Multiple sequence alignment - TraesCS3D01G411000

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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 TraesCS3D01G411000 chr3D 100.000 3911 0 0 1 3911 523765881 523769791 0.000000e+00 7223
1 TraesCS3D01G411000 chr4D 97.557 3930 70 14 1 3911 123318007 123321929 0.000000e+00 6702
2 TraesCS3D01G411000 chrUn 97.350 3925 66 14 1 3911 206781204 206785104 0.000000e+00 6637
3 TraesCS3D01G411000 chr7A 97.195 3922 75 14 1 3911 60261860 60265757 0.000000e+00 6601
4 TraesCS3D01G411000 chr7A 96.610 3923 98 20 1 3911 120858592 120854693 0.000000e+00 6475
5 TraesCS3D01G411000 chr7A 97.194 3100 78 8 816 3911 46420278 46423372 0.000000e+00 5234
6 TraesCS3D01G411000 chr7A 81.982 222 13 10 648 860 60341811 60342014 3.130000e-36 163
7 TraesCS3D01G411000 chr7A 80.526 190 19 4 707 895 60290578 60290750 3.170000e-26 130
8 TraesCS3D01G411000 chr3B 96.917 3925 95 14 1 3911 483383249 483387161 0.000000e+00 6554
9 TraesCS3D01G411000 chr3B 96.889 3922 104 12 1 3911 669797984 669794070 0.000000e+00 6551
10 TraesCS3D01G411000 chr6B 95.921 3923 137 14 1 3911 297455661 297459572 0.000000e+00 6336
11 TraesCS3D01G411000 chr5A 97.484 3100 70 8 816 3911 238849203 238846108 0.000000e+00 5286
12 TraesCS3D01G411000 chr5A 95.161 186 9 0 729 914 57661288 57661473 1.060000e-75 294
13 TraesCS3D01G411000 chr3A 82.301 226 13 9 644 860 272052820 272052613 1.870000e-38 171


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 TraesCS3D01G411000 chr3D 523765881 523769791 3910 False 7223 7223 100.000 1 3911 1 chr3D.!!$F1 3910
1 TraesCS3D01G411000 chr4D 123318007 123321929 3922 False 6702 6702 97.557 1 3911 1 chr4D.!!$F1 3910
2 TraesCS3D01G411000 chrUn 206781204 206785104 3900 False 6637 6637 97.350 1 3911 1 chrUn.!!$F1 3910
3 TraesCS3D01G411000 chr7A 60261860 60265757 3897 False 6601 6601 97.195 1 3911 1 chr7A.!!$F2 3910
4 TraesCS3D01G411000 chr7A 120854693 120858592 3899 True 6475 6475 96.610 1 3911 1 chr7A.!!$R1 3910
5 TraesCS3D01G411000 chr7A 46420278 46423372 3094 False 5234 5234 97.194 816 3911 1 chr7A.!!$F1 3095
6 TraesCS3D01G411000 chr3B 483383249 483387161 3912 False 6554 6554 96.917 1 3911 1 chr3B.!!$F1 3910
7 TraesCS3D01G411000 chr3B 669794070 669797984 3914 True 6551 6551 96.889 1 3911 1 chr3B.!!$R1 3910
8 TraesCS3D01G411000 chr6B 297455661 297459572 3911 False 6336 6336 95.921 1 3911 1 chr6B.!!$F1 3910
9 TraesCS3D01G411000 chr5A 238846108 238849203 3095 True 5286 5286 97.484 816 3911 1 chr5A.!!$R1 3095

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
969 989 1.026182 GTGATGCTGCGGAACCATGA 61.026 55.0 0.0 0.0 0.0 3.07 F
1087 1107 0.036388 ATCACGGATGTTGGTTCGCT 60.036 50.0 0.0 0.0 0.0 4.93 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2214 2240 0.179045 CCACGGAAAGGGATGCTAGG 60.179 60.0 0.0 0.0 0.00 3.02 R
2913 2939 1.779061 TTTCCGCTTCAGCTTCCCCT 61.779 55.0 0.0 0.0 39.32 4.79 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
57 58 2.677914 TCATTCCTATCTCCTTCGGCA 58.322 47.619 0.00 0.00 0.00 5.69
73 74 1.893808 GCATCAGCCCCATGTACCG 60.894 63.158 0.00 0.00 33.58 4.02
208 209 7.841915 TTTTCAGTGAAATCTTGTTTTTCCC 57.158 32.000 18.69 0.00 33.15 3.97
209 210 5.181690 TCAGTGAAATCTTGTTTTTCCCG 57.818 39.130 0.00 0.00 33.15 5.14
211 212 3.383185 AGTGAAATCTTGTTTTTCCCGCA 59.617 39.130 0.00 0.00 33.15 5.69
293 303 2.158871 ACACAAGAGGTTTTAGCACCGA 60.159 45.455 0.00 0.00 42.33 4.69
377 387 7.806487 CCGATTTGAAATGGTGATGAATATGAG 59.194 37.037 0.00 0.00 0.00 2.90
425 435 2.195741 ATGCATCATGGAATCCGGAG 57.804 50.000 11.34 0.00 0.00 4.63
433 443 4.728772 TCATGGAATCCGGAGCATTAAAT 58.271 39.130 11.34 0.00 0.00 1.40
577 587 2.740981 CGAGGGCTTGATATCTCATTGC 59.259 50.000 3.98 1.55 33.27 3.56
634 644 2.028020 ACTCACGAGGTCCTTGATTTCC 60.028 50.000 13.57 0.00 0.00 3.13
642 652 5.105473 CGAGGTCCTTGATTTCCTGTTAGTA 60.105 44.000 0.00 0.00 0.00 1.82
711 727 3.882888 TCCGTTGTTGCTCTTCAGAAAAT 59.117 39.130 0.00 0.00 0.00 1.82
914 934 6.899075 AGATGGGAAATTCCAATGATTCTTCA 59.101 34.615 14.68 0.00 40.62 3.02
969 989 1.026182 GTGATGCTGCGGAACCATGA 61.026 55.000 0.00 0.00 0.00 3.07
1087 1107 0.036388 ATCACGGATGTTGGTTCGCT 60.036 50.000 0.00 0.00 0.00 4.93
1204 1224 9.282247 GTGTCATTCTTTTGTTCATTGCTATAG 57.718 33.333 0.00 0.00 0.00 1.31
1429 1449 1.235281 GCCAGAAACGGGGAGTTGAC 61.235 60.000 0.00 0.00 43.37 3.18
1586 1606 1.868519 CGATAACGGGGCTTCAGTAGC 60.869 57.143 0.00 0.00 41.48 3.58
1718 1738 1.008938 ACTACTGGGCCAAGAGAGGAT 59.991 52.381 16.25 0.00 0.00 3.24
1722 1742 1.839994 CTGGGCCAAGAGAGGATAACA 59.160 52.381 8.04 0.00 0.00 2.41
1737 1757 4.018960 AGGATAACATGTTGTTCCTGCTCT 60.019 41.667 29.72 15.14 40.22 4.09
2063 2089 4.514066 GTGGACAAACATACTTTTCGGTCT 59.486 41.667 0.00 0.00 0.00 3.85
2125 2151 7.415592 TCACATGAGCATAGGGAATCTATAG 57.584 40.000 0.00 0.00 36.59 1.31
2177 2203 3.515562 AGGTGAGGAATCACTCTTGAGT 58.484 45.455 8.18 0.00 40.28 3.41
2214 2240 1.847890 TACAACTTCGCCAAAGCCGC 61.848 55.000 0.00 0.00 38.67 6.53
2326 2352 1.004230 ATGTAGGTAGGGCTGGGCA 59.996 57.895 0.00 0.00 0.00 5.36
2519 2545 2.281276 GGCGTCGACCCAACCTTT 60.281 61.111 10.58 0.00 0.00 3.11
2913 2939 8.364142 CAATTAATCCTCCAAACCAACTAAACA 58.636 33.333 0.00 0.00 0.00 2.83
3265 3291 2.555757 GAGCAGCCCTTATTGCAATAGG 59.444 50.000 18.97 18.97 42.67 2.57
3462 3489 2.223443 TACCAGCCAAGCCAGCTCA 61.223 57.895 0.00 0.00 38.95 4.26
3783 3813 4.355287 ACCCTCTCCTCCTTTTTGAGAAAT 59.645 41.667 0.00 0.00 34.91 2.17
3887 3920 2.159627 CGAAGGGCATTCTGTTGTACAC 59.840 50.000 10.42 0.00 35.61 2.90
3891 3924 3.329520 AGGGCATTCTGTTGTACACCTAA 59.670 43.478 0.00 0.00 0.00 2.69
3906 3939 9.585099 TTGTACACCTAATTTGGTATAGTTACG 57.415 33.333 11.38 0.00 38.45 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
57 58 2.510906 GCGGTACATGGGGCTGAT 59.489 61.111 0.00 0.00 0.00 2.90
73 74 6.977213 TCAATTCAAGTGGTTAGTTTAAGGC 58.023 36.000 0.00 0.00 0.00 4.35
158 159 1.617533 GCCTAACCCCGGGATTTTTCA 60.618 52.381 26.32 0.00 0.00 2.69
206 207 3.600388 GATTCTCCCATAACTATGCGGG 58.400 50.000 0.00 0.00 32.40 6.13
207 208 3.261897 AGGATTCTCCCATAACTATGCGG 59.738 47.826 0.00 0.00 37.19 5.69
208 209 4.543590 AGGATTCTCCCATAACTATGCG 57.456 45.455 0.00 0.00 37.19 4.73
209 210 4.457257 GCAAGGATTCTCCCATAACTATGC 59.543 45.833 0.00 0.00 37.19 3.14
211 212 6.466470 GGAAGCAAGGATTCTCCCATAACTAT 60.466 42.308 0.00 0.00 37.19 2.12
410 420 2.965671 AATGCTCCGGATTCCATGAT 57.034 45.000 3.57 0.00 0.00 2.45
425 435 8.818057 CAACTGTCTACACTACCTATTTAATGC 58.182 37.037 0.00 0.00 0.00 3.56
577 587 2.810274 CGGCCTCATCAATTAGTCATGG 59.190 50.000 0.00 0.00 0.00 3.66
711 727 5.051441 CGACGAAGACTACTTACTATACGCA 60.051 44.000 0.00 0.00 36.39 5.24
783 799 3.762407 TCTTTCACGAACTCCCATGAA 57.238 42.857 0.00 0.00 0.00 2.57
790 806 6.049263 ACAAGAACATTCTTTCACGAACTC 57.951 37.500 4.08 0.00 44.70 3.01
914 934 7.219322 TGTGAGGAATCGACATGATAATGAAT 58.781 34.615 0.00 0.00 35.84 2.57
969 989 4.437239 CTGCGTCTTGAGATCCTAATTGT 58.563 43.478 0.00 0.00 0.00 2.71
1087 1107 3.755905 TGCTCGTTGAAATGCCATAAAGA 59.244 39.130 0.00 0.00 0.00 2.52
1362 1382 0.620410 ACGGGAATGGGAGATGACCA 60.620 55.000 0.00 0.00 43.22 4.02
1395 1415 5.277058 CGTTTCTGGCATGCTATAGTTCTTC 60.277 44.000 18.92 0.00 0.00 2.87
1718 1738 4.072131 GGAAGAGCAGGAACAACATGTTA 58.928 43.478 11.53 0.00 41.28 2.41
1722 1742 3.073650 AGAAGGAAGAGCAGGAACAACAT 59.926 43.478 0.00 0.00 0.00 2.71
1737 1757 1.189524 TCCCCGAAGCGAAGAAGGAA 61.190 55.000 0.00 0.00 0.00 3.36
1769 1789 3.866651 CTTGTGCATGCTCTTACCTACT 58.133 45.455 20.33 0.00 0.00 2.57
2125 2151 2.095252 GCCAAGTCGAAGGCTCGAC 61.095 63.158 23.01 23.01 40.46 4.20
2177 2203 3.664320 TGTAGGCCCCAATAGATCAGAA 58.336 45.455 0.00 0.00 0.00 3.02
2214 2240 0.179045 CCACGGAAAGGGATGCTAGG 60.179 60.000 0.00 0.00 0.00 3.02
2446 2472 2.151202 CAAAAAGCTCTCCACGCCTAA 58.849 47.619 0.00 0.00 0.00 2.69
2519 2545 7.486647 GGAACTGTTATAGTCCGAATACTCAA 58.513 38.462 0.00 0.00 39.18 3.02
2913 2939 1.779061 TTTCCGCTTCAGCTTCCCCT 61.779 55.000 0.00 0.00 39.32 4.79
3757 3787 1.074566 CAAAAAGGAGGAGAGGGTGCT 59.925 52.381 0.00 0.00 0.00 4.40
3768 3798 6.071165 ACAAGCCCATATTTCTCAAAAAGGAG 60.071 38.462 0.00 0.00 36.21 3.69


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

AutoCloner maintained by Alex Coulton.