Multiple sequence alignment - TraesCS2D01G158900

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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 TraesCS2D01G158900 chr2D 100.000 3267 0 0 1 3267 102508821 102505555 0 6034
1 TraesCS2D01G158900 chr2D 95.317 3267 149 2 1 3267 41763749 41760487 0 5182
2 TraesCS2D01G158900 chr2D 95.109 3271 155 3 1 3267 38982212 38978943 0 5149
3 TraesCS2D01G158900 chr7D 95.566 3270 139 6 1 3267 147042076 147045342 0 5230
4 TraesCS2D01G158900 chr7D 95.602 3229 135 6 1 3228 182871971 182875193 0 5169
5 TraesCS2D01G158900 chr7D 93.951 529 32 0 2739 3267 614569086 614569614 0 800
6 TraesCS2D01G158900 chr5D 95.072 3267 159 2 1 3267 318511311 318514575 0 5140
7 TraesCS2D01G158900 chr1D 94.441 3274 172 6 1 3267 32397116 32393846 0 5029
8 TraesCS2D01G158900 chrUn 96.558 2905 94 3 1 2902 91267094 91269995 0 4806
9 TraesCS2D01G158900 chr3D 93.628 3170 188 8 103 3267 39833983 39830823 0 4723
10 TraesCS2D01G158900 chr4B 94.457 3049 162 5 103 3145 57702794 57699747 0 4687


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 TraesCS2D01G158900 chr2D 102505555 102508821 3266 True 6034 6034 100.000 1 3267 1 chr2D.!!$R3 3266
1 TraesCS2D01G158900 chr2D 41760487 41763749 3262 True 5182 5182 95.317 1 3267 1 chr2D.!!$R2 3266
2 TraesCS2D01G158900 chr2D 38978943 38982212 3269 True 5149 5149 95.109 1 3267 1 chr2D.!!$R1 3266
3 TraesCS2D01G158900 chr7D 147042076 147045342 3266 False 5230 5230 95.566 1 3267 1 chr7D.!!$F1 3266
4 TraesCS2D01G158900 chr7D 182871971 182875193 3222 False 5169 5169 95.602 1 3228 1 chr7D.!!$F2 3227
5 TraesCS2D01G158900 chr7D 614569086 614569614 528 False 800 800 93.951 2739 3267 1 chr7D.!!$F3 528
6 TraesCS2D01G158900 chr5D 318511311 318514575 3264 False 5140 5140 95.072 1 3267 1 chr5D.!!$F1 3266
7 TraesCS2D01G158900 chr1D 32393846 32397116 3270 True 5029 5029 94.441 1 3267 1 chr1D.!!$R1 3266
8 TraesCS2D01G158900 chrUn 91267094 91269995 2901 False 4806 4806 96.558 1 2902 1 chrUn.!!$F1 2901
9 TraesCS2D01G158900 chr3D 39830823 39833983 3160 True 4723 4723 93.628 103 3267 1 chr3D.!!$R1 3164
10 TraesCS2D01G158900 chr4B 57699747 57702794 3047 True 4687 4687 94.457 103 3145 1 chr4B.!!$R1 3042

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
879 883 0.605589 CCTCCACGACCCAAACCTTC 60.606 60.0 0.0 0.0 0.0 3.46 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2808 2830 0.685097 GTCACACACCCTTGGCTCTA 59.315 55.0 0.0 0.0 0.0 2.43 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
27 28 2.668250 CGTTTGACGGTGTGTATCTCA 58.332 47.619 0.00 0.00 38.08 3.27
88 89 3.254093 TGTGAGGGGAACTCTACTTCA 57.746 47.619 0.00 0.00 46.72 3.02
264 265 3.976701 AAGATTCGTGCCGCCTGGG 62.977 63.158 0.00 0.00 39.58 4.45
426 429 3.011119 TCCGAAGACTTACTCAGAGAGC 58.989 50.000 3.79 0.00 32.04 4.09
542 545 7.438757 GTGTGAATAGTACTCAGAGAGTATCGA 59.561 40.741 3.79 0.00 45.21 3.59
678 682 1.927174 CACACTATCTAAGCGTGCCAC 59.073 52.381 0.00 0.00 31.85 5.01
706 710 5.047377 AGTGTGTGCTTAAATGGTTTATGGG 60.047 40.000 0.00 0.00 0.00 4.00
879 883 0.605589 CCTCCACGACCCAAACCTTC 60.606 60.000 0.00 0.00 0.00 3.46
934 938 5.619981 GCTCAATTCCGAAAACACTATTGCT 60.620 40.000 0.00 0.00 0.00 3.91
989 993 3.466314 TCAAGGCCGCCATCGCTA 61.466 61.111 13.15 0.00 0.00 4.26
1145 1150 0.971386 CATGGCAAGGAAAAGCTGGT 59.029 50.000 0.00 0.00 0.00 4.00
1375 1382 3.150458 TCCTACAGTTTCGACCTCTCA 57.850 47.619 0.00 0.00 0.00 3.27
1464 1472 7.055667 TCAGTGAAGTTTCTGAAGTAGATGT 57.944 36.000 8.57 0.00 37.69 3.06
1632 1640 8.082852 TGATGTTCTAGTGTAGTTCAGTTTCTC 58.917 37.037 0.00 0.00 0.00 2.87
1633 1641 7.342769 TGTTCTAGTGTAGTTCAGTTTCTCA 57.657 36.000 0.00 0.00 0.00 3.27
2259 2275 7.741027 AGAATTATGACGATCCTTACTACGA 57.259 36.000 0.00 0.00 0.00 3.43
2335 2351 7.346751 TCTGCTTGTCCTTTCTATTGTTTTT 57.653 32.000 0.00 0.00 0.00 1.94
2615 2633 2.204136 TGGGAGGAGTGGCATGGT 60.204 61.111 0.00 0.00 0.00 3.55
2727 2745 4.505922 GTCTCTACAGAAATGAAGGCATCG 59.494 45.833 0.00 0.00 32.35 3.84
2735 2757 1.108776 ATGAAGGCATCGCAAGCATT 58.891 45.000 0.00 0.00 38.86 3.56
2824 2846 0.396811 GTGTAGAGCCAAGGGTGTGT 59.603 55.000 0.00 0.00 0.00 3.72
2975 2997 1.812922 GCAGAGGCATGTGTCGGAG 60.813 63.158 0.00 0.00 40.72 4.63
3056 3078 2.058595 ATGTAAGAGTCGCGGGGCT 61.059 57.895 6.18 6.18 0.00 5.19
3094 3116 0.248289 GATGCAGGCACAAAAGGCAT 59.752 50.000 0.00 0.00 46.91 4.40
3098 3120 0.899720 CAGGCACAAAAGGCATGGAT 59.100 50.000 0.00 0.00 39.22 3.41
3138 3160 2.480587 CGGAAGTGGGGTTTTTGTTGTC 60.481 50.000 0.00 0.00 0.00 3.18
3211 3233 2.480759 GCTTCCGAATACGCAGTTAGGA 60.481 50.000 0.00 0.00 37.78 2.94
3219 3241 0.956633 ACGCAGTTAGGAAGTCACGA 59.043 50.000 0.00 0.00 37.78 4.35
3249 3271 1.465387 CTCTAGAGAGTCACGCGTGTT 59.535 52.381 35.74 25.69 37.40 3.32
3259 3281 2.183504 ACGCGTGTTTGGCATCACA 61.184 52.632 12.93 9.36 34.66 3.58
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
27 28 1.541672 CCAACCACCCTCCCACTTT 59.458 57.895 0.00 0.00 0.00 2.66
55 56 0.673437 CCTCACAAAACAACCGCCAT 59.327 50.000 0.00 0.00 0.00 4.40
88 89 1.202952 TCAGTACACGGGCCCAAATTT 60.203 47.619 24.92 1.63 0.00 1.82
327 330 0.322322 AATTCCAACGTCGGTGCCTA 59.678 50.000 4.27 0.00 0.00 3.93
426 429 3.724374 TCTAAAGACTTCACAACCGTGG 58.276 45.455 0.00 0.00 43.79 4.94
706 710 8.722342 TGATTAAGCACGTAAGAAATGTTTTC 57.278 30.769 0.00 0.00 43.62 2.29
716 720 5.950965 AATCGTCTGATTAAGCACGTAAG 57.049 39.130 4.04 0.00 42.99 2.34
812 816 0.614979 AGTGAGGGCGGTAGACATGT 60.615 55.000 0.00 0.00 0.00 3.21
934 938 2.568956 AGTTGCTAGTTGAGATGGAGCA 59.431 45.455 0.00 0.00 41.23 4.26
989 993 1.739338 CTCCGCCATTACGCTCCTCT 61.739 60.000 0.00 0.00 0.00 3.69
1128 1133 0.752054 CAACCAGCTTTTCCTTGCCA 59.248 50.000 0.00 0.00 0.00 4.92
1295 1302 0.036952 ACAGAGTTCCTCCACGCATG 60.037 55.000 0.00 0.00 0.00 4.06
1375 1382 9.196552 GTGAAAAGCTAATTAAACAGAAGCATT 57.803 29.630 0.00 0.00 35.63 3.56
1464 1472 9.155975 GAGTCAAGTTCAAAATCTATTCTGCTA 57.844 33.333 0.00 0.00 0.00 3.49
1632 1640 8.018520 TCTTAGCCACGTTAACACATAAATTTG 58.981 33.333 6.39 0.00 0.00 2.32
1633 1641 8.101654 TCTTAGCCACGTTAACACATAAATTT 57.898 30.769 6.39 0.00 0.00 1.82
2028 2043 1.352017 TCACACTCCCTGCAACATCAT 59.648 47.619 0.00 0.00 0.00 2.45
2259 2275 8.277490 TCTATGTTTTCGTCATCACTAGTAGT 57.723 34.615 0.00 0.00 0.00 2.73
2335 2351 8.621532 TCTAACAGAAGTAAACTACGAACCTA 57.378 34.615 0.00 0.00 0.00 3.08
2540 2557 8.429493 AAACTGTACTTAGCGTAAAAAGACTT 57.571 30.769 0.00 0.00 0.00 3.01
2615 2633 4.142227 GCCTCTCTAACTGTGTATTCCGAA 60.142 45.833 0.00 0.00 0.00 4.30
2727 2745 1.136147 CGTGCCTCTGAATGCTTGC 59.864 57.895 1.28 0.00 0.00 4.01
2735 2757 3.680786 CCGTCCACGTGCCTCTGA 61.681 66.667 10.91 0.00 37.74 3.27
2808 2830 0.685097 GTCACACACCCTTGGCTCTA 59.315 55.000 0.00 0.00 0.00 2.43
2824 2846 0.701147 TTACATGCCCCATGGTGTCA 59.299 50.000 11.73 5.64 45.16 3.58
2975 2997 1.281899 GTGCATCTCTAACCGAGCAC 58.718 55.000 0.00 0.00 44.31 4.40
3094 3116 1.338105 CCTCTTGCGTCTTCACATCCA 60.338 52.381 0.00 0.00 0.00 3.41
3098 3120 0.880278 GTGCCTCTTGCGTCTTCACA 60.880 55.000 0.00 0.00 45.60 3.58
3138 3160 1.524355 CAGGATTGATAGCTGTTCGCG 59.476 52.381 0.00 0.00 45.59 5.87
3249 3271 4.021559 CCATGCCTGTGATGCCAA 57.978 55.556 0.00 0.00 0.00 4.52


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

AutoCloner maintained by Alex Coulton.