Multiple sequence alignment - TraesCS4B01G263600

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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 TraesCS4B01G263600 chr4B 100.000 2437 0 0 1 2437 534709524 534711960 0.000000e+00 4501
1 TraesCS4B01G263600 chr2B 93.152 1913 119 9 5 1911 159215123 159213217 0.000000e+00 2796
2 TraesCS4B01G263600 chr2B 83.166 1693 267 17 32 1715 441899135 441897452 0.000000e+00 1531
3 TraesCS4B01G263600 chr2B 95.745 470 16 4 1901 2368 412698949 412699416 0.000000e+00 754
4 TraesCS4B01G263600 chr2B 95.329 471 18 4 1901 2368 412636565 412637034 0.000000e+00 745
5 TraesCS4B01G263600 chr2B 90.789 532 38 10 1911 2437 136263694 136263169 0.000000e+00 701
6 TraesCS4B01G263600 chr2B 97.368 114 3 0 2324 2437 412706629 412706742 6.880000e-46 195
7 TraesCS4B01G263600 chr2B 94.355 124 7 0 2314 2437 412637368 412637491 8.890000e-45 191
8 TraesCS4B01G263600 chr7B 93.182 1892 116 10 4 1890 45045419 45043536 0.000000e+00 2767
9 TraesCS4B01G263600 chr2A 89.775 1907 179 15 8 1907 672641164 672639267 0.000000e+00 2427
10 TraesCS4B01G263600 chr2A 88.860 1912 194 12 6 1907 596371856 596373758 0.000000e+00 2333
11 TraesCS4B01G263600 chr5D 89.310 1899 186 12 15 1905 484147928 484146039 0.000000e+00 2366
12 TraesCS4B01G263600 chr4D 88.837 1917 180 20 4 1907 360457162 360459057 0.000000e+00 2324
13 TraesCS4B01G263600 chr4D 91.887 530 38 5 1911 2437 389569125 389569652 0.000000e+00 736
14 TraesCS4B01G263600 chr7D 87.893 1908 200 20 5 1904 203026883 203024999 0.000000e+00 2215
15 TraesCS4B01G263600 chr1D 85.084 1609 232 8 113 1717 379793062 379791458 0.000000e+00 1635
16 TraesCS4B01G263600 chr1B 96.205 527 17 3 1913 2437 316808188 316808713 0.000000e+00 859
17 TraesCS4B01G263600 chr1B 95.094 530 23 3 1910 2437 63880339 63879811 0.000000e+00 832
18 TraesCS4B01G263600 chr3B 94.528 530 27 2 1910 2437 26447504 26448033 0.000000e+00 817
19 TraesCS4B01G263600 chr6D 93.797 532 29 4 1909 2437 359247218 359247748 0.000000e+00 797
20 TraesCS4B01G263600 chr5B 94.670 469 20 5 1904 2368 371685987 371686454 0.000000e+00 723
21 TraesCS4B01G263600 chr3A 89.516 248 20 4 1661 1905 737814663 737814907 2.350000e-80 309


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 TraesCS4B01G263600 chr4B 534709524 534711960 2436 False 4501 4501 100.000 1 2437 1 chr4B.!!$F1 2436
1 TraesCS4B01G263600 chr2B 159213217 159215123 1906 True 2796 2796 93.152 5 1911 1 chr2B.!!$R2 1906
2 TraesCS4B01G263600 chr2B 441897452 441899135 1683 True 1531 1531 83.166 32 1715 1 chr2B.!!$R3 1683
3 TraesCS4B01G263600 chr2B 136263169 136263694 525 True 701 701 90.789 1911 2437 1 chr2B.!!$R1 526
4 TraesCS4B01G263600 chr2B 412636565 412637491 926 False 468 745 94.842 1901 2437 2 chr2B.!!$F3 536
5 TraesCS4B01G263600 chr7B 45043536 45045419 1883 True 2767 2767 93.182 4 1890 1 chr7B.!!$R1 1886
6 TraesCS4B01G263600 chr2A 672639267 672641164 1897 True 2427 2427 89.775 8 1907 1 chr2A.!!$R1 1899
7 TraesCS4B01G263600 chr2A 596371856 596373758 1902 False 2333 2333 88.860 6 1907 1 chr2A.!!$F1 1901
8 TraesCS4B01G263600 chr5D 484146039 484147928 1889 True 2366 2366 89.310 15 1905 1 chr5D.!!$R1 1890
9 TraesCS4B01G263600 chr4D 360457162 360459057 1895 False 2324 2324 88.837 4 1907 1 chr4D.!!$F1 1903
10 TraesCS4B01G263600 chr4D 389569125 389569652 527 False 736 736 91.887 1911 2437 1 chr4D.!!$F2 526
11 TraesCS4B01G263600 chr7D 203024999 203026883 1884 True 2215 2215 87.893 5 1904 1 chr7D.!!$R1 1899
12 TraesCS4B01G263600 chr1D 379791458 379793062 1604 True 1635 1635 85.084 113 1717 1 chr1D.!!$R1 1604
13 TraesCS4B01G263600 chr1B 316808188 316808713 525 False 859 859 96.205 1913 2437 1 chr1B.!!$F1 524
14 TraesCS4B01G263600 chr1B 63879811 63880339 528 True 832 832 95.094 1910 2437 1 chr1B.!!$R1 527
15 TraesCS4B01G263600 chr3B 26447504 26448033 529 False 817 817 94.528 1910 2437 1 chr3B.!!$F1 527
16 TraesCS4B01G263600 chr6D 359247218 359247748 530 False 797 797 93.797 1909 2437 1 chr6D.!!$F1 528

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
562 563 0.106015 GCAAGGGGATATGTGGGCTT 60.106 55.0 0.0 0.0 0.0 4.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2322 2345 0.250513 GGCGGATCTCTTCACAAGGT 59.749 55.0 0.0 0.0 0.0 3.5 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
34 35 5.815581 AGCTAACCAACTTCATGAATACCA 58.184 37.500 8.96 0.00 0.00 3.25
177 178 3.252351 GAGGGGGAAGCTATTGTCCTAT 58.748 50.000 2.26 0.00 34.10 2.57
225 226 5.377478 GCTTGTTTAGCTAGTATCCCCATT 58.623 41.667 0.00 0.00 46.77 3.16
429 430 1.382420 TTTGCTGGGCAGTTGGGTT 60.382 52.632 0.00 0.00 40.61 4.11
431 432 0.539438 TTGCTGGGCAGTTGGGTTAG 60.539 55.000 0.00 0.00 40.61 2.34
466 467 6.608808 CCAAGATGAGGGTAAAATCTGGAAAT 59.391 38.462 0.00 0.00 31.11 2.17
551 552 2.371510 CCTCAAATTTTTGGCAAGGGGA 59.628 45.455 0.00 0.00 38.66 4.81
562 563 0.106015 GCAAGGGGATATGTGGGCTT 60.106 55.000 0.00 0.00 0.00 4.35
567 568 1.479389 GGGGATATGTGGGCTTCCAAG 60.479 57.143 0.00 0.00 43.12 3.61
594 595 3.525800 AAGTTTGGCTACAGATGGGTT 57.474 42.857 0.00 0.00 0.00 4.11
654 655 3.842069 GTTTGGAACCTCCCCACTT 57.158 52.632 0.00 0.00 35.03 3.16
817 818 7.223584 TGAACAAATCATAAAGGAGACTGTGA 58.776 34.615 0.00 0.00 34.67 3.58
826 827 3.777106 AGGAGACTGTGATCAAAGCAA 57.223 42.857 13.13 0.00 41.13 3.91
862 863 3.370953 GGTCTGGCAGTATGAATCCAAGT 60.371 47.826 15.27 0.00 39.69 3.16
870 871 5.455326 GCAGTATGAATCCAAGTGGGTCTAT 60.455 44.000 0.00 0.00 39.69 1.98
954 955 0.755686 TTTGGTCCATTGTTGTGCCC 59.244 50.000 0.00 0.00 0.00 5.36
1109 1110 2.937469 TTTGACTGTGTGGTTGCAAG 57.063 45.000 0.00 0.00 0.00 4.01
1159 1160 7.650104 CGTTTCTTTCCATAGAAGTAGGATCTC 59.350 40.741 0.00 0.00 35.69 2.75
1164 1165 8.707796 TTTCCATAGAAGTAGGATCTCGTTAT 57.292 34.615 0.00 0.00 32.35 1.89
1240 1241 1.832883 TTGTGCTTGTGTCTTGTGGT 58.167 45.000 0.00 0.00 0.00 4.16
1243 1244 1.360192 GCTTGTGTCTTGTGGTGCC 59.640 57.895 0.00 0.00 0.00 5.01
1324 1326 0.326904 TGGTGGCTGATCTGGAGGAT 60.327 55.000 1.46 0.00 37.37 3.24
1353 1355 2.550978 GGTGGATGATTCTGTACACCG 58.449 52.381 7.86 0.00 38.96 4.94
1438 1440 3.230134 TCCAATTGACTTTGGGGTGAAG 58.770 45.455 7.12 0.00 45.21 3.02
1480 1482 0.321919 GTGCCACTCATGCCTCTTCA 60.322 55.000 0.00 0.00 0.00 3.02
1512 1514 3.085952 TGATTCTGGGGCTTGTAAAGG 57.914 47.619 0.00 0.00 46.35 3.11
1528 1530 0.104409 AAGGTGGGTTCCAGAGTCCT 60.104 55.000 0.00 0.00 32.34 3.85
1543 1545 0.687354 GTCCTGACTCTTCAAGGCCA 59.313 55.000 5.01 0.00 28.35 5.36
1643 1645 5.060427 TCAACCCCTCAAGAAGATGAAAA 57.940 39.130 0.00 0.00 0.00 2.29
1675 1677 1.689273 GAGCATATCAAGGAGGTCCGT 59.311 52.381 0.00 0.00 42.08 4.69
1676 1678 1.414181 AGCATATCAAGGAGGTCCGTG 59.586 52.381 5.65 5.65 45.13 4.94
1707 1709 3.730061 GCTGCAAAAGACATGAGGATTCG 60.730 47.826 0.00 0.00 0.00 3.34
1761 1766 4.435651 GCTGTAGTGTTTCATCGGTTTAGC 60.436 45.833 0.00 0.00 0.00 3.09
1773 1783 1.668919 CGGTTTAGCTCAGCGTCAAGA 60.669 52.381 8.82 0.00 0.00 3.02
1779 1789 2.139118 AGCTCAGCGTCAAGAAAAGTC 58.861 47.619 0.00 0.00 0.00 3.01
1786 1796 2.931320 GCGTCAAGAAAAGTCGGATCCT 60.931 50.000 10.75 0.00 0.00 3.24
1787 1797 2.924290 CGTCAAGAAAAGTCGGATCCTC 59.076 50.000 10.75 2.85 0.00 3.71
1836 1846 9.673454 CTTATTTTTGTTACCCTGTACTGTTTC 57.327 33.333 0.00 0.00 0.00 2.78
1838 1848 7.463961 TTTTTGTTACCCTGTACTGTTTCAA 57.536 32.000 0.00 0.00 0.00 2.69
1850 1863 7.043192 CCTGTACTGTTTCAATTTTGCTCTTTG 60.043 37.037 0.00 0.00 0.00 2.77
1877 1894 1.865788 GCGTTTGAGGCATGCTTGGA 61.866 55.000 18.92 0.00 0.00 3.53
1890 1908 3.998913 TGCTTGGATGTTGGACTGATA 57.001 42.857 0.00 0.00 0.00 2.15
2081 2099 0.903942 TTACGGGGCGTTTACTGGAT 59.096 50.000 0.00 0.00 41.54 3.41
2091 2110 2.669950 CGTTTACTGGATTTTTGCCCCG 60.670 50.000 0.00 0.00 0.00 5.73
2254 2275 2.136878 CCGATGCTAGCTCCCCACT 61.137 63.158 17.23 0.00 0.00 4.00
2257 2278 1.381872 ATGCTAGCTCCCCACTCGT 60.382 57.895 17.23 0.00 0.00 4.18
2322 2345 0.550147 CTCCCTTTCCCTTCCTCCCA 60.550 60.000 0.00 0.00 0.00 4.37
2330 2741 1.133809 CCCTTCCTCCCACCTTGTGA 61.134 60.000 0.00 0.00 35.23 3.58
2345 2756 3.074369 TGAAGAGATCCGCCGCCA 61.074 61.111 0.00 0.00 0.00 5.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.909610 TGGTTAGCTCTCCCCCTGTG 60.910 60.000 0.00 0.00 0.00 3.66
2 3 0.253327 GTTGGTTAGCTCTCCCCCTG 59.747 60.000 0.00 0.00 0.00 4.45
3 4 0.119358 AGTTGGTTAGCTCTCCCCCT 59.881 55.000 0.00 0.00 0.00 4.79
6 7 3.055094 TCATGAAGTTGGTTAGCTCTCCC 60.055 47.826 0.00 0.00 0.00 4.30
7 8 4.207891 TCATGAAGTTGGTTAGCTCTCC 57.792 45.455 0.00 0.00 0.00 3.71
11 12 5.815581 TGGTATTCATGAAGTTGGTTAGCT 58.184 37.500 14.54 0.00 0.00 3.32
12 13 6.699575 ATGGTATTCATGAAGTTGGTTAGC 57.300 37.500 14.54 9.97 34.22 3.09
135 136 2.423947 CCAGCCAGCCATCCTCTTTAAT 60.424 50.000 0.00 0.00 0.00 1.40
177 178 7.976734 GCTTTAATGAGAGTTAGTCTAGCAGAA 59.023 37.037 3.25 0.00 34.71 3.02
225 226 6.879458 GGAACTTAAAGAAGGACAGCAGATAA 59.121 38.462 0.00 0.00 36.95 1.75
429 430 4.099633 CCTCATCTTGGGCATATCTCCTA 58.900 47.826 0.00 0.00 0.00 2.94
431 432 2.026449 CCCTCATCTTGGGCATATCTCC 60.026 54.545 0.00 0.00 37.99 3.71
497 498 6.040391 TGGCCTACATGCAAAAATATTAGGAC 59.960 38.462 3.32 2.57 34.31 3.85
529 530 2.552809 CCCCTTGCCAAAAATTTGAGGG 60.553 50.000 17.93 17.93 43.91 4.30
551 552 0.929244 AGCCTTGGAAGCCCACATAT 59.071 50.000 0.00 0.00 43.41 1.78
562 563 2.108250 AGCCAAACTTAAGAGCCTTGGA 59.892 45.455 22.78 0.00 39.70 3.53
567 568 3.939066 TCTGTAGCCAAACTTAAGAGCC 58.061 45.455 10.09 0.00 0.00 4.70
654 655 3.513515 ACAAAGGCCAAAACTGAACAGAA 59.486 39.130 5.01 0.00 0.00 3.02
759 760 1.152819 CTCCATCATGGCAGGGGTG 60.153 63.158 0.00 0.00 37.47 4.61
817 818 6.041637 ACCATAGCATCATCATTTGCTTTGAT 59.958 34.615 14.23 0.00 46.71 2.57
826 827 3.181437 TGCCAGACCATAGCATCATCATT 60.181 43.478 0.00 0.00 0.00 2.57
862 863 4.873010 AGTGAGCTAGAAGAATAGACCCA 58.127 43.478 0.00 0.00 0.00 4.51
870 871 5.420725 TGGCATAAAGTGAGCTAGAAGAA 57.579 39.130 0.00 0.00 0.00 2.52
954 955 3.092301 GAGAAAAACCTGGATTCTGGGG 58.908 50.000 15.24 0.00 33.73 4.96
1028 1029 4.884961 ACAGTCAGGGTTCCTATCTATGT 58.115 43.478 0.00 0.00 29.64 2.29
1109 1110 2.941720 GAGACTGCATCCCAGATGTTTC 59.058 50.000 6.46 1.55 44.64 2.78
1159 1160 8.977505 CCAAAATTTGGCTATGGAATAATAACG 58.022 33.333 12.23 0.00 45.17 3.18
1189 1190 6.699575 AAGCACTTCATGTTTCTTGTTAGT 57.300 33.333 0.00 0.00 0.00 2.24
1240 1241 6.065374 TGTTATTTCTAGTTTTCCACAGGCA 58.935 36.000 0.00 0.00 0.00 4.75
1243 1244 9.965824 AAACATGTTATTTCTAGTTTTCCACAG 57.034 29.630 12.39 0.00 0.00 3.66
1324 1326 3.453717 CAGAATCATCCACCTCTTGAGGA 59.546 47.826 22.10 1.79 35.59 3.71
1353 1355 2.095053 GCATTTTCTCAAGCGAGTCCTC 59.905 50.000 0.00 0.00 40.44 3.71
1438 1440 0.393537 CAGTGCCCATCAGGTTCCTC 60.394 60.000 0.00 0.00 38.26 3.71
1480 1482 3.117738 CCCCAGAATCAAGCTTGGAGTAT 60.118 47.826 25.73 9.49 0.00 2.12
1512 1514 0.321996 GTCAGGACTCTGGAACCCAC 59.678 60.000 0.00 0.00 41.23 4.61
1528 1530 1.768275 TCACTTGGCCTTGAAGAGTCA 59.232 47.619 3.32 0.00 0.00 3.41
1567 1569 4.823276 CTCGAAATCGCCTGAGCT 57.177 55.556 0.00 0.00 39.60 4.09
1569 1571 1.884926 GGGCTCGAAATCGCCTGAG 60.885 63.158 12.59 0.00 45.57 3.35
1691 1693 3.529533 CAGCTCGAATCCTCATGTCTTT 58.470 45.455 0.00 0.00 0.00 2.52
1707 1709 0.747283 CATTCCTCCTGCACCAGCTC 60.747 60.000 0.00 0.00 42.74 4.09
1761 1766 1.457303 CCGACTTTTCTTGACGCTGAG 59.543 52.381 0.00 0.00 0.00 3.35
1813 1823 7.648039 TGAAACAGTACAGGGTAACAAAAAT 57.352 32.000 0.00 0.00 39.74 1.82
1815 1825 7.648039 ATTGAAACAGTACAGGGTAACAAAA 57.352 32.000 0.00 0.00 39.74 2.44
1819 1829 6.419710 GCAAAATTGAAACAGTACAGGGTAAC 59.580 38.462 0.00 0.00 0.00 2.50
1836 1846 5.388061 CGCATGTTCTCAAAGAGCAAAATTG 60.388 40.000 0.00 0.00 38.90 2.32
1838 1848 4.232221 CGCATGTTCTCAAAGAGCAAAAT 58.768 39.130 0.00 0.00 38.90 1.82
1850 1863 0.874390 TGCCTCAAACGCATGTTCTC 59.126 50.000 0.00 0.00 37.31 2.87
1877 1894 4.927267 TGAAACCCTATCAGTCCAACAT 57.073 40.909 0.00 0.00 0.00 2.71
2060 2078 1.278699 TCCAGTAAACGCCCCGTAAAT 59.721 47.619 0.00 0.00 39.99 1.40
2081 2099 0.753479 TGTGAAGCTCGGGGCAAAAA 60.753 50.000 1.17 0.00 44.79 1.94
2254 2275 3.749064 GAGACAGGGCAGCGACGA 61.749 66.667 0.00 0.00 0.00 4.20
2322 2345 0.250513 GGCGGATCTCTTCACAAGGT 59.749 55.000 0.00 0.00 0.00 3.50
2330 2741 3.077556 AGTGGCGGCGGATCTCTT 61.078 61.111 9.78 0.00 0.00 2.85
2345 2756 3.223661 CTGCGAAGAAGAAGGCAGT 57.776 52.632 3.84 0.00 45.84 4.40


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

AutoCloner maintained by Alex Coulton.