Multiple sequence alignment - TraesCS2D01G436500

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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 TraesCS2D01G436500 chr2D 100.000 3671 0 0 1 3671 547144643 547148313 0.000000e+00 6780
1 TraesCS2D01G436500 chr2D 90.000 130 9 2 3544 3669 597886825 597886696 8.160000e-37 165
2 TraesCS2D01G436500 chr2D 89.764 127 12 1 3544 3669 641926602 641926476 1.050000e-35 161
3 TraesCS2D01G436500 chr2A 98.559 3677 40 8 1 3671 690715654 690719323 0.000000e+00 6484
4 TraesCS2D01G436500 chr6B 90.400 125 10 2 3545 3669 576267114 576267236 2.930000e-36 163
5 TraesCS2D01G436500 chr5D 90.323 124 9 2 3546 3669 309687941 309687821 3.790000e-35 159
6 TraesCS2D01G436500 chr1A 90.244 123 10 2 3547 3669 508627149 508627029 3.790000e-35 159
7 TraesCS2D01G436500 chr1A 89.516 124 12 1 3546 3669 583892214 583892092 4.910000e-34 156
8 TraesCS2D01G436500 chr4B 89.062 128 11 3 3544 3669 252980569 252980443 4.910000e-34 156
9 TraesCS2D01G436500 chr2B 85.906 149 11 8 3524 3668 729774556 729774414 2.280000e-32 150


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 TraesCS2D01G436500 chr2D 547144643 547148313 3670 False 6780 6780 100.000 1 3671 1 chr2D.!!$F1 3670
1 TraesCS2D01G436500 chr2A 690715654 690719323 3669 False 6484 6484 98.559 1 3671 1 chr2A.!!$F1 3670

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
839 845 1.081556 TCCGATGTTTCATGCCGACG 61.082 55.000 0.0 0.0 0.0 5.12 F
1396 1402 1.205893 CAGGAGCACTAAGACAGACCC 59.794 57.143 0.0 0.0 0.0 4.46 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2053 2059 0.678950 CGGTTGCCATTGGGAGTTTT 59.321 50.0 4.53 0.0 35.59 2.43 R
3235 3241 1.073216 CGAGATGTCGCCACACTGTC 61.073 60.0 0.00 0.0 39.88 3.51 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
69 70 5.021458 AGATCATGCATAATTTCATCCCCC 58.979 41.667 0.00 0.00 0.00 5.40
143 144 2.093235 CGAAATTGGAGAGGGAGCTCTT 60.093 50.000 14.64 1.93 35.26 2.85
146 147 5.501156 GAAATTGGAGAGGGAGCTCTTTTA 58.499 41.667 14.64 0.00 35.26 1.52
147 148 5.723860 AATTGGAGAGGGAGCTCTTTTAT 57.276 39.130 14.64 0.00 35.26 1.40
148 149 4.762289 TTGGAGAGGGAGCTCTTTTATC 57.238 45.455 14.64 6.25 35.26 1.75
267 270 6.407299 GGCCCAAATGACAGTCAATGATAAAT 60.407 38.462 17.29 0.00 0.00 1.40
268 271 7.201902 GGCCCAAATGACAGTCAATGATAAATA 60.202 37.037 17.29 0.00 0.00 1.40
380 383 4.731313 AAAACTCAGATCCCCTGTTTCT 57.269 40.909 0.00 0.00 43.38 2.52
472 477 3.157949 CTCTCCCCCTTCCTCGCC 61.158 72.222 0.00 0.00 0.00 5.54
564 569 2.421739 CTTCTCCCCCGCCATACG 59.578 66.667 0.00 0.00 43.15 3.06
623 628 2.436646 AGCGATTCGGCCACCTTG 60.437 61.111 2.24 0.00 0.00 3.61
708 714 1.139058 GGTCTGTATGCGATTGAGGGT 59.861 52.381 0.00 0.00 0.00 4.34
839 845 1.081556 TCCGATGTTTCATGCCGACG 61.082 55.000 0.00 0.00 0.00 5.12
1085 1091 5.250235 TCAGTTAAAGATCTAGGCGTCAG 57.750 43.478 0.00 0.00 0.00 3.51
1240 1246 5.540911 ACTTTAGGCATTCAAATGTTGTGG 58.459 37.500 4.76 0.00 38.65 4.17
1287 1293 4.972568 TCAGGCTATCCCAGGTTTGTATTA 59.027 41.667 0.00 0.00 35.39 0.98
1387 1393 2.040278 AGCATTCCAACAGGAGCACTAA 59.960 45.455 0.00 0.00 31.86 2.24
1396 1402 1.205893 CAGGAGCACTAAGACAGACCC 59.794 57.143 0.00 0.00 0.00 4.46
1908 1914 5.880901 AGGTTCATCAACTATGTTGGAGTT 58.119 37.500 10.05 0.00 37.64 3.01
2026 2032 3.939592 GGTAAGACCTAAACTGCATGTCC 59.060 47.826 0.00 0.00 34.73 4.02
2053 2059 5.069781 GGTGTGCCTATAATAAATTGGCCAA 59.930 40.000 23.00 23.00 42.62 4.52
2103 2109 2.293399 ACCATTTCAAGAGGCGTTTGAC 59.707 45.455 6.27 0.00 34.50 3.18
2491 2497 7.009540 GCTTATTGTTTTCATGTATGCAACTCC 59.990 37.037 0.00 0.00 0.00 3.85
2538 2544 8.107095 AGAACAGGGAATTGCTTATACAAACTA 58.893 33.333 0.00 0.00 32.27 2.24
2612 2618 8.427276 ACTGATTGATCATGATCTTAGTTAGCA 58.573 33.333 30.65 17.79 38.60 3.49
2688 2694 3.946824 AGGAATCCTGAGGATGTATGGT 58.053 45.455 15.97 0.00 42.27 3.55
2842 2848 2.158667 TGTCCCCTTCTTGGAGTTGTTC 60.159 50.000 0.00 0.00 38.35 3.18
2869 2875 1.980765 TGTGGTCAAGAGGCTGAAGAT 59.019 47.619 0.00 0.00 0.00 2.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
163 166 2.175202 CACTCTCCTGAGCTTGTACCT 58.825 52.381 0.00 0.00 43.85 3.08
175 178 0.767375 TTTGGCTCTTGCACTCTCCT 59.233 50.000 0.00 0.00 41.91 3.69
314 317 1.139058 GAGTGGGTCTGTCTTGTGTGT 59.861 52.381 0.00 0.00 0.00 3.72
369 372 2.291043 GGGAGCGAGAAACAGGGGA 61.291 63.158 0.00 0.00 0.00 4.81
380 383 2.747686 GGTGAAACAGGGGAGCGA 59.252 61.111 0.00 0.00 39.98 4.93
682 687 0.469917 ATCGCATACAGACCCCCAAG 59.530 55.000 0.00 0.00 0.00 3.61
708 714 5.279506 GGGCGATGACAAATAGAGATCCTAA 60.280 44.000 0.00 0.00 0.00 2.69
1240 1246 5.182001 ACACATCATAGAAGTTTTGGACAGC 59.818 40.000 0.00 0.00 0.00 4.40
1287 1293 1.201429 AGCTTCCGTCCACCCAAGAT 61.201 55.000 0.00 0.00 0.00 2.40
1387 1393 0.902516 GCTCACAGGAGGGTCTGTCT 60.903 60.000 0.00 0.00 45.24 3.41
1396 1402 0.179936 GGATTGAGGGCTCACAGGAG 59.820 60.000 0.00 0.00 44.33 3.69
1761 1767 2.369860 ACCTGACAATCTCTCAACTGCA 59.630 45.455 0.00 0.00 0.00 4.41
1908 1914 1.171308 GTAGTCGGGTGCTGTCTGTA 58.829 55.000 0.00 0.00 0.00 2.74
2053 2059 0.678950 CGGTTGCCATTGGGAGTTTT 59.321 50.000 4.53 0.00 35.59 2.43
2491 2497 3.334691 TGAATCCAGTTTCAAGGCTACG 58.665 45.455 0.00 0.00 32.82 3.51
2688 2694 5.461078 GTCAAGCTAGTTTGTCTCGTTGTTA 59.539 40.000 17.56 0.00 0.00 2.41
2869 2875 4.334552 ACAAGTGATGATTACATGCCACA 58.665 39.130 0.00 0.00 35.25 4.17
3235 3241 1.073216 CGAGATGTCGCCACACTGTC 61.073 60.000 0.00 0.00 39.88 3.51
3323 3329 6.432607 AGATTGTGATGTGAGCAACTTATG 57.567 37.500 0.00 0.00 0.00 1.90
3512 3518 3.126343 AGCTTCTTTATAAAACCGCGTGG 59.874 43.478 14.93 14.93 42.84 4.94
3605 3611 8.739039 TGAAACACGGAGAATATGAAATTTGAT 58.261 29.630 0.00 0.00 0.00 2.57


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

AutoCloner maintained by Alex Coulton.