Multiple sequence alignment - TraesCS4D01G231000

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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 TraesCS4D01G231000 chr4D 100.000 7252 0 0 1 7252 390871355 390864104 0.000000e+00 13393.0
1 TraesCS4D01G231000 chr4D 98.156 7267 84 10 3 7252 448491406 448498639 0.000000e+00 12632.0
2 TraesCS4D01G231000 chr4D 95.872 4312 145 13 1 4297 448405368 448409661 0.000000e+00 6946.0
3 TraesCS4D01G231000 chr4D 96.432 2859 80 5 4295 7132 448420916 448423773 0.000000e+00 4695.0
4 TraesCS4D01G231000 chr4D 85.985 792 102 4 2530 3314 504061912 504062701 0.000000e+00 839.0
5 TraesCS4D01G231000 chr4D 79.866 447 51 23 3157 3590 504062735 504063155 2.560000e-74 291.0
6 TraesCS4D01G231000 chr4D 86.420 81 5 3 706 785 448400120 448400195 4.660000e-12 84.2
7 TraesCS4D01G231000 chr4D 86.076 79 7 1 707 785 448480732 448480806 1.680000e-11 82.4
8 TraesCS4D01G231000 chr6D 80.543 1105 178 28 1703 2796 24460204 24459126 0.000000e+00 815.0
9 TraesCS4D01G231000 chr2D 80.459 1090 179 24 1732 2796 17805444 17804364 0.000000e+00 802.0
10 TraesCS4D01G231000 chr2D 85.112 356 48 4 5910 6260 17799225 17798870 6.920000e-95 359.0
11 TraesCS4D01G231000 chr2D 82.192 365 51 10 6891 7251 326251895 326251541 1.180000e-77 302.0
12 TraesCS4D01G231000 chr2A 80.186 1075 187 21 1737 2797 19084460 19083398 0.000000e+00 782.0
13 TraesCS4D01G231000 chr2A 86.533 349 44 2 5915 6260 19080071 19079723 1.480000e-101 381.0
14 TraesCS4D01G231000 chr2A 83.333 336 49 6 6918 7251 391840714 391841044 3.290000e-78 303.0
15 TraesCS4D01G231000 chr2B 79.715 1124 188 29 1702 2796 29173576 29174688 0.000000e+00 776.0
16 TraesCS4D01G231000 chr2B 80.755 556 91 10 5901 6444 29179127 29179678 3.130000e-113 420.0
17 TraesCS4D01G231000 chr2B 90.517 116 10 1 5995 6109 29502567 29502682 1.260000e-32 152.0
18 TraesCS4D01G231000 chr2B 84.783 92 14 0 1040 1131 29173276 29173367 7.750000e-15 93.5
19 TraesCS4D01G231000 chr7D 83.014 365 51 7 6891 7252 168047174 168046818 3.260000e-83 320.0
20 TraesCS4D01G231000 chr7D 82.527 372 55 8 6885 7252 447077349 447077714 1.170000e-82 318.0
21 TraesCS4D01G231000 chr7D 82.192 365 54 7 6891 7252 58789549 58789193 3.290000e-78 303.0
22 TraesCS4D01G231000 chr1A 82.337 368 51 10 6891 7252 336312336 336311977 2.540000e-79 307.0
23 TraesCS4D01G231000 chr1D 81.694 366 57 8 6891 7252 257349166 257349525 5.500000e-76 296.0
24 TraesCS4D01G231000 chr5D 86.316 95 11 2 6728 6820 218643668 218643574 1.290000e-17 102.0
25 TraesCS4D01G231000 chr5A 85.417 96 12 2 6727 6820 291794011 291793916 1.670000e-16 99.0


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 TraesCS4D01G231000 chr4D 390864104 390871355 7251 True 13393.00 13393 100.0000 1 7252 1 chr4D.!!$R1 7251
1 TraesCS4D01G231000 chr4D 448491406 448498639 7233 False 12632.00 12632 98.1560 3 7252 1 chr4D.!!$F5 7249
2 TraesCS4D01G231000 chr4D 448405368 448409661 4293 False 6946.00 6946 95.8720 1 4297 1 chr4D.!!$F2 4296
3 TraesCS4D01G231000 chr4D 448420916 448423773 2857 False 4695.00 4695 96.4320 4295 7132 1 chr4D.!!$F3 2837
4 TraesCS4D01G231000 chr4D 504061912 504063155 1243 False 565.00 839 82.9255 2530 3590 2 chr4D.!!$F6 1060
5 TraesCS4D01G231000 chr6D 24459126 24460204 1078 True 815.00 815 80.5430 1703 2796 1 chr6D.!!$R1 1093
6 TraesCS4D01G231000 chr2D 17804364 17805444 1080 True 802.00 802 80.4590 1732 2796 1 chr2D.!!$R2 1064
7 TraesCS4D01G231000 chr2A 19079723 19084460 4737 True 581.50 782 83.3595 1737 6260 2 chr2A.!!$R1 4523
8 TraesCS4D01G231000 chr2B 29173276 29174688 1412 False 434.75 776 82.2490 1040 2796 2 chr2B.!!$F3 1756
9 TraesCS4D01G231000 chr2B 29179127 29179678 551 False 420.00 420 80.7550 5901 6444 1 chr2B.!!$F1 543

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
183 186 2.952978 TGCAACGAACAAACCCACTTAT 59.047 40.909 0.00 0.0 0.00 1.73 F
1054 1068 1.768870 ACGAGGTTATTGCTGGCCTAT 59.231 47.619 3.32 0.0 0.00 2.57 F
1438 1574 2.973082 GCCGGATGCCAAGCTTTT 59.027 55.556 5.05 0.0 0.00 2.27 F
2251 2414 3.904800 TGTGACTTTCACCAAGACTCA 57.095 42.857 3.91 0.0 46.40 3.41 F
3117 3878 3.998913 TGACAAGATAGGCATCAACCA 57.001 42.857 0.00 0.0 33.21 3.67 F
3797 4766 3.898741 GAGAGGAATAGAGTTAGTGGGGG 59.101 52.174 0.00 0.0 0.00 5.40 F
5273 6411 4.022242 CACTCACTACCCAACCTATATCCG 60.022 50.000 0.00 0.0 0.00 4.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1054 1068 1.911269 TGTAGGGTCGAGGCTTGCA 60.911 57.895 0.00 0.00 0.00 4.08 R
2248 2411 5.053145 GCTCCACCATAGATTGTAGTTGAG 58.947 45.833 0.00 0.00 0.00 3.02 R
3163 3924 3.650139 TCGAGTCAAGCAGAAACCTAAC 58.350 45.455 0.00 0.00 0.00 2.34 R
3760 4729 3.784178 TCCTCTCTTCCACTCAACAGAT 58.216 45.455 0.00 0.00 0.00 2.90 R
4564 5533 4.875544 TGTTGCATCTAAATTAGGACGC 57.124 40.909 0.00 1.90 0.00 5.19 R
5725 6900 5.163683 CCAAGTGAGATGAATACAAGGCTTG 60.164 44.000 25.06 25.06 0.00 4.01 R
6908 8901 1.452108 CTCTTCGGGGCATCCAACC 60.452 63.158 0.00 0.00 34.36 3.77 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
149 152 8.691797 GGTTTGGTATTCATATGTTACCATTGT 58.308 33.333 26.53 2.77 43.56 2.71
183 186 2.952978 TGCAACGAACAAACCCACTTAT 59.047 40.909 0.00 0.00 0.00 1.73
1054 1068 1.768870 ACGAGGTTATTGCTGGCCTAT 59.231 47.619 3.32 0.00 0.00 2.57
1306 1442 8.282592 TGCATTAATGAATCTTGTCGCTAATAC 58.717 33.333 19.73 0.00 0.00 1.89
1438 1574 2.973082 GCCGGATGCCAAGCTTTT 59.027 55.556 5.05 0.00 0.00 2.27
2206 2369 4.955811 ATGCACCGTATCTTAGGATTCA 57.044 40.909 0.00 0.00 33.71 2.57
2230 2393 5.503002 TGGAGAAGAAATGCTTGATGATGA 58.497 37.500 0.00 0.00 36.83 2.92
2248 2411 4.756642 TGATGATGTGACTTTCACCAAGAC 59.243 41.667 3.91 0.00 46.40 3.01
2251 2414 3.904800 TGTGACTTTCACCAAGACTCA 57.095 42.857 3.91 0.00 46.40 3.41
2683 2855 5.399858 TCTACGAGCCGCAATATTCTTATC 58.600 41.667 0.00 0.00 0.00 1.75
3117 3878 3.998913 TGACAAGATAGGCATCAACCA 57.001 42.857 0.00 0.00 33.21 3.67
3163 3924 6.453643 GTATGCATTCTTCTACATACCACG 57.546 41.667 3.54 0.00 39.16 4.94
3250 4011 8.441608 CACATGATAAGCTAGAGATGTATTTGC 58.558 37.037 0.00 0.00 0.00 3.68
3760 4729 4.471747 TGGCATGGTGAGTTGGTATAGTTA 59.528 41.667 0.00 0.00 0.00 2.24
3797 4766 3.898741 GAGAGGAATAGAGTTAGTGGGGG 59.101 52.174 0.00 0.00 0.00 5.40
3849 4818 8.802267 ACCAACTACACAATTTGCATAACTATT 58.198 29.630 0.00 0.00 0.00 1.73
4609 5578 8.950210 ACAAAATTCATGTTGATAGTGTCTAGG 58.050 33.333 1.16 0.00 0.00 3.02
4979 5960 5.046376 AGCTTTGGGATTAAGGGATTTTGTG 60.046 40.000 0.00 0.00 0.00 3.33
5273 6411 4.022242 CACTCACTACCCAACCTATATCCG 60.022 50.000 0.00 0.00 0.00 4.18
5725 6900 5.446709 CAGCAGTGCTTGTATGCATATAAC 58.553 41.667 16.89 8.80 45.23 1.89
6190 8170 7.201609 GGATTTTATGTACAAGCGTGAAGATGA 60.202 37.037 6.65 0.00 0.00 2.92
6463 8451 3.485394 TGCATTCAGTTGGTATGTGTGT 58.515 40.909 0.00 0.00 0.00 3.72
6677 8670 6.730960 AAGCTATGGATTGCACAATTTTTG 57.269 33.333 0.00 0.00 0.00 2.44
6907 8900 3.622060 TTGCTACCCCCGCAAGAGC 62.622 63.158 0.00 0.00 41.97 4.09
7103 9096 2.636830 CCCTCATCTTGCTAGTTGTGG 58.363 52.381 15.91 15.91 35.75 4.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
13 14 4.466827 GCTAGATAGGAGGATAGCTACCC 58.533 52.174 0.00 0.00 38.07 3.69
183 186 1.742510 GGCTAGTTTAACGCCGGCA 60.743 57.895 28.98 3.37 33.64 5.69
1054 1068 1.911269 TGTAGGGTCGAGGCTTGCA 60.911 57.895 0.00 0.00 0.00 4.08
1244 1380 5.936956 GCTTTAGCATGTTGCCTCTCTATAT 59.063 40.000 0.00 0.00 46.52 0.86
1306 1442 3.620374 CGCTAAATCATGCTATAGCCTGG 59.380 47.826 24.32 13.68 41.18 4.45
2190 2353 5.984695 TCTCCATGAATCCTAAGATACGG 57.015 43.478 0.00 0.00 30.42 4.02
2206 2369 6.127101 TCATCATCAAGCATTTCTTCTCCAT 58.873 36.000 0.00 0.00 31.27 3.41
2248 2411 5.053145 GCTCCACCATAGATTGTAGTTGAG 58.947 45.833 0.00 0.00 0.00 3.02
2251 2414 5.367937 AGATGCTCCACCATAGATTGTAGTT 59.632 40.000 0.00 0.00 0.00 2.24
2683 2855 5.151632 AGTTTTGTTAGCATTATACGCGG 57.848 39.130 12.47 0.00 0.00 6.46
3117 3878 7.759489 ACCAACTTACATGTGTTCATTGTAT 57.241 32.000 9.11 0.00 31.15 2.29
3163 3924 3.650139 TCGAGTCAAGCAGAAACCTAAC 58.350 45.455 0.00 0.00 0.00 2.34
3760 4729 3.784178 TCCTCTCTTCCACTCAACAGAT 58.216 45.455 0.00 0.00 0.00 2.90
4171 5140 8.568617 AATAGAAGGTACCCAGAAAGACATAT 57.431 34.615 8.74 0.00 0.00 1.78
4201 5170 5.914033 ACCAACTAGACATAACACGCATAT 58.086 37.500 0.00 0.00 0.00 1.78
4564 5533 4.875544 TGTTGCATCTAAATTAGGACGC 57.124 40.909 0.00 1.90 0.00 5.19
5725 6900 5.163683 CCAAGTGAGATGAATACAAGGCTTG 60.164 44.000 25.06 25.06 0.00 4.01
6190 8170 7.973048 TTGAGACTAAATGATAGGGTGTACT 57.027 36.000 0.00 0.00 0.00 2.73
6908 8901 1.452108 CTCTTCGGGGCATCCAACC 60.452 63.158 0.00 0.00 34.36 3.77


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

AutoCloner maintained by Alex Coulton.