Multiple sequence alignment - TraesCS7D01G287100

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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 TraesCS7D01G287100 chr7D 100.000 2933 0 0 1 2933 311618196 311621128 0.000000e+00 5417
1 TraesCS7D01G287100 chr3B 96.469 2945 88 4 1 2933 371040525 371037585 0.000000e+00 4848
2 TraesCS7D01G287100 chr3B 92.000 500 25 5 2390 2874 363586967 363586468 0.000000e+00 688
3 TraesCS7D01G287100 chr3B 95.767 189 8 0 1 189 363589204 363589016 3.670000e-79 305
4 TraesCS7D01G287100 chr3B 97.980 99 2 0 2480 2578 406614557 406614655 3.890000e-39 172
5 TraesCS7D01G287100 chr5B 97.646 1912 38 1 580 2484 209634087 209632176 0.000000e+00 3275
6 TraesCS7D01G287100 chr5B 96.453 592 15 2 1 587 209634698 209634108 0.000000e+00 972
7 TraesCS7D01G287100 chr5B 90.000 630 29 16 2304 2933 277765866 277766461 0.000000e+00 784
8 TraesCS7D01G287100 chr4D 95.823 2035 43 13 906 2933 366045591 366047590 0.000000e+00 3249
9 TraesCS7D01G287100 chr5A 96.766 1917 50 6 580 2484 216691791 216693707 0.000000e+00 3186
10 TraesCS7D01G287100 chr5A 96.604 589 14 2 1 584 216691180 216691767 0.000000e+00 972
11 TraesCS7D01G287100 chr5D 96.766 1917 49 6 580 2484 199084070 199085985 0.000000e+00 3184
12 TraesCS7D01G287100 chr5D 96.435 589 15 2 1 584 199083459 199084046 0.000000e+00 966
13 TraesCS7D01G287100 chr6A 94.498 2090 68 15 814 2895 197861226 197859176 0.000000e+00 3179
14 TraesCS7D01G287100 chr2B 95.802 1977 64 5 580 2548 539963643 539965608 0.000000e+00 3173
15 TraesCS7D01G287100 chr2B 93.197 588 34 2 2 584 539963033 539963619 0.000000e+00 859
16 TraesCS7D01G287100 chr2B 97.778 360 7 1 2574 2933 302986019 302986377 1.150000e-173 619
17 TraesCS7D01G287100 chr2B 97.222 360 9 1 2574 2933 371937766 371938124 2.500000e-170 608
18 TraesCS7D01G287100 chr4B 96.302 1839 58 4 1103 2933 149993379 149995215 0.000000e+00 3011
19 TraesCS7D01G287100 chr4B 90.047 643 26 19 2293 2933 338503422 338502816 0.000000e+00 798
20 TraesCS7D01G287100 chr4B 94.475 181 9 1 1 180 175309875 175309695 8.010000e-71 278
21 TraesCS7D01G287100 chr4B 94.475 181 9 1 1 180 531339006 531339186 8.010000e-71 278
22 TraesCS7D01G287100 chr3A 97.451 1726 36 2 814 2532 361576865 361575141 0.000000e+00 2937
23 TraesCS7D01G287100 chr2A 91.769 814 21 15 2128 2933 381722309 381721534 0.000000e+00 1090
24 TraesCS7D01G287100 chr7B 89.891 643 27 17 2293 2933 195988135 195987529 0.000000e+00 793
25 TraesCS7D01G287100 chr7B 97.222 360 9 1 2574 2933 246957091 246956733 2.500000e-170 608
26 TraesCS7D01G287100 chr6B 97.500 360 8 1 2574 2933 252381698 252381340 5.370000e-172 614
27 TraesCS7D01G287100 chr2D 97.500 360 8 1 2574 2933 316863196 316862838 5.370000e-172 614
28 TraesCS7D01G287100 chr7A 97.222 360 9 1 2574 2933 331648175 331648533 2.500000e-170 608


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 TraesCS7D01G287100 chr7D 311618196 311621128 2932 False 5417.0 5417 100.0000 1 2933 1 chr7D.!!$F1 2932
1 TraesCS7D01G287100 chr3B 371037585 371040525 2940 True 4848.0 4848 96.4690 1 2933 1 chr3B.!!$R1 2932
2 TraesCS7D01G287100 chr3B 363586468 363589204 2736 True 496.5 688 93.8835 1 2874 2 chr3B.!!$R2 2873
3 TraesCS7D01G287100 chr5B 209632176 209634698 2522 True 2123.5 3275 97.0495 1 2484 2 chr5B.!!$R1 2483
4 TraesCS7D01G287100 chr5B 277765866 277766461 595 False 784.0 784 90.0000 2304 2933 1 chr5B.!!$F1 629
5 TraesCS7D01G287100 chr4D 366045591 366047590 1999 False 3249.0 3249 95.8230 906 2933 1 chr4D.!!$F1 2027
6 TraesCS7D01G287100 chr5A 216691180 216693707 2527 False 2079.0 3186 96.6850 1 2484 2 chr5A.!!$F1 2483
7 TraesCS7D01G287100 chr5D 199083459 199085985 2526 False 2075.0 3184 96.6005 1 2484 2 chr5D.!!$F1 2483
8 TraesCS7D01G287100 chr6A 197859176 197861226 2050 True 3179.0 3179 94.4980 814 2895 1 chr6A.!!$R1 2081
9 TraesCS7D01G287100 chr2B 539963033 539965608 2575 False 2016.0 3173 94.4995 2 2548 2 chr2B.!!$F3 2546
10 TraesCS7D01G287100 chr4B 149993379 149995215 1836 False 3011.0 3011 96.3020 1103 2933 1 chr4B.!!$F1 1830
11 TraesCS7D01G287100 chr4B 338502816 338503422 606 True 798.0 798 90.0470 2293 2933 1 chr4B.!!$R2 640
12 TraesCS7D01G287100 chr3A 361575141 361576865 1724 True 2937.0 2937 97.4510 814 2532 1 chr3A.!!$R1 1718
13 TraesCS7D01G287100 chr2A 381721534 381722309 775 True 1090.0 1090 91.7690 2128 2933 1 chr2A.!!$R1 805
14 TraesCS7D01G287100 chr7B 195987529 195988135 606 True 793.0 793 89.8910 2293 2933 1 chr7B.!!$R1 640

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
493 499 0.389817 CTCGGTGCATCTCCGTTTCA 60.390 55.000 13.28 0.0 46.86 2.69 F
1361 1400 1.261619 CAGAGCGAAGTGTTTGTGACC 59.738 52.381 0.00 0.0 0.00 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1802 1844 1.745087 GCATGTGGTGGTTGAATCGAT 59.255 47.619 0.00 0.0 0.0 3.59 R
2880 3030 4.006989 ACGCAATGCTCATTTAACCTGTA 58.993 39.130 2.94 0.0 0.0 2.74 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
104 105 4.216472 GTGAAGGAACTCCCAAAAGATGTC 59.784 45.833 0.00 0.00 38.49 3.06
169 170 3.821421 AACTAAAGCCTACTCATCCCG 57.179 47.619 0.00 0.00 0.00 5.14
173 174 1.404843 AAGCCTACTCATCCCGAGAC 58.595 55.000 0.00 0.00 45.45 3.36
386 392 4.523943 TGTTTGGTAAACTACGAGGCTCTA 59.476 41.667 13.50 3.45 41.90 2.43
394 400 1.471684 CTACGAGGCTCTACGGTTTGT 59.528 52.381 13.50 2.85 0.00 2.83
420 426 3.074538 ACCAATAAGGGTTCTTGCAGACT 59.925 43.478 0.00 0.00 43.89 3.24
421 427 4.288626 ACCAATAAGGGTTCTTGCAGACTA 59.711 41.667 0.00 0.00 43.89 2.59
493 499 0.389817 CTCGGTGCATCTCCGTTTCA 60.390 55.000 13.28 0.00 46.86 2.69
1044 1082 6.884836 GGTTTGACAATACAACCTTCCTCTAT 59.115 38.462 0.32 0.00 0.00 1.98
1361 1400 1.261619 CAGAGCGAAGTGTTTGTGACC 59.738 52.381 0.00 0.00 0.00 4.02
1535 1575 8.779303 TCGTCAACAAAGTATTACAAATCACAT 58.221 29.630 0.00 0.00 0.00 3.21
1701 1743 8.400947 CAAATTGAAATACATCTCCGAGTTGAT 58.599 33.333 12.51 1.10 0.00 2.57
1802 1844 4.644234 TGTTTCTTTGAACTGCAGATGGAA 59.356 37.500 23.35 12.02 0.00 3.53
1824 1866 2.027653 TCGATTCAACCACCACATGCTA 60.028 45.455 0.00 0.00 0.00 3.49
2113 2155 0.557729 CCCTCTGGCATACCCCAAAT 59.442 55.000 0.00 0.00 33.73 2.32
2165 2207 4.498009 GGTGCCTAATGACAATGAATTCCG 60.498 45.833 2.27 0.00 0.00 4.30
2194 2246 2.503356 AGAAATTGAGAGGATGCGAGGT 59.497 45.455 0.00 0.00 0.00 3.85
2416 2491 2.408271 TCTCGCATTTCATCTTGCCT 57.592 45.000 0.00 0.00 35.41 4.75
2619 2768 1.984026 CTCCCCAGGCCGCAAAATT 60.984 57.895 0.00 0.00 0.00 1.82
2759 2908 9.853555 TTTGTTGTAATGCCTTATTTGATGTAG 57.146 29.630 0.00 0.00 0.00 2.74
2783 2932 7.646884 AGGATCCCTTTTCTACTTTGAATGAT 58.353 34.615 8.55 0.00 0.00 2.45
2880 3030 2.472695 TGAGCATTGCGTAGTCCTTT 57.527 45.000 2.38 0.00 0.00 3.11
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
53 54 1.768275 ACATGTTGTCTGAGTGTCCCA 59.232 47.619 0.00 0.00 0.00 4.37
104 105 3.763097 TTATGATTGAAACGCAGCAGG 57.237 42.857 0.00 0.00 0.00 4.85
148 149 3.773119 TCGGGATGAGTAGGCTTTAGTTT 59.227 43.478 0.00 0.00 0.00 2.66
169 170 4.333926 GCACCTTCTGAACATAATGGTCTC 59.666 45.833 0.00 0.00 34.53 3.36
173 174 4.096984 GGAAGCACCTTCTGAACATAATGG 59.903 45.833 5.11 0.00 40.07 3.16
421 427 9.357652 CTTTTTCATCATTCGAACAACCATATT 57.642 29.630 0.00 0.00 0.00 1.28
493 499 8.912988 CAAGAGAGAGTATATTGAGACCTCTTT 58.087 37.037 0.00 0.00 36.63 2.52
1404 1444 3.054655 GCATTCCCTCCTAACAGGTAACA 60.055 47.826 0.00 0.00 36.53 2.41
1535 1575 7.962964 ATACTCAAAACTGAAACTGATTCGA 57.037 32.000 0.00 0.00 41.18 3.71
1802 1844 1.745087 GCATGTGGTGGTTGAATCGAT 59.255 47.619 0.00 0.00 0.00 3.59
1812 1854 3.313526 GCAGTATTTCTAGCATGTGGTGG 59.686 47.826 0.00 0.00 0.00 4.61
1824 1866 5.420725 TGTCACTATGGTGCAGTATTTCT 57.579 39.130 3.97 0.00 42.72 2.52
2113 2155 6.015772 TGACCATTATATCCAGAATCGAACGA 60.016 38.462 0.00 0.00 0.00 3.85
2165 2207 5.700373 GCATCCTCTCAATTTCTGATCCTAC 59.300 44.000 0.00 0.00 32.14 3.18
2759 2908 7.888250 ATCATTCAAAGTAGAAAAGGGATCC 57.112 36.000 1.92 1.92 0.00 3.36
2880 3030 4.006989 ACGCAATGCTCATTTAACCTGTA 58.993 39.130 2.94 0.00 0.00 2.74


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

AutoCloner maintained by Alex Coulton.