Multiple sequence alignment - TraesCS1A01G083900

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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 TraesCS1A01G083900 chr1A 100.000 2735 0 0 1 2735 68449747 68452481 0.000000e+00 5051
1 TraesCS1A01G083900 chr1A 92.565 807 56 3 1 806 368383171 368382368 0.000000e+00 1155
2 TraesCS1A01G083900 chr1B 92.296 1934 108 14 807 2735 111046875 111048772 0.000000e+00 2708
3 TraesCS1A01G083900 chr1D 98.357 1522 23 2 807 2328 69192360 69193879 0.000000e+00 2671
4 TraesCS1A01G083900 chr1D 94.315 387 12 2 2349 2735 69194014 69194390 3.920000e-163 584
5 TraesCS1A01G083900 chr7A 92.910 818 50 5 1 810 626352215 626353032 0.000000e+00 1182
6 TraesCS1A01G083900 chr7A 93.069 808 54 2 1 806 30775482 30776289 0.000000e+00 1181
7 TraesCS1A01G083900 chr7A 92.963 810 51 5 1 806 30763071 30763878 0.000000e+00 1175
8 TraesCS1A01G083900 chr7A 92.478 811 56 3 1 806 30753581 30754391 0.000000e+00 1155
9 TraesCS1A01G083900 chr7A 92.478 811 56 2 1 806 665117571 665116761 0.000000e+00 1155
10 TraesCS1A01G083900 chr3B 92.840 810 54 3 1 809 795808796 795809602 0.000000e+00 1171
11 TraesCS1A01G083900 chr2B 92.937 807 53 3 1 806 767899563 767900366 0.000000e+00 1171
12 TraesCS1A01G083900 chr2B 75.152 495 88 27 813 1297 383378703 383378234 1.660000e-47 200
13 TraesCS1A01G083900 chr2A 92.770 816 49 4 1 806 48333607 48334422 0.000000e+00 1171
14 TraesCS1A01G083900 chr2A 75.256 489 92 23 813 1294 419451961 419452427 3.570000e-49 206
15 TraesCS1A01G083900 chr2D 74.494 494 93 28 813 1297 315501229 315500760 1.670000e-42 183


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 TraesCS1A01G083900 chr1A 68449747 68452481 2734 False 5051.0 5051 100.000 1 2735 1 chr1A.!!$F1 2734
1 TraesCS1A01G083900 chr1A 368382368 368383171 803 True 1155.0 1155 92.565 1 806 1 chr1A.!!$R1 805
2 TraesCS1A01G083900 chr1B 111046875 111048772 1897 False 2708.0 2708 92.296 807 2735 1 chr1B.!!$F1 1928
3 TraesCS1A01G083900 chr1D 69192360 69194390 2030 False 1627.5 2671 96.336 807 2735 2 chr1D.!!$F1 1928
4 TraesCS1A01G083900 chr7A 626352215 626353032 817 False 1182.0 1182 92.910 1 810 1 chr7A.!!$F4 809
5 TraesCS1A01G083900 chr7A 30775482 30776289 807 False 1181.0 1181 93.069 1 806 1 chr7A.!!$F3 805
6 TraesCS1A01G083900 chr7A 30763071 30763878 807 False 1175.0 1175 92.963 1 806 1 chr7A.!!$F2 805
7 TraesCS1A01G083900 chr7A 30753581 30754391 810 False 1155.0 1155 92.478 1 806 1 chr7A.!!$F1 805
8 TraesCS1A01G083900 chr7A 665116761 665117571 810 True 1155.0 1155 92.478 1 806 1 chr7A.!!$R1 805
9 TraesCS1A01G083900 chr3B 795808796 795809602 806 False 1171.0 1171 92.840 1 809 1 chr3B.!!$F1 808
10 TraesCS1A01G083900 chr2B 767899563 767900366 803 False 1171.0 1171 92.937 1 806 1 chr2B.!!$F1 805
11 TraesCS1A01G083900 chr2A 48333607 48334422 815 False 1171.0 1171 92.770 1 806 1 chr2A.!!$F1 805

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
186 212 0.247735 CACGATCTGAGACGTCGGAC 60.248 60.0 10.46 6.7 41.08 4.79 F
1017 1047 0.036732 TCATGGAAGCCAGTCACACC 59.963 55.0 0.00 0.0 36.75 4.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1547 1577 1.815003 GCTGGGTGAACTTTGGATCAG 59.185 52.381 0.0 0.0 0.00 2.90 R
2305 2337 2.949177 TAGTATTACCTCCGGGCGTA 57.051 50.000 0.0 0.0 35.63 4.42 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
20 21 1.918262 TCTTCCTCATGCCATTGGAGT 59.082 47.619 6.95 0.00 0.00 3.85
44 45 1.680522 GAAGAGATGAGGCCCTCGCA 61.681 60.000 6.21 0.00 36.38 5.10
73 92 3.222855 CTCCGCTCGCCTCTCCAT 61.223 66.667 0.00 0.00 0.00 3.41
131 157 3.684788 TCACTCCTATGCGCTTCTTTTTC 59.315 43.478 9.73 0.00 0.00 2.29
186 212 0.247735 CACGATCTGAGACGTCGGAC 60.248 60.000 10.46 6.70 41.08 4.79
216 242 1.340017 CCGACTTGGATGTGGGTTCAT 60.340 52.381 0.00 0.00 42.00 2.57
302 328 1.448540 CAGAACGCATCTCCGCCTT 60.449 57.895 0.00 0.00 35.73 4.35
437 467 1.341852 GAGAGAGGGGCGATTAGGTTC 59.658 57.143 0.00 0.00 0.00 3.62
656 686 6.486657 CCCTCTCATGTTTCTTTCTGTTGTAA 59.513 38.462 0.00 0.00 0.00 2.41
709 739 9.662947 TCTACTATATGCGTAGTAAATGCTCTA 57.337 33.333 11.48 0.00 41.03 2.43
798 828 8.742554 AATTTAGTCGAAAAACTGCCTATTTG 57.257 30.769 0.00 0.00 0.00 2.32
811 841 7.369803 ACTGCCTATTTGCTTATCATTATCG 57.630 36.000 0.00 0.00 0.00 2.92
1017 1047 0.036732 TCATGGAAGCCAGTCACACC 59.963 55.000 0.00 0.00 36.75 4.16
1102 1132 3.555956 CCTCGTATTGCAGACCAACATAC 59.444 47.826 0.00 0.00 35.99 2.39
1474 1504 3.437049 GCTGTCCTGCTTTACTAAAGGTG 59.563 47.826 10.03 0.00 38.93 4.00
1547 1577 2.579873 CCTCATGTGGTGGGATGATTC 58.420 52.381 5.61 0.00 0.00 2.52
1615 1645 3.263425 CCTGAGCACCTTCCCTTTTACTA 59.737 47.826 0.00 0.00 0.00 1.82
2305 2337 6.714810 TCTCTTACATTTTGTGGCACAACTAT 59.285 34.615 31.20 23.11 44.16 2.12
2335 2367 7.536159 CGGAGGTAATACTATCCCTACTTTT 57.464 40.000 8.78 0.00 0.00 2.27
2336 2368 7.960262 CGGAGGTAATACTATCCCTACTTTTT 58.040 38.462 8.78 0.00 0.00 1.94
2406 2556 2.003301 GCAAGTTGCTCTACACTAGGC 58.997 52.381 20.71 0.00 40.96 3.93
2412 2562 1.285078 TGCTCTACACTAGGCTCTGGA 59.715 52.381 0.00 0.00 0.00 3.86
2426 2576 2.101582 GCTCTGGACTGATACCGAATGT 59.898 50.000 0.00 0.00 0.00 2.71
2463 2613 2.337849 TCTGTGGCAGATATATGGGCA 58.662 47.619 0.00 6.23 35.39 5.36
2464 2614 2.914941 TCTGTGGCAGATATATGGGCAT 59.085 45.455 11.80 0.00 39.38 4.40
2465 2615 4.103342 TCTGTGGCAGATATATGGGCATA 58.897 43.478 11.80 9.16 39.38 3.14
2466 2616 4.723285 TCTGTGGCAGATATATGGGCATAT 59.277 41.667 11.80 0.00 39.38 1.78
2467 2617 4.784177 TGTGGCAGATATATGGGCATATG 58.216 43.478 11.80 0.00 39.38 1.78
2468 2618 4.139786 GTGGCAGATATATGGGCATATGG 58.860 47.826 4.56 0.00 39.38 2.74
2498 2648 1.208535 CTCCCATTGGCATTGCATGTT 59.791 47.619 11.39 0.00 0.00 2.71
2501 2651 2.937799 CCCATTGGCATTGCATGTTAAC 59.062 45.455 11.39 0.00 0.00 2.01
2511 2661 1.001924 TGCATGTTAACTGCGTTGGTG 60.002 47.619 18.69 4.18 42.62 4.17
2516 2666 5.457140 CATGTTAACTGCGTTGGTGTTTAT 58.543 37.500 7.22 0.00 0.00 1.40
2534 2684 9.016438 GGTGTTTATTTGGTAATAGGTTTCAGA 57.984 33.333 0.00 0.00 0.00 3.27
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
20 21 2.503356 GAGGGCCTCATCTCTTCTCAAA 59.497 50.000 28.55 0.00 0.00 2.69
44 45 2.363147 GCGGAGGAGGAGGAGTGT 60.363 66.667 0.00 0.00 0.00 3.55
131 157 2.678934 TCTCCGTTCCTGACCGGG 60.679 66.667 6.32 0.00 44.32 5.73
186 212 2.125673 CAAGTCGGTAGCCCACGG 60.126 66.667 0.00 0.00 0.00 4.94
216 242 1.215382 CGCGTGAAGAGATGTGGGA 59.785 57.895 0.00 0.00 0.00 4.37
302 328 2.047655 GGAACGATGTGGGCGTGA 60.048 61.111 0.00 0.00 41.75 4.35
312 338 1.449246 GCAGCAGCAGAGGAACGAT 60.449 57.895 0.00 0.00 41.58 3.73
360 389 0.813184 TCTCCCGTCAACCGTGTATC 59.187 55.000 0.00 0.00 33.66 2.24
399 428 0.835276 TCGTACAGGATCCGGAGAGA 59.165 55.000 19.55 10.74 0.00 3.10
544 574 3.591254 GACGGCCTTCTTGTCGGCT 62.591 63.158 0.00 0.00 45.57 5.52
656 686 4.313282 TCTACGCATATCGCTAGTACTGT 58.687 43.478 5.39 0.00 43.23 3.55
722 752 7.380536 ACATTGACAACATTGATAACATGCTT 58.619 30.769 0.00 0.00 33.37 3.91
725 755 8.920509 ATGACATTGACAACATTGATAACATG 57.079 30.769 0.00 0.00 33.37 3.21
779 809 4.160736 AGCAAATAGGCAGTTTTTCGAC 57.839 40.909 0.00 0.00 35.83 4.20
798 828 7.093354 TGAGAAGGATGTCGATAATGATAAGC 58.907 38.462 0.00 0.00 0.00 3.09
919 949 1.524863 CGTTGAGGGTCACTCTCGGT 61.525 60.000 0.00 0.00 46.72 4.69
1017 1047 2.273449 GCCATGGACTCAGGGGTG 59.727 66.667 18.40 0.00 44.41 4.61
1068 1098 3.057734 CAATACGAGGAGTAAATCGCCC 58.942 50.000 0.00 0.00 42.61 6.13
1474 1504 3.181443 ACCGGTAGGATCAAAATCATCCC 60.181 47.826 4.49 0.00 40.90 3.85
1547 1577 1.815003 GCTGGGTGAACTTTGGATCAG 59.185 52.381 0.00 0.00 0.00 2.90
1615 1645 7.385205 GCGTACATGGTCAGTTTCTTCATATAT 59.615 37.037 0.00 0.00 0.00 0.86
1633 1665 4.146616 GCTATTCTGTAACTCGCGTACATG 59.853 45.833 5.77 0.00 0.00 3.21
1914 1946 6.769512 TCAATGCTAACTACTCAAAGGAAGT 58.230 36.000 0.00 0.00 0.00 3.01
2305 2337 2.949177 TAGTATTACCTCCGGGCGTA 57.051 50.000 0.00 0.00 35.63 4.42
2406 2556 4.115516 CAACATTCGGTATCAGTCCAGAG 58.884 47.826 0.00 0.00 0.00 3.35
2412 2562 3.262420 GAGCACAACATTCGGTATCAGT 58.738 45.455 0.00 0.00 0.00 3.41
2426 2576 5.007626 GCCACAGATATAATTTCGAGCACAA 59.992 40.000 0.00 0.00 0.00 3.33
2461 2611 5.102953 TGGGAGATACATAAGCCATATGC 57.897 43.478 0.00 0.00 44.46 3.14
2462 2612 6.544931 CCAATGGGAGATACATAAGCCATATG 59.455 42.308 0.00 0.00 41.21 1.78
2463 2613 6.666678 CCAATGGGAGATACATAAGCCATAT 58.333 40.000 0.00 0.00 35.59 1.78
2464 2614 5.573502 GCCAATGGGAGATACATAAGCCATA 60.574 44.000 0.00 0.00 35.59 2.74
2465 2615 4.812096 GCCAATGGGAGATACATAAGCCAT 60.812 45.833 0.00 0.00 35.59 4.40
2466 2616 3.498481 GCCAATGGGAGATACATAAGCCA 60.498 47.826 0.00 0.00 35.59 4.75
2467 2617 3.084786 GCCAATGGGAGATACATAAGCC 58.915 50.000 0.00 0.00 35.59 4.35
2468 2618 3.754965 TGCCAATGGGAGATACATAAGC 58.245 45.455 0.00 0.00 35.59 3.09
2501 2651 3.363341 ACCAAATAAACACCAACGCAG 57.637 42.857 0.00 0.00 0.00 5.18
2569 2719 4.524802 TCCTGAATCATGCCCAATAGTT 57.475 40.909 0.00 0.00 0.00 2.24
2570 2720 4.736611 ATCCTGAATCATGCCCAATAGT 57.263 40.909 0.00 0.00 0.00 2.12
2612 2762 3.933332 GAGAAAATGAAGGAGGTACACCG 59.067 47.826 0.00 0.00 46.15 4.94


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

AutoCloner maintained by Alex Coulton.