Multiple sequence alignment - TraesCS5B01G006200

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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 TraesCS5B01G006200 chr5B 100.000 1690 0 0 999 2688 7355437 7353748 0.000000e+00 3121
1 TraesCS5B01G006200 chr5B 96.154 780 30 0 999 1778 7304701 7303922 0.000000e+00 1275
2 TraesCS5B01G006200 chr5B 95.769 780 33 0 999 1778 7383267 7382488 0.000000e+00 1258
3 TraesCS5B01G006200 chr5B 90.725 938 55 12 1777 2688 7382516 7381585 0.000000e+00 1221
4 TraesCS5B01G006200 chr5B 89.637 936 61 16 1777 2686 7303950 7303025 0.000000e+00 1158
5 TraesCS5B01G006200 chr5B 100.000 618 0 0 1 618 7356435 7355818 0.000000e+00 1142
6 TraesCS5B01G006200 chr5B 90.081 867 58 15 1848 2688 7148444 7147580 0.000000e+00 1099
7 TraesCS5B01G006200 chr5B 89.965 867 58 16 1848 2688 7184180 7183317 0.000000e+00 1092
8 TraesCS5B01G006200 chr5B 89.619 867 62 15 1848 2688 7162049 7161185 0.000000e+00 1077
9 TraesCS5B01G006200 chr5B 96.296 621 20 3 1 618 7383923 7383303 0.000000e+00 1016
10 TraesCS5B01G006200 chr5B 95.638 619 25 2 1 618 7305352 7304735 0.000000e+00 992
11 TraesCS5B01G006200 chr5B 94.042 621 27 5 1 618 7185606 7184993 0.000000e+00 933
12 TraesCS5B01G006200 chr5D 87.265 1649 149 22 999 2610 7125302 7123678 0.000000e+00 1825
13 TraesCS5B01G006200 chr5D 87.025 1657 158 28 999 2612 7130582 7128940 0.000000e+00 1816
14 TraesCS5B01G006200 chr5D 85.582 1727 178 29 999 2688 3890330 3892022 0.000000e+00 1744
15 TraesCS5B01G006200 chr5D 92.239 786 55 5 999 1778 3875412 3876197 0.000000e+00 1109
16 TraesCS5B01G006200 chr5D 92.229 785 56 3 999 1778 7120000 7119216 0.000000e+00 1107
17 TraesCS5B01G006200 chr5D 92.112 786 56 5 999 1778 3869827 3870612 0.000000e+00 1103
18 TraesCS5B01G006200 chr5D 90.514 622 47 12 4 618 7125952 7125336 0.000000e+00 811
19 TraesCS5B01G006200 chr5D 90.369 623 51 9 1 618 3880085 3880703 0.000000e+00 809
20 TraesCS5B01G006200 chr5D 84.144 864 95 15 1780 2610 7119241 7118387 0.000000e+00 798
21 TraesCS5B01G006200 chr5D 90.016 621 51 11 4 618 7120649 7120034 0.000000e+00 793
22 TraesCS5B01G006200 chr5D 85.037 802 90 17 1833 2604 3870629 3871430 0.000000e+00 789
23 TraesCS5B01G006200 chr5D 89.440 625 53 13 1 618 3869175 3869793 0.000000e+00 776
24 TraesCS5B01G006200 chr5D 84.627 657 70 14 1979 2604 3865482 3866138 2.270000e-175 625
25 TraesCS5B01G006200 chr5A 86.788 1650 169 29 999 2612 4796506 4794870 0.000000e+00 1794
26 TraesCS5B01G006200 chr5A 86.724 1642 160 29 999 2604 4875814 4877433 0.000000e+00 1772
27 TraesCS5B01G006200 chr5A 90.307 619 50 8 1 610 4875124 4875741 0.000000e+00 802
28 TraesCS5B01G006200 chr5A 84.406 808 96 11 1833 2612 4866795 4867600 0.000000e+00 767
29 TraesCS5B01G006200 chr4A 92.219 784 55 4 999 1778 18743010 18742229 0.000000e+00 1105
30 TraesCS5B01G006200 chr4A 92.092 784 57 4 999 1778 18737366 18736584 0.000000e+00 1099
31 TraesCS5B01G006200 chr4A 90.499 621 49 9 4 618 18738016 18737400 0.000000e+00 811


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 TraesCS5B01G006200 chr5B 7353748 7356435 2687 True 2131.500000 3121 100.000000 1 2688 2 chr5B.!!$R5 2687
1 TraesCS5B01G006200 chr5B 7381585 7383923 2338 True 1165.000000 1258 94.263333 1 2688 3 chr5B.!!$R6 2687
2 TraesCS5B01G006200 chr5B 7303025 7305352 2327 True 1141.666667 1275 93.809667 1 2686 3 chr5B.!!$R4 2685
3 TraesCS5B01G006200 chr5B 7147580 7148444 864 True 1099.000000 1099 90.081000 1848 2688 1 chr5B.!!$R1 840
4 TraesCS5B01G006200 chr5B 7161185 7162049 864 True 1077.000000 1077 89.619000 1848 2688 1 chr5B.!!$R2 840
5 TraesCS5B01G006200 chr5B 7183317 7185606 2289 True 1012.500000 1092 92.003500 1 2688 2 chr5B.!!$R3 2687
6 TraesCS5B01G006200 chr5D 3890330 3892022 1692 False 1744.000000 1744 85.582000 999 2688 1 chr5D.!!$F1 1689
7 TraesCS5B01G006200 chr5D 7118387 7130582 12195 True 1191.666667 1825 88.532167 4 2612 6 chr5D.!!$R1 2608
8 TraesCS5B01G006200 chr5D 3865482 3880703 15221 False 868.500000 1109 88.970667 1 2604 6 chr5D.!!$F2 2603
9 TraesCS5B01G006200 chr5A 4794870 4796506 1636 True 1794.000000 1794 86.788000 999 2612 1 chr5A.!!$R1 1613
10 TraesCS5B01G006200 chr5A 4875124 4877433 2309 False 1287.000000 1772 88.515500 1 2604 2 chr5A.!!$F2 2603
11 TraesCS5B01G006200 chr5A 4866795 4867600 805 False 767.000000 767 84.406000 1833 2612 1 chr5A.!!$F1 779
12 TraesCS5B01G006200 chr4A 18742229 18743010 781 True 1105.000000 1105 92.219000 999 1778 1 chr4A.!!$R1 779
13 TraesCS5B01G006200 chr4A 18736584 18738016 1432 True 955.000000 1099 91.295500 4 1778 2 chr4A.!!$R2 1774

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
483 5169 6.07132 GTCAATTCTAGAGGGGGCATTAAAT 58.929 40.0 0.0 0.0 0.0 1.4 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2331 12352 1.112315 GGTGCATGTGGGTTGGAACA 61.112 55.0 0.0 0.0 0.0 3.18 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
453 5139 9.729286 AGGTCAATTCTACCCCTTGGAAACAAA 62.729 40.741 3.34 0.00 43.42 2.83
483 5169 6.071320 GTCAATTCTAGAGGGGGCATTAAAT 58.929 40.000 0.00 0.00 0.00 1.40
1038 10993 3.728864 GCAAGCATTTCACGGTCATACAG 60.729 47.826 0.00 0.00 0.00 2.74
1050 11005 3.448686 GGTCATACAGTCATCAACTCCG 58.551 50.000 0.00 0.00 35.45 4.63
1308 11265 5.478407 GTGAAATCATAAACAACAAGGGGG 58.522 41.667 0.00 0.00 0.00 5.40
1532 11511 6.980577 TGGGTGGATAAATCTCAACCTTATT 58.019 36.000 13.35 0.00 36.44 1.40
1720 11700 6.183360 CGGTATTTTGATTGTCTCCTCCTAGA 60.183 42.308 0.00 0.00 0.00 2.43
1725 11705 7.921041 TTTGATTGTCTCCTCCTAGATGTAT 57.079 36.000 0.00 0.00 0.00 2.29
1753 11733 2.505407 TGGAACTATGGTGGACATCAGG 59.495 50.000 0.00 0.00 41.03 3.86
1755 11735 3.432326 GGAACTATGGTGGACATCAGGAC 60.432 52.174 0.00 0.00 41.03 3.85
1756 11736 2.832838 ACTATGGTGGACATCAGGACA 58.167 47.619 0.00 0.00 41.03 4.02
1757 11737 3.181329 ACTATGGTGGACATCAGGACAA 58.819 45.455 0.00 0.00 41.03 3.18
1758 11738 3.587061 ACTATGGTGGACATCAGGACAAA 59.413 43.478 0.00 0.00 41.03 2.83
1759 11739 3.524095 ATGGTGGACATCAGGACAAAA 57.476 42.857 0.00 0.00 33.53 2.44
1760 11740 3.524095 TGGTGGACATCAGGACAAAAT 57.476 42.857 0.00 0.00 0.00 1.82
1761 11741 3.156293 TGGTGGACATCAGGACAAAATG 58.844 45.455 0.00 0.00 0.00 2.32
1762 11742 3.157087 GGTGGACATCAGGACAAAATGT 58.843 45.455 0.00 0.00 36.37 2.71
1763 11743 4.202514 TGGTGGACATCAGGACAAAATGTA 60.203 41.667 0.00 0.00 33.91 2.29
1764 11744 4.156008 GGTGGACATCAGGACAAAATGTAC 59.844 45.833 0.00 0.00 35.25 2.90
1765 11745 5.003804 GTGGACATCAGGACAAAATGTACT 58.996 41.667 0.00 0.00 43.76 2.73
1766 11746 5.122396 GTGGACATCAGGACAAAATGTACTC 59.878 44.000 0.00 0.00 36.70 2.59
1767 11747 5.013079 TGGACATCAGGACAAAATGTACTCT 59.987 40.000 0.00 0.00 36.70 3.24
1768 11748 6.212589 TGGACATCAGGACAAAATGTACTCTA 59.787 38.462 0.00 0.00 36.70 2.43
1769 11749 7.103641 GGACATCAGGACAAAATGTACTCTAA 58.896 38.462 0.00 0.00 36.70 2.10
1770 11750 7.770897 GGACATCAGGACAAAATGTACTCTAAT 59.229 37.037 0.00 0.00 36.70 1.73
1771 11751 8.723942 ACATCAGGACAAAATGTACTCTAATC 57.276 34.615 0.00 0.00 36.70 1.75
1772 11752 8.543774 ACATCAGGACAAAATGTACTCTAATCT 58.456 33.333 0.00 0.00 36.70 2.40
1773 11753 9.039870 CATCAGGACAAAATGTACTCTAATCTC 57.960 37.037 0.00 0.00 36.70 2.75
1774 11754 8.367660 TCAGGACAAAATGTACTCTAATCTCT 57.632 34.615 0.00 0.00 36.70 3.10
1775 11755 8.470805 TCAGGACAAAATGTACTCTAATCTCTC 58.529 37.037 0.00 0.00 36.70 3.20
1776 11756 8.474025 CAGGACAAAATGTACTCTAATCTCTCT 58.526 37.037 0.00 0.00 36.70 3.10
1777 11757 8.691797 AGGACAAAATGTACTCTAATCTCTCTC 58.308 37.037 0.00 0.00 36.70 3.20
1778 11758 8.470805 GGACAAAATGTACTCTAATCTCTCTCA 58.529 37.037 0.00 0.00 0.00 3.27
1779 11759 9.515020 GACAAAATGTACTCTAATCTCTCTCAG 57.485 37.037 0.00 0.00 0.00 3.35
1813 11800 7.563556 TGTACTCTAATCTCTCTCTCTCTCTCA 59.436 40.741 0.00 0.00 0.00 3.27
1819 11806 3.326297 TCTCTCTCTCTCTCTCACACACA 59.674 47.826 0.00 0.00 0.00 3.72
1821 11808 3.145286 CTCTCTCTCTCTCACACACACA 58.855 50.000 0.00 0.00 0.00 3.72
1823 11810 1.604278 TCTCTCTCTCACACACACACG 59.396 52.381 0.00 0.00 0.00 4.49
1825 11812 1.271446 CTCTCTCACACACACACGCG 61.271 60.000 3.53 3.53 0.00 6.01
1827 11814 4.339809 CTCACACACACACGCGCG 62.340 66.667 30.96 30.96 0.00 6.86
1880 11886 2.234896 TGCATTGGATGGGTGAACAT 57.765 45.000 0.00 0.00 0.00 2.71
1893 11899 7.926018 GGATGGGTGAACATTAATTTCATAACC 59.074 37.037 12.88 14.21 35.47 2.85
1909 11915 0.532862 AACCGACTGTGAAGCACCAG 60.533 55.000 0.00 0.00 32.73 4.00
2042 12050 5.576447 AGAGTGTGGTGTTTGGTTTTAAG 57.424 39.130 0.00 0.00 0.00 1.85
2106 12123 7.499200 TGGATAAGCTAGGGTTTGTTTAGTA 57.501 36.000 0.00 0.00 0.00 1.82
2147 12164 1.065345 TGTCAGCGTCCTCTAGCTACT 60.065 52.381 0.00 0.00 42.52 2.57
2385 12431 2.894126 AGGTCACAGATGAGTTCGTCTT 59.106 45.455 1.13 0.00 40.04 3.01
2393 12442 1.514443 GAGTTCGTCTTCTCCGCCG 60.514 63.158 0.00 0.00 0.00 6.46
2446 12496 2.624838 GTCCAATGGGCATGTTATGGAG 59.375 50.000 0.00 0.00 37.62 3.86
2578 12629 3.365472 AGTGGAAAAGGATACCCAATGC 58.635 45.455 0.00 0.00 33.88 3.56
2632 12683 4.869297 CCAAAATGAAGAAAACACACTGCA 59.131 37.500 0.00 0.00 0.00 4.41
2634 12685 4.989279 AATGAAGAAAACACACTGCACT 57.011 36.364 0.00 0.00 0.00 4.40
2635 12686 6.449635 AAATGAAGAAAACACACTGCACTA 57.550 33.333 0.00 0.00 0.00 2.74
2682 12733 0.453390 GGCTCATGGCTTGCTACAAC 59.547 55.000 6.20 0.00 41.46 3.32
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
453 5139 3.267031 CCCCCTCTAGAATTGACCACTTT 59.733 47.826 0.00 0.00 0.00 2.66
457 5143 1.213296 GCCCCCTCTAGAATTGACCA 58.787 55.000 0.00 0.00 0.00 4.02
1038 10993 3.585862 TCTTGTAAGCGGAGTTGATGAC 58.414 45.455 0.00 0.00 0.00 3.06
1050 11005 3.629142 ATGGGTGGTACTCTTGTAAGC 57.371 47.619 0.00 0.00 0.00 3.09
1123 11078 6.261158 AGAAAAGAAAGTAGCACAAGTCCTTC 59.739 38.462 0.00 0.00 0.00 3.46
1308 11265 5.098211 GCTTACTTTGCTCATCATGTTTCC 58.902 41.667 0.00 0.00 0.00 3.13
1696 11676 7.125792 TCTAGGAGGAGACAATCAAAATACC 57.874 40.000 0.00 0.00 0.00 2.73
1697 11677 8.207545 ACATCTAGGAGGAGACAATCAAAATAC 58.792 37.037 0.00 0.00 0.00 1.89
1720 11700 5.991606 CACCATAGTTCCACGATCAATACAT 59.008 40.000 0.00 0.00 0.00 2.29
1725 11705 2.835156 TCCACCATAGTTCCACGATCAA 59.165 45.455 0.00 0.00 0.00 2.57
1753 11733 9.515020 CTGAGAGAGATTAGAGTACATTTTGTC 57.485 37.037 0.00 0.00 0.00 3.18
1755 11735 8.690884 TCCTGAGAGAGATTAGAGTACATTTTG 58.309 37.037 0.00 0.00 0.00 2.44
1756 11736 8.691797 GTCCTGAGAGAGATTAGAGTACATTTT 58.308 37.037 0.00 0.00 0.00 1.82
1757 11737 7.836685 TGTCCTGAGAGAGATTAGAGTACATTT 59.163 37.037 0.00 0.00 0.00 2.32
1758 11738 7.350382 TGTCCTGAGAGAGATTAGAGTACATT 58.650 38.462 0.00 0.00 0.00 2.71
1759 11739 6.905736 TGTCCTGAGAGAGATTAGAGTACAT 58.094 40.000 0.00 0.00 0.00 2.29
1760 11740 6.314899 TGTCCTGAGAGAGATTAGAGTACA 57.685 41.667 0.00 0.00 0.00 2.90
1761 11741 7.633193 TTTGTCCTGAGAGAGATTAGAGTAC 57.367 40.000 0.00 0.00 0.00 2.73
1762 11742 8.690884 CATTTTGTCCTGAGAGAGATTAGAGTA 58.309 37.037 0.00 0.00 0.00 2.59
1763 11743 7.180051 ACATTTTGTCCTGAGAGAGATTAGAGT 59.820 37.037 0.00 0.00 0.00 3.24
1764 11744 7.555087 ACATTTTGTCCTGAGAGAGATTAGAG 58.445 38.462 0.00 0.00 0.00 2.43
1765 11745 7.487822 ACATTTTGTCCTGAGAGAGATTAGA 57.512 36.000 0.00 0.00 0.00 2.10
1766 11746 8.474025 AGTACATTTTGTCCTGAGAGAGATTAG 58.526 37.037 0.00 0.00 0.00 1.73
1767 11747 8.367660 AGTACATTTTGTCCTGAGAGAGATTA 57.632 34.615 0.00 0.00 0.00 1.75
1768 11748 7.180051 AGAGTACATTTTGTCCTGAGAGAGATT 59.820 37.037 0.00 0.00 0.00 2.40
1769 11749 6.667414 AGAGTACATTTTGTCCTGAGAGAGAT 59.333 38.462 0.00 0.00 0.00 2.75
1770 11750 6.013379 AGAGTACATTTTGTCCTGAGAGAGA 58.987 40.000 0.00 0.00 0.00 3.10
1771 11751 6.279513 AGAGTACATTTTGTCCTGAGAGAG 57.720 41.667 0.00 0.00 0.00 3.20
1772 11752 7.776618 TTAGAGTACATTTTGTCCTGAGAGA 57.223 36.000 0.00 0.00 0.00 3.10
1773 11753 8.474025 AGATTAGAGTACATTTTGTCCTGAGAG 58.526 37.037 0.00 0.00 0.00 3.20
1774 11754 8.367660 AGATTAGAGTACATTTTGTCCTGAGA 57.632 34.615 0.00 0.00 0.00 3.27
1775 11755 8.474025 AGAGATTAGAGTACATTTTGTCCTGAG 58.526 37.037 0.00 0.00 0.00 3.35
1776 11756 8.367660 AGAGATTAGAGTACATTTTGTCCTGA 57.632 34.615 0.00 0.00 0.00 3.86
1777 11757 8.474025 AGAGAGATTAGAGTACATTTTGTCCTG 58.526 37.037 0.00 0.00 0.00 3.86
1778 11758 8.602472 AGAGAGATTAGAGTACATTTTGTCCT 57.398 34.615 0.00 0.00 0.00 3.85
1779 11759 8.691797 AGAGAGAGATTAGAGTACATTTTGTCC 58.308 37.037 0.00 0.00 0.00 4.02
1825 11812 1.857426 GATGTTAACACACGCGCGC 60.857 57.895 32.58 23.91 35.03 6.86
1827 11814 2.166007 GAATGATGTTAACACACGCGC 58.834 47.619 11.22 0.00 35.03 6.86
1880 11886 6.428465 TGCTTCACAGTCGGTTATGAAATTAA 59.572 34.615 0.00 0.00 31.00 1.40
1893 11899 2.654749 TATCTGGTGCTTCACAGTCG 57.345 50.000 0.00 0.00 35.86 4.18
1997 12003 8.553459 TCTTCAACTTGAGAAATCAATAGTCC 57.447 34.615 0.00 0.00 0.00 3.85
2014 12020 3.016736 CCAAACACCACACTCTTCAACT 58.983 45.455 0.00 0.00 0.00 3.16
2042 12050 5.585047 AGGTTTGTGTGTGAAAGAAGTAGTC 59.415 40.000 0.00 0.00 0.00 2.59
2106 12123 1.893801 CCCCTCACTTCTTCTACACGT 59.106 52.381 0.00 0.00 0.00 4.49
2195 12212 3.033659 AGATCAACGGTCCTAGATGGT 57.966 47.619 0.00 0.00 37.07 3.55
2331 12352 1.112315 GGTGCATGTGGGTTGGAACA 61.112 55.000 0.00 0.00 0.00 3.18
2446 12496 8.713271 CCCTTAAAAATTGTCTCGCTATCTATC 58.287 37.037 0.00 0.00 0.00 2.08
2578 12629 5.177142 CACAAGTGTTTGACATCTCTCTCTG 59.823 44.000 0.00 0.00 37.73 3.35
2632 12683 6.293698 TGCTACATGATCAATTGCTGATAGT 58.706 36.000 0.00 0.00 45.23 2.12
2634 12685 6.016860 GGTTGCTACATGATCAATTGCTGATA 60.017 38.462 0.00 0.00 45.23 2.15


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

AutoCloner maintained by Alex Coulton.