Multiple sequence alignment - TraesCS2B01G184200

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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 TraesCS2B01G184200 chr2B 100.000 1970 0 0 472 2441 159256878 159254909 0.000000e+00 3639.0
1 TraesCS2B01G184200 chr2B 100.000 118 0 0 1 118 159257349 159257232 4.090000e-53 219.0
2 TraesCS2B01G184200 chr2D 87.923 2037 116 69 473 2441 109725918 109723944 0.000000e+00 2279.0
3 TraesCS2B01G184200 chr2D 91.228 114 10 0 5 118 109726098 109725985 3.250000e-34 156.0
4 TraesCS2B01G184200 chr2A 88.415 1407 83 37 475 1824 105499443 105498060 0.000000e+00 1622.0
5 TraesCS2B01G184200 chr2A 84.258 559 36 26 1896 2432 105498017 105497489 4.690000e-137 497.0
6 TraesCS2B01G184200 chr2A 93.220 59 4 0 3 61 105508319 105508261 1.200000e-13 87.9
7 TraesCS2B01G184200 chr2A 100.000 37 0 0 82 118 105499520 105499484 4.360000e-08 69.4


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 TraesCS2B01G184200 chr2B 159254909 159257349 2440 True 1929.000000 3639 100.0000 1 2441 2 chr2B.!!$R1 2440
1 TraesCS2B01G184200 chr2D 109723944 109726098 2154 True 1217.500000 2279 89.5755 5 2441 2 chr2D.!!$R1 2436
2 TraesCS2B01G184200 chr2A 105497489 105499520 2031 True 729.466667 1622 90.8910 82 2432 3 chr2A.!!$R2 2350

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
794 811 0.101759 TTTCGTGATCCGGATCCGTC 59.898 55.0 34.25 26.01 37.02 4.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2328 2463 0.166814 GTGGAAGATCAAGCACGCAC 59.833 55.0 0.0 0.0 0.0 5.34 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
19 20 1.600023 CCGCAAACCCTAACTCAACA 58.400 50.000 0.00 0.00 0.00 3.33
20 21 2.159382 CCGCAAACCCTAACTCAACAT 58.841 47.619 0.00 0.00 0.00 2.71
22 23 3.074412 CGCAAACCCTAACTCAACATCT 58.926 45.455 0.00 0.00 0.00 2.90
23 24 3.502211 CGCAAACCCTAACTCAACATCTT 59.498 43.478 0.00 0.00 0.00 2.40
64 65 2.224606 CGCCAATTGAGCCATCTACAT 58.775 47.619 7.12 0.00 0.00 2.29
69 70 4.201657 CAATTGAGCCATCTACATGACCA 58.798 43.478 0.00 0.00 30.57 4.02
79 80 2.365941 TCTACATGACCACAACCGACAA 59.634 45.455 0.00 0.00 0.00 3.18
501 502 1.153289 CCTCCCTGCACTCCATTCG 60.153 63.158 0.00 0.00 0.00 3.34
528 529 1.196012 GGAGGAGGGAAATGACGACT 58.804 55.000 0.00 0.00 0.00 4.18
529 530 1.137282 GGAGGAGGGAAATGACGACTC 59.863 57.143 0.00 0.00 0.00 3.36
536 537 2.875933 GGGAAATGACGACTCACAAACA 59.124 45.455 0.00 0.00 0.00 2.83
574 579 2.730090 GCAGTGTGCCATGAAAATCTCG 60.730 50.000 0.00 0.00 37.42 4.04
667 681 3.004752 AGGGATTATGACACCAAGCAC 57.995 47.619 0.00 0.00 0.00 4.40
694 711 7.507733 TTCTAGGTCGATCCTATCAGTTTAC 57.492 40.000 12.32 0.00 46.43 2.01
771 788 2.542178 CCAAAAGTAAACGCAAAAGCCC 59.458 45.455 0.00 0.00 0.00 5.19
772 789 3.190874 CAAAAGTAAACGCAAAAGCCCA 58.809 40.909 0.00 0.00 0.00 5.36
773 790 2.793278 AAGTAAACGCAAAAGCCCAG 57.207 45.000 0.00 0.00 0.00 4.45
792 809 1.215655 GCTTTCGTGATCCGGATCCG 61.216 60.000 35.72 33.77 37.02 4.18
794 811 0.101759 TTTCGTGATCCGGATCCGTC 59.898 55.000 34.25 26.01 37.02 4.79
840 862 1.527034 GACCGTTAGTTCCAAACCCC 58.473 55.000 0.00 0.00 0.00 4.95
865 887 5.629079 GTCCAACATAAAAGGACTTCCAG 57.371 43.478 0.00 0.00 46.45 3.86
950 972 4.404098 CGGCCGCCAGGTTACCTT 62.404 66.667 14.67 0.00 40.50 3.50
954 976 2.818274 CGCCAGGTTACCTTCGGC 60.818 66.667 19.37 19.37 38.76 5.54
997 1028 0.890996 AAGAGCAAGAAACCCCGCAG 60.891 55.000 0.00 0.00 0.00 5.18
1086 1117 1.817209 CTACACCTTCCTCCGCTCC 59.183 63.158 0.00 0.00 0.00 4.70
1401 1432 1.525077 CTCGGAGGAGGAGGACGAG 60.525 68.421 0.00 0.00 43.85 4.18
1403 1434 2.123640 GGAGGAGGAGGACGAGGG 60.124 72.222 0.00 0.00 0.00 4.30
1404 1435 2.835895 GAGGAGGAGGACGAGGGC 60.836 72.222 0.00 0.00 0.00 5.19
1405 1436 4.467107 AGGAGGAGGACGAGGGCC 62.467 72.222 0.00 0.00 0.00 5.80
1413 1444 2.281484 GACGAGGGCCAGCACAAA 60.281 61.111 6.18 0.00 0.00 2.83
1423 1460 3.884774 AGCACAAAGGCCACGGGA 61.885 61.111 5.01 0.00 0.00 5.14
1577 1624 7.642978 CCACTAGTACGTACACTAATTAAGCTG 59.357 40.741 26.55 2.66 30.77 4.24
1578 1625 7.165483 CACTAGTACGTACACTAATTAAGCTGC 59.835 40.741 26.55 0.00 30.77 5.25
1579 1626 6.205101 AGTACGTACACTAATTAAGCTGCT 57.795 37.500 26.55 0.00 0.00 4.24
1580 1627 7.325660 AGTACGTACACTAATTAAGCTGCTA 57.674 36.000 26.55 0.00 0.00 3.49
1581 1628 7.416022 AGTACGTACACTAATTAAGCTGCTAG 58.584 38.462 26.55 0.00 0.00 3.42
1582 1629 5.041940 ACGTACACTAATTAAGCTGCTAGC 58.958 41.667 8.10 8.10 42.84 3.42
1583 1630 4.444720 CGTACACTAATTAAGCTGCTAGCC 59.555 45.833 13.29 0.00 43.77 3.93
1584 1631 4.487714 ACACTAATTAAGCTGCTAGCCA 57.512 40.909 13.29 0.00 43.77 4.75
1585 1632 4.446371 ACACTAATTAAGCTGCTAGCCAG 58.554 43.478 13.29 10.78 43.77 4.85
1586 1633 3.812053 CACTAATTAAGCTGCTAGCCAGG 59.188 47.826 13.29 3.64 43.77 4.45
1587 1634 2.355010 AATTAAGCTGCTAGCCAGGG 57.645 50.000 13.29 0.99 43.77 4.45
1588 1635 1.511613 ATTAAGCTGCTAGCCAGGGA 58.488 50.000 13.29 0.00 43.77 4.20
1589 1636 1.511613 TTAAGCTGCTAGCCAGGGAT 58.488 50.000 13.29 0.00 43.77 3.85
1595 1655 1.602888 GCTAGCCAGGGATGCATGG 60.603 63.158 14.22 14.22 39.73 3.66
1629 1703 2.831526 TCTGTGGATCGATTCAACTGGA 59.168 45.455 8.28 1.77 30.21 3.86
1630 1704 3.452264 TCTGTGGATCGATTCAACTGGAT 59.548 43.478 8.28 0.00 30.21 3.41
1631 1705 3.797039 TGTGGATCGATTCAACTGGATC 58.203 45.455 8.28 0.00 35.65 3.36
1674 1748 2.817844 GAGCGTGGAACCTGGTTAATTT 59.182 45.455 12.96 0.00 0.00 1.82
1677 1751 3.254903 GCGTGGAACCTGGTTAATTTCTT 59.745 43.478 12.96 0.00 0.00 2.52
1678 1752 4.261867 GCGTGGAACCTGGTTAATTTCTTT 60.262 41.667 12.96 0.00 0.00 2.52
1679 1753 5.048573 GCGTGGAACCTGGTTAATTTCTTTA 60.049 40.000 12.96 0.00 0.00 1.85
1681 1755 7.248437 CGTGGAACCTGGTTAATTTCTTTATC 58.752 38.462 12.96 0.00 0.00 1.75
1734 1810 5.472148 TGTGATGATGGAAGAAACATTTGC 58.528 37.500 0.00 0.00 0.00 3.68
1751 1827 5.523188 ACATTTGCTTACAACAAACACATGG 59.477 36.000 0.00 0.00 39.65 3.66
1755 1831 3.798548 GCTTACAACAAACACATGGTGGG 60.799 47.826 0.00 0.00 42.42 4.61
1756 1832 2.151502 ACAACAAACACATGGTGGGA 57.848 45.000 0.00 0.00 42.42 4.37
1757 1833 2.031120 ACAACAAACACATGGTGGGAG 58.969 47.619 0.00 0.00 42.42 4.30
1758 1834 1.340889 CAACAAACACATGGTGGGAGG 59.659 52.381 0.00 0.00 37.94 4.30
1759 1835 0.178964 ACAAACACATGGTGGGAGGG 60.179 55.000 0.00 0.00 37.94 4.30
1760 1836 0.178964 CAAACACATGGTGGGAGGGT 60.179 55.000 0.00 0.00 37.94 4.34
1772 1848 2.034221 GAGGGTCACTTGGGTGGC 59.966 66.667 0.00 0.00 46.32 5.01
1776 1852 3.685435 GTCACTTGGGTGGCATGG 58.315 61.111 0.00 0.00 46.30 3.66
1777 1853 2.283101 TCACTTGGGTGGCATGGC 60.283 61.111 13.29 13.29 43.17 4.40
1778 1854 2.601067 CACTTGGGTGGCATGGCA 60.601 61.111 19.43 19.43 39.59 4.92
1780 1856 1.985662 ACTTGGGTGGCATGGCATG 60.986 57.895 26.07 22.99 0.00 4.06
1823 1902 2.776072 CTACTTTTGGCCGTCGCG 59.224 61.111 0.00 0.00 35.02 5.87
1874 1957 2.611225 GGATTTCCGAGCATGACTCT 57.389 50.000 13.06 0.00 43.85 3.24
1877 1960 1.996292 TTTCCGAGCATGACTCTTCG 58.004 50.000 13.06 6.38 43.85 3.79
1880 1963 0.171231 CCGAGCATGACTCTTCGTGA 59.829 55.000 13.06 0.00 43.85 4.35
1924 2009 1.741770 GCAACTACCCTGAGGCGTG 60.742 63.158 0.00 0.00 36.11 5.34
1937 2022 1.139947 GGCGTGACCTGAGCTAGTC 59.860 63.158 4.47 4.47 34.51 2.59
1938 2023 1.139947 GCGTGACCTGAGCTAGTCC 59.860 63.158 8.17 0.97 31.76 3.85
1939 2024 1.595993 GCGTGACCTGAGCTAGTCCA 61.596 60.000 8.17 0.00 31.76 4.02
1964 2057 2.012673 GGATGGTCTCAGTGTCAATGC 58.987 52.381 0.00 0.00 0.00 3.56
1965 2058 1.662629 GATGGTCTCAGTGTCAATGCG 59.337 52.381 0.00 0.00 0.00 4.73
1966 2059 0.678950 TGGTCTCAGTGTCAATGCGA 59.321 50.000 0.00 0.00 0.00 5.10
2003 2102 1.980765 GGAGGCCACATAGATGATGGA 59.019 52.381 5.01 0.00 40.18 3.41
2013 2112 0.176680 AGATGATGGACAGACCGTGC 59.823 55.000 0.00 0.00 42.61 5.34
2162 2267 2.855514 CGGGGGCAACTTGTTGGTG 61.856 63.158 14.30 0.00 36.20 4.17
2163 2268 2.506957 GGGGGCAACTTGTTGGTGG 61.507 63.158 14.30 0.00 33.01 4.61
2164 2269 2.506957 GGGGCAACTTGTTGGTGGG 61.507 63.158 14.30 0.00 33.01 4.61
2165 2270 1.760480 GGGCAACTTGTTGGTGGGT 60.760 57.895 14.30 0.00 33.01 4.51
2166 2271 1.739667 GGCAACTTGTTGGTGGGTC 59.260 57.895 14.30 0.00 33.01 4.46
2168 2273 1.098712 GCAACTTGTTGGTGGGTCGA 61.099 55.000 14.30 0.00 33.01 4.20
2169 2274 1.604604 CAACTTGTTGGTGGGTCGAT 58.395 50.000 5.65 0.00 0.00 3.59
2171 2276 0.472471 ACTTGTTGGTGGGTCGATGT 59.528 50.000 0.00 0.00 0.00 3.06
2172 2277 1.156736 CTTGTTGGTGGGTCGATGTC 58.843 55.000 0.00 0.00 0.00 3.06
2222 2334 3.732849 AGCTGCCTAGGCCCCAAC 61.733 66.667 30.81 14.93 41.09 3.77
2325 2460 3.825328 CCTGAATATGTTAAGCCTGCCT 58.175 45.455 0.00 0.00 0.00 4.75
2326 2461 3.567164 CCTGAATATGTTAAGCCTGCCTG 59.433 47.826 0.00 0.00 0.00 4.85
2327 2462 2.951642 TGAATATGTTAAGCCTGCCTGC 59.048 45.455 0.00 0.00 0.00 4.85
2328 2463 1.597742 ATATGTTAAGCCTGCCTGCG 58.402 50.000 0.00 0.00 36.02 5.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.600023 TGTTGAGTTAGGGTTTGCGG 58.400 50.000 0.00 0.00 0.00 5.69
1 2 3.074412 AGATGTTGAGTTAGGGTTTGCG 58.926 45.455 0.00 0.00 0.00 4.85
2 3 4.518970 TCAAGATGTTGAGTTAGGGTTTGC 59.481 41.667 0.23 0.00 37.79 3.68
19 20 6.982160 AGATTCATGCTAGTCTCTCAAGAT 57.018 37.500 0.00 0.00 33.08 2.40
20 21 6.017523 CGTAGATTCATGCTAGTCTCTCAAGA 60.018 42.308 0.00 0.00 0.00 3.02
22 23 5.506483 GCGTAGATTCATGCTAGTCTCTCAA 60.506 44.000 0.00 0.00 0.00 3.02
23 24 4.023622 GCGTAGATTCATGCTAGTCTCTCA 60.024 45.833 0.00 0.00 0.00 3.27
33 34 3.851105 GCTCAATTGGCGTAGATTCATGC 60.851 47.826 5.42 0.00 0.00 4.06
64 65 1.673400 CAACATTGTCGGTTGTGGTCA 59.327 47.619 0.00 0.00 40.48 4.02
69 70 3.738982 TCATCTCAACATTGTCGGTTGT 58.261 40.909 5.33 0.00 44.53 3.32
79 80 3.625853 TCGAGTCTCCTCATCTCAACAT 58.374 45.455 0.00 0.00 37.59 2.71
471 472 2.923568 GGGAGGCCCCGATCTACC 60.924 72.222 0.00 0.00 44.02 3.18
501 502 3.200825 TCATTTCCCTCCTCCATTGACTC 59.799 47.826 0.00 0.00 0.00 3.36
528 529 1.140852 CCACACCTCCTCTGTTTGTGA 59.859 52.381 1.64 0.00 40.02 3.58
529 530 1.597742 CCACACCTCCTCTGTTTGTG 58.402 55.000 0.00 0.00 37.83 3.33
616 630 2.033550 CGCTCTACTGCCTTACTTCGAT 59.966 50.000 0.00 0.00 0.00 3.59
694 711 2.776225 GAGTCGTTGTTTTTGTTGCTCG 59.224 45.455 0.00 0.00 0.00 5.03
739 756 5.577554 GCGTTTACTTTTGGTTTTCCTTTCA 59.422 36.000 0.00 0.00 41.38 2.69
954 976 2.045926 CGGGAGGAACTGGCCAAG 60.046 66.667 7.01 3.48 41.55 3.61
997 1028 2.964978 GTGGTGGTGAGGCATTGC 59.035 61.111 0.00 0.00 0.00 3.56
1365 1396 3.492725 GAGTAGAACTCGACGATCTCG 57.507 52.381 4.30 7.88 44.44 4.04
1404 1435 3.673484 CCGTGGCCTTTGTGCTGG 61.673 66.667 3.32 0.00 0.00 4.85
1405 1436 3.673484 CCCGTGGCCTTTGTGCTG 61.673 66.667 3.32 0.00 0.00 4.41
1411 1442 1.678970 GCTTGATCCCGTGGCCTTT 60.679 57.895 3.32 0.00 0.00 3.11
1413 1444 3.011517 AGCTTGATCCCGTGGCCT 61.012 61.111 3.32 0.00 0.00 5.19
1423 1460 2.393271 AACTAGCGCTTGAGCTTGAT 57.607 45.000 25.45 0.00 46.80 2.57
1497 1544 1.916000 GCTATGGTGTACACGTTCGTC 59.084 52.381 19.41 5.40 0.00 4.20
1501 1548 3.328382 ACATGCTATGGTGTACACGTT 57.672 42.857 19.41 11.61 33.60 3.99
1577 1624 1.602888 CCATGCATCCCTGGCTAGC 60.603 63.158 6.04 6.04 0.00 3.42
1578 1625 0.250640 GACCATGCATCCCTGGCTAG 60.251 60.000 3.91 0.00 35.88 3.42
1579 1626 1.708993 GGACCATGCATCCCTGGCTA 61.709 60.000 3.91 0.00 35.88 3.93
1580 1627 2.599597 GACCATGCATCCCTGGCT 59.400 61.111 3.91 0.00 35.88 4.75
1581 1628 2.520260 GGACCATGCATCCCTGGC 60.520 66.667 3.91 0.00 35.88 4.85
1582 1629 1.454479 GTGGACCATGCATCCCTGG 60.454 63.158 10.79 0.00 35.12 4.45
1583 1630 1.033746 GTGTGGACCATGCATCCCTG 61.034 60.000 10.79 0.00 35.12 4.45
1584 1631 1.304282 GTGTGGACCATGCATCCCT 59.696 57.895 10.79 0.00 35.12 4.20
1585 1632 0.396139 ATGTGTGGACCATGCATCCC 60.396 55.000 10.79 0.00 35.12 3.85
1586 1633 0.742505 CATGTGTGGACCATGCATCC 59.257 55.000 0.00 0.00 33.90 3.51
1587 1634 1.133598 CACATGTGTGGACCATGCATC 59.866 52.381 18.03 0.00 42.74 3.91
1588 1635 1.179152 CACATGTGTGGACCATGCAT 58.821 50.000 18.03 2.55 42.74 3.96
1589 1636 2.643655 CACATGTGTGGACCATGCA 58.356 52.632 18.03 0.00 42.74 3.96
1629 1703 1.233019 GCGCTATGAACCTGCATGAT 58.767 50.000 0.00 0.00 0.00 2.45
1630 1704 1.153597 CGCGCTATGAACCTGCATGA 61.154 55.000 5.56 0.00 0.00 3.07
1631 1705 1.153597 TCGCGCTATGAACCTGCATG 61.154 55.000 5.56 0.00 0.00 4.06
1709 1783 7.123098 AGCAAATGTTTCTTCCATCATCACATA 59.877 33.333 0.00 0.00 0.00 2.29
1734 1810 3.634448 TCCCACCATGTGTTTGTTGTAAG 59.366 43.478 0.00 0.00 0.00 2.34
1751 1827 2.154074 ACCCAAGTGACCCTCCCAC 61.154 63.158 0.00 0.00 34.89 4.61
1823 1902 2.696506 GGGTGTTGCAGTTCTACCTAC 58.303 52.381 0.00 0.00 0.00 3.18
1924 2009 1.066303 CACGATGGACTAGCTCAGGTC 59.934 57.143 0.00 0.00 0.00 3.85
1938 2023 1.205655 ACACTGAGACCATCCACGATG 59.794 52.381 0.00 0.00 39.52 3.84
1939 2024 1.478510 GACACTGAGACCATCCACGAT 59.521 52.381 0.00 0.00 0.00 3.73
1964 2057 1.005037 TGCCTGCCACACTACTTCG 60.005 57.895 0.00 0.00 0.00 3.79
1965 2058 0.674895 CCTGCCTGCCACACTACTTC 60.675 60.000 0.00 0.00 0.00 3.01
1966 2059 1.127567 TCCTGCCTGCCACACTACTT 61.128 55.000 0.00 0.00 0.00 2.24
1994 2093 0.176680 GCACGGTCTGTCCATCATCT 59.823 55.000 0.00 0.00 35.57 2.90
2168 2273 2.102438 TACGCCTCGACGACGACAT 61.102 57.895 13.90 0.00 43.81 3.06
2169 2274 2.738139 TACGCCTCGACGACGACA 60.738 61.111 13.90 0.07 43.81 4.35
2171 2276 3.490759 GGTACGCCTCGACGACGA 61.491 66.667 13.90 9.98 46.56 4.20
2172 2277 3.494336 AGGTACGCCTCGACGACG 61.494 66.667 0.00 0.00 42.67 5.12
2187 2294 2.158652 AGCTGATCCAATCCATCACAGG 60.159 50.000 0.00 0.00 0.00 4.00
2222 2334 2.997986 GCCTGCATTCTGTTTGATTTGG 59.002 45.455 0.00 0.00 0.00 3.28
2325 2460 1.900585 GAAGATCAAGCACGCACGCA 61.901 55.000 0.00 0.00 0.00 5.24
2326 2461 1.225854 GAAGATCAAGCACGCACGC 60.226 57.895 0.00 0.00 0.00 5.34
2327 2462 1.291184 TGGAAGATCAAGCACGCACG 61.291 55.000 0.00 0.00 0.00 5.34
2328 2463 0.166814 GTGGAAGATCAAGCACGCAC 59.833 55.000 0.00 0.00 0.00 5.34


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

AutoCloner maintained by Alex Coulton.