Multiple sequence alignment - TraesCS5B01G109000

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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 TraesCS5B01G109000 chr5B 100.000 2435 0 0 1 2435 152508162 152510596 0.000000e+00 4497.0
1 TraesCS5B01G109000 chr5B 94.098 2050 93 3 1 2050 87588346 87590367 0.000000e+00 3090.0
2 TraesCS5B01G109000 chr5B 96.226 53 1 1 2384 2435 195890158 195890106 4.310000e-13 86.1
3 TraesCS5B01G109000 chr2B 98.075 2389 43 2 1 2388 186776729 186779115 0.000000e+00 4154.0
4 TraesCS5B01G109000 chr2B 97.072 2391 43 8 1 2390 465517789 465515425 0.000000e+00 4002.0
5 TraesCS5B01G109000 chr2B 97.959 49 1 0 2387 2435 139579887 139579839 4.310000e-13 86.1
6 TraesCS5B01G109000 chr2B 96.226 53 1 1 2384 2435 666148050 666147998 4.310000e-13 86.1
7 TraesCS5B01G109000 chr1B 98.031 2387 46 1 2 2388 559438254 559435869 0.000000e+00 4146.0
8 TraesCS5B01G109000 chr1B 97.728 2157 46 3 1 2156 525125245 525127399 0.000000e+00 3709.0
9 TraesCS5B01G109000 chr1B 96.845 1585 44 3 1 1585 92300935 92302513 0.000000e+00 2645.0
10 TraesCS5B01G109000 chr1B 95.725 772 31 2 1618 2388 496144164 496143394 0.000000e+00 1242.0
11 TraesCS5B01G109000 chr1B 92.727 55 3 1 2380 2434 218325770 218325823 7.220000e-11 78.7
12 TraesCS5B01G109000 chrUn 98.206 2230 37 3 1 2229 328534540 328532313 0.000000e+00 3893.0
13 TraesCS5B01G109000 chrUn 98.155 1734 29 3 497 2229 375861244 375859513 0.000000e+00 3022.0
14 TraesCS5B01G109000 chr3B 95.057 1497 61 3 1 1496 733133700 733132216 0.000000e+00 2342.0
15 TraesCS5B01G109000 chr7B 95.766 1181 23 6 1209 2388 256347417 256348571 0.000000e+00 1879.0
16 TraesCS5B01G109000 chr4B 95.725 772 31 2 1618 2388 630329534 630328764 0.000000e+00 1242.0
17 TraesCS5B01G109000 chr4B 96.226 53 1 1 2384 2435 350309327 350309379 4.310000e-13 86.1
18 TraesCS5B01G109000 chr4B 94.340 53 2 1 2384 2435 337204902 337204850 2.010000e-11 80.5
19 TraesCS5B01G109000 chr6B 96.226 53 1 1 2384 2435 390496202 390496150 4.310000e-13 86.1
20 TraesCS5B01G109000 chr7D 94.340 53 2 1 2384 2435 616383548 616383600 2.010000e-11 80.5
21 TraesCS5B01G109000 chr5D 94.340 53 2 1 2384 2435 558747561 558747613 2.010000e-11 80.5


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 TraesCS5B01G109000 chr5B 152508162 152510596 2434 False 4497 4497 100.000 1 2435 1 chr5B.!!$F2 2434
1 TraesCS5B01G109000 chr5B 87588346 87590367 2021 False 3090 3090 94.098 1 2050 1 chr5B.!!$F1 2049
2 TraesCS5B01G109000 chr2B 186776729 186779115 2386 False 4154 4154 98.075 1 2388 1 chr2B.!!$F1 2387
3 TraesCS5B01G109000 chr2B 465515425 465517789 2364 True 4002 4002 97.072 1 2390 1 chr2B.!!$R2 2389
4 TraesCS5B01G109000 chr1B 559435869 559438254 2385 True 4146 4146 98.031 2 2388 1 chr1B.!!$R2 2386
5 TraesCS5B01G109000 chr1B 525125245 525127399 2154 False 3709 3709 97.728 1 2156 1 chr1B.!!$F3 2155
6 TraesCS5B01G109000 chr1B 92300935 92302513 1578 False 2645 2645 96.845 1 1585 1 chr1B.!!$F1 1584
7 TraesCS5B01G109000 chr1B 496143394 496144164 770 True 1242 1242 95.725 1618 2388 1 chr1B.!!$R1 770
8 TraesCS5B01G109000 chrUn 328532313 328534540 2227 True 3893 3893 98.206 1 2229 1 chrUn.!!$R1 2228
9 TraesCS5B01G109000 chrUn 375859513 375861244 1731 True 3022 3022 98.155 497 2229 1 chrUn.!!$R2 1732
10 TraesCS5B01G109000 chr3B 733132216 733133700 1484 True 2342 2342 95.057 1 1496 1 chr3B.!!$R1 1495
11 TraesCS5B01G109000 chr7B 256347417 256348571 1154 False 1879 1879 95.766 1209 2388 1 chr7B.!!$F1 1179
12 TraesCS5B01G109000 chr4B 630328764 630329534 770 True 1242 1242 95.725 1618 2388 1 chr4B.!!$R2 770

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
326 327 1.544724 AACGCCAACTTGCATATGGT 58.455 45.0 4.56 0.0 36.57 3.55 F
1001 1003 1.965083 CGCAGGAGATAACGATACGG 58.035 55.0 0.00 0.0 0.00 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1200 1202 0.251832 AGAGGAAGAAGAGGGCGTCA 60.252 55.0 10.15 0.0 0.00 4.35 R
2395 2429 0.032130 CGGCTCCGCTAAGCTCATAA 59.968 55.0 7.08 0.0 42.13 1.90 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
326 327 1.544724 AACGCCAACTTGCATATGGT 58.455 45.000 4.56 0.00 36.57 3.55
1001 1003 1.965083 CGCAGGAGATAACGATACGG 58.035 55.000 0.00 0.00 0.00 4.02
1200 1202 3.692406 GTCCCCGTCAAGCTCGGT 61.692 66.667 11.03 0.00 45.63 4.69
1440 1443 2.672098 ACAGAATCATAGCCTCGGAGT 58.328 47.619 4.02 0.00 0.00 3.85
1643 1672 2.696125 GGATCTGGGGCCTTGGGA 60.696 66.667 0.84 0.00 0.00 4.37
1841 1871 1.145325 GTCGGGAGGGAGAGGAATAGA 59.855 57.143 0.00 0.00 0.00 1.98
2020 2051 3.920144 GCATCTCGTACTAGTGCGT 57.080 52.632 28.58 10.79 39.65 5.24
2393 2427 6.292150 AGCCCTTTTTCTAGTAGTGATATGC 58.708 40.000 0.00 0.00 0.00 3.14
2394 2428 6.100424 AGCCCTTTTTCTAGTAGTGATATGCT 59.900 38.462 0.00 0.00 0.00 3.79
2395 2429 6.768381 GCCCTTTTTCTAGTAGTGATATGCTT 59.232 38.462 0.00 0.00 0.00 3.91
2396 2430 7.283354 GCCCTTTTTCTAGTAGTGATATGCTTT 59.717 37.037 0.00 0.00 0.00 3.51
2397 2431 9.832445 CCCTTTTTCTAGTAGTGATATGCTTTA 57.168 33.333 0.00 0.00 0.00 1.85
2424 2458 3.102097 CGGAGCCGCCATTTTCTC 58.898 61.111 0.00 0.00 35.94 2.87
2425 2459 1.450312 CGGAGCCGCCATTTTCTCT 60.450 57.895 0.00 0.00 35.94 3.10
2426 2460 0.179084 CGGAGCCGCCATTTTCTCTA 60.179 55.000 0.00 0.00 35.94 2.43
2427 2461 1.742411 CGGAGCCGCCATTTTCTCTAA 60.742 52.381 0.00 0.00 35.94 2.10
2428 2462 2.365582 GGAGCCGCCATTTTCTCTAAA 58.634 47.619 0.00 0.00 36.34 1.85
2429 2463 2.752903 GGAGCCGCCATTTTCTCTAAAA 59.247 45.455 0.00 0.00 38.87 1.52
2430 2464 3.381590 GGAGCCGCCATTTTCTCTAAAAT 59.618 43.478 0.00 0.00 44.35 1.82
2431 2465 4.142160 GGAGCCGCCATTTTCTCTAAAATT 60.142 41.667 0.00 0.00 41.50 1.82
2432 2466 4.747810 AGCCGCCATTTTCTCTAAAATTG 58.252 39.130 0.00 0.00 41.50 2.32
2433 2467 4.462483 AGCCGCCATTTTCTCTAAAATTGA 59.538 37.500 0.00 0.00 41.50 2.57
2434 2468 5.127682 AGCCGCCATTTTCTCTAAAATTGAT 59.872 36.000 0.00 0.00 41.50 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
326 327 1.351017 CAAGGTGGCTGTTTCCTCCTA 59.649 52.381 4.10 0.00 46.35 2.94
545 547 3.887110 ACCAAGTTTACCAGCTACCAAAC 59.113 43.478 7.72 7.72 0.00 2.93
546 548 4.173290 ACCAAGTTTACCAGCTACCAAA 57.827 40.909 0.00 0.00 0.00 3.28
1200 1202 0.251832 AGAGGAAGAAGAGGGCGTCA 60.252 55.000 10.15 0.00 0.00 4.35
1602 1631 4.366684 CACCCCAAGGCCCCAGAC 62.367 72.222 0.00 0.00 36.11 3.51
2393 2427 2.139118 GGCTCCGCTAAGCTCATAAAG 58.861 52.381 7.08 0.00 42.13 1.85
2394 2428 1.538204 CGGCTCCGCTAAGCTCATAAA 60.538 52.381 7.08 0.00 42.13 1.40
2395 2429 0.032130 CGGCTCCGCTAAGCTCATAA 59.968 55.000 7.08 0.00 42.13 1.90
2396 2430 1.660355 CGGCTCCGCTAAGCTCATA 59.340 57.895 7.08 0.00 42.13 2.15
2397 2431 2.419198 CGGCTCCGCTAAGCTCAT 59.581 61.111 7.08 0.00 42.13 2.90
2407 2441 0.179084 TAGAGAAAATGGCGGCTCCG 60.179 55.000 11.43 3.56 43.09 4.63
2408 2442 2.038387 TTAGAGAAAATGGCGGCTCC 57.962 50.000 11.43 0.00 0.00 4.70
2409 2443 4.639135 ATTTTAGAGAAAATGGCGGCTC 57.361 40.909 11.43 0.00 42.46 4.70
2410 2444 4.462483 TCAATTTTAGAGAAAATGGCGGCT 59.538 37.500 11.43 0.00 43.10 5.52
2411 2445 4.743493 TCAATTTTAGAGAAAATGGCGGC 58.257 39.130 0.00 0.00 43.10 6.53


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

AutoCloner maintained by Alex Coulton.