Multiple sequence alignment - TraesCS3A01G287300

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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 TraesCS3A01G287300 chr3A 100.000 2643 0 0 1 2643 515736501 515733859 0.000000e+00 4881.0
1 TraesCS3A01G287300 chr3D 90.743 2571 106 33 120 2643 395651377 395648892 0.000000e+00 3308.0
2 TraesCS3A01G287300 chr3B 91.312 1105 67 14 896 1985 520465215 520464125 0.000000e+00 1482.0
3 TraesCS3A01G287300 chr3B 91.346 728 43 10 29 748 520471959 520471244 0.000000e+00 977.0
4 TraesCS3A01G287300 chr3B 86.890 328 17 7 2333 2643 520463712 520463394 7.000000e-91 344.0
5 TraesCS3A01G287300 chr3B 92.237 219 12 2 2017 2230 520464128 520463910 3.310000e-79 305.0
6 TraesCS3A01G287300 chr3B 97.727 44 1 0 1 44 520472015 520471972 2.820000e-10 76.8


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 TraesCS3A01G287300 chr3A 515733859 515736501 2642 True 4881.000000 4881 100.000000 1 2643 1 chr3A.!!$R1 2642
1 TraesCS3A01G287300 chr3D 395648892 395651377 2485 True 3308.000000 3308 90.743000 120 2643 1 chr3D.!!$R1 2523
2 TraesCS3A01G287300 chr3B 520463394 520465215 1821 True 710.333333 1482 90.146333 896 2643 3 chr3B.!!$R1 1747
3 TraesCS3A01G287300 chr3B 520471244 520472015 771 True 526.900000 977 94.536500 1 748 2 chr3B.!!$R2 747

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
576 618 0.161024 GACAACGCTACTTCACACGC 59.839 55.0 0.0 0.0 0.0 5.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2273 2491 0.45826 ACAAAACCCGCCAAGAACAC 59.542 50.0 0.0 0.0 0.0 3.32 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
54 83 7.894364 AGGTCTTTTTATGTGTAGAGGACTAGA 59.106 37.037 0.00 0.00 0.00 2.43
55 84 8.697292 GGTCTTTTTATGTGTAGAGGACTAGAT 58.303 37.037 0.00 0.00 0.00 1.98
80 109 2.766263 TGACGATGGATTTCTGGCTACT 59.234 45.455 0.00 0.00 0.00 2.57
81 110 3.197766 TGACGATGGATTTCTGGCTACTT 59.802 43.478 0.00 0.00 0.00 2.24
82 111 4.404394 TGACGATGGATTTCTGGCTACTTA 59.596 41.667 0.00 0.00 0.00 2.24
83 112 4.950050 ACGATGGATTTCTGGCTACTTAG 58.050 43.478 0.00 0.00 0.00 2.18
112 141 4.157840 CACTTCCTAGGTTTGGTAATTGGC 59.842 45.833 9.08 0.00 0.00 4.52
116 145 4.017958 TCCTAGGTTTGGTAATTGGCATCA 60.018 41.667 9.08 0.00 0.00 3.07
147 176 4.624024 CGCCTTCTTGACGTGTTCTTATAA 59.376 41.667 0.00 0.00 0.00 0.98
310 352 2.078849 CGAAAGGGATTGGCAAAACC 57.921 50.000 3.01 9.81 39.84 3.27
412 454 1.852942 AAGTACACTGACACTGTGCG 58.147 50.000 7.90 0.00 36.91 5.34
420 462 1.261619 CTGACACTGTGCGGTTTTCTC 59.738 52.381 7.90 0.00 0.00 2.87
462 504 4.338879 AGGGTTCATTTCCTTCTGATGTG 58.661 43.478 0.00 0.00 0.00 3.21
524 566 2.771089 ACATGTTCTGATGTTGCTCGT 58.229 42.857 0.00 0.00 32.38 4.18
545 587 5.992829 TCGTTAATAAGACAAACAGGCAAGA 59.007 36.000 0.00 0.00 0.00 3.02
570 612 2.271800 CATCCAGGACAACGCTACTTC 58.728 52.381 0.00 0.00 0.00 3.01
576 618 0.161024 GACAACGCTACTTCACACGC 59.839 55.000 0.00 0.00 0.00 5.34
580 622 1.516386 CGCTACTTCACACGCGGAT 60.516 57.895 12.47 0.00 41.72 4.18
597 640 4.142687 CGCGGATGTTTATTCTTTCTTGGT 60.143 41.667 0.00 0.00 0.00 3.67
667 710 4.829064 TCTTGTAATGGTTTGACTGTGC 57.171 40.909 0.00 0.00 0.00 4.57
676 719 1.885887 GTTTGACTGTGCTTGCCCATA 59.114 47.619 0.00 0.00 0.00 2.74
681 724 2.357009 GACTGTGCTTGCCCATATTCTG 59.643 50.000 0.00 0.00 0.00 3.02
698 741 7.281774 CCATATTCTGTACTCTGCTTGTTGATT 59.718 37.037 0.00 0.00 0.00 2.57
725 768 1.959042 CCTCGCTGCCTTACATCAAT 58.041 50.000 0.00 0.00 0.00 2.57
801 852 5.514274 TGAAAACAGTTGATCTTGGTTCC 57.486 39.130 0.00 0.00 0.00 3.62
815 866 1.201424 GGTTCCGGGACTCTACCAAT 58.799 55.000 13.96 0.00 0.00 3.16
870 921 3.823873 CGGGACTCTAGCAACTATCAGAT 59.176 47.826 0.00 0.00 0.00 2.90
896 947 8.258007 TGGTAAGACAGTGATATGTTAAAGAGG 58.742 37.037 0.00 0.00 32.25 3.69
974 1028 4.220382 TCTCCGTTGCCATTTCATTTCATT 59.780 37.500 0.00 0.00 0.00 2.57
1087 1141 0.251033 ATGCTTGCAGCTTCCAGACA 60.251 50.000 0.87 0.00 42.97 3.41
1111 1165 1.134670 ACAAGAATCTGGAGCGGCTAC 60.135 52.381 4.92 4.92 0.00 3.58
1284 1338 0.693767 AAGGGAGAGGGGATGAGCAG 60.694 60.000 0.00 0.00 0.00 4.24
1296 1350 1.136695 GATGAGCAGGAGGTGAGTCAG 59.863 57.143 0.00 0.00 0.00 3.51
1340 1394 1.742831 TGCAGCAAAGTGTCTTCGTTT 59.257 42.857 0.00 0.00 0.00 3.60
1354 1408 5.403166 TGTCTTCGTTTGTCCAATAACTACG 59.597 40.000 0.00 0.00 32.78 3.51
1494 1548 2.435938 TGCCGCTAGCCTTTTCCG 60.436 61.111 9.66 0.00 42.71 4.30
1554 1608 2.807676 AGGGATGTGAATGGTTGAACC 58.192 47.619 7.57 7.57 39.22 3.62
1567 1621 2.550180 GGTTGAACCACAGAAGCTCTTC 59.450 50.000 9.98 1.52 38.42 2.87
1660 1714 0.798776 GACCTGATGAGCAACCAACG 59.201 55.000 0.00 0.00 0.00 4.10
1853 1921 5.243981 ACTTCTGTTGAGAGATCAACCATG 58.756 41.667 16.20 8.42 46.74 3.66
1857 1925 4.318332 TGTTGAGAGATCAACCATGACAC 58.682 43.478 16.20 0.00 46.74 3.67
1966 2034 2.632028 AGAGCAAGATCACTGTGTCAGT 59.368 45.455 7.79 0.00 46.51 3.41
1980 2048 5.188555 ACTGTGTCAGTAGGATTCATGTCAT 59.811 40.000 0.27 0.00 43.46 3.06
2006 2074 5.917462 TGTGATATGCGCTATTGCCTATAT 58.083 37.500 9.73 0.01 35.36 0.86
2071 2153 1.153289 CCGTGGGCAGGATGAAGAG 60.153 63.158 0.00 0.00 39.69 2.85
2142 2232 6.936279 AGTAGTCTAAAAGCTGCAGTTGATA 58.064 36.000 16.64 5.55 0.00 2.15
2147 2237 7.041508 AGTCTAAAAGCTGCAGTTGATATATGC 60.042 37.037 16.64 0.00 40.40 3.14
2180 2270 6.914259 TGTGTGAGTAGTGAAGAGTGATTAG 58.086 40.000 0.00 0.00 0.00 1.73
2192 2282 6.314648 TGAAGAGTGATTAGTGATTGTGATGC 59.685 38.462 0.00 0.00 0.00 3.91
2247 2465 8.328014 TGCTATATATATCTGTGGCATTTTGGA 58.672 33.333 0.00 0.00 0.00 3.53
2251 2469 9.758021 ATATATATCTGTGGCATTTTGGATTCA 57.242 29.630 0.00 0.00 0.00 2.57
2264 2482 7.201848 GCATTTTGGATTCATTCTATGTCTCCA 60.202 37.037 0.00 0.00 38.88 3.86
2296 2514 0.681564 TCTTGGCGGGTTTTGTGTGT 60.682 50.000 0.00 0.00 0.00 3.72
2297 2515 0.527385 CTTGGCGGGTTTTGTGTGTG 60.527 55.000 0.00 0.00 0.00 3.82
2298 2516 1.251527 TTGGCGGGTTTTGTGTGTGT 61.252 50.000 0.00 0.00 0.00 3.72
2299 2517 1.226831 GGCGGGTTTTGTGTGTGTG 60.227 57.895 0.00 0.00 0.00 3.82
2300 2518 1.509004 GCGGGTTTTGTGTGTGTGT 59.491 52.632 0.00 0.00 0.00 3.72
2301 2519 0.800300 GCGGGTTTTGTGTGTGTGTG 60.800 55.000 0.00 0.00 0.00 3.82
2302 2520 0.800300 CGGGTTTTGTGTGTGTGTGC 60.800 55.000 0.00 0.00 0.00 4.57
2303 2521 0.800300 GGGTTTTGTGTGTGTGTGCG 60.800 55.000 0.00 0.00 0.00 5.34
2304 2522 1.409982 GGTTTTGTGTGTGTGTGCGC 61.410 55.000 0.00 0.00 0.00 6.09
2305 2523 1.512947 TTTTGTGTGTGTGTGCGCG 60.513 52.632 0.00 0.00 0.00 6.86
2306 2524 4.528740 TTGTGTGTGTGTGCGCGC 62.529 61.111 27.26 27.26 36.27 6.86
2338 2556 3.371898 CGCTCTCATAATTTGTGCACTGA 59.628 43.478 19.41 11.03 0.00 3.41
2513 2737 0.250640 AGCACAGGACCTGCAGAAAG 60.251 55.000 21.95 0.15 37.08 2.62
2612 2853 1.117150 GGGACCGTACTTGCCTATCA 58.883 55.000 0.00 0.00 0.00 2.15
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 2.325484 TGCTCTCCTGGACACTAACAA 58.675 47.619 0.00 0.00 0.00 2.83
54 83 6.305272 AGCCAGAAATCCATCGTCATATAT 57.695 37.500 0.00 0.00 0.00 0.86
55 84 5.745312 AGCCAGAAATCCATCGTCATATA 57.255 39.130 0.00 0.00 0.00 0.86
80 109 7.981142 ACCAAACCTAGGAAGTGAAATACTAA 58.019 34.615 17.98 0.00 39.18 2.24
81 110 7.563724 ACCAAACCTAGGAAGTGAAATACTA 57.436 36.000 17.98 0.00 39.18 1.82
82 111 6.449830 ACCAAACCTAGGAAGTGAAATACT 57.550 37.500 17.98 0.00 42.89 2.12
83 112 8.803397 ATTACCAAACCTAGGAAGTGAAATAC 57.197 34.615 17.98 0.00 0.00 1.89
112 141 6.129393 CGTCAAGAAGGCGTAAAATATGATG 58.871 40.000 0.00 0.00 41.32 3.07
310 352 0.752009 TGCTCCTACGGTCTAGCAGG 60.752 60.000 7.61 0.00 39.92 4.85
335 377 3.372206 GTGAGCTGTGCTACAATTAGTGG 59.628 47.826 0.00 0.00 39.88 4.00
412 454 3.214328 TGCCTTGAGAGTTGAGAAAACC 58.786 45.455 0.00 0.00 0.00 3.27
420 462 3.937706 CCTCTACATTGCCTTGAGAGTTG 59.062 47.826 0.00 0.00 33.28 3.16
462 504 0.320697 AGAACCAAGACGGCAGGTAC 59.679 55.000 5.78 0.00 39.03 3.34
524 566 6.254281 GCTCTTGCCTGTTTGTCTTATTAA 57.746 37.500 0.00 0.00 0.00 1.40
545 587 1.003355 CGTTGTCCTGGATGTGGCT 60.003 57.895 0.00 0.00 0.00 4.75
556 598 0.782384 CGTGTGAAGTAGCGTTGTCC 59.218 55.000 0.00 0.00 0.00 4.02
570 612 3.740044 AAGAATAAACATCCGCGTGTG 57.260 42.857 4.92 5.84 31.49 3.82
576 618 5.640732 CCACCAAGAAAGAATAAACATCCG 58.359 41.667 0.00 0.00 0.00 4.18
580 622 6.222389 CAATGCCACCAAGAAAGAATAAACA 58.778 36.000 0.00 0.00 0.00 2.83
597 640 1.177895 TTTCTTCCGCAGCAATGCCA 61.178 50.000 0.00 0.00 0.00 4.92
663 706 2.512692 ACAGAATATGGGCAAGCACA 57.487 45.000 0.00 0.00 0.00 4.57
667 710 3.812053 GCAGAGTACAGAATATGGGCAAG 59.188 47.826 0.00 0.00 0.00 4.01
676 719 7.516198 AAAATCAACAAGCAGAGTACAGAAT 57.484 32.000 0.00 0.00 0.00 2.40
771 814 7.223387 CCAAGATCAACTGTTTTCAAAAAGGAG 59.777 37.037 0.00 0.00 0.00 3.69
779 822 4.036262 CGGAACCAAGATCAACTGTTTTCA 59.964 41.667 0.00 0.00 0.00 2.69
801 852 2.693591 TCTGCTAATTGGTAGAGTCCCG 59.306 50.000 5.50 0.00 30.50 5.14
815 866 9.618890 AATTAACATCAATAGCTCTTCTGCTAA 57.381 29.630 0.00 0.00 46.81 3.09
870 921 8.258007 CCTCTTTAACATATCACTGTCTTACCA 58.742 37.037 0.00 0.00 0.00 3.25
896 947 8.937884 GGTTTCTCTAGTCTTTCTTTAATGACC 58.062 37.037 0.00 0.00 39.45 4.02
974 1028 4.287781 TCCGTCGAAGTTGCCGCA 62.288 61.111 0.00 0.00 0.00 5.69
1087 1141 1.202463 CCGCTCCAGATTCTTGTCGAT 60.202 52.381 0.00 0.00 0.00 3.59
1111 1165 2.941720 GGGCTCTTAGAAGCAACTGATG 59.058 50.000 6.15 0.00 44.35 3.07
1185 1239 4.907269 TCTATCAATATCCCCAGCTGTTGA 59.093 41.667 13.81 14.58 0.00 3.18
1188 1242 4.288105 CCTTCTATCAATATCCCCAGCTGT 59.712 45.833 13.81 0.00 0.00 4.40
1284 1338 1.548269 CCAGAGAACTGACTCACCTCC 59.452 57.143 0.00 0.00 46.03 4.30
1296 1350 7.170658 GCACTGAACATAGATAATCCAGAGAAC 59.829 40.741 0.00 0.00 0.00 3.01
1340 1394 6.370442 CACTGATTTTCCGTAGTTATTGGACA 59.630 38.462 0.00 0.00 0.00 4.02
1354 1408 4.762251 ACTACCAAAGAGCACTGATTTTCC 59.238 41.667 0.00 0.00 0.00 3.13
1494 1548 8.450180 CAACCAATTTCCCAAAATAAAGTATGC 58.550 33.333 0.00 0.00 33.93 3.14
1554 1608 3.577649 TCTAACCGAAGAGCTTCTGTG 57.422 47.619 7.85 0.42 37.17 3.66
1567 1621 4.095410 TGATGCAAGCAAAATCTAACCG 57.905 40.909 0.00 0.00 0.00 4.44
1853 1921 2.095364 CAGGCAATTCTCAAGCAGTGTC 60.095 50.000 0.00 0.00 0.00 3.67
1857 1925 3.181489 GGATTCAGGCAATTCTCAAGCAG 60.181 47.826 0.00 0.00 0.00 4.24
1966 2034 7.551617 GCATATCACATCATGACATGAATCCTA 59.448 37.037 21.52 10.38 43.84 2.94
1980 2048 2.743664 GGCAATAGCGCATATCACATCA 59.256 45.455 11.47 0.00 43.41 3.07
1993 2061 8.828644 CATCAAATCTCTCATATAGGCAATAGC 58.171 37.037 0.00 0.00 41.10 2.97
2006 2074 5.183969 CCTTTCAGAGCATCAAATCTCTCA 58.816 41.667 0.00 0.00 37.56 3.27
2065 2147 4.607293 TGCAGCTTTTAGACTCTCTTCA 57.393 40.909 0.00 0.00 0.00 3.02
2066 2148 6.148480 TCAAATGCAGCTTTTAGACTCTCTTC 59.852 38.462 5.97 0.00 0.00 2.87
2068 2150 5.555017 TCAAATGCAGCTTTTAGACTCTCT 58.445 37.500 5.97 0.00 0.00 3.10
2071 2153 6.315891 AGAGATCAAATGCAGCTTTTAGACTC 59.684 38.462 5.97 12.75 0.00 3.36
2142 2232 9.534565 CACTACTCACACAACTAATTAGCATAT 57.465 33.333 12.54 0.00 0.00 1.78
2147 2237 9.347934 CTCTTCACTACTCACACAACTAATTAG 57.652 37.037 11.05 11.05 0.00 1.73
2180 2270 2.356695 TGCTAGCATGCATCACAATCAC 59.643 45.455 21.98 0.00 38.12 3.06
2222 2312 8.737168 TCCAAAATGCCACAGATATATATAGC 57.263 34.615 0.00 0.00 0.00 2.97
2264 2482 3.005367 CCCGCCAAGAACACAGTAAAAAT 59.995 43.478 0.00 0.00 0.00 1.82
2273 2491 0.458260 ACAAAACCCGCCAAGAACAC 59.542 50.000 0.00 0.00 0.00 3.32
2311 2529 1.062587 ACAAATTATGAGAGCGCACGC 59.937 47.619 11.47 6.99 42.33 5.34
2312 2530 2.697363 CACAAATTATGAGAGCGCACG 58.303 47.619 11.47 0.00 0.00 5.34
2313 2531 2.159531 TGCACAAATTATGAGAGCGCAC 60.160 45.455 11.47 2.25 0.00 5.34
2314 2532 2.083002 TGCACAAATTATGAGAGCGCA 58.917 42.857 11.47 0.00 0.00 6.09
2315 2533 2.096496 AGTGCACAAATTATGAGAGCGC 59.904 45.455 21.04 0.00 36.42 5.92
2316 2534 3.371898 TCAGTGCACAAATTATGAGAGCG 59.628 43.478 21.04 0.00 0.00 5.03
2317 2535 4.730035 GCTCAGTGCACAAATTATGAGAGC 60.730 45.833 26.72 20.16 42.31 4.09
2318 2536 4.201891 GGCTCAGTGCACAAATTATGAGAG 60.202 45.833 26.72 16.06 45.15 3.20
2319 2537 3.691118 GGCTCAGTGCACAAATTATGAGA 59.309 43.478 26.72 8.53 45.15 3.27
2554 2789 3.701604 CTAGACGGACGGCAGGCAC 62.702 68.421 0.00 0.00 0.00 5.01
2556 2791 2.615262 CTTCTAGACGGACGGCAGGC 62.615 65.000 0.00 0.00 0.00 4.85
2605 2846 1.289380 GTCGGACCGGATGATAGGC 59.711 63.158 15.25 0.00 0.00 3.93
2612 2853 3.912907 GGCATCGTCGGACCGGAT 61.913 66.667 15.25 6.94 0.00 4.18


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

AutoCloner maintained by Alex Coulton.