Multiple sequence alignment - TraesCS5B01G250700

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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 TraesCS5B01G250700 chr5B 100.000 2424 0 0 1 2424 432876724 432879147 0.000000e+00 4477
1 TraesCS5B01G250700 chr5B 96.121 1856 53 8 588 2424 413608022 413609877 0.000000e+00 3011
2 TraesCS5B01G250700 chr3A 96.318 2444 66 10 1 2424 672878432 672875993 0.000000e+00 3993
3 TraesCS5B01G250700 chr2D 96.102 2463 50 7 1 2424 33933816 33936271 0.000000e+00 3975
4 TraesCS5B01G250700 chr2D 96.099 2461 51 8 1 2424 630270293 630272745 0.000000e+00 3971
5 TraesCS5B01G250700 chr3B 95.536 2442 74 8 1 2424 201560774 201558350 0.000000e+00 3873
6 TraesCS5B01G250700 chr3B 95.760 684 28 1 1742 2424 703007384 703006701 0.000000e+00 1101
7 TraesCS5B01G250700 chr3B 98.016 252 5 0 1 252 810472418 810472167 2.860000e-119 438
8 TraesCS5B01G250700 chr3B 98.016 252 5 0 1 252 810482467 810482216 2.860000e-119 438
9 TraesCS5B01G250700 chr3B 95.288 191 9 0 345 535 550898760 550898570 1.090000e-78 303
10 TraesCS5B01G250700 chr4A 94.342 2439 104 7 1 2424 310762406 310764825 0.000000e+00 3709
11 TraesCS5B01G250700 chr4D 95.616 2258 83 5 181 2424 245648863 245651118 0.000000e+00 3607
12 TraesCS5B01G250700 chr7A 92.122 2450 126 27 1 2424 352677445 352675037 0.000000e+00 3393
13 TraesCS5B01G250700 chr5D 95.200 2125 80 11 1 2108 432292718 432290599 0.000000e+00 3339
14 TraesCS5B01G250700 chr1B 95.992 2046 66 5 1 2032 633728864 633726821 0.000000e+00 3310
15 TraesCS5B01G250700 chrUn 95.625 1623 32 6 841 2424 371049286 371050908 0.000000e+00 2567
16 TraesCS5B01G250700 chrUn 97.275 477 8 3 1757 2228 451362693 451362217 0.000000e+00 804
17 TraesCS5B01G250700 chrUn 96.744 430 9 3 2000 2424 451362689 451363118 0.000000e+00 712
18 TraesCS5B01G250700 chr1A 94.507 1420 58 8 1018 2424 371922155 371923567 0.000000e+00 2172
19 TraesCS5B01G250700 chr3D 91.456 831 29 10 1607 2424 182097139 182097940 0.000000e+00 1103
20 TraesCS5B01G250700 chr4B 97.168 459 7 4 1719 2171 1 459 0.000000e+00 771
21 TraesCS5B01G250700 chr5A 97.647 425 8 2 2002 2424 482027372 482026948 0.000000e+00 728


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 TraesCS5B01G250700 chr5B 432876724 432879147 2423 False 4477 4477 100.000 1 2424 1 chr5B.!!$F2 2423
1 TraesCS5B01G250700 chr5B 413608022 413609877 1855 False 3011 3011 96.121 588 2424 1 chr5B.!!$F1 1836
2 TraesCS5B01G250700 chr3A 672875993 672878432 2439 True 3993 3993 96.318 1 2424 1 chr3A.!!$R1 2423
3 TraesCS5B01G250700 chr2D 33933816 33936271 2455 False 3975 3975 96.102 1 2424 1 chr2D.!!$F1 2423
4 TraesCS5B01G250700 chr2D 630270293 630272745 2452 False 3971 3971 96.099 1 2424 1 chr2D.!!$F2 2423
5 TraesCS5B01G250700 chr3B 201558350 201560774 2424 True 3873 3873 95.536 1 2424 1 chr3B.!!$R1 2423
6 TraesCS5B01G250700 chr3B 703006701 703007384 683 True 1101 1101 95.760 1742 2424 1 chr3B.!!$R3 682
7 TraesCS5B01G250700 chr4A 310762406 310764825 2419 False 3709 3709 94.342 1 2424 1 chr4A.!!$F1 2423
8 TraesCS5B01G250700 chr4D 245648863 245651118 2255 False 3607 3607 95.616 181 2424 1 chr4D.!!$F1 2243
9 TraesCS5B01G250700 chr7A 352675037 352677445 2408 True 3393 3393 92.122 1 2424 1 chr7A.!!$R1 2423
10 TraesCS5B01G250700 chr5D 432290599 432292718 2119 True 3339 3339 95.200 1 2108 1 chr5D.!!$R1 2107
11 TraesCS5B01G250700 chr1B 633726821 633728864 2043 True 3310 3310 95.992 1 2032 1 chr1B.!!$R1 2031
12 TraesCS5B01G250700 chrUn 371049286 371050908 1622 False 2567 2567 95.625 841 2424 1 chrUn.!!$F1 1583
13 TraesCS5B01G250700 chr1A 371922155 371923567 1412 False 2172 2172 94.507 1018 2424 1 chr1A.!!$F1 1406
14 TraesCS5B01G250700 chr3D 182097139 182097940 801 False 1103 1103 91.456 1607 2424 1 chr3D.!!$F1 817

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
93 94 4.200092 ACCTCTTCTCAACTTGTTTCACC 58.800 43.478 0.0 0.0 0.0 4.02 F
266 267 4.202121 CGTGCTACAAGGTACATAGGTCAT 60.202 45.833 0.0 0.0 0.0 3.06 F
1113 1119 4.338118 CCCATTTATTCTGCCTTTTCGCTA 59.662 41.667 0.0 0.0 0.0 4.26 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1269 1287 6.590656 ACCCATCTCCAATAGTCCAATAAA 57.409 37.500 0.0 0.0 0.00 1.40 R
1379 1397 7.339466 ACCATGTTCTACTATTTGGTTTGATCC 59.661 37.037 0.0 0.0 33.83 3.36 R
1974 2003 7.890127 TGGATTTCCTATTATGATGGATGGAAC 59.110 37.037 0.0 0.0 36.82 3.62 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
93 94 4.200092 ACCTCTTCTCAACTTGTTTCACC 58.800 43.478 0.00 0.00 0.00 4.02
266 267 4.202121 CGTGCTACAAGGTACATAGGTCAT 60.202 45.833 0.00 0.00 0.00 3.06
298 299 6.388619 AACTACCTTATCCCACACAAATCT 57.611 37.500 0.00 0.00 0.00 2.40
384 385 7.330700 GGCGAATCCACTTTGAATTTGATAAAA 59.669 33.333 0.00 0.00 34.01 1.52
648 649 5.514834 CGGTTACCAATCTCCATAATGGGAT 60.515 44.000 1.13 0.00 38.32 3.85
650 651 7.112779 GGTTACCAATCTCCATAATGGGATAG 58.887 42.308 0.00 0.00 38.32 2.08
651 652 5.184892 ACCAATCTCCATAATGGGATAGC 57.815 43.478 0.00 0.00 38.32 2.97
1066 1072 4.903045 TTTGTTCTTCTACTAGGGGGTG 57.097 45.455 0.00 0.00 0.00 4.61
1113 1119 4.338118 CCCATTTATTCTGCCTTTTCGCTA 59.662 41.667 0.00 0.00 0.00 4.26
1238 1256 7.710475 TCTTGATCATATTCGCTGTAATGTTCA 59.290 33.333 0.00 0.00 0.00 3.18
1269 1287 7.071698 TGGCTCAGAATGGTCTAAAGATAAGAT 59.928 37.037 0.00 0.00 36.16 2.40
1379 1397 6.316390 GTGGTATGGAATTCTTTGGACTACAG 59.684 42.308 5.23 0.00 0.00 2.74
1402 1420 8.109634 ACAGGATCAAACCAAATAGTAGAACAT 58.890 33.333 0.00 0.00 0.00 2.71
1461 1479 8.956426 TCATTTAGCAACCGATTTTTATCTTCT 58.044 29.630 0.00 0.00 0.00 2.85
1906 1935 6.827586 TTTGATAGTCGCCAATTAAAAGGT 57.172 33.333 0.00 0.00 0.00 3.50
2275 2347 9.019764 CAATTTATTGGCTAATTCGAATTCGTT 57.980 29.630 25.89 16.74 36.09 3.85
2280 2352 6.671614 TGGCTAATTCGAATTCGTTTGTAT 57.328 33.333 25.89 10.93 40.80 2.29
2362 2438 4.380531 TCTCTTCACGCTTTCTCACAAAT 58.619 39.130 0.00 0.00 0.00 2.32
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
213 214 5.241403 TGTTGACCATAACTCATGAACCT 57.759 39.130 0.00 0.00 36.69 3.50
266 267 8.480501 GTGTGGGATAAGGTAGTTATGAAACTA 58.519 37.037 0.00 0.00 44.26 2.24
298 299 8.310122 AGGGTAGTGAATCGTTATAGGTAAAA 57.690 34.615 0.00 0.00 0.00 1.52
384 385 6.710295 TGAACACATACTTCACAAGCAATACT 59.290 34.615 0.00 0.00 0.00 2.12
503 504 7.383572 TCAACACAATTGCCACAAAATATACAC 59.616 33.333 5.05 0.00 0.00 2.90
648 649 7.517614 TCCTAATTGTTTGAATTGTGTGCTA 57.482 32.000 0.00 0.00 0.00 3.49
650 651 7.656707 ATTCCTAATTGTTTGAATTGTGTGC 57.343 32.000 0.00 0.00 0.00 4.57
651 652 8.427012 CGAATTCCTAATTGTTTGAATTGTGTG 58.573 33.333 0.00 0.00 37.51 3.82
1066 1072 7.014711 GGGGTTGGTAAGTAATACTACTCCTAC 59.985 44.444 2.69 7.72 37.39 3.18
1238 1256 7.577303 TCTTTAGACCATTCTGAGCCATTTAT 58.423 34.615 0.00 0.00 32.75 1.40
1269 1287 6.590656 ACCCATCTCCAATAGTCCAATAAA 57.409 37.500 0.00 0.00 0.00 1.40
1379 1397 7.339466 ACCATGTTCTACTATTTGGTTTGATCC 59.661 37.037 0.00 0.00 33.83 3.36
1421 1439 9.213799 GGTTGCTAAATGAATTCCAATTTGTTA 57.786 29.630 11.94 0.00 0.00 2.41
1461 1479 9.912634 GAAGAATTATGGAAATGAGTTCAAACA 57.087 29.630 0.00 0.00 38.06 2.83
1974 2003 7.890127 TGGATTTCCTATTATGATGGATGGAAC 59.110 37.037 0.00 0.00 36.82 3.62


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

AutoCloner maintained by Alex Coulton.