Multiple sequence alignment - TraesCS5D01G133300

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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 TraesCS5D01G133300 chr5D 100.000 2627 0 0 1 2627 212626256 212628882 0.000000e+00 4852.0
1 TraesCS5D01G133300 chr5D 96.192 814 12 1 1814 2627 543049637 543050431 0.000000e+00 1314.0
2 TraesCS5D01G133300 chr5D 89.053 1014 78 15 815 1798 213128996 213130006 0.000000e+00 1227.0
3 TraesCS5D01G133300 chr5D 73.585 477 105 18 1067 1535 528230578 528230115 2.090000e-36 163.0
4 TraesCS5D01G133300 chr5D 96.078 51 1 1 694 744 213128378 213128427 6.030000e-12 82.4
5 TraesCS5D01G133300 chr5B 93.646 1385 54 13 458 1815 226758715 226760092 0.000000e+00 2039.0
6 TraesCS5D01G133300 chr5B 89.173 1016 66 19 815 1797 227120765 227121769 0.000000e+00 1227.0
7 TraesCS5D01G133300 chr5B 87.698 252 11 8 177 425 226756734 226756968 2.580000e-70 276.0
8 TraesCS5D01G133300 chr5B 97.015 67 2 0 118 184 226755044 226755110 2.140000e-21 113.0
9 TraesCS5D01G133300 chr5A 94.495 1308 35 20 261 1535 276111019 276112322 0.000000e+00 1982.0
10 TraesCS5D01G133300 chr5A 88.070 1031 65 25 815 1798 276981057 276980038 0.000000e+00 1170.0
11 TraesCS5D01G133300 chr5A 95.156 289 11 2 1527 1815 276113897 276114182 1.110000e-123 453.0
12 TraesCS5D01G133300 chr5A 90.043 231 21 2 23 253 276110490 276110718 5.500000e-77 298.0
13 TraesCS5D01G133300 chr7D 96.437 814 10 2 1814 2627 121779411 121778617 0.000000e+00 1325.0
14 TraesCS5D01G133300 chr7D 95.615 821 17 2 1807 2627 519599664 519598863 0.000000e+00 1299.0
15 TraesCS5D01G133300 chr6D 96.433 813 10 2 1815 2627 301812115 301811322 0.000000e+00 1323.0
16 TraesCS5D01G133300 chr6D 96.064 813 13 1 1815 2627 127949416 127948623 0.000000e+00 1306.0
17 TraesCS5D01G133300 chr4D 96.215 819 11 2 1810 2627 82514448 82513649 0.000000e+00 1323.0
18 TraesCS5D01G133300 chr4D 96.433 813 10 2 1815 2627 488441821 488441028 0.000000e+00 1323.0
19 TraesCS5D01G133300 chr4D 96.310 813 11 2 1815 2627 448353358 448354151 0.000000e+00 1317.0
20 TraesCS5D01G133300 chr4D 96.064 813 13 1 1815 2627 459735540 459736333 0.000000e+00 1306.0
21 TraesCS5D01G133300 chr4D 81.510 649 97 10 998 1627 93841194 93841838 1.800000e-141 512.0
22 TraesCS5D01G133300 chr2D 96.433 813 10 1 1815 2627 435433795 435433002 0.000000e+00 1323.0
23 TraesCS5D01G133300 chr2D 74.170 271 45 19 1098 1354 649338500 649338759 3.600000e-14 89.8
24 TraesCS5D01G133300 chrUn 96.310 813 10 3 1815 2627 95190270 95191062 0.000000e+00 1317.0
25 TraesCS5D01G133300 chrUn 98.893 723 8 0 1905 2627 303582294 303581572 0.000000e+00 1291.0
26 TraesCS5D01G133300 chrUn 98.755 723 9 0 1905 2627 406274058 406274780 0.000000e+00 1286.0
27 TraesCS5D01G133300 chr1D 96.196 815 11 3 1814 2627 436733395 436732600 0.000000e+00 1315.0
28 TraesCS5D01G133300 chr1D 95.443 790 16 8 1815 2604 50899509 50900278 0.000000e+00 1242.0
29 TraesCS5D01G133300 chr4A 82.126 649 93 10 998 1627 487868994 487868350 3.850000e-148 534.0
30 TraesCS5D01G133300 chr4B 81.288 652 93 17 998 1627 132331565 132332209 3.900000e-138 501.0
31 TraesCS5D01G133300 chr2A 74.035 285 48 19 1086 1354 775379060 775378786 2.780000e-15 93.5
32 TraesCS5D01G133300 chr2B 75.000 216 29 17 1069 1270 785208592 785208796 2.800000e-10 76.8


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 TraesCS5D01G133300 chr5D 212626256 212628882 2626 False 4852.000000 4852 100.000000 1 2627 1 chr5D.!!$F1 2626
1 TraesCS5D01G133300 chr5D 543049637 543050431 794 False 1314.000000 1314 96.192000 1814 2627 1 chr5D.!!$F2 813
2 TraesCS5D01G133300 chr5D 213128378 213130006 1628 False 654.700000 1227 92.565500 694 1798 2 chr5D.!!$F3 1104
3 TraesCS5D01G133300 chr5B 227120765 227121769 1004 False 1227.000000 1227 89.173000 815 1797 1 chr5B.!!$F1 982
4 TraesCS5D01G133300 chr5B 226755044 226760092 5048 False 809.333333 2039 92.786333 118 1815 3 chr5B.!!$F2 1697
5 TraesCS5D01G133300 chr5A 276980038 276981057 1019 True 1170.000000 1170 88.070000 815 1798 1 chr5A.!!$R1 983
6 TraesCS5D01G133300 chr5A 276110490 276114182 3692 False 911.000000 1982 93.231333 23 1815 3 chr5A.!!$F1 1792
7 TraesCS5D01G133300 chr7D 121778617 121779411 794 True 1325.000000 1325 96.437000 1814 2627 1 chr7D.!!$R1 813
8 TraesCS5D01G133300 chr7D 519598863 519599664 801 True 1299.000000 1299 95.615000 1807 2627 1 chr7D.!!$R2 820
9 TraesCS5D01G133300 chr6D 301811322 301812115 793 True 1323.000000 1323 96.433000 1815 2627 1 chr6D.!!$R2 812
10 TraesCS5D01G133300 chr6D 127948623 127949416 793 True 1306.000000 1306 96.064000 1815 2627 1 chr6D.!!$R1 812
11 TraesCS5D01G133300 chr4D 82513649 82514448 799 True 1323.000000 1323 96.215000 1810 2627 1 chr4D.!!$R1 817
12 TraesCS5D01G133300 chr4D 488441028 488441821 793 True 1323.000000 1323 96.433000 1815 2627 1 chr4D.!!$R2 812
13 TraesCS5D01G133300 chr4D 448353358 448354151 793 False 1317.000000 1317 96.310000 1815 2627 1 chr4D.!!$F2 812
14 TraesCS5D01G133300 chr4D 459735540 459736333 793 False 1306.000000 1306 96.064000 1815 2627 1 chr4D.!!$F3 812
15 TraesCS5D01G133300 chr4D 93841194 93841838 644 False 512.000000 512 81.510000 998 1627 1 chr4D.!!$F1 629
16 TraesCS5D01G133300 chr2D 435433002 435433795 793 True 1323.000000 1323 96.433000 1815 2627 1 chr2D.!!$R1 812
17 TraesCS5D01G133300 chrUn 95190270 95191062 792 False 1317.000000 1317 96.310000 1815 2627 1 chrUn.!!$F1 812
18 TraesCS5D01G133300 chrUn 303581572 303582294 722 True 1291.000000 1291 98.893000 1905 2627 1 chrUn.!!$R1 722
19 TraesCS5D01G133300 chrUn 406274058 406274780 722 False 1286.000000 1286 98.755000 1905 2627 1 chrUn.!!$F2 722
20 TraesCS5D01G133300 chr1D 436732600 436733395 795 True 1315.000000 1315 96.196000 1814 2627 1 chr1D.!!$R1 813
21 TraesCS5D01G133300 chr1D 50899509 50900278 769 False 1242.000000 1242 95.443000 1815 2604 1 chr1D.!!$F1 789
22 TraesCS5D01G133300 chr4A 487868350 487868994 644 True 534.000000 534 82.126000 998 1627 1 chr4A.!!$R1 629
23 TraesCS5D01G133300 chr4B 132331565 132332209 644 False 501.000000 501 81.288000 998 1627 1 chr4B.!!$F1 629

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
30 31 0.109458 AGCTGCGATGCATGTGTTTG 60.109 50.0 2.46 0.0 38.13 2.93 F
981 5167 0.375803 ACAAACGCGAACCAACTGAC 59.624 50.0 15.93 0.0 0.00 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1574 7358 1.152756 AACTTGAACCCGCTTGCCT 60.153 52.632 0.0 0.0 0.0 4.75 R
2437 8236 3.448301 CCAATTTGAAGGGCTGCTTATCA 59.552 43.478 0.0 0.0 0.0 2.15 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
18 19 3.504021 CTTCTCACTTGAGCTGCGA 57.496 52.632 0.00 0.00 41.80 5.10
19 20 2.007360 CTTCTCACTTGAGCTGCGAT 57.993 50.000 0.00 0.00 41.80 4.58
20 21 1.659601 CTTCTCACTTGAGCTGCGATG 59.340 52.381 0.00 0.00 41.80 3.84
21 22 0.738762 TCTCACTTGAGCTGCGATGC 60.739 55.000 0.00 0.00 41.80 3.91
30 31 0.109458 AGCTGCGATGCATGTGTTTG 60.109 50.000 2.46 0.00 38.13 2.93
32 33 1.609932 CTGCGATGCATGTGTTTGTC 58.390 50.000 2.46 0.00 38.13 3.18
50 51 0.961019 TCTGTGCTGACATTTTGCCC 59.039 50.000 0.00 0.00 0.00 5.36
55 56 1.070445 TGCTGACATTTTGCCCAAAGG 59.930 47.619 0.00 0.00 32.13 3.11
90 91 2.064573 ATTGCGCCTTTGTTTAGCAC 57.935 45.000 4.18 0.00 37.57 4.40
104 105 1.246056 TAGCACTACCTCCGCGTTGT 61.246 55.000 4.92 1.00 0.00 3.32
258 1890 1.922447 TGGGCCTACAGATTTCACCAT 59.078 47.619 4.53 0.00 0.00 3.55
412 2345 2.719739 CAGCTTGGACTCATTGACCAT 58.280 47.619 0.00 0.00 39.98 3.55
429 3860 1.869767 CCATCTGCTGCGATTTAGGAC 59.130 52.381 4.63 0.00 0.00 3.85
433 3864 2.093500 TCTGCTGCGATTTAGGACACAT 60.093 45.455 0.00 0.00 0.00 3.21
452 3883 8.194769 GGACACATATCAAACCCGAAAATAAAT 58.805 33.333 0.00 0.00 0.00 1.40
648 4296 0.600557 CTGCACCGTCTTCTCTGTCT 59.399 55.000 0.00 0.00 0.00 3.41
692 4340 6.671614 TCTCCAACGCAACGATTTTATAAT 57.328 33.333 0.00 0.00 0.00 1.28
922 5095 1.151450 CCAGCACCACACCTTTCCT 59.849 57.895 0.00 0.00 0.00 3.36
981 5167 0.375803 ACAAACGCGAACCAACTGAC 59.624 50.000 15.93 0.00 0.00 3.51
1192 5393 1.251527 GCTCGACCTCTCCAACTCCA 61.252 60.000 0.00 0.00 0.00 3.86
1653 7438 4.577246 GCTAGCTCCGGCGGTCTG 62.577 72.222 27.32 17.71 44.37 3.51
1799 7598 5.384787 GTGCATGGTTTACCGTTTACTTAC 58.615 41.667 0.00 0.00 39.43 2.34
1801 7600 4.388469 GCATGGTTTACCGTTTACTTACGA 59.612 41.667 0.00 0.00 43.99 3.43
1899 7698 8.619146 AGATAATGCATGTTAAATTTCACACG 57.381 30.769 7.34 0.85 0.00 4.49
1900 7699 8.243426 AGATAATGCATGTTAAATTTCACACGT 58.757 29.630 7.34 0.00 0.00 4.49
1901 7700 9.497030 GATAATGCATGTTAAATTTCACACGTA 57.503 29.630 7.34 0.00 0.00 3.57
1902 7701 7.561237 AATGCATGTTAAATTTCACACGTAC 57.439 32.000 7.34 0.00 0.00 3.67
1903 7702 6.061231 TGCATGTTAAATTTCACACGTACA 57.939 33.333 7.34 1.93 0.00 2.90
2328 8127 9.173021 CATCAACCAGTATTCTTGGTGTTTATA 57.827 33.333 0.00 0.00 35.88 0.98
2437 8236 6.475402 CCGTGCAAACTTCAAGATTTAAAACT 59.525 34.615 0.00 0.00 0.00 2.66
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.659601 CATCGCAGCTCAAGTGAGAAG 59.340 52.381 12.54 4.54 44.74 2.85
1 2 1.718396 CATCGCAGCTCAAGTGAGAA 58.282 50.000 12.54 0.00 44.74 2.87
2 3 0.738762 GCATCGCAGCTCAAGTGAGA 60.739 55.000 12.54 0.00 44.74 3.27
5 6 0.248094 CATGCATCGCAGCTCAAGTG 60.248 55.000 0.00 0.00 43.65 3.16
6 7 0.675837 ACATGCATCGCAGCTCAAGT 60.676 50.000 0.00 0.00 43.65 3.16
7 8 0.248094 CACATGCATCGCAGCTCAAG 60.248 55.000 0.00 0.00 43.65 3.02
8 9 0.956902 ACACATGCATCGCAGCTCAA 60.957 50.000 0.00 0.00 43.65 3.02
9 10 0.956902 AACACATGCATCGCAGCTCA 60.957 50.000 0.00 0.00 43.65 4.26
10 11 0.169672 AAACACATGCATCGCAGCTC 59.830 50.000 0.00 0.00 43.65 4.09
11 12 0.109458 CAAACACATGCATCGCAGCT 60.109 50.000 0.00 0.00 43.65 4.24
12 13 0.387622 ACAAACACATGCATCGCAGC 60.388 50.000 0.00 0.00 43.65 5.25
13 14 1.198408 AGACAAACACATGCATCGCAG 59.802 47.619 0.00 0.00 43.65 5.18
14 15 1.069091 CAGACAAACACATGCATCGCA 60.069 47.619 0.00 0.00 44.86 5.10
15 16 1.069022 ACAGACAAACACATGCATCGC 60.069 47.619 0.00 0.00 0.00 4.58
16 17 2.577450 CACAGACAAACACATGCATCG 58.423 47.619 0.00 0.00 0.00 3.84
17 18 2.030540 AGCACAGACAAACACATGCATC 60.031 45.455 0.00 0.00 35.51 3.91
18 19 1.958579 AGCACAGACAAACACATGCAT 59.041 42.857 0.00 0.00 35.51 3.96
19 20 1.065851 CAGCACAGACAAACACATGCA 59.934 47.619 0.00 0.00 35.51 3.96
20 21 1.334556 TCAGCACAGACAAACACATGC 59.665 47.619 0.00 0.00 0.00 4.06
21 22 2.355444 TGTCAGCACAGACAAACACATG 59.645 45.455 4.46 0.00 44.92 3.21
30 31 1.336240 GGGCAAAATGTCAGCACAGAC 60.336 52.381 0.00 0.00 35.41 3.51
32 33 0.675083 TGGGCAAAATGTCAGCACAG 59.325 50.000 0.00 0.00 36.64 3.66
66 67 3.121778 GCTAAACAAAGGCGCAATTTCTG 59.878 43.478 10.83 2.20 0.00 3.02
90 91 2.183555 GGGACAACGCGGAGGTAG 59.816 66.667 12.47 0.00 0.00 3.18
201 1833 0.717896 CGTTCGTTGACGTGCATGTG 60.718 55.000 18.17 1.57 40.80 3.21
235 1867 2.755103 GGTGAAATCTGTAGGCCCAAAG 59.245 50.000 0.00 0.00 0.00 2.77
258 1890 6.427150 GTTCTCGCTAAATCAACAAGAAACA 58.573 36.000 0.00 0.00 0.00 2.83
412 2345 1.275010 TGTGTCCTAAATCGCAGCAGA 59.725 47.619 0.00 0.00 0.00 4.26
452 3883 3.928375 GGAACGGCGATTTCTTTACTGTA 59.072 43.478 16.62 0.00 0.00 2.74
648 4296 4.997395 AGAAGAGAATAGAAGCGTGCAAAA 59.003 37.500 0.00 0.00 0.00 2.44
692 4340 1.484653 CGTAGTGGGTTGATGGATGGA 59.515 52.381 0.00 0.00 0.00 3.41
922 5095 8.061920 TCTTATTCTCTGTAATGAGAGGAGGAA 58.938 37.037 0.00 0.00 43.05 3.36
1574 7358 1.152756 AACTTGAACCCGCTTGCCT 60.153 52.632 0.00 0.00 0.00 4.75
1653 7438 3.718210 CTACCTCTTGCCGGCGACC 62.718 68.421 23.90 0.00 0.00 4.79
1663 7448 4.984146 AGCCAAGAAGAAACTACCTCTT 57.016 40.909 0.00 0.00 35.82 2.85
1799 7598 5.920312 TGTACTAGTCGTGTTAACTTCTCG 58.080 41.667 7.22 6.89 0.00 4.04
1801 7600 6.585322 GCATTGTACTAGTCGTGTTAACTTCT 59.415 38.462 7.22 2.99 0.00 2.85
1842 7641 6.809869 ACTCTTGCAAACTATTTCAAAAGCT 58.190 32.000 0.00 0.00 0.00 3.74
1893 7692 6.508246 CGTGTGAAATTTAACTGTACGTGTGA 60.508 38.462 7.22 0.00 0.00 3.58
1894 7693 5.613983 CGTGTGAAATTTAACTGTACGTGTG 59.386 40.000 7.22 0.00 0.00 3.82
1895 7694 5.291614 ACGTGTGAAATTTAACTGTACGTGT 59.708 36.000 17.38 0.15 40.22 4.49
1896 7695 5.730269 ACGTGTGAAATTTAACTGTACGTG 58.270 37.500 17.38 0.59 40.22 4.49
1897 7696 5.971895 ACGTGTGAAATTTAACTGTACGT 57.028 34.783 14.00 14.00 37.41 3.57
1898 7697 6.865307 TGTACGTGTGAAATTTAACTGTACG 58.135 36.000 22.86 18.66 34.46 3.67
1899 7698 8.000435 GTCTGTACGTGTGAAATTTAACTGTAC 59.000 37.037 22.29 22.29 33.40 2.90
1900 7699 7.705752 TGTCTGTACGTGTGAAATTTAACTGTA 59.294 33.333 7.22 7.13 0.00 2.74
1901 7700 6.535865 TGTCTGTACGTGTGAAATTTAACTGT 59.464 34.615 7.22 8.00 0.00 3.55
1902 7701 6.939627 TGTCTGTACGTGTGAAATTTAACTG 58.060 36.000 7.22 2.65 0.00 3.16
1903 7702 7.542534 TTGTCTGTACGTGTGAAATTTAACT 57.457 32.000 7.22 0.00 0.00 2.24
2328 8127 4.887071 TGAAATGCCAGTTGACTAACAGTT 59.113 37.500 0.00 0.00 39.30 3.16
2437 8236 3.448301 CCAATTTGAAGGGCTGCTTATCA 59.552 43.478 0.00 0.00 0.00 2.15


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

AutoCloner maintained by Alex Coulton.