Multiple sequence alignment - TraesCS1B01G338700

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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 TraesCS1B01G338700 chr1B 100.000 2288 0 0 1 2288 566609765 566612052 0.000000e+00 4226
1 TraesCS1B01G338700 chr1B 95.509 1670 71 4 1 1669 311135942 311134276 0.000000e+00 2665
2 TraesCS1B01G338700 chr1B 99.002 401 4 0 1888 2288 566619756 566620156 0.000000e+00 719
3 TraesCS1B01G338700 chr1B 86.180 644 59 12 1668 2288 287086614 287085978 0.000000e+00 669
4 TraesCS1B01G338700 chr1B 95.771 402 16 1 1888 2288 527336524 527336925 0.000000e+00 647
5 TraesCS1B01G338700 chr1B 95.000 220 9 1 1668 1887 469983677 469983460 6.050000e-91 344
6 TraesCS1B01G338700 chr6B 96.108 1670 63 2 1 1669 643872252 643870584 0.000000e+00 2723
7 TraesCS1B01G338700 chr6B 94.627 1675 79 4 1 1669 671866712 671865043 0.000000e+00 2584
8 TraesCS1B01G338700 chr6B 94.233 1682 85 7 1 1673 643648511 643650189 0.000000e+00 2558
9 TraesCS1B01G338700 chr6B 89.818 275 22 3 1675 1948 451579677 451579946 4.680000e-92 348
10 TraesCS1B01G338700 chr1D 95.988 1670 64 3 1 1669 209755871 209757538 0.000000e+00 2710
11 TraesCS1B01G338700 chr7B 95.749 1670 65 6 1 1669 639855955 639857619 0.000000e+00 2686
12 TraesCS1B01G338700 chr7B 96.010 401 16 0 1888 2288 441174447 441174847 0.000000e+00 652
13 TraesCS1B01G338700 chr3B 95.261 1667 73 6 1 1666 745588843 745590504 0.000000e+00 2636
14 TraesCS1B01G338700 chr5B 94.910 1670 80 3 1 1669 693957763 693956098 0.000000e+00 2608
15 TraesCS1B01G338700 chr5B 94.860 1673 76 8 1 1669 369339841 369338175 0.000000e+00 2604
16 TraesCS1B01G338700 chr5B 95.750 400 15 1 1888 2285 485961751 485962150 0.000000e+00 643
17 TraesCS1B01G338700 chr5B 95.511 401 18 0 1888 2288 532951827 532952227 1.920000e-180 641
18 TraesCS1B01G338700 chr5B 91.322 242 17 3 1668 1909 73209391 73209628 6.090000e-86 327
19 TraesCS1B01G338700 chr2B 95.556 405 17 1 1885 2288 780575363 780574959 0.000000e+00 647
20 TraesCS1B01G338700 chr4B 95.533 403 16 2 1888 2288 36094794 36094392 0.000000e+00 643
21 TraesCS1B01G338700 chr4B 95.511 401 18 0 1888 2288 492198431 492198831 1.920000e-180 641
22 TraesCS1B01G338700 chr7D 82.143 644 79 17 1669 2288 30721147 30721778 9.370000e-144 520
23 TraesCS1B01G338700 chr7D 94.570 221 11 1 1668 1887 394795704 394795924 7.830000e-90 340
24 TraesCS1B01G338700 chr3A 82.409 631 64 33 1676 2278 573941269 573941880 7.290000e-140 507
25 TraesCS1B01G338700 chr6A 81.240 645 83 25 1669 2288 563612571 563613202 9.500000e-134 486
26 TraesCS1B01G338700 chr2A 81.289 636 81 27 1676 2288 593142781 593143401 4.420000e-132 481


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 TraesCS1B01G338700 chr1B 566609765 566612052 2287 False 4226 4226 100.000 1 2288 1 chr1B.!!$F2 2287
1 TraesCS1B01G338700 chr1B 311134276 311135942 1666 True 2665 2665 95.509 1 1669 1 chr1B.!!$R2 1668
2 TraesCS1B01G338700 chr1B 287085978 287086614 636 True 669 669 86.180 1668 2288 1 chr1B.!!$R1 620
3 TraesCS1B01G338700 chr6B 643870584 643872252 1668 True 2723 2723 96.108 1 1669 1 chr6B.!!$R1 1668
4 TraesCS1B01G338700 chr6B 671865043 671866712 1669 True 2584 2584 94.627 1 1669 1 chr6B.!!$R2 1668
5 TraesCS1B01G338700 chr6B 643648511 643650189 1678 False 2558 2558 94.233 1 1673 1 chr6B.!!$F2 1672
6 TraesCS1B01G338700 chr1D 209755871 209757538 1667 False 2710 2710 95.988 1 1669 1 chr1D.!!$F1 1668
7 TraesCS1B01G338700 chr7B 639855955 639857619 1664 False 2686 2686 95.749 1 1669 1 chr7B.!!$F2 1668
8 TraesCS1B01G338700 chr3B 745588843 745590504 1661 False 2636 2636 95.261 1 1666 1 chr3B.!!$F1 1665
9 TraesCS1B01G338700 chr5B 693956098 693957763 1665 True 2608 2608 94.910 1 1669 1 chr5B.!!$R2 1668
10 TraesCS1B01G338700 chr5B 369338175 369339841 1666 True 2604 2604 94.860 1 1669 1 chr5B.!!$R1 1668
11 TraesCS1B01G338700 chr7D 30721147 30721778 631 False 520 520 82.143 1669 2288 1 chr7D.!!$F1 619
12 TraesCS1B01G338700 chr3A 573941269 573941880 611 False 507 507 82.409 1676 2278 1 chr3A.!!$F1 602
13 TraesCS1B01G338700 chr6A 563612571 563613202 631 False 486 486 81.240 1669 2288 1 chr6A.!!$F1 619
14 TraesCS1B01G338700 chr2A 593142781 593143401 620 False 481 481 81.289 1676 2288 1 chr2A.!!$F1 612

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
319 320 0.960364 GCCCAGCGAAGGATGTCAAA 60.960 55.000 0.0 0.0 0.0 2.69 F
897 911 1.369321 GACGAGGGCATGGAGGATC 59.631 63.158 0.0 0.0 0.0 3.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1240 1256 0.537143 TGCTTCCCGCACTTGTTGAT 60.537 50.0 0.0 0.0 45.47 2.57 R
2048 2070 0.693049 AAGTGCCTCCGTGGATTTCT 59.307 50.0 0.0 0.0 38.35 2.52 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
102 103 1.333177 GTCGATCTGCCAGGTAGGAT 58.667 55.000 4.47 0.00 41.22 3.24
238 239 1.398390 GCGGTCATTAGGAGCAAAGTG 59.602 52.381 0.00 0.00 44.30 3.16
240 241 2.615493 CGGTCATTAGGAGCAAAGTGGT 60.615 50.000 0.00 0.00 44.30 4.16
279 280 1.549170 TCTTCCTCTGTTTAGGGTCGC 59.451 52.381 0.00 0.00 37.24 5.19
319 320 0.960364 GCCCAGCGAAGGATGTCAAA 60.960 55.000 0.00 0.00 0.00 2.69
336 337 3.993614 AATGCCATCGCGCCCTTCA 62.994 57.895 0.00 0.00 38.08 3.02
464 465 3.556213 CCATGGTGTTCTCGAACTTGGTA 60.556 47.826 2.57 0.00 41.67 3.25
539 540 2.597510 GGGTTGCCGTTGGAGCTT 60.598 61.111 0.00 0.00 0.00 3.74
615 618 1.917568 GGTGGGTAAATAGTGGTGGGA 59.082 52.381 0.00 0.00 0.00 4.37
650 664 2.365768 GGGGGTGGAGAGGAGGAC 60.366 72.222 0.00 0.00 0.00 3.85
707 721 4.637534 TCTTGAATTAGCCATGAACTCTGC 59.362 41.667 0.00 0.00 0.00 4.26
820 834 1.683365 CCCTTCACCCAATGCCTGG 60.683 63.158 0.00 0.00 45.97 4.45
896 910 2.502492 CGACGAGGGCATGGAGGAT 61.502 63.158 0.00 0.00 0.00 3.24
897 911 1.369321 GACGAGGGCATGGAGGATC 59.631 63.158 0.00 0.00 0.00 3.36
972 988 3.498774 ACTCACTTCTGCAAGGTCATT 57.501 42.857 0.00 0.00 33.37 2.57
1138 1154 2.121689 AGGGTTGGGCCACCTACA 60.122 61.111 13.77 0.00 43.22 2.74
1240 1256 0.460109 CGACGATGGCATTGAGGTCA 60.460 55.000 21.46 0.00 0.00 4.02
1290 1306 3.400054 GCCGCCAAGGAGTAGGGT 61.400 66.667 0.00 0.00 45.00 4.34
1339 1355 5.696724 GTCTGCTATGGTTTATGCGTAGAAT 59.303 40.000 0.00 0.00 0.00 2.40
1686 1706 8.247562 GGCACTGTATGGATTTTATTTTACACA 58.752 33.333 0.00 0.00 0.00 3.72
1744 1765 1.202675 CCCAACCTGCATTGCTGTTTT 60.203 47.619 10.49 2.42 0.00 2.43
1745 1766 2.563702 CCAACCTGCATTGCTGTTTTT 58.436 42.857 10.49 0.04 0.00 1.94
1871 1892 3.209410 ACTTGGAGTGCAAGTCAAGAAG 58.791 45.455 22.87 12.84 38.37 2.85
1873 1894 1.141657 TGGAGTGCAAGTCAAGAAGCT 59.858 47.619 0.00 0.00 38.29 3.74
1874 1895 1.534595 GGAGTGCAAGTCAAGAAGCTG 59.465 52.381 0.00 0.00 38.29 4.24
1875 1896 2.216898 GAGTGCAAGTCAAGAAGCTGT 58.783 47.619 0.00 0.00 35.94 4.40
1893 1915 2.131067 TCGAGGCGGCCATGATACA 61.131 57.895 23.09 0.00 0.00 2.29
2048 2070 5.740290 AGAAAAGTTCTCGGAATGTCCTA 57.260 39.130 0.00 0.00 34.07 2.94
2049 2071 5.725362 AGAAAAGTTCTCGGAATGTCCTAG 58.275 41.667 0.00 0.00 34.07 3.02
2063 2085 1.120530 TCCTAGAAATCCACGGAGGC 58.879 55.000 0.00 0.00 37.29 4.70
2070 2092 2.622064 AATCCACGGAGGCACTTATC 57.378 50.000 0.00 0.00 41.55 1.75
2074 2096 1.414181 CCACGGAGGCACTTATCAGAT 59.586 52.381 0.00 0.00 41.55 2.90
2134 2156 3.681835 ACGGGCTGTCCACGAGAC 61.682 66.667 0.00 0.00 46.51 3.36
2165 2207 2.520982 TCCTATCTCGTGGGCCCG 60.521 66.667 19.37 6.11 0.00 6.13
2167 2209 4.301027 CTATCTCGTGGGCCCGCC 62.301 72.222 29.65 15.56 0.00 6.13
2203 2245 6.208797 CGACCTCAACTCCAACTCCATATATA 59.791 42.308 0.00 0.00 0.00 0.86
2205 2247 6.270231 ACCTCAACTCCAACTCCATATATACC 59.730 42.308 0.00 0.00 0.00 2.73
2206 2248 6.340962 TCAACTCCAACTCCATATATACCG 57.659 41.667 0.00 0.00 0.00 4.02
2208 2250 5.979288 ACTCCAACTCCATATATACCGTC 57.021 43.478 0.00 0.00 0.00 4.79
2249 2291 3.186613 AGGAGAAAGTTTCATCGCGTTTC 59.813 43.478 17.65 7.01 0.00 2.78
2254 2296 1.191647 AGTTTCATCGCGTTTCACGAC 59.808 47.619 5.77 0.00 46.05 4.34
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
132 133 2.815647 GGAAGAAGAGGCGGTGCG 60.816 66.667 0.00 0.00 0.00 5.34
238 239 0.237498 GTGGCGCAAGTACAAGAACC 59.763 55.000 10.83 0.00 41.68 3.62
240 241 1.871039 GAAGTGGCGCAAGTACAAGAA 59.129 47.619 10.83 0.00 41.68 2.52
336 337 1.194781 ACGCTGATTCCTGACCCAGT 61.195 55.000 0.00 0.00 0.00 4.00
556 557 0.121197 AACCTTCCTCCTCCCCATCA 59.879 55.000 0.00 0.00 0.00 3.07
650 664 1.073964 CGGCATGACTGTCACTCTTG 58.926 55.000 13.50 8.63 0.00 3.02
707 721 0.745486 TCATGGAGTCAGGCATTGCG 60.745 55.000 1.91 0.00 0.00 4.85
820 834 3.482783 GCGACAGCTCAACCTCGC 61.483 66.667 0.00 0.00 44.11 5.03
876 890 2.579201 CTCCATGCCCTCGTCGTT 59.421 61.111 0.00 0.00 0.00 3.85
972 988 0.106708 ACTCAAGCTTCGGTGCAAGA 59.893 50.000 0.00 0.00 34.99 3.02
1138 1154 2.234661 TCTTGATCTGATGAACGGCTGT 59.765 45.455 0.00 0.00 0.00 4.40
1240 1256 0.537143 TGCTTCCCGCACTTGTTGAT 60.537 50.000 0.00 0.00 45.47 2.57
1339 1355 4.878439 AGCAGTACGACAGTTCATAACAA 58.122 39.130 0.00 0.00 0.00 2.83
1633 1653 2.359900 GCATACACTTCTCCACCCAAG 58.640 52.381 0.00 0.00 0.00 3.61
1747 1768 6.497785 TCGAAATACCGAAATAGGCAAAAA 57.502 33.333 0.00 0.00 35.42 1.94
1764 1785 7.968405 CCGTTTGATATTCCTTTTCTTCGAAAT 59.032 33.333 0.00 0.00 0.00 2.17
1844 1865 2.557920 CTTGCACTCCAAGTCCTCTT 57.442 50.000 0.00 0.00 44.74 2.85
1860 1881 2.064762 CCTCGACAGCTTCTTGACTTG 58.935 52.381 0.00 0.00 0.00 3.16
1873 1894 2.131067 TATCATGGCCGCCTCGACA 61.131 57.895 11.61 0.00 0.00 4.35
1874 1895 1.664965 GTATCATGGCCGCCTCGAC 60.665 63.158 11.61 0.00 0.00 4.20
1875 1896 1.471829 ATGTATCATGGCCGCCTCGA 61.472 55.000 11.61 7.38 0.00 4.04
1893 1915 6.540438 TGGAAAAGTAGATACGTTGGAGAT 57.460 37.500 0.00 0.00 0.00 2.75
2048 2070 0.693049 AAGTGCCTCCGTGGATTTCT 59.307 50.000 0.00 0.00 38.35 2.52
2049 2071 2.396590 TAAGTGCCTCCGTGGATTTC 57.603 50.000 0.00 0.00 38.35 2.17
2148 2190 2.520982 CGGGCCCACGAGATAGGA 60.521 66.667 24.92 0.00 35.47 2.94
2176 2218 0.966920 GAGTTGGAGTTGAGGTCGGA 59.033 55.000 0.00 0.00 0.00 4.55
2203 2245 2.444281 TTTTTCTCCCCGAGACGGT 58.556 52.632 9.28 0.00 46.80 4.83
2227 2269 2.457366 ACGCGATGAAACTTTCTCCT 57.543 45.000 15.93 0.00 0.00 3.69


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

AutoCloner maintained by Alex Coulton.