Multiple sequence alignment - TraesCS7D01G209900

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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 TraesCS7D01G209900 chr7D 100.000 3173 0 0 1 3173 168065552 168068724 0.000000e+00 5860.0
1 TraesCS7D01G209900 chr7D 95.455 44 2 0 817 860 534456414 534456371 1.580000e-08 71.3
2 TraesCS7D01G209900 chr7B 95.301 2341 48 15 866 3171 133242428 133244741 0.000000e+00 3657.0
3 TraesCS7D01G209900 chr7B 92.546 872 48 12 1 860 708728978 708729844 0.000000e+00 1234.0
4 TraesCS7D01G209900 chr7A 96.554 1480 39 2 869 2345 170188204 170189674 0.000000e+00 2440.0
5 TraesCS7D01G209900 chr7A 94.068 826 28 2 2346 3171 170189703 170190507 0.000000e+00 1234.0
6 TraesCS7D01G209900 chr3D 97.917 864 14 2 1 860 33361935 33361072 0.000000e+00 1493.0
7 TraesCS7D01G209900 chr3D 82.083 240 43 0 2511 2750 587422435 587422196 4.150000e-49 206.0
8 TraesCS7D01G209900 chr6D 97.912 862 15 3 1 860 344159289 344158429 0.000000e+00 1489.0
9 TraesCS7D01G209900 chr6D 97.680 862 17 3 1 860 42506029 42505169 0.000000e+00 1478.0
10 TraesCS7D01G209900 chr6D 96.756 863 24 3 1 860 233688478 233689339 0.000000e+00 1435.0
11 TraesCS7D01G209900 chr2D 96.065 864 29 3 1 860 212009229 212010091 0.000000e+00 1402.0
12 TraesCS7D01G209900 chr2D 83.333 144 10 3 731 860 35976400 35976543 1.550000e-23 121.0
13 TraesCS7D01G209900 chr1A 95.405 827 26 7 1 821 4656253 4657073 0.000000e+00 1306.0
14 TraesCS7D01G209900 chr3B 95.556 450 19 1 84 533 169688868 169689316 0.000000e+00 719.0
15 TraesCS7D01G209900 chr3B 83.830 235 36 2 2510 2743 784455617 784455384 4.120000e-54 222.0
16 TraesCS7D01G209900 chr3B 83.830 235 36 2 2510 2743 784526754 784526521 4.120000e-54 222.0
17 TraesCS7D01G209900 chr3B 81.106 217 36 2 1057 1268 784455975 784455759 5.440000e-38 169.0
18 TraesCS7D01G209900 chr1D 93.709 461 26 2 1 458 32720155 32719695 0.000000e+00 688.0
19 TraesCS7D01G209900 chr1D 91.270 126 8 2 445 567 32719750 32719625 5.440000e-38 169.0
20 TraesCS7D01G209900 chr1D 96.226 53 0 2 810 860 379870795 379870743 5.640000e-13 86.1
21 TraesCS7D01G209900 chr2B 87.676 284 25 9 534 809 553880572 553880291 3.950000e-84 322.0
22 TraesCS7D01G209900 chr4B 90.000 250 17 7 575 820 665900511 665900266 1.840000e-82 316.0
23 TraesCS7D01G209900 chr5A 86.348 293 26 13 537 819 310728464 310728752 1.110000e-79 307.0
24 TraesCS7D01G209900 chr5D 90.323 62 3 2 800 858 551015184 551015123 9.440000e-11 78.7


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 TraesCS7D01G209900 chr7D 168065552 168068724 3172 False 5860.0 5860 100.0000 1 3173 1 chr7D.!!$F1 3172
1 TraesCS7D01G209900 chr7B 133242428 133244741 2313 False 3657.0 3657 95.3010 866 3171 1 chr7B.!!$F1 2305
2 TraesCS7D01G209900 chr7B 708728978 708729844 866 False 1234.0 1234 92.5460 1 860 1 chr7B.!!$F2 859
3 TraesCS7D01G209900 chr7A 170188204 170190507 2303 False 1837.0 2440 95.3110 869 3171 2 chr7A.!!$F1 2302
4 TraesCS7D01G209900 chr3D 33361072 33361935 863 True 1493.0 1493 97.9170 1 860 1 chr3D.!!$R1 859
5 TraesCS7D01G209900 chr6D 344158429 344159289 860 True 1489.0 1489 97.9120 1 860 1 chr6D.!!$R2 859
6 TraesCS7D01G209900 chr6D 42505169 42506029 860 True 1478.0 1478 97.6800 1 860 1 chr6D.!!$R1 859
7 TraesCS7D01G209900 chr6D 233688478 233689339 861 False 1435.0 1435 96.7560 1 860 1 chr6D.!!$F1 859
8 TraesCS7D01G209900 chr2D 212009229 212010091 862 False 1402.0 1402 96.0650 1 860 1 chr2D.!!$F2 859
9 TraesCS7D01G209900 chr1A 4656253 4657073 820 False 1306.0 1306 95.4050 1 821 1 chr1A.!!$F1 820
10 TraesCS7D01G209900 chr1D 32719625 32720155 530 True 428.5 688 92.4895 1 567 2 chr1D.!!$R2 566


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
904 946 1.342819 GAGTAGCACCAGCCCAGATAG 59.657 57.143 0.0 0.0 43.56 2.08 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2667 2740 0.592637 CACCAAAATCGCAGTGCTCA 59.407 50.0 14.33 0.0 0.0 4.26 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
860 899 4.634443 CGAAAATAAACCTGGAACGGAGAT 59.366 41.667 0.00 0.00 36.31 2.75
861 900 5.813672 CGAAAATAAACCTGGAACGGAGATA 59.186 40.000 0.00 0.00 36.31 1.98
862 901 6.018994 CGAAAATAAACCTGGAACGGAGATAG 60.019 42.308 0.00 0.00 36.31 2.08
863 902 6.555463 AAATAAACCTGGAACGGAGATAGA 57.445 37.500 0.00 0.00 36.31 1.98
864 903 5.793030 ATAAACCTGGAACGGAGATAGAG 57.207 43.478 0.00 0.00 36.31 2.43
874 913 2.887783 ACGGAGATAGAGATGAACGCAT 59.112 45.455 0.00 0.00 37.47 4.73
904 946 1.342819 GAGTAGCACCAGCCCAGATAG 59.657 57.143 0.00 0.00 43.56 2.08
946 988 2.867647 GCAAAACAAGCCCAATCACTCC 60.868 50.000 0.00 0.00 0.00 3.85
967 1009 1.571773 ATTACCCCTTTCCTGCCGCT 61.572 55.000 0.00 0.00 0.00 5.52
968 1010 2.478335 TTACCCCTTTCCTGCCGCTG 62.478 60.000 0.00 0.00 0.00 5.18
1809 1851 3.445008 AGAGCACTTCAGATGGGAGTTA 58.555 45.455 0.00 0.00 0.00 2.24
2049 2091 3.837731 AGAAGAAGAGGAGGAAAGGTGAG 59.162 47.826 0.00 0.00 0.00 3.51
2187 2229 3.262405 ACCGGTGATTGGTGTATGTAAGT 59.738 43.478 6.12 0.00 38.60 2.24
2202 2244 3.928754 TGTAAGTCTGATGCCCCTCTAT 58.071 45.455 0.00 0.00 0.00 1.98
2230 2275 8.491331 TTGTTGAACGAATGATGATATCTTGA 57.509 30.769 3.98 0.00 0.00 3.02
2360 2433 1.885887 CCCAAAATCGGAGAACTGCAA 59.114 47.619 0.00 0.00 43.58 4.08
2433 2506 4.952335 CCCTTCAGGATAAAAGCAATCACT 59.048 41.667 0.00 0.00 38.24 3.41
2453 2526 9.566432 AATCACTTATGGATTCTCCTAAATGAC 57.434 33.333 0.00 0.00 37.46 3.06
2517 2590 5.754890 GGAAACCAAACATATGGATGCAATC 59.245 40.000 7.80 3.90 43.54 2.67
2596 2669 5.067674 TGCCAATGCAAACTGGTCTTATATC 59.932 40.000 12.82 0.00 46.66 1.63
2667 2740 7.744087 TGTGCAATTGACTATCTACAAAAGT 57.256 32.000 10.34 0.00 0.00 2.66
2690 2763 1.468054 GCACTGCGATTTTGGTGGATC 60.468 52.381 0.00 0.00 0.00 3.36
2909 2983 9.696917 ACTTTACAAAAATTCATTCATGTCCTC 57.303 29.630 0.00 0.00 0.00 3.71
3025 3099 0.531974 TTTGGCACTGAGTCGTGGAC 60.532 55.000 14.17 0.00 35.47 4.02
3094 3168 1.032114 GTAACAGTCCATGGGCCTGC 61.032 60.000 24.07 7.45 0.00 4.85
3171 3245 5.290493 TGCTGATGTTGGGGTATAAGTAG 57.710 43.478 0.00 0.00 0.00 2.57
3172 3246 4.966168 TGCTGATGTTGGGGTATAAGTAGA 59.034 41.667 0.00 0.00 0.00 2.59
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
289 293 3.643595 TTCCCCAATGCGGCCTCAG 62.644 63.158 0.18 0.00 0.00 3.35
860 899 4.560128 GCTATGGAATGCGTTCATCTCTA 58.440 43.478 19.95 3.55 36.01 2.43
861 900 3.397482 GCTATGGAATGCGTTCATCTCT 58.603 45.455 19.95 2.60 36.01 3.10
862 901 2.481952 GGCTATGGAATGCGTTCATCTC 59.518 50.000 19.95 3.55 36.01 2.75
863 902 2.498167 GGCTATGGAATGCGTTCATCT 58.502 47.619 19.95 6.55 36.01 2.90
864 903 1.195448 CGGCTATGGAATGCGTTCATC 59.805 52.381 19.95 4.61 36.01 2.92
874 913 0.750850 GGTGCTACTCGGCTATGGAA 59.249 55.000 0.00 0.00 0.00 3.53
904 946 4.020751 TGCTCATGGGCTGATAGTCTATTC 60.021 45.833 20.42 0.00 32.10 1.75
946 988 0.751643 CGGCAGGAAAGGGGTAATGG 60.752 60.000 0.00 0.00 0.00 3.16
1248 1290 1.004440 GGTGAAGCCGAAGCAGAGT 60.004 57.895 0.00 0.00 43.56 3.24
1563 1605 4.443266 GAGTTGCTCGCCGAGGCT 62.443 66.667 16.95 0.00 39.32 4.58
1632 1674 3.867857 GGAGTTGAAGTCCTCCATCTTC 58.132 50.000 11.78 0.00 45.47 2.87
1809 1851 2.121992 CTGTGTCTTCTGGCAGCCCT 62.122 60.000 9.64 0.00 0.00 5.19
2049 2091 5.308825 TCTTCTTCCTTCTTCACATCAACC 58.691 41.667 0.00 0.00 0.00 3.77
2187 2229 3.928754 ACAAGTATAGAGGGGCATCAGA 58.071 45.455 0.00 0.00 0.00 3.27
2202 2244 9.599866 AAGATATCATCATTCGTTCAACAAGTA 57.400 29.630 5.32 0.00 0.00 2.24
2230 2275 8.531982 TGTCACTCTTATTGCTTTAGTGTATCT 58.468 33.333 0.00 0.00 38.88 1.98
2360 2433 2.746375 CCTGGCTGGCCGGTATTCT 61.746 63.158 14.55 0.00 40.80 2.40
2453 2526 7.461182 TTTACACCAGAATTCCACCATTTAG 57.539 36.000 0.65 0.00 0.00 1.85
2517 2590 7.015226 TCTTTCTCACACACATTGTTACTTG 57.985 36.000 0.00 0.00 35.67 3.16
2518 2591 7.307396 CGATCTTTCTCACACACATTGTTACTT 60.307 37.037 0.00 0.00 35.67 2.24
2519 2592 6.146184 CGATCTTTCTCACACACATTGTTACT 59.854 38.462 0.00 0.00 35.67 2.24
2520 2593 6.145534 TCGATCTTTCTCACACACATTGTTAC 59.854 38.462 0.00 0.00 35.67 2.50
2521 2594 6.145534 GTCGATCTTTCTCACACACATTGTTA 59.854 38.462 0.00 0.00 35.67 2.41
2522 2595 5.050091 GTCGATCTTTCTCACACACATTGTT 60.050 40.000 0.00 0.00 35.67 2.83
2523 2596 4.449068 GTCGATCTTTCTCACACACATTGT 59.551 41.667 0.00 0.00 39.97 2.71
2596 2669 5.405797 TCATGATTTCTGTTCTCTCTGACG 58.594 41.667 0.00 0.00 0.00 4.35
2667 2740 0.592637 CACCAAAATCGCAGTGCTCA 59.407 50.000 14.33 0.00 0.00 4.26
2690 2763 2.684881 ACAACTCCAACTGTGCTCAAAG 59.315 45.455 0.00 0.00 0.00 2.77
2885 2959 9.912634 GAGAGGACATGAATGAATTTTTGTAAA 57.087 29.630 0.00 0.00 0.00 2.01
2889 2963 8.954350 ACTAGAGAGGACATGAATGAATTTTTG 58.046 33.333 0.00 0.00 0.00 2.44
2960 3034 2.158900 CGTAAGGACAAGGCATCATCCT 60.159 50.000 0.00 0.00 43.66 3.24
3019 3093 3.695060 AGTCATTAGTCCAGTAGTCCACG 59.305 47.826 0.00 0.00 0.00 4.94
3025 3099 5.664457 TGCAATGAGTCATTAGTCCAGTAG 58.336 41.667 17.86 4.13 32.35 2.57
3094 3168 5.953183 TGAGCAAGCTGTTAATTGGTTATG 58.047 37.500 0.00 0.00 37.27 1.90



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

AutoCloner maintained by Alex Coulton.