Multiple sequence alignment - TraesCS7B01G492200

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 TraesCS7B01G492200 chr7B 100.000 4450 0 0 1 4450 744442823 744447272 0.000000e+00 8218.0
1 TraesCS7B01G492200 chr7B 98.318 2853 41 4 1 2846 744481227 744484079 0.000000e+00 4996.0
2 TraesCS7B01G492200 chr7B 97.540 2846 69 1 1 2846 744503730 744506574 0.000000e+00 4867.0
3 TraesCS7B01G492200 chr7B 97.449 2078 52 1 1 2078 744492472 744494548 0.000000e+00 3542.0
4 TraesCS7B01G492200 chr7B 97.974 1876 37 1 971 2846 744460477 744462351 0.000000e+00 3253.0
5 TraesCS7B01G492200 chr7B 97.449 1607 28 3 2855 4450 744484302 744485906 0.000000e+00 2728.0
6 TraesCS7B01G492200 chr7B 96.017 1607 38 5 2855 4450 744495204 744496795 0.000000e+00 2590.0
7 TraesCS7B01G492200 chr7B 95.958 1608 36 8 2855 4450 744506797 744508387 0.000000e+00 2582.0
8 TraesCS7B01G492200 chr7B 94.897 1607 34 7 2855 4450 744462574 744464143 0.000000e+00 2470.0
9 TraesCS7B01G492200 chr7B 97.867 422 9 0 2425 2846 744494560 744494981 0.000000e+00 730.0
10 TraesCS7B01G492200 chr7B 95.724 421 18 0 1 421 744526042 744526462 0.000000e+00 678.0
11 TraesCS7B01G492200 chr7A 95.975 2857 102 6 1 2846 735396995 735394141 0.000000e+00 4626.0
12 TraesCS7B01G492200 chr7A 95.940 2857 103 6 1 2846 735360702 735357848 0.000000e+00 4621.0
13 TraesCS7B01G492200 chr7A 95.870 2857 105 6 1 2846 735378928 735376074 0.000000e+00 4610.0
14 TraesCS7B01G492200 chr7A 97.089 1580 35 2 2881 4450 735393956 735392378 0.000000e+00 2652.0
15 TraesCS7B01G492200 chr7A 97.029 1582 34 3 2881 4450 735375889 735374309 0.000000e+00 2649.0
16 TraesCS7B01G492200 chr7A 96.944 1440 42 2 3011 4450 735343035 735341598 0.000000e+00 2414.0
17 TraesCS7B01G492200 chr7A 92.361 144 1 1 2881 3014 735357645 735357502 3.510000e-46 196.0
18 TraesCS7B01G492200 chr7D 91.976 2480 173 13 388 2846 632351754 632354228 0.000000e+00 3454.0
19 TraesCS7B01G492200 chr7D 91.710 2485 171 17 388 2846 632360144 632362619 0.000000e+00 3415.0
20 TraesCS7B01G492200 chr7D 92.292 999 54 10 2855 3840 632362842 632363830 0.000000e+00 1397.0
21 TraesCS7B01G492200 chr7D 91.992 999 58 9 2855 3840 632354451 632355440 0.000000e+00 1382.0
22 TraesCS7B01G492200 chr7D 91.148 305 27 0 1 305 632340906 632341210 8.910000e-112 414.0
23 TraesCS7B01G492200 chr7D 100.000 61 0 0 335 395 632341322 632341382 3.640000e-21 113.0
24 TraesCS7B01G492200 chr2D 89.560 613 56 7 3840 4449 216964907 216964300 0.000000e+00 771.0
25 TraesCS7B01G492200 chr6D 89.141 617 55 9 3838 4449 158216716 158217325 0.000000e+00 758.0
26 TraesCS7B01G492200 chr1D 88.961 616 64 4 3837 4449 225493020 225493634 0.000000e+00 758.0
27 TraesCS7B01G492200 chr6B 87.234 94 8 2 600 693 709999443 709999354 2.190000e-18 104.0
28 TraesCS7B01G492200 chr2B 92.453 53 4 0 543 595 98114323 98114375 4.770000e-10 76.8
29 TraesCS7B01G492200 chr2A 100.000 30 0 0 327 356 593510507 593510478 6.220000e-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 TraesCS7B01G492200 chr7B 744442823 744447272 4449 False 8218.000000 8218 100.0000 1 4450 1 chr7B.!!$F1 4449
1 TraesCS7B01G492200 chr7B 744481227 744485906 4679 False 3862.000000 4996 97.8835 1 4450 2 chr7B.!!$F4 4449
2 TraesCS7B01G492200 chr7B 744503730 744508387 4657 False 3724.500000 4867 96.7490 1 4450 2 chr7B.!!$F6 4449
3 TraesCS7B01G492200 chr7B 744460477 744464143 3666 False 2861.500000 3253 96.4355 971 4450 2 chr7B.!!$F3 3479
4 TraesCS7B01G492200 chr7B 744492472 744496795 4323 False 2287.333333 3542 97.1110 1 4450 3 chr7B.!!$F5 4449
5 TraesCS7B01G492200 chr7A 735392378 735396995 4617 True 3639.000000 4626 96.5320 1 4450 2 chr7A.!!$R4 4449
6 TraesCS7B01G492200 chr7A 735374309 735378928 4619 True 3629.500000 4610 96.4495 1 4450 2 chr7A.!!$R3 4449
7 TraesCS7B01G492200 chr7A 735341598 735343035 1437 True 2414.000000 2414 96.9440 3011 4450 1 chr7A.!!$R1 1439
8 TraesCS7B01G492200 chr7A 735357502 735360702 3200 True 2408.500000 4621 94.1505 1 3014 2 chr7A.!!$R2 3013
9 TraesCS7B01G492200 chr7D 632351754 632355440 3686 False 2418.000000 3454 91.9840 388 3840 2 chr7D.!!$F2 3452
10 TraesCS7B01G492200 chr7D 632360144 632363830 3686 False 2406.000000 3415 92.0010 388 3840 2 chr7D.!!$F3 3452
11 TraesCS7B01G492200 chr2D 216964300 216964907 607 True 771.000000 771 89.5600 3840 4449 1 chr2D.!!$R1 609
12 TraesCS7B01G492200 chr6D 158216716 158217325 609 False 758.000000 758 89.1410 3838 4449 1 chr6D.!!$F1 611
13 TraesCS7B01G492200 chr1D 225493020 225493634 614 False 758.000000 758 88.9610 3837 4449 1 chr1D.!!$F1 612

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
234 235 0.249031 ACGCAGTGGCAAAGAAAAGC 60.249 50.000 0.00 0.0 42.51 3.51 F
1781 1794 3.747854 AACCCTAATAGCTAGGTTCGC 57.252 47.619 8.87 0.0 45.42 4.70 F
3111 3472 0.831711 TTTGCTCTTTTGCCCCCTCC 60.832 55.000 0.00 0.0 0.00 4.30 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2137 2161 2.183478 AAGGATGACACATGCGACAA 57.817 45.000 0.0 0.0 0.00 3.18 R
3273 3634 2.239907 GTTCCTCTACTCAAAGGCCCAT 59.760 50.000 0.0 0.0 32.37 4.00 R
3921 4292 1.613630 AGCCGGTGATGGGAAGACT 60.614 57.895 1.9 0.0 0.00 3.24 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
234 235 0.249031 ACGCAGTGGCAAAGAAAAGC 60.249 50.000 0.00 0.00 42.51 3.51
485 495 4.933400 GCAGAAAGTACCCAACGAATCTTA 59.067 41.667 0.00 0.00 0.00 2.10
831 843 4.553330 ACCGAAGATACCAATGTTGTCT 57.447 40.909 0.00 0.00 0.00 3.41
1528 1541 5.837979 TCCATCCTTTGATTTGTTCCTTGAA 59.162 36.000 0.00 0.00 0.00 2.69
1781 1794 3.747854 AACCCTAATAGCTAGGTTCGC 57.252 47.619 8.87 0.00 45.42 4.70
2137 2161 7.092174 TGTTGGTTTATCATAGATAGGGTGGTT 60.092 37.037 0.00 0.00 0.00 3.67
2730 2783 4.871993 AAGATTTCGATCTCACATGTGC 57.128 40.909 21.38 6.05 0.00 4.57
2853 2906 4.258543 TCTAACTTTATTGTTCCCTGCGG 58.741 43.478 0.00 0.00 0.00 5.69
3111 3472 0.831711 TTTGCTCTTTTGCCCCCTCC 60.832 55.000 0.00 0.00 0.00 4.30
3439 3802 9.553064 TTATTCAGTGGTTATGTTTGCAAAAAT 57.447 25.926 18.63 18.63 0.00 1.82
3454 3822 8.603181 GTTTGCAAAAATAATATGGTGGTCATC 58.397 33.333 14.67 0.00 37.30 2.92
3569 3938 5.324697 GCTTCTTCGTTGGTTATTCATGTC 58.675 41.667 0.00 0.00 0.00 3.06
3635 4004 0.317479 AGACGGTCCTTGTTCTTCCG 59.683 55.000 4.14 0.00 45.53 4.30
3921 4292 1.530655 TCTGTGACTCCACTGCCGA 60.531 57.895 0.00 0.00 43.55 5.54
4063 4434 0.980231 GAGAGGCTGACAGTGGGGAT 60.980 60.000 3.99 0.00 0.00 3.85
4104 4476 2.594303 TGCAACCGCCTCCTTGTG 60.594 61.111 0.00 0.00 37.32 3.33
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
485 495 2.540515 CTTCACCGCTATGAACGATGT 58.459 47.619 0.00 0.00 34.84 3.06
498 508 2.287188 ACATACGCGTATACCTTCACCG 60.287 50.000 29.79 16.85 0.00 4.94
742 754 3.277133 CCCACATGGCGAAGGTTG 58.723 61.111 0.00 0.00 0.00 3.77
1781 1794 4.679373 ATATAGCTCCCCAGATAATGCG 57.321 45.455 0.00 0.00 0.00 4.73
1812 1825 7.229306 GCATATTAGACCAGATGAACATGGAAA 59.771 37.037 0.00 0.00 39.02 3.13
1903 1916 9.761504 CTCAATCATCATCCCATATATGTAGTC 57.238 37.037 11.73 0.00 0.00 2.59
2137 2161 2.183478 AAGGATGACACATGCGACAA 57.817 45.000 0.00 0.00 0.00 3.18
2730 2783 7.013559 TGGAATATGTATTGCAAGTGAAGATGG 59.986 37.037 4.94 0.00 40.34 3.51
2847 2900 9.222581 CATTCCTCATGATAAATGATCCGCAGG 62.223 44.444 18.61 3.64 42.64 4.85
2849 2902 4.622260 TCCTCATGATAAATGATCCGCA 57.378 40.909 0.00 0.00 33.07 5.69
2850 2903 5.413833 ACATTCCTCATGATAAATGATCCGC 59.586 40.000 25.45 0.00 36.24 5.54
3111 3472 4.335647 AGGTGGTTCGCAGCCTGG 62.336 66.667 0.00 0.00 0.00 4.45
3273 3634 2.239907 GTTCCTCTACTCAAAGGCCCAT 59.760 50.000 0.00 0.00 32.37 4.00
3569 3938 5.510674 GCATCTTGATCGATGAACAAAACAG 59.489 40.000 0.54 0.00 42.63 3.16
3830 4201 7.416213 GCAGTCAGTAGAGAATAACATCACTCT 60.416 40.741 0.00 0.00 41.61 3.24
3921 4292 1.613630 AGCCGGTGATGGGAAGACT 60.614 57.895 1.90 0.00 0.00 3.24
4063 4434 2.756400 GTCCATGGACCTGGTGCA 59.244 61.111 31.37 23.55 38.41 4.57
4104 4476 7.166970 GGGAGGAATAATTTTTATTTTCGCGTC 59.833 37.037 5.77 0.00 0.00 5.19


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

AutoCloner maintained by Alex Coulton.