Multiple sequence alignment - TraesCS5B01G253100

Loading Multiple Alignment...

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 TraesCS5B01G253100 chr5B 100.000 3738 0 0 1 3738 436095400 436099137 0.000000e+00 6903.0
1 TraesCS5B01G253100 chr5B 94.820 2143 80 10 175 2294 436152291 436154425 0.000000e+00 3314.0
2 TraesCS5B01G253100 chr5B 90.525 1657 144 4 637 2282 436162916 436164570 0.000000e+00 2178.0
3 TraesCS5B01G253100 chr5B 86.887 1815 204 22 480 2283 436209055 436210846 0.000000e+00 2002.0
4 TraesCS5B01G253100 chr5B 95.987 897 23 5 2289 3173 436154556 436155451 0.000000e+00 1445.0
5 TraesCS5B01G253100 chr5B 94.291 578 12 6 3163 3738 436156106 436156664 0.000000e+00 865.0
6 TraesCS5B01G253100 chr5B 77.450 1051 154 40 2292 3266 436210987 436212030 5.460000e-153 551.0
7 TraesCS5B01G253100 chr5B 85.659 258 31 3 202 454 436162165 436162421 2.210000e-67 267.0
8 TraesCS5B01G253100 chr5B 86.466 133 17 1 346 478 436208894 436209025 1.080000e-30 145.0
9 TraesCS5B01G253100 chr5B 85.366 123 7 6 3 119 435948563 435948680 2.360000e-22 117.0
10 TraesCS5B01G253100 chr5D 95.319 2307 85 8 1 2294 368028894 368031190 0.000000e+00 3640.0
11 TraesCS5B01G253100 chr5D 92.776 2118 119 14 175 2284 368078219 368080310 0.000000e+00 3033.0
12 TraesCS5B01G253100 chr5D 95.964 1462 38 9 2289 3738 368031321 368032773 0.000000e+00 2353.0
13 TraesCS5B01G253100 chr5D 90.548 1661 139 5 637 2282 368244606 368246263 0.000000e+00 2182.0
14 TraesCS5B01G253100 chr5D 86.047 1978 205 38 346 2283 368285766 368287712 0.000000e+00 2058.0
15 TraesCS5B01G253100 chr5D 87.989 1074 97 9 2292 3338 368080455 368081523 0.000000e+00 1240.0
16 TraesCS5B01G253100 chr5D 78.100 758 113 33 2672 3394 368288274 368289013 7.420000e-117 431.0
17 TraesCS5B01G253100 chr5D 86.312 263 29 4 197 454 368244165 368244425 2.840000e-71 279.0
18 TraesCS5B01G253100 chr5D 84.483 116 9 5 9 119 367990255 367990366 5.110000e-19 106.0
19 TraesCS5B01G253100 chr5A 92.363 2239 114 27 93 2294 470076032 470078250 0.000000e+00 3134.0
20 TraesCS5B01G253100 chr5A 96.375 1462 31 7 2289 3738 470078381 470079832 0.000000e+00 2386.0
21 TraesCS5B01G253100 chr5A 86.997 1815 199 24 480 2283 470170324 470172112 0.000000e+00 2010.0
22 TraesCS5B01G253100 chr5A 78.883 1146 163 49 2308 3394 469900344 469901469 0.000000e+00 702.0
23 TraesCS5B01G253100 chr5A 78.336 1154 179 43 2292 3394 470172253 470173386 0.000000e+00 680.0
24 TraesCS5B01G253100 chr5A 87.047 193 5 4 1 191 470075803 470075977 2.280000e-47 200.0
25 TraesCS5B01G253100 chr5A 84.211 133 21 0 346 478 470170162 470170294 3.030000e-26 130.0
26 TraesCS5B01G253100 chr5A 97.222 36 0 1 52 86 470076002 470076037 4.030000e-05 60.2
27 TraesCS5B01G253100 chr2D 87.172 343 41 3 3395 3735 605779617 605779958 1.630000e-103 387.0
28 TraesCS5B01G253100 chr6D 86.994 346 37 6 3395 3735 119466750 119466408 2.110000e-102 383.0
29 TraesCS5B01G253100 chr3A 85.465 344 42 8 3394 3734 218898 218560 5.940000e-93 351.0
30 TraesCS5B01G253100 chr6A 85.143 350 43 8 3391 3735 598023611 598023956 2.140000e-92 350.0
31 TraesCS5B01G253100 chr1D 85.629 334 44 3 3395 3725 2107770 2108102 7.680000e-92 348.0
32 TraesCS5B01G253100 chr1A 85.131 343 38 8 3397 3735 550838757 550838424 4.620000e-89 339.0


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 TraesCS5B01G253100 chr5B 436095400 436099137 3737 False 6903.000000 6903 100.000000 1 3738 1 chr5B.!!$F2 3737
1 TraesCS5B01G253100 chr5B 436152291 436156664 4373 False 1874.666667 3314 95.032667 175 3738 3 chr5B.!!$F3 3563
2 TraesCS5B01G253100 chr5B 436162165 436164570 2405 False 1222.500000 2178 88.092000 202 2282 2 chr5B.!!$F4 2080
3 TraesCS5B01G253100 chr5B 436208894 436212030 3136 False 899.333333 2002 83.601000 346 3266 3 chr5B.!!$F5 2920
4 TraesCS5B01G253100 chr5D 368028894 368032773 3879 False 2996.500000 3640 95.641500 1 3738 2 chr5D.!!$F2 3737
5 TraesCS5B01G253100 chr5D 368078219 368081523 3304 False 2136.500000 3033 90.382500 175 3338 2 chr5D.!!$F3 3163
6 TraesCS5B01G253100 chr5D 368285766 368289013 3247 False 1244.500000 2058 82.073500 346 3394 2 chr5D.!!$F5 3048
7 TraesCS5B01G253100 chr5D 368244165 368246263 2098 False 1230.500000 2182 88.430000 197 2282 2 chr5D.!!$F4 2085
8 TraesCS5B01G253100 chr5A 470075803 470079832 4029 False 1445.050000 3134 93.251750 1 3738 4 chr5A.!!$F2 3737
9 TraesCS5B01G253100 chr5A 470170162 470173386 3224 False 940.000000 2010 83.181333 346 3394 3 chr5A.!!$F3 3048
10 TraesCS5B01G253100 chr5A 469900344 469901469 1125 False 702.000000 702 78.883000 2308 3394 1 chr5A.!!$F1 1086

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
276 429 0.449388 CCCTCAAATTGCTGAGCGTC 59.551 55.0 0.00 0.00 41.36 5.19 F
1324 1879 0.179000 AGTGATTGGGCCTGACGATC 59.821 55.0 4.53 1.38 0.00 3.69 F
2031 2587 0.179137 TCATACTGCAAGGTCGCGAG 60.179 55.0 10.24 0.00 39.30 5.03 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2275 2831 0.321564 CCATGAAGGCGAGTCCACAA 60.322 55.000 0.00 0.0 37.29 3.33 R
2302 2995 1.783284 GCATCATCCAAGATACGCGA 58.217 50.000 15.93 0.0 0.00 5.87 R
3236 4708 1.867233 CTGAGTGTGCTAGCAAACGTT 59.133 47.619 28.18 15.1 39.08 3.99 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
130 133 2.676822 AGACGAAGCGAGGCCTCA 60.677 61.111 31.67 0.00 0.00 3.86
158 161 2.364448 GCTCGAGGGAGGGGAAGT 60.364 66.667 15.58 0.00 40.80 3.01
247 398 2.686106 GGTAAGCTCCGACCCCCA 60.686 66.667 0.00 0.00 0.00 4.96
276 429 0.449388 CCCTCAAATTGCTGAGCGTC 59.551 55.000 0.00 0.00 41.36 5.19
525 740 6.324819 CGTTATCTGCTTGTTTCATCCAATT 58.675 36.000 0.00 0.00 0.00 2.32
563 778 9.787435 ACTATTTCTAAAGTTGTATGGTTGTCA 57.213 29.630 0.00 0.00 0.00 3.58
587 1123 1.336125 TGATGCACACATTTTGTCGCA 59.664 42.857 0.00 4.33 42.55 5.10
639 1175 7.065216 GGCTAGAATTTTGCCAGAAAATTTC 57.935 36.000 10.96 0.00 45.46 2.17
712 1248 9.109393 TGTATATCTCACCATGCTTTTAGTTTC 57.891 33.333 0.00 0.00 0.00 2.78
824 1360 1.726853 CTACAGCTGGTGCCACTTAC 58.273 55.000 19.93 0.00 40.80 2.34
1230 1785 6.433847 TTCCTATTCTTTCCACAAGAGTCA 57.566 37.500 0.00 0.00 0.00 3.41
1272 1827 3.736720 TGCTGATGCTATCCTGATTGAC 58.263 45.455 0.00 0.00 40.48 3.18
1324 1879 0.179000 AGTGATTGGGCCTGACGATC 59.821 55.000 4.53 1.38 0.00 3.69
1608 2163 4.478206 TGGTGATGAGAAATGGAGAGAC 57.522 45.455 0.00 0.00 0.00 3.36
1884 2439 0.908198 CCTGTCCTTCTCTTCCCAGG 59.092 60.000 0.00 0.00 34.10 4.45
1973 2529 4.737855 ACAATATTCAGTACTCGCCAGT 57.262 40.909 0.00 0.00 36.55 4.00
1987 2543 1.541379 GCCAGTTTACATTCCGGGTT 58.459 50.000 0.00 0.00 0.00 4.11
2001 2557 2.362717 TCCGGGTTCAAATTTGGTTCAC 59.637 45.455 17.90 9.57 0.00 3.18
2023 2579 6.988580 TCACAGGAATAAGATCATACTGCAAG 59.011 38.462 0.00 0.00 42.29 4.01
2031 2587 0.179137 TCATACTGCAAGGTCGCGAG 60.179 55.000 10.24 0.00 39.30 5.03
2275 2831 6.183360 GCACCAGCTCTCTGATTATGAAAAAT 60.183 38.462 0.00 0.00 42.95 1.82
2302 2995 1.376424 CGCCTTCATGGTCTGCTGT 60.376 57.895 0.00 0.00 38.35 4.40
2374 3067 4.671831 TCAAATATGTCCAAGCCTTCCAA 58.328 39.130 0.00 0.00 0.00 3.53
2563 3265 1.202114 CGGCTTAATTGTGTGGCACAT 59.798 47.619 24.95 10.30 44.16 3.21
2601 3303 9.822185 GGAAAATTTATCTGCTTGTTTGGATAT 57.178 29.630 0.00 0.00 0.00 1.63
2727 3490 5.426504 AGGCTTCAAAGAGTATCATGAGTG 58.573 41.667 0.09 0.00 37.82 3.51
3236 4708 7.446931 TGTTATTGTCTGCAGTTCCATTCTTAA 59.553 33.333 14.67 3.72 0.00 1.85
3307 4787 5.237815 TGCTAACAGGGCATCGAATTATAG 58.762 41.667 0.00 0.00 34.56 1.31
3440 4926 4.343239 GCTCCATGAAGGCCTTAATTTGAT 59.657 41.667 20.54 0.90 37.29 2.57
3595 5082 5.133221 ACTGGGGCTTTTTAGCATATGTAG 58.867 41.667 4.29 0.00 36.33 2.74
3612 5099 7.466455 GCATATGTAGTGTTCATCCTCAAAGTG 60.466 40.741 4.29 0.00 0.00 3.16
3707 5194 9.720667 CATTACATCCTTGTATACATGTGTTTG 57.279 33.333 16.55 11.97 38.12 2.93
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
29 31 2.721906 GGGGAATGGAGATTGGGGAATA 59.278 50.000 0.00 0.00 0.00 1.75
247 398 2.815503 GCAATTTGAGGGCAGCAAAAAT 59.184 40.909 0.00 0.00 38.57 1.82
276 429 0.449388 GATGGAAAGCTTGCGAGTGG 59.551 55.000 0.00 0.00 0.00 4.00
376 549 6.090763 TGCAGATGTATAAACAGTTCTCAACG 59.909 38.462 0.00 0.00 39.49 4.10
378 551 9.098355 GTATGCAGATGTATAAACAGTTCTCAA 57.902 33.333 0.00 0.00 39.49 3.02
379 552 8.478066 AGTATGCAGATGTATAAACAGTTCTCA 58.522 33.333 0.00 0.00 39.49 3.27
547 762 4.776349 TCAGTGTGACAACCATACAACTT 58.224 39.130 0.00 0.00 39.09 2.66
563 778 3.548616 CGACAAAATGTGTGCATCAGTGT 60.549 43.478 0.00 0.00 41.96 3.55
587 1123 2.978824 CCCCGAATGACACTCCGT 59.021 61.111 0.00 0.00 0.00 4.69
639 1175 3.349006 GTGGGTGCGACACTGCTG 61.349 66.667 9.31 0.00 35.98 4.41
780 1316 0.035056 ATGGAGCCCTGTGTTGCTAC 60.035 55.000 0.00 0.00 38.11 3.58
920 1464 5.735766 ACAATAGGGAGAAGTGAGTAAAGC 58.264 41.667 0.00 0.00 0.00 3.51
1230 1785 0.842635 GATGGGGCTCACCTGAGATT 59.157 55.000 6.49 0.00 44.74 2.40
1272 1827 2.892425 GATGGCGACCAGGCTTCG 60.892 66.667 4.26 4.26 46.88 3.79
1324 1879 3.581755 CATTGCATGAACCACAAAGGAG 58.418 45.455 0.00 0.00 41.22 3.69
1608 2163 2.800250 AGGGCTTCTGGAGTTTTGATG 58.200 47.619 0.00 0.00 0.00 3.07
1884 2439 1.912371 GCAGCGTACCAACAAGCCTC 61.912 60.000 0.00 0.00 0.00 4.70
1973 2529 5.070580 ACCAAATTTGAACCCGGAATGTAAA 59.929 36.000 19.86 0.00 0.00 2.01
1987 2543 7.831691 TCTTATTCCTGTGAACCAAATTTGA 57.168 32.000 19.86 0.00 32.13 2.69
2001 2557 6.294473 ACCTTGCAGTATGATCTTATTCCTG 58.706 40.000 0.00 0.00 39.69 3.86
2031 2587 5.763876 ACTCATAGGAATATAGGTTGCCC 57.236 43.478 0.00 0.00 0.00 5.36
2275 2831 0.321564 CCATGAAGGCGAGTCCACAA 60.322 55.000 0.00 0.00 37.29 3.33
2302 2995 1.783284 GCATCATCCAAGATACGCGA 58.217 50.000 15.93 0.00 0.00 5.87
2563 3265 8.850156 GCAGATAAATTTTCCCTATCTTGCTTA 58.150 33.333 0.00 0.00 31.45 3.09
2620 3334 8.636213 CCTCAATGATCTGGCTTGTAAATTTAT 58.364 33.333 0.31 0.00 0.00 1.40
2727 3490 8.703604 TGATTTTCTACAGCACTAAGTATCAC 57.296 34.615 0.00 0.00 0.00 3.06
2808 3571 7.063593 ACAGATATAGGAGACAAGAACTAGCA 58.936 38.462 0.00 0.00 0.00 3.49
3236 4708 1.867233 CTGAGTGTGCTAGCAAACGTT 59.133 47.619 28.18 15.10 39.08 3.99
3307 4787 7.625828 ACTTGATAGCAACCAAAGTATAACC 57.374 36.000 0.00 0.00 0.00 2.85
3440 4926 9.936759 AAGTGAAAAGTTTGGATTTTGAAGTTA 57.063 25.926 0.00 0.00 30.22 2.24
3595 5082 3.503363 TCATGCACTTTGAGGATGAACAC 59.497 43.478 0.00 0.00 40.23 3.32


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

AutoCloner maintained by Alex Coulton.