Multiple sequence alignment - TraesCS3D01G308300

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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 TraesCS3D01G308300 chr3D 100.000 2414 0 0 1 2414 422408457 422410870 0.000000e+00 4458
1 TraesCS3D01G308300 chr3D 96.350 904 33 0 1 904 563378747 563377844 0.000000e+00 1487
2 TraesCS3D01G308300 chr3D 96.239 904 32 2 1 902 424380105 424381008 0.000000e+00 1480
3 TraesCS3D01G308300 chr3D 95.833 912 37 1 1 911 170279748 170280659 0.000000e+00 1472
4 TraesCS3D01G308300 chr3D 95.833 912 36 2 1 911 454114896 454115806 0.000000e+00 1472
5 TraesCS3D01G308300 chr5D 95.996 999 29 9 1426 2414 94600572 94601569 0.000000e+00 1613
6 TraesCS3D01G308300 chr5D 95.700 1000 31 8 1426 2414 132681561 132682559 0.000000e+00 1598
7 TraesCS3D01G308300 chr2B 95.792 998 30 8 1426 2414 158693164 158694158 0.000000e+00 1600
8 TraesCS3D01G308300 chr7D 95.305 1001 35 7 1426 2414 125048669 125047669 0.000000e+00 1578
9 TraesCS3D01G308300 chr7D 96.495 913 29 3 1 911 199849643 199850554 0.000000e+00 1506
10 TraesCS3D01G308300 chr7D 95.838 913 35 3 1 911 561475401 561476312 0.000000e+00 1472
11 TraesCS3D01G308300 chr7D 97.701 522 12 0 907 1428 616134307 616134828 0.000000e+00 898
12 TraesCS3D01G308300 chr7D 87.327 434 51 4 993 1423 616055578 616056010 6.000000e-136 494
13 TraesCS3D01G308300 chr7D 86.998 423 52 2 1001 1420 616068180 616068602 7.810000e-130 473
14 TraesCS3D01G308300 chr2D 95.291 998 38 6 1426 2414 302440594 302441591 0.000000e+00 1574
15 TraesCS3D01G308300 chr2D 95.210 1002 35 8 1426 2414 429261676 429262677 0.000000e+00 1572
16 TraesCS3D01G308300 chr2D 95.733 914 37 2 1 912 520863543 520862630 0.000000e+00 1471
17 TraesCS3D01G308300 chr6D 95.195 999 37 8 1426 2414 469305760 469306757 0.000000e+00 1568
18 TraesCS3D01G308300 chr6D 95.095 999 36 8 1426 2414 301324065 301323070 0.000000e+00 1561
19 TraesCS3D01G308300 chr6D 95.643 918 36 4 1 914 187050582 187049665 0.000000e+00 1471
20 TraesCS3D01G308300 chr4D 95.272 994 38 7 1429 2414 380119277 380118285 0.000000e+00 1567
21 TraesCS3D01G308300 chr1D 96.239 904 34 0 1 904 98975387 98974484 0.000000e+00 1482
22 TraesCS3D01G308300 chr7A 90.207 531 29 3 913 1422 709129460 709129988 0.000000e+00 671
23 TraesCS3D01G308300 chr7A 88.497 539 40 7 907 1423 709121796 709122334 1.220000e-177 632
24 TraesCS3D01G308300 chr7A 87.470 423 53 0 1001 1423 708913267 708913689 2.790000e-134 488
25 TraesCS3D01G308300 chr7A 87.438 406 46 4 1019 1420 708919292 708919696 1.690000e-126 462
26 TraesCS3D01G308300 chr7B 86.852 540 47 10 909 1426 709378066 709378603 1.240000e-162 582
27 TraesCS3D01G308300 chr7B 85.581 430 60 2 995 1423 709258612 709259040 1.320000e-122 449


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 TraesCS3D01G308300 chr3D 422408457 422410870 2413 False 4458 4458 100.000 1 2414 1 chr3D.!!$F2 2413
1 TraesCS3D01G308300 chr3D 563377844 563378747 903 True 1487 1487 96.350 1 904 1 chr3D.!!$R1 903
2 TraesCS3D01G308300 chr3D 424380105 424381008 903 False 1480 1480 96.239 1 902 1 chr3D.!!$F3 901
3 TraesCS3D01G308300 chr3D 170279748 170280659 911 False 1472 1472 95.833 1 911 1 chr3D.!!$F1 910
4 TraesCS3D01G308300 chr3D 454114896 454115806 910 False 1472 1472 95.833 1 911 1 chr3D.!!$F4 910
5 TraesCS3D01G308300 chr5D 94600572 94601569 997 False 1613 1613 95.996 1426 2414 1 chr5D.!!$F1 988
6 TraesCS3D01G308300 chr5D 132681561 132682559 998 False 1598 1598 95.700 1426 2414 1 chr5D.!!$F2 988
7 TraesCS3D01G308300 chr2B 158693164 158694158 994 False 1600 1600 95.792 1426 2414 1 chr2B.!!$F1 988
8 TraesCS3D01G308300 chr7D 125047669 125048669 1000 True 1578 1578 95.305 1426 2414 1 chr7D.!!$R1 988
9 TraesCS3D01G308300 chr7D 199849643 199850554 911 False 1506 1506 96.495 1 911 1 chr7D.!!$F1 910
10 TraesCS3D01G308300 chr7D 561475401 561476312 911 False 1472 1472 95.838 1 911 1 chr7D.!!$F2 910
11 TraesCS3D01G308300 chr7D 616134307 616134828 521 False 898 898 97.701 907 1428 1 chr7D.!!$F5 521
12 TraesCS3D01G308300 chr2D 302440594 302441591 997 False 1574 1574 95.291 1426 2414 1 chr2D.!!$F1 988
13 TraesCS3D01G308300 chr2D 429261676 429262677 1001 False 1572 1572 95.210 1426 2414 1 chr2D.!!$F2 988
14 TraesCS3D01G308300 chr2D 520862630 520863543 913 True 1471 1471 95.733 1 912 1 chr2D.!!$R1 911
15 TraesCS3D01G308300 chr6D 469305760 469306757 997 False 1568 1568 95.195 1426 2414 1 chr6D.!!$F1 988
16 TraesCS3D01G308300 chr6D 301323070 301324065 995 True 1561 1561 95.095 1426 2414 1 chr6D.!!$R2 988
17 TraesCS3D01G308300 chr6D 187049665 187050582 917 True 1471 1471 95.643 1 914 1 chr6D.!!$R1 913
18 TraesCS3D01G308300 chr4D 380118285 380119277 992 True 1567 1567 95.272 1429 2414 1 chr4D.!!$R1 985
19 TraesCS3D01G308300 chr1D 98974484 98975387 903 True 1482 1482 96.239 1 904 1 chr1D.!!$R1 903
20 TraesCS3D01G308300 chr7A 709129460 709129988 528 False 671 671 90.207 913 1422 1 chr7A.!!$F4 509
21 TraesCS3D01G308300 chr7A 709121796 709122334 538 False 632 632 88.497 907 1423 1 chr7A.!!$F3 516
22 TraesCS3D01G308300 chr7B 709378066 709378603 537 False 582 582 86.852 909 1426 1 chr7B.!!$F2 517

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
968 973 0.730265 GGACGAACAACAGTGCAACA 59.27 50.0 0.0 0.0 41.43 3.33 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2209 2251 1.544825 GGCCCCCTTTCTTCTTTGGC 61.545 60.0 0.0 0.0 36.68 4.52 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
411 415 4.275838 TGTTTTCGGATTCGTTTCGTTT 57.724 36.364 0.00 0.00 37.69 3.60
864 869 9.096160 GATGGTGATATTAGATTCATGCTAGTG 57.904 37.037 0.00 0.00 0.00 2.74
865 870 7.966812 TGGTGATATTAGATTCATGCTAGTGT 58.033 34.615 0.00 0.00 0.00 3.55
866 871 7.874528 TGGTGATATTAGATTCATGCTAGTGTG 59.125 37.037 0.00 0.00 0.00 3.82
867 872 7.875041 GGTGATATTAGATTCATGCTAGTGTGT 59.125 37.037 0.00 0.00 0.00 3.72
868 873 9.914131 GTGATATTAGATTCATGCTAGTGTGTA 57.086 33.333 0.00 0.00 0.00 2.90
873 878 9.618890 ATTAGATTCATGCTAGTGTGTAATTGT 57.381 29.630 0.00 0.00 0.00 2.71
874 879 7.312657 AGATTCATGCTAGTGTGTAATTGTG 57.687 36.000 0.00 0.00 0.00 3.33
875 880 7.105588 AGATTCATGCTAGTGTGTAATTGTGA 58.894 34.615 0.00 0.00 0.00 3.58
876 881 7.607607 AGATTCATGCTAGTGTGTAATTGTGAA 59.392 33.333 0.00 0.00 0.00 3.18
877 882 7.686438 TTCATGCTAGTGTGTAATTGTGAAT 57.314 32.000 0.00 0.00 0.00 2.57
878 883 7.686438 TCATGCTAGTGTGTAATTGTGAATT 57.314 32.000 0.00 0.00 34.90 2.17
879 884 8.109705 TCATGCTAGTGTGTAATTGTGAATTT 57.890 30.769 0.00 0.00 32.38 1.82
880 885 9.225436 TCATGCTAGTGTGTAATTGTGAATTTA 57.775 29.630 0.00 0.00 32.38 1.40
881 886 9.838975 CATGCTAGTGTGTAATTGTGAATTTAA 57.161 29.630 0.00 0.00 32.38 1.52
883 888 9.278978 TGCTAGTGTGTAATTGTGAATTTAAGA 57.721 29.630 0.00 0.00 32.38 2.10
884 889 9.543018 GCTAGTGTGTAATTGTGAATTTAAGAC 57.457 33.333 0.00 0.00 32.38 3.01
887 892 9.897744 AGTGTGTAATTGTGAATTTAAGACATG 57.102 29.630 0.00 0.00 32.38 3.21
888 893 8.638565 GTGTGTAATTGTGAATTTAAGACATGC 58.361 33.333 0.00 0.00 32.38 4.06
889 894 8.575589 TGTGTAATTGTGAATTTAAGACATGCT 58.424 29.630 0.00 0.00 32.38 3.79
890 895 9.410556 GTGTAATTGTGAATTTAAGACATGCTT 57.589 29.630 7.40 7.40 35.18 3.91
891 896 9.409312 TGTAATTGTGAATTTAAGACATGCTTG 57.591 29.630 11.24 0.00 33.91 4.01
892 897 9.410556 GTAATTGTGAATTTAAGACATGCTTGT 57.589 29.630 4.68 4.68 33.91 3.16
893 898 7.878477 ATTGTGAATTTAAGACATGCTTGTG 57.122 32.000 10.37 0.00 37.42 3.33
894 899 6.389830 TGTGAATTTAAGACATGCTTGTGT 57.610 33.333 10.37 2.89 37.42 3.72
895 900 6.804677 TGTGAATTTAAGACATGCTTGTGTT 58.195 32.000 17.45 17.45 41.72 3.32
896 901 6.696583 TGTGAATTTAAGACATGCTTGTGTTG 59.303 34.615 21.06 0.00 39.47 3.33
897 902 6.917477 GTGAATTTAAGACATGCTTGTGTTGA 59.083 34.615 21.06 12.76 39.47 3.18
898 903 7.113965 GTGAATTTAAGACATGCTTGTGTTGAG 59.886 37.037 21.06 0.00 39.47 3.02
899 904 5.437289 TTTAAGACATGCTTGTGTTGAGG 57.563 39.130 21.06 0.00 39.47 3.86
900 905 2.645838 AGACATGCTTGTGTTGAGGT 57.354 45.000 10.37 0.00 35.79 3.85
901 906 2.936202 AGACATGCTTGTGTTGAGGTT 58.064 42.857 10.37 0.00 35.79 3.50
902 907 3.290710 AGACATGCTTGTGTTGAGGTTT 58.709 40.909 10.37 0.00 35.79 3.27
903 908 3.067180 AGACATGCTTGTGTTGAGGTTTG 59.933 43.478 10.37 0.00 35.79 2.93
904 909 2.129607 CATGCTTGTGTTGAGGTTTGC 58.870 47.619 0.00 0.00 0.00 3.68
905 910 1.180907 TGCTTGTGTTGAGGTTTGCA 58.819 45.000 0.00 0.00 0.00 4.08
968 973 0.730265 GGACGAACAACAGTGCAACA 59.270 50.000 0.00 0.00 41.43 3.33
1017 1044 1.803922 CATGGCTACGTTCGCGACA 60.804 57.895 9.15 1.03 44.71 4.35
1020 1047 1.515519 GGCTACGTTCGCGACATCA 60.516 57.895 9.15 0.00 44.71 3.07
1677 1707 4.189231 TGCTTCGAGGGCTAATAAACTTC 58.811 43.478 12.40 0.00 0.00 3.01
1768 1800 1.848652 TTGCTAGCCTCTTCGGTACT 58.151 50.000 13.29 0.00 34.25 2.73
1782 1814 0.811281 GGTACTGTGCATTGCCCTTC 59.189 55.000 6.12 0.00 0.00 3.46
1899 1931 2.395619 ACAGCCACCATACCTACCTAC 58.604 52.381 0.00 0.00 0.00 3.18
2193 2225 3.766545 TCATTATTAGAGCATTGCCCCC 58.233 45.455 4.70 0.00 0.00 5.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
204 206 5.360714 ACACTTCATCCACACAAAACTCAAT 59.639 36.000 0.00 0.00 0.00 2.57
411 415 5.062528 TCCAAGATTTGCACATATCGCATA 58.937 37.500 0.00 0.00 39.58 3.14
668 672 6.480763 TCTTTCTACAAAAGATATGCCCACA 58.519 36.000 0.00 0.00 33.05 4.17
853 858 7.686438 ATTCACAATTACACACTAGCATGAA 57.314 32.000 0.00 0.00 0.00 2.57
864 869 8.970691 AGCATGTCTTAAATTCACAATTACAC 57.029 30.769 0.00 0.00 0.00 2.90
865 870 9.409312 CAAGCATGTCTTAAATTCACAATTACA 57.591 29.630 0.00 0.00 32.74 2.41
866 871 9.410556 ACAAGCATGTCTTAAATTCACAATTAC 57.589 29.630 0.00 0.00 33.41 1.89
867 872 9.409312 CACAAGCATGTCTTAAATTCACAATTA 57.591 29.630 0.00 0.00 37.82 1.40
868 873 7.927629 ACACAAGCATGTCTTAAATTCACAATT 59.072 29.630 0.00 0.00 37.82 2.32
869 874 7.436118 ACACAAGCATGTCTTAAATTCACAAT 58.564 30.769 0.00 0.00 37.82 2.71
870 875 6.804677 ACACAAGCATGTCTTAAATTCACAA 58.195 32.000 0.00 0.00 37.82 3.33
871 876 6.389830 ACACAAGCATGTCTTAAATTCACA 57.610 33.333 0.00 0.00 37.82 3.58
872 877 6.917477 TCAACACAAGCATGTCTTAAATTCAC 59.083 34.615 0.00 0.00 37.82 3.18
873 878 7.036996 TCAACACAAGCATGTCTTAAATTCA 57.963 32.000 0.00 0.00 37.82 2.57
874 879 6.583806 CCTCAACACAAGCATGTCTTAAATTC 59.416 38.462 0.00 0.00 37.82 2.17
875 880 6.040842 ACCTCAACACAAGCATGTCTTAAATT 59.959 34.615 0.00 0.00 37.82 1.82
876 881 5.536161 ACCTCAACACAAGCATGTCTTAAAT 59.464 36.000 0.00 0.00 37.82 1.40
877 882 4.887071 ACCTCAACACAAGCATGTCTTAAA 59.113 37.500 0.00 0.00 37.82 1.52
878 883 4.460263 ACCTCAACACAAGCATGTCTTAA 58.540 39.130 0.00 0.00 37.82 1.85
879 884 4.085357 ACCTCAACACAAGCATGTCTTA 57.915 40.909 0.00 0.00 37.82 2.10
880 885 2.936202 ACCTCAACACAAGCATGTCTT 58.064 42.857 0.00 0.00 37.82 3.01
881 886 2.645838 ACCTCAACACAAGCATGTCT 57.354 45.000 0.00 0.00 37.82 3.41
882 887 3.374745 CAAACCTCAACACAAGCATGTC 58.625 45.455 0.00 0.00 37.82 3.06
883 888 2.481795 GCAAACCTCAACACAAGCATGT 60.482 45.455 0.00 0.00 41.61 3.21
884 889 2.129607 GCAAACCTCAACACAAGCATG 58.870 47.619 0.00 0.00 0.00 4.06
885 890 1.755959 TGCAAACCTCAACACAAGCAT 59.244 42.857 0.00 0.00 0.00 3.79
886 891 1.180907 TGCAAACCTCAACACAAGCA 58.819 45.000 0.00 0.00 0.00 3.91
887 892 2.195922 CTTGCAAACCTCAACACAAGC 58.804 47.619 0.00 0.00 0.00 4.01
888 893 2.195922 GCTTGCAAACCTCAACACAAG 58.804 47.619 0.00 0.00 38.00 3.16
889 894 1.134848 GGCTTGCAAACCTCAACACAA 60.135 47.619 11.75 0.00 0.00 3.33
890 895 0.459489 GGCTTGCAAACCTCAACACA 59.541 50.000 11.75 0.00 0.00 3.72
891 896 0.249447 GGGCTTGCAAACCTCAACAC 60.249 55.000 18.06 0.00 0.00 3.32
892 897 0.396974 AGGGCTTGCAAACCTCAACA 60.397 50.000 18.06 0.00 0.00 3.33
893 898 0.752658 AAGGGCTTGCAAACCTCAAC 59.247 50.000 18.06 2.01 32.29 3.18
894 899 2.373335 TAAGGGCTTGCAAACCTCAA 57.627 45.000 18.06 9.17 32.29 3.02
895 900 2.603075 ATAAGGGCTTGCAAACCTCA 57.397 45.000 18.06 6.97 32.29 3.86
896 901 5.451937 GGATTTATAAGGGCTTGCAAACCTC 60.452 44.000 18.06 8.74 32.29 3.85
897 902 4.405680 GGATTTATAAGGGCTTGCAAACCT 59.594 41.667 18.06 16.35 35.78 3.50
898 903 4.161377 TGGATTTATAAGGGCTTGCAAACC 59.839 41.667 10.57 10.57 0.00 3.27
899 904 5.109210 GTGGATTTATAAGGGCTTGCAAAC 58.891 41.667 0.00 0.00 0.00 2.93
900 905 4.161377 GGTGGATTTATAAGGGCTTGCAAA 59.839 41.667 0.00 0.00 0.00 3.68
901 906 3.704061 GGTGGATTTATAAGGGCTTGCAA 59.296 43.478 0.00 0.00 0.00 4.08
902 907 3.295973 GGTGGATTTATAAGGGCTTGCA 58.704 45.455 0.00 0.00 0.00 4.08
903 908 2.293399 CGGTGGATTTATAAGGGCTTGC 59.707 50.000 0.00 0.00 0.00 4.01
904 909 2.884639 CCGGTGGATTTATAAGGGCTTG 59.115 50.000 0.00 0.00 0.00 4.01
905 910 2.781174 TCCGGTGGATTTATAAGGGCTT 59.219 45.455 0.00 0.00 0.00 4.35
968 973 6.942532 TGACACAAAGCAGAGTATTTCTTT 57.057 33.333 0.00 0.00 32.41 2.52
1017 1044 2.420547 CCACATCACCACCGAAGATGAT 60.421 50.000 8.46 0.00 0.00 2.45
1020 1047 0.984230 ACCACATCACCACCGAAGAT 59.016 50.000 0.00 0.00 0.00 2.40
1131 1158 2.474561 CACCTCGTAGTGCGTCCTA 58.525 57.895 0.00 0.00 42.13 2.94
1168 1195 2.188994 GATCTCGCCCTTGCTGCT 59.811 61.111 0.00 0.00 34.43 4.24
1169 1196 1.712977 CTTGATCTCGCCCTTGCTGC 61.713 60.000 0.00 0.00 34.43 5.25
1413 1440 5.084519 TCTTTATATCGCCTGTCCTACCAT 58.915 41.667 0.00 0.00 0.00 3.55
1451 1478 2.632377 CACAACTACCCACTAGCATGG 58.368 52.381 0.00 0.00 39.71 3.66
1637 1667 1.732259 GCAAAGTACTGCTACGCATGT 59.268 47.619 0.00 0.00 38.13 3.21
1647 1677 1.079503 GCCCTCGAAGCAAAGTACTG 58.920 55.000 0.00 0.00 0.00 2.74
1691 1721 7.221067 GGACTCACATTAGTCATAAAGAACTCG 59.779 40.741 6.37 0.00 46.40 4.18
1768 1800 0.895100 GTGAGGAAGGGCAATGCACA 60.895 55.000 11.17 0.00 32.33 4.57
2057 2089 2.157738 GGGATGTGCAATGATCTAGCC 58.842 52.381 0.00 0.00 0.00 3.93
2206 2242 1.550327 CCCCTTTCTTCTTTGGCCTC 58.450 55.000 3.32 0.00 0.00 4.70
2209 2251 1.544825 GGCCCCCTTTCTTCTTTGGC 61.545 60.000 0.00 0.00 36.68 4.52
2211 2253 1.715785 TTGGCCCCCTTTCTTCTTTG 58.284 50.000 0.00 0.00 0.00 2.77
2215 2257 1.895798 CTTCTTTGGCCCCCTTTCTTC 59.104 52.381 0.00 0.00 0.00 2.87
2218 2261 1.544825 GGCTTCTTTGGCCCCCTTTC 61.545 60.000 0.00 0.00 43.49 2.62


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

AutoCloner maintained by Alex Coulton.