Multiple sequence alignment - TraesCS4D01G187900

Loading Multiple Alignment...

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 TraesCS4D01G187900 chr4D 100.000 2714 0 0 1 2714 326982403 326979690 0.000000e+00 5012.0
1 TraesCS4D01G187900 chr4D 92.888 703 40 6 1 695 109369603 109370303 0.000000e+00 1013.0
2 TraesCS4D01G187900 chr4B 95.381 1169 25 8 826 1965 406465757 406464589 0.000000e+00 1832.0
3 TraesCS4D01G187900 chr4B 95.266 676 32 0 1964 2639 406464547 406463872 0.000000e+00 1072.0
4 TraesCS4D01G187900 chr4B 96.429 84 1 2 2632 2714 406463702 406463620 1.310000e-28 137.0
5 TraesCS4D01G187900 chr4B 98.611 72 1 0 739 810 406465812 406465741 7.890000e-26 128.0
6 TraesCS4D01G187900 chr4A 96.872 1023 29 3 944 1965 144356367 144357387 0.000000e+00 1709.0
7 TraesCS4D01G187900 chr4A 90.576 764 41 17 1964 2714 144357430 144358175 0.000000e+00 983.0
8 TraesCS4D01G187900 chr4A 87.879 132 5 4 826 946 144355787 144355918 7.830000e-31 145.0
9 TraesCS4D01G187900 chr4A 96.154 78 3 0 733 810 144355726 144355803 7.890000e-26 128.0
10 TraesCS4D01G187900 chr5B 91.198 977 53 11 1004 1964 700924388 700923429 0.000000e+00 1297.0
11 TraesCS4D01G187900 chr5B 92.837 349 16 5 1963 2306 700923386 700923042 5.220000e-137 497.0
12 TraesCS4D01G187900 chr5B 86.585 410 24 10 2306 2714 700922922 700922543 8.980000e-115 424.0
13 TraesCS4D01G187900 chr5B 76.536 179 36 6 1316 1492 534639932 534640106 2.880000e-15 93.5
14 TraesCS4D01G187900 chr5B 96.296 54 2 0 686 739 523909948 523909895 3.720000e-14 89.8
15 TraesCS4D01G187900 chr5B 75.978 179 37 6 1316 1492 534600493 534600667 1.340000e-13 87.9
16 TraesCS4D01G187900 chr2A 90.750 973 55 15 1004 1964 582969299 582968350 0.000000e+00 1266.0
17 TraesCS4D01G187900 chr2A 84.714 700 83 22 1 687 478385512 478384824 0.000000e+00 678.0
18 TraesCS4D01G187900 chr2A 93.123 349 15 5 1963 2306 582968307 582967963 1.120000e-138 503.0
19 TraesCS4D01G187900 chr2A 88.264 409 24 6 2307 2714 582967842 582967457 4.090000e-128 468.0
20 TraesCS4D01G187900 chr1D 93.305 702 38 6 1 695 15419958 15419259 0.000000e+00 1027.0
21 TraesCS4D01G187900 chr1D 93.103 58 4 0 682 739 384133327 384133384 4.810000e-13 86.1
22 TraesCS4D01G187900 chr6D 93.133 699 35 8 1 689 162260017 162260712 0.000000e+00 1013.0
23 TraesCS4D01G187900 chr7D 85.694 699 82 14 1 687 529359468 529360160 0.000000e+00 721.0
24 TraesCS4D01G187900 chr7D 96.296 54 2 0 686 739 45431110 45431163 3.720000e-14 89.8
25 TraesCS4D01G187900 chr7D 96.296 54 2 0 686 739 48249552 48249605 3.720000e-14 89.8
26 TraesCS4D01G187900 chr7D 94.444 54 3 0 686 739 454842456 454842403 1.730000e-12 84.2
27 TraesCS4D01G187900 chr2D 85.470 702 78 20 2 686 9242791 9243485 0.000000e+00 710.0
28 TraesCS4D01G187900 chr7B 85.244 698 82 17 4 687 510189136 510188446 0.000000e+00 699.0
29 TraesCS4D01G187900 chr7B 89.706 68 6 1 686 752 747586288 747586355 4.810000e-13 86.1
30 TraesCS4D01G187900 chr7A 85.949 669 74 16 30 686 208802264 208802924 0.000000e+00 697.0
31 TraesCS4D01G187900 chr7A 94.545 55 3 0 685 739 208802968 208803022 4.810000e-13 86.1
32 TraesCS4D01G187900 chr7A 94.545 55 3 0 686 740 678623342 678623396 4.810000e-13 86.1
33 TraesCS4D01G187900 chr6B 85.630 682 68 24 26 687 609645252 609645923 0.000000e+00 689.0
34 TraesCS4D01G187900 chr1B 94.828 58 3 0 686 743 683441989 683442046 1.030000e-14 91.6
35 TraesCS4D01G187900 chr5D 73.180 261 55 12 1220 1478 439734018 439734265 2.240000e-11 80.5


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 TraesCS4D01G187900 chr4D 326979690 326982403 2713 True 5012.000000 5012 100.000000 1 2714 1 chr4D.!!$R1 2713
1 TraesCS4D01G187900 chr4D 109369603 109370303 700 False 1013.000000 1013 92.888000 1 695 1 chr4D.!!$F1 694
2 TraesCS4D01G187900 chr4B 406463620 406465812 2192 True 792.250000 1832 96.421750 739 2714 4 chr4B.!!$R1 1975
3 TraesCS4D01G187900 chr4A 144355726 144358175 2449 False 741.250000 1709 92.870250 733 2714 4 chr4A.!!$F1 1981
4 TraesCS4D01G187900 chr5B 700922543 700924388 1845 True 739.333333 1297 90.206667 1004 2714 3 chr5B.!!$R2 1710
5 TraesCS4D01G187900 chr2A 582967457 582969299 1842 True 745.666667 1266 90.712333 1004 2714 3 chr2A.!!$R2 1710
6 TraesCS4D01G187900 chr2A 478384824 478385512 688 True 678.000000 678 84.714000 1 687 1 chr2A.!!$R1 686
7 TraesCS4D01G187900 chr1D 15419259 15419958 699 True 1027.000000 1027 93.305000 1 695 1 chr1D.!!$R1 694
8 TraesCS4D01G187900 chr6D 162260017 162260712 695 False 1013.000000 1013 93.133000 1 689 1 chr6D.!!$F1 688
9 TraesCS4D01G187900 chr7D 529359468 529360160 692 False 721.000000 721 85.694000 1 687 1 chr7D.!!$F3 686
10 TraesCS4D01G187900 chr2D 9242791 9243485 694 False 710.000000 710 85.470000 2 686 1 chr2D.!!$F1 684
11 TraesCS4D01G187900 chr7B 510188446 510189136 690 True 699.000000 699 85.244000 4 687 1 chr7B.!!$R1 683
12 TraesCS4D01G187900 chr7A 208802264 208803022 758 False 391.550000 697 90.247000 30 739 2 chr7A.!!$F2 709
13 TraesCS4D01G187900 chr6B 609645252 609645923 671 False 689.000000 689 85.630000 26 687 1 chr6B.!!$F1 661

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
812 895 0.03779 AGCTGAGTTCTCACGCTTCC 60.038 55.0 15.49 0.0 0.0 3.46 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2046 2679 1.493446 AGAATGATCTGCCATGGAGCA 59.507 47.619 18.4 3.69 41.46 4.26 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
73 76 9.838975 AAAACAAATTTTGGAAAATGTTCAGAC 57.161 25.926 13.42 0.00 38.53 3.51
538 575 4.142609 TCCCTCGATTGAAAGGATTGAG 57.857 45.455 0.00 0.00 35.61 3.02
568 605 5.753438 GCGTAGATTGAATAACTCATGGACA 59.247 40.000 0.00 0.00 32.78 4.02
636 674 5.913137 TCAATGAATGGAAAAATAGCGGT 57.087 34.783 0.00 0.00 0.00 5.68
646 684 6.516718 TGGAAAAATAGCGGTTTGATTTTCA 58.483 32.000 19.10 9.61 38.09 2.69
662 700 1.896339 TTCATTCACACGCGGCGAAG 61.896 55.000 30.94 22.01 0.00 3.79
810 893 0.320247 CCAGCTGAGTTCTCACGCTT 60.320 55.000 17.39 6.97 0.00 4.68
811 894 1.066914 CAGCTGAGTTCTCACGCTTC 58.933 55.000 8.42 1.22 0.00 3.86
812 895 0.037790 AGCTGAGTTCTCACGCTTCC 60.038 55.000 15.49 0.00 0.00 3.46
813 896 1.016653 GCTGAGTTCTCACGCTTCCC 61.017 60.000 13.04 0.00 0.00 3.97
814 897 0.605589 CTGAGTTCTCACGCTTCCCT 59.394 55.000 0.00 0.00 0.00 4.20
815 898 0.603569 TGAGTTCTCACGCTTCCCTC 59.396 55.000 0.00 0.00 0.00 4.30
816 899 0.603569 GAGTTCTCACGCTTCCCTCA 59.396 55.000 0.00 0.00 0.00 3.86
817 900 1.000955 GAGTTCTCACGCTTCCCTCAA 59.999 52.381 0.00 0.00 0.00 3.02
818 901 1.416401 AGTTCTCACGCTTCCCTCAAA 59.584 47.619 0.00 0.00 0.00 2.69
819 902 2.158813 AGTTCTCACGCTTCCCTCAAAA 60.159 45.455 0.00 0.00 0.00 2.44
820 903 2.616842 GTTCTCACGCTTCCCTCAAAAA 59.383 45.455 0.00 0.00 0.00 1.94
841 924 2.246719 AAAAGCTGAGTTCTCACGCT 57.753 45.000 15.49 15.49 0.00 5.07
846 929 1.869754 GCTGAGTTCTCACGCTGACAA 60.870 52.381 13.04 0.00 0.00 3.18
960 1519 1.450533 CACGCATAGTATACGCAACCG 59.549 52.381 2.59 1.40 41.14 4.44
1021 1583 4.521062 CCTCCGAGGCTCGCAAGG 62.521 72.222 29.77 29.77 38.82 3.61
1341 1911 3.487042 GCGTCTACTACTTCATCGAGCAA 60.487 47.826 0.00 0.00 0.00 3.91
1353 1923 2.460330 CGAGCAATTCGTCTGGCTT 58.540 52.632 0.00 0.00 44.27 4.35
1356 1926 1.153958 GCAATTCGTCTGGCTTGCC 60.154 57.895 4.43 4.43 38.39 4.52
1641 2219 1.551019 GGAAGGGGTTGCTCGGTAGT 61.551 60.000 0.00 0.00 0.00 2.73
1989 2622 5.124457 GCTTATGGCTGACTTCAAAGATGAA 59.876 40.000 0.00 0.00 39.43 2.57
2007 2640 2.025981 TGAATGCTTGGCTCCATAGTGT 60.026 45.455 0.00 0.00 0.00 3.55
2046 2679 3.490348 ACATGCCTACAAGAGCAAAACT 58.510 40.909 0.00 0.00 43.36 2.66
2065 2699 1.977056 TGCTCCATGGCAGATCATTC 58.023 50.000 6.96 0.00 37.29 2.67
2339 3110 6.194796 ACCACATGCTACAATGTTACATTC 57.805 37.500 7.71 0.00 38.75 2.67
2340 3111 5.945784 ACCACATGCTACAATGTTACATTCT 59.054 36.000 7.71 0.00 38.75 2.40
2373 3144 9.354673 TGAATCAGCTTAAAAGGAATAATAGGG 57.645 33.333 0.00 0.00 0.00 3.53
2419 3190 9.426837 CAGACCAAAATATTGTTTCATTCACAT 57.573 29.630 0.00 0.00 34.60 3.21
2462 3240 1.197492 CTGTAAACTGCAATGCTCGCA 59.803 47.619 6.82 0.00 37.88 5.10
2471 3249 0.431984 CAATGCTCGCACGCAAAAAG 59.568 50.000 0.72 0.00 44.06 2.27
2486 3264 8.103924 GCACGCAAAAAGAATGAATAAATACAG 58.896 33.333 0.00 0.00 0.00 2.74
2521 3299 5.393135 CGATATGTAGATCATGTAGCCCGTT 60.393 44.000 0.00 0.00 37.91 4.44
2525 3303 3.627395 AGATCATGTAGCCCGTTTTGA 57.373 42.857 0.00 0.00 0.00 2.69
2702 3657 0.252421 ACTGACCTGGCTCTGATGGA 60.252 55.000 0.00 0.00 0.00 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
73 76 8.592105 TCAAAATAGCAACAAGATTTTGGAAG 57.408 30.769 15.51 0.00 44.82 3.46
286 304 6.987386 ACGGGAACATATGTTGAAAATTCAA 58.013 32.000 25.42 4.52 44.31 2.69
538 575 6.273825 TGAGTTATTCAATCTACGCTTCCTC 58.726 40.000 0.00 0.00 31.34 3.71
568 605 0.030369 GTCGTCGTATGCCGGAGAAT 59.970 55.000 5.05 0.00 37.11 2.40
636 674 3.304257 CCGCGTGTGAATGAAAATCAAA 58.696 40.909 4.92 0.00 0.00 2.69
646 684 3.788766 GCTTCGCCGCGTGTGAAT 61.789 61.111 19.11 0.00 42.33 2.57
726 809 1.486310 TGGGTCTCACTGGCACATATC 59.514 52.381 0.00 0.00 38.20 1.63
735 818 0.588252 CTTTGCGTTGGGTCTCACTG 59.412 55.000 0.00 0.00 0.00 3.66
821 904 2.289002 CAGCGTGAGAACTCAGCTTTTT 59.711 45.455 18.49 4.28 39.92 1.94
822 905 1.869767 CAGCGTGAGAACTCAGCTTTT 59.130 47.619 18.49 4.52 39.92 2.27
823 906 1.069204 TCAGCGTGAGAACTCAGCTTT 59.931 47.619 18.49 5.00 39.92 3.51
824 907 0.676184 TCAGCGTGAGAACTCAGCTT 59.324 50.000 18.49 8.16 39.92 3.74
825 908 0.038709 GTCAGCGTGAGAACTCAGCT 60.039 55.000 16.66 16.66 41.36 4.24
826 909 0.319040 TGTCAGCGTGAGAACTCAGC 60.319 55.000 4.67 10.43 40.75 4.26
827 910 2.057316 CTTGTCAGCGTGAGAACTCAG 58.943 52.381 4.67 1.72 40.75 3.35
828 911 1.869754 GCTTGTCAGCGTGAGAACTCA 60.870 52.381 0.00 0.00 35.91 3.41
829 912 0.787183 GCTTGTCAGCGTGAGAACTC 59.213 55.000 0.00 0.00 35.91 3.01
830 913 2.906047 GCTTGTCAGCGTGAGAACT 58.094 52.632 0.00 0.00 35.91 3.01
926 1033 2.534019 GCGTGTATGATGCGGGGTG 61.534 63.158 0.00 0.00 0.00 4.61
960 1519 4.468689 GAGGTACGGGTGGGCTGC 62.469 72.222 0.00 0.00 0.00 5.25
1356 1926 2.044551 GGGAGGAGGCCAGCTTTG 60.045 66.667 5.01 0.00 0.00 2.77
1482 2052 2.890109 CGCCAGCCGCATCTTGATC 61.890 63.158 0.00 0.00 37.30 2.92
1943 2529 6.327934 AGCAATGAAGCATCTGTTTGTATTC 58.672 36.000 0.00 0.00 36.85 1.75
1946 2535 5.710513 AAGCAATGAAGCATCTGTTTGTA 57.289 34.783 0.00 0.00 36.85 2.41
1948 2537 5.518847 CCATAAGCAATGAAGCATCTGTTTG 59.481 40.000 0.89 0.00 37.86 2.93
1989 2622 3.931907 TTACACTATGGAGCCAAGCAT 57.068 42.857 0.00 0.00 0.00 3.79
2007 2640 5.280945 GCATGTTCAGTGCTTCTGTTTTTA 58.719 37.500 8.75 0.00 43.97 1.52
2046 2679 1.493446 AGAATGATCTGCCATGGAGCA 59.507 47.619 18.40 3.69 41.46 4.26
2065 2699 3.497297 TTGTGCATCTTATTGCTGCAG 57.503 42.857 10.11 10.11 46.63 4.41
2339 3110 7.605449 TCCTTTTAAGCTGATTCAATTGGAAG 58.395 34.615 5.42 0.00 39.30 3.46
2340 3111 7.537596 TCCTTTTAAGCTGATTCAATTGGAA 57.462 32.000 5.42 0.00 40.46 3.53
2373 3144 7.227314 TGGTCTGATATGTATGAACTGCATTTC 59.773 37.037 9.72 9.72 38.44 2.17
2462 3240 9.906660 TTCTGTATTTATTCATTCTTTTTGCGT 57.093 25.926 0.00 0.00 0.00 5.24
2486 3264 9.911980 CATGATCTACATATCGTTGCATATTTC 57.088 33.333 0.00 0.00 37.46 2.17
2521 3299 6.127925 CCAGTGCAATAAGTTATGAGCTCAAA 60.128 38.462 22.50 13.30 0.00 2.69
2525 3303 4.848357 ACCAGTGCAATAAGTTATGAGCT 58.152 39.130 16.84 0.00 0.00 4.09


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

AutoCloner maintained by Alex Coulton.