Multiple sequence alignment - TraesCS5B01G197000

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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 TraesCS5B01G197000 chr5B 100.000 2237 0 0 1 2237 354716397 354714161 0.000000e+00 4132.0
1 TraesCS5B01G197000 chr5A 89.316 2265 166 31 4 2237 402658884 402656665 0.000000e+00 2772.0
2 TraesCS5B01G197000 chr5D 91.072 1781 103 31 2 1739 309402944 309401177 0.000000e+00 2357.0
3 TraesCS5B01G197000 chr5D 96.594 411 10 2 1768 2177 309401178 309400771 0.000000e+00 678.0
4 TraesCS5B01G197000 chr1D 82.796 93 16 0 418 510 7337666 7337574 1.420000e-12 84.2
5 TraesCS5B01G197000 chr3D 77.982 109 22 2 421 529 303583470 303583364 1.430000e-07 67.6


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 TraesCS5B01G197000 chr5B 354714161 354716397 2236 True 4132.0 4132 100.000 1 2237 1 chr5B.!!$R1 2236
1 TraesCS5B01G197000 chr5A 402656665 402658884 2219 True 2772.0 2772 89.316 4 2237 1 chr5A.!!$R1 2233
2 TraesCS5B01G197000 chr5D 309400771 309402944 2173 True 1517.5 2357 93.833 2 2177 2 chr5D.!!$R1 2175

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
85 86 0.107831 TCCTGTTTTGGTGGACTCGG 59.892 55.0 0.00 0.00 0.0 4.63 F
440 449 0.179145 AACGCCTTCATAGTCGACGG 60.179 55.0 10.46 5.18 0.0 4.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1011 1056 2.124693 CAGCGACCTCCTCCTCCTC 61.125 68.421 0.0 0.0 0.0 3.71 R
2103 2161 1.198637 GAGCAAGCCAAACAGTAGCAG 59.801 52.381 0.0 0.0 0.0 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
23 24 4.560108 GCATGTTGAATTTGAGGCTTGACT 60.560 41.667 0.00 0.00 0.00 3.41
41 42 6.560003 TTGACTGGAGCTAGGATGAAATTA 57.440 37.500 0.00 0.00 0.00 1.40
63 64 2.910319 TGCTAGGGTTGTATTGGTCAGT 59.090 45.455 0.00 0.00 0.00 3.41
65 66 2.762535 AGGGTTGTATTGGTCAGTCG 57.237 50.000 0.00 0.00 0.00 4.18
85 86 0.107831 TCCTGTTTTGGTGGACTCGG 59.892 55.000 0.00 0.00 0.00 4.63
112 113 3.128589 GCAGAAGCGTTGGGAATATTTGA 59.871 43.478 0.00 0.00 0.00 2.69
119 120 5.585047 AGCGTTGGGAATATTTGAAGTAGAC 59.415 40.000 0.00 0.00 0.00 2.59
121 122 6.674760 GCGTTGGGAATATTTGAAGTAGACAC 60.675 42.308 0.00 0.00 0.00 3.67
133 134 6.751514 TGAAGTAGACACATGTGTTTTGTT 57.248 33.333 31.03 20.68 45.05 2.83
166 170 4.308899 ACGTCCTTAATGAAGATCGAGG 57.691 45.455 11.62 1.31 34.25 4.63
175 179 9.944376 CCTTAATGAAGATCGAGGGATTAAATA 57.056 33.333 0.00 0.00 34.25 1.40
181 185 8.762645 TGAAGATCGAGGGATTAAATATGCTAT 58.237 33.333 0.00 0.00 31.51 2.97
208 212 9.871238 AACTACAAGTTGTCATAATAGGTAGTG 57.129 33.333 12.82 0.00 38.94 2.74
279 283 1.000955 TCTTGTCTCGCTGAACCCTTC 59.999 52.381 0.00 0.00 0.00 3.46
354 362 1.004044 AGGCATCCAGTCCTTGTGAAG 59.996 52.381 0.00 0.00 0.00 3.02
397 406 2.506444 GGTACAAACCCGGATGAACAA 58.494 47.619 0.73 0.00 40.21 2.83
404 413 3.433306 ACCCGGATGAACAAATGAGAA 57.567 42.857 0.73 0.00 0.00 2.87
412 421 6.611381 GGATGAACAAATGAGAATGACGAAA 58.389 36.000 0.00 0.00 0.00 3.46
440 449 0.179145 AACGCCTTCATAGTCGACGG 60.179 55.000 10.46 5.18 0.00 4.79
472 481 6.580791 CACTTTACAATAAACCAACATCACCG 59.419 38.462 0.00 0.00 0.00 4.94
477 486 5.069251 ACAATAAACCAACATCACCGGAAAA 59.931 36.000 9.46 0.00 0.00 2.29
510 520 3.374220 TCAGAAAAATGCAAGCACCAG 57.626 42.857 0.00 0.00 0.00 4.00
513 523 4.022935 TCAGAAAAATGCAAGCACCAGTAG 60.023 41.667 0.00 0.00 0.00 2.57
578 601 4.992381 AACTACACTCACTTCGCAATTC 57.008 40.909 0.00 0.00 0.00 2.17
579 602 3.990092 ACTACACTCACTTCGCAATTCA 58.010 40.909 0.00 0.00 0.00 2.57
710 754 1.224069 GCTGTCAGACACGTGTGCAT 61.224 55.000 28.82 9.01 0.00 3.96
781 825 2.435586 GCCACAGCTCACGCTCAT 60.436 61.111 0.00 0.00 45.15 2.90
800 844 1.108132 TTTTTACGCGCAACCCCCTT 61.108 50.000 5.73 0.00 0.00 3.95
852 896 0.618981 CCCTCCCCTATTTATCCCGC 59.381 60.000 0.00 0.00 0.00 6.13
1011 1056 2.279451 TTCGGCATGGAGATCGCG 60.279 61.111 0.00 0.00 0.00 5.87
1239 1284 0.669619 GCGACTCCCCTAGCTAGTTC 59.330 60.000 19.31 6.72 0.00 3.01
1263 1308 1.556911 ACCTCTGCTCTTGTGGTATGG 59.443 52.381 0.00 0.00 30.61 2.74
1266 1311 0.108186 CTGCTCTTGTGGTATGGCGA 60.108 55.000 0.00 0.00 0.00 5.54
1361 1407 3.521947 AATTGAGTACCTAGGTGCGAC 57.478 47.619 25.33 20.77 35.88 5.19
1449 1503 0.179174 AATTTTCGCGGCCGATTCAC 60.179 50.000 33.48 9.92 43.97 3.18
1558 1613 6.844388 TCGCACCTATATAATCCCCTTATCAT 59.156 38.462 0.00 0.00 32.26 2.45
1568 1623 2.143602 CCCCTTATCATCCCCCTTTGA 58.856 52.381 0.00 0.00 0.00 2.69
1634 1689 5.125417 TGCATTGTTAACTGGAAATAGGAGC 59.875 40.000 7.22 0.00 0.00 4.70
1649 1704 7.361799 GGAAATAGGAGCGTGTATCTTGTTTTT 60.362 37.037 0.00 0.00 0.00 1.94
1679 1734 1.188219 TCACCACTCTCAGACCCTGC 61.188 60.000 0.00 0.00 0.00 4.85
1690 1745 0.842467 AGACCCTGCCCTATATGCCC 60.842 60.000 0.00 0.00 0.00 5.36
1736 1793 7.107250 TCAGACGGCTGATGAACAGTACTAC 62.107 48.000 19.45 0.00 45.88 2.73
1738 1795 9.890582 TCAGACGGCTGATGAACAGTACTACTA 62.891 44.444 19.45 0.00 45.88 1.82
1743 1800 6.665474 CTGATGAACAGTACTACTACTCGT 57.335 41.667 0.00 0.00 41.30 4.18
1744 1801 6.418585 TGATGAACAGTACTACTACTCGTG 57.581 41.667 0.00 0.00 30.03 4.35
1745 1802 6.168389 TGATGAACAGTACTACTACTCGTGA 58.832 40.000 0.00 0.00 30.03 4.35
1746 1803 6.313164 TGATGAACAGTACTACTACTCGTGAG 59.687 42.308 0.00 0.00 30.03 3.51
1747 1804 5.787380 TGAACAGTACTACTACTCGTGAGA 58.213 41.667 3.44 0.00 30.03 3.27
1748 1805 6.404708 TGAACAGTACTACTACTCGTGAGAT 58.595 40.000 3.44 0.00 40.84 2.75
1749 1806 6.534436 TGAACAGTACTACTACTCGTGAGATC 59.466 42.308 3.44 0.00 40.84 2.75
1750 1807 5.975282 ACAGTACTACTACTCGTGAGATCA 58.025 41.667 3.44 0.00 40.84 2.92
1751 1808 6.584488 ACAGTACTACTACTCGTGAGATCAT 58.416 40.000 3.44 0.00 40.84 2.45
1752 1809 6.702723 ACAGTACTACTACTCGTGAGATCATC 59.297 42.308 3.44 0.00 40.84 2.92
1753 1810 6.926826 CAGTACTACTACTCGTGAGATCATCT 59.073 42.308 3.44 0.00 40.84 2.90
1754 1811 7.439955 CAGTACTACTACTCGTGAGATCATCTT 59.560 40.741 3.44 0.00 40.84 2.40
1755 1812 7.988599 AGTACTACTACTCGTGAGATCATCTTT 59.011 37.037 3.44 0.00 40.84 2.52
1756 1813 7.022055 ACTACTACTCGTGAGATCATCTTTG 57.978 40.000 3.44 0.00 40.84 2.77
1757 1814 5.906113 ACTACTCGTGAGATCATCTTTGT 57.094 39.130 3.44 0.00 40.84 2.83
1758 1815 6.274157 ACTACTCGTGAGATCATCTTTGTT 57.726 37.500 3.44 0.00 40.84 2.83
1759 1816 7.392494 ACTACTCGTGAGATCATCTTTGTTA 57.608 36.000 3.44 0.00 40.84 2.41
1760 1817 7.827701 ACTACTCGTGAGATCATCTTTGTTAA 58.172 34.615 3.44 0.00 40.84 2.01
1761 1818 6.952935 ACTCGTGAGATCATCTTTGTTAAC 57.047 37.500 3.44 0.00 40.84 2.01
1762 1819 6.692486 ACTCGTGAGATCATCTTTGTTAACT 58.308 36.000 7.22 0.00 40.84 2.24
1763 1820 6.587990 ACTCGTGAGATCATCTTTGTTAACTG 59.412 38.462 7.22 0.00 40.84 3.16
1764 1821 5.869344 TCGTGAGATCATCTTTGTTAACTGG 59.131 40.000 7.22 0.00 33.31 4.00
1890 1948 4.755266 ATGCTGTCTATCCGTTTTAGGT 57.245 40.909 0.00 0.00 0.00 3.08
2103 2161 8.776376 ATCATTGTTAATTGAATGGAAACCAC 57.224 30.769 0.00 0.00 35.80 4.16
2172 2230 7.824672 AGAAGACAAAAGCTTTGATGGAATAG 58.175 34.615 13.54 0.00 0.00 1.73
2180 2238 7.579761 AAGCTTTGATGGAATAGGATTCTTC 57.420 36.000 0.00 0.00 0.00 2.87
2187 2245 4.370776 TGGAATAGGATTCTTCAGGGTCA 58.629 43.478 0.00 0.00 0.00 4.02
2188 2246 4.164221 TGGAATAGGATTCTTCAGGGTCAC 59.836 45.833 0.00 0.00 0.00 3.67
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.676646 GTCAAGCCTCAAATTCAACATGC 59.323 43.478 0.00 0.00 0.00 4.06
23 24 5.573380 AGCATAATTTCATCCTAGCTCCA 57.427 39.130 0.00 0.00 0.00 3.86
41 42 3.523564 ACTGACCAATACAACCCTAGCAT 59.476 43.478 0.00 0.00 0.00 3.79
63 64 3.390003 GTCCACCAAAACAGGACGA 57.610 52.632 0.00 0.00 42.02 4.20
85 86 0.884704 TCCCAACGCTTCTGCTCAAC 60.885 55.000 0.00 0.00 36.97 3.18
112 113 6.677920 GCAGAACAAAACACATGTGTCTACTT 60.678 38.462 30.64 18.57 44.13 2.24
119 120 3.162202 TGGCAGAACAAAACACATGTG 57.838 42.857 24.25 24.25 0.00 3.21
121 122 2.477375 GCATGGCAGAACAAAACACATG 59.523 45.455 0.00 0.00 37.77 3.21
133 134 2.359850 GGACGTTGGCATGGCAGA 60.360 61.111 22.17 10.70 0.00 4.26
193 197 6.746120 ACACGATTCCACTACCTATTATGAC 58.254 40.000 0.00 0.00 0.00 3.06
196 200 8.311836 CCATAACACGATTCCACTACCTATTAT 58.688 37.037 0.00 0.00 0.00 1.28
208 212 2.540101 CGAGAAGCCATAACACGATTCC 59.460 50.000 0.00 0.00 0.00 3.01
255 259 0.670854 GTTCAGCGAGACAAGACCCC 60.671 60.000 0.00 0.00 0.00 4.95
331 335 1.815003 CACAAGGACTGGATGCCTTTC 59.185 52.381 0.00 0.00 42.41 2.62
336 340 2.191128 ACTTCACAAGGACTGGATGC 57.809 50.000 0.00 0.00 0.00 3.91
376 384 1.700739 TGTTCATCCGGGTTTGTACCT 59.299 47.619 0.00 0.00 44.38 3.08
412 421 4.517285 ACTATGAAGGCGTTTGTGATGAT 58.483 39.130 0.00 0.00 0.00 2.45
440 449 7.697291 TGTTGGTTTATTGTAAAGTGACGTTTC 59.303 33.333 0.00 0.00 0.00 2.78
448 457 6.294286 CCGGTGATGTTGGTTTATTGTAAAGT 60.294 38.462 0.00 0.00 0.00 2.66
452 461 4.907809 TCCGGTGATGTTGGTTTATTGTA 58.092 39.130 0.00 0.00 0.00 2.41
456 465 5.714806 AGATTTTCCGGTGATGTTGGTTTAT 59.285 36.000 0.00 0.00 0.00 1.40
462 471 4.764679 TTCAGATTTTCCGGTGATGTTG 57.235 40.909 0.00 0.00 0.00 3.33
534 544 2.215942 ATGGTTTGGTTCTAGCCCAC 57.784 50.000 0.84 0.00 0.00 4.61
578 601 6.194796 ACCTTCGGAATACAAATTCATGTG 57.805 37.500 0.00 0.00 42.88 3.21
579 602 6.659242 AGAACCTTCGGAATACAAATTCATGT 59.341 34.615 0.00 0.00 42.88 3.21
592 636 2.557317 GTGTGTTCAGAACCTTCGGAA 58.443 47.619 10.93 0.00 38.69 4.30
595 639 1.787155 CTCGTGTGTTCAGAACCTTCG 59.213 52.381 10.93 11.60 0.00 3.79
781 825 1.108132 AAGGGGGTTGCGCGTAAAAA 61.108 50.000 12.24 0.00 0.00 1.94
800 844 1.595929 GGGAGCGGACGTTTCAACA 60.596 57.895 0.00 0.00 0.00 3.33
957 1002 6.789262 ACAATCAATGAAATGTGCTAGCTAC 58.211 36.000 17.23 12.72 0.00 3.58
1011 1056 2.124693 CAGCGACCTCCTCCTCCTC 61.125 68.421 0.00 0.00 0.00 3.71
1263 1308 6.304683 TGCGATATATGCACGTATATATTCGC 59.695 38.462 26.80 26.80 42.77 4.70
1449 1503 8.839914 CACACGTACATGAATACAAAAAGAATG 58.160 33.333 0.00 0.00 0.00 2.67
1525 1580 6.456501 GGATTATATAGGTGCGACAGAACTT 58.543 40.000 0.00 0.00 0.00 2.66
1526 1581 5.047235 GGGATTATATAGGTGCGACAGAACT 60.047 44.000 0.00 0.00 0.00 3.01
1527 1582 5.169295 GGGATTATATAGGTGCGACAGAAC 58.831 45.833 0.00 0.00 0.00 3.01
1568 1623 8.641541 TGTATTTCTTTGATTCTTTCTTTGCCT 58.358 29.630 0.00 0.00 0.00 4.75
1598 1653 8.888716 CCAGTTAACAATGCATACTGTGTATAA 58.111 33.333 20.00 7.57 35.58 0.98
1602 1657 5.312895 TCCAGTTAACAATGCATACTGTGT 58.687 37.500 20.00 10.15 35.58 3.72
1649 1704 4.893608 TGAGAGTGGTGAAAATCGATCAA 58.106 39.130 0.00 0.00 0.00 2.57
1679 1734 4.229123 AGATCAAAGATGGGGCATATAGGG 59.771 45.833 0.00 0.00 0.00 3.53
1690 1745 8.301720 TCTGATTTGTTTTGAGATCAAAGATGG 58.698 33.333 7.95 0.00 45.34 3.51
1736 1793 7.971168 AGTTAACAAAGATGATCTCACGAGTAG 59.029 37.037 8.61 0.00 0.00 2.57
1737 1794 7.755373 CAGTTAACAAAGATGATCTCACGAGTA 59.245 37.037 8.61 0.00 0.00 2.59
1738 1795 6.587990 CAGTTAACAAAGATGATCTCACGAGT 59.412 38.462 8.61 0.00 0.00 4.18
1739 1796 6.035435 CCAGTTAACAAAGATGATCTCACGAG 59.965 42.308 8.61 0.00 0.00 4.18
1740 1797 5.869344 CCAGTTAACAAAGATGATCTCACGA 59.131 40.000 8.61 0.00 0.00 4.35
1741 1798 5.869344 TCCAGTTAACAAAGATGATCTCACG 59.131 40.000 8.61 0.00 0.00 4.35
1742 1799 6.876257 ACTCCAGTTAACAAAGATGATCTCAC 59.124 38.462 8.61 0.00 0.00 3.51
1743 1800 7.009179 ACTCCAGTTAACAAAGATGATCTCA 57.991 36.000 8.61 0.00 0.00 3.27
1744 1801 8.254508 ACTACTCCAGTTAACAAAGATGATCTC 58.745 37.037 8.61 0.00 31.59 2.75
1745 1802 8.140112 ACTACTCCAGTTAACAAAGATGATCT 57.860 34.615 8.61 0.00 31.59 2.75
1746 1803 9.303537 GTACTACTCCAGTTAACAAAGATGATC 57.696 37.037 8.61 0.00 38.80 2.92
1747 1804 9.036980 AGTACTACTCCAGTTAACAAAGATGAT 57.963 33.333 8.61 0.00 38.80 2.45
1748 1805 8.418597 AGTACTACTCCAGTTAACAAAGATGA 57.581 34.615 8.61 0.00 38.80 2.92
1749 1806 9.490379 AAAGTACTACTCCAGTTAACAAAGATG 57.510 33.333 8.61 0.00 38.80 2.90
1890 1948 4.986875 TTACACGTATGCGCTTTACAAA 57.013 36.364 9.73 0.92 42.83 2.83
2103 2161 1.198637 GAGCAAGCCAAACAGTAGCAG 59.801 52.381 0.00 0.00 0.00 4.24
2172 2230 5.501156 ACAAATAGTGACCCTGAAGAATCC 58.499 41.667 0.00 0.00 0.00 3.01
2180 2238 5.163457 ACCAAACAAACAAATAGTGACCCTG 60.163 40.000 0.00 0.00 0.00 4.45
2187 2245 9.930693 TTACTTTGAACCAAACAAACAAATAGT 57.069 25.926 0.00 0.00 34.30 2.12


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

AutoCloner maintained by Alex Coulton.