Multiple sequence alignment - TraesCS7B01G492500

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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 TraesCS7B01G492500 chr7B 100.000 4640 0 0 1 4640 744503711 744508350 0.000000e+00 8569.0
1 TraesCS7B01G492500 chr7B 96.977 4664 115 11 1 4640 744481208 744485869 0.000000e+00 7808.0
2 TraesCS7B01G492500 chr7B 97.154 3654 78 6 989 4640 744460477 744464106 0.000000e+00 6148.0
3 TraesCS7B01G492500 chr7B 97.522 2865 70 1 1 2864 744442804 744445668 0.000000e+00 4896.0
4 TraesCS7B01G492500 chr7B 98.273 2200 35 2 2443 4640 744494560 744496758 0.000000e+00 3849.0
5 TraesCS7B01G492500 chr7B 97.330 2097 54 2 1 2096 744492453 744494548 0.000000e+00 3561.0
6 TraesCS7B01G492500 chr7B 95.863 1571 36 8 3087 4640 744445677 744447235 0.000000e+00 2514.0
7 TraesCS7B01G492500 chr7B 94.773 440 23 0 1 440 744526023 744526462 0.000000e+00 686.0
8 TraesCS7B01G492500 chr7D 92.268 3699 249 22 407 4080 632351754 632355440 0.000000e+00 5212.0
9 TraesCS7B01G492500 chr7D 92.090 3704 246 25 407 4080 632360144 632363830 0.000000e+00 5173.0
10 TraesCS7B01G492500 chr7D 87.085 542 54 8 4078 4604 398377766 398378306 2.390000e-167 599.0
11 TraesCS7B01G492500 chr7D 91.667 324 27 0 1 324 632340887 632341210 2.550000e-122 449.0
12 TraesCS7B01G492500 chr7D 96.667 60 2 0 355 414 632341323 632341382 2.950000e-17 100.0
13 TraesCS7B01G492500 chr7D 81.250 96 12 5 605 698 233939140 233939231 6.440000e-09 73.1
14 TraesCS7B01G492500 chr7A 95.655 3061 119 6 1 3049 735397014 735393956 0.000000e+00 4903.0
15 TraesCS7B01G492500 chr7A 95.524 3061 123 6 1 3049 735378947 735375889 0.000000e+00 4881.0
16 TraesCS7B01G492500 chr7A 95.492 3017 122 5 1 3005 735360721 735357707 0.000000e+00 4806.0
17 TraesCS7B01G492500 chr7A 96.241 1543 41 5 3114 4640 735393956 735392415 0.000000e+00 2512.0
18 TraesCS7B01G492500 chr7A 96.181 1545 40 5 3114 4640 735375889 735374346 0.000000e+00 2508.0
19 TraesCS7B01G492500 chr7A 95.435 1402 48 5 3254 4640 735343035 735341635 0.000000e+00 2220.0
20 TraesCS7B01G492500 chr7A 98.611 144 2 0 3114 3257 735357645 735357502 5.960000e-64 255.0
21 TraesCS7B01G492500 chr7A 100.000 40 0 0 3010 3049 735357684 735357645 1.790000e-09 75.0
22 TraesCS7B01G492500 chr1D 86.411 574 61 8 4077 4634 225493020 225493592 3.070000e-171 612.0
23 TraesCS7B01G492500 chr1D 81.609 87 15 1 626 712 411109919 411109834 2.320000e-08 71.3
24 TraesCS7B01G492500 chr1D 80.519 77 15 0 622 698 316838391 316838467 5.010000e-05 60.2
25 TraesCS7B01G492500 chr1D 78.125 96 16 4 605 698 384298660 384298752 6.490000e-04 56.5
26 TraesCS7B01G492500 chr2D 86.411 574 56 14 4078 4634 236458738 236459306 3.970000e-170 608.0
27 TraesCS7B01G492500 chr2D 83.182 220 19 6 4437 4640 539811397 539811614 7.930000e-43 185.0
28 TraesCS7B01G492500 chr5B 85.813 578 64 8 4078 4639 244391519 244392094 8.590000e-167 597.0
29 TraesCS7B01G492500 chr4A 76.051 547 98 24 3008 3535 732780171 732780703 2.140000e-63 254.0
30 TraesCS7B01G492500 chr2B 90.566 53 5 0 562 614 98114323 98114375 2.320000e-08 71.3
31 TraesCS7B01G492500 chr1B 90.196 51 5 0 562 612 381597720 381597670 3.000000e-07 67.6
32 TraesCS7B01G492500 chr1B 100.000 28 0 0 347 374 664957483 664957456 8.000000e-03 52.8
33 TraesCS7B01G492500 chr4D 80.460 87 16 1 626 712 72780032 72780117 1.080000e-06 65.8
34 TraesCS7B01G492500 chr3A 77.477 111 21 4 605 713 681088121 681088013 3.880000e-06 63.9
35 TraesCS7B01G492500 chr6D 78.125 96 17 4 605 698 147855312 147855405 1.800000e-04 58.4
36 TraesCS7B01G492500 chr2A 100.000 30 0 0 344 373 35382591 35382562 6.490000e-04 56.5
37 TraesCS7B01G492500 chr1A 100.000 28 0 0 346 373 126021074 126021047 8.000000e-03 52.8


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 TraesCS7B01G492500 chr7B 744503711 744508350 4639 False 8569.0 8569 100.000000 1 4640 1 chr7B.!!$F3 4639
1 TraesCS7B01G492500 chr7B 744481208 744485869 4661 False 7808.0 7808 96.977000 1 4640 1 chr7B.!!$F2 4639
2 TraesCS7B01G492500 chr7B 744460477 744464106 3629 False 6148.0 6148 97.154000 989 4640 1 chr7B.!!$F1 3651
3 TraesCS7B01G492500 chr7B 744442804 744447235 4431 False 3705.0 4896 96.692500 1 4640 2 chr7B.!!$F5 4639
4 TraesCS7B01G492500 chr7B 744492453 744496758 4305 False 3705.0 3849 97.801500 1 4640 2 chr7B.!!$F6 4639
5 TraesCS7B01G492500 chr7D 632351754 632355440 3686 False 5212.0 5212 92.268000 407 4080 1 chr7D.!!$F3 3673
6 TraesCS7B01G492500 chr7D 632360144 632363830 3686 False 5173.0 5173 92.090000 407 4080 1 chr7D.!!$F4 3673
7 TraesCS7B01G492500 chr7D 398377766 398378306 540 False 599.0 599 87.085000 4078 4604 1 chr7D.!!$F2 526
8 TraesCS7B01G492500 chr7A 735392415 735397014 4599 True 3707.5 4903 95.948000 1 4640 2 chr7A.!!$R4 4639
9 TraesCS7B01G492500 chr7A 735374346 735378947 4601 True 3694.5 4881 95.852500 1 4640 2 chr7A.!!$R3 4639
10 TraesCS7B01G492500 chr7A 735341635 735343035 1400 True 2220.0 2220 95.435000 3254 4640 1 chr7A.!!$R1 1386
11 TraesCS7B01G492500 chr7A 735357502 735360721 3219 True 1712.0 4806 98.034333 1 3257 3 chr7A.!!$R2 3256
12 TraesCS7B01G492500 chr1D 225493020 225493592 572 False 612.0 612 86.411000 4077 4634 1 chr1D.!!$F1 557
13 TraesCS7B01G492500 chr2D 236458738 236459306 568 False 608.0 608 86.411000 4078 4634 1 chr2D.!!$F1 556
14 TraesCS7B01G492500 chr5B 244391519 244392094 575 False 597.0 597 85.813000 4078 4639 1 chr5B.!!$F1 561
15 TraesCS7B01G492500 chr4A 732780171 732780703 532 False 254.0 254 76.051000 3008 3535 1 chr4A.!!$F1 527

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
396 406 3.490933 CGGTGATGGTCGATGTATCAACT 60.491 47.826 16.99 0.0 36.6 3.16 F
983 996 5.187186 CCCGTAAGCTACATATCTACCCATT 59.813 44.000 0.00 0.0 0.0 3.16 F
1380 1394 0.888736 CAAAGGCCACCGACACATCA 60.889 55.000 5.01 0.0 0.0 3.07 F
1470 1484 3.118592 TCAAAAACTGGGACGCCAATTTT 60.119 39.130 0.00 0.0 0.0 1.82 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1335 1348 1.937899 ACGTGTTTGTTGCAGTACTCC 59.062 47.619 0.00 0.00 0.00 3.85 R
2536 2581 4.995124 TCTCGTGATTTAGCTACAAGGAC 58.005 43.478 0.00 0.00 0.00 3.85 R
3418 3573 1.359459 GGCGTCTTTCCCGTGATCAC 61.359 60.000 16.21 16.21 0.00 3.06 R
3950 4117 9.841880 GTTACCATAAAAATTTCAGGTCTTCTC 57.158 33.333 6.97 0.00 32.14 2.87 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
83 84 6.298361 TCAAATCTTGTCCTGAAATGAGTCA 58.702 36.000 0.00 0.00 0.00 3.41
188 189 3.973516 AGACAGAACGCGTCGGCA 61.974 61.111 14.44 0.00 39.92 5.69
396 406 3.490933 CGGTGATGGTCGATGTATCAACT 60.491 47.826 16.99 0.00 36.60 3.16
410 420 9.208022 CGATGTATCAACTTGTAATATCCACAT 57.792 33.333 0.00 0.00 0.00 3.21
454 464 6.414694 CAGCCGCAAAAACAATATATGTGTAG 59.585 38.462 0.00 0.00 42.99 2.74
865 878 6.862469 ATGTGTCCTCATCAAATTGGAAAT 57.138 33.333 0.00 0.00 0.00 2.17
983 996 5.187186 CCCGTAAGCTACATATCTACCCATT 59.813 44.000 0.00 0.00 0.00 3.16
1335 1348 4.080695 TCAAAGATCCTCTCCAAGGTCATG 60.081 45.833 0.00 0.00 46.32 3.07
1380 1394 0.888736 CAAAGGCCACCGACACATCA 60.889 55.000 5.01 0.00 0.00 3.07
1470 1484 3.118592 TCAAAAACTGGGACGCCAATTTT 60.119 39.130 0.00 0.00 0.00 1.82
2126 2151 6.434018 AGATCTGCTCTGAATTTGTTTAGC 57.566 37.500 0.00 0.00 31.12 3.09
2265 2290 7.417612 TCACACACTTCTTTCTAATTTTGCTC 58.582 34.615 0.00 0.00 0.00 4.26
2314 2359 6.367374 TTCACTACTGGTCCATATGTCAAA 57.633 37.500 1.24 0.00 0.00 2.69
2400 2445 6.373495 TGATAGCTAAATCACATGATCATGCC 59.627 38.462 31.17 12.08 42.39 4.40
3879 4044 1.272807 CGGTCCTTGTTCTTCCCCTA 58.727 55.000 0.00 0.00 0.00 3.53
3977 4144 9.588096 AGAAGACCTGAAATTTTTATGGTAACT 57.412 29.630 0.00 0.00 37.61 2.24
4273 4450 2.404923 ACGAGAGTCATCGGAAGAGA 57.595 50.000 13.90 0.00 46.91 3.10
4396 4574 2.660802 CTGGGACCCACCACGTAC 59.339 66.667 9.95 0.00 41.20 3.67
4435 4613 0.984961 TGCCTCCTTATGCCTGCTCT 60.985 55.000 0.00 0.00 0.00 4.09
4471 4649 3.044986 CACCAACAACATCTTTGCTTCG 58.955 45.455 0.00 0.00 0.00 3.79
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
83 84 0.531974 TCCGCTTTTTGTCTGCTCGT 60.532 50.000 0.00 0.00 0.00 4.18
188 189 4.505039 GGTGTCTAAGACCAACTCCAATGT 60.505 45.833 0.00 0.00 33.25 2.71
338 339 6.380079 AAAGGATGTTGGAGTACTCTTGAT 57.620 37.500 21.88 9.38 0.00 2.57
454 464 6.485648 AGCTCACGGGGTACATATTTAATTTC 59.514 38.462 0.00 0.00 0.00 2.17
661 673 0.818296 ACAGTAACTGGCTCTAGGCG 59.182 55.000 0.00 0.00 44.42 5.52
696 708 6.507958 TGCCGAATGATTTTCTGTCAAATA 57.492 33.333 0.00 0.00 0.00 1.40
731 743 7.970384 TCTATTTATTGTTTTGCGAATCGACT 58.030 30.769 6.91 0.00 0.00 4.18
865 878 8.950007 AAGGGGTCAAACTAGAAAATTCATAA 57.050 30.769 0.00 0.00 0.00 1.90
916 929 9.643693 AGCCAAATAATACAAAACAAGATGAAG 57.356 29.630 0.00 0.00 0.00 3.02
983 996 0.237235 GCCGATTGAGCAACGTTTGA 59.763 50.000 0.00 0.00 0.00 2.69
1335 1348 1.937899 ACGTGTTTGTTGCAGTACTCC 59.062 47.619 0.00 0.00 0.00 3.85
1380 1394 2.507471 CCTAGCTCCTCCACCAAAATCT 59.493 50.000 0.00 0.00 0.00 2.40
1470 1484 2.028484 GCCGTGTCGACCTTGACA 59.972 61.111 14.12 0.00 46.15 3.58
2126 2151 9.658799 CACCCTATCTATGATAAACCAACATAG 57.341 37.037 0.00 0.00 42.45 2.23
2536 2581 4.995124 TCTCGTGATTTAGCTACAAGGAC 58.005 43.478 0.00 0.00 0.00 3.85
3418 3573 1.359459 GGCGTCTTTCCCGTGATCAC 61.359 60.000 16.21 16.21 0.00 3.06
3950 4117 9.841880 GTTACCATAAAAATTTCAGGTCTTCTC 57.158 33.333 6.97 0.00 32.14 2.87
3977 4144 2.930950 GCCTTGCCATGGTCATAAGTA 58.069 47.619 14.67 0.00 0.00 2.24
4273 4450 3.704566 TGTCAGCCTCTCCACGTATAATT 59.295 43.478 0.00 0.00 0.00 1.40
4360 4538 3.144506 CAGCTTTCATGGCGAGGAATAT 58.855 45.455 0.00 0.00 34.52 1.28
4369 4547 2.054453 GGGTCCCAGCTTTCATGGC 61.054 63.158 1.78 0.00 36.43 4.40
4435 4613 2.836154 GTGGGTCCCAGCTGTCAA 59.164 61.111 12.21 0.00 32.34 3.18


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

AutoCloner maintained by Alex Coulton.