Multiple sequence alignment - TraesCS7B01G138800

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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 TraesCS7B01G138800 chr7B 100.000 3425 0 0 1 3425 174568709 174565285 0 6325
1 TraesCS7B01G138800 chr7D 95.937 2732 87 17 704 3425 222146914 222149631 0 4409
2 TraesCS7B01G138800 chr7D 96.040 707 18 5 1 701 222144774 222145476 0 1142
3 TraesCS7B01G138800 chr7A 93.857 2735 93 22 704 3425 236621654 236624326 0 4050
4 TraesCS7B01G138800 chr7A 95.621 708 21 6 1 701 236620059 236620763 0 1127


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 TraesCS7B01G138800 chr7B 174565285 174568709 3424 True 6325.0 6325 100.0000 1 3425 1 chr7B.!!$R1 3424
1 TraesCS7B01G138800 chr7D 222144774 222149631 4857 False 2775.5 4409 95.9885 1 3425 2 chr7D.!!$F1 3424
2 TraesCS7B01G138800 chr7A 236620059 236624326 4267 False 2588.5 4050 94.7390 1 3425 2 chr7A.!!$F1 3424

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
948 2411 0.739462 CCACTATTTGCGACCGCTCA 60.739 55.0 15.61 2.45 42.51 4.26 F
1728 3200 1.641577 CTGCTAGTTCGTTACAGCCC 58.358 55.0 0.00 0.00 33.00 5.19 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2135 3607 0.535780 TCTGTGTGCAGCAAGAAGGG 60.536 55.0 0.0 0.0 42.29 3.95 R
2945 4418 1.826385 ACAATGGTTAGCAGGACAGC 58.174 50.0 0.0 0.0 0.00 4.40 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
29 30 5.179929 GCACTTTGGCTTCAATTTTAATGCT 59.820 36.000 0.00 0.00 0.00 3.79
172 174 5.739935 GCAAATGAGATTGGTTGGTGACTTT 60.740 40.000 0.00 0.00 0.00 2.66
276 278 2.095059 CCAATGTAGTTTCTGGTGCTGC 60.095 50.000 0.00 0.00 0.00 5.25
277 279 1.442769 ATGTAGTTTCTGGTGCTGCG 58.557 50.000 0.00 0.00 0.00 5.18
299 301 2.357075 GGACCGACATTTTTCTCCTCC 58.643 52.381 0.00 0.00 0.00 4.30
301 303 1.985895 ACCGACATTTTTCTCCTCCCT 59.014 47.619 0.00 0.00 0.00 4.20
355 357 4.335594 GGCAGTTGACGATAATTTAGGCTT 59.664 41.667 0.00 0.00 0.00 4.35
622 630 3.943381 TGTGGTCTGATTGATCTGCATTC 59.057 43.478 0.00 0.00 0.00 2.67
701 709 4.721776 TCTGGGGTATGAGTTAGCTTTGAT 59.278 41.667 0.00 0.00 0.00 2.57
702 710 5.036117 TGGGGTATGAGTTAGCTTTGATC 57.964 43.478 0.00 0.00 0.00 2.92
731 2183 1.070175 GGTCATCGAAACAACACACGG 60.070 52.381 0.00 0.00 0.00 4.94
776 2229 8.749499 CACAACACAAGAAGAAAAATTCAGATC 58.251 33.333 0.00 0.00 0.00 2.75
873 2327 1.433534 CCTTCACTTCTTGCCGTCTC 58.566 55.000 0.00 0.00 0.00 3.36
895 2349 1.890894 GTCTCGCCCTCTGTTGCTA 59.109 57.895 0.00 0.00 0.00 3.49
925 2388 2.287373 GCGATGCATTGAGAGAGGAAAG 59.713 50.000 18.58 0.00 0.00 2.62
933 2396 1.150135 TGAGAGAGGAAAGTCCCCACT 59.850 52.381 0.00 0.00 37.19 4.00
942 2405 2.109425 AAGTCCCCACTATTTGCGAC 57.891 50.000 0.00 0.00 30.14 5.19
948 2411 0.739462 CCACTATTTGCGACCGCTCA 60.739 55.000 15.61 2.45 42.51 4.26
1011 2480 1.667830 CGACTCAATGGCGGTGTGT 60.668 57.895 0.00 0.00 44.96 3.72
1073 2542 1.767681 CATCTCCTTCTCCTTCCCCAG 59.232 57.143 0.00 0.00 0.00 4.45
1327 2796 3.187699 CTCGTCGGCCCAGAGATCG 62.188 68.421 10.31 3.35 34.13 3.69
1728 3200 1.641577 CTGCTAGTTCGTTACAGCCC 58.358 55.000 0.00 0.00 33.00 5.19
1962 3434 4.215613 GTCGCAAGGAACTATTTTGGACTT 59.784 41.667 0.00 0.00 38.49 3.01
2009 3481 3.171277 GTGTTGGCGATGCTATTCAAAC 58.829 45.455 0.00 0.00 0.00 2.93
2085 3557 1.909302 GTGGATCTTGACTCCCCTGAA 59.091 52.381 0.00 0.00 31.32 3.02
2091 3563 3.454858 TCTTGACTCCCCTGAAGCTATT 58.545 45.455 0.00 0.00 0.00 1.73
2135 3607 2.435805 TGGAGATGACCCATAGAAGCAC 59.564 50.000 0.00 0.00 0.00 4.40
2150 3622 2.195567 GCACCCTTCTTGCTGCACA 61.196 57.895 0.00 0.00 37.00 4.57
2319 3791 0.254462 TTGTTGCCAGAGTGTCACCA 59.746 50.000 0.00 0.00 0.00 4.17
2324 3796 0.886490 GCCAGAGTGTCACCAACTGG 60.886 60.000 24.74 24.74 43.91 4.00
2450 3922 4.910195 TGCTGTTTGAAGTCATGACCTAT 58.090 39.130 22.21 9.11 0.00 2.57
2454 3926 6.989169 GCTGTTTGAAGTCATGACCTATAGAT 59.011 38.462 22.21 0.00 0.00 1.98
2560 4032 3.711190 ACCCAATCAAGAAAGCCTGTTTT 59.289 39.130 0.00 0.00 0.00 2.43
2561 4033 4.164030 ACCCAATCAAGAAAGCCTGTTTTT 59.836 37.500 0.00 0.00 0.00 1.94
2609 4081 6.768029 TTGCTTTTGTTATTTTGCTGCTAG 57.232 33.333 0.00 0.00 0.00 3.42
2688 4160 5.186992 TGAACTTCATATTGTCTTCCGAGGA 59.813 40.000 0.00 0.00 0.00 3.71
2711 4183 3.066342 TGAATACTTTAGGAGGAGCGACG 59.934 47.826 0.00 0.00 0.00 5.12
2945 4418 5.975344 GGTGCATATGTTCATGAAGATTGTG 59.025 40.000 21.75 19.79 0.00 3.33
2955 4428 1.072806 TGAAGATTGTGCTGTCCTGCT 59.927 47.619 0.00 0.00 0.00 4.24
3049 4522 9.305925 CCAGAATTCTATTTTTAGCCATTTGAC 57.694 33.333 7.86 0.00 0.00 3.18
3096 4569 6.515340 CGACGAGCAGTAATTTTGTTTTACTC 59.485 38.462 0.00 0.00 37.71 2.59
3118 4591 7.560368 ACTCTCAAGAAGAATTATGGTGTAGG 58.440 38.462 0.00 0.00 32.23 3.18
3249 4722 7.979786 TGGCTTTTATGGGGTATAAAAATGA 57.020 32.000 0.00 0.00 45.63 2.57
3352 4826 3.956848 CAATTGATCTCTCCTTTTCCCCC 59.043 47.826 0.00 0.00 0.00 5.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
29 30 8.489489 AGCCAGATTAAGAGAGTAAATGAATGA 58.511 33.333 0.00 0.00 0.00 2.57
86 88 4.518970 GCAGTTCAGAAAATCCCTACACAA 59.481 41.667 0.00 0.00 0.00 3.33
172 174 0.543410 TGGGTAGAAAGCCGTCTCCA 60.543 55.000 0.00 0.00 46.91 3.86
277 279 1.004394 AGGAGAAAAATGTCGGTCCCC 59.996 52.381 0.00 0.00 0.00 4.81
299 301 6.423302 GCATCTGTATTCATAAGACTGACAGG 59.577 42.308 7.51 0.00 34.23 4.00
301 303 6.982724 CAGCATCTGTATTCATAAGACTGACA 59.017 38.462 0.00 0.00 34.23 3.58
355 357 1.804151 CGCTCGACCTTGGAATTTCAA 59.196 47.619 0.00 0.00 0.00 2.69
672 680 3.933861 AACTCATACCCCAGATGTTCC 57.066 47.619 0.00 0.00 0.00 3.62
678 686 4.101114 TCAAAGCTAACTCATACCCCAGA 58.899 43.478 0.00 0.00 0.00 3.86
679 687 4.487714 TCAAAGCTAACTCATACCCCAG 57.512 45.455 0.00 0.00 0.00 4.45
701 709 3.006430 TGTTTCGATGACCTGCTTAGTGA 59.994 43.478 0.00 0.00 0.00 3.41
702 710 3.325870 TGTTTCGATGACCTGCTTAGTG 58.674 45.455 0.00 0.00 0.00 2.74
744 2197 7.810766 TTTTTCTTCTTGTGTTGTGTTGATC 57.189 32.000 0.00 0.00 0.00 2.92
776 2229 8.410030 TCTGATTTCATTCTTGTGTTGTTTTG 57.590 30.769 0.00 0.00 0.00 2.44
883 2337 1.408822 GGGACCAATAGCAACAGAGGG 60.409 57.143 0.00 0.00 0.00 4.30
895 2349 1.453745 AATGCATCGCGGGACCAAT 60.454 52.632 6.13 0.00 0.00 3.16
925 2388 1.087771 CGGTCGCAAATAGTGGGGAC 61.088 60.000 6.23 6.23 43.75 4.46
933 2396 0.668096 ACGTTGAGCGGTCGCAAATA 60.668 50.000 17.71 0.00 46.52 1.40
995 2464 2.260869 GCACACACCGCCATTGAGT 61.261 57.895 0.00 0.00 0.00 3.41
1073 2542 2.434359 CGTCGTGGAGGAAAGGGC 60.434 66.667 0.00 0.00 0.00 5.19
1860 3332 1.661463 TGGACATTGGAAGAGCTCCT 58.339 50.000 10.93 0.00 45.64 3.69
2009 3481 3.129113 TCCATGTGCAAAATCCTGAATCG 59.871 43.478 0.00 0.00 0.00 3.34
2085 3557 2.154462 GCACTGACACCACAAATAGCT 58.846 47.619 0.00 0.00 0.00 3.32
2091 3563 2.899838 GGCGCACTGACACCACAA 60.900 61.111 10.83 0.00 0.00 3.33
2135 3607 0.535780 TCTGTGTGCAGCAAGAAGGG 60.536 55.000 0.00 0.00 42.29 3.95
2150 3622 6.990939 CACTCCATGATGATGTAGAATTCTGT 59.009 38.462 18.47 3.96 0.00 3.41
2319 3791 1.494721 TCAAGAAGGGTGCTTCCAGTT 59.505 47.619 0.00 0.00 38.11 3.16
2324 3796 4.579869 TGAACTATCAAGAAGGGTGCTTC 58.420 43.478 0.00 0.00 30.99 3.86
2560 4032 4.455533 CCAGCAGTTCTGTAGTAATGCAAA 59.544 41.667 12.20 0.00 41.25 3.68
2561 4033 4.002982 CCAGCAGTTCTGTAGTAATGCAA 58.997 43.478 12.20 0.00 41.25 4.08
2562 4034 3.599343 CCAGCAGTTCTGTAGTAATGCA 58.401 45.455 12.20 0.00 41.25 3.96
2634 4106 7.594351 TGCTCACTCAGATATGATCTAAAGT 57.406 36.000 0.00 0.00 37.58 2.66
2688 4160 4.261656 CGTCGCTCCTCCTAAAGTATTCAT 60.262 45.833 0.00 0.00 0.00 2.57
2831 4304 3.411446 CCTAAGCTTGTCAACATGTGGA 58.589 45.455 9.86 0.00 0.00 4.02
2872 4345 7.710044 AGCATCTCATGTAACTTAGTTGATCTG 59.290 37.037 8.00 0.86 0.00 2.90
2945 4418 1.826385 ACAATGGTTAGCAGGACAGC 58.174 50.000 0.00 0.00 0.00 4.40
2955 4428 6.514947 ACACTTTACTGTCGTACAATGGTTA 58.485 36.000 0.00 0.00 0.00 2.85
3096 4569 6.889198 TCCCTACACCATAATTCTTCTTGAG 58.111 40.000 0.00 0.00 0.00 3.02
3118 4591 6.683974 TGTATTCTGCTTTGAGCTAAATCC 57.316 37.500 1.29 0.00 42.97 3.01
3249 4722 8.633561 GGCAACCTTAGAAGCATATTTAAAGAT 58.366 33.333 0.00 0.00 0.00 2.40
3265 4738 5.531287 AGTTTACTGAACAAGGCAACCTTAG 59.469 40.000 0.00 0.00 42.67 2.18
3329 4803 3.382865 GGGGAAAAGGAGAGATCAATTGC 59.617 47.826 0.00 0.00 0.00 3.56
3352 4826 7.388500 ACATCAATTCCAACCTAAAAGCAAATG 59.612 33.333 0.00 0.00 0.00 2.32


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

AutoCloner maintained by Alex Coulton.