Multiple sequence alignment - TraesCS5B01G025800

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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 TraesCS5B01G025800 chr5B 100.000 4549 0 0 1 4549 24373308 24377856 0.000000e+00 8401.0
1 TraesCS5B01G025800 chr5B 98.633 2853 29 6 1 2850 24330032 24332877 0.000000e+00 5044.0
2 TraesCS5B01G025800 chr5B 98.486 2245 28 2 607 2850 24313379 24315618 0.000000e+00 3952.0
3 TraesCS5B01G025800 chr5B 99.001 1702 17 0 2848 4549 24315956 24317657 0.000000e+00 3049.0
4 TraesCS5B01G025800 chr5B 98.766 1702 20 1 2848 4549 24333216 24334916 0.000000e+00 3025.0
5 TraesCS5B01G025800 chr5B 98.531 1702 23 2 2848 4549 24358929 24360628 0.000000e+00 3003.0
6 TraesCS5B01G025800 chr5B 98.228 1467 19 4 3088 4549 24298657 24300121 0.000000e+00 2558.0
7 TraesCS5B01G025800 chr5B 98.885 1345 13 2 1508 2850 24357247 24358591 0.000000e+00 2399.0
8 TraesCS5B01G025800 chr5B 92.599 1635 82 16 904 2518 6659213 6660828 0.000000e+00 2313.0
9 TraesCS5B01G025800 chr5B 87.985 1057 96 19 2988 4022 31114617 31113570 0.000000e+00 1219.0
10 TraesCS5B01G025800 chr5B 98.548 551 8 0 1 551 24312836 24313386 0.000000e+00 974.0
11 TraesCS5B01G025800 chr5B 94.876 605 30 1 1307 1910 31117723 31117119 0.000000e+00 944.0
12 TraesCS5B01G025800 chr5B 95.636 527 21 1 4023 4549 30919280 30918756 0.000000e+00 845.0
13 TraesCS5B01G025800 chr5B 95.446 527 22 1 4023 4549 30993413 30992889 0.000000e+00 839.0
14 TraesCS5B01G025800 chr5B 83.660 612 35 18 717 1308 31118336 31117770 2.430000e-142 516.0
15 TraesCS5B01G025800 chr5B 84.388 474 55 10 4093 4549 24424843 24424372 8.980000e-122 448.0
16 TraesCS5B01G025800 chr5B 85.202 446 44 9 1911 2354 31117081 31116656 5.400000e-119 438.0
17 TraesCS5B01G025800 chr5B 99.281 139 1 0 2 140 24390647 24390785 7.550000e-63 252.0
18 TraesCS5B01G025800 chr5B 96.026 151 3 3 711 859 6659053 6659202 4.550000e-60 243.0
19 TraesCS5B01G025800 chr5B 89.116 147 14 2 568 713 31118683 31118538 1.010000e-41 182.0
20 TraesCS5B01G025800 chr5B 91.339 127 11 0 2361 2487 31115167 31115041 1.680000e-39 174.0
21 TraesCS5B01G025800 chr5B 96.053 76 3 0 2775 2850 6660827 6660902 1.720000e-24 124.0
22 TraesCS5B01G025800 chr5D 94.525 1169 49 10 2863 4021 5117609 5116446 0.000000e+00 1790.0
23 TraesCS5B01G025800 chr5D 91.070 1019 60 17 1311 2321 5118603 5117608 0.000000e+00 1349.0
24 TraesCS5B01G025800 chr5D 89.163 526 50 3 1379 1900 5163917 5163395 0.000000e+00 649.0
25 TraesCS5B01G025800 chr5D 91.228 342 29 1 3222 3562 5154292 5153951 8.910000e-127 464.0
26 TraesCS5B01G025800 chr5D 82.393 585 52 24 711 1283 5119232 5118687 3.210000e-126 462.0
27 TraesCS5B01G025800 chr5D 84.665 463 63 5 2048 2505 5156627 5156168 5.360000e-124 455.0
28 TraesCS5B01G025800 chr5D 81.132 371 40 12 934 1283 5164398 5164037 2.090000e-68 270.0
29 TraesCS5B01G025800 chr5D 82.486 177 30 1 2952 3128 519275240 519275065 2.190000e-33 154.0
30 TraesCS5B01G025800 chr5D 90.196 51 1 1 667 713 5164813 5164763 3.800000e-06 63.9
31 TraesCS5B01G025800 chr5D 100.000 31 0 0 447 477 6935002 6935032 1.770000e-04 58.4
32 TraesCS5B01G025800 chr5D 100.000 31 0 0 447 477 13912196 13912166 1.770000e-04 58.4
33 TraesCS5B01G025800 chr5A 84.662 1167 126 29 1385 2505 3556109 3557268 0.000000e+00 1114.0
34 TraesCS5B01G025800 chr5A 89.840 748 66 7 1308 2052 3699380 3700120 0.000000e+00 952.0
35 TraesCS5B01G025800 chr5A 85.938 832 78 26 2916 3729 3700818 3701628 0.000000e+00 852.0
36 TraesCS5B01G025800 chr5A 92.239 335 26 0 3225 3559 3558752 3559086 4.120000e-130 475.0
37 TraesCS5B01G025800 chr5A 86.168 441 49 11 2049 2487 3700152 3700582 2.480000e-127 466.0
38 TraesCS5B01G025800 chr5A 81.667 600 51 26 711 1282 3698729 3699297 1.160000e-120 444.0
39 TraesCS5B01G025800 chr5A 92.075 265 18 2 2515 2776 34842169 34841905 2.000000e-98 370.0
40 TraesCS5B01G025800 chr5A 84.444 315 29 10 904 1216 3555606 3555902 4.450000e-75 292.0
41 TraesCS5B01G025800 chr5A 93.333 150 9 1 711 859 3555446 3555595 2.130000e-53 220.0
42 TraesCS5B01G025800 chr5A 87.952 166 17 3 287 452 305331783 305331621 4.640000e-45 193.0
43 TraesCS5B01G025800 chr5A 93.651 126 7 1 586 710 3555173 3555298 2.160000e-43 187.0
44 TraesCS5B01G025800 chr5A 95.876 97 4 0 3716 3812 3701944 3702040 1.690000e-34 158.0
45 TraesCS5B01G025800 chr5A 81.818 121 11 7 165 278 3698321 3698437 1.740000e-14 91.6
46 TraesCS5B01G025800 chr5A 100.000 31 0 0 447 477 401136541 401136571 1.770000e-04 58.4
47 TraesCS5B01G025800 chr5A 100.000 29 0 0 542 570 678194063 678194091 2.000000e-03 54.7
48 TraesCS5B01G025800 chr1D 90.602 266 25 0 2512 2777 365323994 365323729 2.010000e-93 353.0
49 TraesCS5B01G025800 chr1D 90.494 263 25 0 2516 2778 2211379 2211641 9.370000e-92 348.0
50 TraesCS5B01G025800 chr2D 91.154 260 22 1 2519 2777 112871208 112870949 7.240000e-93 351.0
51 TraesCS5B01G025800 chr2D 90.262 267 24 2 2513 2777 180881758 180881492 9.370000e-92 348.0
52 TraesCS5B01G025800 chr2D 85.629 167 22 2 288 454 67240648 67240484 1.680000e-39 174.0
53 TraesCS5B01G025800 chr2D 83.871 155 19 4 287 437 551460364 551460212 4.740000e-30 143.0
54 TraesCS5B01G025800 chr6D 90.226 266 24 2 2513 2777 426200977 426200713 3.370000e-91 346.0
55 TraesCS5B01G025800 chr4B 79.747 316 49 9 2848 3160 639253909 639253606 9.910000e-52 215.0
56 TraesCS5B01G025800 chr4B 84.940 166 23 1 287 452 506915268 506915105 2.810000e-37 167.0
57 TraesCS5B01G025800 chr4B 84.524 168 24 2 287 454 255386292 255386127 1.010000e-36 165.0
58 TraesCS5B01G025800 chr4B 100.000 31 0 0 447 477 38023488 38023458 1.770000e-04 58.4
59 TraesCS5B01G025800 chr6B 82.700 237 32 9 2887 3118 23285703 23285471 7.720000e-48 202.0
60 TraesCS5B01G025800 chr6A 82.203 236 36 5 2928 3160 614360008 614360240 9.980000e-47 198.0
61 TraesCS5B01G025800 chr6A 92.105 38 3 0 2222 2259 356987635 356987598 2.000000e-03 54.7
62 TraesCS5B01G025800 chr6A 100.000 28 0 0 4299 4326 55899704 55899677 8.000000e-03 52.8
63 TraesCS5B01G025800 chr7A 87.349 166 18 3 287 452 117353533 117353371 2.160000e-43 187.0
64 TraesCS5B01G025800 chr4A 83.146 178 26 3 279 454 313633659 313633834 4.710000e-35 159.0
65 TraesCS5B01G025800 chr4A 76.587 252 53 5 2848 3095 691439786 691439537 2.860000e-27 134.0
66 TraesCS5B01G025800 chr4A 76.349 241 51 5 2848 3084 691455746 691455508 1.720000e-24 124.0
67 TraesCS5B01G025800 chr7D 82.941 170 26 3 285 454 430228601 430228435 2.830000e-32 150.0
68 TraesCS5B01G025800 chr4D 90.164 61 2 4 1355 1415 509114621 509114677 4.880000e-10 76.8
69 TraesCS5B01G025800 chr4D 82.022 89 10 4 482 569 293377813 293377730 2.270000e-08 71.3
70 TraesCS5B01G025800 chr1B 100.000 31 0 0 447 477 168354970 168355000 1.770000e-04 58.4
71 TraesCS5B01G025800 chr1A 100.000 31 0 0 447 477 39635202 39635172 1.770000e-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 TraesCS5B01G025800 chr5B 24373308 24377856 4548 False 8401.000000 8401 100.000000 1 4549 1 chr5B.!!$F2 4548
1 TraesCS5B01G025800 chr5B 24330032 24334916 4884 False 4034.500000 5044 98.699500 1 4549 2 chr5B.!!$F6 4548
2 TraesCS5B01G025800 chr5B 24357247 24360628 3381 False 2701.000000 3003 98.708000 1508 4549 2 chr5B.!!$F7 3041
3 TraesCS5B01G025800 chr5B 24312836 24317657 4821 False 2658.333333 3952 98.678333 1 4549 3 chr5B.!!$F5 4548
4 TraesCS5B01G025800 chr5B 24298657 24300121 1464 False 2558.000000 2558 98.228000 3088 4549 1 chr5B.!!$F1 1461
5 TraesCS5B01G025800 chr5B 6659053 6660902 1849 False 893.333333 2313 94.892667 711 2850 3 chr5B.!!$F4 2139
6 TraesCS5B01G025800 chr5B 30918756 30919280 524 True 845.000000 845 95.636000 4023 4549 1 chr5B.!!$R2 526
7 TraesCS5B01G025800 chr5B 30992889 30993413 524 True 839.000000 839 95.446000 4023 4549 1 chr5B.!!$R3 526
8 TraesCS5B01G025800 chr5B 31113570 31118683 5113 True 578.833333 1219 88.696333 568 4022 6 chr5B.!!$R4 3454
9 TraesCS5B01G025800 chr5D 5116446 5119232 2786 True 1200.333333 1790 89.329333 711 4021 3 chr5D.!!$R3 3310
10 TraesCS5B01G025800 chr5D 5153951 5156627 2676 True 459.500000 464 87.946500 2048 3562 2 chr5D.!!$R4 1514
11 TraesCS5B01G025800 chr5D 5163395 5164813 1418 True 327.633333 649 86.830333 667 1900 3 chr5D.!!$R5 1233
12 TraesCS5B01G025800 chr5A 3698321 3702040 3719 False 493.933333 952 86.884500 165 3812 6 chr5A.!!$F4 3647
13 TraesCS5B01G025800 chr5A 3555173 3559086 3913 False 457.600000 1114 89.665800 586 3559 5 chr5A.!!$F3 2973

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
861 1120 0.684535 TCATCTGGAGGTTGTGCGAA 59.315 50.0 0.0 0.0 0.0 4.7 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
3836 7781 2.972713 GCATCCACTATTGAGGGTCCTA 59.027 50.0 0.0 0.0 0.0 2.94 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
282 289 7.548097 TCAAGTGAAGGTCTAATAGCTACAAG 58.452 38.462 0.00 0.00 33.87 3.16
320 327 3.195825 ACAAGATATATAGGCGCTGACCC 59.804 47.826 7.64 0.00 0.00 4.46
859 1118 1.012086 CATCATCTGGAGGTTGTGCG 58.988 55.000 0.00 0.00 0.00 5.34
860 1119 0.904649 ATCATCTGGAGGTTGTGCGA 59.095 50.000 0.00 0.00 0.00 5.10
861 1120 0.684535 TCATCTGGAGGTTGTGCGAA 59.315 50.000 0.00 0.00 0.00 4.70
862 1121 1.081892 CATCTGGAGGTTGTGCGAAG 58.918 55.000 0.00 0.00 0.00 3.79
902 1161 1.813337 GAAAGGAGGCGAGCTGCTC 60.813 63.158 19.53 19.53 45.43 4.26
2595 4600 8.294954 TGTAAAGTTTGACCAAATTTGTAGGA 57.705 30.769 16.73 0.00 31.87 2.94
2964 5950 1.826720 GTCCATTCAACATGCATGGGT 59.173 47.619 29.41 14.93 40.78 4.51
3681 7293 4.811555 TGATTCCTCTGTTTCAAACACG 57.188 40.909 0.00 0.00 36.25 4.49
4081 8027 7.068103 TGTGAATCCAAACAGAAACTACACATT 59.932 33.333 0.00 0.00 0.00 2.71
4226 8172 2.375174 AGGCCACTGATACAACCTTTCA 59.625 45.455 5.01 0.00 0.00 2.69
4397 8344 7.282585 AGAGGTCTATGTTAATATGCTGCAAA 58.717 34.615 6.36 0.00 0.00 3.68
4518 8465 8.416329 GCACTAATGATTGAAACCCTCATAAAT 58.584 33.333 0.00 0.00 32.78 1.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
282 289 1.670811 CTTGTCTTGGGTGTGTGTGTC 59.329 52.381 0.00 0.0 0.00 3.67
320 327 0.107654 GTTAGGGGTAGTGCTGCTGG 60.108 60.000 0.00 0.0 0.00 4.85
326 333 3.512724 TCTTGTAGTGTTAGGGGTAGTGC 59.487 47.826 0.00 0.0 0.00 4.40
617 626 2.945008 TGTGCATTAGCTCATGGTAAGC 59.055 45.455 9.85 0.0 39.15 3.09
634 643 4.559153 ACTATTTGGAGTTTGCAATGTGC 58.441 39.130 0.00 0.0 45.29 4.57
3836 7781 2.972713 GCATCCACTATTGAGGGTCCTA 59.027 50.000 0.00 0.0 0.00 2.94
4104 8050 8.275632 CGTTTCCCATTTCTTTCTTTTCATTTC 58.724 33.333 0.00 0.0 0.00 2.17
4182 8128 6.663093 CCTATAGAGCCTGAGAGAACATGTAT 59.337 42.308 0.00 0.0 0.00 2.29


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

AutoCloner maintained by Alex Coulton.