Multiple sequence alignment - TraesCS4D01G250900

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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 TraesCS4D01G250900 chr4D 100.000 4526 0 0 1 4526 419315864 419311339 0 8359
1 TraesCS4D01G250900 chr4A 94.430 2639 106 18 1 2622 45335448 45338062 0 4021
2 TraesCS4D01G250900 chr4A 95.266 1859 74 6 2653 4501 45338060 45339914 0 2933
3 TraesCS4D01G250900 chr4B 93.091 1925 82 18 2 1918 517276366 517274485 0 2771
4 TraesCS4D01G250900 chr4B 96.049 1544 52 4 1944 3478 517274489 517272946 0 2505
5 TraesCS4D01G250900 chr4B 94.986 1037 44 4 3492 4526 517267279 517266249 0 1620


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 TraesCS4D01G250900 chr4D 419311339 419315864 4525 True 8359 8359 100.000 1 4526 1 chr4D.!!$R1 4525
1 TraesCS4D01G250900 chr4A 45335448 45339914 4466 False 3477 4021 94.848 1 4501 2 chr4A.!!$F1 4500
2 TraesCS4D01G250900 chr4B 517272946 517276366 3420 True 2638 2771 94.570 2 3478 2 chr4B.!!$R2 3476
3 TraesCS4D01G250900 chr4B 517266249 517267279 1030 True 1620 1620 94.986 3492 4526 1 chr4B.!!$R1 1034

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
433 446 0.536724 ATGCTACTCATGTGACGGCA 59.463 50.000 0.94 8.71 33.26 5.69 F
551 569 1.285373 ACTGTGTACCCCCAACAACAA 59.715 47.619 0.00 0.00 0.00 2.83 F
1510 1532 1.868713 TTCCAGCGGAGTACCCAATA 58.131 50.000 0.00 0.00 31.21 1.90 F
2629 2654 0.687354 TCAAGGACCTCCAGAACTGC 59.313 55.000 0.00 0.00 38.89 4.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1489 1511 0.251916 TTGGGTACTCCGCTGGAATG 59.748 55.000 0.0 0.0 38.76 2.67 R
1536 1558 1.133915 TCTGGCAACTTCGAACCCTTT 60.134 47.619 0.0 0.0 37.61 3.11 R
2700 2731 0.449388 CGTCAATTTCAGCAGCCTCC 59.551 55.000 0.0 0.0 0.00 4.30 R
4366 4406 0.946221 AGAGAGCGAAACAACTGGCG 60.946 55.000 0.0 0.0 0.00 5.69 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
205 207 8.960591 AGTTGGTGAAGAAATAAATGATAGTGG 58.039 33.333 0.00 0.00 0.00 4.00
216 218 9.686683 AAATAAATGATAGTGGAAGCTAGTTGT 57.313 29.630 0.00 0.00 0.00 3.32
227 229 0.811616 GCTAGTTGTGAGGATGGGCG 60.812 60.000 0.00 0.00 0.00 6.13
333 335 7.362920 GCACTTTCAGGCCTATTATTTTTCTCA 60.363 37.037 3.98 0.00 0.00 3.27
378 380 9.793259 ACTCTTCAATAATTGTTTTCAGAGGTA 57.207 29.630 14.38 0.00 0.00 3.08
395 397 6.071334 TCAGAGGTATGAACATCGAACTTCTT 60.071 38.462 0.00 0.00 41.29 2.52
433 446 0.536724 ATGCTACTCATGTGACGGCA 59.463 50.000 0.94 8.71 33.26 5.69
536 554 6.855836 ACATTTGCCTTGTTATGATACTGTG 58.144 36.000 0.00 0.00 0.00 3.66
538 556 7.609918 ACATTTGCCTTGTTATGATACTGTGTA 59.390 33.333 0.00 0.00 0.00 2.90
551 569 1.285373 ACTGTGTACCCCCAACAACAA 59.715 47.619 0.00 0.00 0.00 2.83
581 599 7.531871 CAGCATATCAATTGTCACGCTATAAAC 59.468 37.037 5.13 0.00 0.00 2.01
721 739 9.811995 AACTGTAATTTAAGATGACGCATACTA 57.188 29.630 0.00 0.00 0.00 1.82
735 753 5.927819 ACGCATACTACCTTACTCTAGAGT 58.072 41.667 27.72 27.72 45.02 3.24
828 846 4.283467 TGGTACAGTTCTGTGATGCTAACT 59.717 41.667 14.69 0.00 32.52 2.24
829 847 5.479027 TGGTACAGTTCTGTGATGCTAACTA 59.521 40.000 14.69 0.00 31.20 2.24
963 985 7.039784 TCCAATTCAAAAGGAATAACACTCAGG 60.040 37.037 0.00 0.00 45.46 3.86
1357 1379 7.113965 GTGTTGTTCACAAGATAAAATCAGCAG 59.886 37.037 0.00 0.00 45.51 4.24
1510 1532 1.868713 TTCCAGCGGAGTACCCAATA 58.131 50.000 0.00 0.00 31.21 1.90
1736 1758 8.157476 AGATAAAAGTACTCTGAAAGGAAAGCA 58.843 33.333 0.00 0.00 0.00 3.91
1871 1893 1.826385 CCCAGAACACCATTCTCCAC 58.174 55.000 0.00 0.00 0.00 4.02
1911 1933 6.902341 TGCATCTGTTGAATTACAAGAAGAC 58.098 36.000 0.00 0.00 39.30 3.01
2059 2081 6.805160 TCAGATGATGACTTGGACATGTCCA 61.805 44.000 38.19 38.19 44.99 4.02
2060 2082 8.049349 TCAGATGATGACTTGGACATGTCCAT 62.049 42.308 40.80 30.17 45.52 3.41
2135 2160 6.845908 AGGATGTGCAAGGTTCATCTATTAT 58.154 36.000 12.41 0.00 38.28 1.28
2161 2186 0.898326 TCTGGTGGAGTCAGCGCTAA 60.898 55.000 10.99 0.00 43.77 3.09
2332 2357 8.631480 ATTGCAGCTATCATTTGATAATCAGA 57.369 30.769 0.00 0.00 36.66 3.27
2437 2462 4.686972 TGAAGACATCCGAACAGATGATC 58.313 43.478 8.44 4.73 45.43 2.92
2480 2505 5.971895 AAACAATTAACAGCTGTGCAAAG 57.028 34.783 22.49 15.63 0.00 2.77
2579 2604 5.177696 GTGTGGAGTCTGTAATCACTGAAAC 59.822 44.000 0.00 0.00 34.78 2.78
2629 2654 0.687354 TCAAGGACCTCCAGAACTGC 59.313 55.000 0.00 0.00 38.89 4.40
2630 2655 0.689623 CAAGGACCTCCAGAACTGCT 59.310 55.000 0.00 0.00 38.89 4.24
2631 2656 1.072965 CAAGGACCTCCAGAACTGCTT 59.927 52.381 0.00 0.00 38.89 3.91
2633 2658 0.687354 GGACCTCCAGAACTGCTTGA 59.313 55.000 0.00 0.00 35.64 3.02
2634 2659 1.280421 GGACCTCCAGAACTGCTTGAT 59.720 52.381 0.00 0.00 35.64 2.57
2636 2661 1.980765 ACCTCCAGAACTGCTTGATGA 59.019 47.619 0.00 0.00 0.00 2.92
2655 2686 4.090761 TGATAAACATGCTGAGGATCCC 57.909 45.455 8.55 0.11 0.00 3.85
2678 2709 4.310769 GAGTATTGCCTCGATTGCACTAT 58.689 43.478 9.07 4.79 38.72 2.12
2700 2731 9.113838 ACTATAGGAAATGTAGCTGAAAATGTG 57.886 33.333 4.43 0.00 0.00 3.21
2774 2805 9.558396 TTGCCAATCAATTTTAGAAACTTCATT 57.442 25.926 0.00 0.00 0.00 2.57
2777 2808 8.863049 CCAATCAATTTTAGAAACTTCATTCGG 58.137 33.333 0.00 0.00 34.46 4.30
2920 2951 5.489792 TGCTCAACAGTTAGAGGAAGAAT 57.510 39.130 12.11 0.00 32.54 2.40
3016 3047 4.934356 AGGAGAAGCAATCAACCCAAATA 58.066 39.130 0.00 0.00 0.00 1.40
3021 3052 7.418254 GGAGAAGCAATCAACCCAAATAATGAT 60.418 37.037 0.00 0.00 34.11 2.45
3547 3582 7.931407 TGTAGATTATGCACATCTTACGGAATT 59.069 33.333 14.03 0.00 32.94 2.17
3696 3731 6.455360 AGGTTTGGATTATTACAGTGCATG 57.545 37.500 0.00 0.00 0.00 4.06
3846 3881 7.875554 AGTGTTGGTTTGAAATTTGTTACAAGT 59.124 29.630 0.00 0.00 0.00 3.16
3852 3887 9.685828 GGTTTGAAATTTGTTACAAGTATGCTA 57.314 29.630 0.00 0.00 0.00 3.49
3969 4004 6.753180 TGTTGCAATGCCTATTTTCTTACAA 58.247 32.000 0.59 0.00 0.00 2.41
4001 4036 5.419760 CATCTTGAAGATGTATGCACAGG 57.580 43.478 23.50 0.00 45.33 4.00
4154 4194 7.891183 ACAATACATAACTGTTGTGAGACTC 57.109 36.000 21.72 0.00 36.79 3.36
4173 4213 2.796593 CTCATATCGCATTCAAGTCGCA 59.203 45.455 0.00 0.00 0.00 5.10
4176 4216 0.673333 ATCGCATTCAAGTCGCACCA 60.673 50.000 0.00 0.00 0.00 4.17
4184 4224 4.582701 TTCAAGTCGCACCATTCATTTT 57.417 36.364 0.00 0.00 0.00 1.82
4363 4403 7.348815 TGATCCTTGTCATTTCCTGATTGTAT 58.651 34.615 0.00 0.00 35.97 2.29
4366 4406 6.603201 TCCTTGTCATTTCCTGATTGTATTCC 59.397 38.462 0.00 0.00 35.97 3.01
4416 4456 1.987770 CGCAACCTGCAATTTAGCAAG 59.012 47.619 0.00 0.00 45.36 4.01
4449 4490 4.222588 CCTTCAGCCCCATCATTTTGTAAA 59.777 41.667 0.00 0.00 0.00 2.01
4456 4497 7.769970 CAGCCCCATCATTTTGTAAATAATTGT 59.230 33.333 0.00 0.00 0.00 2.71
4506 4548 4.650972 TGCACATAAGGATTATACCCCC 57.349 45.455 0.00 0.00 39.78 5.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
158 160 4.515191 ACTGTTATTGTACCAACTGCACTG 59.485 41.667 0.00 0.00 0.00 3.66
166 168 6.358178 TCTTCACCAACTGTTATTGTACCAA 58.642 36.000 0.00 0.00 0.00 3.67
205 207 2.911484 CCCATCCTCACAACTAGCTTC 58.089 52.381 0.00 0.00 0.00 3.86
216 218 1.064758 ACAATAAAGCGCCCATCCTCA 60.065 47.619 2.29 0.00 0.00 3.86
333 335 6.332976 AGAGTGTATCCAAATCCAATTCCT 57.667 37.500 0.00 0.00 0.00 3.36
369 371 5.661056 AGTTCGATGTTCATACCTCTGAA 57.339 39.130 0.00 0.00 32.84 3.02
378 380 8.954950 AAGATATCAAGAAGTTCGATGTTCAT 57.045 30.769 5.32 0.00 0.00 2.57
395 397 6.266131 AGCATACCCCAAAAGAAGATATCA 57.734 37.500 5.32 0.00 0.00 2.15
433 446 9.740710 AAGTCTTAAGCACAACCTAGATAAAAT 57.259 29.630 0.00 0.00 0.00 1.82
499 513 4.985538 AGGCAAATGTTCTTCCTACAAGA 58.014 39.130 0.00 0.00 0.00 3.02
536 554 0.671796 GCTGTTGTTGTTGGGGGTAC 59.328 55.000 0.00 0.00 0.00 3.34
538 556 1.000993 TGCTGTTGTTGTTGGGGGT 59.999 52.632 0.00 0.00 0.00 4.95
551 569 3.064408 CGTGACAATTGATATGCTGCTGT 59.936 43.478 13.59 0.00 0.00 4.40
642 660 0.965363 CCCAACCGCTTACTGGCATT 60.965 55.000 0.00 0.00 0.00 3.56
713 731 5.759273 ACACTCTAGAGTAAGGTAGTATGCG 59.241 44.000 24.75 10.29 40.20 4.73
721 739 3.508012 CACTGCACACTCTAGAGTAAGGT 59.492 47.826 24.75 15.82 40.20 3.50
735 753 4.335400 TCTTATCTGTGAACACTGCACA 57.665 40.909 6.51 0.00 43.41 4.57
919 941 4.862902 TGGAGAATATCTAGACTGCTGC 57.137 45.455 0.00 0.00 0.00 5.25
963 985 3.119173 AGCTGAGATAGTGCTTGTCTCAC 60.119 47.826 11.99 9.98 42.36 3.51
1357 1379 0.307146 GATGCAGCGCCTCTCAAATC 59.693 55.000 2.29 0.00 0.00 2.17
1489 1511 0.251916 TTGGGTACTCCGCTGGAATG 59.748 55.000 0.00 0.00 38.76 2.67
1533 1555 2.223745 GGCAACTTCGAACCCTTTACA 58.776 47.619 0.00 0.00 0.00 2.41
1536 1558 1.133915 TCTGGCAACTTCGAACCCTTT 60.134 47.619 0.00 0.00 37.61 3.11
1736 1758 7.284034 CAGTAATAATTGCTGGTGAAGAAGGAT 59.716 37.037 0.00 0.00 39.36 3.24
1871 1893 5.349817 ACAGATGCAATAAACTCGTCTTCAG 59.650 40.000 0.00 0.00 0.00 3.02
1911 1933 5.628606 TGTAACACATGAATTTTGCACATCG 59.371 36.000 0.00 0.00 0.00 3.84
2059 2081 5.987953 CAGATTGGACAGACGATGATGTTAT 59.012 40.000 0.00 0.00 0.00 1.89
2060 2082 5.127031 TCAGATTGGACAGACGATGATGTTA 59.873 40.000 0.00 0.00 0.00 2.41
2161 2186 4.256920 GTGGCATGTGAAGATAGTTCTGT 58.743 43.478 0.00 0.00 30.72 3.41
2332 2357 6.651225 GGTTTACTGAGCATAGTCTTGAGTTT 59.349 38.462 0.00 0.00 32.19 2.66
2437 2462 1.143620 GTAGCTGGCAGAGAGCTGG 59.856 63.158 20.86 0.00 46.44 4.85
2579 2604 1.691434 GAGCTCCCATGTCCTCCTTAG 59.309 57.143 0.87 0.00 0.00 2.18
2629 2654 6.072618 GGATCCTCAGCATGTTTATCATCAAG 60.073 42.308 3.84 0.00 37.40 3.02
2630 2655 5.766670 GGATCCTCAGCATGTTTATCATCAA 59.233 40.000 3.84 0.00 37.40 2.57
2631 2656 5.311265 GGATCCTCAGCATGTTTATCATCA 58.689 41.667 3.84 0.00 37.40 3.07
2633 2658 4.660168 GGGATCCTCAGCATGTTTATCAT 58.340 43.478 12.58 0.00 37.40 2.45
2634 2659 3.494924 CGGGATCCTCAGCATGTTTATCA 60.495 47.826 12.58 0.00 37.40 2.15
2636 2661 2.705658 TCGGGATCCTCAGCATGTTTAT 59.294 45.455 12.58 0.00 37.40 1.40
2678 2709 6.480763 TCCACATTTTCAGCTACATTTCCTA 58.519 36.000 0.00 0.00 0.00 2.94
2700 2731 0.449388 CGTCAATTTCAGCAGCCTCC 59.551 55.000 0.00 0.00 0.00 4.30
2774 2805 0.679505 CTCCAGAAGTTCACCACCGA 59.320 55.000 5.50 0.00 0.00 4.69
2777 2808 1.967319 TTGCTCCAGAAGTTCACCAC 58.033 50.000 5.50 0.00 0.00 4.16
3016 3047 5.970592 GCCTTTAGCCTTTGAAGAATCATT 58.029 37.500 0.00 0.00 32.91 2.57
3238 3269 7.792032 TCAGTAGGAACACCATTATTTCTAGG 58.208 38.462 0.00 0.00 0.00 3.02
3240 3271 7.272978 GCTCAGTAGGAACACCATTATTTCTA 58.727 38.462 0.00 0.00 0.00 2.10
3480 3511 7.679164 GCCTTTTCATCTTCATCTTGAGCTAAG 60.679 40.741 0.00 0.00 37.76 2.18
3547 3582 7.603404 CCAGAACATTAATGAGAAAATTTGGCA 59.397 33.333 22.16 0.00 0.00 4.92
3846 3881 7.857456 TCAAACCCAAGATTAAGAGTAGCATA 58.143 34.615 0.00 0.00 0.00 3.14
3852 3887 7.015584 AGCAAATTCAAACCCAAGATTAAGAGT 59.984 33.333 0.00 0.00 0.00 3.24
3935 3970 1.780860 GCATTGCAACAGAACACGTTC 59.219 47.619 0.00 1.54 39.78 3.95
4001 4036 8.406297 GGATGATGAAAAGTACCAAGGAATTAC 58.594 37.037 0.00 0.00 0.00 1.89
4139 4179 4.177026 GCGATATGAGTCTCACAACAGTT 58.823 43.478 4.21 0.00 0.00 3.16
4140 4180 3.193479 TGCGATATGAGTCTCACAACAGT 59.807 43.478 4.21 0.00 0.00 3.55
4154 4194 2.348872 GGTGCGACTTGAATGCGATATG 60.349 50.000 0.00 0.00 0.00 1.78
4184 4224 8.557864 CATTGCCATTCTACAAAATTTGAAACA 58.442 29.630 13.19 0.00 0.00 2.83
4363 4403 1.503818 GAGCGAAACAACTGGCGGAA 61.504 55.000 0.00 0.00 0.00 4.30
4366 4406 0.946221 AGAGAGCGAAACAACTGGCG 60.946 55.000 0.00 0.00 0.00 5.69
4416 4456 1.611936 GGGGCTGAAGGAACTGAGAAC 60.612 57.143 0.00 0.00 40.86 3.01
4470 4511 7.816995 TCCTTATGTGCAAAACCAAATCATTAC 59.183 33.333 0.00 0.00 0.00 1.89


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

AutoCloner maintained by Alex Coulton.