Multiple sequence alignment - TraesCS7D01G073500

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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 TraesCS7D01G073500 chr7D 100.000 2393 0 0 1 2393 43130876 43133268 0.000000e+00 4420
1 TraesCS7D01G073500 chr7D 100.000 462 0 0 2886 3347 43133761 43134222 0.000000e+00 854
2 TraesCS7D01G073500 chr4A 95.440 1557 66 4 839 2393 650847825 650846272 0.000000e+00 2477
3 TraesCS7D01G073500 chr4A 89.627 482 23 7 2886 3346 650846252 650845777 3.720000e-164 588
4 TraesCS7D01G073500 chr4A 93.052 403 24 3 839 1240 650856102 650855703 1.340000e-163 586
5 TraesCS7D01G073500 chr4A 77.966 354 48 18 2992 3337 650843790 650843459 9.480000e-46 195
6 TraesCS7D01G073500 chr7A 94.098 1525 72 1 869 2393 42976415 42977921 0.000000e+00 2302
7 TraesCS7D01G073500 chr7A 89.189 296 16 6 2886 3173 42977942 42978229 4.110000e-94 355
8 TraesCS7D01G073500 chr7A 77.399 469 56 22 2887 3346 42979862 42980289 2.010000e-57 233
9 TraesCS7D01G073500 chr7A 90.667 150 5 1 3206 3346 42978233 42978382 1.230000e-44 191
10 TraesCS7D01G073500 chr7A 96.000 100 4 0 3248 3347 42978482 42978581 2.670000e-36 163
11 TraesCS7D01G073500 chr6D 93.341 841 40 6 1 839 349901568 349900742 0.000000e+00 1229
12 TraesCS7D01G073500 chr6D 92.857 840 43 7 4 841 366706202 366705378 0.000000e+00 1203
13 TraesCS7D01G073500 chr2D 93.238 843 39 7 1 841 78077382 78078208 0.000000e+00 1225
14 TraesCS7D01G073500 chr3D 93.128 844 40 8 1 841 475028388 475029216 0.000000e+00 1221
15 TraesCS7D01G073500 chr3D 92.654 844 46 5 1 842 286226230 286225401 0.000000e+00 1201
16 TraesCS7D01G073500 chr5D 92.781 845 43 8 1 842 212483659 212484488 0.000000e+00 1206
17 TraesCS7D01G073500 chr5D 84.140 372 51 5 1311 1678 286938204 286937837 1.480000e-93 353
18 TraesCS7D01G073500 chr6A 92.671 846 41 11 1 842 31268099 31267271 0.000000e+00 1199
19 TraesCS7D01G073500 chr4D 92.509 841 49 4 1 839 449446045 449446873 0.000000e+00 1192
20 TraesCS7D01G073500 chr1B 92.099 848 55 4 1 845 380642360 380641522 0.000000e+00 1184
21 TraesCS7D01G073500 chr7B 88.760 258 29 0 1671 1928 710696862 710697119 1.940000e-82 316
22 TraesCS7D01G073500 chr7B 87.984 258 31 0 1671 1928 710339275 710339532 4.200000e-79 305


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 TraesCS7D01G073500 chr7D 43130876 43134222 3346 False 2637.000000 4420 100.000000 1 3347 2 chr7D.!!$F1 3346
1 TraesCS7D01G073500 chr4A 650843459 650847825 4366 True 1086.666667 2477 87.677667 839 3346 3 chr4A.!!$R2 2507
2 TraesCS7D01G073500 chr7A 42976415 42980289 3874 False 648.800000 2302 89.470600 869 3347 5 chr7A.!!$F1 2478
3 TraesCS7D01G073500 chr6D 349900742 349901568 826 True 1229.000000 1229 93.341000 1 839 1 chr6D.!!$R1 838
4 TraesCS7D01G073500 chr6D 366705378 366706202 824 True 1203.000000 1203 92.857000 4 841 1 chr6D.!!$R2 837
5 TraesCS7D01G073500 chr2D 78077382 78078208 826 False 1225.000000 1225 93.238000 1 841 1 chr2D.!!$F1 840
6 TraesCS7D01G073500 chr3D 475028388 475029216 828 False 1221.000000 1221 93.128000 1 841 1 chr3D.!!$F1 840
7 TraesCS7D01G073500 chr3D 286225401 286226230 829 True 1201.000000 1201 92.654000 1 842 1 chr3D.!!$R1 841
8 TraesCS7D01G073500 chr5D 212483659 212484488 829 False 1206.000000 1206 92.781000 1 842 1 chr5D.!!$F1 841
9 TraesCS7D01G073500 chr6A 31267271 31268099 828 True 1199.000000 1199 92.671000 1 842 1 chr6A.!!$R1 841
10 TraesCS7D01G073500 chr4D 449446045 449446873 828 False 1192.000000 1192 92.509000 1 839 1 chr4D.!!$F1 838
11 TraesCS7D01G073500 chr1B 380641522 380642360 838 True 1184.000000 1184 92.099000 1 845 1 chr1B.!!$R1 844

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
850 857 1.065418 AGTTGGCCTAAATCCGGAGTG 60.065 52.381 11.34 0.00 0.0 3.51 F
1863 1872 1.006102 GTATGAGCGGCGCCACTAT 60.006 57.895 30.40 19.11 0.0 2.12 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1920 1929 1.375908 GAACTCCATCGCACCAGCA 60.376 57.895 0.0 0.0 42.27 4.41 R
3281 3307 0.608130 GGCACCAGGACCATTTTTCC 59.392 55.000 0.0 0.0 0.00 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
173 174 6.916360 AAGAGATTTGCCCAAATGTAAGAA 57.084 33.333 10.69 0.00 40.77 2.52
191 193 8.974060 TGTAAGAAAGTGTTAGAAAGGATTGT 57.026 30.769 0.00 0.00 0.00 2.71
378 380 9.412460 TGATTATCAAGGTGAAAATATTGAGCT 57.588 29.630 0.00 0.00 35.31 4.09
746 751 4.100084 CGGCCACTGCATCCCAGA 62.100 66.667 2.24 0.00 44.64 3.86
787 794 2.045634 GCCCTACCCAAACGGACC 60.046 66.667 0.00 0.00 34.64 4.46
790 797 1.619807 CCCTACCCAAACGGACCGAT 61.620 60.000 23.38 5.64 34.64 4.18
849 856 1.209747 GAGTTGGCCTAAATCCGGAGT 59.790 52.381 11.34 3.58 0.00 3.85
850 857 1.065418 AGTTGGCCTAAATCCGGAGTG 60.065 52.381 11.34 0.00 0.00 3.51
856 863 2.879026 GCCTAAATCCGGAGTGATTTCC 59.121 50.000 11.34 0.00 42.44 3.13
863 870 1.649664 CGGAGTGATTTCCTCTGCTG 58.350 55.000 0.00 0.00 34.96 4.41
911 919 1.078426 CCTGCAAACCCTAGTCCCG 60.078 63.158 0.00 0.00 0.00 5.14
1368 1377 2.408022 CGGGAGGACTTCTACGCG 59.592 66.667 3.53 3.53 0.00 6.01
1371 1380 2.278013 GAGGACTTCTACGCGGCG 60.278 66.667 22.36 22.36 0.00 6.46
1509 1518 2.811317 GTGCTCTTCTCCGCCGTG 60.811 66.667 0.00 0.00 0.00 4.94
1863 1872 1.006102 GTATGAGCGGCGCCACTAT 60.006 57.895 30.40 19.11 0.00 2.12
1920 1929 0.464870 AGAAGCTGCTCATGCTCGAT 59.535 50.000 1.00 0.00 40.22 3.59
1923 1932 1.888172 GCTGCTCATGCTCGATGCT 60.888 57.895 8.07 0.00 43.37 3.79
1926 1935 1.523258 GCTCATGCTCGATGCTGGT 60.523 57.895 8.07 0.00 43.37 4.00
2019 2028 1.574526 AAGGCAGGATTGGGCTGCTA 61.575 55.000 0.00 0.00 43.02 3.49
2365 2374 4.425180 TGAACTGGTAAACTTGCTACCA 57.575 40.909 2.18 2.18 45.23 3.25
2980 2989 9.474313 ACAAACCACACAATAACTATTGGATAT 57.526 29.630 12.80 0.00 45.54 1.63
3029 3038 0.112412 TCTTGCTCCAAAGTTCCCCC 59.888 55.000 0.00 0.00 0.00 5.40
3059 3068 1.889170 CTTTCCAAGGAGGCAAGGTTC 59.111 52.381 0.00 0.00 37.04 3.62
3098 3113 6.667414 AGTTTTGGGCATAATAGGAAATGTGA 59.333 34.615 0.00 0.00 0.00 3.58
3101 3116 6.012337 TGGGCATAATAGGAAATGTGAAGA 57.988 37.500 0.00 0.00 0.00 2.87
3143 3160 4.036734 GTCAACTGAGCATTGAAGGACAAA 59.963 41.667 0.00 0.00 42.03 2.83
3173 3190 6.385649 TTGAAGTGACCTACATTTGTTTCC 57.614 37.500 0.00 0.00 0.00 3.13
3196 3213 6.899075 TCCAAGGGAGTAATTAACTAGCTGTA 59.101 38.462 0.00 0.00 39.07 2.74
3204 3221 8.425577 AGTAATTAACTAGCTGTATGCACTTG 57.574 34.615 0.00 0.00 45.94 3.16
3259 3285 1.100463 TTCGTGGCTGCAACACACAT 61.100 50.000 18.04 0.00 38.74 3.21
3262 3288 2.006169 CGTGGCTGCAACACACATATA 58.994 47.619 18.04 0.00 38.74 0.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
173 174 6.293244 GCACGTTACAATCCTTTCTAACACTT 60.293 38.462 0.00 0.0 0.00 3.16
191 193 1.384525 AGCACACCAAAAGCACGTTA 58.615 45.000 0.00 0.0 0.00 3.18
378 380 3.636231 CCGGGTCTTGGTGCAGGA 61.636 66.667 0.00 0.0 0.00 3.86
660 665 1.370810 CGCCAGGGCCAAAAATGTT 59.629 52.632 6.18 0.0 37.98 2.71
661 666 2.582493 CCGCCAGGGCCAAAAATGT 61.582 57.895 6.18 0.0 37.98 2.71
746 751 2.351276 GTCATGTCCGGGCCTGTT 59.649 61.111 11.58 0.0 0.00 3.16
849 856 6.149973 CAGAATAACAACAGCAGAGGAAATCA 59.850 38.462 0.00 0.0 0.00 2.57
850 857 6.150140 ACAGAATAACAACAGCAGAGGAAATC 59.850 38.462 0.00 0.0 0.00 2.17
856 863 3.369147 CCGACAGAATAACAACAGCAGAG 59.631 47.826 0.00 0.0 0.00 3.35
863 870 3.797256 CCGAGATCCGACAGAATAACAAC 59.203 47.826 5.32 0.0 41.76 3.32
911 919 0.441921 GCAAGAAGAGTGAAGCGAGC 59.558 55.000 0.00 0.0 0.00 5.03
944 952 1.641192 GGGAGAGGGGAACTGGATTTT 59.359 52.381 0.00 0.0 0.00 1.82
1920 1929 1.375908 GAACTCCATCGCACCAGCA 60.376 57.895 0.00 0.0 42.27 4.41
2019 2028 5.422012 GTCCAATGTGTTCCTCCCAATATTT 59.578 40.000 0.00 0.0 0.00 1.40
2365 2374 6.421485 ACTGCTGAAAACAAGAGGATGATAT 58.579 36.000 0.00 0.0 0.00 1.63
2903 2912 6.884295 TGTAATTTTGTGGACAGAGGGAATAG 59.116 38.462 0.00 0.0 0.00 1.73
2980 2989 9.412460 AGGAATGATGATAATTGACTTTTAGCA 57.588 29.630 0.00 0.0 30.42 3.49
2988 2997 9.947669 CAAGAGAAAGGAATGATGATAATTGAC 57.052 33.333 0.00 0.0 0.00 3.18
2989 2998 8.627403 GCAAGAGAAAGGAATGATGATAATTGA 58.373 33.333 0.00 0.0 0.00 2.57
2990 2999 8.630917 AGCAAGAGAAAGGAATGATGATAATTG 58.369 33.333 0.00 0.0 0.00 2.32
2991 3000 8.763984 AGCAAGAGAAAGGAATGATGATAATT 57.236 30.769 0.00 0.0 0.00 1.40
2992 3001 7.447853 GGAGCAAGAGAAAGGAATGATGATAAT 59.552 37.037 0.00 0.0 0.00 1.28
3059 3068 2.607771 CCAAAACTCCCATGAACAAGCG 60.608 50.000 0.00 0.0 0.00 4.68
3098 3113 6.321181 TGACAATTTTGTAGGCACTTCTTCTT 59.679 34.615 0.00 0.0 42.43 2.52
3101 3116 6.096846 AGTTGACAATTTTGTAGGCACTTCTT 59.903 34.615 0.00 0.0 42.43 2.52
3143 3160 9.665719 ACAAATGTAGGTCACTTCAAAATTTTT 57.334 25.926 0.00 0.0 0.00 1.94
3150 3167 5.888724 TGGAAACAAATGTAGGTCACTTCAA 59.111 36.000 0.00 0.0 37.44 2.69
3151 3168 5.441500 TGGAAACAAATGTAGGTCACTTCA 58.558 37.500 0.00 0.0 37.44 3.02
3173 3190 7.171678 GCATACAGCTAGTTAATTACTCCCTTG 59.828 40.741 0.00 0.0 41.15 3.61
3196 3213 6.225981 AGAAAAGAAAAAGGACAAGTGCAT 57.774 33.333 0.00 0.0 0.00 3.96
3204 3221 9.947669 GTAGGAACTAAAGAAAAGAAAAAGGAC 57.052 33.333 0.00 0.0 45.48 3.85
3262 3288 8.537728 TTTTTCCTGATATATCTTTGGCATGT 57.462 30.769 13.79 0.0 0.00 3.21
3281 3307 0.608130 GGCACCAGGACCATTTTTCC 59.392 55.000 0.00 0.0 0.00 3.13


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

AutoCloner maintained by Alex Coulton.