Multiple sequence alignment - TraesCS5A01G199000

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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 TraesCS5A01G199000 chr5A 100.000 6083 0 0 1 6083 403872235 403878317 0.000000e+00 11234.0
1 TraesCS5A01G199000 chr3A 98.538 6087 83 4 1 6083 112331774 112325690 0.000000e+00 10743.0
2 TraesCS5A01G199000 chr3A 97.064 2350 50 5 1439 3771 726090769 726088422 0.000000e+00 3940.0
3 TraesCS5A01G199000 chr3A 96.266 2357 50 8 1439 3771 732788619 732790961 0.000000e+00 3831.0
4 TraesCS5A01G199000 chr3A 97.908 1864 37 2 3763 5624 732791358 732793221 0.000000e+00 3225.0
5 TraesCS5A01G199000 chr3A 97.532 1864 43 3 3763 5624 726088059 726086197 0.000000e+00 3184.0
6 TraesCS5A01G199000 chr3A 98.536 1434 18 3 1 1434 726092331 726090901 0.000000e+00 2529.0
7 TraesCS5A01G199000 chr3A 98.188 1435 19 3 1 1434 732787059 732788487 0.000000e+00 2499.0
8 TraesCS5A01G199000 chr3A 93.559 1273 61 12 1439 2703 506234911 506233652 0.000000e+00 1877.0
9 TraesCS5A01G199000 chr3A 97.195 927 26 0 1439 2365 184605960 184605034 0.000000e+00 1568.0
10 TraesCS5A01G199000 chr3A 94.152 684 38 2 2692 3375 506233266 506232585 0.000000e+00 1040.0
11 TraesCS5A01G199000 chr3A 97.835 462 9 1 5623 6083 726086292 726085831 0.000000e+00 797.0
12 TraesCS5A01G199000 chr3A 97.624 463 9 2 5623 6083 732793126 732793588 0.000000e+00 793.0
13 TraesCS5A01G199000 chr3A 98.958 96 1 0 5623 5718 112326244 112326149 8.110000e-39 172.0
14 TraesCS5A01G199000 chr3A 84.615 65 9 1 3835 3898 496705730 496705666 5.090000e-06 63.9
15 TraesCS5A01G199000 chr7A 97.315 2719 66 6 1 2718 297443664 297440952 0.000000e+00 4610.0
16 TraesCS5A01G199000 chr7A 96.618 1863 34 11 3763 5624 297439564 297437730 0.000000e+00 3064.0
17 TraesCS5A01G199000 chr7A 95.445 988 39 4 2788 3771 297440946 297439961 0.000000e+00 1570.0
18 TraesCS5A01G199000 chr7A 97.835 462 8 2 5623 6083 297437825 297437365 0.000000e+00 797.0
19 TraesCS5A01G199000 chr7A 86.986 292 34 4 2697 2985 283296434 283296144 5.880000e-85 326.0
20 TraesCS5A01G199000 chr7A 93.714 175 9 1 3599 3771 283295141 283294967 1.680000e-65 261.0
21 TraesCS5A01G199000 chr6A 94.799 1942 93 7 1439 3375 521441942 521440004 0.000000e+00 3020.0
22 TraesCS5A01G199000 chr6A 90.335 507 48 1 4176 4681 295824076 295823570 0.000000e+00 664.0
23 TraesCS5A01G199000 chr6A 87.356 261 32 1 4877 5137 295818482 295818223 1.280000e-76 298.0
24 TraesCS5A01G199000 chr1B 97.838 1434 30 1 1 1434 30444946 30446378 0.000000e+00 2475.0
25 TraesCS5A01G199000 chr1B 97.352 1435 31 3 1 1434 12321029 12319601 0.000000e+00 2433.0
26 TraesCS5A01G199000 chr1B 97.195 927 26 0 1439 2365 30446508 30447434 0.000000e+00 1568.0
27 TraesCS5A01G199000 chr1B 93.863 717 40 3 3058 3771 12310640 12309925 0.000000e+00 1077.0
28 TraesCS5A01G199000 chr1B 94.504 564 25 2 3763 4320 12309533 12308970 0.000000e+00 865.0
29 TraesCS5A01G199000 chr1B 90.018 571 33 9 2462 3020 12311198 12310640 0.000000e+00 717.0
30 TraesCS5A01G199000 chr2B 97.071 1434 41 1 1 1434 258775094 258776526 0.000000e+00 2414.0
31 TraesCS5A01G199000 chr2B 97.195 927 26 0 1439 2365 258776656 258777582 0.000000e+00 1568.0
32 TraesCS5A01G199000 chr2B 92.820 571 38 1 5050 5620 232921526 232922093 0.000000e+00 824.0
33 TraesCS5A01G199000 chr2B 92.077 467 36 1 5617 6082 232921996 232922462 0.000000e+00 656.0
34 TraesCS5A01G199000 chr2B 91.702 470 33 5 5617 6082 791411047 791411514 0.000000e+00 647.0
35 TraesCS5A01G199000 chr2B 89.547 287 27 1 5336 5622 791410863 791411146 1.610000e-95 361.0
36 TraesCS5A01G199000 chr2B 97.619 210 4 1 5050 5258 791410663 791410872 5.800000e-95 359.0
37 TraesCS5A01G199000 chr2B 87.730 163 18 2 3962 4122 601334877 601335039 8.050000e-44 189.0
38 TraesCS5A01G199000 chr6B 96.936 1436 37 4 1 1435 33894591 33896020 0.000000e+00 2401.0
39 TraesCS5A01G199000 chr6B 96.932 1434 38 3 1 1434 33877442 33878869 0.000000e+00 2399.0
40 TraesCS5A01G199000 chr6B 89.803 304 31 0 5307 5610 76774786 76774483 2.060000e-104 390.0
41 TraesCS5A01G199000 chr6B 93.464 153 7 2 3975 4124 340155547 340155699 2.210000e-54 224.0
42 TraesCS5A01G199000 chr6B 87.898 157 17 2 3968 4122 157476257 157476101 3.740000e-42 183.0
43 TraesCS5A01G199000 chr6B 87.898 157 17 2 3968 4122 157477106 157476950 3.740000e-42 183.0
44 TraesCS5A01G199000 chr1A 97.303 927 25 0 1439 2365 487558559 487559485 0.000000e+00 1574.0
45 TraesCS5A01G199000 chr1A 95.946 74 3 0 2584 2657 371922537 371922610 2.980000e-23 121.0
46 TraesCS5A01G199000 chr7B 90.391 1124 59 9 4519 5624 330980065 330978973 0.000000e+00 1432.0
47 TraesCS5A01G199000 chr7B 89.263 801 47 14 3763 4529 330980976 330980181 0.000000e+00 966.0
48 TraesCS5A01G199000 chr7B 85.958 527 55 12 4247 4769 711745164 711745675 4.150000e-151 545.0
49 TraesCS5A01G199000 chr7B 93.069 303 19 2 5623 5925 330979068 330978768 5.600000e-120 442.0
50 TraesCS5A01G199000 chr7D 89.171 748 44 11 3053 3771 592881765 592881026 0.000000e+00 898.0
51 TraesCS5A01G199000 chr7D 89.354 526 45 8 4247 4769 617523119 617523636 0.000000e+00 651.0
52 TraesCS5A01G199000 chr7D 87.089 395 38 10 2660 3047 592882348 592881960 9.360000e-118 435.0
53 TraesCS5A01G199000 chr7D 98.485 66 1 0 3771 3836 32508926 32508991 3.850000e-22 117.0
54 TraesCS5A01G199000 chr7D 98.485 66 1 0 3771 3836 168796359 168796294 3.850000e-22 117.0
55 TraesCS5A01G199000 chr7D 93.333 45 3 0 2998 3042 592882131 592882087 3.930000e-07 67.6
56 TraesCS5A01G199000 chr4A 88.980 735 65 7 3053 3771 645673967 645674701 0.000000e+00 894.0
57 TraesCS5A01G199000 chr4A 89.167 720 71 6 3059 3771 689340491 689339772 0.000000e+00 891.0
58 TraesCS5A01G199000 chr4A 91.621 549 45 1 5075 5623 49236296 49235749 0.000000e+00 758.0
59 TraesCS5A01G199000 chr4A 91.247 457 37 2 5626 6082 49235840 49235387 2.410000e-173 619.0
60 TraesCS5A01G199000 chr4A 86.316 380 38 9 2678 3047 645673401 645673776 9.500000e-108 401.0
61 TraesCS5A01G199000 chr4A 87.500 256 25 7 5829 6080 656931863 656931611 7.710000e-74 289.0
62 TraesCS5A01G199000 chr4A 93.827 81 3 2 2585 2665 219338485 219338407 2.980000e-23 121.0
63 TraesCS5A01G199000 chr6D 88.963 598 58 7 4176 4769 212315274 212315867 0.000000e+00 732.0
64 TraesCS5A01G199000 chr6D 87.759 482 44 6 4877 5348 212316205 212316681 3.210000e-152 549.0
65 TraesCS5A01G199000 chr6D 86.337 344 35 6 5743 6082 212316986 212317321 1.250000e-96 364.0
66 TraesCS5A01G199000 chr6D 79.508 122 22 3 2471 2590 254550684 254550804 3.910000e-12 84.2
67 TraesCS5A01G199000 chrUn 86.973 261 33 1 4877 5137 321894292 321894033 5.960000e-75 292.0
68 TraesCS5A01G199000 chrUn 94.792 96 3 2 4675 4769 321894725 321894631 1.370000e-31 148.0
69 TraesCS5A01G199000 chr4D 98.485 66 1 0 3771 3836 462821457 462821522 3.850000e-22 117.0
70 TraesCS5A01G199000 chr3B 91.111 45 4 0 3854 3898 487909511 487909467 1.830000e-05 62.1
71 TraesCS5A01G199000 chr3D 92.500 40 3 0 3854 3893 374209276 374209237 2.370000e-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 TraesCS5A01G199000 chr5A 403872235 403878317 6082 False 11234.000000 11234 100.000000 1 6083 1 chr5A.!!$F1 6082
1 TraesCS5A01G199000 chr3A 112325690 112331774 6084 True 10743.000000 10743 98.538000 1 6083 1 chr3A.!!$R1 6082
2 TraesCS5A01G199000 chr3A 726085831 726092331 6500 True 2612.500000 3940 97.741750 1 6083 4 chr3A.!!$R6 6082
3 TraesCS5A01G199000 chr3A 732787059 732793588 6529 False 2587.000000 3831 97.496500 1 6083 4 chr3A.!!$F1 6082
4 TraesCS5A01G199000 chr3A 184605034 184605960 926 True 1568.000000 1568 97.195000 1439 2365 1 chr3A.!!$R3 926
5 TraesCS5A01G199000 chr3A 506232585 506234911 2326 True 1458.500000 1877 93.855500 1439 3375 2 chr3A.!!$R5 1936
6 TraesCS5A01G199000 chr7A 297437365 297443664 6299 True 2510.250000 4610 96.803250 1 6083 4 chr7A.!!$R2 6082
7 TraesCS5A01G199000 chr7A 283294967 283296434 1467 True 293.500000 326 90.350000 2697 3771 2 chr7A.!!$R1 1074
8 TraesCS5A01G199000 chr6A 521440004 521441942 1938 True 3020.000000 3020 94.799000 1439 3375 1 chr6A.!!$R3 1936
9 TraesCS5A01G199000 chr6A 295823570 295824076 506 True 664.000000 664 90.335000 4176 4681 1 chr6A.!!$R2 505
10 TraesCS5A01G199000 chr1B 12319601 12321029 1428 True 2433.000000 2433 97.352000 1 1434 1 chr1B.!!$R1 1433
11 TraesCS5A01G199000 chr1B 30444946 30447434 2488 False 2021.500000 2475 97.516500 1 2365 2 chr1B.!!$F1 2364
12 TraesCS5A01G199000 chr1B 12308970 12311198 2228 True 886.333333 1077 92.795000 2462 4320 3 chr1B.!!$R2 1858
13 TraesCS5A01G199000 chr2B 258775094 258777582 2488 False 1991.000000 2414 97.133000 1 2365 2 chr2B.!!$F3 2364
14 TraesCS5A01G199000 chr2B 232921526 232922462 936 False 740.000000 824 92.448500 5050 6082 2 chr2B.!!$F2 1032
15 TraesCS5A01G199000 chr2B 791410663 791411514 851 False 455.666667 647 92.956000 5050 6082 3 chr2B.!!$F4 1032
16 TraesCS5A01G199000 chr6B 33894591 33896020 1429 False 2401.000000 2401 96.936000 1 1435 1 chr6B.!!$F2 1434
17 TraesCS5A01G199000 chr6B 33877442 33878869 1427 False 2399.000000 2399 96.932000 1 1434 1 chr6B.!!$F1 1433
18 TraesCS5A01G199000 chr1A 487558559 487559485 926 False 1574.000000 1574 97.303000 1439 2365 1 chr1A.!!$F2 926
19 TraesCS5A01G199000 chr7B 330978768 330980976 2208 True 946.666667 1432 90.907667 3763 5925 3 chr7B.!!$R1 2162
20 TraesCS5A01G199000 chr7B 711745164 711745675 511 False 545.000000 545 85.958000 4247 4769 1 chr7B.!!$F1 522
21 TraesCS5A01G199000 chr7D 617523119 617523636 517 False 651.000000 651 89.354000 4247 4769 1 chr7D.!!$F2 522
22 TraesCS5A01G199000 chr7D 592881026 592882348 1322 True 466.866667 898 89.864333 2660 3771 3 chr7D.!!$R2 1111
23 TraesCS5A01G199000 chr4A 689339772 689340491 719 True 891.000000 891 89.167000 3059 3771 1 chr4A.!!$R3 712
24 TraesCS5A01G199000 chr4A 49235387 49236296 909 True 688.500000 758 91.434000 5075 6082 2 chr4A.!!$R4 1007
25 TraesCS5A01G199000 chr4A 645673401 645674701 1300 False 647.500000 894 87.648000 2678 3771 2 chr4A.!!$F1 1093
26 TraesCS5A01G199000 chr6D 212315274 212317321 2047 False 548.333333 732 87.686333 4176 6082 3 chr6D.!!$F2 1906
27 TraesCS5A01G199000 chrUn 321894033 321894725 692 True 220.000000 292 90.882500 4675 5137 2 chrUn.!!$R1 462

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
556 559 4.919774 TTGCTTGGATTAAGTGGGAGTA 57.080 40.909 0.00 0.0 38.70 2.59 F
1246 1250 1.352156 GATGGTCGTCGTTGGACAGC 61.352 60.000 0.00 0.0 43.61 4.40 F
2253 2386 1.063616 CAACTGAAGATGAGGCATGCG 59.936 52.381 12.44 0.0 0.00 4.73 F
3544 4617 0.953727 GATGTGAGTTGTTGCTGCCA 59.046 50.000 0.00 0.0 0.00 4.92 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1523 1653 0.958822 GTTGTTCGGGGTGCTCAAAT 59.041 50.000 0.00 0.0 0.00 2.32 R
2489 2622 1.136329 AGGAGTGGAACAGCACCCAT 61.136 55.000 0.00 0.0 41.80 4.00 R
3861 5366 4.381825 GGGCACATGCATGATTTTTCACTA 60.382 41.667 32.75 0.0 44.36 2.74 R
5409 7349 1.585297 TCATACATGCGTGCCATCTG 58.415 50.000 5.64 0.0 29.71 2.90 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
556 559 4.919774 TTGCTTGGATTAAGTGGGAGTA 57.080 40.909 0.00 0.00 38.70 2.59
1246 1250 1.352156 GATGGTCGTCGTTGGACAGC 61.352 60.000 0.00 0.00 43.61 4.40
1523 1653 3.192541 TGCAGTTGACAAGCTTACAGA 57.807 42.857 0.00 0.00 0.00 3.41
1660 1793 1.202592 ACAATGACGTGGTACTGCACA 60.203 47.619 0.00 0.00 0.00 4.57
1815 1948 9.363763 CTGATTATGCTTTGATGTATAGATCGT 57.636 33.333 5.48 0.00 0.00 3.73
1979 2112 9.208022 TGATATTGCAAAATAGATTAGACGGAG 57.792 33.333 1.71 0.00 0.00 4.63
2145 2278 9.162764 TGTATGCTTCTCCTTTTATCAACTTAC 57.837 33.333 0.00 0.00 0.00 2.34
2253 2386 1.063616 CAACTGAAGATGAGGCATGCG 59.936 52.381 12.44 0.00 0.00 4.73
2497 2630 3.391665 GACGCTGCCTATGGGTGCT 62.392 63.158 11.84 1.96 34.12 4.40
2783 3366 5.985175 TGATCAGGTGGGACCAAATTATA 57.015 39.130 0.00 0.00 41.95 0.98
3348 4405 6.015772 GCTGAACAAGGTAGGTTTGGAAATTA 60.016 38.462 0.00 0.00 0.00 1.40
3544 4617 0.953727 GATGTGAGTTGTTGCTGCCA 59.046 50.000 0.00 0.00 0.00 4.92
3597 4670 2.125147 ACACTGTGTGCACGTGCT 60.125 55.556 37.59 16.84 42.66 4.40
3861 5366 3.864789 TGCTGACCTTCTCCTTCTTTT 57.135 42.857 0.00 0.00 0.00 2.27
3989 5495 9.585099 TCATGACCATAAAATTTTAATGCAGTC 57.415 29.630 14.35 14.91 0.00 3.51
4163 5671 3.808174 GGGAAATGTATACTTCGGCAGAC 59.192 47.826 4.17 0.00 0.00 3.51
4935 6815 6.543100 ACACCCGTTTGAGTGAAAAGTAATAA 59.457 34.615 0.00 0.00 37.43 1.40
5409 7349 6.014755 TCTCTCAATCCATGTACCAGATCATC 60.015 42.308 0.00 0.00 0.00 2.92
5638 7578 3.691575 TGTTTGAAGTTCTTGTGGTCCA 58.308 40.909 4.17 0.00 0.00 4.02
5989 7940 4.455606 AGAAGTGAACTTTGAGAACCCTG 58.544 43.478 0.00 0.00 36.11 4.45
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
609 612 1.532437 CAAACACTCGCAGCAATCTCA 59.468 47.619 0.00 0.00 0.00 3.27
1285 1289 9.394767 TGCAAGAGATGTGTAATATACATGTTT 57.605 29.630 2.30 0.00 41.34 2.83
1523 1653 0.958822 GTTGTTCGGGGTGCTCAAAT 59.041 50.000 0.00 0.00 0.00 2.32
1979 2112 4.136796 TCCATGGCAATGCTATGTACTTC 58.863 43.478 25.86 0.00 44.21 3.01
2145 2278 8.950210 AGCATGTCCCATTAATATAATTTCTCG 58.050 33.333 0.00 0.00 0.00 4.04
2484 2617 1.302949 GGAACAGCACCCATAGGCA 59.697 57.895 0.00 0.00 36.11 4.75
2489 2622 1.136329 AGGAGTGGAACAGCACCCAT 61.136 55.000 0.00 0.00 41.80 4.00
2783 3366 7.560991 AGAGATTCATGAGAGATCTACACAGTT 59.439 37.037 8.12 0.00 0.00 3.16
2835 3674 8.245701 AGAAATTTCAGTCGTGAGAGAAATAC 57.754 34.615 19.99 7.38 41.36 1.89
3851 5356 8.084073 TGCATGATTTTTCACTAAAAGAAGGAG 58.916 33.333 0.00 0.00 39.00 3.69
3861 5366 4.381825 GGGCACATGCATGATTTTTCACTA 60.382 41.667 32.75 0.00 44.36 2.74
4785 6545 4.866508 TTTCCTCGAGAAAGACTTGCTA 57.133 40.909 15.71 0.00 39.60 3.49
4935 6815 7.403231 TCAAAAAGTGATACTCCCTCTTATCCT 59.597 37.037 0.00 0.00 0.00 3.24
5409 7349 1.585297 TCATACATGCGTGCCATCTG 58.415 50.000 5.64 0.00 29.71 2.90
5638 7578 7.725844 ACTGTTTTTATTGATCCTTCCAACTCT 59.274 33.333 0.00 0.00 0.00 3.24
5989 7940 5.689068 GGAATTTTCATTGATCGGAATGAGC 59.311 40.000 8.11 0.00 42.04 4.26


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

AutoCloner maintained by Alex Coulton.