Multiple sequence alignment - TraesCS7B01G111400

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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 TraesCS7B01G111400 chr7B 100.000 3434 0 0 1 3434 127775799 127772366 0.000000e+00 6342.0
1 TraesCS7B01G111400 chr7B 97.355 3440 77 8 1 3434 128072037 128068606 0.000000e+00 5836.0
2 TraesCS7B01G111400 chr7B 98.432 2679 40 2 1 2677 127654278 127651600 0.000000e+00 4713.0
3 TraesCS7B01G111400 chr7B 97.271 1869 36 5 761 2617 128436445 128438310 0.000000e+00 3155.0
4 TraesCS7B01G111400 chr7B 85.773 485 33 16 2228 2677 134493384 134493867 6.670000e-132 481.0
5 TraesCS7B01G111400 chr7B 76.433 314 57 14 413 724 651193647 651193349 1.650000e-33 154.0
6 TraesCS7B01G111400 chr7D 90.956 1957 117 31 760 2677 164752991 164751056 0.000000e+00 2579.0
7 TraesCS7B01G111400 chr7D 90.033 1535 100 21 1189 2677 165118315 165119842 0.000000e+00 1938.0
8 TraesCS7B01G111400 chr7D 86.943 942 82 23 1762 2677 169421831 169420905 0.000000e+00 1020.0
9 TraesCS7B01G111400 chr7D 85.495 910 79 24 1762 2636 169025261 169026152 0.000000e+00 900.0
10 TraesCS7B01G111400 chr7D 84.200 981 84 22 1765 2677 169440249 169439272 0.000000e+00 887.0
11 TraesCS7B01G111400 chr7D 83.333 744 104 15 950 1680 169440989 169440253 0.000000e+00 669.0
12 TraesCS7B01G111400 chr7D 89.873 79 8 0 588 666 260698117 260698039 6.060000e-18 102.0
13 TraesCS7B01G111400 chr7A 90.359 1950 133 26 771 2677 166869089 166871026 0.000000e+00 2508.0
14 TraesCS7B01G111400 chr7A 90.748 1859 127 24 774 2598 166491748 166489901 0.000000e+00 2438.0
15 TraesCS7B01G111400 chr7A 87.625 897 60 18 1802 2677 166595046 166594180 0.000000e+00 994.0
16 TraesCS7B01G111400 chr7A 82.754 835 117 18 911 1728 171439523 171438699 0.000000e+00 719.0
17 TraesCS7B01G111400 chr7A 90.548 529 42 8 2723 3248 527158635 527158112 0.000000e+00 693.0
18 TraesCS7B01G111400 chr7A 88.354 395 26 13 1 378 166492577 166492186 1.120000e-124 457.0
19 TraesCS7B01G111400 chr7A 88.354 395 26 13 1 378 166868263 166868654 1.120000e-124 457.0
20 TraesCS7B01G111400 chr7A 76.689 296 52 14 413 706 726503833 726504113 7.680000e-32 148.0
21 TraesCS7B01G111400 chrUn 88.832 788 55 13 1916 2677 218480268 218481048 0.000000e+00 937.0
22 TraesCS7B01G111400 chr6A 83.226 775 106 14 972 1728 124423003 124423771 0.000000e+00 689.0
23 TraesCS7B01G111400 chr6A 83.097 775 107 14 972 1728 124916868 124916100 0.000000e+00 684.0
24 TraesCS7B01G111400 chr3B 89.031 547 44 12 2723 3264 776949696 776950231 0.000000e+00 664.0
25 TraesCS7B01G111400 chr5A 88.462 546 55 7 2722 3264 44406444 44406984 0.000000e+00 652.0
26 TraesCS7B01G111400 chr5A 77.070 314 55 14 413 724 570379416 570379118 7.620000e-37 165.0
27 TraesCS7B01G111400 chr1B 90.792 467 37 5 2740 3205 175675004 175674543 1.350000e-173 619.0
28 TraesCS7B01G111400 chr1B 87.293 543 48 11 2724 3263 28450088 28449564 4.900000e-168 601.0
29 TraesCS7B01G111400 chr1B 81.181 271 36 9 3147 3412 679718695 679718955 1.620000e-48 204.0
30 TraesCS7B01G111400 chr2B 90.046 432 39 4 2834 3264 682344033 682343605 1.080000e-154 556.0
31 TraesCS7B01G111400 chr2B 84.967 153 20 3 561 712 131882990 131883140 5.940000e-33 152.0
32 TraesCS7B01G111400 chr1A 90.046 432 35 6 2834 3264 552256417 552255993 1.390000e-153 553.0
33 TraesCS7B01G111400 chr1A 91.262 206 16 2 2723 2926 588379120 588379325 2.610000e-71 279.0
34 TraesCS7B01G111400 chr5B 85.066 529 67 10 2731 3254 636335207 636334686 2.350000e-146 529.0
35 TraesCS7B01G111400 chr4A 95.238 126 6 0 3290 3415 648656227 648656352 2.090000e-47 200.0
36 TraesCS7B01G111400 chr1D 76.115 314 58 15 413 724 67973430 67973132 7.680000e-32 148.0
37 TraesCS7B01G111400 chr6B 89.873 79 8 0 588 666 399048992 399049070 6.060000e-18 102.0
38 TraesCS7B01G111400 chr6D 95.652 46 2 0 1762 1807 103052603 103052648 1.320000e-09 75.0
39 TraesCS7B01G111400 chr4D 97.059 34 1 0 2686 2719 386019765 386019732 1.330000e-04 58.4


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 TraesCS7B01G111400 chr7B 127772366 127775799 3433 True 6342.0 6342 100.0000 1 3434 1 chr7B.!!$R2 3433
1 TraesCS7B01G111400 chr7B 128068606 128072037 3431 True 5836.0 5836 97.3550 1 3434 1 chr7B.!!$R3 3433
2 TraesCS7B01G111400 chr7B 127651600 127654278 2678 True 4713.0 4713 98.4320 1 2677 1 chr7B.!!$R1 2676
3 TraesCS7B01G111400 chr7B 128436445 128438310 1865 False 3155.0 3155 97.2710 761 2617 1 chr7B.!!$F1 1856
4 TraesCS7B01G111400 chr7D 164751056 164752991 1935 True 2579.0 2579 90.9560 760 2677 1 chr7D.!!$R1 1917
5 TraesCS7B01G111400 chr7D 165118315 165119842 1527 False 1938.0 1938 90.0330 1189 2677 1 chr7D.!!$F1 1488
6 TraesCS7B01G111400 chr7D 169420905 169421831 926 True 1020.0 1020 86.9430 1762 2677 1 chr7D.!!$R2 915
7 TraesCS7B01G111400 chr7D 169025261 169026152 891 False 900.0 900 85.4950 1762 2636 1 chr7D.!!$F2 874
8 TraesCS7B01G111400 chr7D 169439272 169440989 1717 True 778.0 887 83.7665 950 2677 2 chr7D.!!$R4 1727
9 TraesCS7B01G111400 chr7A 166868263 166871026 2763 False 1482.5 2508 89.3565 1 2677 2 chr7A.!!$F2 2676
10 TraesCS7B01G111400 chr7A 166489901 166492577 2676 True 1447.5 2438 89.5510 1 2598 2 chr7A.!!$R4 2597
11 TraesCS7B01G111400 chr7A 166594180 166595046 866 True 994.0 994 87.6250 1802 2677 1 chr7A.!!$R1 875
12 TraesCS7B01G111400 chr7A 171438699 171439523 824 True 719.0 719 82.7540 911 1728 1 chr7A.!!$R2 817
13 TraesCS7B01G111400 chr7A 527158112 527158635 523 True 693.0 693 90.5480 2723 3248 1 chr7A.!!$R3 525
14 TraesCS7B01G111400 chrUn 218480268 218481048 780 False 937.0 937 88.8320 1916 2677 1 chrUn.!!$F1 761
15 TraesCS7B01G111400 chr6A 124423003 124423771 768 False 689.0 689 83.2260 972 1728 1 chr6A.!!$F1 756
16 TraesCS7B01G111400 chr6A 124916100 124916868 768 True 684.0 684 83.0970 972 1728 1 chr6A.!!$R1 756
17 TraesCS7B01G111400 chr3B 776949696 776950231 535 False 664.0 664 89.0310 2723 3264 1 chr3B.!!$F1 541
18 TraesCS7B01G111400 chr5A 44406444 44406984 540 False 652.0 652 88.4620 2722 3264 1 chr5A.!!$F1 542
19 TraesCS7B01G111400 chr1B 28449564 28450088 524 True 601.0 601 87.2930 2724 3263 1 chr1B.!!$R1 539
20 TraesCS7B01G111400 chr5B 636334686 636335207 521 True 529.0 529 85.0660 2731 3254 1 chr5B.!!$R1 523

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
692 784 0.593128 AGTGGTGAGATTTTGCGTGC 59.407 50.000 0.00 0.00 0.0 5.34 F
866 1071 1.439679 GAAATTTGACGCGTCCTCCT 58.560 50.000 34.34 16.25 0.0 3.69 F
1698 1971 1.823470 TGCAATGTATGGCCCGCTC 60.823 57.895 0.00 0.00 0.0 5.03 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1698 1971 0.249073 CAGGGAAGATGGTACGAGCG 60.249 60.000 0.0 0.0 0.0 5.03 R
1730 2027 1.209128 GATTGACGCTGGTACATCCG 58.791 55.000 0.0 0.0 38.2 4.18 R
2935 3332 4.566426 AGAAGTCTTTTGATGGGGAGAG 57.434 45.455 0.0 0.0 0.0 3.20 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
303 326 3.500343 ACTTTAAATTGCAGGCTGAGGT 58.500 40.909 20.86 0.00 0.00 3.85
692 784 0.593128 AGTGGTGAGATTTTGCGTGC 59.407 50.000 0.00 0.00 0.00 5.34
792 997 4.036262 CCAGGTTTCAGAAAATTGACGTGA 59.964 41.667 0.00 0.00 0.00 4.35
866 1071 1.439679 GAAATTTGACGCGTCCTCCT 58.560 50.000 34.34 16.25 0.00 3.69
1165 1412 3.801997 CCAAGGATCTGGCCGCCT 61.802 66.667 11.61 0.00 0.00 5.52
1698 1971 1.823470 TGCAATGTATGGCCCGCTC 60.823 57.895 0.00 0.00 0.00 5.03
1730 2027 0.620556 TTCCCTGTTCAGGATGCTCC 59.379 55.000 19.12 0.00 36.58 4.70
1875 2196 0.545171 CCCAGTCAGATGTGCTGGAT 59.455 55.000 25.01 0.00 44.47 3.41
2045 2397 8.324306 TGAAGAACTAATGAGAATGATGGAAGT 58.676 33.333 0.00 0.00 0.00 3.01
2648 3037 2.550855 GCTCTGTTTCCTGTGATGGACA 60.551 50.000 0.00 0.00 35.58 4.02
2688 3077 1.203758 CTTTTTGTACCCCGGGAATGC 59.796 52.381 26.32 14.27 0.00 3.56
2935 3332 8.347771 TGCATGCATGTTAAAATATTCTCTCTC 58.652 33.333 26.79 5.09 0.00 3.20
2936 3333 8.566260 GCATGCATGTTAAAATATTCTCTCTCT 58.434 33.333 26.79 0.00 0.00 3.10
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
303 326 4.624015 CCTGCTCTTTTTCATTTTGCTGA 58.376 39.130 0.00 0.00 0.00 4.26
309 332 2.967887 ACTGGCCTGCTCTTTTTCATTT 59.032 40.909 9.95 0.00 0.00 2.32
314 337 1.466851 GCCACTGGCCTGCTCTTTTT 61.467 55.000 9.13 0.00 44.06 1.94
355 378 5.518128 GCTACATGAAGTGACTAGACATGTG 59.482 44.000 26.91 20.88 46.69 3.21
792 997 3.184736 CCGATTCGGTCCCCAATTT 57.815 52.632 17.08 0.00 42.73 1.82
866 1071 1.741401 CGATGGACTTGCAGGCGAA 60.741 57.895 0.00 0.00 0.00 4.70
1698 1971 0.249073 CAGGGAAGATGGTACGAGCG 60.249 60.000 0.00 0.00 0.00 5.03
1730 2027 1.209128 GATTGACGCTGGTACATCCG 58.791 55.000 0.00 0.00 38.20 4.18
1875 2196 5.129634 TGTTGGCTGTAATTCTTGACAGAA 58.870 37.500 9.75 0.00 44.88 3.02
2045 2397 1.610624 GCTCCACTTCAATTGGGTCGA 60.611 52.381 5.42 3.08 34.56 4.20
2648 3037 6.688637 AAAGGTAAGAGCAGTTTTAACGTT 57.311 33.333 5.88 5.88 0.00 3.99
2935 3332 4.566426 AGAAGTCTTTTGATGGGGAGAG 57.434 45.455 0.00 0.00 0.00 3.20
2936 3333 6.215431 TGAATAGAAGTCTTTTGATGGGGAGA 59.785 38.462 0.00 0.00 0.00 3.71


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

AutoCloner maintained by Alex Coulton.