Multiple sequence alignment - TraesCS2D01G579500

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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 TraesCS2D01G579500 chr2D 100.000 4833 0 0 1 4833 641959797 641964629 0.000000e+00 8925
1 TraesCS2D01G579500 chr2D 98.769 3819 39 5 1018 4833 597940115 597943928 0.000000e+00 6785
2 TraesCS2D01G579500 chr2D 99.301 1573 7 1 1 1573 597938536 597940104 0.000000e+00 2841
3 TraesCS2D01G579500 chr2D 86.709 158 21 0 997 1154 513093661 513093818 4.970000e-40 176
4 TraesCS2D01G579500 chrUn 100.000 394 0 0 2968 3361 479437173 479436780 0.000000e+00 728
5 TraesCS2D01G579500 chr6D 80.448 491 68 21 984 1454 6982156 6982638 2.770000e-92 350
6 TraesCS2D01G579500 chr1A 81.074 391 50 15 965 1349 61575806 61576178 1.700000e-74 291
7 TraesCS2D01G579500 chr1A 78.673 422 61 20 888 1302 61713563 61713962 2.230000e-63 254
8 TraesCS2D01G579500 chr1D 78.657 417 59 21 944 1349 63543526 63543923 2.890000e-62 250
9 TraesCS2D01G579500 chr1B 85.185 243 27 7 944 1178 101591860 101591619 1.740000e-59 241
10 TraesCS2D01G579500 chr1B 86.512 215 26 2 967 1178 101519209 101519423 2.910000e-57 233


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 TraesCS2D01G579500 chr2D 641959797 641964629 4832 False 8925 8925 100.000 1 4833 1 chr2D.!!$F2 4832
1 TraesCS2D01G579500 chr2D 597938536 597943928 5392 False 4813 6785 99.035 1 4833 2 chr2D.!!$F3 4832

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
594 595 0.899717 AATGCAAGGCGTTGGATGGT 60.900 50.000 23.97 9.13 43.42 3.55 F
640 641 2.768527 TCCAGATCATCCTTGTCCTGAC 59.231 50.000 0.00 0.00 0.00 3.51 F
2372 2939 2.017049 GTGGCCCATCAACACAGATAC 58.983 52.381 0.00 0.00 35.30 2.24 F
2966 3534 1.821216 AAACCGGACCAATGCAGTAG 58.179 50.000 9.46 0.00 0.00 2.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2190 2757 1.268845 CGTTTCCAAAAACCTCGGTGG 60.269 52.381 0.0 0.0 41.46 4.61 R
2509 3077 9.646427 TTGCACTTTTGTAAAAATACTTGAACT 57.354 25.926 0.0 0.0 0.00 3.01 R
3595 4164 1.956477 TCCAGCACCTTTTTCAGCTTC 59.044 47.619 0.0 0.0 34.61 3.86 R
4731 5301 0.671251 TGTAAAAAGGGCGGTTGCTG 59.329 50.000 0.0 0.0 42.25 4.41 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
37 38 2.517450 GCTGAAATCGCCGGAGTCG 61.517 63.158 5.05 0.00 0.00 4.18
38 39 1.138883 CTGAAATCGCCGGAGTCGA 59.861 57.895 5.05 5.08 46.40 4.20
45 46 3.532155 GCCGGAGTCGATCAGCCT 61.532 66.667 5.05 0.00 39.00 4.58
135 136 2.806244 ACCTCAACAGTGTTAATCGCAC 59.194 45.455 8.49 0.00 37.13 5.34
151 152 9.289303 GTTAATCGCACAACTGAATATTCATTT 57.711 29.630 18.26 15.75 36.46 2.32
154 155 6.314018 TCGCACAACTGAATATTCATTTCAC 58.686 36.000 18.26 9.40 36.46 3.18
594 595 0.899717 AATGCAAGGCGTTGGATGGT 60.900 50.000 23.97 9.13 43.42 3.55
640 641 2.768527 TCCAGATCATCCTTGTCCTGAC 59.231 50.000 0.00 0.00 0.00 3.51
1573 2140 6.988622 TGTTAATTTTGGGGTATCAGTACG 57.011 37.500 0.00 0.00 0.00 3.67
1589 2156 5.250235 CAGTACGTACTGTTCATGATCCT 57.750 43.478 36.61 8.29 46.51 3.24
1604 2171 9.988815 GTTCATGATCCTAATCAACAGTAGTAT 57.011 33.333 0.00 0.00 44.85 2.12
1657 2224 3.175240 CTGACGGCTCGAGTTGCG 61.175 66.667 15.13 0.26 42.69 4.85
1976 2543 7.010738 CCCAGTTACGTCGTGTTCATATTAATT 59.989 37.037 8.47 0.00 0.00 1.40
1977 2544 9.022915 CCAGTTACGTCGTGTTCATATTAATTA 57.977 33.333 8.47 0.00 0.00 1.40
2182 2749 3.432326 CCCTCTACACCAAGTTCCATAGC 60.432 52.174 0.00 0.00 0.00 2.97
2255 2822 4.024670 AGGATAAAGCGAGAAGTACACCT 58.975 43.478 0.00 0.00 0.00 4.00
2372 2939 2.017049 GTGGCCCATCAACACAGATAC 58.983 52.381 0.00 0.00 35.30 2.24
2374 2941 2.040947 TGGCCCATCAACACAGATACAA 59.959 45.455 0.00 0.00 0.00 2.41
2966 3534 1.821216 AAACCGGACCAATGCAGTAG 58.179 50.000 9.46 0.00 0.00 2.57
3446 4015 4.455606 CAATCTGATGAGGGAAGGTAACC 58.544 47.826 0.00 0.00 37.17 2.85
3459 4028 3.141767 AGGTAACCTGAAAGAAGCCAC 57.858 47.619 0.00 0.00 34.07 5.01
3619 4188 3.009473 AGCTGAAAAAGGTGCTGGAGATA 59.991 43.478 0.00 0.00 34.56 1.98
3748 4317 3.889538 CAGTCCTATTCGACTCATACCCA 59.110 47.826 0.00 0.00 41.23 4.51
4178 4748 4.546829 AGCTAAACCATTAACACGGAGA 57.453 40.909 0.00 0.00 0.00 3.71
4236 4806 1.466858 AGGATCAACCCCTTTCCCAA 58.533 50.000 0.00 0.00 40.05 4.12
4439 5009 0.323725 CATTGGGTCCTCCTGTTGGG 60.324 60.000 0.00 0.00 36.20 4.12
4517 5087 3.564511 GCGTACAACGTTTACTCCACTA 58.435 45.455 0.00 0.00 44.73 2.74
4588 5158 3.547746 TCGCTATTTTTACCCATCCCAC 58.452 45.455 0.00 0.00 0.00 4.61
4775 5345 9.859427 CATTTTCTTGGTGATTTATGTGTACAT 57.141 29.630 0.00 2.75 40.22 2.29
4789 5359 8.702163 TTATGTGTACATGATGTGTTCTACTG 57.298 34.615 8.61 0.00 42.29 2.74
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
37 38 1.068434 GAGTAGTGCAGGAGGCTGATC 59.932 57.143 0.00 0.00 45.15 2.92
38 39 1.118838 GAGTAGTGCAGGAGGCTGAT 58.881 55.000 0.00 0.00 45.15 2.90
39 40 0.251787 TGAGTAGTGCAGGAGGCTGA 60.252 55.000 0.00 0.00 45.15 4.26
40 41 0.610174 TTGAGTAGTGCAGGAGGCTG 59.390 55.000 0.00 0.00 45.15 4.85
45 46 1.901833 TCAGCATTGAGTAGTGCAGGA 59.098 47.619 0.00 0.00 43.63 3.86
118 119 3.968096 CAGTTGTGCGATTAACACTGTTG 59.032 43.478 4.57 0.00 38.86 3.33
135 136 7.430211 CCACATCGTGAAATGAATATTCAGTTG 59.570 37.037 29.86 19.41 44.40 3.16
151 152 3.056179 TGCATAGAAGTTCCACATCGTGA 60.056 43.478 0.00 0.00 35.23 4.35
154 155 5.390251 GCATATGCATAGAAGTTCCACATCG 60.390 44.000 22.84 0.00 41.59 3.84
594 595 7.440523 GGAGAATTTAGAGTTCTGCTTTCAA 57.559 36.000 0.93 0.00 39.87 2.69
640 641 9.289303 CTACCGTGAATTATCCTTTTTCATTTG 57.711 33.333 0.00 0.00 32.48 2.32
1573 2140 8.136057 CTGTTGATTAGGATCATGAACAGTAC 57.864 38.462 12.68 0.00 40.50 2.73
1657 2224 7.544566 TCTTAACTATGTTCACCGAACTTGATC 59.455 37.037 8.23 0.00 42.39 2.92
1753 2320 8.186821 ACACGTAACGTCTAAAGCTCTAAATAT 58.813 33.333 0.00 0.00 38.32 1.28
1977 2544 9.725019 TGAATTCAAACTAGTCATCTGTGTATT 57.275 29.630 5.45 0.00 0.00 1.89
1978 2545 9.896645 ATGAATTCAAACTAGTCATCTGTGTAT 57.103 29.630 13.09 0.00 0.00 2.29
1979 2546 9.154847 CATGAATTCAAACTAGTCATCTGTGTA 57.845 33.333 13.09 0.00 0.00 2.90
2190 2757 1.268845 CGTTTCCAAAAACCTCGGTGG 60.269 52.381 0.00 0.00 41.46 4.61
2509 3077 9.646427 TTGCACTTTTGTAAAAATACTTGAACT 57.354 25.926 0.00 0.00 0.00 3.01
2895 3463 2.825205 TGCTTCTCTTTTGCCTTTTGC 58.175 42.857 0.00 0.00 41.77 3.68
2966 3534 7.430992 AGTACACTAGTTTTCCCGATTTTTC 57.569 36.000 0.00 0.00 0.00 2.29
3446 4015 3.293311 CACCATTGTGGCTTCTTTCAG 57.707 47.619 0.00 0.00 42.67 3.02
3459 4028 2.158827 TCGGTCCATATGTCCACCATTG 60.159 50.000 13.44 1.73 34.86 2.82
3595 4164 1.956477 TCCAGCACCTTTTTCAGCTTC 59.044 47.619 0.00 0.00 34.61 3.86
3619 4188 3.627395 TTGGACAAATGCTCCTCGTAT 57.373 42.857 0.00 0.00 0.00 3.06
4178 4748 5.077564 GGTTTTTCCTTCTTGGGATGTAGT 58.922 41.667 0.00 0.00 35.07 2.73
4439 5009 2.046285 AAGCCCAATAGCACACGGC 61.046 57.895 0.00 0.00 45.30 5.68
4542 5112 2.287188 GGCACACAATTCATCGCATAGG 60.287 50.000 0.00 0.00 0.00 2.57
4621 5191 6.410388 GGATTGGATGGGTAATGTTCCTCTTA 60.410 42.308 0.00 0.00 0.00 2.10
4731 5301 0.671251 TGTAAAAAGGGCGGTTGCTG 59.329 50.000 0.00 0.00 42.25 4.41
4775 5345 4.623932 AAAGAGGCAGTAGAACACATCA 57.376 40.909 0.00 0.00 0.00 3.07
4789 5359 5.177511 GCAAAACAAGGATTACAAAAGAGGC 59.822 40.000 0.00 0.00 0.00 4.70


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

AutoCloner maintained by Alex Coulton.