Multiple sequence alignment - TraesCS2A01G589800

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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 TraesCS2A01G589800 chr2A 100.000 2264 0 0 1 2264 778395549 778397812 0 4181
1 TraesCS2A01G589800 chr2A 94.912 1081 48 1 385 1458 677899071 677897991 0 1685
2 TraesCS2A01G589800 chr2A 99.754 814 0 2 1453 2264 778404022 778404835 0 1491
3 TraesCS2A01G589800 chr2A 98.405 815 9 4 1453 2264 760363569 760364382 0 1430
4 TraesCS2A01G589800 chr2A 98.403 814 11 2 1453 2264 777226857 777227670 0 1430
5 TraesCS2A01G589800 chr7A 95.515 1360 43 7 1 1348 16878262 16876909 0 2158
6 TraesCS2A01G589800 chr7A 93.429 1461 66 14 1 1458 643609221 643610654 0 2139
7 TraesCS2A01G589800 chr7A 93.087 1461 70 15 1 1458 192624653 192626085 0 2109
8 TraesCS2A01G589800 chr7A 95.293 871 41 0 588 1458 134596484 134597354 0 1382
9 TraesCS2A01G589800 chr7A 94.604 871 47 0 588 1458 699322383 699321513 0 1349
10 TraesCS2A01G589800 chr7A 96.064 813 20 4 1 801 134595921 134596733 0 1314
11 TraesCS2A01G589800 chr7A 95.567 812 25 5 1 801 699322945 699322134 0 1290
12 TraesCS2A01G589800 chr1B 92.905 1480 71 22 1 1458 357902171 357900704 0 2121
13 TraesCS2A01G589800 chr1B 92.400 921 46 13 546 1458 629308537 629309441 0 1291
14 TraesCS2A01G589800 chrUn 100.000 807 0 0 1458 2264 377369000 377369806 0 1491
15 TraesCS2A01G589800 chr6A 98.885 807 9 0 1458 2264 16987474 16988280 0 1441
16 TraesCS2A01G589800 chr6A 98.528 815 12 0 1450 2264 21034262 21035076 0 1439
17 TraesCS2A01G589800 chr6A 98.526 814 10 2 1453 2264 16994489 16995302 0 1435
18 TraesCS2A01G589800 chr6A 98.637 807 11 0 1458 2264 24595579 24594773 0 1430
19 TraesCS2A01G589800 chr6A 98.637 807 11 0 1458 2264 29306580 29305774 0 1430
20 TraesCS2A01G589800 chr1A 93.647 913 45 5 558 1458 559590014 559590925 0 1352
21 TraesCS2A01G589800 chr1A 95.600 841 36 1 618 1458 480958750 480959589 0 1347
22 TraesCS2A01G589800 chr1A 95.519 848 27 4 1 837 559589422 559590269 0 1345
23 TraesCS2A01G589800 chr5A 95.818 813 22 4 1 801 288269129 288268317 0 1303
24 TraesCS2A01G589800 chr4A 96.268 777 17 4 1 765 637837252 637836476 0 1264


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 TraesCS2A01G589800 chr2A 778395549 778397812 2263 False 4181.0 4181 100.0000 1 2264 1 chr2A.!!$F3 2263
1 TraesCS2A01G589800 chr2A 677897991 677899071 1080 True 1685.0 1685 94.9120 385 1458 1 chr2A.!!$R1 1073
2 TraesCS2A01G589800 chr2A 778404022 778404835 813 False 1491.0 1491 99.7540 1453 2264 1 chr2A.!!$F4 811
3 TraesCS2A01G589800 chr2A 760363569 760364382 813 False 1430.0 1430 98.4050 1453 2264 1 chr2A.!!$F1 811
4 TraesCS2A01G589800 chr2A 777226857 777227670 813 False 1430.0 1430 98.4030 1453 2264 1 chr2A.!!$F2 811
5 TraesCS2A01G589800 chr7A 16876909 16878262 1353 True 2158.0 2158 95.5150 1 1348 1 chr7A.!!$R1 1347
6 TraesCS2A01G589800 chr7A 643609221 643610654 1433 False 2139.0 2139 93.4290 1 1458 1 chr7A.!!$F2 1457
7 TraesCS2A01G589800 chr7A 192624653 192626085 1432 False 2109.0 2109 93.0870 1 1458 1 chr7A.!!$F1 1457
8 TraesCS2A01G589800 chr7A 134595921 134597354 1433 False 1348.0 1382 95.6785 1 1458 2 chr7A.!!$F3 1457
9 TraesCS2A01G589800 chr7A 699321513 699322945 1432 True 1319.5 1349 95.0855 1 1458 2 chr7A.!!$R2 1457
10 TraesCS2A01G589800 chr1B 357900704 357902171 1467 True 2121.0 2121 92.9050 1 1458 1 chr1B.!!$R1 1457
11 TraesCS2A01G589800 chr1B 629308537 629309441 904 False 1291.0 1291 92.4000 546 1458 1 chr1B.!!$F1 912
12 TraesCS2A01G589800 chrUn 377369000 377369806 806 False 1491.0 1491 100.0000 1458 2264 1 chrUn.!!$F1 806
13 TraesCS2A01G589800 chr6A 16987474 16988280 806 False 1441.0 1441 98.8850 1458 2264 1 chr6A.!!$F1 806
14 TraesCS2A01G589800 chr6A 21034262 21035076 814 False 1439.0 1439 98.5280 1450 2264 1 chr6A.!!$F3 814
15 TraesCS2A01G589800 chr6A 16994489 16995302 813 False 1435.0 1435 98.5260 1453 2264 1 chr6A.!!$F2 811
16 TraesCS2A01G589800 chr6A 24594773 24595579 806 True 1430.0 1430 98.6370 1458 2264 1 chr6A.!!$R1 806
17 TraesCS2A01G589800 chr6A 29305774 29306580 806 True 1430.0 1430 98.6370 1458 2264 1 chr6A.!!$R2 806
18 TraesCS2A01G589800 chr1A 559589422 559590925 1503 False 1348.5 1352 94.5830 1 1458 2 chr1A.!!$F2 1457
19 TraesCS2A01G589800 chr1A 480958750 480959589 839 False 1347.0 1347 95.6000 618 1458 1 chr1A.!!$F1 840
20 TraesCS2A01G589800 chr5A 288268317 288269129 812 True 1303.0 1303 95.8180 1 801 1 chr5A.!!$R1 800
21 TraesCS2A01G589800 chr4A 637836476 637837252 776 True 1264.0 1264 96.2680 1 765 1 chr4A.!!$R1 764

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
592 636 0.035458 GCACAACTGCTAGAGGTGGT 59.965 55.0 10.66 2.05 44.67 4.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1413 1677 4.143333 GGCGCTGCCTCCGTAAGA 62.143 66.667 7.64 0.0 46.69 2.1 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
276 277 0.478072 TTGGACCAATCACAGTGGCT 59.522 50.000 1.69 0.00 40.02 4.75
398 399 2.954318 GCTGGATACACTGGCATGAAAT 59.046 45.455 0.00 0.00 46.17 2.17
404 405 7.715657 TGGATACACTGGCATGAAATAATTTC 58.284 34.615 0.00 0.00 46.17 2.17
565 573 4.636435 GGTGACGGTGGTGGTGGG 62.636 72.222 0.00 0.00 0.00 4.61
580 624 2.032681 GGGCGAGGAAGCACAACT 59.967 61.111 0.00 0.00 40.96 3.16
581 625 2.328099 GGGCGAGGAAGCACAACTG 61.328 63.158 0.00 0.00 40.96 3.16
582 626 2.558313 GCGAGGAAGCACAACTGC 59.442 61.111 0.00 0.00 44.63 4.40
591 635 2.846371 GCACAACTGCTAGAGGTGG 58.154 57.895 10.66 1.52 44.67 4.61
592 636 0.035458 GCACAACTGCTAGAGGTGGT 59.965 55.000 10.66 2.05 44.67 4.16
593 637 1.800805 CACAACTGCTAGAGGTGGTG 58.199 55.000 10.66 9.39 44.67 4.17
594 638 0.687354 ACAACTGCTAGAGGTGGTGG 59.313 55.000 10.66 0.00 44.67 4.61
595 639 0.687354 CAACTGCTAGAGGTGGTGGT 59.313 55.000 0.00 0.00 35.49 4.16
596 640 0.977395 AACTGCTAGAGGTGGTGGTC 59.023 55.000 0.00 0.00 0.00 4.02
597 641 1.251527 ACTGCTAGAGGTGGTGGTCG 61.252 60.000 0.00 0.00 0.00 4.79
598 642 0.965866 CTGCTAGAGGTGGTGGTCGA 60.966 60.000 0.00 0.00 0.00 4.20
599 643 0.965866 TGCTAGAGGTGGTGGTCGAG 60.966 60.000 0.00 0.00 0.00 4.04
600 644 1.810532 CTAGAGGTGGTGGTCGAGC 59.189 63.158 7.89 7.89 0.00 5.03
601 645 0.965866 CTAGAGGTGGTGGTCGAGCA 60.966 60.000 14.39 14.39 0.00 4.26
602 646 0.965866 TAGAGGTGGTGGTCGAGCAG 60.966 60.000 19.24 0.00 30.97 4.24
603 647 3.302347 GAGGTGGTGGTCGAGCAGG 62.302 68.421 19.24 0.00 30.97 4.85
605 649 4.314440 GTGGTGGTCGAGCAGGCA 62.314 66.667 19.24 0.00 30.97 4.75
606 650 3.321648 TGGTGGTCGAGCAGGCAT 61.322 61.111 19.24 0.00 0.00 4.40
720 911 1.192146 GCTAGAGGTGGTGGTGGTCA 61.192 60.000 0.00 0.00 0.00 4.02
805 1068 2.182030 GGTCGGAGAGGAAGCACG 59.818 66.667 0.00 0.00 36.95 5.34
809 1072 0.035725 TCGGAGAGGAAGCACGAGTA 60.036 55.000 0.00 0.00 0.00 2.59
879 1142 5.357032 CCTTCGGTTATTTGCTTAATCCAGT 59.643 40.000 0.00 0.00 0.00 4.00
889 1152 4.661222 TGCTTAATCCAGTTGGTTGATCA 58.339 39.130 0.00 0.00 36.34 2.92
1154 1418 0.106769 TGCAAGCTGAAGGTGTCCAA 60.107 50.000 0.00 0.00 0.00 3.53
1373 1637 7.482169 AAGTACTTCACTTGGATAGATCACA 57.518 36.000 1.12 0.00 46.01 3.58
1413 1677 1.893801 AGAGGACCAACGTCGAGATTT 59.106 47.619 0.00 0.00 40.17 2.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
182 183 1.255882 TGCATCCGCATGGTTTTTCT 58.744 45.000 0.00 0.00 45.36 2.52
276 277 1.595311 ATGAGGGCCATGGTACTCAA 58.405 50.000 30.87 20.16 42.55 3.02
577 621 0.977395 GACCACCACCTCTAGCAGTT 59.023 55.000 0.00 0.00 0.00 3.16
578 622 1.251527 CGACCACCACCTCTAGCAGT 61.252 60.000 0.00 0.00 0.00 4.40
579 623 0.965866 TCGACCACCACCTCTAGCAG 60.966 60.000 0.00 0.00 0.00 4.24
580 624 0.965866 CTCGACCACCACCTCTAGCA 60.966 60.000 0.00 0.00 0.00 3.49
581 625 1.810532 CTCGACCACCACCTCTAGC 59.189 63.158 0.00 0.00 0.00 3.42
582 626 0.965866 TGCTCGACCACCACCTCTAG 60.966 60.000 0.00 0.00 0.00 2.43
583 627 0.965866 CTGCTCGACCACCACCTCTA 60.966 60.000 0.00 0.00 0.00 2.43
584 628 2.203640 TGCTCGACCACCACCTCT 60.204 61.111 0.00 0.00 0.00 3.69
585 629 2.262915 CTGCTCGACCACCACCTC 59.737 66.667 0.00 0.00 0.00 3.85
586 630 3.314331 CCTGCTCGACCACCACCT 61.314 66.667 0.00 0.00 0.00 4.00
588 632 2.238847 TATGCCTGCTCGACCACCAC 62.239 60.000 0.00 0.00 0.00 4.16
589 633 1.549243 TTATGCCTGCTCGACCACCA 61.549 55.000 0.00 0.00 0.00 4.17
590 634 0.811616 CTTATGCCTGCTCGACCACC 60.812 60.000 0.00 0.00 0.00 4.61
591 635 0.108138 ACTTATGCCTGCTCGACCAC 60.108 55.000 0.00 0.00 0.00 4.16
592 636 0.108186 CACTTATGCCTGCTCGACCA 60.108 55.000 0.00 0.00 0.00 4.02
593 637 1.432270 GCACTTATGCCTGCTCGACC 61.432 60.000 0.00 0.00 46.97 4.79
594 638 2.009888 GCACTTATGCCTGCTCGAC 58.990 57.895 0.00 0.00 46.97 4.20
595 639 4.521075 GCACTTATGCCTGCTCGA 57.479 55.556 0.00 0.00 46.97 4.04
604 648 2.501723 ACCACCACCTCTAGCACTTATG 59.498 50.000 0.00 0.00 0.00 1.90
605 649 2.766828 GACCACCACCTCTAGCACTTAT 59.233 50.000 0.00 0.00 0.00 1.73
606 650 2.176889 GACCACCACCTCTAGCACTTA 58.823 52.381 0.00 0.00 0.00 2.24
720 911 1.055040 AGCACTTGTGCTTCCTCTCT 58.945 50.000 20.95 0.00 43.52 3.10
805 1068 2.100989 CCACCACCACCTCTAGTACTC 58.899 57.143 0.00 0.00 0.00 2.59
809 1072 0.898789 CGACCACCACCACCTCTAGT 60.899 60.000 0.00 0.00 0.00 2.57
960 1224 5.888691 TTGTTAGCACAAGACACAAAGAA 57.111 34.783 0.00 0.00 38.03 2.52
1032 1296 3.390521 TCCTCTTGGTCCGCGCAT 61.391 61.111 8.75 0.00 34.23 4.73
1154 1418 0.036010 CCATGACTTCTTGCGGTCCT 60.036 55.000 0.00 0.00 0.00 3.85
1280 1544 9.725019 AGACATATGAGTTCAAAGTTGTTGATA 57.275 29.630 10.38 0.00 0.00 2.15
1373 1637 5.316987 CTCTTGGACATCTTTTGGTACCTT 58.683 41.667 14.36 0.00 0.00 3.50
1413 1677 4.143333 GGCGCTGCCTCCGTAAGA 62.143 66.667 7.64 0.00 46.69 2.10


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

AutoCloner maintained by Alex Coulton.