Multiple sequence alignment - TraesCS5B01G190900

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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 TraesCS5B01G190900 chr5B 100.000 2786 0 0 1 2786 344629966 344632751 0 5145
1 TraesCS5B01G190900 chr5B 97.236 1664 25 4 2 1663 82189942 82188298 0 2798
2 TraesCS5B01G190900 chr5B 97.115 1525 40 3 2 1525 443102767 443101246 0 2569
3 TraesCS5B01G190900 chr5B 98.422 1014 16 0 1773 2786 82176590 82175577 0 1784
4 TraesCS5B01G190900 chr5B 98.323 1014 17 0 1773 2786 443096501 443095488 0 1779
5 TraesCS5B01G190900 chrUn 98.646 1772 21 2 2 1772 15876322 15874553 0 3136
6 TraesCS5B01G190900 chrUn 99.014 1014 10 0 1773 2786 15872626 15871613 0 1818
7 TraesCS5B01G190900 chr4B 98.031 1270 24 1 503 1772 74330788 74332056 0 2206
8 TraesCS5B01G190900 chr4B 97.480 1270 30 1 503 1772 635891517 635892784 0 2167
9 TraesCS5B01G190900 chr4B 97.239 1014 28 0 1773 2786 74335766 74336779 0 1718
10 TraesCS5B01G190900 chr7B 97.799 1272 24 3 503 1772 688939657 688940926 0 2191
11 TraesCS5B01G190900 chr2B 97.874 1270 19 5 503 1772 408281285 408280024 0 2189
12 TraesCS5B01G190900 chr2B 97.482 1271 27 4 503 1772 571306518 571305252 0 2165
13 TraesCS5B01G190900 chr2B 97.929 1014 20 1 1773 2786 200684575 200683563 0 1755
14 TraesCS5B01G190900 chr2B 97.649 808 15 3 2 809 200689183 200688380 0 1384
15 TraesCS5B01G190900 chr2B 94.504 746 33 4 2 739 548109215 548109960 0 1144
16 TraesCS5B01G190900 chr4A 97.874 1270 15 5 503 1772 667698472 667697215 0 2185
17 TraesCS5B01G190900 chr4A 99.014 1014 10 0 1773 2786 667695133 667694120 0 1818
18 TraesCS5B01G190900 chr3B 98.225 1014 18 0 1773 2786 485245986 485246999 0 1773
19 TraesCS5B01G190900 chr3B 97.535 1014 25 0 1773 2786 823971105 823970092 0 1735
20 TraesCS5B01G190900 chr3B 97.164 811 17 3 2 809 161305118 161304311 0 1365
21 TraesCS5B01G190900 chr3B 97.425 699 16 2 2 699 823973615 823972918 0 1190
22 TraesCS5B01G190900 chr1B 98.028 1014 20 0 1773 2786 324871960 324872973 0 1762
23 TraesCS5B01G190900 chr1B 97.564 698 17 0 2 699 324865208 324865905 0 1195
24 TraesCS5B01G190900 chr6B 96.084 715 25 3 2 714 708345804 708345091 0 1162


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 TraesCS5B01G190900 chr5B 344629966 344632751 2785 False 5145.0 5145 100.000 1 2786 1 chr5B.!!$F1 2785
1 TraesCS5B01G190900 chr5B 82188298 82189942 1644 True 2798.0 2798 97.236 2 1663 1 chr5B.!!$R2 1661
2 TraesCS5B01G190900 chr5B 443101246 443102767 1521 True 2569.0 2569 97.115 2 1525 1 chr5B.!!$R4 1523
3 TraesCS5B01G190900 chr5B 82175577 82176590 1013 True 1784.0 1784 98.422 1773 2786 1 chr5B.!!$R1 1013
4 TraesCS5B01G190900 chr5B 443095488 443096501 1013 True 1779.0 1779 98.323 1773 2786 1 chr5B.!!$R3 1013
5 TraesCS5B01G190900 chrUn 15871613 15876322 4709 True 2477.0 3136 98.830 2 2786 2 chrUn.!!$R1 2784
6 TraesCS5B01G190900 chr4B 635891517 635892784 1267 False 2167.0 2167 97.480 503 1772 1 chr4B.!!$F1 1269
7 TraesCS5B01G190900 chr4B 74330788 74336779 5991 False 1962.0 2206 97.635 503 2786 2 chr4B.!!$F2 2283
8 TraesCS5B01G190900 chr7B 688939657 688940926 1269 False 2191.0 2191 97.799 503 1772 1 chr7B.!!$F1 1269
9 TraesCS5B01G190900 chr2B 408280024 408281285 1261 True 2189.0 2189 97.874 503 1772 1 chr2B.!!$R1 1269
10 TraesCS5B01G190900 chr2B 571305252 571306518 1266 True 2165.0 2165 97.482 503 1772 1 chr2B.!!$R2 1269
11 TraesCS5B01G190900 chr2B 200683563 200689183 5620 True 1569.5 1755 97.789 2 2786 2 chr2B.!!$R3 2784
12 TraesCS5B01G190900 chr2B 548109215 548109960 745 False 1144.0 1144 94.504 2 739 1 chr2B.!!$F1 737
13 TraesCS5B01G190900 chr4A 667694120 667698472 4352 True 2001.5 2185 98.444 503 2786 2 chr4A.!!$R1 2283
14 TraesCS5B01G190900 chr3B 485245986 485246999 1013 False 1773.0 1773 98.225 1773 2786 1 chr3B.!!$F1 1013
15 TraesCS5B01G190900 chr3B 823970092 823973615 3523 True 1462.5 1735 97.480 2 2786 2 chr3B.!!$R2 2784
16 TraesCS5B01G190900 chr3B 161304311 161305118 807 True 1365.0 1365 97.164 2 809 1 chr3B.!!$R1 807
17 TraesCS5B01G190900 chr1B 324871960 324872973 1013 False 1762.0 1762 98.028 1773 2786 1 chr1B.!!$F2 1013
18 TraesCS5B01G190900 chr1B 324865208 324865905 697 False 1195.0 1195 97.564 2 699 1 chr1B.!!$F1 697
19 TraesCS5B01G190900 chr6B 708345091 708345804 713 True 1162.0 1162 96.084 2 714 1 chr6B.!!$R1 712

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
247 251 1.687563 CGGGAGTTTGGTGGAGTTTT 58.312 50.000 0.00 0.0 0.00 2.43 F
492 496 2.696707 TGCTCCGGTAATATTTCGGACT 59.303 45.455 21.23 0.0 46.48 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1355 1628 1.303317 GGATCGTTGCCACCTTGGT 60.303 57.895 0.00 0.00 40.46 3.67 R
2249 7029 2.190841 TCAGTGACGACGTCTGGCA 61.191 57.895 26.86 12.71 33.15 4.92 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
247 251 1.687563 CGGGAGTTTGGTGGAGTTTT 58.312 50.000 0.00 0.00 0.00 2.43
417 421 5.221541 TGGTGAGCATTTTATTTTCCCGTTT 60.222 36.000 0.00 0.00 0.00 3.60
418 422 5.699001 GGTGAGCATTTTATTTTCCCGTTTT 59.301 36.000 0.00 0.00 0.00 2.43
419 423 6.347321 GGTGAGCATTTTATTTTCCCGTTTTG 60.347 38.462 0.00 0.00 0.00 2.44
423 427 7.217906 AGCATTTTATTTTCCCGTTTTGGTTA 58.782 30.769 0.00 0.00 35.15 2.85
424 428 7.386573 AGCATTTTATTTTCCCGTTTTGGTTAG 59.613 33.333 0.00 0.00 35.15 2.34
425 429 7.514805 CATTTTATTTTCCCGTTTTGGTTAGC 58.485 34.615 0.00 0.00 35.15 3.09
426 430 5.786264 TTATTTTCCCGTTTTGGTTAGCA 57.214 34.783 0.00 0.00 35.15 3.49
430 434 4.674281 TTCCCGTTTTGGTTAGCATTTT 57.326 36.364 0.00 0.00 35.15 1.82
431 435 5.786264 TTCCCGTTTTGGTTAGCATTTTA 57.214 34.783 0.00 0.00 35.15 1.52
432 436 5.986501 TCCCGTTTTGGTTAGCATTTTAT 57.013 34.783 0.00 0.00 35.15 1.40
437 441 8.030106 CCCGTTTTGGTTAGCATTTTATTTAGA 58.970 33.333 0.00 0.00 35.15 2.10
438 442 9.581099 CCGTTTTGGTTAGCATTTTATTTAGAT 57.419 29.630 0.00 0.00 0.00 1.98
456 460 4.685169 AGATGTCAACTAATTGGTTGCG 57.315 40.909 25.17 7.59 44.19 4.85
460 464 5.752892 TGTCAACTAATTGGTTGCGTAAA 57.247 34.783 25.17 8.94 44.19 2.01
461 465 6.132791 TGTCAACTAATTGGTTGCGTAAAA 57.867 33.333 25.17 8.29 44.19 1.52
463 467 7.203910 TGTCAACTAATTGGTTGCGTAAAAAT 58.796 30.769 25.17 0.00 44.19 1.82
464 468 7.168302 TGTCAACTAATTGGTTGCGTAAAAATG 59.832 33.333 25.17 3.64 44.19 2.32
468 472 7.649973 ACTAATTGGTTGCGTAAAAATGTGTA 58.350 30.769 0.00 0.00 0.00 2.90
469 473 7.806014 ACTAATTGGTTGCGTAAAAATGTGTAG 59.194 33.333 0.00 0.00 0.00 2.74
470 474 5.502153 TTGGTTGCGTAAAAATGTGTAGT 57.498 34.783 0.00 0.00 0.00 2.73
471 475 5.502153 TGGTTGCGTAAAAATGTGTAGTT 57.498 34.783 0.00 0.00 0.00 2.24
472 476 5.274718 TGGTTGCGTAAAAATGTGTAGTTG 58.725 37.500 0.00 0.00 0.00 3.16
473 477 4.147479 GGTTGCGTAAAAATGTGTAGTTGC 59.853 41.667 0.00 0.00 0.00 4.17
474 478 4.822036 TGCGTAAAAATGTGTAGTTGCT 57.178 36.364 0.00 0.00 0.00 3.91
475 479 4.778904 TGCGTAAAAATGTGTAGTTGCTC 58.221 39.130 0.00 0.00 0.00 4.26
476 480 4.156182 GCGTAAAAATGTGTAGTTGCTCC 58.844 43.478 0.00 0.00 0.00 4.70
481 485 3.688694 AATGTGTAGTTGCTCCGGTAA 57.311 42.857 0.00 0.00 0.00 2.85
483 487 5.347620 AATGTGTAGTTGCTCCGGTAATA 57.652 39.130 0.00 0.00 0.00 0.98
484 488 5.546621 ATGTGTAGTTGCTCCGGTAATAT 57.453 39.130 0.00 0.00 0.00 1.28
485 489 5.347620 TGTGTAGTTGCTCCGGTAATATT 57.652 39.130 0.00 0.00 0.00 1.28
488 492 5.045215 TGTAGTTGCTCCGGTAATATTTCG 58.955 41.667 0.00 0.00 0.00 3.46
491 495 3.102052 TGCTCCGGTAATATTTCGGAC 57.898 47.619 21.23 18.36 46.48 4.79
492 496 2.696707 TGCTCCGGTAATATTTCGGACT 59.303 45.455 21.23 0.00 46.48 3.85
497 501 6.696148 GCTCCGGTAATATTTCGGACTATATG 59.304 42.308 21.23 14.55 46.48 1.78
498 502 7.415989 GCTCCGGTAATATTTCGGACTATATGA 60.416 40.741 21.23 6.21 46.48 2.15
499 503 8.352137 TCCGGTAATATTTCGGACTATATGAA 57.648 34.615 21.23 4.30 46.48 2.57
500 504 8.974238 TCCGGTAATATTTCGGACTATATGAAT 58.026 33.333 21.23 0.00 46.48 2.57
631 697 6.067263 TGTGTAAAAATGTGTAGTTGCTCC 57.933 37.500 0.00 0.00 0.00 4.70
641 707 5.113383 TGTGTAGTTGCTCCGGTAATATTG 58.887 41.667 0.00 0.00 0.00 1.90
642 708 4.025145 GTGTAGTTGCTCCGGTAATATTGC 60.025 45.833 0.00 0.00 0.00 3.56
1355 1628 0.036732 GGGGTCACTGCACATGAAGA 59.963 55.000 0.00 0.00 0.00 2.87
1511 1785 4.547671 CAGAATAGTCAGGTAGAAGGGGA 58.452 47.826 0.00 0.00 0.00 4.81
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
332 336 4.235939 ACAATAATTGCACGCAACTTCA 57.764 36.364 6.60 0.00 38.88 3.02
442 446 6.981559 ACACATTTTTACGCAACCAATTAGTT 59.018 30.769 0.00 0.00 0.00 2.24
444 448 7.806014 ACTACACATTTTTACGCAACCAATTAG 59.194 33.333 0.00 0.00 0.00 1.73
446 450 6.508777 ACTACACATTTTTACGCAACCAATT 58.491 32.000 0.00 0.00 0.00 2.32
448 452 5.502153 ACTACACATTTTTACGCAACCAA 57.498 34.783 0.00 0.00 0.00 3.67
449 453 5.274718 CAACTACACATTTTTACGCAACCA 58.725 37.500 0.00 0.00 0.00 3.67
450 454 4.147479 GCAACTACACATTTTTACGCAACC 59.853 41.667 0.00 0.00 0.00 3.77
453 457 4.319911 GGAGCAACTACACATTTTTACGCA 60.320 41.667 0.00 0.00 0.00 5.24
454 458 4.156182 GGAGCAACTACACATTTTTACGC 58.844 43.478 0.00 0.00 0.00 4.42
455 459 4.391358 CGGAGCAACTACACATTTTTACG 58.609 43.478 0.00 0.00 0.00 3.18
456 460 4.214758 ACCGGAGCAACTACACATTTTTAC 59.785 41.667 9.46 0.00 0.00 2.01
460 464 2.561478 ACCGGAGCAACTACACATTT 57.439 45.000 9.46 0.00 0.00 2.32
461 465 3.688694 TTACCGGAGCAACTACACATT 57.311 42.857 9.46 0.00 0.00 2.71
463 467 5.347620 AATATTACCGGAGCAACTACACA 57.652 39.130 9.46 0.00 0.00 3.72
464 468 5.051240 CGAAATATTACCGGAGCAACTACAC 60.051 44.000 9.46 0.00 0.00 2.90
468 472 3.133362 TCCGAAATATTACCGGAGCAACT 59.867 43.478 21.13 0.00 46.17 3.16
469 473 3.460103 TCCGAAATATTACCGGAGCAAC 58.540 45.455 21.13 0.00 46.17 4.17
470 474 3.823281 TCCGAAATATTACCGGAGCAA 57.177 42.857 21.13 0.00 46.17 3.91
497 501 9.990888 CGTTTACTACTCGAGCAAATAATATTC 57.009 33.333 13.61 0.00 0.00 1.75
498 502 9.525409 ACGTTTACTACTCGAGCAAATAATATT 57.475 29.630 13.61 0.00 0.00 1.28
501 505 8.915871 TTACGTTTACTACTCGAGCAAATAAT 57.084 30.769 13.61 0.00 0.00 1.28
502 506 8.741101 TTTACGTTTACTACTCGAGCAAATAA 57.259 30.769 13.61 3.70 0.00 1.40
504 508 7.823149 ATTTACGTTTACTACTCGAGCAAAT 57.177 32.000 13.61 0.00 0.00 2.32
505 509 8.915871 ATATTTACGTTTACTACTCGAGCAAA 57.084 30.769 13.61 5.22 0.00 3.68
602 668 9.458374 GCAACTACACATTTTTACACAACTAAT 57.542 29.630 0.00 0.00 0.00 1.73
609 675 5.144359 CGGAGCAACTACACATTTTTACAC 58.856 41.667 0.00 0.00 0.00 2.90
631 697 7.654568 TCCATATATAGTCCGCAATATTACCG 58.345 38.462 0.00 0.00 0.00 4.02
641 707 6.452494 AGTACACATCCATATATAGTCCGC 57.548 41.667 0.00 0.00 0.00 5.54
983 1253 3.452627 AGACATCTCGGCTCACCTATTTT 59.547 43.478 0.00 0.00 0.00 1.82
1355 1628 1.303317 GGATCGTTGCCACCTTGGT 60.303 57.895 0.00 0.00 40.46 3.67
1511 1785 5.350633 CATTGTATTCACCATCGGCATTTT 58.649 37.500 0.00 0.00 0.00 1.82
2249 7029 2.190841 TCAGTGACGACGTCTGGCA 61.191 57.895 26.86 12.71 33.15 4.92
2420 7200 6.163476 TGTTGTACGAGCATTCTGTTCTATT 58.837 36.000 0.00 0.00 0.00 1.73


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

AutoCloner maintained by Alex Coulton.