Multiple sequence alignment - TraesCS2B01G554000

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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 TraesCS2B01G554000 chr2B 100.000 3019 0 0 1 3019 749226282 749223264 0.000000e+00 5576.0
1 TraesCS2B01G554000 chr2B 84.337 664 55 22 834 1490 749404224 749403603 3.790000e-169 604.0
2 TraesCS2B01G554000 chr2B 87.908 521 33 15 793 1308 749307072 749306577 1.370000e-163 586.0
3 TraesCS2B01G554000 chr2B 82.336 702 78 12 798 1476 749175266 749174588 4.970000e-158 568.0
4 TraesCS2B01G554000 chr2B 84.411 526 35 18 970 1490 749410837 749410354 1.110000e-129 473.0
5 TraesCS2B01G554000 chr2B 87.500 184 23 0 851 1034 749415232 749415049 2.680000e-51 213.0
6 TraesCS2B01G554000 chr2B 100.000 96 0 0 3334 3429 749222949 749222854 9.780000e-41 178.0
7 TraesCS2B01G554000 chr2B 78.656 253 29 19 1505 1744 749414953 749414713 9.920000e-31 145.0
8 TraesCS2B01G554000 chr2B 95.349 86 4 0 3342 3427 749223399 749223314 1.660000e-28 137.0
9 TraesCS2B01G554000 chr2B 73.469 245 45 16 1505 1742 749174514 749174283 1.320000e-09 75.0
10 TraesCS2B01G554000 chr7B 96.532 1211 36 6 1812 3019 60477546 60476339 0.000000e+00 1999.0
11 TraesCS2B01G554000 chr7B 79.845 1161 159 39 1920 3019 616774635 616775781 0.000000e+00 778.0
12 TraesCS2B01G554000 chr7B 88.013 317 35 3 2705 3019 60476059 60475744 4.180000e-99 372.0
13 TraesCS2B01G554000 chr7B 96.875 96 3 0 3334 3429 60475886 60475791 9.850000e-36 161.0
14 TraesCS2B01G554000 chr7B 96.512 86 3 0 3342 3427 60476420 60476335 3.570000e-30 143.0
15 TraesCS2B01G554000 chr7B 96.429 84 3 0 3346 3429 60476089 60476006 4.610000e-29 139.0
16 TraesCS2B01G554000 chr7B 93.671 79 5 0 1812 1890 616773383 616773461 6.010000e-23 119.0
17 TraesCS2B01G554000 chr7B 89.888 89 8 1 3342 3429 60475986 60475898 2.800000e-21 113.0
18 TraesCS2B01G554000 chr5B 97.835 1155 23 2 1813 2965 350395677 350394523 0.000000e+00 1993.0
19 TraesCS2B01G554000 chr5B 98.958 96 1 0 3334 3429 350393873 350393778 4.550000e-39 172.0
20 TraesCS2B01G554000 chr5B 89.286 84 8 1 3347 3429 350394654 350394571 1.680000e-18 104.0
21 TraesCS2B01G554000 chr2D 95.082 1098 31 8 714 1810 614826861 614825786 0.000000e+00 1707.0
22 TraesCS2B01G554000 chr2D 91.895 1024 40 22 793 1810 615006779 615005793 0.000000e+00 1391.0
23 TraesCS2B01G554000 chr2D 92.937 807 42 7 1 801 614827657 614826860 0.000000e+00 1160.0
24 TraesCS2B01G554000 chr2D 88.809 697 42 19 797 1490 615023856 615023193 0.000000e+00 822.0
25 TraesCS2B01G554000 chr2D 84.389 679 102 4 10 686 353021409 353020733 0.000000e+00 664.0
26 TraesCS2B01G554000 chr2D 86.522 460 34 16 834 1291 615057086 615056653 6.660000e-132 481.0
27 TraesCS2B01G554000 chr2D 90.090 111 10 1 1365 1474 615056621 615056511 3.570000e-30 143.0
28 TraesCS2B01G554000 chr2D 82.540 126 12 8 1506 1631 615056442 615056327 6.050000e-18 102.0
29 TraesCS2B01G554000 chr2D 91.489 47 4 0 1506 1552 615053869 615053823 7.940000e-07 65.8
30 TraesCS2B01G554000 chr2A 91.174 1133 79 16 1896 3019 695320161 695321281 0.000000e+00 1519.0
31 TraesCS2B01G554000 chr2A 88.050 1046 56 26 793 1810 745148122 745147118 0.000000e+00 1175.0
32 TraesCS2B01G554000 chr2A 84.679 966 66 41 793 1731 745216493 745215583 0.000000e+00 889.0
33 TraesCS2B01G554000 chr2A 82.331 815 87 34 851 1631 745259414 745258623 0.000000e+00 654.0
34 TraesCS2B01G554000 chr2A 83.475 708 69 22 789 1490 745256634 745255969 1.750000e-172 616.0
35 TraesCS2B01G554000 chr2A 89.623 318 30 3 2705 3019 695321071 695321388 5.330000e-108 401.0
36 TraesCS2B01G554000 chr2A 79.661 236 21 12 1261 1488 745103235 745103019 9.920000e-31 145.0
37 TraesCS2B01G554000 chr2A 91.667 84 7 0 3346 3429 695321257 695321340 2.160000e-22 117.0
38 TraesCS2B01G554000 chr2A 73.585 265 41 22 1505 1750 745102930 745102676 1.320000e-09 75.0
39 TraesCS2B01G554000 chr6A 91.895 1024 62 14 1896 2911 546476134 546475124 0.000000e+00 1411.0
40 TraesCS2B01G554000 chr6A 95.098 102 3 2 1813 1914 546476247 546476148 3.540000e-35 159.0
41 TraesCS2B01G554000 chr6A 94.048 84 5 0 3346 3429 546474744 546474661 9.990000e-26 128.0
42 TraesCS2B01G554000 chr6B 90.106 566 39 8 2406 2968 551661852 551662403 0.000000e+00 719.0
43 TraesCS2B01G554000 chr4A 78.680 1121 148 48 1967 3019 675522484 675521387 0.000000e+00 662.0
44 TraesCS2B01G554000 chr4A 82.403 699 117 6 1 695 596578803 596578107 3.790000e-169 604.0
45 TraesCS2B01G554000 chr4A 94.737 76 4 0 1815 1890 675524836 675524761 6.010000e-23 119.0
46 TraesCS2B01G554000 chr7D 84.544 647 90 10 1 643 506030776 506031416 1.740000e-177 632.0
47 TraesCS2B01G554000 chr7A 84.591 636 92 5 46 677 579017697 579018330 8.080000e-176 627.0
48 TraesCS2B01G554000 chr7A 83.636 660 101 7 23 679 573447383 573448038 6.290000e-172 614.0
49 TraesCS2B01G554000 chr1D 82.714 700 113 8 1 697 487775880 487776574 1.750000e-172 616.0
50 TraesCS2B01G554000 chr1B 82.690 699 113 8 2 697 178726240 178726933 6.290000e-172 614.0
51 TraesCS2B01G554000 chr5A 82.920 685 111 6 3 683 593398555 593397873 2.260000e-171 612.0
52 TraesCS2B01G554000 chr3B 75.508 1082 202 48 1969 3019 52765908 52764859 4.010000e-129 472.0
53 TraesCS2B01G554000 chr3B 97.059 34 0 1 2457 2490 471483106 471483074 4.780000e-04 56.5


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 TraesCS2B01G554000 chr2B 749222854 749226282 3428 True 1963.666667 5576 98.449667 1 3429 3 chr2B.!!$R4 3428
1 TraesCS2B01G554000 chr2B 749403603 749404224 621 True 604.000000 604 84.337000 834 1490 1 chr2B.!!$R2 656
2 TraesCS2B01G554000 chr2B 749174283 749175266 983 True 321.500000 568 77.902500 798 1742 2 chr2B.!!$R3 944
3 TraesCS2B01G554000 chr2B 749410354 749415232 4878 True 277.000000 473 83.522333 851 1744 3 chr2B.!!$R5 893
4 TraesCS2B01G554000 chr7B 60475744 60477546 1802 True 487.833333 1999 94.041500 1812 3429 6 chr7B.!!$R1 1617
5 TraesCS2B01G554000 chr7B 616773383 616775781 2398 False 448.500000 778 86.758000 1812 3019 2 chr7B.!!$F1 1207
6 TraesCS2B01G554000 chr5B 350393778 350395677 1899 True 756.333333 1993 95.359667 1813 3429 3 chr5B.!!$R1 1616
7 TraesCS2B01G554000 chr2D 614825786 614827657 1871 True 1433.500000 1707 94.009500 1 1810 2 chr2D.!!$R4 1809
8 TraesCS2B01G554000 chr2D 615005793 615006779 986 True 1391.000000 1391 91.895000 793 1810 1 chr2D.!!$R2 1017
9 TraesCS2B01G554000 chr2D 615023193 615023856 663 True 822.000000 822 88.809000 797 1490 1 chr2D.!!$R3 693
10 TraesCS2B01G554000 chr2D 353020733 353021409 676 True 664.000000 664 84.389000 10 686 1 chr2D.!!$R1 676
11 TraesCS2B01G554000 chr2A 745147118 745148122 1004 True 1175.000000 1175 88.050000 793 1810 1 chr2A.!!$R1 1017
12 TraesCS2B01G554000 chr2A 745215583 745216493 910 True 889.000000 889 84.679000 793 1731 1 chr2A.!!$R2 938
13 TraesCS2B01G554000 chr2A 695320161 695321388 1227 False 679.000000 1519 90.821333 1896 3429 3 chr2A.!!$F1 1533
14 TraesCS2B01G554000 chr2A 745255969 745259414 3445 True 635.000000 654 82.903000 789 1631 2 chr2A.!!$R4 842
15 TraesCS2B01G554000 chr6A 546474661 546476247 1586 True 566.000000 1411 93.680333 1813 3429 3 chr6A.!!$R1 1616
16 TraesCS2B01G554000 chr6B 551661852 551662403 551 False 719.000000 719 90.106000 2406 2968 1 chr6B.!!$F1 562
17 TraesCS2B01G554000 chr4A 596578107 596578803 696 True 604.000000 604 82.403000 1 695 1 chr4A.!!$R1 694
18 TraesCS2B01G554000 chr4A 675521387 675524836 3449 True 390.500000 662 86.708500 1815 3019 2 chr4A.!!$R2 1204
19 TraesCS2B01G554000 chr7D 506030776 506031416 640 False 632.000000 632 84.544000 1 643 1 chr7D.!!$F1 642
20 TraesCS2B01G554000 chr7A 579017697 579018330 633 False 627.000000 627 84.591000 46 677 1 chr7A.!!$F2 631
21 TraesCS2B01G554000 chr7A 573447383 573448038 655 False 614.000000 614 83.636000 23 679 1 chr7A.!!$F1 656
22 TraesCS2B01G554000 chr1D 487775880 487776574 694 False 616.000000 616 82.714000 1 697 1 chr1D.!!$F1 696
23 TraesCS2B01G554000 chr1B 178726240 178726933 693 False 614.000000 614 82.690000 2 697 1 chr1B.!!$F1 695
24 TraesCS2B01G554000 chr5A 593397873 593398555 682 True 612.000000 612 82.920000 3 683 1 chr5A.!!$R1 680
25 TraesCS2B01G554000 chr3B 52764859 52765908 1049 True 472.000000 472 75.508000 1969 3019 1 chr3B.!!$R1 1050

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
697 710 0.027455 TCTGCAGAACAAAACGCGTG 59.973 50.0 15.67 2.21 0.00 5.34 F
738 751 1.052617 TGACTTTCATGGTCCGGACA 58.947 50.0 34.40 21.15 33.22 4.02 F
2065 9192 0.107508 CGGTCCATTGGAGATGCAGT 60.108 55.0 5.39 0.00 29.39 4.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1810 6267 2.859165 TGAGTTTTAGGCACTCCCTG 57.141 50.00 0.83 0.0 45.91 4.45 R
2128 9275 4.665212 CACGCATTCAGCATTGTTAGATT 58.335 39.13 0.00 0.0 46.13 2.40 R
2990 11403 0.599728 TGCATGTTTTTGAAGGCCGC 60.600 50.00 0.00 0.0 0.00 6.53 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
34 35 2.845752 CTTTGGCGCATGCAATGGCT 62.846 55.000 19.57 0.00 46.86 4.75
272 274 1.608055 TGGCACAACAACTCATCCTG 58.392 50.000 0.00 0.00 31.92 3.86
309 312 4.452825 TCACCATCCTTCGTACTCTAGAG 58.547 47.826 18.49 18.49 0.00 2.43
380 384 2.048597 GCGTGGTGTCCGTCATGA 60.049 61.111 0.00 0.00 0.00 3.07
565 573 4.589908 GGATGCAAAGTAAGAGGGAGAAA 58.410 43.478 0.00 0.00 0.00 2.52
665 678 1.210722 GACTCCCACAAATCTCCTCCC 59.789 57.143 0.00 0.00 0.00 4.30
697 710 0.027455 TCTGCAGAACAAAACGCGTG 59.973 50.000 15.67 2.21 0.00 5.34
699 712 1.585002 GCAGAACAAAACGCGTGCA 60.585 52.632 14.98 0.00 0.00 4.57
738 751 1.052617 TGACTTTCATGGTCCGGACA 58.947 50.000 34.40 21.15 33.22 4.02
744 757 1.218047 CATGGTCCGGACATCACGT 59.782 57.895 34.40 16.42 0.00 4.49
787 800 1.903404 CGCCTTGGAGGTGCCTTTT 60.903 57.895 0.00 0.00 39.28 2.27
788 801 1.463553 CGCCTTGGAGGTGCCTTTTT 61.464 55.000 0.00 0.00 39.28 1.94
820 833 8.385491 TGGTAGTAATCATATCAAGCAATGGAT 58.615 33.333 0.00 0.00 0.00 3.41
840 854 4.282195 GGATACAGCTATAGGACAGCAAGT 59.718 45.833 1.04 0.00 41.66 3.16
841 855 5.221541 GGATACAGCTATAGGACAGCAAGTT 60.222 44.000 1.04 0.00 41.66 2.66
842 856 3.866651 ACAGCTATAGGACAGCAAGTTG 58.133 45.455 1.04 0.00 41.66 3.16
843 857 3.201290 CAGCTATAGGACAGCAAGTTGG 58.799 50.000 4.75 0.00 41.66 3.77
844 858 2.840651 AGCTATAGGACAGCAAGTTGGT 59.159 45.455 0.63 0.63 41.66 3.67
845 859 4.030913 AGCTATAGGACAGCAAGTTGGTA 58.969 43.478 7.35 0.00 41.66 3.25
847 861 4.141914 GCTATAGGACAGCAAGTTGGTACT 60.142 45.833 7.35 8.94 38.93 2.73
848 862 2.841442 AGGACAGCAAGTTGGTACTC 57.159 50.000 7.35 5.42 31.99 2.59
849 863 2.047061 AGGACAGCAAGTTGGTACTCA 58.953 47.619 7.35 0.00 31.99 3.41
850 864 2.438021 AGGACAGCAAGTTGGTACTCAA 59.562 45.455 7.35 0.00 31.99 3.02
900 4157 3.620374 ACGATGCTGTGTTGATCTGAATC 59.380 43.478 0.00 0.00 0.00 2.52
901 4158 3.302286 CGATGCTGTGTTGATCTGAATCG 60.302 47.826 0.00 0.00 36.51 3.34
902 4159 3.044235 TGCTGTGTTGATCTGAATCGT 57.956 42.857 0.00 0.00 34.39 3.73
903 4160 2.738314 TGCTGTGTTGATCTGAATCGTG 59.262 45.455 0.00 0.00 34.39 4.35
906 4163 4.805719 GCTGTGTTGATCTGAATCGTGATA 59.194 41.667 0.00 0.00 34.39 2.15
908 4165 5.965922 TGTGTTGATCTGAATCGTGATACT 58.034 37.500 0.00 0.00 34.39 2.12
910 4167 6.036470 GTGTTGATCTGAATCGTGATACTCA 58.964 40.000 0.00 0.00 34.39 3.41
911 4176 6.531594 GTGTTGATCTGAATCGTGATACTCAA 59.468 38.462 0.00 0.00 34.39 3.02
1104 4578 4.636648 GGTTCAGATTGACGAGAGAGTAGA 59.363 45.833 0.00 0.00 0.00 2.59
1105 4579 5.298276 GGTTCAGATTGACGAGAGAGTAGAT 59.702 44.000 0.00 0.00 0.00 1.98
1106 4580 6.483974 GGTTCAGATTGACGAGAGAGTAGATA 59.516 42.308 0.00 0.00 0.00 1.98
1107 4581 7.307751 GGTTCAGATTGACGAGAGAGTAGATAG 60.308 44.444 0.00 0.00 0.00 2.08
1543 5086 7.164230 TCTGAAAGTTGAAACAAAGGCTTTA 57.836 32.000 12.95 0.00 33.76 1.85
1810 6267 4.403734 TCACCCCAATGAGGTAAAGAAAC 58.596 43.478 0.00 0.00 35.24 2.78
1928 9007 1.927487 TGTTCCTCGTAACCAGGCTA 58.073 50.000 0.00 0.00 0.00 3.93
1954 9033 0.608856 TCCAACGCGGTCTAGTGGTA 60.609 55.000 12.47 0.00 35.57 3.25
1957 9036 1.941999 AACGCGGTCTAGTGGTAGCC 61.942 60.000 12.47 0.00 0.00 3.93
2065 9192 0.107508 CGGTCCATTGGAGATGCAGT 60.108 55.000 5.39 0.00 29.39 4.40
2128 9275 6.291377 GCTTATATGGGATCTTGAACTCACA 58.709 40.000 0.00 0.00 0.00 3.58
2960 10740 3.871485 TGCCTTGAAAAGTTGCAATTGT 58.129 36.364 0.59 0.00 44.25 2.71
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
8 9 2.034879 CATGCGCCAAAGGACGAGT 61.035 57.895 4.18 0.00 0.00 4.18
34 35 1.067846 ACGTCAACTCGATGCAAGCTA 60.068 47.619 0.00 0.00 33.53 3.32
309 312 8.693542 AGCTTATTTCAAATGCTATGTTGTTC 57.306 30.769 0.00 0.00 31.71 3.18
380 384 1.923148 CCACCCCCTATCAAAGACCTT 59.077 52.381 0.00 0.00 0.00 3.50
557 564 2.122954 ACTCCGCCCTTTCTCCCT 59.877 61.111 0.00 0.00 0.00 4.20
565 573 0.698818 ATTTCCTTTCACTCCGCCCT 59.301 50.000 0.00 0.00 0.00 5.19
665 678 5.240891 TGTTCTGCAGATTAGAGACAAAGG 58.759 41.667 19.04 0.00 0.00 3.11
697 710 1.067142 TCAACGTGGGTCTGTATCTGC 60.067 52.381 0.00 0.00 0.00 4.26
699 712 3.513912 TCATTCAACGTGGGTCTGTATCT 59.486 43.478 0.00 0.00 0.00 1.98
790 803 7.603180 TGCTTGATATGATTACTACCAGAGT 57.397 36.000 0.00 0.00 42.69 3.24
791 804 8.933807 CATTGCTTGATATGATTACTACCAGAG 58.066 37.037 0.00 0.00 0.00 3.35
795 808 8.798859 ATCCATTGCTTGATATGATTACTACC 57.201 34.615 0.00 0.00 0.00 3.18
820 833 4.141937 CCAACTTGCTGTCCTATAGCTGTA 60.142 45.833 0.00 0.00 41.66 2.74
840 854 3.202906 GTGCAGAGTTGTTGAGTACCAA 58.797 45.455 0.00 0.00 0.00 3.67
841 855 2.169561 TGTGCAGAGTTGTTGAGTACCA 59.830 45.455 0.00 0.00 0.00 3.25
842 856 2.833794 TGTGCAGAGTTGTTGAGTACC 58.166 47.619 0.00 0.00 0.00 3.34
843 857 3.248602 CCTTGTGCAGAGTTGTTGAGTAC 59.751 47.826 0.00 0.00 0.00 2.73
844 858 3.118408 ACCTTGTGCAGAGTTGTTGAGTA 60.118 43.478 0.00 0.00 0.00 2.59
845 859 2.292267 CCTTGTGCAGAGTTGTTGAGT 58.708 47.619 0.00 0.00 0.00 3.41
847 861 2.092968 AGACCTTGTGCAGAGTTGTTGA 60.093 45.455 0.00 0.00 0.00 3.18
848 862 2.032550 CAGACCTTGTGCAGAGTTGTTG 59.967 50.000 0.00 0.00 0.00 3.33
849 863 2.292267 CAGACCTTGTGCAGAGTTGTT 58.708 47.619 0.00 0.00 0.00 2.83
850 864 1.959042 CAGACCTTGTGCAGAGTTGT 58.041 50.000 0.00 0.00 0.00 3.32
852 866 0.882042 CGCAGACCTTGTGCAGAGTT 60.882 55.000 0.00 0.00 41.26 3.01
853 867 1.301244 CGCAGACCTTGTGCAGAGT 60.301 57.895 0.00 0.00 41.26 3.24
903 4160 1.343821 CGCACGCCGTTTGAGTATC 59.656 57.895 0.00 0.00 0.00 2.24
953 4227 2.558359 GCTTTAGTGTTGCACCTCCATT 59.442 45.455 0.00 0.00 34.49 3.16
1104 4578 2.821366 GCACCTGCACGCTGCTAT 60.821 61.111 10.54 0.00 45.31 2.97
1241 4716 1.213013 CGACTTGGTGGTCTCCTCG 59.787 63.158 0.00 0.00 34.38 4.63
1437 4934 1.729470 CCTCCGATCCTCCTGACACG 61.729 65.000 0.00 0.00 0.00 4.49
1543 5086 5.929992 CACACATTGAAAATCTCCAGCAAAT 59.070 36.000 0.00 0.00 0.00 2.32
1810 6267 2.859165 TGAGTTTTAGGCACTCCCTG 57.141 50.000 0.83 0.00 45.91 4.45
1957 9036 5.649782 AACAATTTGACAGCCCAATAGAG 57.350 39.130 2.79 0.00 0.00 2.43
2065 9192 4.769345 TTATGACCCATGTGATACAGCA 57.231 40.909 0.00 0.00 0.00 4.41
2128 9275 4.665212 CACGCATTCAGCATTGTTAGATT 58.335 39.130 0.00 0.00 46.13 2.40
2988 11401 1.873486 GCATGTTTTTGAAGGCCGCTT 60.873 47.619 0.00 0.00 0.00 4.68
2990 11403 0.599728 TGCATGTTTTTGAAGGCCGC 60.600 50.000 0.00 0.00 0.00 6.53
3336 11749 2.130426 TTTTTGAAGGGCGGCTGCA 61.130 52.632 21.31 1.58 45.35 4.41
3340 11753 1.291184 GCATGTTTTTGAAGGGCGGC 61.291 55.000 0.00 0.00 0.00 6.53


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

AutoCloner maintained by Alex Coulton.