Multiple sequence alignment - TraesCS3A01G234300

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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 TraesCS3A01G234300 chr3A 100.000 2618 0 0 1 2618 437700172 437702789 0.000000e+00 4835
1 TraesCS3A01G234300 chr3A 96.753 2618 81 2 1 2618 542176335 542178948 0.000000e+00 4361
2 TraesCS3A01G234300 chr3A 94.945 2275 108 3 344 2618 285802474 285800207 0.000000e+00 3557
3 TraesCS3A01G234300 chr3A 79.820 1219 230 15 101 1311 532607395 532608605 0.000000e+00 874
4 TraesCS3A01G234300 chr3A 94.571 350 19 0 1 350 285810880 285810531 2.290000e-150 542
5 TraesCS3A01G234300 chr7A 96.715 2618 86 0 1 2618 193084493 193081876 0.000000e+00 4359
6 TraesCS3A01G234300 chr4B 92.577 2627 182 9 1 2618 527732545 527735167 0.000000e+00 3759
7 TraesCS3A01G234300 chr2A 92.316 2629 187 9 1 2618 398975337 398972713 0.000000e+00 3722
8 TraesCS3A01G234300 chr2A 91.974 2629 196 9 1 2618 398344233 398346857 0.000000e+00 3672
9 TraesCS3A01G234300 chr1B 91.273 2624 214 10 1 2618 149498369 149495755 0.000000e+00 3563
10 TraesCS3A01G234300 chr6D 89.341 1623 145 10 25 1645 240017706 240019302 0.000000e+00 2013
11 TraesCS3A01G234300 chr6D 87.303 890 109 3 1730 2618 240019425 240020311 0.000000e+00 1014
12 TraesCS3A01G234300 chr4D 94.379 1014 53 3 1606 2618 304278841 304279851 0.000000e+00 1554
13 TraesCS3A01G234300 chr4D 95.955 890 30 4 681 1570 304277957 304278840 0.000000e+00 1439


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 TraesCS3A01G234300 chr3A 437700172 437702789 2617 False 4835.0 4835 100.000 1 2618 1 chr3A.!!$F1 2617
1 TraesCS3A01G234300 chr3A 542176335 542178948 2613 False 4361.0 4361 96.753 1 2618 1 chr3A.!!$F3 2617
2 TraesCS3A01G234300 chr3A 285800207 285802474 2267 True 3557.0 3557 94.945 344 2618 1 chr3A.!!$R1 2274
3 TraesCS3A01G234300 chr3A 532607395 532608605 1210 False 874.0 874 79.820 101 1311 1 chr3A.!!$F2 1210
4 TraesCS3A01G234300 chr7A 193081876 193084493 2617 True 4359.0 4359 96.715 1 2618 1 chr7A.!!$R1 2617
5 TraesCS3A01G234300 chr4B 527732545 527735167 2622 False 3759.0 3759 92.577 1 2618 1 chr4B.!!$F1 2617
6 TraesCS3A01G234300 chr2A 398972713 398975337 2624 True 3722.0 3722 92.316 1 2618 1 chr2A.!!$R1 2617
7 TraesCS3A01G234300 chr2A 398344233 398346857 2624 False 3672.0 3672 91.974 1 2618 1 chr2A.!!$F1 2617
8 TraesCS3A01G234300 chr1B 149495755 149498369 2614 True 3563.0 3563 91.273 1 2618 1 chr1B.!!$R1 2617
9 TraesCS3A01G234300 chr6D 240017706 240020311 2605 False 1513.5 2013 88.322 25 2618 2 chr6D.!!$F1 2593
10 TraesCS3A01G234300 chr4D 304277957 304279851 1894 False 1496.5 1554 95.167 681 2618 2 chr4D.!!$F1 1937

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
641 642 1.00444 GAGGCTGTCTCGCAAAGGT 60.004 57.895 0.0 0.0 32.18 3.5 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2168 2242 1.064825 GGGGAGTGAAGTGGAGGAAA 58.935 55.0 0.0 0.0 0.0 3.13 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
130 131 4.949238 CCATTGGTAATTCACATCCTGTCA 59.051 41.667 0.00 0.00 0.00 3.58
273 274 5.333568 GGTTCGCGTTACAGTTAACTTCAAT 60.334 40.000 5.07 0.00 36.22 2.57
568 569 6.346040 CCACTTTTCTGAACAAATGCGAAATC 60.346 38.462 0.00 0.00 0.00 2.17
624 625 5.363868 CCCAGATGTAGTTGAATACAGGAGA 59.636 44.000 0.00 0.00 38.96 3.71
641 642 1.004440 GAGGCTGTCTCGCAAAGGT 60.004 57.895 0.00 0.00 32.18 3.50
682 683 5.194740 TGATGGTGAATATCCTTTACCCCAA 59.805 40.000 0.00 0.00 0.00 4.12
1197 1210 1.918957 AGCTCTCCCCTGCATAACTTT 59.081 47.619 0.00 0.00 0.00 2.66
1200 1213 3.873801 GCTCTCCCCTGCATAACTTTCAA 60.874 47.826 0.00 0.00 0.00 2.69
1396 1409 3.449737 TGGTAACTACATAGGTGCTGTCC 59.550 47.826 0.00 0.00 37.61 4.02
1413 1426 4.498241 CTGTCCTTTCAATCTGTGATCGA 58.502 43.478 0.00 0.00 35.70 3.59
1447 1460 3.055819 GGCTGTATCTGAGTCACTTCCAA 60.056 47.826 0.00 0.00 0.00 3.53
1581 1594 7.614494 CATTTGGTTATCCAGAGGAACAAAAT 58.386 34.615 10.39 5.54 45.22 1.82
1669 1711 3.642141 ACCTGTTGTCCTTTTGGTTCAT 58.358 40.909 0.00 0.00 41.38 2.57
1682 1724 3.719268 TGGTTCATGTGCTGTAATCCT 57.281 42.857 0.00 0.00 0.00 3.24
1716 1758 7.445707 TGGTGTTGAACTTAATTAGTACATGCA 59.554 33.333 0.00 0.00 35.54 3.96
1765 1838 1.002544 GTGTGCTGGGCTAACTCTCTT 59.997 52.381 0.00 0.00 0.00 2.85
1819 1893 2.029739 TCTTCGTCGCAGTTGGTTATCA 60.030 45.455 0.00 0.00 0.00 2.15
1926 2000 5.880054 ATGTGCTACTGTGTTAAATCACC 57.120 39.130 0.00 0.00 37.51 4.02
2004 2078 3.974642 AGGAGTCCTGGTACAAAAGAACT 59.025 43.478 12.07 0.00 38.70 3.01
2081 2155 2.359169 CCCTACTTGGCTGGAGCGA 61.359 63.158 0.00 0.00 43.26 4.93
2097 2171 0.109226 GCGACGGCTTCTACTGTTCT 60.109 55.000 0.00 0.00 35.83 3.01
2104 2178 3.427638 CGGCTTCTACTGTTCTTCATCGA 60.428 47.826 0.00 0.00 0.00 3.59
2168 2242 0.616111 AACCACTCGCTCTGATCCCT 60.616 55.000 0.00 0.00 0.00 4.20
2286 2361 6.494491 AGATGAAGAAGAGCACATCTAGCTAT 59.506 38.462 0.00 0.00 44.67 2.97
2342 2417 3.930229 CCGTTGTATTTCGATCTGGTTCA 59.070 43.478 0.00 0.00 0.00 3.18
2422 2497 0.179097 GCTCTTCCCTTCGATTCGCT 60.179 55.000 0.00 0.00 0.00 4.93
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
36 37 4.133820 CAAGGCGGTCAATATATGGTTCA 58.866 43.478 0.00 0.00 0.00 3.18
96 97 7.341512 TGTGAATTACCAATGGATGAATAGCAA 59.658 33.333 6.16 0.00 0.00 3.91
130 131 8.771702 AACACCATTGTAGCATCCTGCAGTAT 62.772 42.308 13.81 0.00 39.82 2.12
149 150 2.739943 TGTGTGGGATTTTGAACACCA 58.260 42.857 2.64 0.00 41.75 4.17
273 274 2.314852 TCCAGGATCCAGACCAGAAGTA 59.685 50.000 15.82 0.00 0.00 2.24
544 545 5.947503 TTTCGCATTTGTTCAGAAAAGTG 57.052 34.783 0.00 0.00 0.00 3.16
568 569 2.892425 GAGGTTCATCGCAGCCGG 60.892 66.667 0.00 0.00 34.56 6.13
624 625 1.302033 CACCTTTGCGAGACAGCCT 60.302 57.895 0.00 0.00 36.02 4.58
641 642 3.057104 CCATCACATTCTTCTTTGCAGCA 60.057 43.478 0.00 0.00 0.00 4.41
682 683 5.221722 ACGGATAATGCAGTTGGTGATATCT 60.222 40.000 3.98 0.00 0.00 1.98
726 727 1.601759 GCGGGCACATCCTATGCAT 60.602 57.895 3.79 3.79 45.27 3.96
1197 1210 9.554395 TGAGAAACTACATCTATTGTGTTTTGA 57.446 29.630 0.00 0.00 38.50 2.69
1327 1340 6.920817 TCGTTTCATCTTTCTCAGCTAGTAA 58.079 36.000 0.00 0.00 0.00 2.24
1396 1409 8.494347 GGAAGATATTCGATCACAGATTGAAAG 58.506 37.037 12.31 0.00 37.92 2.62
1413 1426 6.328672 ACTCAGATACAGCCAAGGAAGATATT 59.671 38.462 0.00 0.00 0.00 1.28
1581 1594 1.522092 GGCATCCGAGTCACCATCA 59.478 57.895 0.00 0.00 0.00 3.07
1669 1711 3.719268 AATCACCAGGATTACAGCACA 57.281 42.857 0.00 0.00 44.38 4.57
1682 1724 6.723298 ATTAAGTTCAACACCAAATCACCA 57.277 33.333 0.00 0.00 0.00 4.17
1801 1875 2.536365 GATGATAACCAACTGCGACGA 58.464 47.619 0.00 0.00 0.00 4.20
1819 1893 1.758122 GCTTTTGGGATGGGCCGAT 60.758 57.895 0.00 0.00 37.63 4.18
1863 1937 2.618442 TGCCATCATCGCTAATGTGA 57.382 45.000 0.00 0.00 36.68 3.58
2004 2078 1.381928 GGTGGTCTAGCGATCGTCCA 61.382 60.000 17.81 13.98 0.00 4.02
2081 2155 3.673594 CGATGAAGAACAGTAGAAGCCGT 60.674 47.826 0.00 0.00 0.00 5.68
2097 2171 1.143838 CACCTCCCGCATCGATGAA 59.856 57.895 29.20 9.49 0.00 2.57
2104 2178 2.705658 TGAATAGAATCACCTCCCGCAT 59.294 45.455 0.00 0.00 0.00 4.73
2168 2242 1.064825 GGGGAGTGAAGTGGAGGAAA 58.935 55.000 0.00 0.00 0.00 3.13
2286 2361 3.627395 ACCTGCCGTAAAGATCAATCA 57.373 42.857 0.00 0.00 0.00 2.57
2342 2417 3.959495 AGCAAACCCATGTCCATAGAT 57.041 42.857 0.00 0.00 0.00 1.98
2422 2497 2.041755 TGGCCTAGAGTTCTCAGAGACA 59.958 50.000 3.32 0.00 0.00 3.41
2584 2659 9.623350 GGCATTGCAAATTTGTGTATTTATTTT 57.377 25.926 19.03 0.00 0.00 1.82
2592 2667 5.293814 GCATATGGCATTGCAAATTTGTGTA 59.706 36.000 19.03 5.86 43.97 2.90


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

AutoCloner maintained by Alex Coulton.