Multiple sequence alignment - TraesCS2D01G222800

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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 TraesCS2D01G222800 chr2D 100.000 2794 0 0 1 2794 189855010 189857803 0.000000e+00 5160
1 TraesCS2D01G222800 chr2D 97.638 1863 36 5 1 1859 637321081 637319223 0.000000e+00 3190
2 TraesCS2D01G222800 chr2D 95.183 955 34 3 1852 2794 39577676 39576722 0.000000e+00 1498
3 TraesCS2D01G222800 chr2D 94.154 958 40 6 1852 2794 39703993 39703037 0.000000e+00 1445
4 TraesCS2D01G222800 chr2D 95.981 821 27 2 1980 2794 200912074 200911254 0.000000e+00 1328
5 TraesCS2D01G222800 chr5A 97.311 1934 42 7 1 1928 73031640 73033569 0.000000e+00 3275
6 TraesCS2D01G222800 chr5A 96.224 821 25 2 1980 2794 614342221 614343041 0.000000e+00 1339
7 TraesCS2D01G222800 chr1B 97.206 1933 45 6 1 1928 638749961 638748033 0.000000e+00 3262
8 TraesCS2D01G222800 chr7A 97.155 1933 42 9 1 1928 60106948 60105024 0.000000e+00 3253
9 TraesCS2D01G222800 chr7A 96.955 821 19 2 1980 2794 4947632 4946812 0.000000e+00 1373
10 TraesCS2D01G222800 chr3B 96.999 1933 49 7 1 1928 575754675 575752747 0.000000e+00 3240
11 TraesCS2D01G222800 chr2B 96.586 1933 57 6 1 1928 500714167 500716095 0.000000e+00 3195
12 TraesCS2D01G222800 chr2B 96.046 1922 69 6 1 1918 751970335 751968417 0.000000e+00 3121
13 TraesCS2D01G222800 chr6D 97.638 1863 36 5 1 1859 108464397 108466255 0.000000e+00 3190
14 TraesCS2D01G222800 chr6B 96.482 1933 58 7 1 1928 388367584 388365657 0.000000e+00 3184
15 TraesCS2D01G222800 chr6B 96.102 821 25 3 1980 2794 388183039 388183858 0.000000e+00 1332
16 TraesCS2D01G222800 chr6B 95.859 821 28 2 1980 2794 388300264 388301084 0.000000e+00 1323
17 TraesCS2D01G222800 chr7D 96.421 978 29 2 1607 2578 467054499 467055476 0.000000e+00 1607
18 TraesCS2D01G222800 chr7B 96.346 821 24 4 1980 2794 47133085 47132265 0.000000e+00 1345
19 TraesCS2D01G222800 chrUn 92.053 151 5 2 1852 1996 233525248 233525099 3.650000e-49 206
20 TraesCS2D01G222800 chrUn 92.053 151 5 2 1852 1996 257944132 257944281 3.650000e-49 206
21 TraesCS2D01G222800 chr4D 92.053 151 5 2 1852 1996 123688981 123689130 3.650000e-49 206


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 TraesCS2D01G222800 chr2D 189855010 189857803 2793 False 5160 5160 100.000 1 2794 1 chr2D.!!$F1 2793
1 TraesCS2D01G222800 chr2D 637319223 637321081 1858 True 3190 3190 97.638 1 1859 1 chr2D.!!$R4 1858
2 TraesCS2D01G222800 chr2D 39576722 39577676 954 True 1498 1498 95.183 1852 2794 1 chr2D.!!$R1 942
3 TraesCS2D01G222800 chr2D 39703037 39703993 956 True 1445 1445 94.154 1852 2794 1 chr2D.!!$R2 942
4 TraesCS2D01G222800 chr2D 200911254 200912074 820 True 1328 1328 95.981 1980 2794 1 chr2D.!!$R3 814
5 TraesCS2D01G222800 chr5A 73031640 73033569 1929 False 3275 3275 97.311 1 1928 1 chr5A.!!$F1 1927
6 TraesCS2D01G222800 chr5A 614342221 614343041 820 False 1339 1339 96.224 1980 2794 1 chr5A.!!$F2 814
7 TraesCS2D01G222800 chr1B 638748033 638749961 1928 True 3262 3262 97.206 1 1928 1 chr1B.!!$R1 1927
8 TraesCS2D01G222800 chr7A 60105024 60106948 1924 True 3253 3253 97.155 1 1928 1 chr7A.!!$R2 1927
9 TraesCS2D01G222800 chr7A 4946812 4947632 820 True 1373 1373 96.955 1980 2794 1 chr7A.!!$R1 814
10 TraesCS2D01G222800 chr3B 575752747 575754675 1928 True 3240 3240 96.999 1 1928 1 chr3B.!!$R1 1927
11 TraesCS2D01G222800 chr2B 500714167 500716095 1928 False 3195 3195 96.586 1 1928 1 chr2B.!!$F1 1927
12 TraesCS2D01G222800 chr2B 751968417 751970335 1918 True 3121 3121 96.046 1 1918 1 chr2B.!!$R1 1917
13 TraesCS2D01G222800 chr6D 108464397 108466255 1858 False 3190 3190 97.638 1 1859 1 chr6D.!!$F1 1858
14 TraesCS2D01G222800 chr6B 388365657 388367584 1927 True 3184 3184 96.482 1 1928 1 chr6B.!!$R1 1927
15 TraesCS2D01G222800 chr6B 388183039 388183858 819 False 1332 1332 96.102 1980 2794 1 chr6B.!!$F1 814
16 TraesCS2D01G222800 chr6B 388300264 388301084 820 False 1323 1323 95.859 1980 2794 1 chr6B.!!$F2 814
17 TraesCS2D01G222800 chr7D 467054499 467055476 977 False 1607 1607 96.421 1607 2578 1 chr7D.!!$F1 971
18 TraesCS2D01G222800 chr7B 47132265 47133085 820 True 1345 1345 96.346 1980 2794 1 chr7B.!!$R1 814

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
647 649 0.186386 CTCCCGAGGGATAGACCACT 59.814 60.0 11.86 0.0 44.24 4.0 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2134 2155 0.734253 GTGCACTCGTAGGTGAGCTG 60.734 60.0 10.32 0.0 39.68 4.24 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
83 84 4.024670 ACTAAGTAAGATGCCGGAGAAGT 58.975 43.478 5.05 0.00 0.00 3.01
107 108 7.758076 AGTGACGAAATATACGAGATCACAAAA 59.242 33.333 17.62 0.00 37.03 2.44
273 274 0.325602 TATTTTCACGGGTCGCCCTT 59.674 50.000 12.26 1.15 42.67 3.95
294 295 5.296035 CCTTGTTCCGTAGTTGAGTTCTTTT 59.704 40.000 0.00 0.00 0.00 2.27
582 583 5.184671 ACGTAAAGGGTAGTACTCTTGGAAG 59.815 44.000 16.23 11.64 38.11 3.46
583 584 5.416952 CGTAAAGGGTAGTACTCTTGGAAGA 59.583 44.000 16.23 0.00 38.11 2.87
606 607 0.716108 GAAGATCACCGCGTGAACAG 59.284 55.000 13.81 0.00 45.96 3.16
640 642 2.317040 GAATGTCACTCCCGAGGGATA 58.683 52.381 11.86 0.00 43.66 2.59
647 649 0.186386 CTCCCGAGGGATAGACCACT 59.814 60.000 11.86 0.00 44.24 4.00
648 650 1.424302 CTCCCGAGGGATAGACCACTA 59.576 57.143 11.86 0.00 44.24 2.74
741 743 1.689273 GAAGTCAGAGTCTGGGTGTGT 59.311 52.381 19.99 0.32 31.51 3.72
1070 1072 1.134907 GCCTATTTCGGGTTCACTCGA 60.135 52.381 0.00 0.00 0.00 4.04
1394 1398 5.022787 TGGGTTTTAGATCCTTGGGAAATG 58.977 41.667 0.00 0.00 34.34 2.32
1477 1484 0.250989 ATCGCGGGGAAGGAAAAACA 60.251 50.000 6.13 0.00 0.00 2.83
1537 1544 5.023452 TCTAGTATCCACTGGCTTTCAAGA 58.977 41.667 0.00 0.00 36.14 3.02
1574 1581 1.742750 GCACCCTCCACTATTTCGGAC 60.743 57.143 0.00 0.00 0.00 4.79
1750 1757 2.550606 GGCATTTTGTAGACGTGGTTCA 59.449 45.455 0.00 0.00 0.00 3.18
1834 1841 4.035675 GTGGATTGAGGAATAAAAGCTCGG 59.964 45.833 0.00 0.00 0.00 4.63
1870 1883 6.371278 ACTTCTCCGGGTACTCAAGATATTA 58.629 40.000 0.00 0.00 0.00 0.98
1926 1947 5.105310 CCGAGAAGACCAGGAAAAGATAAGA 60.105 44.000 0.00 0.00 0.00 2.10
2083 2104 7.345653 CCCTGGCTAAGAATCTATATCATACCA 59.654 40.741 0.00 0.00 0.00 3.25
2134 2155 3.686726 AGAACACATGAATCCTCGCTTTC 59.313 43.478 0.00 0.00 0.00 2.62
2237 2263 8.833231 TTAGAGACGATCAAGTTTGAGAAAAT 57.167 30.769 0.74 0.00 41.08 1.82
2247 2273 8.633075 TCAAGTTTGAGAAAATAAAAGTGCAG 57.367 30.769 0.00 0.00 32.50 4.41
2252 2278 5.060506 TGAGAAAATAAAAGTGCAGACCGA 58.939 37.500 0.00 0.00 0.00 4.69
2275 2301 1.491668 TATGCCTCGGAAAGCTACCA 58.508 50.000 9.92 0.00 0.00 3.25
2489 2517 2.066262 AGTTATTGTCGCACACTTCCG 58.934 47.619 0.00 0.00 0.00 4.30
2514 2542 7.158021 GTCTAGGAGATGCATGTTAAGCTATT 58.842 38.462 2.46 0.00 0.00 1.73
2742 2770 8.705048 AGAAAAGAGCTAAGGAACTATTTACG 57.295 34.615 0.00 0.00 38.49 3.18
2773 2801 1.429463 GGGTGCTGAACGAACTACTG 58.571 55.000 0.00 0.00 0.00 2.74
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
20 21 0.320771 AAAGCCGCTCCACAGTAGTG 60.321 55.000 0.00 0.00 45.47 2.74
83 84 7.758076 ACTTTTGTGATCTCGTATATTTCGTCA 59.242 33.333 0.00 0.00 0.00 4.35
124 125 9.346725 GAAAGCTTTCGTCTCAATTCATATTTT 57.653 29.630 22.66 0.00 0.00 1.82
273 274 4.034742 GCAAAAGAACTCAACTACGGAACA 59.965 41.667 0.00 0.00 0.00 3.18
294 295 6.020984 CACGAAAAATGATACGAGAAATGCA 58.979 36.000 0.00 0.00 0.00 3.96
582 583 1.135373 TCACGCGGTGATCTTCTCTTC 60.135 52.381 12.47 0.00 37.67 2.87
583 584 0.888619 TCACGCGGTGATCTTCTCTT 59.111 50.000 12.47 0.00 37.67 2.85
606 607 7.415653 GGGAGTGACATTCATTACTTTGGATTC 60.416 40.741 0.00 0.00 0.00 2.52
981 983 0.537828 TAAACCACTTTGCCCCGGTC 60.538 55.000 0.00 0.00 0.00 4.79
1070 1072 0.466555 TACGGTGGTTGCCAAAGCTT 60.467 50.000 0.00 0.00 40.80 3.74
1111 1113 0.321346 GTTGCACCCCCTTGAAATGG 59.679 55.000 0.00 0.00 0.00 3.16
1174 1176 0.469917 AGAACATCCCGCCACCATAG 59.530 55.000 0.00 0.00 0.00 2.23
1371 1375 4.750833 TTTCCCAAGGATCTAAAACCCA 57.249 40.909 0.00 0.00 0.00 4.51
1394 1398 6.295973 GGAGAATAGGGGTATTAAGAAGAGGC 60.296 46.154 0.00 0.00 0.00 4.70
1537 1544 5.528337 AGGGTGCTTGGTAATATTCCATTT 58.472 37.500 7.26 0.00 34.75 2.32
1834 1841 3.580731 CCGGAGAAGTTCTCTTTGTCTC 58.419 50.000 27.68 11.70 42.95 3.36
1870 1883 5.505181 ACAATCTACACCTCTCCAAACAT 57.495 39.130 0.00 0.00 0.00 2.71
1926 1947 9.775854 CTCCTGAGATACATGACATTCTTTATT 57.224 33.333 0.00 0.00 0.00 1.40
1941 1962 5.183140 GGAAGTGATCTAGCTCCTGAGATAC 59.817 48.000 0.00 0.00 32.47 2.24
2083 2104 4.326826 TCAAGAAGACGGAATGATTGCTT 58.673 39.130 0.00 0.00 0.00 3.91
2134 2155 0.734253 GTGCACTCGTAGGTGAGCTG 60.734 60.000 10.32 0.00 39.68 4.24
2219 2240 8.420189 GCACTTTTATTTTCTCAAACTTGATCG 58.580 33.333 0.00 0.00 36.46 3.69
2237 2263 4.094294 GCATAATGTCGGTCTGCACTTTTA 59.906 41.667 0.00 0.00 33.13 1.52
2247 2273 2.900528 CCGAGGCATAATGTCGGTC 58.099 57.895 1.80 0.00 46.66 4.79
2252 2278 2.717639 AGCTTTCCGAGGCATAATGT 57.282 45.000 0.00 0.00 0.00 2.71
2265 2291 4.455606 AGCTATGAATGGTGGTAGCTTTC 58.544 43.478 0.00 0.00 45.48 2.62
2275 2301 7.281774 CAGACAGTGAATAAAGCTATGAATGGT 59.718 37.037 0.00 0.00 0.00 3.55
2489 2517 4.954875 AGCTTAACATGCATCTCCTAGAC 58.045 43.478 0.00 0.00 0.00 2.59
2514 2542 5.616975 TCTCCTAGGCTATAATCCAAGGA 57.383 43.478 2.96 0.00 0.00 3.36
2674 2702 4.887071 CGGTTGAAATGGAATTGGATCCTA 59.113 41.667 14.23 5.68 40.35 2.94
2740 2768 0.677842 GCACCCGATTAGGTATCCGT 59.322 55.000 0.00 0.00 38.39 4.69
2742 2770 1.968493 TCAGCACCCGATTAGGTATCC 59.032 52.381 0.00 0.00 38.39 2.59


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

AutoCloner maintained by Alex Coulton.