Multiple sequence alignment - TraesCS2B01G437600

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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 TraesCS2B01G437600 chr2B 100.000 2426 0 0 1 2426 629656839 629659264 0.000000e+00 4481
1 TraesCS2B01G437600 chr2B 90.641 983 61 16 1445 2420 419998334 419999292 0.000000e+00 1277
2 TraesCS2B01G437600 chr2B 93.032 818 47 2 1 818 208612158 208611351 0.000000e+00 1186
3 TraesCS2B01G437600 chr7B 98.071 985 16 1 1445 2426 658053218 658054202 0.000000e+00 1711
4 TraesCS2B01G437600 chr7B 95.025 985 34 5 1445 2426 606733053 606732081 0.000000e+00 1533
5 TraesCS2B01G437600 chr7B 80.662 574 83 14 173 733 484845418 484845976 1.040000e-113 420
6 TraesCS2B01G437600 chr7B 80.454 573 84 14 173 732 484831162 484831719 1.740000e-111 412
7 TraesCS2B01G437600 chr4B 92.510 988 57 10 1444 2425 624110997 624110021 0.000000e+00 1399
8 TraesCS2B01G437600 chr4B 81.923 697 105 15 33 714 59049146 59048456 9.730000e-159 569
9 TraesCS2B01G437600 chr2A 94.370 817 44 2 1 817 741973440 741974254 0.000000e+00 1253
10 TraesCS2B01G437600 chr2A 88.822 1002 93 14 1437 2426 4064310 4065304 0.000000e+00 1212
11 TraesCS2B01G437600 chr2A 93.813 598 31 3 857 1449 674416902 674417498 0.000000e+00 894
12 TraesCS2B01G437600 chr2A 87.844 436 46 3 1017 1445 674491873 674492308 2.780000e-139 505
13 TraesCS2B01G437600 chr7D 89.484 989 89 10 1447 2426 531978162 531979144 0.000000e+00 1236
14 TraesCS2B01G437600 chr7D 80.662 574 81 14 173 732 86081182 86081739 3.730000e-113 418
15 TraesCS2B01G437600 chr6A 89.200 1000 92 11 1436 2426 615950613 615951605 0.000000e+00 1234
16 TraesCS2B01G437600 chr6A 87.413 1001 105 14 1435 2426 428336453 428335465 0.000000e+00 1131
17 TraesCS2B01G437600 chr1B 93.009 658 43 3 1769 2426 183370764 183370110 0.000000e+00 957
18 TraesCS2B01G437600 chr1B 92.705 658 45 3 1769 2426 183425634 183424980 0.000000e+00 946
19 TraesCS2B01G437600 chr4D 84.478 1005 96 23 1437 2426 91260494 91261453 0.000000e+00 937
20 TraesCS2B01G437600 chr2D 93.843 536 17 3 914 1449 529650777 529651296 0.000000e+00 793
21 TraesCS2B01G437600 chr2D 91.892 74 4 2 857 930 529649219 529649290 4.270000e-18 102
22 TraesCS2B01G437600 chr1D 82.158 695 104 15 33 714 48890053 48889366 1.620000e-161 579
23 TraesCS2B01G437600 chr3B 81.779 697 105 16 33 714 693347453 693346764 4.530000e-157 564
24 TraesCS2B01G437600 chrUn 81.001 679 111 14 9 675 49601629 49602301 7.690000e-145 523
25 TraesCS2B01G437600 chr6D 93.590 312 17 1 1 309 348841631 348841942 1.700000e-126 462
26 TraesCS2B01G437600 chr5D 78.846 676 91 27 1 661 276269235 276268597 2.250000e-110 409


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 TraesCS2B01G437600 chr2B 629656839 629659264 2425 False 4481.0 4481 100.0000 1 2426 1 chr2B.!!$F2 2425
1 TraesCS2B01G437600 chr2B 419998334 419999292 958 False 1277.0 1277 90.6410 1445 2420 1 chr2B.!!$F1 975
2 TraesCS2B01G437600 chr2B 208611351 208612158 807 True 1186.0 1186 93.0320 1 818 1 chr2B.!!$R1 817
3 TraesCS2B01G437600 chr7B 658053218 658054202 984 False 1711.0 1711 98.0710 1445 2426 1 chr7B.!!$F3 981
4 TraesCS2B01G437600 chr7B 606732081 606733053 972 True 1533.0 1533 95.0250 1445 2426 1 chr7B.!!$R1 981
5 TraesCS2B01G437600 chr7B 484845418 484845976 558 False 420.0 420 80.6620 173 733 1 chr7B.!!$F2 560
6 TraesCS2B01G437600 chr7B 484831162 484831719 557 False 412.0 412 80.4540 173 732 1 chr7B.!!$F1 559
7 TraesCS2B01G437600 chr4B 624110021 624110997 976 True 1399.0 1399 92.5100 1444 2425 1 chr4B.!!$R2 981
8 TraesCS2B01G437600 chr4B 59048456 59049146 690 True 569.0 569 81.9230 33 714 1 chr4B.!!$R1 681
9 TraesCS2B01G437600 chr2A 741973440 741974254 814 False 1253.0 1253 94.3700 1 817 1 chr2A.!!$F4 816
10 TraesCS2B01G437600 chr2A 4064310 4065304 994 False 1212.0 1212 88.8220 1437 2426 1 chr2A.!!$F1 989
11 TraesCS2B01G437600 chr2A 674416902 674417498 596 False 894.0 894 93.8130 857 1449 1 chr2A.!!$F2 592
12 TraesCS2B01G437600 chr7D 531978162 531979144 982 False 1236.0 1236 89.4840 1447 2426 1 chr7D.!!$F2 979
13 TraesCS2B01G437600 chr7D 86081182 86081739 557 False 418.0 418 80.6620 173 732 1 chr7D.!!$F1 559
14 TraesCS2B01G437600 chr6A 615950613 615951605 992 False 1234.0 1234 89.2000 1436 2426 1 chr6A.!!$F1 990
15 TraesCS2B01G437600 chr6A 428335465 428336453 988 True 1131.0 1131 87.4130 1435 2426 1 chr6A.!!$R1 991
16 TraesCS2B01G437600 chr1B 183370110 183370764 654 True 957.0 957 93.0090 1769 2426 1 chr1B.!!$R1 657
17 TraesCS2B01G437600 chr1B 183424980 183425634 654 True 946.0 946 92.7050 1769 2426 1 chr1B.!!$R2 657
18 TraesCS2B01G437600 chr4D 91260494 91261453 959 False 937.0 937 84.4780 1437 2426 1 chr4D.!!$F1 989
19 TraesCS2B01G437600 chr2D 529649219 529651296 2077 False 447.5 793 92.8675 857 1449 2 chr2D.!!$F1 592
20 TraesCS2B01G437600 chr1D 48889366 48890053 687 True 579.0 579 82.1580 33 714 1 chr1D.!!$R1 681
21 TraesCS2B01G437600 chr3B 693346764 693347453 689 True 564.0 564 81.7790 33 714 1 chr3B.!!$R1 681
22 TraesCS2B01G437600 chrUn 49601629 49602301 672 False 523.0 523 81.0010 9 675 1 chrUn.!!$F1 666
23 TraesCS2B01G437600 chr5D 276268597 276269235 638 True 409.0 409 78.8460 1 661 1 chr5D.!!$R1 660

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
830 870 0.459585 TGACTTAAGATGACGGGCGC 60.46 55.0 10.09 0.0 0.0 6.53 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1983 3549 2.928801 TTGCAGTAGAGCCACAAGAA 57.071 45.0 0.0 0.0 0.0 2.52 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
30 37 4.592485 ATCTACCTGTTTGCCTCTATCG 57.408 45.455 0.00 0.00 0.00 2.92
44 51 6.115446 TGCCTCTATCGATTTTGTGAATTCT 58.885 36.000 1.71 0.00 0.00 2.40
403 422 8.932945 TGATCTACAGTTGAAGTGATGAATAC 57.067 34.615 7.07 2.59 0.00 1.89
450 470 9.520515 AAGCATCTTTAACAAAAGGAGAAGATA 57.479 29.630 0.00 0.00 33.46 1.98
454 474 8.281212 TCTTTAACAAAAGGAGAAGATATGCC 57.719 34.615 0.00 0.00 0.00 4.40
650 685 5.825679 TCAGTAGCACCAACTTTTTACATGT 59.174 36.000 2.69 2.69 0.00 3.21
723 763 5.416952 CCTCTTTGCAGGAAGTATGAAATGT 59.583 40.000 0.00 0.00 35.20 2.71
727 767 7.828717 TCTTTGCAGGAAGTATGAAATGTATCA 59.171 33.333 0.00 0.00 0.00 2.15
740 780 7.967771 TGAAATGTATCAAACGCACATTATG 57.032 32.000 0.06 0.00 40.94 1.90
751 791 8.511321 TCAAACGCACATTATGTTCTTAAGATT 58.489 29.630 5.89 0.00 0.00 2.40
776 816 3.019564 GCTGAAGTTGCAGGATTATGGT 58.980 45.455 0.00 0.00 36.41 3.55
777 817 3.065925 GCTGAAGTTGCAGGATTATGGTC 59.934 47.826 0.00 0.00 36.41 4.02
783 823 1.134128 TGCAGGATTATGGTCGCACAT 60.134 47.619 0.00 0.00 34.90 3.21
795 835 4.606961 TGGTCGCACATTTTCTTTCTTTC 58.393 39.130 0.00 0.00 0.00 2.62
796 836 4.338118 TGGTCGCACATTTTCTTTCTTTCT 59.662 37.500 0.00 0.00 0.00 2.52
818 858 9.567776 TTTCTTTGACCATAGAACATGACTTAA 57.432 29.630 0.00 0.00 30.14 1.85
819 859 8.777865 TCTTTGACCATAGAACATGACTTAAG 57.222 34.615 0.00 0.00 0.00 1.85
820 860 8.593679 TCTTTGACCATAGAACATGACTTAAGA 58.406 33.333 10.09 0.00 0.00 2.10
821 861 9.388506 CTTTGACCATAGAACATGACTTAAGAT 57.611 33.333 10.09 0.00 0.00 2.40
822 862 8.722480 TTGACCATAGAACATGACTTAAGATG 57.278 34.615 10.09 6.05 0.00 2.90
823 863 8.078060 TGACCATAGAACATGACTTAAGATGA 57.922 34.615 10.09 0.00 0.00 2.92
824 864 7.981789 TGACCATAGAACATGACTTAAGATGAC 59.018 37.037 10.09 4.26 0.00 3.06
825 865 6.980978 ACCATAGAACATGACTTAAGATGACG 59.019 38.462 10.09 0.00 0.00 4.35
826 866 6.422100 CCATAGAACATGACTTAAGATGACGG 59.578 42.308 10.09 0.00 0.00 4.79
827 867 4.759782 AGAACATGACTTAAGATGACGGG 58.240 43.478 10.09 0.00 0.00 5.28
828 868 2.906354 ACATGACTTAAGATGACGGGC 58.094 47.619 10.09 0.00 0.00 6.13
829 869 1.860950 CATGACTTAAGATGACGGGCG 59.139 52.381 10.09 0.00 0.00 6.13
830 870 0.459585 TGACTTAAGATGACGGGCGC 60.460 55.000 10.09 0.00 0.00 6.53
831 871 1.480219 GACTTAAGATGACGGGCGCG 61.480 60.000 22.69 22.69 0.00 6.86
832 872 2.202824 TTAAGATGACGGGCGCGG 60.203 61.111 27.52 9.49 0.00 6.46
833 873 4.884257 TAAGATGACGGGCGCGGC 62.884 66.667 26.39 26.39 0.00 6.53
847 887 2.202414 CGGCAATGCGCGCTTTTA 60.202 55.556 33.29 12.75 43.84 1.52
848 888 1.586042 CGGCAATGCGCGCTTTTAT 60.586 52.632 33.29 14.80 43.84 1.40
849 889 1.800332 CGGCAATGCGCGCTTTTATG 61.800 55.000 33.29 21.06 43.84 1.90
850 890 1.481819 GGCAATGCGCGCTTTTATGG 61.482 55.000 33.29 19.66 43.84 2.74
851 891 0.801836 GCAATGCGCGCTTTTATGGT 60.802 50.000 33.29 6.72 0.00 3.55
852 892 1.191096 CAATGCGCGCTTTTATGGTC 58.809 50.000 33.29 0.00 0.00 4.02
853 893 1.094785 AATGCGCGCTTTTATGGTCT 58.905 45.000 33.29 5.09 0.00 3.85
854 894 1.948104 ATGCGCGCTTTTATGGTCTA 58.052 45.000 33.29 7.30 0.00 2.59
855 895 1.286501 TGCGCGCTTTTATGGTCTAG 58.713 50.000 33.29 0.00 0.00 2.43
903 943 5.824624 GCTCCCAATCTCAATCTCAAACATA 59.175 40.000 0.00 0.00 0.00 2.29
942 2486 3.777925 CGACACGAAAGCAGCCGG 61.778 66.667 0.00 0.00 0.00 6.13
962 2506 2.423446 GCGGCTCGATTCCCTCAT 59.577 61.111 0.00 0.00 0.00 2.90
1041 2585 3.428763 TCCAATCGGGATGGAACAGGAA 61.429 50.000 2.80 0.00 43.84 3.36
1098 2642 2.685388 TCTAGTCGAGATGCAACAGGAG 59.315 50.000 0.00 0.00 0.00 3.69
1282 2826 3.616560 GCAGGACCAGTTCGATTCTTACA 60.617 47.826 0.00 0.00 0.00 2.41
1374 2918 2.398554 CCAGGTCGCGGTGGAAATG 61.399 63.158 15.47 2.15 35.67 2.32
1814 3376 0.469917 CGGAGGGCATACCAGACAAT 59.530 55.000 0.00 0.00 43.89 2.71
1945 3509 8.806429 TTAAATGGTGATGTGAGTGATTACAT 57.194 30.769 0.00 0.00 40.04 2.29
1954 3518 6.114187 TGTGAGTGATTACATCTTTCCTGT 57.886 37.500 0.00 0.00 0.00 4.00
2020 3606 3.638160 TGCAAATTCTTTCCTGCAGACTT 59.362 39.130 17.39 0.00 39.77 3.01
2188 3775 7.378461 AGCAAACAAAATATGACAAAGTGTACG 59.622 33.333 0.00 0.00 0.00 3.67
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
30 37 5.617751 CGGTGTCAGGAGAATTCACAAAATC 60.618 44.000 8.44 0.00 0.00 2.17
44 51 1.627864 TTCAGTGATCGGTGTCAGGA 58.372 50.000 0.00 0.00 0.00 3.86
160 173 5.432885 TGCAACCTAAACAAGCTTAGTTC 57.567 39.130 0.00 0.00 0.00 3.01
291 309 1.342174 GTGGCCCAATCAAGCATATGG 59.658 52.381 0.00 0.00 0.00 2.74
366 385 3.295093 CTGTAGATCAGAGCCTCCTTGA 58.705 50.000 0.00 0.00 46.27 3.02
403 422 3.754965 TCTTGTCCAAGGTTCCAGAATG 58.245 45.455 7.16 0.00 38.88 2.67
450 470 6.607198 GGGGTGTATTATTAGCATATTGGCAT 59.393 38.462 0.00 0.00 35.83 4.40
685 725 2.819608 CAAAGAGGGAAAGAATCGCCAA 59.180 45.455 0.00 0.00 41.76 4.52
723 763 9.157104 TCTTAAGAACATAATGTGCGTTTGATA 57.843 29.630 1.68 0.00 28.94 2.15
727 767 7.692291 CGAATCTTAAGAACATAATGTGCGTTT 59.308 33.333 9.71 0.00 28.94 3.60
740 780 5.847670 ACTTCAGCACGAATCTTAAGAAC 57.152 39.130 9.71 6.15 31.69 3.01
751 791 0.035317 ATCCTGCAACTTCAGCACGA 59.965 50.000 0.00 0.00 37.02 4.35
776 816 6.472163 GTCAAAGAAAGAAAGAAAATGTGCGA 59.528 34.615 0.00 0.00 0.00 5.10
777 817 6.291796 GGTCAAAGAAAGAAAGAAAATGTGCG 60.292 38.462 0.00 0.00 0.00 5.34
795 835 8.777865 TCTTAAGTCATGTTCTATGGTCAAAG 57.222 34.615 1.63 0.00 0.00 2.77
796 836 9.166173 CATCTTAAGTCATGTTCTATGGTCAAA 57.834 33.333 1.63 0.00 0.00 2.69
830 870 1.586042 ATAAAAGCGCGCATTGCCG 60.586 52.632 35.10 13.08 42.08 5.69
831 871 1.481819 CCATAAAAGCGCGCATTGCC 61.482 55.000 35.10 1.61 42.08 4.52
832 872 0.801836 ACCATAAAAGCGCGCATTGC 60.802 50.000 35.10 2.36 41.47 3.56
833 873 1.191096 GACCATAAAAGCGCGCATTG 58.809 50.000 35.10 20.74 0.00 2.82
834 874 1.094785 AGACCATAAAAGCGCGCATT 58.905 45.000 35.10 26.27 0.00 3.56
835 875 1.867233 CTAGACCATAAAAGCGCGCAT 59.133 47.619 35.10 20.88 0.00 4.73
836 876 1.286501 CTAGACCATAAAAGCGCGCA 58.713 50.000 35.10 13.52 0.00 6.09
837 877 1.287425 ACTAGACCATAAAAGCGCGC 58.713 50.000 26.66 26.66 0.00 6.86
850 890 0.463204 GGCTTTCCGGGGTACTAGAC 59.537 60.000 0.00 0.00 0.00 2.59
851 891 0.688749 GGGCTTTCCGGGGTACTAGA 60.689 60.000 0.00 0.00 0.00 2.43
852 892 1.693152 GGGGCTTTCCGGGGTACTAG 61.693 65.000 0.00 0.00 36.01 2.57
853 893 1.690283 GGGGCTTTCCGGGGTACTA 60.690 63.158 0.00 0.00 36.01 1.82
854 894 3.013327 GGGGCTTTCCGGGGTACT 61.013 66.667 0.00 0.00 36.01 2.73
855 895 4.119363 GGGGGCTTTCCGGGGTAC 62.119 72.222 0.00 0.00 36.01 3.34
962 2506 5.180304 GCTTTTGTTTTCCCTGTTTGTTTGA 59.820 36.000 0.00 0.00 0.00 2.69
1041 2585 0.743345 GCGGCTTGAACGGGAAGTAT 60.743 55.000 0.00 0.00 0.00 2.12
1054 2598 1.188219 TCCTCTTCTGTCTGCGGCTT 61.188 55.000 0.00 0.00 0.00 4.35
1098 2642 2.046217 GGCTGGAACGGGAACTCC 60.046 66.667 0.00 0.00 33.56 3.85
1189 2733 1.621301 CGCTCGTCCTGTTGCTTCAG 61.621 60.000 2.54 2.54 35.45 3.02
1282 2826 0.477204 CCCTCCATCATGTGCTCCAT 59.523 55.000 0.00 0.00 0.00 3.41
1379 2923 4.451150 GATCCGCCCGCTGACACA 62.451 66.667 0.00 0.00 0.00 3.72
1954 3518 9.474313 AGCCATAACAGAATATAGTTTTTCCAA 57.526 29.630 0.00 0.00 0.00 3.53
1965 3531 7.284034 CCACAAGAAGAAGCCATAACAGAATAT 59.716 37.037 0.00 0.00 0.00 1.28
1983 3549 2.928801 TTGCAGTAGAGCCACAAGAA 57.071 45.000 0.00 0.00 0.00 2.52
2028 3614 6.483307 CCTCAGTTACATTTCTGACAAGTTCA 59.517 38.462 0.00 0.00 36.04 3.18
2032 3618 5.641209 CCTCCTCAGTTACATTTCTGACAAG 59.359 44.000 0.00 0.00 36.04 3.16
2037 3623 4.256920 CACCCTCCTCAGTTACATTTCTG 58.743 47.826 0.00 0.00 0.00 3.02
2038 3624 3.910627 ACACCCTCCTCAGTTACATTTCT 59.089 43.478 0.00 0.00 0.00 2.52
2039 3625 4.287766 ACACCCTCCTCAGTTACATTTC 57.712 45.455 0.00 0.00 0.00 2.17


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

AutoCloner maintained by Alex Coulton.