Multiple sequence alignment - TraesCS4B01G162300

Loading Multiple Alignment...

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 TraesCS4B01G162300 chr4B 100.000 2573 0 0 1 2573 326093253 326095825 0.000000e+00 4752
1 TraesCS4B01G162300 chr1A 91.678 2283 93 39 325 2573 490893234 490895453 0.000000e+00 3073
2 TraesCS4B01G162300 chr1A 86.726 226 21 3 76 292 490893008 490893233 2.560000e-60 243
3 TraesCS4B01G162300 chr1D 91.883 2119 86 27 474 2564 394409943 394407883 0.000000e+00 2881
4 TraesCS4B01G162300 chr1D 90.180 1222 52 26 549 1759 394452594 394451430 0.000000e+00 1530
5 TraesCS4B01G162300 chr1D 90.123 405 26 7 33 431 394453041 394452645 4.910000e-142 514
6 TraesCS4B01G162300 chr1D 87.731 432 27 12 28 442 394410373 394409951 4.980000e-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 TraesCS4B01G162300 chr4B 326093253 326095825 2572 False 4752 4752 100.0000 1 2573 1 chr4B.!!$F1 2572
1 TraesCS4B01G162300 chr1A 490893008 490895453 2445 False 1658 3073 89.2020 76 2573 2 chr1A.!!$F1 2497
2 TraesCS4B01G162300 chr1D 394407883 394410373 2490 True 1681 2881 89.8070 28 2564 2 chr1D.!!$R1 2536
3 TraesCS4B01G162300 chr1D 394451430 394453041 1611 True 1022 1530 90.1515 33 1759 2 chr1D.!!$R2 1726

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
103 105 0.034059 ATGGATAAGCGGCCGAGAAG 59.966 55.0 33.48 0.0 0.0 2.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1713 1789 0.107848 AGGTACGGTAGCCACATTGC 60.108 55.0 13.34 0.0 0.0 3.56 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
26 27 8.293867 TGTGTGGTGAAATGTTTAAATACTAGC 58.706 33.333 0.00 0.00 0.00 3.42
73 74 1.009389 CGGCAACCACGAAGAGAGAC 61.009 60.000 0.00 0.00 0.00 3.36
81 82 0.393267 ACGAAGAGAGACGGAGAGGG 60.393 60.000 0.00 0.00 0.00 4.30
97 99 2.985847 GGGCATGGATAAGCGGCC 60.986 66.667 0.00 0.00 43.86 6.13
103 105 0.034059 ATGGATAAGCGGCCGAGAAG 59.966 55.000 33.48 0.00 0.00 2.85
112 114 0.245539 CGGCCGAGAAGAGGTTGTAA 59.754 55.000 24.07 0.00 0.00 2.41
127 129 7.787028 AGAGGTTGTAATCTTGTAGATTCTCC 58.213 38.462 5.26 5.14 40.75 3.71
213 224 0.035820 GTAGGACGGCCAATTCACCA 60.036 55.000 11.69 0.00 36.29 4.17
215 226 0.394352 AGGACGGCCAATTCACCATC 60.394 55.000 11.69 0.00 36.29 3.51
389 416 1.983224 CCACAAGTCGTCCATCCCT 59.017 57.895 0.00 0.00 0.00 4.20
421 448 2.158959 GTGACCAGCGATCCGAACG 61.159 63.158 0.00 0.00 0.00 3.95
463 490 7.559897 TCCCGGCAAATTAAGAAGAAGAATATT 59.440 33.333 0.00 0.00 0.00 1.28
561 595 2.437359 AGTTGCCCATCAGCTCGC 60.437 61.111 0.00 0.00 29.69 5.03
581 615 4.933064 CTCGCGGCTAGCTTCCGG 62.933 72.222 22.98 15.24 46.51 5.14
643 684 0.601841 GACGGCCGAGGACTTTGAAA 60.602 55.000 35.90 0.00 0.00 2.69
649 690 4.671766 CGGCCGAGGACTTTGAAATTTTAG 60.672 45.833 24.07 0.00 0.00 1.85
661 702 4.778904 TGAAATTTTAGAAACCACGCTCG 58.221 39.130 0.00 0.00 0.00 5.03
662 703 4.273969 TGAAATTTTAGAAACCACGCTCGT 59.726 37.500 0.00 0.00 0.00 4.18
663 704 4.400036 AATTTTAGAAACCACGCTCGTC 57.600 40.909 0.00 0.00 0.00 4.20
664 705 1.787012 TTTAGAAACCACGCTCGTCC 58.213 50.000 0.00 0.00 0.00 4.79
750 791 0.464036 TGCCACGATATTTCCTCGCT 59.536 50.000 0.00 0.00 39.71 4.93
751 792 1.140816 GCCACGATATTTCCTCGCTC 58.859 55.000 0.00 0.00 39.71 5.03
752 793 1.409412 CCACGATATTTCCTCGCTCG 58.591 55.000 0.00 0.00 39.71 5.03
753 794 0.778815 CACGATATTTCCTCGCTCGC 59.221 55.000 0.00 0.00 39.71 5.03
754 795 0.669077 ACGATATTTCCTCGCTCGCT 59.331 50.000 0.00 0.00 39.71 4.93
755 796 1.067212 ACGATATTTCCTCGCTCGCTT 59.933 47.619 0.00 0.00 39.71 4.68
756 797 1.453524 CGATATTTCCTCGCTCGCTTG 59.546 52.381 0.00 0.00 0.00 4.01
757 798 1.193426 GATATTTCCTCGCTCGCTTGC 59.807 52.381 0.00 0.00 0.00 4.01
758 799 0.175760 TATTTCCTCGCTCGCTTGCT 59.824 50.000 0.00 0.00 0.00 3.91
759 800 0.674895 ATTTCCTCGCTCGCTTGCTT 60.675 50.000 0.00 0.00 0.00 3.91
760 801 1.568612 TTTCCTCGCTCGCTTGCTTG 61.569 55.000 0.00 0.00 0.00 4.01
761 802 4.157958 CCTCGCTCGCTTGCTTGC 62.158 66.667 0.00 0.00 0.00 4.01
799 848 3.557903 ATCGCCTGCACCACAAGCT 62.558 57.895 0.00 0.00 33.24 3.74
800 849 4.034258 CGCCTGCACCACAAGCTG 62.034 66.667 0.00 0.00 33.24 4.24
802 851 3.677648 CCTGCACCACAAGCTGGC 61.678 66.667 0.00 0.00 45.32 4.85
942 995 2.108157 TCCAAGCTCGTGCACGTT 59.892 55.556 35.74 21.94 42.74 3.99
945 998 1.641140 CAAGCTCGTGCACGTTGAA 59.359 52.632 35.74 18.00 42.74 2.69
954 1015 4.194312 CACGTTGAAGCTTGCGTG 57.806 55.556 23.68 23.68 46.28 5.34
955 1016 2.005537 CACGTTGAAGCTTGCGTGC 61.006 57.895 24.60 5.27 45.86 5.34
956 1017 2.792543 CGTTGAAGCTTGCGTGCG 60.793 61.111 2.10 0.00 38.13 5.34
957 1018 2.327940 GTTGAAGCTTGCGTGCGT 59.672 55.556 2.10 0.00 38.13 5.24
1081 1142 0.933047 CGTCGACGACAGCAACTTCA 60.933 55.000 33.35 0.00 43.02 3.02
1082 1143 1.419374 GTCGACGACAGCAACTTCAT 58.581 50.000 22.66 0.00 32.09 2.57
1161 1222 2.496817 GCCGTCTGCCTCTACCTG 59.503 66.667 0.00 0.00 0.00 4.00
1407 1483 4.278513 CTGGTGGCCGGGGACAAA 62.279 66.667 2.18 0.00 33.39 2.83
1610 1686 4.077188 GTGCTCGCACGCCAAGTC 62.077 66.667 6.25 0.00 37.19 3.01
1665 1741 3.056035 ACCTGTAAGCCACTTACTGCTAC 60.056 47.826 16.16 0.00 44.49 3.58
1713 1789 5.222631 GGTTTAACAACAGAGCCAAATGAG 58.777 41.667 0.00 0.00 34.15 2.90
1725 1801 3.155093 CCAAATGAGCAATGTGGCTAC 57.845 47.619 0.00 0.00 45.99 3.58
1727 1803 1.382522 AATGAGCAATGTGGCTACCG 58.617 50.000 0.00 0.00 45.99 4.02
1728 1804 0.253044 ATGAGCAATGTGGCTACCGT 59.747 50.000 0.00 0.00 45.99 4.83
1731 1807 0.107848 AGCAATGTGGCTACCGTACC 60.108 55.000 0.00 0.00 43.70 3.34
1732 1808 0.107848 GCAATGTGGCTACCGTACCT 60.108 55.000 0.00 0.00 0.00 3.08
1734 1810 1.066430 CAATGTGGCTACCGTACCTGT 60.066 52.381 0.00 0.00 0.00 4.00
1738 1821 2.429767 GGCTACCGTACCTGTCCCC 61.430 68.421 0.00 0.00 0.00 4.81
1744 1827 2.753043 GTACCTGTCCCCGCGAGA 60.753 66.667 8.23 0.00 0.00 4.04
1745 1828 2.753043 TACCTGTCCCCGCGAGAC 60.753 66.667 18.73 18.73 34.72 3.36
1896 1983 1.068121 CCTCCAAAGGGAAGGACAGT 58.932 55.000 0.00 0.00 44.38 3.55
1943 2030 5.878332 TTTGTGCCATGAGTATTGTAGTG 57.122 39.130 0.00 0.00 0.00 2.74
2014 2101 5.913514 GCATCTCGATGTGTACGTAGTTTAT 59.086 40.000 8.54 0.00 40.77 1.40
2053 2140 3.118371 AGCTCACCCTTAATTAAGTCCCG 60.118 47.826 20.99 8.02 0.00 5.14
2184 2271 1.866925 GAAAAGGTTGCGTCTCCGG 59.133 57.895 0.00 0.00 33.68 5.14
2185 2272 0.601841 GAAAAGGTTGCGTCTCCGGA 60.602 55.000 2.93 2.93 33.68 5.14
2294 2385 5.287226 AGGCGACTAAAATTAGTACGATGG 58.713 41.667 19.64 5.28 43.64 3.51
2313 2404 0.824182 GAGGATCCGGATCAGGACGT 60.824 60.000 38.29 18.93 44.07 4.34
2331 2422 0.524862 GTCCGTCTTCGTCTGGCTAA 59.475 55.000 0.00 0.00 35.01 3.09
2466 2559 4.135153 CGCCACGGCTAGAGCACT 62.135 66.667 6.48 0.00 44.36 4.40
2467 2560 2.202810 GCCACGGCTAGAGCACTC 60.203 66.667 0.00 0.00 44.36 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 8.293867 GCTAGTATTTAAACATTTCACCACACA 58.706 33.333 0.00 0.00 0.00 3.72
1 2 8.293867 TGCTAGTATTTAAACATTTCACCACAC 58.706 33.333 0.00 0.00 0.00 3.82
2 3 8.397575 TGCTAGTATTTAAACATTTCACCACA 57.602 30.769 0.00 0.00 0.00 4.17
3 4 9.685828 TTTGCTAGTATTTAAACATTTCACCAC 57.314 29.630 0.00 0.00 0.00 4.16
4 5 9.685828 GTTTGCTAGTATTTAAACATTTCACCA 57.314 29.630 0.00 0.00 34.19 4.17
5 6 9.135843 GGTTTGCTAGTATTTAAACATTTCACC 57.864 33.333 0.00 0.00 35.35 4.02
6 7 9.135843 GGGTTTGCTAGTATTTAAACATTTCAC 57.864 33.333 0.00 0.00 35.35 3.18
7 8 9.084533 AGGGTTTGCTAGTATTTAAACATTTCA 57.915 29.630 0.00 0.00 35.35 2.69
10 11 9.185680 CCTAGGGTTTGCTAGTATTTAAACATT 57.814 33.333 0.00 0.00 35.35 2.71
11 12 8.554011 TCCTAGGGTTTGCTAGTATTTAAACAT 58.446 33.333 9.46 0.00 35.35 2.71
12 13 7.920227 TCCTAGGGTTTGCTAGTATTTAAACA 58.080 34.615 9.46 0.00 35.35 2.83
13 14 7.012138 GCTCCTAGGGTTTGCTAGTATTTAAAC 59.988 40.741 9.46 0.00 33.48 2.01
14 15 7.052248 GCTCCTAGGGTTTGCTAGTATTTAAA 58.948 38.462 9.46 0.00 0.00 1.52
15 16 6.157297 TGCTCCTAGGGTTTGCTAGTATTTAA 59.843 38.462 9.46 0.00 0.00 1.52
16 17 5.664006 TGCTCCTAGGGTTTGCTAGTATTTA 59.336 40.000 9.46 0.00 0.00 1.40
17 18 4.473559 TGCTCCTAGGGTTTGCTAGTATTT 59.526 41.667 9.46 0.00 0.00 1.40
18 19 4.037927 TGCTCCTAGGGTTTGCTAGTATT 58.962 43.478 9.46 0.00 0.00 1.89
19 20 3.388350 GTGCTCCTAGGGTTTGCTAGTAT 59.612 47.826 9.46 0.00 0.00 2.12
20 21 2.764572 GTGCTCCTAGGGTTTGCTAGTA 59.235 50.000 9.46 0.00 0.00 1.82
21 22 1.555533 GTGCTCCTAGGGTTTGCTAGT 59.444 52.381 9.46 0.00 0.00 2.57
22 23 1.471676 CGTGCTCCTAGGGTTTGCTAG 60.472 57.143 9.46 0.00 0.00 3.42
23 24 0.535335 CGTGCTCCTAGGGTTTGCTA 59.465 55.000 9.46 0.00 0.00 3.49
24 25 1.296715 CGTGCTCCTAGGGTTTGCT 59.703 57.895 9.46 0.00 0.00 3.91
25 26 1.003718 ACGTGCTCCTAGGGTTTGC 60.004 57.895 9.46 9.23 0.00 3.68
26 27 0.391263 GGACGTGCTCCTAGGGTTTG 60.391 60.000 9.46 0.00 35.89 2.93
73 74 0.322975 CTTATCCATGCCCCTCTCCG 59.677 60.000 0.00 0.00 0.00 4.63
81 82 3.357079 CGGCCGCTTATCCATGCC 61.357 66.667 14.67 0.00 38.74 4.40
97 99 6.853720 TCTACAAGATTACAACCTCTTCTCG 58.146 40.000 0.00 0.00 29.34 4.04
103 105 6.987404 GGGAGAATCTACAAGATTACAACCTC 59.013 42.308 2.25 4.93 44.41 3.85
112 114 4.339814 GTGACTCGGGAGAATCTACAAGAT 59.660 45.833 2.08 0.00 35.84 2.40
187 197 4.208686 GGCCGTCCTACTCCTGCG 62.209 72.222 0.00 0.00 0.00 5.18
213 224 4.458989 AGTTGTGACAATTACATTGCCGAT 59.541 37.500 0.00 0.00 43.98 4.18
215 226 4.159377 AGTTGTGACAATTACATTGCCG 57.841 40.909 0.00 0.00 43.98 5.69
235 250 0.109132 GGCGAATTTGTGGCTGGAAG 60.109 55.000 0.00 0.00 0.00 3.46
261 276 6.276091 GGATCTTTGACTGGCAATTATTTCC 58.724 40.000 0.00 0.00 36.15 3.13
368 387 1.021390 GGATGGACGACTTGTGGCAG 61.021 60.000 0.00 0.00 0.00 4.85
372 399 1.676014 GGAAGGGATGGACGACTTGTG 60.676 57.143 0.00 0.00 0.00 3.33
441 468 8.811378 GTGCAATATTCTTCTTCTTAATTTGCC 58.189 33.333 0.00 0.00 35.96 4.52
643 684 2.740447 GGACGAGCGTGGTTTCTAAAAT 59.260 45.455 0.00 0.00 0.00 1.82
649 690 2.741211 GGGGACGAGCGTGGTTTC 60.741 66.667 0.00 0.00 0.00 2.78
661 702 3.412624 GAGCTGCTGGATGGGGGAC 62.413 68.421 7.01 0.00 0.00 4.46
662 703 3.092511 GAGCTGCTGGATGGGGGA 61.093 66.667 7.01 0.00 0.00 4.81
663 704 3.414193 TGAGCTGCTGGATGGGGG 61.414 66.667 7.01 0.00 0.00 5.40
664 705 2.124403 GTGAGCTGCTGGATGGGG 60.124 66.667 7.01 0.00 0.00 4.96
757 798 4.767255 AAGGAGCGGGCGAGCAAG 62.767 66.667 6.37 0.00 40.15 4.01
758 799 4.760047 GAAGGAGCGGGCGAGCAA 62.760 66.667 6.37 0.00 40.15 3.91
761 802 4.856607 GTCGAAGGAGCGGGCGAG 62.857 72.222 0.00 0.00 33.00 5.03
902 955 3.438297 TCTTGGACTAATCAGCTACGC 57.562 47.619 0.00 0.00 0.00 4.42
904 957 5.105310 TGGACTTCTTGGACTAATCAGCTAC 60.105 44.000 0.00 0.00 0.00 3.58
913 966 2.231478 CGAGCTTGGACTTCTTGGACTA 59.769 50.000 0.00 0.00 0.00 2.59
942 995 4.312231 GCACGCACGCAAGCTTCA 62.312 61.111 0.00 0.00 45.62 3.02
954 1015 4.415501 CGAACTCTGCACGCACGC 62.416 66.667 0.00 0.00 0.00 5.34
955 1016 3.030308 ACGAACTCTGCACGCACG 61.030 61.111 0.00 0.00 0.00 5.34
956 1017 1.487452 TTCACGAACTCTGCACGCAC 61.487 55.000 0.00 0.00 0.00 5.34
957 1018 1.215014 CTTCACGAACTCTGCACGCA 61.215 55.000 0.00 0.00 0.00 5.24
1344 1405 4.200283 GCCTGCTCCTCGTCTCCG 62.200 72.222 0.00 0.00 0.00 4.63
1407 1483 3.394836 GGAGGGAGCGCCTTCACT 61.395 66.667 19.93 1.14 41.84 3.41
1608 1684 2.668280 GCTTCGGTGAGTTGGCGAC 61.668 63.158 0.00 0.00 0.00 5.19
1609 1685 2.357034 GCTTCGGTGAGTTGGCGA 60.357 61.111 0.00 0.00 0.00 5.54
1610 1686 2.034879 ATGCTTCGGTGAGTTGGCG 61.035 57.895 0.00 0.00 0.00 5.69
1611 1687 0.955428 TCATGCTTCGGTGAGTTGGC 60.955 55.000 0.00 0.00 0.00 4.52
1612 1688 0.798776 GTCATGCTTCGGTGAGTTGG 59.201 55.000 0.00 0.00 0.00 3.77
1613 1689 1.511850 TGTCATGCTTCGGTGAGTTG 58.488 50.000 0.00 0.00 0.00 3.16
1614 1690 2.146342 CTTGTCATGCTTCGGTGAGTT 58.854 47.619 0.00 0.00 0.00 3.01
1615 1691 1.800805 CTTGTCATGCTTCGGTGAGT 58.199 50.000 0.00 0.00 0.00 3.41
1713 1789 0.107848 AGGTACGGTAGCCACATTGC 60.108 55.000 13.34 0.00 0.00 3.56
1727 1803 2.753043 TCTCGCGGGGACAGGTAC 60.753 66.667 5.94 0.00 0.00 3.34
1728 1804 2.753043 GTCTCGCGGGGACAGGTA 60.753 66.667 21.62 0.00 34.23 3.08
1836 1923 1.280457 AGAAAAGTGGCCGGAGAGAT 58.720 50.000 5.05 0.00 0.00 2.75
1896 1983 9.469097 AATAATTTTAATGTACAGCCTACACCA 57.531 29.630 0.33 0.00 0.00 4.17
1924 2011 2.614057 GGCACTACAATACTCATGGCAC 59.386 50.000 0.00 0.00 33.20 5.01
2014 2101 3.519973 CTGCCCGTGTCAGTGCTGA 62.520 63.158 0.00 0.00 37.24 4.26
2053 2140 1.134551 GGTGACAAGCAGAGAGATCCC 60.135 57.143 0.00 0.00 0.00 3.85
2184 2271 1.949465 AGAAACGGTGAGGTGTTGTC 58.051 50.000 0.00 0.00 0.00 3.18
2185 2272 2.285977 GAAGAAACGGTGAGGTGTTGT 58.714 47.619 0.00 0.00 0.00 3.32
2252 2343 4.268359 GCCTAATCAATCCTCCATCCATC 58.732 47.826 0.00 0.00 0.00 3.51
2253 2344 3.307975 CGCCTAATCAATCCTCCATCCAT 60.308 47.826 0.00 0.00 0.00 3.41
2254 2345 2.038952 CGCCTAATCAATCCTCCATCCA 59.961 50.000 0.00 0.00 0.00 3.41
2255 2346 2.303022 TCGCCTAATCAATCCTCCATCC 59.697 50.000 0.00 0.00 0.00 3.51
2288 2379 0.178961 TGATCCGGATCCTCCATCGT 60.179 55.000 35.72 4.08 35.91 3.73
2294 2385 0.824182 ACGTCCTGATCCGGATCCTC 60.824 60.000 35.72 22.65 37.02 3.71
2313 2404 0.809385 CTTAGCCAGACGAAGACGGA 59.191 55.000 0.00 0.00 44.46 4.69
2466 2559 2.007049 GCCGCTCGAAAAAGATCCAGA 61.007 52.381 0.00 0.00 0.00 3.86
2467 2560 0.375106 GCCGCTCGAAAAAGATCCAG 59.625 55.000 0.00 0.00 0.00 3.86


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

AutoCloner maintained by Alex Coulton.