Multiple sequence alignment - TraesCS5A01G351500

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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 TraesCS5A01G351500 chr5A 100.000 3289 0 0 1 3289 554183623 554180335 0.000000e+00 6074
1 TraesCS5A01G351500 chr5A 82.771 1689 217 50 817 2458 554236183 554234522 0.000000e+00 1439
2 TraesCS5A01G351500 chr5A 81.746 1627 238 42 806 2385 554201341 554199727 0.000000e+00 1304
3 TraesCS5A01G351500 chr5A 83.905 1224 160 24 815 2011 554218709 554217496 0.000000e+00 1134
4 TraesCS5A01G351500 chr5A 80.685 409 72 4 16 419 554236986 554236580 8.860000e-81 311
5 TraesCS5A01G351500 chr5D 94.784 2914 110 19 415 3289 438569904 438566994 0.000000e+00 4501
6 TraesCS5A01G351500 chr5D 83.411 1724 232 36 817 2504 438722385 438720680 0.000000e+00 1550
7 TraesCS5A01G351500 chr5D 82.002 1628 226 40 806 2385 438589668 438588060 0.000000e+00 1321
8 TraesCS5A01G351500 chr5D 80.542 1475 235 41 840 2288 438455199 438453751 0.000000e+00 1086
9 TraesCS5A01G351500 chr5D 82.887 970 121 22 817 1761 438658500 438657551 0.000000e+00 830
10 TraesCS5A01G351500 chr5D 95.704 419 18 0 1 419 438570360 438569942 0.000000e+00 675
11 TraesCS5A01G351500 chr5D 83.629 733 96 19 1762 2482 438624306 438623586 0.000000e+00 667
12 TraesCS5A01G351500 chr5D 79.564 597 87 12 2493 3065 542293467 542294052 8.550000e-106 394
13 TraesCS5A01G351500 chr5D 79.724 434 68 10 1 419 438659322 438658894 2.480000e-76 296
14 TraesCS5A01G351500 chr5D 79.426 418 68 8 16 419 438723196 438722783 2.500000e-71 279
15 TraesCS5A01G351500 chr5B 93.056 1685 106 8 811 2490 533451392 533449714 0.000000e+00 2453
16 TraesCS5A01G351500 chr5B 83.363 1671 199 51 817 2440 533573078 533571440 0.000000e+00 1472
17 TraesCS5A01G351500 chr5B 83.181 1641 217 39 816 2408 533515388 533513759 0.000000e+00 1447
18 TraesCS5A01G351500 chr5B 81.561 1627 232 43 806 2385 533494258 533492653 0.000000e+00 1280
19 TraesCS5A01G351500 chr5B 82.489 1422 190 42 1053 2443 533565266 533563873 0.000000e+00 1192
20 TraesCS5A01G351500 chr5B 92.822 404 29 0 16 419 533472989 533472586 1.310000e-163 586
21 TraesCS5A01G351500 chr5B 87.069 348 36 5 440 782 533459232 533458889 5.150000e-103 385
22 TraesCS5A01G351500 chr5B 80.896 424 73 5 1 419 533573894 533573474 8.800000e-86 327
23 TraesCS5A01G351500 chr5B 80.825 412 53 7 2678 3065 691198167 691197758 1.920000e-77 300
24 TraesCS5A01G351500 chr5B 80.997 321 46 11 15 324 533523844 533523528 1.180000e-59 241
25 TraesCS5A01G351500 chr5B 87.805 123 8 3 3068 3183 533449722 533449600 1.590000e-28 137
26 TraesCS5A01G351500 chr1B 85.110 591 65 7 2494 3065 236998330 236997744 1.700000e-162 582
27 TraesCS5A01G351500 chr3B 84.370 595 63 7 2499 3065 741433273 741433865 1.030000e-154 556
28 TraesCS5A01G351500 chr3B 82.266 406 48 6 2683 3065 95571158 95570754 2.450000e-86 329
29 TraesCS5A01G351500 chr3B 82.323 396 47 5 2683 3056 220790928 220791322 4.090000e-84 322
30 TraesCS5A01G351500 chr2B 85.179 560 53 6 2528 3065 180054482 180053931 6.200000e-152 547
31 TraesCS5A01G351500 chr2D 83.418 591 61 7 2493 3061 126146117 126145542 6.290000e-142 514
32 TraesCS5A01G351500 chr2D 82.245 597 74 13 2494 3065 27583468 27582879 1.370000e-133 486
33 TraesCS5A01G351500 chr2D 80.000 405 56 4 2684 3065 44919799 44919397 3.230000e-70 276
34 TraesCS5A01G351500 chr4D 83.082 597 68 7 2493 3065 315085148 315084561 2.260000e-141 512
35 TraesCS5A01G351500 chr7A 83.390 584 60 13 2495 3056 477022187 477022755 1.050000e-139 507
36 TraesCS5A01G351500 chr3D 82.741 591 70 7 2494 3062 45032245 45031665 6.340000e-137 497
37 TraesCS5A01G351500 chr1A 83.734 541 61 7 2495 3016 171465828 171465296 1.370000e-133 486
38 TraesCS5A01G351500 chr1A 89.296 355 38 0 2488 2842 412463178 412463532 2.330000e-121 446
39 TraesCS5A01G351500 chr3A 80.431 603 78 9 2493 3065 487361045 487360453 1.090000e-114 424


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 TraesCS5A01G351500 chr5A 554180335 554183623 3288 True 6074.0 6074 100.0000 1 3289 1 chr5A.!!$R1 3288
1 TraesCS5A01G351500 chr5A 554199727 554201341 1614 True 1304.0 1304 81.7460 806 2385 1 chr5A.!!$R2 1579
2 TraesCS5A01G351500 chr5A 554217496 554218709 1213 True 1134.0 1134 83.9050 815 2011 1 chr5A.!!$R3 1196
3 TraesCS5A01G351500 chr5A 554234522 554236986 2464 True 875.0 1439 81.7280 16 2458 2 chr5A.!!$R4 2442
4 TraesCS5A01G351500 chr5D 438566994 438570360 3366 True 2588.0 4501 95.2440 1 3289 2 chr5D.!!$R4 3288
5 TraesCS5A01G351500 chr5D 438588060 438589668 1608 True 1321.0 1321 82.0020 806 2385 1 chr5D.!!$R2 1579
6 TraesCS5A01G351500 chr5D 438453751 438455199 1448 True 1086.0 1086 80.5420 840 2288 1 chr5D.!!$R1 1448
7 TraesCS5A01G351500 chr5D 438720680 438723196 2516 True 914.5 1550 81.4185 16 2504 2 chr5D.!!$R6 2488
8 TraesCS5A01G351500 chr5D 438623586 438624306 720 True 667.0 667 83.6290 1762 2482 1 chr5D.!!$R3 720
9 TraesCS5A01G351500 chr5D 438657551 438659322 1771 True 563.0 830 81.3055 1 1761 2 chr5D.!!$R5 1760
10 TraesCS5A01G351500 chr5D 542293467 542294052 585 False 394.0 394 79.5640 2493 3065 1 chr5D.!!$F1 572
11 TraesCS5A01G351500 chr5B 533513759 533515388 1629 True 1447.0 1447 83.1810 816 2408 1 chr5B.!!$R4 1592
12 TraesCS5A01G351500 chr5B 533449600 533451392 1792 True 1295.0 2453 90.4305 811 3183 2 chr5B.!!$R8 2372
13 TraesCS5A01G351500 chr5B 533492653 533494258 1605 True 1280.0 1280 81.5610 806 2385 1 chr5B.!!$R3 1579
14 TraesCS5A01G351500 chr5B 533563873 533565266 1393 True 1192.0 1192 82.4890 1053 2443 1 chr5B.!!$R6 1390
15 TraesCS5A01G351500 chr5B 533571440 533573894 2454 True 899.5 1472 82.1295 1 2440 2 chr5B.!!$R9 2439
16 TraesCS5A01G351500 chr1B 236997744 236998330 586 True 582.0 582 85.1100 2494 3065 1 chr1B.!!$R1 571
17 TraesCS5A01G351500 chr3B 741433273 741433865 592 False 556.0 556 84.3700 2499 3065 1 chr3B.!!$F2 566
18 TraesCS5A01G351500 chr2B 180053931 180054482 551 True 547.0 547 85.1790 2528 3065 1 chr2B.!!$R1 537
19 TraesCS5A01G351500 chr2D 126145542 126146117 575 True 514.0 514 83.4180 2493 3061 1 chr2D.!!$R3 568
20 TraesCS5A01G351500 chr2D 27582879 27583468 589 True 486.0 486 82.2450 2494 3065 1 chr2D.!!$R1 571
21 TraesCS5A01G351500 chr4D 315084561 315085148 587 True 512.0 512 83.0820 2493 3065 1 chr4D.!!$R1 572
22 TraesCS5A01G351500 chr7A 477022187 477022755 568 False 507.0 507 83.3900 2495 3056 1 chr7A.!!$F1 561
23 TraesCS5A01G351500 chr3D 45031665 45032245 580 True 497.0 497 82.7410 2494 3062 1 chr3D.!!$R1 568
24 TraesCS5A01G351500 chr1A 171465296 171465828 532 True 486.0 486 83.7340 2495 3016 1 chr1A.!!$R1 521
25 TraesCS5A01G351500 chr3A 487360453 487361045 592 True 424.0 424 80.4310 2493 3065 1 chr3A.!!$R1 572

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
644 703 0.178767 TCTTGTCACACAGCTGCTGT 59.821 50.000 28.49 28.49 46.51 4.40 F
1514 1634 2.693591 TCACGAAGACTCAAGGTTCACT 59.306 45.455 0.00 0.00 0.00 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1591 1711 0.179073 ATCACCAAAGATCCTCGCCG 60.179 55.000 0.0 0.0 0.0 6.46 R
3049 3293 1.072331 TCAAGGTCTCTTCAGTTGGGC 59.928 52.381 0.0 0.0 0.0 5.36 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
19 20 2.730550 ACCATTGCTTTGTTGCTAGC 57.269 45.000 8.10 8.10 37.89 3.42
115 121 8.584157 TGATGTTAAAATTCAATGGCTGTTAGT 58.416 29.630 0.00 0.00 0.00 2.24
131 137 6.595716 GGCTGTTAGTGATGACTTAGAACAAT 59.404 38.462 0.00 0.00 31.04 2.71
222 237 4.367386 AGAATAAAGAGCAATGCAGTGC 57.633 40.909 30.52 30.52 45.28 4.40
316 331 9.884814 ATTCAGAGGTATGTTTAGTATACTCCT 57.115 33.333 9.12 7.70 32.81 3.69
355 370 3.482156 TTGCCCAGATTATGAGAGAGC 57.518 47.619 0.00 0.00 0.00 4.09
528 586 9.241919 TCCACATGTTAGATAAATCACATTGTT 57.758 29.630 0.00 0.00 0.00 2.83
595 654 9.136323 CCTTTTCTAATAAAGGGTGATATTGCT 57.864 33.333 7.16 0.00 46.81 3.91
641 700 1.233019 ACATCTTGTCACACAGCTGC 58.767 50.000 15.27 0.00 0.00 5.25
644 703 0.178767 TCTTGTCACACAGCTGCTGT 59.821 50.000 28.49 28.49 46.51 4.40
838 926 9.457436 GGGAAGTGACTTTTAACATTATAGGAA 57.543 33.333 0.00 0.00 0.00 3.36
926 1014 4.515191 CGAATGTGAAGAAGAAAACCCTCA 59.485 41.667 0.00 0.00 0.00 3.86
949 1037 6.829811 TCACTATGATCAAGCATTTCCATTCA 59.170 34.615 0.00 0.00 0.00 2.57
1349 1455 9.408648 AGATTCTACCCTTTTTGGTACATATTG 57.591 33.333 0.00 0.00 39.30 1.90
1479 1599 5.530915 CGTATAATCAAAGGGATTGCAAGGA 59.469 40.000 4.94 0.00 45.70 3.36
1514 1634 2.693591 TCACGAAGACTCAAGGTTCACT 59.306 45.455 0.00 0.00 0.00 3.41
1553 1673 4.768583 TGAAAGCTGGAAATGTTTTGCTT 58.231 34.783 0.00 0.00 41.67 3.91
1555 1675 3.116079 AGCTGGAAATGTTTTGCTTGG 57.884 42.857 0.00 0.00 0.00 3.61
1591 1711 5.193679 ACCCAAGATAGCTGATTTTGGTAC 58.806 41.667 16.86 0.00 44.77 3.34
1616 1750 4.816385 GCGAGGATCTTTGGTGATAATGAA 59.184 41.667 0.00 0.00 0.00 2.57
1740 1895 2.767644 TAGTGGCTACATGGCTCCTA 57.232 50.000 2.02 0.00 42.34 2.94
1921 2085 4.219288 ACTTTCATTTCCAGAAGTGCATCC 59.781 41.667 0.00 0.00 0.00 3.51
2025 2199 3.252554 AGGAAGACAAGACTGAGGAGT 57.747 47.619 0.00 0.00 33.98 3.85
2334 2521 2.996621 CGAACTGCTCTCGAAGGAAAAT 59.003 45.455 0.00 0.00 38.61 1.82
2614 2828 2.289631 CCAAGGCATGATACATAGGCGA 60.290 50.000 0.00 0.00 0.00 5.54
2869 3105 5.988561 GTCCGAAGATAGAGCAGATTTTCAT 59.011 40.000 0.00 0.00 0.00 2.57
3049 3293 2.291043 ACCCAAGACCCGCCACTAG 61.291 63.158 0.00 0.00 0.00 2.57
3067 3311 1.439543 AGCCCAACTGAAGAGACCTT 58.560 50.000 0.00 0.00 34.81 3.50
3070 3314 2.290577 GCCCAACTGAAGAGACCTTGAT 60.291 50.000 0.00 0.00 31.62 2.57
3158 3408 5.531287 ACACTTCAATGAAGGTGACCTTTAC 59.469 40.000 24.77 7.23 44.82 2.01
3222 3472 8.451908 AAATACTTCCTGTGTCCAATATAAGC 57.548 34.615 0.00 0.00 0.00 3.09
3235 3485 4.211164 CCAATATAAGCGTTGCTGATTCGA 59.789 41.667 0.00 0.00 39.62 3.71
3238 3488 4.974103 ATAAGCGTTGCTGATTCGATAC 57.026 40.909 0.00 0.00 39.62 2.24
3241 3491 2.348666 AGCGTTGCTGATTCGATACAAC 59.651 45.455 0.00 0.00 37.57 3.32
3260 3510 6.323203 ACAACTTTAGTACTAAGTCAGCGA 57.677 37.500 14.73 0.00 0.00 4.93
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
13 14 4.141937 ACCGAGAAATGACTATTGCTAGCA 60.142 41.667 14.93 14.93 32.05 3.49
19 20 6.516718 AGTATGGACCGAGAAATGACTATTG 58.483 40.000 0.00 0.00 0.00 1.90
187 202 7.039784 TGCTCTTTATTCTTTTACCTGTGCAAT 60.040 33.333 0.00 0.00 0.00 3.56
222 237 2.083167 AAAATTGGCAGCACAATCCG 57.917 45.000 8.92 0.00 40.01 4.18
338 353 4.620589 ATGTGCTCTCTCATAATCTGGG 57.379 45.455 0.00 0.00 0.00 4.45
355 370 1.211709 GTTCGGCCGGGAAAATGTG 59.788 57.895 27.83 0.00 0.00 3.21
427 485 3.710209 AGCTGAACCATGCTCTAAACT 57.290 42.857 0.00 0.00 33.90 2.66
528 586 2.418368 ATATGGAAAGCGGCAAGACA 57.582 45.000 1.45 0.00 0.00 3.41
591 650 9.145865 CTTGTTTTTAACCTCTTTAACAAGCAA 57.854 29.630 11.19 0.00 42.79 3.91
641 700 2.614779 CAGACACAGCCATAGTGACAG 58.385 52.381 0.00 0.00 40.16 3.51
644 703 1.644509 ACCAGACACAGCCATAGTGA 58.355 50.000 0.00 0.00 40.16 3.41
834 922 6.156083 TCCAATTTTTGTTCTTTCCTGTTCCT 59.844 34.615 0.00 0.00 0.00 3.36
838 926 6.790232 TCTCCAATTTTTGTTCTTTCCTGT 57.210 33.333 0.00 0.00 0.00 4.00
881 969 3.193691 GTCAGAGATACCCATACCATCCG 59.806 52.174 0.00 0.00 0.00 4.18
926 1014 7.834881 ATGAATGGAAATGCTTGATCATAGT 57.165 32.000 0.00 0.00 0.00 2.12
949 1037 7.669722 TGTGAGGGCAATTTCTTCTAGTTTTAT 59.330 33.333 0.00 0.00 0.00 1.40
1128 1234 5.036916 TCTTGACCACCTAACATTCCCTAT 58.963 41.667 0.00 0.00 0.00 2.57
1397 1505 7.715265 TGACTCATCTAACAGAAGAAACAAC 57.285 36.000 0.00 0.00 0.00 3.32
1409 1529 8.316640 ACATCAGTTTTCTTGACTCATCTAAC 57.683 34.615 0.00 0.00 0.00 2.34
1553 1673 3.198635 TCTTGGGTTTCAAATTTGCACCA 59.801 39.130 27.50 21.41 34.61 4.17
1555 1675 5.120674 GCTATCTTGGGTTTCAAATTTGCAC 59.879 40.000 13.54 11.70 34.56 4.57
1591 1711 0.179073 ATCACCAAAGATCCTCGCCG 60.179 55.000 0.00 0.00 0.00 6.46
1616 1750 3.006323 TGCGTTGGGTATTTGCATTTTCT 59.994 39.130 0.00 0.00 0.00 2.52
1740 1895 4.851639 AGACTCCTTCCATTGCATACTT 57.148 40.909 0.00 0.00 0.00 2.24
1921 2085 7.532571 TGTGTCAAAAGATGCTTCAGATATTG 58.467 34.615 2.07 0.73 0.00 1.90
1959 2133 9.784531 AAATAACCAAGAACATCGATCATATCT 57.215 29.630 0.00 0.00 0.00 1.98
2025 2199 3.969312 TCTATGATGGATGAGTCAGGCAA 59.031 43.478 0.00 0.00 0.00 4.52
2417 2617 4.870426 CGACTACTAGGCAACACATGAAAT 59.130 41.667 0.00 0.00 41.41 2.17
2614 2828 2.029649 GGAATTGTGTTGCTGTGCTCAT 60.030 45.455 0.00 0.00 0.00 2.90
2731 2945 2.094390 CGGTGTCGTATCCTTCCTGAAA 60.094 50.000 0.00 0.00 0.00 2.69
2869 3105 2.836154 GGTGACTGTTGGCCAGGA 59.164 61.111 5.11 0.00 46.06 3.86
3049 3293 1.072331 TCAAGGTCTCTTCAGTTGGGC 59.928 52.381 0.00 0.00 0.00 5.36
3158 3408 6.122277 ACCACCTAATCACTTGTATCCAATG 58.878 40.000 0.00 0.00 0.00 2.82
3204 3454 4.188462 CAACGCTTATATTGGACACAGGA 58.812 43.478 0.00 0.00 0.00 3.86
3222 3472 4.584029 AAGTTGTATCGAATCAGCAACG 57.416 40.909 0.00 0.00 42.72 4.10
3235 3485 7.967303 GTCGCTGACTTAGTACTAAAGTTGTAT 59.033 37.037 15.95 0.00 0.00 2.29
3238 3488 6.087820 GTGTCGCTGACTTAGTACTAAAGTTG 59.912 42.308 15.95 7.32 33.15 3.16
3241 3491 5.940595 AGTGTCGCTGACTTAGTACTAAAG 58.059 41.667 15.95 11.63 33.15 1.85
3260 3510 2.224450 CCCTCCGTCCTAAAAACAGTGT 60.224 50.000 0.00 0.00 0.00 3.55


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

AutoCloner maintained by Alex Coulton.