Multiple sequence alignment - TraesCS2B01G325700

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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 TraesCS2B01G325700 chr2B 100.000 2378 0 0 1 2378 465517759 465515382 0 4392
1 TraesCS2B01G325700 chr2B 96.780 2360 46 10 1 2333 186776759 186779115 0 3910
2 TraesCS2B01G325700 chr5B 97.078 2361 42 8 1 2335 152508192 152510551 0 3952
3 TraesCS2B01G325700 chr5B 95.186 1994 94 2 1 1994 87588376 87590367 0 3149
4 TraesCS2B01G325700 chr1B 96.776 2357 48 3 3 2333 559438223 559435869 0 3906
5 TraesCS2B01G325700 chr1B 96.335 2128 48 12 1 2101 525125275 525127399 0 3470
6 TraesCS2B01G325700 chr1B 96.592 1555 48 2 1 1555 92300964 92302513 0 2573
7 TraesCS2B01G325700 chr1B 94.961 774 38 1 1560 2333 496144166 496143394 0 1212
8 TraesCS2B01G325700 chrUn 96.955 2200 39 9 1 2174 328534510 328532313 0 3666
9 TraesCS2B01G325700 chr3B 95.024 1467 60 3 1 1466 733133670 733132216 0 2292
10 TraesCS2B01G325700 chr7B 97.749 1155 26 0 1179 2333 256347417 256348571 0 1989
11 TraesCS2B01G325700 chr7B 94.629 782 39 2 1557 2335 590705076 590705857 0 1208
12 TraesCS2B01G325700 chr1A 93.897 1278 77 1 57 1334 414251982 414250706 0 1927
13 TraesCS2B01G325700 chr4B 95.402 783 35 1 1551 2333 630329545 630328764 0 1245
14 TraesCS2B01G325700 chr3A 94.968 775 38 1 1560 2333 633413509 633412735 0 1214


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 TraesCS2B01G325700 chr2B 465515382 465517759 2377 True 4392 4392 100.000 1 2378 1 chr2B.!!$R1 2377
1 TraesCS2B01G325700 chr2B 186776759 186779115 2356 False 3910 3910 96.780 1 2333 1 chr2B.!!$F1 2332
2 TraesCS2B01G325700 chr5B 152508192 152510551 2359 False 3952 3952 97.078 1 2335 1 chr5B.!!$F2 2334
3 TraesCS2B01G325700 chr5B 87588376 87590367 1991 False 3149 3149 95.186 1 1994 1 chr5B.!!$F1 1993
4 TraesCS2B01G325700 chr1B 559435869 559438223 2354 True 3906 3906 96.776 3 2333 1 chr1B.!!$R2 2330
5 TraesCS2B01G325700 chr1B 525125275 525127399 2124 False 3470 3470 96.335 1 2101 1 chr1B.!!$F2 2100
6 TraesCS2B01G325700 chr1B 92300964 92302513 1549 False 2573 2573 96.592 1 1555 1 chr1B.!!$F1 1554
7 TraesCS2B01G325700 chr1B 496143394 496144166 772 True 1212 1212 94.961 1560 2333 1 chr1B.!!$R1 773
8 TraesCS2B01G325700 chrUn 328532313 328534510 2197 True 3666 3666 96.955 1 2174 1 chrUn.!!$R1 2173
9 TraesCS2B01G325700 chr3B 733132216 733133670 1454 True 2292 2292 95.024 1 1466 1 chr3B.!!$R1 1465
10 TraesCS2B01G325700 chr7B 256347417 256348571 1154 False 1989 1989 97.749 1179 2333 1 chr7B.!!$F1 1154
11 TraesCS2B01G325700 chr7B 590705076 590705857 781 False 1208 1208 94.629 1557 2335 1 chr7B.!!$F2 778
12 TraesCS2B01G325700 chr1A 414250706 414251982 1276 True 1927 1927 93.897 57 1334 1 chr1A.!!$R1 1277
13 TraesCS2B01G325700 chr4B 630328764 630329545 781 True 1245 1245 95.402 1551 2333 1 chr4B.!!$R1 782
14 TraesCS2B01G325700 chr3A 633412735 633413509 774 True 1214 1214 94.968 1560 2333 1 chr3A.!!$R1 773

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
180 181 0.235665 AGCACGACATTTGCGTTGAG 59.764 50.0 0.0 0.0 45.15 3.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1733 1761 0.838122 CCTTCCCCCTCACTCACACT 60.838 60.0 0.0 0.0 0.0 3.55 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
94 95 7.661536 ATGTTACCTATTCTCTAGAACAGCA 57.338 36.000 0.00 0.00 36.80 4.41
180 181 0.235665 AGCACGACATTTGCGTTGAG 59.764 50.000 0.00 0.00 45.15 3.02
254 255 7.148540 GCATTTCAAACATGCATATTGTTCACT 60.149 33.333 18.62 0.00 45.50 3.41
407 408 4.628333 CCAAAAGCTGCGATTTTGATCAAT 59.372 37.500 23.67 0.00 46.01 2.57
520 521 3.801698 TCAGCTCACCATAGAGAATTGC 58.198 45.455 0.00 0.00 37.87 3.56
679 680 9.170890 TGACTTTATTCATCCCTATCCAGTATT 57.829 33.333 0.00 0.00 0.00 1.89
681 682 8.606830 ACTTTATTCATCCCTATCCAGTATTCC 58.393 37.037 0.00 0.00 0.00 3.01
1032 1033 2.185350 GCTCTGGCGCTGCTTCTA 59.815 61.111 7.64 0.00 0.00 2.10
1173 1174 4.514577 CCCGTCAAGCTCGGCGAT 62.515 66.667 11.27 0.00 45.71 4.58
1618 1646 3.699894 CTCCACCTGCAGCTCGGT 61.700 66.667 8.66 0.00 0.00 4.69
1832 1860 1.677966 CGAAGTCGAGGGAGGTGGA 60.678 63.158 0.00 0.00 43.02 4.02
2087 2121 1.594293 CGCACTTTCCGACAGGTGT 60.594 57.895 0.00 0.00 39.05 4.16
2335 2370 9.435570 TCTATAGCCCTTTTTCTAGTAGTGATT 57.564 33.333 0.00 0.00 0.00 2.57
2336 2371 9.699703 CTATAGCCCTTTTTCTAGTAGTGATTC 57.300 37.037 0.00 0.00 0.00 2.52
2337 2372 6.628644 AGCCCTTTTTCTAGTAGTGATTCT 57.371 37.500 0.00 0.00 0.00 2.40
2338 2373 7.021998 AGCCCTTTTTCTAGTAGTGATTCTT 57.978 36.000 0.00 0.00 0.00 2.52
2339 2374 7.106890 AGCCCTTTTTCTAGTAGTGATTCTTC 58.893 38.462 0.00 0.00 0.00 2.87
2340 2375 6.879458 GCCCTTTTTCTAGTAGTGATTCTTCA 59.121 38.462 0.00 0.00 0.00 3.02
2341 2376 7.065204 GCCCTTTTTCTAGTAGTGATTCTTCAG 59.935 40.741 0.00 0.00 30.85 3.02
2342 2377 8.097662 CCCTTTTTCTAGTAGTGATTCTTCAGT 58.902 37.037 0.00 0.00 38.99 3.41
2343 2378 9.495572 CCTTTTTCTAGTAGTGATTCTTCAGTT 57.504 33.333 0.00 0.00 36.84 3.16
2346 2381 9.698309 TTTTCTAGTAGTGATTCTTCAGTTGAG 57.302 33.333 0.00 0.00 36.84 3.02
2347 2382 7.397892 TCTAGTAGTGATTCTTCAGTTGAGG 57.602 40.000 0.00 0.00 36.84 3.86
2348 2383 7.175797 TCTAGTAGTGATTCTTCAGTTGAGGA 58.824 38.462 0.00 0.00 36.84 3.71
2349 2384 6.672266 AGTAGTGATTCTTCAGTTGAGGAA 57.328 37.500 8.80 8.80 42.91 3.36
2351 2386 7.684529 AGTAGTGATTCTTCAGTTGAGGAATT 58.315 34.615 17.21 7.55 46.49 2.17
2352 2387 8.160106 AGTAGTGATTCTTCAGTTGAGGAATTT 58.840 33.333 17.21 10.70 46.49 1.82
2353 2388 7.211966 AGTGATTCTTCAGTTGAGGAATTTG 57.788 36.000 17.21 0.00 46.49 2.32
2354 2389 7.000472 AGTGATTCTTCAGTTGAGGAATTTGA 59.000 34.615 17.21 5.87 46.49 2.69
2355 2390 7.503566 AGTGATTCTTCAGTTGAGGAATTTGAA 59.496 33.333 17.21 5.30 46.49 2.69
2356 2391 7.592903 GTGATTCTTCAGTTGAGGAATTTGAAC 59.407 37.037 17.21 11.38 46.49 3.18
2357 2392 7.285172 TGATTCTTCAGTTGAGGAATTTGAACA 59.715 33.333 17.21 9.73 46.49 3.18
2358 2393 7.403312 TTCTTCAGTTGAGGAATTTGAACAA 57.597 32.000 2.92 0.00 35.60 2.83
2359 2394 7.403312 TCTTCAGTTGAGGAATTTGAACAAA 57.597 32.000 2.48 2.48 34.46 2.83
2360 2395 7.483307 TCTTCAGTTGAGGAATTTGAACAAAG 58.517 34.615 6.18 0.00 33.32 2.77
2361 2396 6.147864 TCAGTTGAGGAATTTGAACAAAGG 57.852 37.500 6.18 0.00 33.32 3.11
2362 2397 5.890985 TCAGTTGAGGAATTTGAACAAAGGA 59.109 36.000 6.18 0.00 33.32 3.36
2363 2398 6.039717 TCAGTTGAGGAATTTGAACAAAGGAG 59.960 38.462 6.18 0.00 33.32 3.69
2364 2399 5.893824 AGTTGAGGAATTTGAACAAAGGAGT 59.106 36.000 6.18 0.00 33.32 3.85
2365 2400 6.381133 AGTTGAGGAATTTGAACAAAGGAGTT 59.619 34.615 6.18 0.00 33.32 3.01
2366 2401 6.391227 TGAGGAATTTGAACAAAGGAGTTC 57.609 37.500 6.18 0.00 46.22 3.01
2367 2402 6.129179 TGAGGAATTTGAACAAAGGAGTTCT 58.871 36.000 8.13 0.00 46.19 3.01
2368 2403 6.263168 TGAGGAATTTGAACAAAGGAGTTCTC 59.737 38.462 8.13 5.65 46.19 2.87
2369 2404 6.368805 AGGAATTTGAACAAAGGAGTTCTCT 58.631 36.000 8.13 2.96 46.19 3.10
2370 2405 6.264067 AGGAATTTGAACAAAGGAGTTCTCTG 59.736 38.462 8.13 0.00 46.19 3.35
2371 2406 6.263168 GGAATTTGAACAAAGGAGTTCTCTGA 59.737 38.462 8.13 0.00 46.19 3.27
2372 2407 7.201821 GGAATTTGAACAAAGGAGTTCTCTGAA 60.202 37.037 8.13 0.27 46.19 3.02
2373 2408 6.683974 TTTGAACAAAGGAGTTCTCTGAAG 57.316 37.500 8.13 0.00 46.19 3.02
2374 2409 5.614324 TGAACAAAGGAGTTCTCTGAAGA 57.386 39.130 8.13 0.00 46.19 2.87
2375 2410 5.989477 TGAACAAAGGAGTTCTCTGAAGAA 58.011 37.500 8.13 0.00 46.19 2.52
2376 2411 6.051717 TGAACAAAGGAGTTCTCTGAAGAAG 58.948 40.000 8.13 0.00 46.19 2.85
2377 2412 5.622346 ACAAAGGAGTTCTCTGAAGAAGT 57.378 39.130 0.00 0.00 45.84 3.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
94 95 4.022416 TGCGTTGCTTATTTTGGAATCAGT 60.022 37.500 0.00 0.00 0.00 3.41
180 181 1.960417 GGCTATTCAGAGAGGCCAAC 58.040 55.000 5.01 0.00 42.08 3.77
407 408 1.308069 GCCGATTGAAGCCTTGCTCA 61.308 55.000 0.00 0.00 38.25 4.26
520 521 3.502211 CACCAACCAAGTTTACCAGCTAG 59.498 47.826 0.00 0.00 0.00 3.42
679 680 3.451402 TCACTTCTGCACTAGTAGGGA 57.549 47.619 2.75 0.00 34.28 4.20
681 682 5.934625 ACAAATTCACTTCTGCACTAGTAGG 59.065 40.000 1.45 0.00 0.00 3.18
1032 1033 1.514983 TGGAGGTCATGGAGATGCAT 58.485 50.000 0.00 0.00 0.00 3.96
1173 1174 1.622725 GGGTAGAGGAAGAAGAGGGCA 60.623 57.143 0.00 0.00 0.00 5.36
1733 1761 0.838122 CCTTCCCCCTCACTCACACT 60.838 60.000 0.00 0.00 0.00 3.55
1832 1860 0.987294 CTTCCTCCTGACACACCCAT 59.013 55.000 0.00 0.00 0.00 4.00
1922 1952 4.799586 GCCATTGCTATCTACACGTATGGT 60.800 45.833 8.11 0.00 35.01 3.55
2335 2370 7.403312 TTTGTTCAAATTCCTCAACTGAAGA 57.597 32.000 0.00 0.00 0.00 2.87
2336 2371 6.698766 CCTTTGTTCAAATTCCTCAACTGAAG 59.301 38.462 0.00 0.00 0.00 3.02
2337 2372 6.379703 TCCTTTGTTCAAATTCCTCAACTGAA 59.620 34.615 0.00 0.00 0.00 3.02
2338 2373 5.890985 TCCTTTGTTCAAATTCCTCAACTGA 59.109 36.000 0.00 0.00 0.00 3.41
2339 2374 6.147864 TCCTTTGTTCAAATTCCTCAACTG 57.852 37.500 0.00 0.00 0.00 3.16
2340 2375 5.893824 ACTCCTTTGTTCAAATTCCTCAACT 59.106 36.000 0.00 0.00 0.00 3.16
2341 2376 6.149129 ACTCCTTTGTTCAAATTCCTCAAC 57.851 37.500 0.00 0.00 0.00 3.18
2342 2377 6.607198 AGAACTCCTTTGTTCAAATTCCTCAA 59.393 34.615 9.56 0.00 46.19 3.02
2343 2378 6.129179 AGAACTCCTTTGTTCAAATTCCTCA 58.871 36.000 9.56 0.00 46.19 3.86
2344 2379 6.488344 AGAGAACTCCTTTGTTCAAATTCCTC 59.512 38.462 9.56 0.00 46.19 3.71
2345 2380 6.264067 CAGAGAACTCCTTTGTTCAAATTCCT 59.736 38.462 9.56 0.00 46.19 3.36
2346 2381 6.263168 TCAGAGAACTCCTTTGTTCAAATTCC 59.737 38.462 9.56 0.00 46.19 3.01
2347 2382 7.264373 TCAGAGAACTCCTTTGTTCAAATTC 57.736 36.000 9.56 1.04 46.19 2.17
2348 2383 7.557719 TCTTCAGAGAACTCCTTTGTTCAAATT 59.442 33.333 9.56 0.00 46.19 1.82
2349 2384 7.056635 TCTTCAGAGAACTCCTTTGTTCAAAT 58.943 34.615 9.56 0.00 46.19 2.32
2350 2385 6.414732 TCTTCAGAGAACTCCTTTGTTCAAA 58.585 36.000 9.56 0.00 46.19 2.69
2351 2386 5.989477 TCTTCAGAGAACTCCTTTGTTCAA 58.011 37.500 9.56 0.00 46.19 2.69
2352 2387 5.614324 TCTTCAGAGAACTCCTTTGTTCA 57.386 39.130 9.56 0.00 46.19 3.18
2353 2388 6.052360 ACTTCTTCAGAGAACTCCTTTGTTC 58.948 40.000 0.00 0.00 44.67 3.18
2354 2389 5.995446 ACTTCTTCAGAGAACTCCTTTGTT 58.005 37.500 0.00 0.00 36.99 2.83
2355 2390 5.622346 ACTTCTTCAGAGAACTCCTTTGT 57.378 39.130 0.00 0.00 36.99 2.83


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

AutoCloner maintained by Alex Coulton.