Multiple sequence alignment - TraesCS5D01G185800

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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 TraesCS5D01G185800 chr5D 100.000 2971 0 0 1 2971 287809659 287806689 0.000000e+00 5487
1 TraesCS5D01G185800 chr5D 88.462 260 27 3 2635 2892 315935973 315936231 8.000000e-81 311
2 TraesCS5D01G185800 chr5B 95.490 2572 65 20 444 2971 326918631 326916067 0.000000e+00 4060
3 TraesCS5D01G185800 chr5B 88.337 463 20 7 1 440 326919165 326918714 2.620000e-145 525
4 TraesCS5D01G185800 chr5B 88.077 260 28 3 2635 2892 364139531 364139789 3.720000e-79 305
5 TraesCS5D01G185800 chr5A 94.383 2368 82 25 444 2784 380226163 380223820 0.000000e+00 3589
6 TraesCS5D01G185800 chr5A 87.607 468 26 16 1 440 380226710 380226247 5.680000e-142 514
7 TraesCS5D01G185800 chr5A 94.709 189 9 1 2784 2971 380222999 380222811 2.900000e-75 292
8 TraesCS5D01G185800 chr5A 85.824 261 29 5 2635 2892 410512837 410513092 1.360000e-68 270
9 TraesCS5D01G185800 chr4B 86.842 266 32 3 2633 2896 317763549 317763285 8.050000e-76 294
10 TraesCS5D01G185800 chr6B 84.848 264 35 5 2633 2892 100682040 100681778 8.170000e-66 261
11 TraesCS5D01G185800 chr6A 88.780 205 18 4 2694 2896 582938529 582938730 2.290000e-61 246
12 TraesCS5D01G185800 chr1A 82.510 263 39 6 2633 2892 508734877 508735135 1.070000e-54 224


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 TraesCS5D01G185800 chr5D 287806689 287809659 2970 True 5487.0 5487 100.0000 1 2971 1 chr5D.!!$R1 2970
1 TraesCS5D01G185800 chr5B 326916067 326919165 3098 True 2292.5 4060 91.9135 1 2971 2 chr5B.!!$R1 2970
2 TraesCS5D01G185800 chr5A 380222811 380226710 3899 True 1465.0 3589 92.2330 1 2971 3 chr5A.!!$R1 2970

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
223 230 0.111061 TTGTGCAGCCAACCAGAGAT 59.889 50.000 0.00 0.0 0.00 2.75 F
1256 1405 1.135689 GCCAATGTGGACACGTTCATC 60.136 52.381 6.92 0.0 40.96 2.92 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1579 1728 1.328279 TTCGACTGCTGAGAAGACCA 58.672 50.0 0.00 0.0 0.0 4.02 R
2931 3930 0.099436 GTGATTCGTGCATGGCCTTC 59.901 55.0 3.32 0.0 0.0 3.46 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
48 49 5.961272 AGACCTCGCAAAAAGAAAGAAAAA 58.039 33.333 0.00 0.00 0.00 1.94
55 56 6.816140 TCGCAAAAAGAAAGAAAAACCAAGAT 59.184 30.769 0.00 0.00 0.00 2.40
87 90 6.947376 AATCTTGGGGTTACTGTTACTACT 57.053 37.500 0.00 0.00 0.00 2.57
88 91 8.439964 AAATCTTGGGGTTACTGTTACTACTA 57.560 34.615 0.00 0.00 0.00 1.82
89 92 6.840780 TCTTGGGGTTACTGTTACTACTAC 57.159 41.667 0.00 0.00 0.00 2.73
99 102 9.913451 GTTACTGTTACTACTACTTATGACTCG 57.087 37.037 0.00 0.00 0.00 4.18
143 148 1.452108 GCCCCCTGAATCTTGGTCG 60.452 63.158 0.00 0.00 0.00 4.79
193 198 6.207417 TGATGGTTTCTTGTCTTCATTCCTTC 59.793 38.462 0.00 0.00 0.00 3.46
223 230 0.111061 TTGTGCAGCCAACCAGAGAT 59.889 50.000 0.00 0.00 0.00 2.75
262 290 1.205893 TGTTTTGTGGTGTTTGCCCTC 59.794 47.619 0.00 0.00 0.00 4.30
267 295 1.832167 TGGTGTTTGCCCTCTTGCC 60.832 57.895 0.00 0.00 0.00 4.52
318 346 2.770164 TAGGAGCTTCTTGCAGTTCC 57.230 50.000 0.00 0.00 42.99 3.62
327 355 3.594603 TCTTGCAGTTCCAGTACTAGC 57.405 47.619 0.00 0.00 0.00 3.42
351 397 6.404708 CAGTAGTACTCAGTAGTCAGTACCA 58.595 44.000 8.03 0.00 44.19 3.25
352 398 6.535865 CAGTAGTACTCAGTAGTCAGTACCAG 59.464 46.154 8.03 0.00 44.19 4.00
353 399 5.502089 AGTACTCAGTAGTCAGTACCAGT 57.498 43.478 8.03 0.00 44.19 4.00
354 400 6.617782 AGTACTCAGTAGTCAGTACCAGTA 57.382 41.667 8.03 0.00 44.19 2.74
355 401 6.405538 AGTACTCAGTAGTCAGTACCAGTAC 58.594 44.000 15.87 15.87 44.19 2.73
356 402 5.502089 ACTCAGTAGTCAGTACCAGTACT 57.498 43.478 4.61 4.61 46.52 2.73
357 403 5.490159 ACTCAGTAGTCAGTACCAGTACTC 58.510 45.833 7.50 0.00 43.98 2.59
358 404 4.841422 TCAGTAGTCAGTACCAGTACTCC 58.159 47.826 7.50 2.40 43.98 3.85
412 458 6.989759 TCAAGCCGATTCTGCAGTAATTAATA 59.010 34.615 14.67 0.00 0.00 0.98
457 584 1.350019 AGGTACTTCTTTTGGTCCGGG 59.650 52.381 0.00 0.00 27.25 5.73
509 636 4.021544 CAGCTTTGGTGCCTTGGTATTTTA 60.022 41.667 0.00 0.00 0.00 1.52
514 641 4.211920 TGGTGCCTTGGTATTTTATAGCC 58.788 43.478 0.00 0.00 0.00 3.93
515 642 4.211920 GGTGCCTTGGTATTTTATAGCCA 58.788 43.478 0.00 0.00 0.00 4.75
516 643 4.832823 GGTGCCTTGGTATTTTATAGCCAT 59.167 41.667 0.00 0.00 0.00 4.40
517 644 6.007703 GGTGCCTTGGTATTTTATAGCCATA 58.992 40.000 0.00 0.00 0.00 2.74
574 702 5.123502 ACTGATTGCTTTAATCTGCTGACAG 59.876 40.000 0.00 0.00 44.20 3.51
593 721 4.958509 ACAGATGTGATCATAAGCCAGAG 58.041 43.478 0.00 0.00 34.06 3.35
609 737 1.669779 CAGAGCAGCCAAGACATTAGC 59.330 52.381 0.00 0.00 0.00 3.09
626 754 8.090831 AGACATTAGCGCAGAAAATCATAGATA 58.909 33.333 11.47 0.00 0.00 1.98
628 756 9.224267 ACATTAGCGCAGAAAATCATAGATAAT 57.776 29.630 11.47 0.00 0.00 1.28
629 757 9.699985 CATTAGCGCAGAAAATCATAGATAATC 57.300 33.333 11.47 0.00 0.00 1.75
649 777 9.149225 GATAATCTGTCTAACATCATGCTAAGG 57.851 37.037 0.00 0.00 0.00 2.69
930 1079 7.766278 GGTCTCTCATGTGTGTTATTACTGAAT 59.234 37.037 0.00 0.00 0.00 2.57
1256 1405 1.135689 GCCAATGTGGACACGTTCATC 60.136 52.381 6.92 0.00 40.96 2.92
1579 1728 0.550914 TTGACAGGGGAGCACAAGTT 59.449 50.000 0.00 0.00 0.00 2.66
1625 1774 0.555769 TTGAGGGTTGGTTCCAGCTT 59.444 50.000 5.74 0.00 0.00 3.74
1916 2065 2.552031 GCATCGGAGGAACTTAAGGAC 58.448 52.381 7.53 0.09 41.55 3.85
2101 2250 7.065803 CCAGTGGTAGTACACAATATTTCCTTG 59.934 40.741 0.00 0.00 43.72 3.61
2114 2263 7.611855 ACAATATTTCCTTGACAACTAGAAGGG 59.388 37.037 0.00 0.00 37.45 3.95
2115 2264 4.367039 TTTCCTTGACAACTAGAAGGGG 57.633 45.455 0.00 0.00 37.45 4.79
2125 2274 1.909986 ACTAGAAGGGGCTTTCTGTCC 59.090 52.381 12.82 0.00 37.91 4.02
2214 2364 7.906527 GCCCGTTGTAAACTTGTAATACAATAG 59.093 37.037 6.27 0.00 46.99 1.73
2346 2498 2.980541 CAAGCATTGGGACCATGGT 58.019 52.632 19.89 19.89 43.94 3.55
2347 2499 1.269012 CAAGCATTGGGACCATGGTT 58.731 50.000 20.85 2.15 43.94 3.67
2349 2501 2.028561 AGCATTGGGACCATGGTTTT 57.971 45.000 20.85 0.00 0.00 2.43
2350 2502 1.624813 AGCATTGGGACCATGGTTTTG 59.375 47.619 20.85 13.00 0.00 2.44
2380 2552 0.902531 AGCTGTGGTATACTTGCGGT 59.097 50.000 2.25 0.00 35.63 5.68
2385 2557 3.359033 TGTGGTATACTTGCGGTAGTCT 58.641 45.455 2.25 0.00 33.51 3.24
2391 2563 0.324943 ACTTGCGGTAGTCTGGCAAT 59.675 50.000 7.85 0.00 44.71 3.56
2427 2599 2.687935 TGGTTTTGCCTGAACTCTTGAC 59.312 45.455 0.00 0.00 38.35 3.18
2434 2606 0.969894 CTGAACTCTTGACGGGAGGT 59.030 55.000 0.00 0.00 35.34 3.85
2435 2607 0.966920 TGAACTCTTGACGGGAGGTC 59.033 55.000 2.25 2.25 44.97 3.85
2543 2715 2.769663 TGTAACCTCGGTAGCATGGATT 59.230 45.455 7.12 1.90 0.00 3.01
2931 3930 0.954452 GGGTGTTCTTCAACAGGCTG 59.046 55.000 14.16 14.16 43.42 4.85
2956 3955 1.875514 CCATGCACGAATCACCCATAG 59.124 52.381 0.00 0.00 0.00 2.23
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
55 56 8.541899 ACAGTAACCCCAAGATTTTTCTTTTA 57.458 30.769 0.00 0.00 0.00 1.52
87 90 3.257375 ACACAGGCAACGAGTCATAAGTA 59.743 43.478 0.00 0.00 46.39 2.24
88 91 2.037251 ACACAGGCAACGAGTCATAAGT 59.963 45.455 0.00 0.00 46.39 2.24
89 92 2.413112 CACACAGGCAACGAGTCATAAG 59.587 50.000 0.00 0.00 46.39 1.73
99 102 1.394917 CGCTAAGATCACACAGGCAAC 59.605 52.381 0.00 0.00 0.00 4.17
131 135 2.267642 CGCCCCGACCAAGATTCA 59.732 61.111 0.00 0.00 0.00 2.57
163 168 4.889409 TGAAGACAAGAAACCATCAGCTTT 59.111 37.500 0.00 0.00 0.00 3.51
193 198 3.715495 TGGCTGCACAAACAAATAACAG 58.285 40.909 0.50 0.00 0.00 3.16
223 230 2.973600 CGCGTTCGTTTTGGGGGA 60.974 61.111 0.00 0.00 0.00 4.81
262 290 0.882927 TTTCCGACGAACAGGGCAAG 60.883 55.000 0.00 0.00 0.00 4.01
267 295 2.334838 CCTAAGTTTCCGACGAACAGG 58.665 52.381 0.00 0.00 0.00 4.00
327 355 6.404708 TGGTACTGACTACTGAGTACTACTG 58.595 44.000 0.00 0.00 42.79 2.74
351 397 0.323542 AGCCGTGCTACTGGAGTACT 60.324 55.000 6.56 0.00 38.56 2.73
352 398 0.531200 AAGCCGTGCTACTGGAGTAC 59.469 55.000 0.00 0.00 38.25 2.73
353 399 1.263356 AAAGCCGTGCTACTGGAGTA 58.737 50.000 0.00 0.00 38.25 2.59
354 400 0.396811 AAAAGCCGTGCTACTGGAGT 59.603 50.000 0.00 0.00 38.25 3.85
355 401 0.798776 CAAAAGCCGTGCTACTGGAG 59.201 55.000 0.00 0.00 38.25 3.86
356 402 1.234615 GCAAAAGCCGTGCTACTGGA 61.235 55.000 0.00 0.00 38.25 3.86
357 403 1.210155 GCAAAAGCCGTGCTACTGG 59.790 57.895 0.00 0.00 38.25 4.00
358 404 0.110056 CTGCAAAAGCCGTGCTACTG 60.110 55.000 5.57 1.87 42.69 2.74
440 486 2.038033 CTGACCCGGACCAAAAGAAGTA 59.962 50.000 0.73 0.00 0.00 2.24
442 488 1.071699 TCTGACCCGGACCAAAAGAAG 59.928 52.381 0.73 0.00 0.00 2.85
447 574 0.841289 AAAGTCTGACCCGGACCAAA 59.159 50.000 0.73 0.00 40.33 3.28
457 584 2.411904 CTCTGCTCACCAAAGTCTGAC 58.588 52.381 0.00 0.00 0.00 3.51
509 636 9.833917 CATGAATCATGAGAGTATTATGGCTAT 57.166 33.333 17.76 0.00 43.81 2.97
514 641 6.091713 TGCGCATGAATCATGAGAGTATTATG 59.908 38.462 26.87 0.00 43.81 1.90
515 642 6.168389 TGCGCATGAATCATGAGAGTATTAT 58.832 36.000 26.87 0.00 43.81 1.28
516 643 5.540911 TGCGCATGAATCATGAGAGTATTA 58.459 37.500 26.87 5.95 43.81 0.98
517 644 4.383173 TGCGCATGAATCATGAGAGTATT 58.617 39.130 26.87 0.00 43.81 1.89
574 702 3.736720 TGCTCTGGCTTATGATCACATC 58.263 45.455 0.00 0.00 39.59 3.06
593 721 1.063166 GCGCTAATGTCTTGGCTGC 59.937 57.895 0.00 0.00 36.76 5.25
609 737 8.531622 AGACAGATTATCTATGATTTTCTGCG 57.468 34.615 14.05 0.00 34.00 5.18
626 754 6.294473 CCCTTAGCATGATGTTAGACAGATT 58.706 40.000 0.00 0.00 0.00 2.40
628 756 4.443457 GCCCTTAGCATGATGTTAGACAGA 60.443 45.833 0.00 0.00 42.97 3.41
629 757 3.812053 GCCCTTAGCATGATGTTAGACAG 59.188 47.826 0.00 0.00 42.97 3.51
637 765 4.210331 AGTTTAAGGCCCTTAGCATGATG 58.790 43.478 2.94 0.00 46.50 3.07
649 777 0.528017 GGCAGCAAGAGTTTAAGGCC 59.472 55.000 0.00 0.00 0.00 5.19
759 894 8.131455 ACTCTTAATGACGCATAATTACACAG 57.869 34.615 0.00 0.00 0.00 3.66
930 1079 5.192927 ACCAGATTATTCGCCTGAAATTGA 58.807 37.500 0.00 0.00 37.71 2.57
1256 1405 2.668457 CGGAGTCAAGGATCTGAAAACG 59.332 50.000 0.00 0.00 0.00 3.60
1579 1728 1.328279 TTCGACTGCTGAGAAGACCA 58.672 50.000 0.00 0.00 0.00 4.02
1625 1774 2.031919 ACCGCGACAAAGGCATCA 59.968 55.556 8.23 0.00 0.00 3.07
1772 1921 1.675641 GGCGTGCTTGTCCCAGATT 60.676 57.895 0.00 0.00 0.00 2.40
1916 2065 1.858091 ACTCAGCACTGTCACTTTCG 58.142 50.000 0.00 0.00 0.00 3.46
2101 2250 3.244596 ACAGAAAGCCCCTTCTAGTTGTC 60.245 47.826 0.00 0.00 33.81 3.18
2114 2263 2.067013 GAGTAACACGGACAGAAAGCC 58.933 52.381 0.00 0.00 0.00 4.35
2115 2264 2.750948 TGAGTAACACGGACAGAAAGC 58.249 47.619 0.00 0.00 0.00 3.51
2125 2274 6.387465 TCTTCCAGTAGAAATGAGTAACACG 58.613 40.000 0.00 0.00 32.88 4.49
2173 2323 1.338107 CGGGCATCACTCCTACCATA 58.662 55.000 0.00 0.00 0.00 2.74
2300 2452 2.523015 CAAAGCATCTGGACGCAAATC 58.477 47.619 0.00 0.00 0.00 2.17
2341 2493 0.958091 TGTTCCGAGGCAAAACCATG 59.042 50.000 0.00 0.00 43.14 3.66
2342 2494 1.613437 CTTGTTCCGAGGCAAAACCAT 59.387 47.619 0.00 0.00 43.14 3.55
2343 2495 1.028905 CTTGTTCCGAGGCAAAACCA 58.971 50.000 0.00 0.00 43.14 3.67
2344 2496 0.318699 GCTTGTTCCGAGGCAAAACC 60.319 55.000 0.00 0.00 39.61 3.27
2345 2497 0.668535 AGCTTGTTCCGAGGCAAAAC 59.331 50.000 0.00 0.00 0.00 2.43
2346 2498 0.667993 CAGCTTGTTCCGAGGCAAAA 59.332 50.000 0.00 0.00 0.00 2.44
2347 2499 0.465460 ACAGCTTGTTCCGAGGCAAA 60.465 50.000 0.00 0.00 0.00 3.68
2349 2501 1.597854 CACAGCTTGTTCCGAGGCA 60.598 57.895 0.00 0.00 0.00 4.75
2350 2502 2.328099 CCACAGCTTGTTCCGAGGC 61.328 63.158 0.00 0.00 0.00 4.70
2380 2552 6.939730 TGTTAAGAAACATCATTGCCAGACTA 59.060 34.615 0.00 0.00 40.69 2.59
2427 2599 2.376695 TACCTGGATTAGACCTCCCG 57.623 55.000 0.00 0.00 31.32 5.14
2434 2606 3.637229 CTCTTCGCCTTACCTGGATTAGA 59.363 47.826 0.00 0.00 0.00 2.10
2435 2607 3.243907 CCTCTTCGCCTTACCTGGATTAG 60.244 52.174 0.00 0.00 0.00 1.73
2503 2675 4.465632 ACAACATAAGCACGACTATCCA 57.534 40.909 0.00 0.00 0.00 3.41
2543 2715 4.574674 ATGCCATAAACTCTGTGAAGGA 57.425 40.909 0.00 0.00 0.00 3.36
2882 3881 7.289549 GGGTACATGTACTTTAATACTCCCTCT 59.710 40.741 29.89 0.00 36.36 3.69
2931 3930 0.099436 GTGATTCGTGCATGGCCTTC 59.901 55.000 3.32 0.00 0.00 3.46


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

AutoCloner maintained by Alex Coulton.