Multiple sequence alignment - TraesCS3B01G081300

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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 TraesCS3B01G081300 chr3B 100.000 3425 0 0 1 3425 51228477 51231901 0.000000e+00 6325
1 TraesCS3B01G081300 chr3B 98.108 3435 53 4 1 3425 51947732 51951164 0.000000e+00 5973
2 TraesCS3B01G081300 chr3B 98.450 1807 27 1 1 1806 51771556 51773362 0.000000e+00 3181
3 TraesCS3B01G081300 chr3B 85.164 2649 369 22 1 2633 52853770 52851130 0.000000e+00 2693
4 TraesCS3B01G081300 chr3B 84.937 2629 377 18 17 2633 52426290 52428911 0.000000e+00 2643
5 TraesCS3B01G081300 chr3B 83.850 2644 399 23 3 2630 51726991 51729622 0.000000e+00 2492
6 TraesCS3B01G081300 chr3B 80.801 1573 276 25 1074 2633 51926133 51927692 0.000000e+00 1208
7 TraesCS3B01G081300 chr3B 83.673 1127 165 17 1520 2633 52415613 52416733 0.000000e+00 1044
8 TraesCS3B01G081300 chr3B 82.869 467 78 2 2662 3127 52739995 52739530 5.290000e-113 418
9 TraesCS3B01G081300 chr3B 80.374 428 78 4 2643 3065 51805262 51805688 1.530000e-83 320
10 TraesCS3B01G081300 chr3B 80.929 409 69 7 2701 3101 52775060 52774653 7.130000e-82 315
11 TraesCS3B01G081300 chr3B 89.916 119 8 1 3017 3131 51859916 51860034 2.130000e-32 150
12 TraesCS3B01G081300 chr3A 83.050 3121 484 28 39 3121 41616700 41619813 0.000000e+00 2791
13 TraesCS3B01G081300 chr3A 85.028 2645 371 21 3 2633 41537175 41539808 0.000000e+00 2667
14 TraesCS3B01G081300 chr3A 92.154 1848 137 8 1 1843 40918026 40919870 0.000000e+00 2603
15 TraesCS3B01G081300 chr3A 83.994 2649 368 34 2 2633 41368776 41371385 0.000000e+00 2492
16 TraesCS3B01G081300 chr3A 83.442 2597 409 20 47 2630 40936368 40938956 0.000000e+00 2394
17 TraesCS3B01G081300 chr3A 82.878 2634 404 30 11 2630 41117756 41120356 0.000000e+00 2322
18 TraesCS3B01G081300 chr3A 84.542 731 85 16 2714 3422 40939085 40939809 0.000000e+00 699
19 TraesCS3B01G081300 chr3A 81.744 493 80 9 2644 3131 42019547 42020034 1.480000e-108 403
20 TraesCS3B01G081300 chr3A 80.632 506 94 4 2132 2633 41611554 41612059 4.140000e-104 388
21 TraesCS3B01G081300 chr3A 80.242 496 83 12 2643 3135 41239676 41240159 3.250000e-95 359
22 TraesCS3B01G081300 chr3A 80.093 432 80 5 2639 3065 41371439 41371869 1.980000e-82 316
23 TraesCS3B01G081300 chr3D 82.857 490 80 4 2644 3131 30280961 30281448 1.460000e-118 436


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 TraesCS3B01G081300 chr3B 51228477 51231901 3424 False 6325.0 6325 100.0000 1 3425 1 chr3B.!!$F1 3424
1 TraesCS3B01G081300 chr3B 51947732 51951164 3432 False 5973.0 5973 98.1080 1 3425 1 chr3B.!!$F7 3424
2 TraesCS3B01G081300 chr3B 51771556 51773362 1806 False 3181.0 3181 98.4500 1 1806 1 chr3B.!!$F3 1805
3 TraesCS3B01G081300 chr3B 52851130 52853770 2640 True 2693.0 2693 85.1640 1 2633 1 chr3B.!!$R3 2632
4 TraesCS3B01G081300 chr3B 52426290 52428911 2621 False 2643.0 2643 84.9370 17 2633 1 chr3B.!!$F9 2616
5 TraesCS3B01G081300 chr3B 51726991 51729622 2631 False 2492.0 2492 83.8500 3 2630 1 chr3B.!!$F2 2627
6 TraesCS3B01G081300 chr3B 51926133 51927692 1559 False 1208.0 1208 80.8010 1074 2633 1 chr3B.!!$F6 1559
7 TraesCS3B01G081300 chr3B 52415613 52416733 1120 False 1044.0 1044 83.6730 1520 2633 1 chr3B.!!$F8 1113
8 TraesCS3B01G081300 chr3A 41616700 41619813 3113 False 2791.0 2791 83.0500 39 3121 1 chr3A.!!$F6 3082
9 TraesCS3B01G081300 chr3A 41537175 41539808 2633 False 2667.0 2667 85.0280 3 2633 1 chr3A.!!$F4 2630
10 TraesCS3B01G081300 chr3A 40918026 40919870 1844 False 2603.0 2603 92.1540 1 1843 1 chr3A.!!$F1 1842
11 TraesCS3B01G081300 chr3A 41117756 41120356 2600 False 2322.0 2322 82.8780 11 2630 1 chr3A.!!$F2 2619
12 TraesCS3B01G081300 chr3A 40936368 40939809 3441 False 1546.5 2394 83.9920 47 3422 2 chr3A.!!$F8 3375
13 TraesCS3B01G081300 chr3A 41368776 41371869 3093 False 1404.0 2492 82.0435 2 3065 2 chr3A.!!$F9 3063
14 TraesCS3B01G081300 chr3A 41611554 41612059 505 False 388.0 388 80.6320 2132 2633 1 chr3A.!!$F5 501

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
630 637 5.179555 GGACTTAGTTCATTCACACAAGGAC 59.82 44.0 0.0 0.0 0.0 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2603 2623 1.353091 AAGACCACTCCTCCCAGTTC 58.647 55.0 0.0 0.0 0.0 3.01 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
232 238 5.941788 AGAAAAGGAGGACAAAAGAGCTAA 58.058 37.500 0.00 0.00 0.00 3.09
311 317 6.373759 TCCTAGATGTGGCTAGATGTAAAGA 58.626 40.000 0.00 0.00 40.20 2.52
630 637 5.179555 GGACTTAGTTCATTCACACAAGGAC 59.820 44.000 0.00 0.00 0.00 3.85
1045 1052 3.801050 CCATCGAGTTGATCTCATGTCAC 59.199 47.826 0.00 0.00 42.88 3.67
1139 1150 7.880160 AAAACATCGGGATTGAGATTATTCA 57.120 32.000 0.00 0.00 0.00 2.57
1685 1699 3.666345 ACCTAGAGTCGATAAGGTGGT 57.334 47.619 9.36 2.58 40.83 4.16
2483 2500 7.872113 ACCCAACTTGAAATATCTGAGAATC 57.128 36.000 0.00 0.00 0.00 2.52
2659 2727 1.117150 GTGGATGCCCATTCTGCAAT 58.883 50.000 0.00 0.00 45.68 3.56
3042 3113 1.534175 GCGAAGACCTGGATGTCTACG 60.534 57.143 0.00 0.00 44.68 3.51
3059 3131 0.815734 ACGCGCTGTCTACCAGTTAT 59.184 50.000 5.73 0.00 43.55 1.89
3140 3217 4.566004 TGTGTCTTTAATTCTCTGGACCG 58.434 43.478 0.00 0.00 0.00 4.79
3191 3269 3.213506 TGCAAGCTTCGTATGGCATTAT 58.786 40.909 4.78 0.00 0.00 1.28
3221 3299 6.541641 TGCACCAGAAATGCTTAAATTTGTTT 59.458 30.769 0.00 0.00 43.77 2.83
3222 3300 7.066766 TGCACCAGAAATGCTTAAATTTGTTTT 59.933 29.630 0.00 0.00 43.77 2.43
3290 3368 3.611057 GCAGATTGCAGGCATATACAAGC 60.611 47.826 0.00 0.00 44.26 4.01
3296 3374 4.572909 TGCAGGCATATACAAGCTATCAG 58.427 43.478 0.00 0.00 0.00 2.90
3332 3410 4.201724 GCTCTAAGTTGCTTATGTGTTCCG 60.202 45.833 0.00 0.00 0.00 4.30
3349 3427 6.183360 TGTGTTCCGTAGTATATGCTCATCAA 60.183 38.462 0.00 0.00 0.00 2.57
3362 3453 4.491676 TGCTCATCAAAACTACTACGGTC 58.508 43.478 0.00 0.00 0.00 4.79
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
232 238 3.385193 GCCAAGCCAATTGTTTACTGT 57.615 42.857 4.43 0.00 37.17 3.55
311 317 6.060788 GGATCATCAGGAAGTATCTTGCTTT 58.939 40.000 1.02 0.00 32.94 3.51
630 637 8.454106 ACAATAGCAAGCTTGTAAGACTTATTG 58.546 33.333 26.55 23.78 33.96 1.90
893 900 2.103537 TGACTGCCACACATCATCTG 57.896 50.000 0.00 0.00 0.00 2.90
1045 1052 0.105246 AGCTCCCATCCCACCTCTAG 60.105 60.000 0.00 0.00 0.00 2.43
1139 1150 1.529244 GGGAGGCAGCCGCATTTAT 60.529 57.895 17.96 0.00 41.24 1.40
1685 1699 7.015064 ACTTAGGAAAGTCCTCACCTTAACTA 58.985 38.462 0.00 0.00 45.66 2.24
1834 1848 8.144478 GCCAGTATAATTCAGATCAAGTAGACA 58.856 37.037 0.00 0.00 0.00 3.41
2483 2500 2.738846 GGTAACTGCATATGCTCCATCG 59.261 50.000 27.13 11.45 42.66 3.84
2523 2540 1.668826 TCACCCTTCCTACAGCCAAT 58.331 50.000 0.00 0.00 0.00 3.16
2603 2623 1.353091 AAGACCACTCCTCCCAGTTC 58.647 55.000 0.00 0.00 0.00 3.01
2998 3069 2.612212 TGAACTCGCTGGTTCTGTTTTC 59.388 45.455 15.91 0.00 44.02 2.29
3059 3131 3.164268 ACCTTGTGCTTTCATTGCCATA 58.836 40.909 0.00 0.00 0.00 2.74
3140 3217 8.629158 TGTGTATCCAATGAGGCATAAAATTAC 58.371 33.333 0.00 0.00 37.29 1.89
3191 3269 1.825090 AGCATTTCTGGTGCATCGAA 58.175 45.000 0.00 0.00 44.87 3.71
3221 3299 7.469537 TCTTTTCAAAGGTGTACAAGGAAAA 57.530 32.000 0.00 8.74 36.67 2.29
3222 3300 6.405397 GCTCTTTTCAAAGGTGTACAAGGAAA 60.405 38.462 0.00 1.13 36.67 3.13
3235 3313 8.017946 GGACATGTACTAAAGCTCTTTTCAAAG 58.982 37.037 0.00 0.00 37.36 2.77
3290 3368 3.141398 AGCAACACACAACACCTGATAG 58.859 45.455 0.00 0.00 0.00 2.08
3296 3374 2.943033 ACTTAGAGCAACACACAACACC 59.057 45.455 0.00 0.00 0.00 4.16
3349 3427 6.655078 TTAGGAAACAGACCGTAGTAGTTT 57.345 37.500 0.00 0.00 37.15 2.66
3362 3453 6.769822 AGTCCAGCATATGAATTAGGAAACAG 59.230 38.462 6.97 0.00 0.00 3.16
3400 3499 0.322456 ATGCTTTGCCCGCTGAAGTA 60.322 50.000 0.00 2.47 0.00 2.24


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

AutoCloner maintained by Alex Coulton.