Multiple sequence alignment - TraesCS7B01G236500

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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 TraesCS7B01G236500 chr7B 100.000 2303 0 0 1 2303 440807929 440810231 0.000000e+00 4253
1 TraesCS7B01G236500 chr7A 94.294 2331 62 18 1 2303 509474838 509472551 0.000000e+00 3502
2 TraesCS7B01G236500 chr7D 93.130 1703 77 17 1 1687 423703856 423705534 0.000000e+00 2460
3 TraesCS7B01G236500 chr7D 90.278 360 27 5 1945 2303 423705599 423705951 4.480000e-127 464


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 TraesCS7B01G236500 chr7B 440807929 440810231 2302 False 4253 4253 100.000 1 2303 1 chr7B.!!$F1 2302
1 TraesCS7B01G236500 chr7A 509472551 509474838 2287 True 3502 3502 94.294 1 2303 1 chr7A.!!$R1 2302
2 TraesCS7B01G236500 chr7D 423703856 423705951 2095 False 1462 2460 91.704 1 2303 2 chr7D.!!$F1 2302


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
891 910 0.111061 TCAGTTTCAGCCACAGCCAT 59.889 50.0 0.0 0.0 41.25 4.4 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1868 1892 1.489481 CTGGGACCTATCACTGAGCA 58.511 55.0 0.0 0.0 28.7 4.26 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
156 165 2.351455 GCTTGTAGCTCCCACTCTTTC 58.649 52.381 0.00 0.00 38.45 2.62
192 201 1.674359 CGTATGGTTATGCTTGCCCA 58.326 50.000 0.00 0.00 0.00 5.36
241 250 3.030291 AGTTGGCAAAACCTGATCAACA 58.970 40.909 0.00 0.00 40.33 3.33
272 281 7.912056 AAACTTGTCAGCATATATCGCATAT 57.088 32.000 9.01 0.00 0.00 1.78
308 318 4.931027 ACTCTGGAGTCTGGTTACTCTA 57.069 45.455 4.20 0.00 44.42 2.43
310 320 3.949113 CTCTGGAGTCTGGTTACTCTACC 59.051 52.174 4.20 0.00 44.42 3.18
341 351 5.622770 ATTTCTTGTTAACCGTGCTAAGG 57.377 39.130 2.48 0.00 0.00 2.69
342 352 3.756933 TCTTGTTAACCGTGCTAAGGT 57.243 42.857 2.48 0.00 45.29 3.50
343 353 3.395639 TCTTGTTAACCGTGCTAAGGTG 58.604 45.455 2.48 0.00 41.95 4.00
344 354 1.515081 TGTTAACCGTGCTAAGGTGC 58.485 50.000 2.48 0.00 41.95 5.01
345 355 0.800631 GTTAACCGTGCTAAGGTGCC 59.199 55.000 0.00 0.00 41.95 5.01
346 356 0.688487 TTAACCGTGCTAAGGTGCCT 59.312 50.000 0.00 0.00 41.95 4.75
347 357 1.559368 TAACCGTGCTAAGGTGCCTA 58.441 50.000 0.00 0.00 41.95 3.93
348 358 0.688487 AACCGTGCTAAGGTGCCTAA 59.312 50.000 0.00 0.00 41.95 2.69
349 359 0.249398 ACCGTGCTAAGGTGCCTAAG 59.751 55.000 0.00 0.00 41.10 2.18
382 392 3.261897 TCCCTTGAGTTGAGATCTGTTCC 59.738 47.826 0.00 0.00 0.00 3.62
392 402 1.347707 AGATCTGTTCCGAAACCTGCA 59.652 47.619 0.00 0.00 34.28 4.41
473 483 1.471684 CACAAAGCTGAGGATGCCTTC 59.528 52.381 0.00 0.00 31.76 3.46
562 573 3.129462 GGAAGAGTAAATTGGAGCTTGGC 59.871 47.826 0.00 0.00 0.00 4.52
579 590 0.391263 GGCTTCTGTTACGGTCCTGG 60.391 60.000 0.00 0.00 0.00 4.45
592 603 2.158900 CGGTCCTGGTATGAATGCTCTT 60.159 50.000 0.00 0.00 0.00 2.85
607 618 4.600692 TGCTCTTGTTTACTGCAGTCTA 57.399 40.909 25.56 10.29 0.00 2.59
675 687 6.592994 CCCAGCATCAGATATGTACATAAGTG 59.407 42.308 19.11 17.56 0.00 3.16
692 704 6.369890 ACATAAGTGCAGTATGTCAAGTCTTG 59.630 38.462 14.49 6.21 37.59 3.02
882 901 0.315251 GCCCACCTTTCAGTTTCAGC 59.685 55.000 0.00 0.00 0.00 4.26
891 910 0.111061 TCAGTTTCAGCCACAGCCAT 59.889 50.000 0.00 0.00 41.25 4.40
892 911 1.350684 TCAGTTTCAGCCACAGCCATA 59.649 47.619 0.00 0.00 41.25 2.74
893 912 2.161855 CAGTTTCAGCCACAGCCATAA 58.838 47.619 0.00 0.00 41.25 1.90
1119 1138 1.455217 CGAGTCCTACCGTCCCCAT 60.455 63.158 0.00 0.00 0.00 4.00
1158 1177 2.295602 TTTCTACCCTGGCCCGTCC 61.296 63.158 0.00 0.00 0.00 4.79
1246 1265 0.338467 TAGCTCCTTCCCTGGCACTA 59.662 55.000 0.00 0.00 0.00 2.74
1496 1520 6.472486 GTCTTTGTAAAAGACTTGTTCTTGGC 59.528 38.462 20.42 0.00 44.41 4.52
1556 1580 1.532316 TCGTGGGTTCGAAGTCCCT 60.532 57.895 21.04 0.00 41.44 4.20
1586 1610 4.292186 TCTTTGATTTGGAGAGTGAGGG 57.708 45.455 0.00 0.00 0.00 4.30
1646 1670 2.100252 TGTTCCGTGTCTCGTCTCTTTT 59.900 45.455 0.00 0.00 37.94 2.27
1657 1681 7.597743 GTGTCTCGTCTCTTTTAAGTATTTCCA 59.402 37.037 0.00 0.00 0.00 3.53
1699 1723 9.409312 TGCTTTCAGTTTATTATGTTGTTGATG 57.591 29.630 0.00 0.00 0.00 3.07
1786 1810 4.065088 GCGGCATCATCTTTAGTTATGGA 58.935 43.478 0.00 0.00 0.00 3.41
1787 1811 4.515191 GCGGCATCATCTTTAGTTATGGAA 59.485 41.667 0.00 0.00 0.00 3.53
1788 1812 5.560953 GCGGCATCATCTTTAGTTATGGAAC 60.561 44.000 0.00 0.00 35.64 3.62
1802 1826 2.198827 TGGAACACTGGGTAGCATTG 57.801 50.000 0.00 0.00 0.00 2.82
1803 1827 1.702401 TGGAACACTGGGTAGCATTGA 59.298 47.619 0.00 0.00 0.00 2.57
1804 1828 2.308570 TGGAACACTGGGTAGCATTGAT 59.691 45.455 0.00 0.00 0.00 2.57
1805 1829 3.521531 TGGAACACTGGGTAGCATTGATA 59.478 43.478 0.00 0.00 0.00 2.15
1806 1830 4.165950 TGGAACACTGGGTAGCATTGATAT 59.834 41.667 0.00 0.00 0.00 1.63
1807 1831 5.133221 GGAACACTGGGTAGCATTGATATT 58.867 41.667 0.00 0.00 0.00 1.28
1808 1832 5.009010 GGAACACTGGGTAGCATTGATATTG 59.991 44.000 0.00 0.00 0.00 1.90
1809 1833 5.116084 ACACTGGGTAGCATTGATATTGT 57.884 39.130 0.00 0.00 0.00 2.71
1810 1834 4.883585 ACACTGGGTAGCATTGATATTGTG 59.116 41.667 0.00 0.00 0.00 3.33
1811 1835 3.885297 ACTGGGTAGCATTGATATTGTGC 59.115 43.478 0.00 0.00 39.10 4.57
1894 1918 2.026822 AGTGATAGGTCCCAGCTTGTTG 60.027 50.000 0.00 0.00 0.00 3.33
2148 2179 9.649167 GTCTAAAAGTACCTCTGTAATTGCTAA 57.351 33.333 0.00 0.00 35.58 3.09
2225 2256 3.532542 ACGAAGTATAAGAAGGGCAAGC 58.467 45.455 0.00 0.00 41.94 4.01
2269 2300 8.328864 GCCGATTAGTTTTCATTACTAGTTCTG 58.671 37.037 0.00 0.00 30.36 3.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
98 107 8.000780 AGAACAACAAAGCTAGAAAGTTCAAT 57.999 30.769 17.80 2.42 37.25 2.57
147 156 4.214332 GCAACAAACTAGAGGAAAGAGTGG 59.786 45.833 0.00 0.00 0.00 4.00
156 165 1.878953 ACGGTGCAACAAACTAGAGG 58.121 50.000 0.98 0.00 39.98 3.69
182 191 0.681175 GTCCAAAACTGGGCAAGCAT 59.319 50.000 0.00 0.00 32.88 3.79
241 250 7.653713 CGATATATGCTGACAAGTTTTCCTAGT 59.346 37.037 0.00 0.00 0.00 2.57
272 281 7.973048 ACTCCAGAGTCCAGTATAACAAATA 57.027 36.000 0.00 0.00 36.92 1.40
341 351 4.591072 AGGGATAGAAGATGACTTAGGCAC 59.409 45.833 0.00 0.00 36.39 5.01
342 352 4.820775 AGGGATAGAAGATGACTTAGGCA 58.179 43.478 0.00 0.00 36.39 4.75
343 353 5.305644 TCAAGGGATAGAAGATGACTTAGGC 59.694 44.000 0.00 0.00 36.39 3.93
344 354 6.553100 ACTCAAGGGATAGAAGATGACTTAGG 59.447 42.308 0.00 0.00 36.39 2.69
345 355 7.595819 ACTCAAGGGATAGAAGATGACTTAG 57.404 40.000 0.00 0.00 36.39 2.18
346 356 7.619698 TCAACTCAAGGGATAGAAGATGACTTA 59.380 37.037 0.00 0.00 36.39 2.24
347 357 6.441924 TCAACTCAAGGGATAGAAGATGACTT 59.558 38.462 0.00 0.00 39.24 3.01
348 358 5.960811 TCAACTCAAGGGATAGAAGATGACT 59.039 40.000 0.00 0.00 0.00 3.41
349 359 6.097554 TCTCAACTCAAGGGATAGAAGATGAC 59.902 42.308 0.00 0.00 0.00 3.06
382 392 4.414852 CAATAAAGGACATGCAGGTTTCG 58.585 43.478 5.07 0.00 0.00 3.46
392 402 8.877864 TGTAACATTTCTCCAATAAAGGACAT 57.122 30.769 0.00 0.00 33.19 3.06
473 483 2.163010 CAGGTAGGTCTGCAGCAAATTG 59.837 50.000 9.47 0.00 0.00 2.32
562 573 3.446161 TCATACCAGGACCGTAACAGAAG 59.554 47.826 0.00 0.00 0.00 2.85
579 590 6.128172 ACTGCAGTAAACAAGAGCATTCATAC 60.128 38.462 20.16 0.00 34.35 2.39
592 603 2.637872 AGGCCTTAGACTGCAGTAAACA 59.362 45.455 21.73 3.24 0.00 2.83
607 618 2.282462 CGAGGGTTGCAAGGCCTT 60.282 61.111 13.78 13.78 0.00 4.35
675 687 2.704572 AGCCAAGACTTGACATACTGC 58.295 47.619 16.99 9.21 0.00 4.40
692 704 6.934048 AGCTTGAGTTAAGATCATAAAGCC 57.066 37.500 7.97 0.00 38.76 4.35
720 739 5.925509 ACATGTTTACTCTGTTGGTGTACT 58.074 37.500 0.00 0.00 0.00 2.73
882 901 1.518325 TCGTTGTGTTATGGCTGTGG 58.482 50.000 0.00 0.00 0.00 4.17
891 910 3.398406 ACTGTGCATGATCGTTGTGTTA 58.602 40.909 0.00 0.00 0.00 2.41
892 911 2.221169 ACTGTGCATGATCGTTGTGTT 58.779 42.857 0.00 0.00 0.00 3.32
893 912 1.882912 ACTGTGCATGATCGTTGTGT 58.117 45.000 0.00 0.00 0.00 3.72
1119 1138 1.540797 CCACCGAACCCAAAGACGTTA 60.541 52.381 0.00 0.00 0.00 3.18
1158 1177 1.503818 CCGGAAACACCCAGTTGACG 61.504 60.000 0.00 0.00 41.19 4.35
1525 1549 1.202710 ACCCACGACAGCAATACAACA 60.203 47.619 0.00 0.00 0.00 3.33
1556 1580 6.716628 ACTCTCCAAATCAAAGATACAGCAAA 59.283 34.615 0.00 0.00 0.00 3.68
1586 1610 2.424956 GATCCAGCTCATGGGTTCAAAC 59.575 50.000 0.00 0.00 45.07 2.93
1646 1670 9.605275 CACTGAGAAGAATGATGGAAATACTTA 57.395 33.333 0.00 0.00 0.00 2.24
1657 1681 5.311265 TGAAAGCACACTGAGAAGAATGAT 58.689 37.500 0.00 0.00 0.00 2.45
1699 1723 8.937634 AGAACAAAGATATGGAAATGCATTTC 57.062 30.769 34.36 34.36 44.08 2.17
1786 1810 5.357878 CACAATATCAATGCTACCCAGTGTT 59.642 40.000 0.00 0.00 40.29 3.32
1787 1811 4.883585 CACAATATCAATGCTACCCAGTGT 59.116 41.667 0.00 0.00 40.29 3.55
1788 1812 4.261322 GCACAATATCAATGCTACCCAGTG 60.261 45.833 0.00 0.00 40.73 3.66
1789 1813 3.885297 GCACAATATCAATGCTACCCAGT 59.115 43.478 0.00 0.00 36.40 4.00
1790 1814 3.884693 TGCACAATATCAATGCTACCCAG 59.115 43.478 7.17 0.00 40.13 4.45
1791 1815 3.631686 GTGCACAATATCAATGCTACCCA 59.368 43.478 13.17 0.00 40.13 4.51
1792 1816 3.631686 TGTGCACAATATCAATGCTACCC 59.368 43.478 19.28 0.00 40.13 3.69
1793 1817 4.898829 TGTGCACAATATCAATGCTACC 57.101 40.909 19.28 0.00 40.13 3.18
1794 1818 5.688621 CCAATGTGCACAATATCAATGCTAC 59.311 40.000 25.72 0.00 40.13 3.58
1795 1819 5.360429 ACCAATGTGCACAATATCAATGCTA 59.640 36.000 25.72 0.00 40.13 3.49
1796 1820 4.160814 ACCAATGTGCACAATATCAATGCT 59.839 37.500 25.72 0.00 40.13 3.79
1797 1821 4.435425 ACCAATGTGCACAATATCAATGC 58.565 39.130 25.72 0.00 39.88 3.56
1798 1822 7.254185 GCTTAACCAATGTGCACAATATCAATG 60.254 37.037 25.72 13.20 0.00 2.82
1799 1823 6.757947 GCTTAACCAATGTGCACAATATCAAT 59.242 34.615 25.72 9.63 0.00 2.57
1800 1824 6.098679 GCTTAACCAATGTGCACAATATCAA 58.901 36.000 25.72 12.48 0.00 2.57
1801 1825 5.184671 TGCTTAACCAATGTGCACAATATCA 59.815 36.000 25.72 9.28 0.00 2.15
1802 1826 5.649557 TGCTTAACCAATGTGCACAATATC 58.350 37.500 25.72 6.85 0.00 1.63
1803 1827 5.657826 TGCTTAACCAATGTGCACAATAT 57.342 34.783 25.72 10.56 0.00 1.28
1867 1891 2.045524 CTGGGACCTATCACTGAGCAT 58.954 52.381 0.00 0.00 28.70 3.79
1868 1892 1.489481 CTGGGACCTATCACTGAGCA 58.511 55.000 0.00 0.00 28.70 4.26
1912 1940 3.774766 GGGGAAAAGGCCATAAACTTGAT 59.225 43.478 5.01 0.00 0.00 2.57
2119 2150 8.657729 GCAATTACAGAGGTACTTTTAGACTTC 58.342 37.037 0.00 0.00 41.55 3.01
2148 2179 3.919834 AGAAATTAGCATCAAGGGCCAT 58.080 40.909 6.18 0.00 0.00 4.40
2225 2256 3.438360 CGGCTTAAATGCTAAAAGCTGG 58.562 45.455 7.13 0.00 44.98 4.85
2269 2300 3.915437 TCGGGAGCATTTTTCTTGAAC 57.085 42.857 0.00 0.00 0.00 3.18



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

AutoCloner maintained by Alex Coulton.