Multiple sequence alignment - TraesCS5A01G405200

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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 TraesCS5A01G405200 chr5A 100.000 2277 0 0 479 2755 596581713 596579437 0.000000e+00 4205
1 TraesCS5A01G405200 chr5A 100.000 138 0 0 1 138 596582191 596582054 3.520000e-64 255
2 TraesCS5A01G405200 chr5D 92.758 2306 108 22 482 2755 477394600 477392322 0.000000e+00 3278
3 TraesCS5A01G405200 chr5D 89.701 301 21 5 1228 1528 7043680 7043390 2.590000e-100 375
4 TraesCS5A01G405200 chr5D 89.130 138 4 2 1 138 477394751 477394625 7.900000e-36 161
5 TraesCS5A01G405200 chr5B 91.255 2287 116 31 479 2719 585024991 585022743 0.000000e+00 3038
6 TraesCS5A01G405200 chr5B 89.855 138 3 4 1 138 585025140 585025014 1.700000e-37 167
7 TraesCS5A01G405200 chr6A 84.385 301 21 8 1228 1528 583369193 583368919 3.500000e-69 272
8 TraesCS5A01G405200 chr1A 91.026 156 14 0 1229 1384 31028866 31028711 7.730000e-51 211


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 TraesCS5A01G405200 chr5A 596579437 596582191 2754 True 2230.0 4205 100.000 1 2755 2 chr5A.!!$R1 2754
1 TraesCS5A01G405200 chr5D 477392322 477394751 2429 True 1719.5 3278 90.944 1 2755 2 chr5D.!!$R2 2754
2 TraesCS5A01G405200 chr5B 585022743 585025140 2397 True 1602.5 3038 90.555 1 2719 2 chr5B.!!$R1 2718

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
682 683 0.401738 CCCGCCTGGTGATTGGATAT 59.598 55.0 9.25 0.0 0.0 1.63 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2565 2617 0.629058 TTCTCCCTATTGTTGGGGCC 59.371 55.0 0.0 0.0 43.36 5.8 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
596 597 2.974698 CGATCCGCCCTCCATTGC 60.975 66.667 0.00 0.00 0.00 3.56
682 683 0.401738 CCCGCCTGGTGATTGGATAT 59.598 55.000 9.25 0.00 0.00 1.63
730 731 1.502190 CGAGAAGAAAAAGGCGGCC 59.498 57.895 12.11 12.11 0.00 6.13
731 732 1.234615 CGAGAAGAAAAAGGCGGCCA 61.235 55.000 23.09 0.00 0.00 5.36
732 733 0.958822 GAGAAGAAAAAGGCGGCCAA 59.041 50.000 23.09 0.00 0.00 4.52
733 734 0.961753 AGAAGAAAAAGGCGGCCAAG 59.038 50.000 23.09 0.00 0.00 3.61
791 792 1.448893 TAAATGCAGGACCCGCGTC 60.449 57.895 4.92 0.00 38.38 5.19
864 865 1.343506 CGCGCCGGGTCTATAAATAC 58.656 55.000 2.18 0.00 0.00 1.89
911 912 0.755698 TTTCCCCGATCCCTCTCTCG 60.756 60.000 0.00 0.00 34.73 4.04
914 915 2.265182 CCCGATCCCTCTCTCGAGC 61.265 68.421 7.81 0.00 37.05 5.03
915 916 2.265182 CCGATCCCTCTCTCGAGCC 61.265 68.421 7.81 0.00 37.05 4.70
956 957 4.499037 ACGGTTTAGTCCTTCATTTTGC 57.501 40.909 0.00 0.00 0.00 3.68
962 963 1.615392 AGTCCTTCATTTTGCTGTGGC 59.385 47.619 0.00 0.00 39.26 5.01
967 968 2.512485 TCATTTTGCTGTGGCTGTTG 57.488 45.000 0.00 0.00 39.59 3.33
983 984 0.872388 GTTGGCGTTAAGTGTCAGGG 59.128 55.000 0.00 0.00 0.00 4.45
991 992 3.746492 CGTTAAGTGTCAGGGGAAAGAAG 59.254 47.826 0.00 0.00 0.00 2.85
1553 1566 2.243810 CTCATGACCTACTAGGAGGGC 58.756 57.143 25.50 23.68 46.08 5.19
1555 1568 3.445888 GACCTACTAGGAGGGCGC 58.554 66.667 25.50 10.28 41.36 6.53
1802 1834 4.158209 TCGTCCGTCACCTGATGTAAATTA 59.842 41.667 0.00 0.00 0.00 1.40
1803 1835 5.047847 CGTCCGTCACCTGATGTAAATTAT 58.952 41.667 0.00 0.00 0.00 1.28
1804 1836 5.522460 CGTCCGTCACCTGATGTAAATTATT 59.478 40.000 0.00 0.00 0.00 1.40
1927 1959 1.149148 GCACCGGTCTCTCTGTTTTC 58.851 55.000 2.59 0.00 0.00 2.29
2000 2039 2.813779 AGATGCGCGTCTTCATTTTC 57.186 45.000 26.28 0.00 0.00 2.29
2029 2068 0.804364 ATTCACCGTCAGCGTACGTA 59.196 50.000 17.90 0.00 41.27 3.57
2084 2128 2.356553 GCGCAGGTTGACGTACCA 60.357 61.111 10.09 0.00 40.82 3.25
2090 2135 0.879765 AGGTTGACGTACCAGTCTCG 59.120 55.000 10.09 0.00 40.82 4.04
2175 2224 0.389817 GGCCAAACGGAAAAGATGCC 60.390 55.000 0.00 0.00 0.00 4.40
2277 2326 3.623060 CCGTGGTGATAGAATTTGACAGG 59.377 47.826 0.00 0.00 0.00 4.00
2371 2420 2.493675 GCAAGAGCTTAAAAAGGAGGGG 59.506 50.000 0.00 0.00 37.91 4.79
2431 2483 1.813513 ACAGTTGCTTCCAGATTCCG 58.186 50.000 0.00 0.00 0.00 4.30
2472 2524 2.287977 ACTTCAACAGGCCCCTAAAC 57.712 50.000 0.00 0.00 0.00 2.01
2489 2541 2.344093 AACACATAGTCCCCAGTCCT 57.656 50.000 0.00 0.00 0.00 3.85
2545 2597 3.836562 AGGAAAAGCAAGATGCCAAGATT 59.163 39.130 0.00 0.00 46.52 2.40
2553 2605 5.244626 AGCAAGATGCCAAGATTTAACAAGT 59.755 36.000 0.00 0.00 46.52 3.16
2565 2617 9.329913 CAAGATTTAACAAGTCTTCCAATTACG 57.670 33.333 0.00 0.00 30.19 3.18
2596 2648 7.213178 ACAATAGGGAGAATGATACAACCTT 57.787 36.000 0.00 0.00 0.00 3.50
2598 2650 7.092444 ACAATAGGGAGAATGATACAACCTTGA 60.092 37.037 0.00 0.00 0.00 3.02
2604 2656 6.199937 AGAATGATACAACCTTGATGCAAC 57.800 37.500 0.00 0.00 0.00 4.17
2605 2657 4.621068 ATGATACAACCTTGATGCAACG 57.379 40.909 0.00 0.00 0.00 4.10
2606 2658 2.746904 TGATACAACCTTGATGCAACGG 59.253 45.455 0.00 0.00 0.00 4.44
2614 2666 2.023741 GATGCAACGGCGCTGATG 59.976 61.111 25.98 23.26 45.35 3.07
2660 2712 4.021925 GCACCGCAGAACCTCCCT 62.022 66.667 0.00 0.00 0.00 4.20
2707 2759 2.244651 CCGTATGCCTTGTAGCCGC 61.245 63.158 0.00 0.00 0.00 6.53
2741 2793 4.777896 TCCATAACCCTAGATATGGCTGTC 59.222 45.833 17.62 0.00 45.38 3.51
2742 2794 4.532126 CCATAACCCTAGATATGGCTGTCA 59.468 45.833 13.06 0.00 41.41 3.58
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
667 668 5.163311 TGTGACAGTATATCCAATCACCAGG 60.163 44.000 0.00 0.00 36.47 4.45
672 673 4.501400 CGGCTGTGACAGTATATCCAATCA 60.501 45.833 14.82 0.00 33.43 2.57
682 683 3.353557 AGATTCTACGGCTGTGACAGTA 58.646 45.455 14.82 0.00 33.43 2.74
730 731 0.598065 CCCGGTGGCTTTCTTTCTTG 59.402 55.000 0.00 0.00 0.00 3.02
731 732 0.539669 CCCCGGTGGCTTTCTTTCTT 60.540 55.000 0.00 0.00 0.00 2.52
732 733 1.074951 CCCCGGTGGCTTTCTTTCT 59.925 57.895 0.00 0.00 0.00 2.52
733 734 3.681473 CCCCGGTGGCTTTCTTTC 58.319 61.111 0.00 0.00 0.00 2.62
864 865 2.464459 GCGATGAGGAAACTGGCGG 61.464 63.158 0.00 0.00 44.43 6.13
915 916 1.446016 AATTCCGGGAATCTAGGGGG 58.554 55.000 21.95 0.00 30.29 5.40
942 943 1.615392 GCCACAGCAAAATGAAGGACT 59.385 47.619 0.00 0.00 39.53 3.85
956 957 0.238289 CTTAACGCCAACAGCCACAG 59.762 55.000 0.00 0.00 38.78 3.66
962 963 1.531149 CCTGACACTTAACGCCAACAG 59.469 52.381 0.00 0.00 0.00 3.16
967 968 0.035739 TTCCCCTGACACTTAACGCC 59.964 55.000 0.00 0.00 0.00 5.68
983 984 4.764308 AGAGACAGCATTTTCCTTCTTTCC 59.236 41.667 0.00 0.00 0.00 3.13
991 992 1.471684 CCTGCAGAGACAGCATTTTCC 59.528 52.381 17.39 0.00 41.82 3.13
1118 1119 4.131088 GACGAGCTGGGGGACGAC 62.131 72.222 0.00 0.00 0.00 4.34
1202 1206 2.431942 CGGTTCGACACCTTCCGG 60.432 66.667 12.80 0.00 44.69 5.14
1578 1599 4.736896 GTGACCTCCGTCCGTGGC 62.737 72.222 0.00 0.00 38.32 5.01
1802 1834 6.183360 GCGGCAGTAGTTTTCCATTTAGTAAT 60.183 38.462 0.00 0.00 0.00 1.89
1803 1835 5.122711 GCGGCAGTAGTTTTCCATTTAGTAA 59.877 40.000 0.00 0.00 0.00 2.24
1804 1836 4.632688 GCGGCAGTAGTTTTCCATTTAGTA 59.367 41.667 0.00 0.00 0.00 1.82
1899 1931 1.870055 GAGACCGGTGCGTCAACCTA 61.870 60.000 14.63 0.00 38.14 3.08
1927 1959 5.206299 GTCGACGTTAGATAATCCAGAGTG 58.794 45.833 0.00 0.00 0.00 3.51
1987 2026 4.870426 TCAGTGGATAGAAAATGAAGACGC 59.130 41.667 0.00 0.00 0.00 5.19
2000 2039 3.711086 CTGACGGTGAATCAGTGGATAG 58.289 50.000 0.00 0.00 39.04 2.08
2045 2084 1.933115 ATGCCGACGACCATTTTGGC 61.933 55.000 0.00 0.00 42.67 4.52
2084 2128 1.583054 AAGCGAAAAACAGCGAGACT 58.417 45.000 0.00 0.00 38.61 3.24
2090 2135 4.913345 ACCGTTAAATAAGCGAAAAACAGC 59.087 37.500 0.00 0.00 0.00 4.40
2175 2224 0.750850 TCCGATAGAAAAGAGGCCGG 59.249 55.000 0.00 0.00 39.76 6.13
2213 2262 2.433664 GGGGTGGCTCACGTTACG 60.434 66.667 2.19 2.19 34.83 3.18
2225 2274 1.950909 TGTTTTCACTAAAGCGGGGTG 59.049 47.619 0.00 0.00 0.00 4.61
2226 2275 2.351706 TGTTTTCACTAAAGCGGGGT 57.648 45.000 0.00 0.00 0.00 4.95
2228 2277 4.561735 TCTTTGTTTTCACTAAAGCGGG 57.438 40.909 0.00 0.00 32.81 6.13
2277 2326 5.105716 TGCTTAGTAACTCAGTGATCTGTCC 60.106 44.000 0.00 0.00 41.91 4.02
2291 2340 1.467342 CGGCCACCTTTGCTTAGTAAC 59.533 52.381 2.24 0.00 0.00 2.50
2325 2374 6.263168 CCTTTGCCCTACTTATTCGATTCAAT 59.737 38.462 0.00 0.00 0.00 2.57
2371 2420 6.071952 AGTCTTCTAGCTAGCATATCTCTTGC 60.072 42.308 18.83 0.00 40.45 4.01
2472 2524 2.166907 AGAGGACTGGGGACTATGTG 57.833 55.000 0.00 0.00 0.00 3.21
2489 2541 4.565652 CCCAACCTCTAAAAGCTGCTTAGA 60.566 45.833 16.31 14.25 34.85 2.10
2545 2597 4.456566 GGCCGTAATTGGAAGACTTGTTAA 59.543 41.667 0.00 0.00 0.00 2.01
2553 2605 0.699399 TTGGGGCCGTAATTGGAAGA 59.301 50.000 0.00 0.00 0.00 2.87
2565 2617 0.629058 TTCTCCCTATTGTTGGGGCC 59.371 55.000 0.00 0.00 43.36 5.80
2585 2637 2.746904 CCGTTGCATCAAGGTTGTATCA 59.253 45.455 0.00 0.00 0.00 2.15
2590 2642 1.442520 CGCCGTTGCATCAAGGTTG 60.443 57.895 0.00 0.00 37.32 3.77
2596 2648 2.436469 ATCAGCGCCGTTGCATCA 60.436 55.556 2.29 0.00 37.32 3.07
2598 2650 3.511595 CCATCAGCGCCGTTGCAT 61.512 61.111 2.29 0.00 37.32 3.96
2604 2656 3.869272 GAAGCACCATCAGCGCCG 61.869 66.667 2.29 0.00 37.01 6.46
2605 2657 3.512516 GGAAGCACCATCAGCGCC 61.513 66.667 2.29 0.00 38.79 6.53
2606 2658 2.747460 TGGAAGCACCATCAGCGC 60.747 61.111 0.00 0.00 44.64 5.92
2660 2712 3.961484 TGGAGAGGAGAGAGAGCATAA 57.039 47.619 0.00 0.00 0.00 1.90
2707 2759 1.475213 GGGTTATGGAAGGGCGAAGAG 60.475 57.143 0.00 0.00 0.00 2.85


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

AutoCloner maintained by Alex Coulton.