Multiple sequence alignment - TraesCS1D01G329600

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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 TraesCS1D01G329600 chr1D 100.000 2318 0 0 1 2318 420648454 420650771 0.000000e+00 4281.0
1 TraesCS1D01G329600 chr1A 93.679 2104 78 21 1 2085 517095452 517097519 0.000000e+00 3097.0
2 TraesCS1D01G329600 chr1A 96.957 230 6 1 2090 2318 517097726 517097955 3.610000e-103 385.0
3 TraesCS1D01G329600 chr1B 94.743 1750 63 14 593 2318 568962559 568964303 0.000000e+00 2695.0
4 TraesCS1D01G329600 chr7A 97.778 45 1 0 500 544 732467563 732467607 6.870000e-11 78.7
5 TraesCS1D01G329600 chr7A 97.674 43 1 0 501 543 167261685 167261643 8.880000e-10 75.0
6 TraesCS1D01G329600 chr7D 95.745 47 2 0 497 543 90810993 90810947 2.470000e-10 76.8
7 TraesCS1D01G329600 chr7B 97.727 44 1 0 501 544 129535858 129535815 2.470000e-10 76.8
8 TraesCS1D01G329600 chr6A 95.833 48 0 2 495 541 33013678 33013724 2.470000e-10 76.8
9 TraesCS1D01G329600 chr5D 94.000 50 3 0 494 543 528402878 528402829 2.470000e-10 76.8
10 TraesCS1D01G329600 chr5A 94.000 50 3 0 494 543 656467819 656467770 2.470000e-10 76.8
11 TraesCS1D01G329600 chr2A 90.741 54 3 2 495 546 32146209 32146262 1.150000e-08 71.3


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 TraesCS1D01G329600 chr1D 420648454 420650771 2317 False 4281 4281 100.000 1 2318 1 chr1D.!!$F1 2317
1 TraesCS1D01G329600 chr1A 517095452 517097955 2503 False 1741 3097 95.318 1 2318 2 chr1A.!!$F1 2317
2 TraesCS1D01G329600 chr1B 568962559 568964303 1744 False 2695 2695 94.743 593 2318 1 chr1B.!!$F1 1725

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
904 922 0.554792 CTAGTCCCGAGGTCCCCTTA 59.445 60.0 0.0 0.0 31.76 2.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2096 2336 3.181464 CCTTAAAGTAGGGGTAGAGCAGC 60.181 52.174 0.0 0.0 0.0 5.25 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
32 33 3.664107 GGCTACACAAGATGACTCACAA 58.336 45.455 0.00 0.00 0.00 3.33
50 51 5.550290 TCACAAGAGAACAATAGTGCATGA 58.450 37.500 0.00 0.00 0.00 3.07
72 73 1.190643 CTCAGTCTCAGGGACCTTCC 58.809 60.000 0.00 0.00 45.54 3.46
74 75 0.900647 CAGTCTCAGGGACCTTCCGT 60.901 60.000 0.00 0.00 45.54 4.69
144 145 5.105187 CGGTACATCATATCATCCATCCACT 60.105 44.000 0.00 0.00 0.00 4.00
187 188 3.802377 CGTTTGCGACGTGGTAAAA 57.198 47.368 14.70 6.02 46.49 1.52
188 189 1.378347 CGTTTGCGACGTGGTAAAAC 58.622 50.000 14.70 15.32 46.49 2.43
226 232 1.351707 CATTACGTGCATCCACCGC 59.648 57.895 0.00 0.00 38.79 5.68
265 272 1.067565 GCAAGACGGAGATGTGACAGA 60.068 52.381 0.00 0.00 0.00 3.41
268 275 3.351794 AGACGGAGATGTGACAGAGTA 57.648 47.619 0.00 0.00 0.00 2.59
269 276 3.892284 AGACGGAGATGTGACAGAGTAT 58.108 45.455 0.00 0.00 0.00 2.12
395 402 7.362574 GCAGCAAAAGTATAAGGTTACAATGGA 60.363 37.037 0.00 0.00 0.00 3.41
396 403 7.968405 CAGCAAAAGTATAAGGTTACAATGGAC 59.032 37.037 0.00 0.00 0.00 4.02
397 404 7.888546 AGCAAAAGTATAAGGTTACAATGGACT 59.111 33.333 0.00 0.00 0.00 3.85
398 405 7.968405 GCAAAAGTATAAGGTTACAATGGACTG 59.032 37.037 0.00 0.00 0.00 3.51
399 406 8.458843 CAAAAGTATAAGGTTACAATGGACTGG 58.541 37.037 0.00 0.00 0.00 4.00
407 414 2.867109 ACAATGGACTGGAGTTGAGG 57.133 50.000 0.00 0.00 0.00 3.86
409 416 2.304180 ACAATGGACTGGAGTTGAGGAG 59.696 50.000 0.00 0.00 0.00 3.69
411 418 2.398754 TGGACTGGAGTTGAGGAGAA 57.601 50.000 0.00 0.00 0.00 2.87
421 428 7.119846 ACTGGAGTTGAGGAGAATAAAATTTCG 59.880 37.037 0.00 0.00 0.00 3.46
450 458 2.483714 GGATCCACATGAGCACATACGT 60.484 50.000 6.95 0.00 35.09 3.57
521 531 8.012957 AGATGTACTACCTCTGTTCCTAAATG 57.987 38.462 0.00 0.00 0.00 2.32
527 537 7.838884 ACTACCTCTGTTCCTAAATGTAAGAC 58.161 38.462 0.00 0.00 0.00 3.01
533 543 8.441312 TCTGTTCCTAAATGTAAGACGTTTTT 57.559 30.769 0.00 0.00 38.23 1.94
903 921 1.310373 CTAGTCCCGAGGTCCCCTT 59.690 63.158 0.00 0.00 31.76 3.95
904 922 0.554792 CTAGTCCCGAGGTCCCCTTA 59.445 60.000 0.00 0.00 31.76 2.69
993 1011 1.716050 CGCATATCGTCTCCATCAACG 59.284 52.381 0.00 0.00 40.17 4.10
1383 1403 6.054295 GCTCTGAGTCATCTTTGGACATTAT 58.946 40.000 6.53 0.00 37.74 1.28
1384 1404 7.147672 TGCTCTGAGTCATCTTTGGACATTATA 60.148 37.037 6.53 0.00 37.74 0.98
1385 1405 7.712639 GCTCTGAGTCATCTTTGGACATTATAA 59.287 37.037 6.53 0.00 37.74 0.98
1531 1552 1.933181 TCCGAATGTATGCAAGCTTCG 59.067 47.619 10.04 10.04 35.56 3.79
1585 1606 7.394077 TCTGCCTTCATGTTATTTTTCATGAGA 59.606 33.333 0.00 0.00 46.79 3.27
1587 1608 8.533657 TGCCTTCATGTTATTTTTCATGAGAAT 58.466 29.630 0.00 5.70 46.79 2.40
1588 1609 9.028185 GCCTTCATGTTATTTTTCATGAGAATC 57.972 33.333 9.01 0.00 46.79 2.52
1771 1797 7.667635 TCAATGTGTTCCTTTGTTACCATATCA 59.332 33.333 0.00 0.00 31.79 2.15
1865 1891 5.871396 TTCCAGAGAAAACTGTCTACTGT 57.129 39.130 0.00 0.00 36.30 3.55
1951 1978 6.379386 GTTTGGAATACTGTAAAGCCAGAAC 58.621 40.000 0.00 4.67 36.30 3.01
2009 2036 6.345329 CGCGATGAAGATACAACTCACATTAG 60.345 42.308 0.00 0.00 0.00 1.73
2010 2037 6.477033 GCGATGAAGATACAACTCACATTAGT 59.523 38.462 0.00 0.00 0.00 2.24
2146 2387 8.073768 CGTGAAAGTTGTAAAAGGATGTGTATT 58.926 33.333 0.00 0.00 0.00 1.89
2299 2540 3.308530 GCAACCAGCACAACATTTAGAC 58.691 45.455 0.00 0.00 44.79 2.59
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 0.824109 TCATCTTGTGTAGCCGGGAG 59.176 55.000 2.18 0.00 0.00 4.30
9 10 1.204704 TGAGTCATCTTGTGTAGCCGG 59.795 52.381 0.00 0.00 0.00 6.13
11 12 3.319137 TGTGAGTCATCTTGTGTAGCC 57.681 47.619 0.00 0.00 0.00 3.93
12 13 4.560128 TCTTGTGAGTCATCTTGTGTAGC 58.440 43.478 0.00 0.00 0.00 3.58
32 33 5.186603 TGAGAGTCATGCACTATTGTTCTCT 59.813 40.000 16.06 14.09 34.41 3.10
50 51 1.080638 AGGTCCCTGAGACTGAGAGT 58.919 55.000 0.00 0.00 45.54 3.24
87 88 2.399580 AGGTAGACATGGTAGAAGGGC 58.600 52.381 0.00 0.00 0.00 5.19
90 91 6.037786 TGTTCAAGGTAGACATGGTAGAAG 57.962 41.667 0.00 0.00 0.00 2.85
91 92 6.428083 TTGTTCAAGGTAGACATGGTAGAA 57.572 37.500 0.00 0.00 0.00 2.10
144 145 3.719924 ACCGATGAACTGTTTTACGACA 58.280 40.909 12.80 0.00 0.00 4.35
170 171 2.103388 GTGTTTTACCACGTCGCAAAC 58.897 47.619 0.00 0.00 0.00 2.93
171 172 2.455295 GTGTTTTACCACGTCGCAAA 57.545 45.000 0.00 0.00 0.00 3.68
179 180 1.202320 CGGTCGCGTGTTTTACCAC 59.798 57.895 5.77 0.00 32.04 4.16
180 181 2.596795 GCGGTCGCGTGTTTTACCA 61.597 57.895 5.77 0.00 32.04 3.25
181 182 2.171701 GCGGTCGCGTGTTTTACC 59.828 61.111 5.77 3.83 0.00 2.85
208 214 1.089481 AGCGGTGGATGCACGTAATG 61.089 55.000 11.52 0.04 33.85 1.90
250 257 2.952978 GGATACTCTGTCACATCTCCGT 59.047 50.000 0.00 0.00 0.00 4.69
252 259 4.832266 AGATGGATACTCTGTCACATCTCC 59.168 45.833 0.00 0.00 40.53 3.71
265 272 3.906846 CCTTGGAGGCTAAGATGGATACT 59.093 47.826 0.00 0.00 37.61 2.12
314 321 4.107820 AGTTGAGAATAAGGGGAAGCTCT 58.892 43.478 0.00 0.00 0.00 4.09
395 402 7.119846 CGAAATTTTATTCTCCTCAACTCCAGT 59.880 37.037 0.00 0.00 0.00 4.00
396 403 7.414540 CCGAAATTTTATTCTCCTCAACTCCAG 60.415 40.741 0.00 0.00 0.00 3.86
397 404 6.374333 CCGAAATTTTATTCTCCTCAACTCCA 59.626 38.462 0.00 0.00 0.00 3.86
398 405 6.678164 GCCGAAATTTTATTCTCCTCAACTCC 60.678 42.308 0.00 0.00 0.00 3.85
399 406 6.094186 AGCCGAAATTTTATTCTCCTCAACTC 59.906 38.462 0.00 0.00 0.00 3.01
407 414 5.820947 TCCCAGTAGCCGAAATTTTATTCTC 59.179 40.000 0.00 0.00 0.00 2.87
409 416 6.294010 GGATCCCAGTAGCCGAAATTTTATTC 60.294 42.308 0.00 0.00 0.00 1.75
411 418 5.070685 GGATCCCAGTAGCCGAAATTTTAT 58.929 41.667 0.00 0.00 0.00 1.40
421 428 1.071385 CTCATGTGGATCCCAGTAGCC 59.929 57.143 9.90 0.00 32.34 3.93
465 473 6.468956 GTCGTTGCATGTTTCTTATGTTATGG 59.531 38.462 0.00 0.00 0.00 2.74
466 474 6.468956 GGTCGTTGCATGTTTCTTATGTTATG 59.531 38.462 0.00 0.00 0.00 1.90
467 475 6.551736 GGTCGTTGCATGTTTCTTATGTTAT 58.448 36.000 0.00 0.00 0.00 1.89
468 476 5.390040 CGGTCGTTGCATGTTTCTTATGTTA 60.390 40.000 0.00 0.00 0.00 2.41
469 477 4.612712 CGGTCGTTGCATGTTTCTTATGTT 60.613 41.667 0.00 0.00 0.00 2.71
470 478 3.120338 CGGTCGTTGCATGTTTCTTATGT 60.120 43.478 0.00 0.00 0.00 2.29
471 479 3.120338 ACGGTCGTTGCATGTTTCTTATG 60.120 43.478 0.00 0.00 0.00 1.90
472 480 3.071479 ACGGTCGTTGCATGTTTCTTAT 58.929 40.909 0.00 0.00 0.00 1.73
473 481 2.485903 ACGGTCGTTGCATGTTTCTTA 58.514 42.857 0.00 0.00 0.00 2.10
474 482 1.305201 ACGGTCGTTGCATGTTTCTT 58.695 45.000 0.00 0.00 0.00 2.52
475 483 1.305201 AACGGTCGTTGCATGTTTCT 58.695 45.000 8.00 0.00 36.91 2.52
476 484 2.953640 TAACGGTCGTTGCATGTTTC 57.046 45.000 17.57 0.00 38.92 2.78
477 485 2.873472 TCTTAACGGTCGTTGCATGTTT 59.127 40.909 17.57 0.00 38.92 2.83
521 531 5.741982 ACATTGAACTGCAAAAACGTCTTAC 59.258 36.000 0.00 0.00 40.48 2.34
527 537 3.117832 CGCTACATTGAACTGCAAAAACG 59.882 43.478 0.00 0.00 40.48 3.60
533 543 0.669012 TCGCGCTACATTGAACTGCA 60.669 50.000 5.56 0.00 0.00 4.41
586 596 3.339093 GGTAACCCAGCTGGCCCT 61.339 66.667 28.39 15.34 37.83 5.19
588 598 3.971109 GACGGTAACCCAGCTGGCC 62.971 68.421 28.39 21.03 37.83 5.36
855 873 8.899771 GCTAGCCTACTTGTATGGAAAATTTTA 58.100 33.333 2.29 0.00 0.00 1.52
903 921 1.404391 GACGAACAGAAGGGAGCGATA 59.596 52.381 0.00 0.00 0.00 2.92
904 922 0.173708 GACGAACAGAAGGGAGCGAT 59.826 55.000 0.00 0.00 0.00 4.58
993 1011 1.367659 GCTCAGTGTCCATCTTCAGC 58.632 55.000 0.00 0.00 0.00 4.26
1311 1329 6.349445 CGAAAAGCTTCTCACCTAGTTAGAGA 60.349 42.308 0.00 2.85 36.68 3.10
1383 1403 5.363562 AGATTGGCAGACTCACATCATTA 57.636 39.130 0.00 0.00 0.00 1.90
1384 1404 4.232188 AGATTGGCAGACTCACATCATT 57.768 40.909 0.00 0.00 0.00 2.57
1385 1405 3.928005 AGATTGGCAGACTCACATCAT 57.072 42.857 0.00 0.00 0.00 2.45
1504 1525 5.008019 AGCTTGCATACATTCGGAAACATAG 59.992 40.000 0.00 0.00 0.00 2.23
1531 1552 7.275920 ACCAGTTTCATATATCTCCAGTGAAC 58.724 38.462 0.00 0.00 0.00 3.18
1587 1608 9.778741 AGACAAACAAATGTAGATGAAGTTAGA 57.221 29.630 0.00 0.00 32.57 2.10
1634 1658 6.175471 ACTGCATCAGTTGAGAATGATAACA 58.825 36.000 0.00 0.00 42.59 2.41
1686 1710 9.376075 CTGTTCACTCACTCTACATTATCATTT 57.624 33.333 0.00 0.00 0.00 2.32
1771 1797 8.596293 TCAAATCTTATTCCAAATTTTCTGGCT 58.404 29.630 0.00 0.00 33.63 4.75
1865 1891 4.157849 TCTGTTTGTACATGTTGGTGGA 57.842 40.909 2.30 0.00 32.86 4.02
1951 1978 5.654603 TGATGTTGGTACACTAGTGGTAG 57.345 43.478 26.12 1.91 39.29 3.18
2096 2336 3.181464 CCTTAAAGTAGGGGTAGAGCAGC 60.181 52.174 0.00 0.00 0.00 5.25
2146 2387 4.468713 TGGTTGAGAAACATCCACAATCA 58.531 39.130 0.00 0.00 41.66 2.57


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

AutoCloner maintained by Alex Coulton.