Multiple sequence alignment - TraesCS5B01G250600

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 TraesCS5B01G250600 chr5B 100.000 2456 0 0 1 2456 432875919 432878374 0.000000e+00 4536
1 TraesCS5B01G250600 chr5B 96.071 1069 37 3 1393 2456 413608022 413609090 0.000000e+00 1736
2 TraesCS5B01G250600 chr5B 97.279 147 3 1 3 148 538681572 538681718 5.240000e-62 248
3 TraesCS5B01G250600 chr3B 96.627 2461 77 4 1 2456 201561580 201559121 0.000000e+00 4080
4 TraesCS5B01G250600 chr3A 96.545 2460 77 6 1 2456 672879237 672876782 0.000000e+00 4065
5 TraesCS5B01G250600 chr1B 96.463 2460 81 4 1 2456 633729670 633727213 0.000000e+00 4056
6 TraesCS5B01G250600 chr5D 95.739 2464 92 10 1 2456 432293525 432291067 0.000000e+00 3956
7 TraesCS5B01G250600 chr4A 95.087 2463 111 8 1 2456 310761600 310764059 0.000000e+00 3869
8 TraesCS5B01G250600 chr4A 94.110 2462 116 16 1 2456 219340674 219338236 0.000000e+00 3716
9 TraesCS5B01G250600 chr2D 97.282 2171 48 3 290 2456 33933300 33935463 0.000000e+00 3672
10 TraesCS5B01G250600 chr2D 96.274 1986 48 10 1 1976 272802469 272800500 0.000000e+00 3234
11 TraesCS5B01G250600 chr2D 97.188 1707 36 4 754 2456 630270241 630271939 0.000000e+00 2876
12 TraesCS5B01G250600 chr2D 97.405 1503 34 2 1 1498 630268418 630269920 0.000000e+00 2555
13 TraesCS5B01G250600 chr4D 95.794 1474 57 3 986 2456 245648863 245650334 0.000000e+00 2374
14 TraesCS5B01G250600 chr2B 94.479 326 16 2 1 325 528568007 528568331 3.650000e-138 501
15 TraesCS5B01G250600 chr2A 92.576 229 16 1 1 228 499294799 499294571 6.550000e-86 327


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 TraesCS5B01G250600 chr5B 432875919 432878374 2455 False 4536.0 4536 100.0000 1 2456 1 chr5B.!!$F2 2455
1 TraesCS5B01G250600 chr5B 413608022 413609090 1068 False 1736.0 1736 96.0710 1393 2456 1 chr5B.!!$F1 1063
2 TraesCS5B01G250600 chr3B 201559121 201561580 2459 True 4080.0 4080 96.6270 1 2456 1 chr3B.!!$R1 2455
3 TraesCS5B01G250600 chr3A 672876782 672879237 2455 True 4065.0 4065 96.5450 1 2456 1 chr3A.!!$R1 2455
4 TraesCS5B01G250600 chr1B 633727213 633729670 2457 True 4056.0 4056 96.4630 1 2456 1 chr1B.!!$R1 2455
5 TraesCS5B01G250600 chr5D 432291067 432293525 2458 True 3956.0 3956 95.7390 1 2456 1 chr5D.!!$R1 2455
6 TraesCS5B01G250600 chr4A 310761600 310764059 2459 False 3869.0 3869 95.0870 1 2456 1 chr4A.!!$F1 2455
7 TraesCS5B01G250600 chr4A 219338236 219340674 2438 True 3716.0 3716 94.1100 1 2456 1 chr4A.!!$R1 2455
8 TraesCS5B01G250600 chr2D 33933300 33935463 2163 False 3672.0 3672 97.2820 290 2456 1 chr2D.!!$F1 2166
9 TraesCS5B01G250600 chr2D 272800500 272802469 1969 True 3234.0 3234 96.2740 1 1976 1 chr2D.!!$R1 1975
10 TraesCS5B01G250600 chr2D 630268418 630271939 3521 False 2715.5 2876 97.2965 1 2456 2 chr2D.!!$F2 2455
11 TraesCS5B01G250600 chr4D 245648863 245650334 1471 False 2374.0 2374 95.7940 986 2456 1 chr4D.!!$F1 1470

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
187 189 2.235402 TCTAGCGGACGGAATTCCTTTT 59.765 45.455 22.05 6.38 32.88 2.27 F
538 546 3.118884 GCGGAGGAAGAATTAGTACCACA 60.119 47.826 0.00 0.00 0.00 4.17 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1018 2094 5.241403 TGTTGACCATAACTCATGAACCT 57.759 39.13 0.0 0.0 36.69 3.5 R
2074 3171 6.590656 ACCCATCTCCAATAGTCCAATAAA 57.409 37.50 0.0 0.0 0.00 1.4 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
153 155 5.620738 AAGGATGAGATCAATTCGGAAGA 57.379 39.130 0.00 0.00 39.20 2.87
172 174 6.508721 CGGAAGAGCTTTTTCTTATTCTAGCG 60.509 42.308 10.56 1.49 37.53 4.26
187 189 2.235402 TCTAGCGGACGGAATTCCTTTT 59.765 45.455 22.05 6.38 32.88 2.27
534 542 5.044558 CAGAAGCGGAGGAAGAATTAGTAC 58.955 45.833 0.00 0.00 0.00 2.73
537 545 3.132467 AGCGGAGGAAGAATTAGTACCAC 59.868 47.826 0.00 0.00 0.00 4.16
538 546 3.118884 GCGGAGGAAGAATTAGTACCACA 60.119 47.826 0.00 0.00 0.00 4.17
547 555 9.185680 GGAAGAATTAGTACCACATTACCAAAT 57.814 33.333 0.00 0.00 0.00 2.32
898 1974 4.200092 ACCTCTTCTCAACTTGTTTCACC 58.800 43.478 0.00 0.00 0.00 4.02
1071 2147 4.202121 CGTGCTACAAGGTACATAGGTCAT 60.202 45.833 0.00 0.00 0.00 3.06
1103 2179 6.388619 AACTACCTTATCCCACACAAATCT 57.611 37.500 0.00 0.00 0.00 2.40
1189 2265 7.330700 GGCGAATCCACTTTGAATTTGATAAAA 59.669 33.333 0.00 0.00 34.01 1.52
1453 2529 5.514834 CGGTTACCAATCTCCATAATGGGAT 60.515 44.000 1.13 0.00 38.32 3.85
1455 2531 7.112779 GGTTACCAATCTCCATAATGGGATAG 58.887 42.308 0.00 0.00 38.32 2.08
1456 2532 5.184892 ACCAATCTCCATAATGGGATAGC 57.815 43.478 0.00 0.00 38.32 2.97
1871 2966 4.903045 TTTGTTCTTCTACTAGGGGGTG 57.097 45.455 0.00 0.00 0.00 4.61
1918 3013 4.338118 CCCATTTATTCTGCCTTTTCGCTA 59.662 41.667 0.00 0.00 0.00 4.26
2007 3104 7.100458 GCACAACTTCTTATTTATGTGGGAT 57.900 36.000 5.93 0.00 38.78 3.85
2043 3140 7.710475 TCTTGATCATATTCGCTGTAATGTTCA 59.290 33.333 0.00 0.00 0.00 3.18
2074 3171 7.071698 TGGCTCAGAATGGTCTAAAGATAAGAT 59.928 37.037 0.00 0.00 36.16 2.40
2184 3281 6.316390 GTGGTATGGAATTCTTTGGACTACAG 59.684 42.308 5.23 0.00 0.00 2.74
2207 3304 8.109634 ACAGGATCAAACCAAATAGTAGAACAT 58.890 33.333 0.00 0.00 0.00 2.71
2266 3363 8.956426 TCATTTAGCAACCGATTTTTATCTTCT 58.044 29.630 0.00 0.00 0.00 2.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
153 155 4.567159 CGTCCGCTAGAATAAGAAAAAGCT 59.433 41.667 0.00 0.00 0.00 3.74
172 174 6.510879 AATTAGACAAAAGGAATTCCGTCC 57.489 37.500 18.82 6.43 42.08 4.79
534 542 6.922957 CCGGAATATTCAATTTGGTAATGTGG 59.077 38.462 17.07 0.00 0.00 4.17
537 545 9.840427 GATACCGGAATATTCAATTTGGTAATG 57.160 33.333 17.07 0.00 34.67 1.90
538 546 9.581289 TGATACCGGAATATTCAATTTGGTAAT 57.419 29.630 17.07 9.69 34.67 1.89
547 555 9.581289 AACCATATTTGATACCGGAATATTCAA 57.419 29.630 17.07 6.82 0.00 2.69
628 636 1.517832 CACCCGCCCAAGTAGAGAG 59.482 63.158 0.00 0.00 0.00 3.20
1018 2094 5.241403 TGTTGACCATAACTCATGAACCT 57.759 39.130 0.00 0.00 36.69 3.50
1071 2147 8.480501 GTGTGGGATAAGGTAGTTATGAAACTA 58.519 37.037 0.00 0.00 44.26 2.24
1103 2179 8.310122 AGGGTAGTGAATCGTTATAGGTAAAA 57.690 34.615 0.00 0.00 0.00 1.52
1189 2265 6.710295 TGAACACATACTTCACAAGCAATACT 59.290 34.615 0.00 0.00 0.00 2.12
1308 2384 7.383572 TCAACACAATTGCCACAAAATATACAC 59.616 33.333 5.05 0.00 0.00 2.90
1453 2529 7.517614 TCCTAATTGTTTGAATTGTGTGCTA 57.482 32.000 0.00 0.00 0.00 3.49
1455 2531 7.656707 ATTCCTAATTGTTTGAATTGTGTGC 57.343 32.000 0.00 0.00 0.00 4.57
1456 2532 8.427012 CGAATTCCTAATTGTTTGAATTGTGTG 58.573 33.333 0.00 0.00 37.51 3.82
1871 2966 7.014711 GGGGTTGGTAAGTAATACTACTCCTAC 59.985 44.444 2.69 7.72 37.39 3.18
2007 3104 7.879677 AGCGAATATGATCAAGACATTTATGGA 59.120 33.333 0.00 0.00 0.00 3.41
2043 3140 7.577303 TCTTTAGACCATTCTGAGCCATTTAT 58.423 34.615 0.00 0.00 32.75 1.40
2074 3171 6.590656 ACCCATCTCCAATAGTCCAATAAA 57.409 37.500 0.00 0.00 0.00 1.40
2184 3281 7.339466 ACCATGTTCTACTATTTGGTTTGATCC 59.661 37.037 0.00 0.00 33.83 3.36
2226 3323 9.213799 GGTTGCTAAATGAATTCCAATTTGTTA 57.786 29.630 11.94 0.00 0.00 2.41
2266 3363 9.912634 GAAGAATTATGGAAATGAGTTCAAACA 57.087 29.630 0.00 0.00 38.06 2.83


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

AutoCloner maintained by Alex Coulton.