Multiple sequence alignment - TraesCS3D01G280000

Loading Multiple Alignment...

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 TraesCS3D01G280000 chr3D 100.000 2546 0 0 1 2546 388382148 388379603 0.000000e+00 4702
1 TraesCS3D01G280000 chr3B 94.997 1519 54 8 549 2050 505017153 505015640 0.000000e+00 2364
2 TraesCS3D01G280000 chr3B 94.326 564 22 3 1 555 505017756 505017194 0.000000e+00 856
3 TraesCS3D01G280000 chr3B 88.699 292 19 6 2268 2546 505015508 505015218 6.740000e-91 344
4 TraesCS3D01G280000 chr3B 88.806 134 13 2 2088 2219 505015641 505015508 2.030000e-36 163
5 TraesCS3D01G280000 chr3B 95.238 84 4 0 1 84 505019213 505019130 1.590000e-27 134
6 TraesCS3D01G280000 chr3A 96.459 819 22 4 1735 2546 509443856 509443038 0.000000e+00 1345
7 TraesCS3D01G280000 chr3A 95.030 845 23 9 919 1762 509444684 509443858 0.000000e+00 1310
8 TraesCS3D01G280000 chr3A 83.007 306 28 11 10 293 509445501 509445198 3.250000e-64 255
9 TraesCS3D01G280000 chr3A 97.000 100 3 0 456 555 509445194 509445095 4.360000e-38 169
10 TraesCS3D01G280000 chr2D 89.091 165 13 3 293 457 571079116 571078957 1.540000e-47 200
11 TraesCS3D01G280000 chr7A 88.554 166 11 5 293 457 652302328 652302170 7.190000e-46 195
12 TraesCS3D01G280000 chr5A 86.932 176 17 4 285 459 558675663 558675493 2.580000e-45 193
13 TraesCS3D01G280000 chr4A 88.095 168 12 4 293 458 5222619 5222458 2.580000e-45 193
14 TraesCS3D01G280000 chr7D 87.574 169 16 3 288 456 500775620 500775457 9.300000e-45 191
15 TraesCS3D01G280000 chr1D 86.782 174 16 5 293 464 155961832 155961664 1.200000e-43 187
16 TraesCS3D01G280000 chr6A 86.628 172 17 4 285 456 47465883 47465718 4.330000e-43 185
17 TraesCS3D01G280000 chr5B 86.905 168 17 3 290 457 352378605 352378767 1.560000e-42 183
18 TraesCS3D01G280000 chr1B 83.168 202 31 3 992 1192 591359703 591359504 5.600000e-42 182


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 TraesCS3D01G280000 chr3D 388379603 388382148 2545 True 4702.00 4702 100.0000 1 2546 1 chr3D.!!$R1 2545
1 TraesCS3D01G280000 chr3B 505015218 505019213 3995 True 772.20 2364 92.4132 1 2546 5 chr3B.!!$R1 2545
2 TraesCS3D01G280000 chr3A 509443038 509445501 2463 True 769.75 1345 92.8740 10 2546 4 chr3A.!!$R1 2536

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
784 2340 0.599991 TGTGTGGAGCTAACAGTGCG 60.6 55.0 2.01 0.0 35.28 5.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1643 3213 2.225382 TTACATGAGTCACCTCCCGA 57.775 50.0 0.0 0.0 36.86 5.14 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
201 1688 0.938168 GCGGTAGCTATGCGTACCAC 60.938 60.000 0.00 0.00 39.00 4.16
234 1721 8.899771 TCAGATTTTTAGGATATTTTCGGGAAC 58.100 33.333 0.00 0.00 0.00 3.62
254 1741 7.598493 CGGGAACTGTGTGAATTATTGAATTTT 59.402 33.333 0.00 0.00 35.33 1.82
298 1786 8.575649 TTCTTGAGTTGTTTTATATTCCCTCC 57.424 34.615 0.00 0.00 0.00 4.30
301 1789 6.478129 TGAGTTGTTTTATATTCCCTCCGTT 58.522 36.000 0.00 0.00 0.00 4.44
316 1804 7.909485 TCCCTCCGTTTCTAAATATAAGTCT 57.091 36.000 0.00 0.00 0.00 3.24
467 1955 6.989155 ACGGAGGTAGTATATGAAAATCCA 57.011 37.500 0.00 0.00 0.00 3.41
468 1956 6.756221 ACGGAGGTAGTATATGAAAATCCAC 58.244 40.000 0.00 0.00 0.00 4.02
593 2128 0.683973 ATAATGGAGCAGGGCGAGAG 59.316 55.000 0.00 0.00 0.00 3.20
608 2158 1.402852 CGAGAGCATTCCGTCAACTCA 60.403 52.381 0.00 0.00 0.00 3.41
650 2200 6.713762 TGAATAAAAGTTCAGGGCCATATG 57.286 37.500 6.18 0.00 33.41 1.78
653 2203 6.715347 ATAAAAGTTCAGGGCCATATGTTC 57.285 37.500 6.18 0.00 0.00 3.18
684 2239 5.066593 AGCCTGCTGTTTATTAATAGGAGC 58.933 41.667 4.55 12.31 38.86 4.70
784 2340 0.599991 TGTGTGGAGCTAACAGTGCG 60.600 55.000 2.01 0.00 35.28 5.34
795 2351 3.670359 GCTAACAGTGCGCATGAATTTGA 60.670 43.478 15.91 0.00 0.00 2.69
811 2367 9.326339 CATGAATTTGAGCTATCATATGTTTCG 57.674 33.333 1.90 0.00 34.73 3.46
814 2370 6.510746 TTTGAGCTATCATATGTTTCGTCG 57.489 37.500 1.90 0.00 34.73 5.12
917 2473 7.771927 ACCTTGCTTCTAGTTAAGTACTACA 57.228 36.000 0.00 0.00 38.33 2.74
964 2531 8.463930 AATCTTTTGTTTCAGATTGTAGGACA 57.536 30.769 0.00 0.00 38.16 4.02
1229 2796 9.596308 TGCTAGGAATGTCTAATAACCATAGTA 57.404 33.333 0.00 0.00 0.00 1.82
1565 3135 6.446318 TGTGAAACAGCTTGTCCAATAAATC 58.554 36.000 0.00 0.00 45.67 2.17
1566 3136 6.040278 TGTGAAACAGCTTGTCCAATAAATCA 59.960 34.615 0.00 0.00 45.67 2.57
1575 3145 3.191162 TGTCCAATAAATCACACTGCTGC 59.809 43.478 0.00 0.00 0.00 5.25
1643 3213 6.327386 ACCAGTCCACCAATATCTTGTATT 57.673 37.500 0.00 0.00 0.00 1.89
1714 3284 5.385198 TCTTTAGCAGGAACACCTTTTCAT 58.615 37.500 0.00 0.00 30.75 2.57
1762 3332 7.411486 TTTCTGTTGGTCTTATAGAGAGAGG 57.589 40.000 0.00 0.00 34.31 3.69
1865 3464 8.552034 GCTCATCTATAATTGTGACCAGTAAAC 58.448 37.037 0.00 0.00 0.00 2.01
2029 3630 0.815615 CGATCCCAGTAAGGCCTTGC 60.816 60.000 28.77 26.66 35.39 4.01
2097 3698 2.419324 CTCAGAATCAGCTTTGCCACTC 59.581 50.000 0.00 0.00 0.00 3.51
2101 3702 1.542492 ATCAGCTTTGCCACTCAAGG 58.458 50.000 0.00 0.00 35.84 3.61
2146 3749 8.021396 AGAAAATAGCCGTTTGTTTCAGATTAC 58.979 33.333 0.00 0.00 31.94 1.89
2380 3989 6.018669 GGAGTAGTGCATATGCTAAAACAGAC 60.019 42.308 27.13 17.29 42.66 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 9.807649 CTGGACAATTTTTCTCCCTTTATAATG 57.192 33.333 0.00 0.00 0.00 1.90
7 8 7.122650 CAGCTGGACAATTTTTCTCCCTTTATA 59.877 37.037 5.57 0.00 0.00 0.98
213 1700 7.449086 ACACAGTTCCCGAAAATATCCTAAAAA 59.551 33.333 0.00 0.00 0.00 1.94
234 1721 9.350357 CTCAGGAAAATTCAATAATTCACACAG 57.650 33.333 0.00 0.00 34.12 3.66
254 1741 5.310409 AGAAACTGGAAAATGTCTCAGGA 57.690 39.130 0.00 0.00 32.03 3.86
339 1827 2.146342 CTTTGCTCCGCCCTATATGTG 58.854 52.381 0.00 0.00 0.00 3.21
445 1933 5.862323 CGTGGATTTTCATATACTACCTCCG 59.138 44.000 0.00 0.00 0.00 4.63
467 1955 3.057734 GAGAATTCGTTTGGACTGACGT 58.942 45.455 0.00 0.00 40.03 4.34
468 1956 3.057019 TGAGAATTCGTTTGGACTGACG 58.943 45.455 0.00 0.00 40.43 4.35
593 2128 1.398390 GGTGATGAGTTGACGGAATGC 59.602 52.381 0.00 0.00 0.00 3.56
599 2134 0.175760 ATCCCGGTGATGAGTTGACG 59.824 55.000 0.00 0.00 30.54 4.35
608 2158 2.026356 TCAACATGAACATCCCGGTGAT 60.026 45.455 0.00 0.00 0.00 3.06
650 2200 7.736447 ATAAACAGCAGGCTATTCATAGAAC 57.264 36.000 0.00 0.00 32.05 3.01
678 2228 6.803366 ATATGCTGTCATATGATGCTCCTA 57.197 37.500 24.26 16.77 42.61 2.94
760 2316 4.067896 CACTGTTAGCTCCACACAGAAAT 58.932 43.478 17.60 0.00 40.43 2.17
784 2340 9.125906 GAAACATATGATAGCTCAAATTCATGC 57.874 33.333 10.38 0.00 34.37 4.06
795 2351 5.915758 GTCTTCGACGAAACATATGATAGCT 59.084 40.000 12.03 0.00 0.00 3.32
811 2367 5.461078 TGCACTACACTAAAAAGTCTTCGAC 59.539 40.000 0.00 0.00 0.00 4.20
814 2370 5.179555 CCCTGCACTACACTAAAAAGTCTTC 59.820 44.000 0.00 0.00 0.00 2.87
819 2375 3.437049 GCTCCCTGCACTACACTAAAAAG 59.563 47.826 0.00 0.00 42.31 2.27
889 2445 8.975663 AGTACTTAACTAGAAGCAAGGTTTTT 57.024 30.769 0.00 0.00 36.36 1.94
964 2531 1.761784 CTGCTAGATGCTTGGACTCCT 59.238 52.381 0.00 0.00 43.37 3.69
1565 3135 2.683859 CCGTCATGGCAGCAGTGTG 61.684 63.158 0.00 0.00 0.00 3.82
1566 3136 2.359107 CCGTCATGGCAGCAGTGT 60.359 61.111 0.00 0.00 0.00 3.55
1643 3213 2.225382 TTACATGAGTCACCTCCCGA 57.775 50.000 0.00 0.00 36.86 5.14
1714 3284 4.383989 GGGGCCAAATGAGCAATAATTCAA 60.384 41.667 4.39 0.00 0.00 2.69
1762 3332 6.482308 ACATTGGTAACTTGTAACACAGAGAC 59.518 38.462 0.00 0.00 32.89 3.36
1865 3464 5.041191 AGTATGCATTTAGAAGAGGGGTG 57.959 43.478 3.54 0.00 0.00 4.61
1897 3497 4.521130 TGTTTCGCTCTCTAGACACAAT 57.479 40.909 0.00 0.00 0.00 2.71
2029 3630 5.163723 TGACAGAAGTTGAAGCTGAAACAAG 60.164 40.000 12.80 3.96 33.94 3.16
2097 3698 2.357034 CACGTCCCGGTGTCCTTG 60.357 66.667 0.00 0.00 33.24 3.61
2101 3702 2.737376 GAAGCACGTCCCGGTGTC 60.737 66.667 0.00 0.00 40.08 3.67
2380 3989 9.485206 AATTTGTTCATTTTCAGGAGAAGAATG 57.515 29.630 0.00 0.00 35.69 2.67


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

AutoCloner maintained by Alex Coulton.