Multiple sequence alignment - TraesCS3D01G457300

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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 TraesCS3D01G457300 chr3D 100.000 2951 0 0 1 2951 562632780 562629830 0 5450
1 TraesCS3D01G457300 chr3D 95.482 2966 111 13 1 2951 562588961 562591918 0 4713
2 TraesCS3D01G457300 chr4D 93.146 2918 138 29 1 2866 95772745 95769838 0 4224
3 TraesCS3D01G457300 chr4D 91.348 3005 171 46 1 2951 95673885 95676854 0 4026
4 TraesCS3D01G457300 chr2A 91.672 2966 195 20 3 2951 553441931 553444861 0 4061
5 TraesCS3D01G457300 chr2A 92.857 1428 90 4 1533 2951 100665646 100664222 0 2061
6 TraesCS3D01G457300 chr2A 92.577 1428 94 4 1533 2951 623557015 623555591 0 2039
7 TraesCS3D01G457300 chr2D 91.266 2977 183 39 3 2951 344358041 344355114 0 3986
8 TraesCS3D01G457300 chr7A 93.340 2057 120 7 910 2950 563787036 563784981 0 3024
9 TraesCS3D01G457300 chr7A 92.857 1428 90 4 1533 2951 67664729 67663305 0 2061
10 TraesCS3D01G457300 chr7A 92.787 1428 91 4 1533 2951 353833700 353832276 0 2056
11 TraesCS3D01G457300 chr3B 93.245 2028 121 10 935 2951 27206655 27208677 0 2972
12 TraesCS3D01G457300 chr3B 89.699 864 70 9 3 850 743260018 743259158 0 1085
13 TraesCS3D01G457300 chr6B 92.991 2026 130 4 935 2951 125371590 125373612 0 2944
14 TraesCS3D01G457300 chr1B 92.892 2026 132 4 935 2951 483138002 483135980 0 2933
15 TraesCS3D01G457300 chr5B 91.994 1986 126 5 935 2912 503113581 503111621 0 2756
16 TraesCS3D01G457300 chr5B 93.383 801 48 3 1 800 536192033 536191237 0 1181
17 TraesCS3D01G457300 chr3A 93.778 1816 85 10 3 1807 697692793 697694591 0 2702
18 TraesCS3D01G457300 chr3A 93.680 1076 43 9 2 1063 697727594 697726530 0 1587
19 TraesCS3D01G457300 chr4A 92.927 1428 89 4 1533 2951 16490792 16492216 0 2067
20 TraesCS3D01G457300 chr4A 86.893 885 73 19 4 850 16489332 16490211 0 952
21 TraesCS3D01G457300 chr4B 92.495 1439 96 4 1522 2951 653531120 653532555 0 2049
22 TraesCS3D01G457300 chrUn 89.699 864 70 9 3 850 231941892 231941032 0 1085


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 TraesCS3D01G457300 chr3D 562629830 562632780 2950 True 5450.0 5450 100.000 1 2951 1 chr3D.!!$R1 2950
1 TraesCS3D01G457300 chr3D 562588961 562591918 2957 False 4713.0 4713 95.482 1 2951 1 chr3D.!!$F1 2950
2 TraesCS3D01G457300 chr4D 95769838 95772745 2907 True 4224.0 4224 93.146 1 2866 1 chr4D.!!$R1 2865
3 TraesCS3D01G457300 chr4D 95673885 95676854 2969 False 4026.0 4026 91.348 1 2951 1 chr4D.!!$F1 2950
4 TraesCS3D01G457300 chr2A 553441931 553444861 2930 False 4061.0 4061 91.672 3 2951 1 chr2A.!!$F1 2948
5 TraesCS3D01G457300 chr2A 100664222 100665646 1424 True 2061.0 2061 92.857 1533 2951 1 chr2A.!!$R1 1418
6 TraesCS3D01G457300 chr2A 623555591 623557015 1424 True 2039.0 2039 92.577 1533 2951 1 chr2A.!!$R2 1418
7 TraesCS3D01G457300 chr2D 344355114 344358041 2927 True 3986.0 3986 91.266 3 2951 1 chr2D.!!$R1 2948
8 TraesCS3D01G457300 chr7A 563784981 563787036 2055 True 3024.0 3024 93.340 910 2950 1 chr7A.!!$R3 2040
9 TraesCS3D01G457300 chr7A 67663305 67664729 1424 True 2061.0 2061 92.857 1533 2951 1 chr7A.!!$R1 1418
10 TraesCS3D01G457300 chr7A 353832276 353833700 1424 True 2056.0 2056 92.787 1533 2951 1 chr7A.!!$R2 1418
11 TraesCS3D01G457300 chr3B 27206655 27208677 2022 False 2972.0 2972 93.245 935 2951 1 chr3B.!!$F1 2016
12 TraesCS3D01G457300 chr3B 743259158 743260018 860 True 1085.0 1085 89.699 3 850 1 chr3B.!!$R1 847
13 TraesCS3D01G457300 chr6B 125371590 125373612 2022 False 2944.0 2944 92.991 935 2951 1 chr6B.!!$F1 2016
14 TraesCS3D01G457300 chr1B 483135980 483138002 2022 True 2933.0 2933 92.892 935 2951 1 chr1B.!!$R1 2016
15 TraesCS3D01G457300 chr5B 503111621 503113581 1960 True 2756.0 2756 91.994 935 2912 1 chr5B.!!$R1 1977
16 TraesCS3D01G457300 chr5B 536191237 536192033 796 True 1181.0 1181 93.383 1 800 1 chr5B.!!$R2 799
17 TraesCS3D01G457300 chr3A 697692793 697694591 1798 False 2702.0 2702 93.778 3 1807 1 chr3A.!!$F1 1804
18 TraesCS3D01G457300 chr3A 697726530 697727594 1064 True 1587.0 1587 93.680 2 1063 1 chr3A.!!$R1 1061
19 TraesCS3D01G457300 chr4A 16489332 16492216 2884 False 1509.5 2067 89.910 4 2951 2 chr4A.!!$F1 2947
20 TraesCS3D01G457300 chr4B 653531120 653532555 1435 False 2049.0 2049 92.495 1522 2951 1 chr4B.!!$F1 1429
21 TraesCS3D01G457300 chrUn 231941032 231941892 860 True 1085.0 1085 89.699 3 850 1 chrUn.!!$R1 847

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
446 492 0.947180 TTGTAGTGCTTCCCGCGAAC 60.947 55.000 8.23 0.0 43.27 3.95 F
1672 1933 1.267806 ACTTGCTGACTGATTTTGCCG 59.732 47.619 0.00 0.0 0.00 5.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1681 1942 0.041839 GCAACGTCAGTCAGCAAGTG 60.042 55.000 0.0 0.0 33.32 3.16 R
2515 2797 1.001641 CTGCAGCCCTTAAGCCACT 60.002 57.895 0.0 0.0 0.00 4.00 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
143 147 1.529244 CCCCTCGCCCAATCATTCC 60.529 63.158 0.00 0.00 0.00 3.01
226 247 1.952635 GGCGTTGTCGTCGGACTTT 60.953 57.895 6.57 0.00 43.79 2.66
266 287 1.880186 CCTACCGCGCACCAAATTT 59.120 52.632 8.75 0.00 0.00 1.82
446 492 0.947180 TTGTAGTGCTTCCCGCGAAC 60.947 55.000 8.23 0.00 43.27 3.95
481 530 4.713824 TTGGGTAGTCGATTGTAGTCTG 57.286 45.455 0.00 0.00 0.00 3.51
897 971 7.117236 TCACTTTAGTTAAGGATGCAGTTAACG 59.883 37.037 17.08 9.80 41.85 3.18
1128 1209 3.012518 GCTTGACTATGTTGATGCTGGT 58.987 45.455 0.00 0.00 0.00 4.00
1188 1269 4.416513 TGGTTGGGATATCCTGTCAATGAT 59.583 41.667 21.18 0.00 36.20 2.45
1350 1431 6.748333 TTCATCAGTAATTTCAGGCAAGAG 57.252 37.500 0.00 0.00 0.00 2.85
1520 1601 2.958355 ACAACTTGCTGGCTAATGTTGT 59.042 40.909 14.47 14.47 41.75 3.32
1610 1781 3.082698 GCACTTGCTGTTTGATGTTGA 57.917 42.857 0.00 0.00 38.21 3.18
1623 1854 6.712095 TGTTTGATGTTGAAGTAGAAGAGCAT 59.288 34.615 0.00 0.00 0.00 3.79
1666 1927 5.163281 AGAAGATCACTTGCTGACTGATT 57.837 39.130 0.00 0.00 36.39 2.57
1667 1928 5.558818 AGAAGATCACTTGCTGACTGATTT 58.441 37.500 0.00 0.00 36.39 2.17
1668 1929 6.002704 AGAAGATCACTTGCTGACTGATTTT 58.997 36.000 0.00 0.00 36.39 1.82
1669 1930 5.624344 AGATCACTTGCTGACTGATTTTG 57.376 39.130 0.00 0.00 0.00 2.44
1670 1931 3.631145 TCACTTGCTGACTGATTTTGC 57.369 42.857 0.00 0.00 0.00 3.68
1671 1932 2.294233 TCACTTGCTGACTGATTTTGCC 59.706 45.455 0.00 0.00 0.00 4.52
1672 1933 1.267806 ACTTGCTGACTGATTTTGCCG 59.732 47.619 0.00 0.00 0.00 5.69
1673 1934 1.536766 CTTGCTGACTGATTTTGCCGA 59.463 47.619 0.00 0.00 0.00 5.54
1674 1935 1.603456 TGCTGACTGATTTTGCCGAA 58.397 45.000 0.00 0.00 0.00 4.30
1675 1936 1.536766 TGCTGACTGATTTTGCCGAAG 59.463 47.619 0.00 0.00 0.00 3.79
1676 1937 1.806542 GCTGACTGATTTTGCCGAAGA 59.193 47.619 0.00 0.00 0.00 2.87
1677 1938 2.226437 GCTGACTGATTTTGCCGAAGAA 59.774 45.455 0.00 0.00 0.00 2.52
1678 1939 3.669023 GCTGACTGATTTTGCCGAAGAAG 60.669 47.826 0.00 0.00 0.00 2.85
1679 1940 2.813754 TGACTGATTTTGCCGAAGAAGG 59.186 45.455 0.00 0.00 0.00 3.46
1680 1941 2.814336 GACTGATTTTGCCGAAGAAGGT 59.186 45.455 0.00 0.00 0.00 3.50
1681 1942 2.814336 ACTGATTTTGCCGAAGAAGGTC 59.186 45.455 0.00 0.00 0.00 3.85
1682 1943 2.813754 CTGATTTTGCCGAAGAAGGTCA 59.186 45.455 0.00 0.00 0.00 4.02
1683 1944 2.552315 TGATTTTGCCGAAGAAGGTCAC 59.448 45.455 0.00 0.00 0.00 3.67
1684 1945 2.341846 TTTTGCCGAAGAAGGTCACT 57.658 45.000 0.00 0.00 0.00 3.41
1685 1946 2.341846 TTTGCCGAAGAAGGTCACTT 57.658 45.000 0.00 0.00 40.34 3.16
1686 1947 1.593196 TTGCCGAAGAAGGTCACTTG 58.407 50.000 0.00 0.00 36.97 3.16
1687 1948 0.884704 TGCCGAAGAAGGTCACTTGC 60.885 55.000 0.00 0.00 36.97 4.01
1688 1949 0.603975 GCCGAAGAAGGTCACTTGCT 60.604 55.000 0.00 0.00 36.97 3.91
1689 1950 1.151668 CCGAAGAAGGTCACTTGCTG 58.848 55.000 0.00 0.00 36.97 4.41
1690 1951 1.270305 CCGAAGAAGGTCACTTGCTGA 60.270 52.381 0.00 0.00 36.97 4.26
1738 2000 7.148188 TGCTTTCAGATTCATATTTCAGTGACC 60.148 37.037 0.00 0.00 0.00 4.02
1753 2015 6.215495 TCAGTGACCGTGATTATGACATAA 57.785 37.500 10.26 10.26 0.00 1.90
1819 2084 3.884693 TGTTGATGAAGAAGCTGAGCAAA 59.115 39.130 7.39 0.00 0.00 3.68
1832 2097 1.271597 TGAGCAAAAGGAGGAAGAGGC 60.272 52.381 0.00 0.00 0.00 4.70
1857 2122 6.043411 GGAACCTGACTATGTACTTGATGAC 58.957 44.000 0.00 0.00 0.00 3.06
1950 2231 5.771165 GGTGGACATGAAAAACCCTAAGTAA 59.229 40.000 0.00 0.00 0.00 2.24
2124 2406 3.138283 TGACAACAGGACAGGAGGATTTT 59.862 43.478 0.00 0.00 0.00 1.82
2135 2417 4.021916 CAGGAGGATTTTTCATCAAGGCT 58.978 43.478 0.00 0.00 0.00 4.58
2257 2539 6.639686 CAGAAGATGTCACTTGGAACATTTTG 59.360 38.462 0.00 0.00 39.30 2.44
2299 2581 7.505923 GGAGTTTAATTGCACCCCTAATAGATT 59.494 37.037 0.00 0.00 0.00 2.40
2313 2595 6.665680 CCCTAATAGATTGAAGCTAGCTAGGA 59.334 42.308 19.70 6.99 33.40 2.94
2349 2631 5.685861 GCACTGAAGAAGATCCATGGTGATA 60.686 44.000 12.58 0.00 0.00 2.15
2391 2673 7.013823 AGACTATGGGATTATGGACATGAAG 57.986 40.000 0.00 0.00 0.00 3.02
2515 2797 4.769488 GTCATATGATGCCTGTAGGAGAGA 59.231 45.833 9.02 0.00 37.39 3.10
2585 2867 9.573133 CATATGAAAAATAGGTTCAAAGGTGTC 57.427 33.333 0.00 0.00 38.44 3.67
2655 2937 2.057922 CTATGGGCTGGGTGGAAGTAT 58.942 52.381 0.00 0.00 0.00 2.12
2713 2995 8.400184 ACTTTGAAAGATGATCTGAACATCAA 57.600 30.769 24.10 12.27 44.29 2.57
2717 2999 8.344446 TGAAAGATGATCTGAACATCAACAAT 57.656 30.769 24.10 9.51 44.29 2.71
2785 3067 0.746659 GCTGTCCACAAAGTTTGGCT 59.253 50.000 19.45 0.00 33.71 4.75
2800 3082 0.614812 TGGCTAGATGCAGAGCACAA 59.385 50.000 17.04 2.91 43.04 3.33
2806 3088 4.393062 GCTAGATGCAGAGCACAAGTTTTA 59.607 41.667 11.95 0.00 43.04 1.52
2869 3152 2.563179 GAGAGGTACTGAAGCAAGACCA 59.437 50.000 0.00 0.00 41.55 4.02
2914 3198 4.954875 ACAAGTTGAAGTGGAGAGAGAAG 58.045 43.478 10.54 0.00 0.00 2.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
263 284 0.820074 TTGACACCGAACGGCCAAAT 60.820 50.000 13.32 0.00 39.32 2.32
266 287 2.589442 GTTGACACCGAACGGCCA 60.589 61.111 13.32 6.35 39.32 5.36
446 492 4.320870 ACTACCCAATAACCAGTTTGACG 58.679 43.478 0.00 0.00 0.00 4.35
481 530 0.756294 CCAACTTCACCCAAAACCCC 59.244 55.000 0.00 0.00 0.00 4.95
529 579 4.749598 GTCTGGCCGAAAAACATTCAAAAT 59.250 37.500 0.00 0.00 0.00 1.82
649 701 5.600696 ACATTGGCCAAACAAAGTTTAGAG 58.399 37.500 24.71 2.02 28.92 2.43
884 958 4.391830 TGAATCTTCACGTTAACTGCATCC 59.608 41.667 3.71 0.00 31.01 3.51
897 971 9.070149 GCATCTTCAAGTTAAATGAATCTTCAC 57.930 33.333 5.65 0.00 40.49 3.18
933 1008 8.133627 GCACAAGCATCAATAAAGATAACTGAT 58.866 33.333 0.00 0.00 41.58 2.90
1128 1209 8.206189 TCTTCAATGACTGCATATGAGAATGTA 58.794 33.333 6.97 0.00 33.44 2.29
1188 1269 4.441773 GGCATGCACCAATAAATGATGTGA 60.442 41.667 21.36 0.00 0.00 3.58
1350 1431 4.122776 CTGCTCCCACTGTACATATCAAC 58.877 47.826 0.00 0.00 0.00 3.18
1623 1854 4.338964 TCTTCAGCAAAATCAGTCAGCAAA 59.661 37.500 0.00 0.00 0.00 3.68
1666 1927 1.946768 CAAGTGACCTTCTTCGGCAAA 59.053 47.619 0.00 0.00 0.00 3.68
1667 1928 1.593196 CAAGTGACCTTCTTCGGCAA 58.407 50.000 0.00 0.00 0.00 4.52
1668 1929 0.884704 GCAAGTGACCTTCTTCGGCA 60.885 55.000 0.00 0.00 0.00 5.69
1669 1930 0.603975 AGCAAGTGACCTTCTTCGGC 60.604 55.000 0.00 0.00 0.00 5.54
1670 1931 1.151668 CAGCAAGTGACCTTCTTCGG 58.848 55.000 0.00 0.00 0.00 4.30
1671 1932 2.154854 TCAGCAAGTGACCTTCTTCG 57.845 50.000 0.00 0.00 0.00 3.79
1680 1941 1.570813 CAACGTCAGTCAGCAAGTGA 58.429 50.000 0.00 0.00 34.86 3.41
1681 1942 0.041839 GCAACGTCAGTCAGCAAGTG 60.042 55.000 0.00 0.00 33.32 3.16
1682 1943 0.461870 TGCAACGTCAGTCAGCAAGT 60.462 50.000 0.00 0.00 38.02 3.16
1683 1944 0.234106 CTGCAACGTCAGTCAGCAAG 59.766 55.000 0.00 0.00 39.60 4.01
1684 1945 0.179086 TCTGCAACGTCAGTCAGCAA 60.179 50.000 4.38 0.00 39.60 3.91
1685 1946 0.179086 TTCTGCAACGTCAGTCAGCA 60.179 50.000 4.38 0.00 38.43 4.41
1686 1947 0.510359 CTTCTGCAACGTCAGTCAGC 59.490 55.000 4.38 0.00 35.63 4.26
1687 1948 2.140065 TCTTCTGCAACGTCAGTCAG 57.860 50.000 4.38 5.47 35.63 3.51
1688 1949 2.224042 ACATCTTCTGCAACGTCAGTCA 60.224 45.455 4.38 0.00 35.63 3.41
1689 1950 2.408050 ACATCTTCTGCAACGTCAGTC 58.592 47.619 4.38 0.00 35.63 3.51
1690 1951 2.533266 ACATCTTCTGCAACGTCAGT 57.467 45.000 4.38 0.00 35.63 3.41
1691 1952 3.366121 CACTACATCTTCTGCAACGTCAG 59.634 47.826 0.00 0.00 35.46 3.51
1692 1953 3.317150 CACTACATCTTCTGCAACGTCA 58.683 45.455 0.00 0.00 0.00 4.35
1693 1954 2.092838 GCACTACATCTTCTGCAACGTC 59.907 50.000 0.00 0.00 0.00 4.34
1694 1955 2.069273 GCACTACATCTTCTGCAACGT 58.931 47.619 0.00 0.00 0.00 3.99
1695 1956 2.341257 AGCACTACATCTTCTGCAACG 58.659 47.619 0.00 0.00 31.71 4.10
1738 2000 8.538409 TCTCCATCATTTATGTCATAATCACG 57.462 34.615 6.11 0.00 33.34 4.35
1819 2084 1.554583 GGTTCCGCCTCTTCCTCCTT 61.555 60.000 0.00 0.00 0.00 3.36
1832 2097 4.713824 TCAAGTACATAGTCAGGTTCCG 57.286 45.455 0.00 0.00 0.00 4.30
1857 2122 6.957984 TCTCTTGACAGATTCAAATCTTCG 57.042 37.500 2.47 0.00 43.90 3.79
1950 2231 2.619849 CCACATCAGCAAAGACCATCCT 60.620 50.000 0.00 0.00 0.00 3.24
2099 2381 3.516586 TCCTCCTGTCCTGTTGTCATTA 58.483 45.455 0.00 0.00 0.00 1.90
2124 2406 6.327365 TGATCTCCATAGTAAGCCTTGATGAA 59.673 38.462 0.00 0.00 0.00 2.57
2299 2581 3.202373 TGTCCTAGTCCTAGCTAGCTTCA 59.798 47.826 24.88 4.52 37.66 3.02
2313 2595 2.965831 TCTTCAGTGCTGTTGTCCTAGT 59.034 45.455 0.00 0.00 0.00 2.57
2349 2631 7.768120 CCATAGTCTACTGAATTGCTCTTCTTT 59.232 37.037 0.00 0.00 0.00 2.52
2391 2673 2.835156 AGCCAGGGTTCTTCTCTCTTAC 59.165 50.000 0.00 0.00 0.00 2.34
2515 2797 1.001641 CTGCAGCCCTTAAGCCACT 60.002 57.895 0.00 0.00 0.00 4.00
2655 2937 3.820467 CACTCCCAAGAACTTGTGCATTA 59.180 43.478 12.54 0.00 38.85 1.90
2713 2995 4.357918 AGTGTGAAAGGAGCACTATTGT 57.642 40.909 0.00 0.00 41.12 2.71
2717 2999 5.246203 ACTCATAAGTGTGAAAGGAGCACTA 59.754 40.000 0.00 0.00 41.94 2.74
2785 3067 5.939883 ACATAAAACTTGTGCTCTGCATCTA 59.060 36.000 0.00 0.00 41.91 1.98
2800 3082 8.588290 TTGGTAAATATGCCTCACATAAAACT 57.412 30.769 0.00 0.00 44.36 2.66
2806 3088 8.538701 TGAAATTTTGGTAAATATGCCTCACAT 58.461 29.630 0.00 0.00 43.18 3.21
2914 3198 4.549458 CTGTGACCATCCATTTTTCACAC 58.451 43.478 0.00 0.00 41.20 3.82


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

AutoCloner maintained by Alex Coulton.