Multiple sequence alignment - TraesCS3D01G191900

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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 TraesCS3D01G191900 chr3D 100.000 3439 0 0 1 3439 182084067 182087505 0.000000e+00 6351.0
1 TraesCS3D01G191900 chr3D 98.366 2816 42 1 628 3439 356978263 356975448 0.000000e+00 4942.0
2 TraesCS3D01G191900 chr3D 90.909 1221 68 17 627 1814 16121893 16120683 0.000000e+00 1600.0
3 TraesCS3D01G191900 chr3D 99.301 858 6 0 1825 2682 152703969 152704826 0.000000e+00 1552.0
4 TraesCS3D01G191900 chr3D 89.053 1215 75 23 631 1803 468666174 468664976 0.000000e+00 1454.0
5 TraesCS3D01G191900 chr3D 98.993 695 7 0 2745 3439 152705151 152705845 0.000000e+00 1245.0
6 TraesCS3D01G191900 chr3D 93.118 465 13 3 1162 1607 578353343 578352879 0.000000e+00 664.0
7 TraesCS3D01G191900 chr3D 100.000 71 0 0 1733 1803 578322911 578322841 7.740000e-27 132.0
8 TraesCS3D01G191900 chr3D 98.485 66 1 0 2894 2959 152704832 152704897 2.170000e-22 117.0
9 TraesCS3D01G191900 chr3D 100.000 46 0 0 1683 1728 578322983 578322938 6.120000e-13 86.1
10 TraesCS3D01G191900 chr1D 98.151 2812 31 4 628 3439 346200511 346197721 0.000000e+00 4885.0
11 TraesCS3D01G191900 chr1D 95.070 852 27 5 627 1476 481961643 481960805 0.000000e+00 1327.0
12 TraesCS3D01G191900 chr1D 97.541 488 9 1 2955 3439 481959326 481958839 0.000000e+00 832.0
13 TraesCS3D01G191900 chr5D 98.343 2052 27 3 628 2678 78754566 78756611 0.000000e+00 3594.0
14 TraesCS3D01G191900 chr5D 99.767 858 2 0 1825 2682 125658751 125659608 0.000000e+00 1574.0
15 TraesCS3D01G191900 chr5D 98.628 802 9 2 1825 2626 423750024 423750823 0.000000e+00 1419.0
16 TraesCS3D01G191900 chr5D 95.216 857 23 8 626 1477 423748936 423749779 0.000000e+00 1339.0
17 TraesCS3D01G191900 chr5D 94.737 855 30 5 624 1476 474542529 474543370 0.000000e+00 1315.0
18 TraesCS3D01G191900 chr5D 95.545 651 6 7 2789 3439 125660081 125660708 0.000000e+00 1020.0
19 TraesCS3D01G191900 chr5D 97.546 489 9 1 2954 3439 78756710 78757198 0.000000e+00 833.0
20 TraesCS3D01G191900 chr5D 97.336 488 10 1 2955 3439 474544558 474545045 0.000000e+00 826.0
21 TraesCS3D01G191900 chr5D 96.000 75 2 1 1733 1806 284885996 284886070 1.680000e-23 121.0
22 TraesCS3D01G191900 chr5D 97.561 41 1 0 2894 2934 78756682 78756722 1.710000e-08 71.3
23 TraesCS3D01G191900 chr7D 97.919 2066 23 4 627 2678 574241588 574239529 0.000000e+00 3559.0
24 TraesCS3D01G191900 chr7D 98.638 1615 22 0 1825 3439 65816016 65817630 0.000000e+00 2861.0
25 TraesCS3D01G191900 chr7D 88.915 2102 111 45 628 2634 154001438 154003512 0.000000e+00 2479.0
26 TraesCS3D01G191900 chr7D 94.595 851 26 6 628 1476 508795049 508795881 0.000000e+00 1299.0
27 TraesCS3D01G191900 chr7D 97.541 488 9 1 2955 3439 508797497 508797984 0.000000e+00 832.0
28 TraesCS3D01G191900 chr7D 97.131 488 11 1 2955 3439 135865111 135865598 0.000000e+00 821.0
29 TraesCS3D01G191900 chr7D 96.495 485 13 3 2955 3439 574239372 574238892 0.000000e+00 798.0
30 TraesCS3D01G191900 chr2D 98.504 802 10 2 1825 2626 102620845 102621644 0.000000e+00 1413.0
31 TraesCS3D01G191900 chr4A 86.328 1258 84 44 627 1814 693356867 693355628 0.000000e+00 1290.0
32 TraesCS3D01G191900 chr4A 95.652 138 6 0 1408 1545 693356024 693355887 4.470000e-54 222.0
33 TraesCS3D01G191900 chr3B 97.280 625 17 0 1 625 260354792 260355416 0.000000e+00 1061.0
34 TraesCS3D01G191900 chr3B 86.705 173 15 4 1549 1713 392293144 392292972 5.860000e-43 185.0
35 TraesCS3D01G191900 chr6D 76.684 579 111 18 1 564 304994623 304995192 2.010000e-77 300.0
36 TraesCS3D01G191900 chr6B 76.348 575 120 12 1 564 472302281 472301712 9.330000e-76 294.0
37 TraesCS3D01G191900 chr6B 84.083 289 18 11 1408 1668 149424939 149425227 1.580000e-63 254.0
38 TraesCS3D01G191900 chr4D 98.230 113 2 0 2789 2901 353864532 353864644 7.530000e-47 198.0
39 TraesCS3D01G191900 chr4D 96.460 113 4 0 2789 2901 152889011 152889123 1.630000e-43 187.0
40 TraesCS3D01G191900 chr6A 72.987 596 140 13 1 584 410232230 410231644 4.530000e-44 189.0
41 TraesCS3D01G191900 chr6A 93.805 113 7 0 2789 2901 569404658 569404546 1.640000e-38 171.0
42 TraesCS3D01G191900 chr3A 94.690 113 6 0 2789 2901 351706817 351706929 3.530000e-40 176.0
43 TraesCS3D01G191900 chr3A 97.590 83 2 0 543 625 229153488 229153570 3.580000e-30 143.0
44 TraesCS3D01G191900 chr5B 93.103 87 5 1 2596 2682 696511404 696511319 3.600000e-25 126.0
45 TraesCS3D01G191900 chr7B 96.226 53 1 1 2627 2678 719467361 719467309 6.120000e-13 86.1


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 TraesCS3D01G191900 chr3D 182084067 182087505 3438 False 6351.000000 6351 100.000000 1 3439 1 chr3D.!!$F1 3438
1 TraesCS3D01G191900 chr3D 356975448 356978263 2815 True 4942.000000 4942 98.366000 628 3439 1 chr3D.!!$R2 2811
2 TraesCS3D01G191900 chr3D 16120683 16121893 1210 True 1600.000000 1600 90.909000 627 1814 1 chr3D.!!$R1 1187
3 TraesCS3D01G191900 chr3D 468664976 468666174 1198 True 1454.000000 1454 89.053000 631 1803 1 chr3D.!!$R3 1172
4 TraesCS3D01G191900 chr3D 152703969 152705845 1876 False 971.333333 1552 98.926333 1825 3439 3 chr3D.!!$F2 1614
5 TraesCS3D01G191900 chr1D 346197721 346200511 2790 True 4885.000000 4885 98.151000 628 3439 1 chr1D.!!$R1 2811
6 TraesCS3D01G191900 chr1D 481958839 481961643 2804 True 1079.500000 1327 96.305500 627 3439 2 chr1D.!!$R2 2812
7 TraesCS3D01G191900 chr5D 78754566 78757198 2632 False 1499.433333 3594 97.816667 628 3439 3 chr5D.!!$F2 2811
8 TraesCS3D01G191900 chr5D 423748936 423750823 1887 False 1379.000000 1419 96.922000 626 2626 2 chr5D.!!$F4 2000
9 TraesCS3D01G191900 chr5D 125658751 125660708 1957 False 1297.000000 1574 97.656000 1825 3439 2 chr5D.!!$F3 1614
10 TraesCS3D01G191900 chr5D 474542529 474545045 2516 False 1070.500000 1315 96.036500 624 3439 2 chr5D.!!$F5 2815
11 TraesCS3D01G191900 chr7D 65816016 65817630 1614 False 2861.000000 2861 98.638000 1825 3439 1 chr7D.!!$F1 1614
12 TraesCS3D01G191900 chr7D 154001438 154003512 2074 False 2479.000000 2479 88.915000 628 2634 1 chr7D.!!$F3 2006
13 TraesCS3D01G191900 chr7D 574238892 574241588 2696 True 2178.500000 3559 97.207000 627 3439 2 chr7D.!!$R1 2812
14 TraesCS3D01G191900 chr7D 508795049 508797984 2935 False 1065.500000 1299 96.068000 628 3439 2 chr7D.!!$F4 2811
15 TraesCS3D01G191900 chr2D 102620845 102621644 799 False 1413.000000 1413 98.504000 1825 2626 1 chr2D.!!$F1 801
16 TraesCS3D01G191900 chr4A 693355628 693356867 1239 True 756.000000 1290 90.990000 627 1814 2 chr4A.!!$R1 1187
17 TraesCS3D01G191900 chr3B 260354792 260355416 624 False 1061.000000 1061 97.280000 1 625 1 chr3B.!!$F1 624
18 TraesCS3D01G191900 chr6D 304994623 304995192 569 False 300.000000 300 76.684000 1 564 1 chr6D.!!$F1 563
19 TraesCS3D01G191900 chr6B 472301712 472302281 569 True 294.000000 294 76.348000 1 564 1 chr6B.!!$R1 563

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
771 782 0.524414 GCCGCAGTTAACCCGATTTT 59.476 50.000 15.40 0.00 0.0 1.82 F
842 853 1.597578 GTGGGTTGACGGCCGTTAA 60.598 57.895 34.65 31.77 0.0 2.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2275 2550 4.884164 CCTTCCTTGTGTTCCTAATGATCC 59.116 45.833 0.00 0.0 0.0 3.36 R
2897 3764 8.415950 TTCTATTCTAAAAGATTTTGGCCACA 57.584 30.769 3.88 0.0 0.0 4.17 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
349 356 2.671619 GTAGGCCCGTTGCAGCAA 60.672 61.111 2.83 2.83 43.89 3.91
678 689 5.046448 TGAAGTTAAAGCATCCAATTGCCAT 60.046 36.000 0.00 0.00 43.83 4.40
771 782 0.524414 GCCGCAGTTAACCCGATTTT 59.476 50.000 15.40 0.00 0.00 1.82
775 786 3.119637 CCGCAGTTAACCCGATTTTTGAT 60.120 43.478 15.40 0.00 0.00 2.57
842 853 1.597578 GTGGGTTGACGGCCGTTAA 60.598 57.895 34.65 31.77 0.00 2.01
1344 1372 3.713248 TCTATGGATGTGCTGTTCCTCAT 59.287 43.478 0.00 0.00 32.95 2.90
1556 1762 6.475076 TGTCAGTAAATGAAACATGTTTGCAC 59.525 34.615 27.85 14.18 40.43 4.57
2580 2856 9.683870 TTTTCTACAAAACTACCTCCAGTTAAA 57.316 29.630 0.00 0.00 37.78 1.52
2897 3764 2.737544 TGCTGCCATGTTACATCCAAT 58.262 42.857 0.00 0.00 0.00 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
73 74 4.697756 ACATCGTGGTGGTGGCCG 62.698 66.667 0.00 0.00 0.00 6.13
331 338 3.483788 TTGCTGCAACGGGCCTACA 62.484 57.895 11.69 0.00 43.89 2.74
349 356 2.367202 CCCATCTGCCCCTACACGT 61.367 63.158 0.00 0.00 0.00 4.49
661 672 2.568062 TGTGATGGCAATTGGATGCTTT 59.432 40.909 7.72 0.00 45.68 3.51
678 689 0.459585 GGGACGCGCTAGAAATGTGA 60.460 55.000 5.73 0.00 0.00 3.58
842 853 1.414919 TCTGTTTTGTACCGACAGCCT 59.585 47.619 12.82 0.00 40.36 4.58
1344 1372 5.818678 ACCCTAGTTTGATAACACTGACA 57.181 39.130 0.00 0.00 36.70 3.58
1556 1762 6.040247 ACTGACATAAATTGATGCTTGCATG 58.960 36.000 13.18 0.15 0.00 4.06
2275 2550 4.884164 CCTTCCTTGTGTTCCTAATGATCC 59.116 45.833 0.00 0.00 0.00 3.36
2897 3764 8.415950 TTCTATTCTAAAAGATTTTGGCCACA 57.584 30.769 3.88 0.00 0.00 4.17
2925 3840 0.106268 TGAGCCCAAGCCTTGTTTGA 60.106 50.000 3.37 0.00 41.25 2.69
2926 3841 0.752054 TTGAGCCCAAGCCTTGTTTG 59.248 50.000 3.37 0.00 41.25 2.93
2927 3842 1.043022 CTTGAGCCCAAGCCTTGTTT 58.957 50.000 3.37 0.00 42.72 2.83
2929 3844 1.228675 CCTTGAGCCCAAGCCTTGT 60.229 57.895 1.75 0.00 46.42 3.16
2931 3846 1.228675 CACCTTGAGCCCAAGCCTT 60.229 57.895 1.75 0.00 46.42 4.35
2932 3847 2.437897 CACCTTGAGCCCAAGCCT 59.562 61.111 1.75 0.00 46.42 4.58


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

AutoCloner maintained by Alex Coulton.