Multiple sequence alignment - TraesCS3D01G488500

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 TraesCS3D01G488500 chr3D 100.000 2201 0 0 1 2201 583170856 583168656 0.000000e+00 4065.0
1 TraesCS3D01G488500 chr3D 92.620 2046 111 25 12 2039 583225695 583223672 0.000000e+00 2905.0
2 TraesCS3D01G488500 chr3D 90.364 2200 143 41 38 2191 583278975 583276799 0.000000e+00 2824.0
3 TraesCS3D01G488500 chr3D 88.989 2116 148 53 38 2097 583182371 583180285 0.000000e+00 2538.0
4 TraesCS3D01G488500 chr3D 94.490 1452 69 8 627 2068 583284625 583283175 0.000000e+00 2228.0
5 TraesCS3D01G488500 chr3D 88.006 1876 164 36 247 2068 583188165 583186297 0.000000e+00 2161.0
6 TraesCS3D01G488500 chr3D 88.015 1310 135 10 906 2201 583289841 583288540 0.000000e+00 1530.0
7 TraesCS3D01G488500 chr3D 82.822 1368 178 31 847 2201 583028957 583027634 0.000000e+00 1171.0
8 TraesCS3D01G488500 chr3D 100.000 183 0 0 2598 2780 583168259 583168077 3.430000e-89 339.0
9 TraesCS3D01G488500 chr3D 97.727 176 4 0 2605 2780 583276608 583276433 1.250000e-78 303.0
10 TraesCS3D01G488500 chr3B 89.428 2081 143 44 38 2068 780302807 780300754 0.000000e+00 2553.0
11 TraesCS3D01G488500 chr3B 85.436 2204 199 66 38 2188 780326876 780324742 0.000000e+00 2180.0
12 TraesCS3D01G488500 chr3B 85.390 2204 200 66 38 2188 780322271 780320137 0.000000e+00 2174.0
13 TraesCS3D01G488500 chr3B 85.299 2204 202 66 38 2188 780316897 780314763 0.000000e+00 2163.0
14 TraesCS3D01G488500 chr3B 86.682 1314 123 24 906 2201 780355463 780354184 0.000000e+00 1410.0
15 TraesCS3D01G488500 chr6A 86.933 1301 130 25 906 2188 34282127 34280849 0.000000e+00 1424.0
16 TraesCS3D01G488500 chr6A 77.551 392 45 29 393 748 34388896 34388512 2.180000e-46 196.0
17 TraesCS3D01G488500 chr6A 86.517 89 10 1 2100 2188 34393522 34393436 2.280000e-16 97.1
18 TraesCS3D01G488500 chr7A 81.588 1184 185 25 970 2132 287552241 287553412 0.000000e+00 948.0
19 TraesCS3D01G488500 chr7A 95.385 65 2 1 353 416 39273807 39273743 4.900000e-18 102.0
20 TraesCS3D01G488500 chr7A 83.871 93 12 2 2099 2188 287849866 287849958 4.930000e-13 86.1
21 TraesCS3D01G488500 chr7D 85.158 411 38 12 311 709 39552972 39552573 1.550000e-107 399.0
22 TraesCS3D01G488500 chr7D 82.292 96 14 2 2099 2191 264320998 264321093 2.300000e-11 80.5
23 TraesCS3D01G488500 chr4A 83.575 414 46 11 311 709 645784641 645784235 4.370000e-98 368.0
24 TraesCS3D01G488500 chr4A 81.436 404 49 15 311 709 645729063 645728681 9.670000e-80 307.0
25 TraesCS3D01G488500 chr4A 81.481 405 47 14 311 709 645762259 645761877 9.670000e-80 307.0
26 TraesCS3D01G488500 chr4A 90.000 110 10 1 316 424 645687077 645686968 1.040000e-29 141.0


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 TraesCS3D01G488500 chr3D 583168077 583170856 2779 True 2202.000000 4065 100.0000 1 2780 2 chr3D.!!$R3 2779
1 TraesCS3D01G488500 chr3D 583223672 583225695 2023 True 2905.000000 2905 92.6200 12 2039 1 chr3D.!!$R2 2027
2 TraesCS3D01G488500 chr3D 583180285 583188165 7880 True 2349.500000 2538 88.4975 38 2097 2 chr3D.!!$R4 2059
3 TraesCS3D01G488500 chr3D 583283175 583289841 6666 True 1879.000000 2228 91.2525 627 2201 2 chr3D.!!$R6 1574
4 TraesCS3D01G488500 chr3D 583276433 583278975 2542 True 1563.500000 2824 94.0455 38 2780 2 chr3D.!!$R5 2742
5 TraesCS3D01G488500 chr3D 583027634 583028957 1323 True 1171.000000 1171 82.8220 847 2201 1 chr3D.!!$R1 1354
6 TraesCS3D01G488500 chr3B 780300754 780302807 2053 True 2553.000000 2553 89.4280 38 2068 1 chr3B.!!$R1 2030
7 TraesCS3D01G488500 chr3B 780314763 780326876 12113 True 2172.333333 2180 85.3750 38 2188 3 chr3B.!!$R3 2150
8 TraesCS3D01G488500 chr3B 780354184 780355463 1279 True 1410.000000 1410 86.6820 906 2201 1 chr3B.!!$R2 1295
9 TraesCS3D01G488500 chr6A 34280849 34282127 1278 True 1424.000000 1424 86.9330 906 2188 1 chr6A.!!$R1 1282
10 TraesCS3D01G488500 chr7A 287552241 287553412 1171 False 948.000000 948 81.5880 970 2132 1 chr7A.!!$F1 1162

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
498 544 1.088340 CCTCGTGCAGATGAGCTTGG 61.088 60.0 5.26 0.0 34.28 3.61 F
1552 9703 0.316841 GGCCAAGGCTAGAGAGATCG 59.683 60.0 11.40 0.0 41.60 3.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1555 9706 0.681733 GTGGACTCCAGCAGAGACAA 59.318 55.0 10.46 0.0 46.50 3.18 R
2698 19674 7.510428 AACAAGCATAATAAAGCGTTGATTG 57.490 32.0 0.00 0.0 39.05 2.67 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
134 139 5.464168 ACACATGAAGCTAAGAAATTGTGC 58.536 37.500 0.00 0.00 37.36 4.57
185 190 3.960571 ACATGGGTCCAGATCTCAAAAG 58.039 45.455 0.00 0.00 0.00 2.27
322 341 9.123902 CTTGAACACCCATAATCTATGAATGAA 57.876 33.333 0.00 0.00 38.45 2.57
447 478 1.399440 CAACCTGGAACATGCGATGAG 59.601 52.381 0.00 0.00 38.20 2.90
450 481 1.293924 CTGGAACATGCGATGAGGTC 58.706 55.000 0.00 0.00 38.20 3.85
494 540 1.812922 CACCCTCGTGCAGATGAGC 60.813 63.158 5.26 0.00 34.28 4.26
498 544 1.088340 CCTCGTGCAGATGAGCTTGG 61.088 60.000 5.26 0.00 34.28 3.61
509 555 1.604604 TGAGCTTGGCACTAACAACC 58.395 50.000 0.00 0.00 0.00 3.77
549 595 1.471119 CAGTGGCAAGGCATGAAGAT 58.529 50.000 0.00 0.00 0.00 2.40
732 8840 1.628846 GGGACAAACTCTCAGGGCTTA 59.371 52.381 0.00 0.00 0.00 3.09
767 8876 7.718753 AGATTCCACTAAAATGATAGCTTGAGG 59.281 37.037 0.00 0.00 0.00 3.86
887 8996 4.574674 TGTGTTGGGATCTCTATGCTTT 57.425 40.909 0.00 0.00 0.00 3.51
1433 9575 0.457851 GATGACGCAGCTACTCAGGT 59.542 55.000 0.00 0.00 0.00 4.00
1470 9612 1.291877 CCCGCTTGGTGAAGAAGTCG 61.292 60.000 0.00 0.00 0.00 4.18
1552 9703 0.316841 GGCCAAGGCTAGAGAGATCG 59.683 60.000 11.40 0.00 41.60 3.69
1555 9706 1.686052 CCAAGGCTAGAGAGATCGCTT 59.314 52.381 0.00 0.00 0.00 4.68
1785 9940 9.237187 CTCAACATCCTTAGCTCATAGATACTA 57.763 37.037 0.00 0.00 0.00 1.82
1857 18772 9.638176 AATAGCTGATCTTCATACAATTTTCCT 57.362 29.630 0.00 0.00 0.00 3.36
2009 18969 4.215827 GGATCTTGCTCCTTATGCATGAAG 59.784 45.833 10.16 8.92 44.01 3.02
2197 19173 7.765819 ACTCAGATTTTAACATCATCGACATCA 59.234 33.333 4.50 0.00 0.00 3.07
2637 19613 3.473625 AGAACCACAGTTTTTCCTACGG 58.526 45.455 0.00 0.00 35.94 4.02
2748 19724 8.463930 TCAAACTTCACCAGAAATAAAGACAT 57.536 30.769 0.00 0.00 32.35 3.06
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.032549 GCTTATGTACCATGCTTCGCTG 60.033 50.000 0.00 0.00 0.00 5.18
2 3 2.213499 AGCTTATGTACCATGCTTCGC 58.787 47.619 0.00 0.00 0.00 4.70
4 5 4.399303 ACCAAAGCTTATGTACCATGCTTC 59.601 41.667 0.00 0.00 42.23 3.86
5 6 4.344104 ACCAAAGCTTATGTACCATGCTT 58.656 39.130 0.00 10.25 44.51 3.91
6 7 3.968265 ACCAAAGCTTATGTACCATGCT 58.032 40.909 0.00 0.00 35.30 3.79
7 8 5.828299 TTACCAAAGCTTATGTACCATGC 57.172 39.130 0.00 0.00 0.00 4.06
118 122 4.846779 TTTCCGCACAATTTCTTAGCTT 57.153 36.364 0.00 0.00 0.00 3.74
134 139 9.579768 TTGGACAAATATGTTGATAAATTTCCG 57.420 29.630 0.00 0.00 40.74 4.30
185 190 7.703621 AGTTTATAGTTGAATGAACATGCATGC 59.296 33.333 26.53 11.82 36.98 4.06
254 271 6.514705 GCCCAAAAATGCTTAAATTTTCTGCA 60.515 34.615 12.48 12.48 38.49 4.41
322 341 4.738740 GCGTGCTTACAATTCGTCTAGTAT 59.261 41.667 0.00 0.00 0.00 2.12
450 481 0.675083 TTGGTGCTTGCTGGTCATTG 59.325 50.000 0.00 0.00 0.00 2.82
498 544 1.263217 CCGTGTCTTGGTTGTTAGTGC 59.737 52.381 0.00 0.00 0.00 4.40
509 555 2.330372 ATGCTGCAGCCGTGTCTTG 61.330 57.895 34.64 0.00 41.18 3.02
533 579 1.324740 GCCATCTTCATGCCTTGCCA 61.325 55.000 0.00 0.00 0.00 4.92
549 595 0.536724 ATGTGCGTGATGACTAGCCA 59.463 50.000 0.00 0.00 0.00 4.75
592 652 1.507141 GGCAAACTCACACACGAGGG 61.507 60.000 0.00 0.00 37.34 4.30
709 8817 1.296715 CCTGAGAGTTTGTCCCCCG 59.703 63.158 0.00 0.00 0.00 5.73
732 8840 8.463930 TCATTTTAGTGGAATCTTGTCAGTTT 57.536 30.769 0.00 0.00 0.00 2.66
767 8876 5.761726 TGATGGATCTTCACATAGTTGCATC 59.238 40.000 0.00 0.00 40.35 3.91
1433 9575 2.434336 CGGGTGTAGGATTGGATCTTGA 59.566 50.000 0.00 0.00 0.00 3.02
1552 9703 1.437625 GACTCCAGCAGAGACAAAGC 58.562 55.000 10.46 0.00 46.50 3.51
1555 9706 0.681733 GTGGACTCCAGCAGAGACAA 59.318 55.000 10.46 0.00 46.50 3.18
1803 9958 2.247437 GCGGATGCCAATCGGAGAC 61.247 63.158 0.00 0.00 35.66 3.36
1804 9959 2.108976 GCGGATGCCAATCGGAGA 59.891 61.111 0.00 0.00 35.66 3.71
2009 18969 1.814394 TGTGACTTTGATCTGGCATGC 59.186 47.619 9.90 9.90 0.00 4.06
2145 19121 7.535139 ACATTAATTTGGACTTCGTTGTATGG 58.465 34.615 0.00 0.00 0.00 2.74
2601 19577 8.747538 ACTGTGGTTCTAGAGTAAATGTTTTT 57.252 30.769 0.00 0.00 0.00 1.94
2602 19578 8.747538 AACTGTGGTTCTAGAGTAAATGTTTT 57.252 30.769 0.00 0.00 0.00 2.43
2603 19579 8.747538 AAACTGTGGTTCTAGAGTAAATGTTT 57.252 30.769 0.00 0.56 34.14 2.83
2698 19674 7.510428 AACAAGCATAATAAAGCGTTGATTG 57.490 32.000 0.00 0.00 39.05 2.67


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

AutoCloner maintained by Alex Coulton.