Multiple sequence alignment - TraesCS3A01G486200

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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 TraesCS3A01G486200 chr3A 100.000 3215 0 0 1 3215 714629541 714632755 0.000000e+00 5938
1 TraesCS3A01G486200 chr3A 88.095 336 19 8 610 942 714638903 714638586 2.340000e-101 379
2 TraesCS3A01G486200 chr4A 97.059 2618 48 9 610 3215 573670097 573672697 0.000000e+00 4381
3 TraesCS3A01G486200 chr4A 96.715 2618 65 7 610 3215 608866351 608863743 0.000000e+00 4338
4 TraesCS3A01G486200 chr4A 89.318 337 15 6 609 942 573683393 573683075 1.390000e-108 403
5 TraesCS3A01G486200 chr4A 92.941 255 14 4 615 868 608840830 608841081 5.070000e-98 368
6 TraesCS3A01G486200 chr4D 96.286 2639 63 13 603 3215 477884454 477881825 0.000000e+00 4298
7 TraesCS3A01G486200 chr4D 95.391 2647 73 12 610 3215 433387019 433384381 0.000000e+00 4167
8 TraesCS3A01G486200 chr4D 95.992 524 15 3 52 574 312585200 312584682 0.000000e+00 846
9 TraesCS3A01G486200 chr4D 87.143 350 21 8 597 942 477875811 477876140 3.030000e-100 375
10 TraesCS3A01G486200 chr4D 91.954 261 18 2 610 868 433378511 433378770 2.360000e-96 363
11 TraesCS3A01G486200 chr5D 95.983 2564 69 12 678 3215 375442802 375445357 0.000000e+00 4133
12 TraesCS3A01G486200 chr5D 92.990 2625 120 23 611 3215 449913470 449916050 0.000000e+00 3770
13 TraesCS3A01G486200 chr5A 92.199 2628 136 25 610 3215 396679715 396677135 0.000000e+00 3653
14 TraesCS3A01G486200 chr3D 91.151 2633 149 38 610 3215 149758703 149761278 0.000000e+00 3494
15 TraesCS3A01G486200 chr2B 94.011 1603 65 9 1513 3103 685368725 685367142 0.000000e+00 2399
16 TraesCS3A01G486200 chr4B 93.399 1515 87 12 810 2315 14640307 14638797 0.000000e+00 2231
17 TraesCS3A01G486200 chr4B 94.469 922 33 5 2307 3215 14630829 14629913 0.000000e+00 1404
18 TraesCS3A01G486200 chr6A 96.853 572 16 2 2 572 586990667 586990097 0.000000e+00 955
19 TraesCS3A01G486200 chr6A 95.924 368 14 1 205 572 50190162 50189796 2.140000e-166 595
20 TraesCS3A01G486200 chr2D 93.712 493 25 6 2 492 485050993 485050505 0.000000e+00 734
21 TraesCS3A01G486200 chr7B 93.093 333 19 2 2 334 733671436 733671764 4.820000e-133 484
22 TraesCS3A01G486200 chr7B 91.940 335 23 2 2 336 399257277 399256947 1.750000e-127 466
23 TraesCS3A01G486200 chr7B 93.380 287 15 3 2 285 742898947 742898662 3.830000e-114 422
24 TraesCS3A01G486200 chr7B 93.380 287 15 3 2 285 742902221 742901936 3.830000e-114 422
25 TraesCS3A01G486200 chr7B 93.304 224 11 3 2 222 741958440 741958662 8.600000e-86 327
26 TraesCS3A01G486200 chr7B 90.558 233 21 1 377 609 399256945 399256714 1.120000e-79 307
27 TraesCS3A01G486200 chrUn 93.031 287 16 3 2 285 344285714 344285999 1.780000e-112 416


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 TraesCS3A01G486200 chr3A 714629541 714632755 3214 False 5938.0 5938 100.000 1 3215 1 chr3A.!!$F1 3214
1 TraesCS3A01G486200 chr4A 573670097 573672697 2600 False 4381.0 4381 97.059 610 3215 1 chr4A.!!$F1 2605
2 TraesCS3A01G486200 chr4A 608863743 608866351 2608 True 4338.0 4338 96.715 610 3215 1 chr4A.!!$R2 2605
3 TraesCS3A01G486200 chr4D 477881825 477884454 2629 True 4298.0 4298 96.286 603 3215 1 chr4D.!!$R3 2612
4 TraesCS3A01G486200 chr4D 433384381 433387019 2638 True 4167.0 4167 95.391 610 3215 1 chr4D.!!$R2 2605
5 TraesCS3A01G486200 chr4D 312584682 312585200 518 True 846.0 846 95.992 52 574 1 chr4D.!!$R1 522
6 TraesCS3A01G486200 chr5D 375442802 375445357 2555 False 4133.0 4133 95.983 678 3215 1 chr5D.!!$F1 2537
7 TraesCS3A01G486200 chr5D 449913470 449916050 2580 False 3770.0 3770 92.990 611 3215 1 chr5D.!!$F2 2604
8 TraesCS3A01G486200 chr5A 396677135 396679715 2580 True 3653.0 3653 92.199 610 3215 1 chr5A.!!$R1 2605
9 TraesCS3A01G486200 chr3D 149758703 149761278 2575 False 3494.0 3494 91.151 610 3215 1 chr3D.!!$F1 2605
10 TraesCS3A01G486200 chr2B 685367142 685368725 1583 True 2399.0 2399 94.011 1513 3103 1 chr2B.!!$R1 1590
11 TraesCS3A01G486200 chr4B 14638797 14640307 1510 True 2231.0 2231 93.399 810 2315 1 chr4B.!!$R2 1505
12 TraesCS3A01G486200 chr4B 14629913 14630829 916 True 1404.0 1404 94.469 2307 3215 1 chr4B.!!$R1 908
13 TraesCS3A01G486200 chr6A 586990097 586990667 570 True 955.0 955 96.853 2 572 1 chr6A.!!$R2 570
14 TraesCS3A01G486200 chr7B 742898662 742902221 3559 True 422.0 422 93.380 2 285 2 chr7B.!!$R2 283
15 TraesCS3A01G486200 chr7B 399256714 399257277 563 True 386.5 466 91.249 2 609 2 chr7B.!!$R1 607

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
776 821 0.249868 CCCGTTTCTGACAGCAGTGA 60.250 55.0 0.0 0.0 42.84 3.41 F
982 1049 0.960861 TGCTTCTTCTCGCTCTCCGA 60.961 55.0 0.0 0.0 45.15 4.55 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1961 3951 1.163554 CTTTGCCTGCTCCTCAAGTC 58.836 55.000 0.0 0.0 0.0 3.01 R
2962 5219 1.484240 GTAGCAGTGCAGGAAGAGGAT 59.516 52.381 19.2 0.0 0.0 3.24 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
244 249 2.548067 GCCATATCCGACGACAGGAATT 60.548 50.000 0.00 0.00 41.69 2.17
339 344 2.317609 CCGCACCCTTTCGTGACAG 61.318 63.158 0.00 0.00 35.68 3.51
361 366 1.872773 AAAGCGGATCTCCTCCTTCT 58.127 50.000 0.00 0.00 42.47 2.85
369 374 3.551846 GATCTCCTCCTTCTCTCGAACT 58.448 50.000 0.00 0.00 0.00 3.01
401 445 0.817634 TGCCCCACTTCGTCAAGTTG 60.818 55.000 0.00 0.00 41.24 3.16
500 544 2.271944 AAACGCCCTAGTTTTGAGCT 57.728 45.000 0.00 0.00 41.04 4.09
581 625 1.139734 CCGAGACACATCCGGTCTG 59.860 63.158 0.00 2.96 45.21 3.51
605 649 0.395724 GTCAAATCTCCCCCGCCATT 60.396 55.000 0.00 0.00 0.00 3.16
736 781 8.284693 GCTAAAAACTACCAAGTTGACGAATTA 58.715 33.333 3.87 0.00 45.37 1.40
776 821 0.249868 CCCGTTTCTGACAGCAGTGA 60.250 55.000 0.00 0.00 42.84 3.41
982 1049 0.960861 TGCTTCTTCTCGCTCTCCGA 60.961 55.000 0.00 0.00 45.15 4.55
1023 1090 1.210967 CCGTCCTGGCCCAATAGTAAA 59.789 52.381 0.00 0.00 0.00 2.01
1238 1308 2.334307 GCTGCAGCAAACTCCTGAA 58.666 52.632 33.36 0.00 41.59 3.02
1474 2828 9.283768 AGTTGTTGTTTTTCTGAATTTTCCTTT 57.716 25.926 0.00 0.00 0.00 3.11
1764 3754 6.442885 TCTGGGATATGTATCATGAGCAGAAT 59.557 38.462 0.09 1.62 34.40 2.40
1795 3785 2.573462 GCCCAGGATAATGAGGCTCATA 59.427 50.000 29.02 17.43 35.76 2.15
1832 3822 6.625740 GCAAAACTGCATAAGGAGCTTGATTA 60.626 38.462 6.21 0.00 36.54 1.75
1857 3847 2.303022 GGCCAATCAGTATAGCCAGCTA 59.697 50.000 0.00 1.10 43.32 3.32
1961 3951 1.548269 ACTGAAGGAGAAGAAGAGGCG 59.452 52.381 0.00 0.00 0.00 5.52
2734 4782 6.704493 TGACGAAACTGAATTAGCTAACACTT 59.296 34.615 8.70 0.00 0.00 3.16
2962 5219 1.370051 CTGCAAGTCGTCGTCGTCA 60.370 57.895 1.33 0.00 38.33 4.35
3020 5296 0.108186 CGGAGCAACATAGCAGTGGA 60.108 55.000 0.00 0.00 36.85 4.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
244 249 3.518634 TTATGTGTATCGACTGCTGCA 57.481 42.857 0.88 0.88 0.00 4.41
401 445 1.153349 GGCCGTGGATGAGGAGAAC 60.153 63.158 0.00 0.00 0.00 3.01
452 496 2.742372 GATGTTGTGGCGACGGCT 60.742 61.111 22.70 0.00 39.81 5.52
500 544 4.283403 GGCAGCGGCAAACAAGCA 62.283 61.111 11.88 0.00 43.71 3.91
575 619 3.083600 GATTTGACGCCGCAGACCG 62.084 63.158 0.00 0.00 0.00 4.79
581 625 3.202706 GGGGAGATTTGACGCCGC 61.203 66.667 0.00 0.00 35.91 6.53
736 781 6.072342 ACGGGTTTAAACGCTCTAAAATGATT 60.072 34.615 26.77 0.00 39.45 2.57
738 783 4.756135 ACGGGTTTAAACGCTCTAAAATGA 59.244 37.500 26.77 0.00 39.45 2.57
831 876 4.217159 GCGACGGCCGGGTCTAAT 62.217 66.667 31.76 5.85 39.04 1.73
1023 1090 2.661399 TCGTCGTCCGAGGTCTCT 59.339 61.111 8.95 0.00 41.60 3.10
1238 1308 3.584848 AGAAGCTTGGGTCTATCACAGTT 59.415 43.478 2.10 0.00 0.00 3.16
1301 1371 2.610546 TTGCCTGCCCTCTGCCTA 60.611 61.111 0.00 0.00 40.16 3.93
1474 2828 9.990360 TCAGACATACATAAGTTTTCACACTTA 57.010 29.630 0.00 0.00 42.22 2.24
1764 3754 3.414759 TTATCCTGGGCTCTACCAAGA 57.585 47.619 0.00 0.00 43.15 3.02
1795 3785 2.301346 CAGTTTTGCAACCTCTGTCCT 58.699 47.619 0.00 0.00 32.70 3.85
1832 3822 2.981784 TGGCTATACTGATTGGCCAGAT 59.018 45.455 5.11 2.42 46.35 2.90
1857 3847 3.181440 ACAACTTGGACACATCATCCACT 60.181 43.478 0.00 0.00 46.09 4.00
1961 3951 1.163554 CTTTGCCTGCTCCTCAAGTC 58.836 55.000 0.00 0.00 0.00 3.01
2693 4741 3.591023 TCGTCAGTGTTCACAAGTTCAA 58.409 40.909 5.74 0.00 0.00 2.69
2734 4782 6.574465 GCCTAAGTGAACCTATCTCTGAAACA 60.574 42.308 0.00 0.00 32.37 2.83
2962 5219 1.484240 GTAGCAGTGCAGGAAGAGGAT 59.516 52.381 19.20 0.00 0.00 3.24


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

AutoCloner maintained by Alex Coulton.