Multiple sequence alignment - TraesCS3B01G067100

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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 TraesCS3B01G067100 chr3B 100.000 3394 0 0 1 3394 39847340 39843947 0 6268
1 TraesCS3B01G067100 chr7B 97.996 3394 65 1 1 3394 716910709 716907319 0 5888
2 TraesCS3B01G067100 chr7B 97.820 3394 70 1 1 3394 742954454 742957843 0 5854
3 TraesCS3B01G067100 chr7B 97.790 3394 71 2 1 3394 716778892 716775503 0 5849
4 TraesCS3B01G067100 chr7B 96.582 3394 110 3 1 3394 139593629 139590242 0 5620
5 TraesCS3B01G067100 chr5A 97.938 3394 67 1 1 3394 16538866 16535476 0 5877
6 TraesCS3B01G067100 chr7A 97.936 3392 68 1 1 3392 60349344 60345955 0 5875
7 TraesCS3B01G067100 chr2B 97.761 3394 73 2 1 3394 391172728 391169338 0 5843
8 TraesCS3B01G067100 chr1B 97.643 3394 76 1 1 3394 583567264 583570653 0 5821
9 TraesCS3B01G067100 chr4B 97.407 3394 84 1 1 3394 209224810 209221421 0 5777


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 TraesCS3B01G067100 chr3B 39843947 39847340 3393 True 6268 6268 100.000 1 3394 1 chr3B.!!$R1 3393
1 TraesCS3B01G067100 chr7B 716907319 716910709 3390 True 5888 5888 97.996 1 3394 1 chr7B.!!$R3 3393
2 TraesCS3B01G067100 chr7B 742954454 742957843 3389 False 5854 5854 97.820 1 3394 1 chr7B.!!$F1 3393
3 TraesCS3B01G067100 chr7B 716775503 716778892 3389 True 5849 5849 97.790 1 3394 1 chr7B.!!$R2 3393
4 TraesCS3B01G067100 chr7B 139590242 139593629 3387 True 5620 5620 96.582 1 3394 1 chr7B.!!$R1 3393
5 TraesCS3B01G067100 chr5A 16535476 16538866 3390 True 5877 5877 97.938 1 3394 1 chr5A.!!$R1 3393
6 TraesCS3B01G067100 chr7A 60345955 60349344 3389 True 5875 5875 97.936 1 3392 1 chr7A.!!$R1 3391
7 TraesCS3B01G067100 chr2B 391169338 391172728 3390 True 5843 5843 97.761 1 3394 1 chr2B.!!$R1 3393
8 TraesCS3B01G067100 chr1B 583567264 583570653 3389 False 5821 5821 97.643 1 3394 1 chr1B.!!$F1 3393
9 TraesCS3B01G067100 chr4B 209221421 209224810 3389 True 5777 5777 97.407 1 3394 1 chr4B.!!$R1 3393

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
133 134 0.955428 GTCGAAGCATGCCAGAACCA 60.955 55.000 15.66 0.0 0.00 3.67 F
421 422 1.369321 CCTAGCGGATTCTCCCTGC 59.631 63.158 0.00 0.0 31.13 4.85 F
1766 1767 0.807667 CGCTGGCGCTCTTTGATAGT 60.808 55.000 7.64 0.0 0.00 2.12 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1004 1005 1.079127 CGTTCTCCCGTGCTTCCAT 60.079 57.895 0.0 0.0 0.00 3.41 R
2278 2280 1.048724 TGGCCGAGGACTTCCATAGG 61.049 60.000 0.0 0.0 38.89 2.57 R
3267 3270 1.269723 CGACCCCCTTTTTGCTTTCTC 59.730 52.381 0.0 0.0 0.00 2.87 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
133 134 0.955428 GTCGAAGCATGCCAGAACCA 60.955 55.000 15.66 0.00 0.00 3.67
243 244 4.202040 TGTCATGTTCAAAGCAGGTTTCTG 60.202 41.667 0.00 0.00 43.64 3.02
323 324 6.305272 TCAGTTTCATCCTCTTTATGAGCT 57.695 37.500 0.00 0.00 41.35 4.09
421 422 1.369321 CCTAGCGGATTCTCCCTGC 59.631 63.158 0.00 0.00 31.13 4.85
424 425 2.175202 CTAGCGGATTCTCCCTGCTAT 58.825 52.381 0.00 0.00 37.53 2.97
462 463 3.118956 CCGCAGTCAAAACTCTCCTCTAT 60.119 47.826 0.00 0.00 31.71 1.98
632 633 4.080526 ACACACACATATTCCTCCCTTACC 60.081 45.833 0.00 0.00 0.00 2.85
635 636 5.193728 ACACACATATTCCTCCCTTACCAAT 59.806 40.000 0.00 0.00 0.00 3.16
738 739 6.466326 GGAAGTCATCATCATCCCCTTTATCA 60.466 42.308 0.00 0.00 0.00 2.15
743 744 7.614583 GTCATCATCATCCCCTTTATCAATCAT 59.385 37.037 0.00 0.00 0.00 2.45
871 872 2.102420 TCCAGCGAAAAGAACAGTCTCA 59.898 45.455 0.00 0.00 30.70 3.27
1004 1005 4.760530 AATTGGTAGAGCTCAGCATGTA 57.239 40.909 17.77 3.92 37.40 2.29
1155 1156 8.167392 TGGAAAAATAGGAGATTTAGTTCCACA 58.833 33.333 10.20 0.00 35.05 4.17
1331 1332 6.200878 AGGAAAGAAAGAATAGGGTTGTCA 57.799 37.500 0.00 0.00 0.00 3.58
1433 1434 5.911280 GCATAATCGGTTGTTCATGATCTTG 59.089 40.000 0.00 2.18 0.00 3.02
1460 1461 1.974265 TGGACCAAAGTCGCAAATCA 58.026 45.000 0.00 0.00 44.54 2.57
1766 1767 0.807667 CGCTGGCGCTCTTTGATAGT 60.808 55.000 7.64 0.00 0.00 2.12
1789 1790 4.199310 GCATTATCTACAACCCTGAAGCA 58.801 43.478 0.00 0.00 0.00 3.91
1904 1905 4.345854 AGAAGAAGGAATGTCGACCTACT 58.654 43.478 14.12 3.12 35.25 2.57
1915 1916 2.683933 ACCTACTGCTCCGTGGGG 60.684 66.667 8.19 0.00 39.61 4.96
1937 1938 4.112634 GTTTGAACCTTGCTTTTCTGTCC 58.887 43.478 0.00 0.00 0.00 4.02
1958 1959 4.342378 TCCAATTCTCAGACGCTATAGCTT 59.658 41.667 21.98 13.52 39.32 3.74
2213 2215 2.194271 GCTGAGGAAGGATTTCGTACG 58.806 52.381 9.53 9.53 33.98 3.67
2278 2280 5.816258 GCCTACCTAGTTGAAATAGGAACAC 59.184 44.000 23.81 7.96 42.15 3.32
2435 2437 6.001449 AGATCGAACCTATCCCATTTTGAA 57.999 37.500 0.00 0.00 0.00 2.69
2455 2457 6.028146 TGAAAGTACGATGGTTAGCTGTTA 57.972 37.500 0.00 0.00 0.00 2.41
2490 2492 7.517417 GCTGTACTAGAATGACAACACATATGC 60.517 40.741 1.58 0.00 0.00 3.14
2568 2570 2.352127 GGCCTTCATCTTTGACAGCAAC 60.352 50.000 0.00 0.00 33.65 4.17
2744 2747 5.869579 AGAAGCAGAATCTACAACTTTGGA 58.130 37.500 0.00 0.00 0.00 3.53
3138 3141 2.550855 GGCTGGTTGTGAGACATCTTCA 60.551 50.000 0.00 0.00 0.00 3.02
3267 3270 8.557864 CAGATGCTATTCCTTCAAGAAAGTATG 58.442 37.037 0.00 0.00 32.69 2.39
3283 3286 5.728637 AAGTATGAGAAAGCAAAAAGGGG 57.271 39.130 0.00 0.00 0.00 4.79
3284 3287 4.089361 AGTATGAGAAAGCAAAAAGGGGG 58.911 43.478 0.00 0.00 0.00 5.40
3309 3312 1.610038 TCACCGTATCGCGTCCAATAT 59.390 47.619 5.77 0.00 39.32 1.28
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
133 134 4.915158 GGTACGGCTCACTACTAAAGAT 57.085 45.455 0.00 0.00 0.00 2.40
243 244 5.049405 CAGTGATGTTTTCCAAGGTGTCTAC 60.049 44.000 0.00 0.00 0.00 2.59
323 324 7.348815 AGAATTGTTGACCCATATGATCTCAA 58.651 34.615 3.65 10.93 0.00 3.02
421 422 1.337118 GGAGAGGCAGGTCCAGATAG 58.663 60.000 0.00 0.00 37.29 2.08
424 425 2.039624 GGGAGAGGCAGGTCCAGA 59.960 66.667 0.00 0.00 37.29 3.86
565 566 6.176975 TCGATTTAGCGTTGTCATTTTCAT 57.823 33.333 0.00 0.00 0.00 2.57
738 739 2.708325 GGTGGAGGAAGAGGCTATGATT 59.292 50.000 0.00 0.00 0.00 2.57
743 744 0.343372 ATGGGTGGAGGAAGAGGCTA 59.657 55.000 0.00 0.00 0.00 3.93
829 830 7.174080 GCTGGAGAAAGAGAACACTTCTTTTAT 59.826 37.037 2.20 0.00 43.07 1.40
830 831 6.483640 GCTGGAGAAAGAGAACACTTCTTTTA 59.516 38.462 2.20 0.00 43.07 1.52
1004 1005 1.079127 CGTTCTCCCGTGCTTCCAT 60.079 57.895 0.00 0.00 0.00 3.41
1155 1156 3.330701 TCCCTTCTGCTACCAATCAAAGT 59.669 43.478 0.00 0.00 0.00 2.66
1331 1332 5.339008 TCTAATCCAAACAGCGTATCAGT 57.661 39.130 0.00 0.00 0.00 3.41
1408 1409 5.125356 AGATCATGAACAACCGATTATGCA 58.875 37.500 0.00 0.00 0.00 3.96
1433 1434 3.438781 TGCGACTTTGGTCCATGAATTAC 59.561 43.478 0.00 0.00 39.15 1.89
1766 1767 4.199310 GCTTCAGGGTTGTAGATAATGCA 58.801 43.478 0.00 0.00 0.00 3.96
1904 1905 1.527380 GTTCAAACCCCACGGAGCA 60.527 57.895 0.00 0.00 0.00 4.26
1915 1916 4.112634 GGACAGAAAAGCAAGGTTCAAAC 58.887 43.478 0.00 0.00 0.00 2.93
1958 1959 8.545420 GTGAGAAATCGAGTACTGTTTTTACAA 58.455 33.333 0.00 0.00 0.00 2.41
2009 2011 6.915544 AATCAGTGACTAATATGCACACAG 57.084 37.500 0.00 0.00 35.08 3.66
2213 2215 2.923121 TCTATCAAGAGCATTGTGGCC 58.077 47.619 0.00 0.00 0.00 5.36
2278 2280 1.048724 TGGCCGAGGACTTCCATAGG 61.049 60.000 0.00 0.00 38.89 2.57
2435 2437 4.860907 CGTTAACAGCTAACCATCGTACTT 59.139 41.667 6.39 0.00 37.22 2.24
2455 2457 6.096423 TGTCATTCTAGTACAGCTAATCCGTT 59.904 38.462 0.00 0.00 0.00 4.44
2568 2570 2.940890 AATACCGCGGCCTGTCATGG 62.941 60.000 28.58 0.00 0.00 3.66
2744 2747 8.542497 TCTTTTGCAGTCTGTAAATACGTATT 57.458 30.769 15.07 15.07 32.29 1.89
2964 2967 9.809096 TTCACTAAGAGCTAATGACTAGAAATG 57.191 33.333 0.00 0.00 0.00 2.32
3138 3141 5.749462 AGAAGCCATTTGTAGCACTAAGAT 58.251 37.500 0.00 0.00 0.00 2.40
3267 3270 1.269723 CGACCCCCTTTTTGCTTTCTC 59.730 52.381 0.00 0.00 0.00 2.87
3309 3312 2.571653 AGGTCAACTTGTGGCATAGCTA 59.428 45.455 0.00 0.00 31.37 3.32


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

AutoCloner maintained by Alex Coulton.