Multiple sequence alignment - TraesCS5A01G171500

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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 TraesCS5A01G171500 chr5A 100.000 3071 0 0 1 3071 364959903 364956833 0.000000e+00 5672.0
1 TraesCS5A01G171500 chr5A 100.000 28 0 0 3019 3046 306188532 306188559 6.000000e-03 52.8
2 TraesCS5A01G171500 chr5B 95.173 2258 82 14 830 3071 313210863 313208617 0.000000e+00 3541.0
3 TraesCS5A01G171500 chr5B 100.000 28 0 0 3019 3046 251506237 251506264 6.000000e-03 52.8
4 TraesCS5A01G171500 chr5D 94.651 2262 75 24 779 3012 276455133 276452890 0.000000e+00 3465.0
5 TraesCS5A01G171500 chr1B 94.865 779 39 1 1 779 185229037 185228260 0.000000e+00 1216.0
6 TraesCS5A01G171500 chr1B 94.723 777 40 1 1 777 566122133 566121358 0.000000e+00 1206.0
7 TraesCS5A01G171500 chr6B 94.330 776 44 0 1 776 132110954 132111729 0.000000e+00 1190.0
8 TraesCS5A01G171500 chr6B 94.223 779 44 1 1 779 283228281 283227504 0.000000e+00 1188.0
9 TraesCS5A01G171500 chr2D 94.337 777 40 2 1 773 610245890 610245114 0.000000e+00 1188.0
10 TraesCS5A01G171500 chr2D 87.826 115 13 1 1403 1517 624320867 624320754 1.920000e-27 134.0
11 TraesCS5A01G171500 chr3B 94.423 771 41 2 1 770 52193305 52192536 0.000000e+00 1184.0
12 TraesCS5A01G171500 chr4B 93.997 783 44 3 1 780 13967346 13966564 0.000000e+00 1182.0
13 TraesCS5A01G171500 chr4B 94.087 778 45 1 1 778 404848112 404847336 0.000000e+00 1181.0
14 TraesCS5A01G171500 chr3D 94.293 771 43 1 1 770 586598864 586598094 0.000000e+00 1179.0
15 TraesCS5A01G171500 chr4D 85.340 191 24 4 1341 1530 480846801 480846988 8.690000e-46 195.0


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 TraesCS5A01G171500 chr5A 364956833 364959903 3070 True 5672 5672 100.000 1 3071 1 chr5A.!!$R1 3070
1 TraesCS5A01G171500 chr5B 313208617 313210863 2246 True 3541 3541 95.173 830 3071 1 chr5B.!!$R1 2241
2 TraesCS5A01G171500 chr5D 276452890 276455133 2243 True 3465 3465 94.651 779 3012 1 chr5D.!!$R1 2233
3 TraesCS5A01G171500 chr1B 185228260 185229037 777 True 1216 1216 94.865 1 779 1 chr1B.!!$R1 778
4 TraesCS5A01G171500 chr1B 566121358 566122133 775 True 1206 1206 94.723 1 777 1 chr1B.!!$R2 776
5 TraesCS5A01G171500 chr6B 132110954 132111729 775 False 1190 1190 94.330 1 776 1 chr6B.!!$F1 775
6 TraesCS5A01G171500 chr6B 283227504 283228281 777 True 1188 1188 94.223 1 779 1 chr6B.!!$R1 778
7 TraesCS5A01G171500 chr2D 610245114 610245890 776 True 1188 1188 94.337 1 773 1 chr2D.!!$R1 772
8 TraesCS5A01G171500 chr3B 52192536 52193305 769 True 1184 1184 94.423 1 770 1 chr3B.!!$R1 769
9 TraesCS5A01G171500 chr4B 13966564 13967346 782 True 1182 1182 93.997 1 780 1 chr4B.!!$R1 779
10 TraesCS5A01G171500 chr4B 404847336 404848112 776 True 1181 1181 94.087 1 778 1 chr4B.!!$R2 777
11 TraesCS5A01G171500 chr3D 586598094 586598864 770 True 1179 1179 94.293 1 770 1 chr3D.!!$R1 769

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
980 987 0.107214 TCTGATTCCCCAATCGCCAC 60.107 55.0 0.0 0.0 41.41 5.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2436 2462 0.03601 CGGCATCAAGGAGGACAAGT 60.036 55.0 0.0 0.0 0.0 3.16 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
25 26 0.173708 CTCGGGTCTGTTCACTAGGC 59.826 60.000 0.00 0.00 0.00 3.93
26 27 0.251653 TCGGGTCTGTTCACTAGGCT 60.252 55.000 0.00 0.00 0.00 4.58
355 359 3.645268 GATCCTGCTTTGCCCGGGT 62.645 63.158 24.63 0.00 0.00 5.28
361 365 2.035626 CTTTGCCCGGGTGGATGT 59.964 61.111 24.63 0.00 37.49 3.06
441 445 1.798813 CTTTTCGCGGTACTCAAAGCT 59.201 47.619 6.13 0.00 0.00 3.74
501 505 3.079478 ATGCCCTCTCAGCGCTGA 61.079 61.111 35.97 35.97 38.06 4.26
516 520 2.932622 GCGCTGATGTCAAGAAAGGAGA 60.933 50.000 0.00 0.00 0.00 3.71
522 526 5.132502 TGATGTCAAGAAAGGAGAAAGCAA 58.867 37.500 0.00 0.00 0.00 3.91
539 543 0.170116 CAACGTGGCGGCAATTGTAT 59.830 50.000 15.50 1.64 0.00 2.29
543 547 1.292061 GTGGCGGCAATTGTATCGTA 58.708 50.000 15.50 1.31 0.00 3.43
567 571 3.119280 TCGAAGACGATGACCTATTTGCA 60.119 43.478 0.00 0.00 43.81 4.08
608 612 1.349026 CTGCAGGGGTCTTCTCTCAAA 59.651 52.381 5.57 0.00 0.00 2.69
635 639 0.543277 GATGATGACACAGGGCTCCA 59.457 55.000 0.00 0.00 0.00 3.86
665 669 7.732025 TCTTCTTGTGTTATGGTTGTCTTAGA 58.268 34.615 0.00 0.00 0.00 2.10
707 711 5.096849 GTCCTTTGTTTTTGCGTTTCAGTA 58.903 37.500 0.00 0.00 0.00 2.74
712 716 5.425577 TGTTTTTGCGTTTCAGTATGCTA 57.574 34.783 0.00 0.00 34.76 3.49
720 724 4.441079 GCGTTTCAGTATGCTAGTAAGGGA 60.441 45.833 0.00 0.00 34.76 4.20
887 891 7.006509 TCTCCAGGAGAAGAACAAAATCAAAT 58.993 34.615 17.67 0.00 35.59 2.32
888 892 7.175641 TCTCCAGGAGAAGAACAAAATCAAATC 59.824 37.037 17.67 0.00 35.59 2.17
889 893 6.777091 TCCAGGAGAAGAACAAAATCAAATCA 59.223 34.615 0.00 0.00 0.00 2.57
890 894 7.287466 TCCAGGAGAAGAACAAAATCAAATCAA 59.713 33.333 0.00 0.00 0.00 2.57
891 895 7.927629 CCAGGAGAAGAACAAAATCAAATCAAA 59.072 33.333 0.00 0.00 0.00 2.69
929 936 2.121538 GGCCTCTCCAATTTCCGGC 61.122 63.158 0.00 0.00 36.83 6.13
933 940 3.876198 CTCCAATTTCCGGCCGCG 61.876 66.667 22.85 13.93 0.00 6.46
980 987 0.107214 TCTGATTCCCCAATCGCCAC 60.107 55.000 0.00 0.00 41.41 5.01
1546 1559 4.851214 AGAGCCTCTCGCCCTCCC 62.851 72.222 0.00 0.00 38.78 4.30
1709 1722 4.056125 GGCTTTCGGTGGGCAAGC 62.056 66.667 0.00 0.00 41.93 4.01
1849 1862 0.035915 GGAGAGAGGGCTTTCACCAC 60.036 60.000 0.00 0.00 0.00 4.16
2196 2211 8.461222 CACATTTCTCATTGGCTTAAAGATACA 58.539 33.333 0.00 0.00 0.00 2.29
2362 2388 9.685276 ATACATTACATGATTCCAGTTCTTTGA 57.315 29.630 0.00 0.00 0.00 2.69
2363 2389 8.048534 ACATTACATGATTCCAGTTCTTTGAG 57.951 34.615 0.00 0.00 0.00 3.02
2436 2462 3.913799 TCATCCTAGTTCCTTGGGTTCAA 59.086 43.478 0.00 0.00 0.00 2.69
2497 2523 1.556911 AGGTATCCAAGCTGTGACAGG 59.443 52.381 15.24 0.00 33.68 4.00
2509 2536 5.865085 AGCTGTGACAGGTTATCAACTTAA 58.135 37.500 12.08 0.00 39.27 1.85
2638 2672 2.046507 GGACACTGCTGCCTCCAG 60.047 66.667 0.00 0.00 42.13 3.86
2898 2942 4.607293 TCATCGGAAATCCTGTATCCAG 57.393 45.455 0.00 0.00 38.50 3.86
2901 2945 3.572642 TCGGAAATCCTGTATCCAGCTA 58.427 45.455 0.00 0.00 37.38 3.32
3015 3063 7.948034 TGTTCCTTAAAATCGGGTCATATTT 57.052 32.000 0.00 0.00 0.00 1.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
25 26 1.278127 CCTAACCCTACCACACACCAG 59.722 57.143 0.00 0.00 0.00 4.00
26 27 1.354101 CCTAACCCTACCACACACCA 58.646 55.000 0.00 0.00 0.00 4.17
76 77 0.173935 TTATTCCGACGCGACACCAT 59.826 50.000 15.93 1.19 0.00 3.55
124 125 2.071778 AGACAAAGGCAAAAGCCTCA 57.928 45.000 9.77 0.00 39.63 3.86
139 140 2.037367 ACCGCTGGCTCCTAGACA 59.963 61.111 0.00 0.00 0.00 3.41
226 227 1.539560 ATCGCCCATCTGAGGATCCG 61.540 60.000 5.98 0.00 0.00 4.18
441 445 0.036765 AACAGCCGTCGCCATCTTTA 60.037 50.000 0.00 0.00 34.57 1.85
501 505 4.023707 CGTTGCTTTCTCCTTTCTTGACAT 60.024 41.667 0.00 0.00 0.00 3.06
516 520 2.362329 AATTGCCGCCACGTTGCTTT 62.362 50.000 10.16 0.00 0.00 3.51
522 526 1.701545 CGATACAATTGCCGCCACGT 61.702 55.000 5.05 0.00 0.00 4.49
552 556 3.009723 ACCAGTTGCAAATAGGTCATCG 58.990 45.455 13.02 0.00 31.36 3.84
567 571 3.019564 GCAGAAGGATATGCAACCAGTT 58.980 45.455 9.88 0.00 42.11 3.16
608 612 3.372349 CCCTGTGTCATCATCCCTGAATT 60.372 47.826 0.00 0.00 34.37 2.17
635 639 6.773638 ACAACCATAACACAAGAAGATCTCT 58.226 36.000 0.00 0.00 35.13 3.10
665 669 8.925338 CAAAGGACCATAAATACCTAGAGTACT 58.075 37.037 0.00 0.00 32.46 2.73
707 711 4.079096 AGAGTAGGTGTCCCTTACTAGCAT 60.079 45.833 0.00 0.00 42.66 3.79
712 716 3.829728 ACAGAGTAGGTGTCCCTTACT 57.170 47.619 0.00 0.00 42.66 2.24
720 724 4.156190 CACGAATCAGTACAGAGTAGGTGT 59.844 45.833 9.67 0.00 0.00 4.16
816 820 0.032815 TCAATCGACGTGGCTGTTCA 59.967 50.000 0.00 0.00 0.00 3.18
887 891 7.308830 GCCAATAGCTTTTCTTTCTCTCTTTGA 60.309 37.037 0.00 0.00 38.99 2.69
888 892 6.805760 GCCAATAGCTTTTCTTTCTCTCTTTG 59.194 38.462 0.00 0.00 38.99 2.77
889 893 6.071672 GGCCAATAGCTTTTCTTTCTCTCTTT 60.072 38.462 0.00 0.00 43.05 2.52
890 894 5.417266 GGCCAATAGCTTTTCTTTCTCTCTT 59.583 40.000 0.00 0.00 43.05 2.85
891 895 4.946772 GGCCAATAGCTTTTCTTTCTCTCT 59.053 41.667 0.00 0.00 43.05 3.10
929 936 3.605749 TTCTTCTCTTGCCCCGCGG 62.606 63.158 21.04 21.04 0.00 6.46
933 940 0.112412 TGGGTTTCTTCTCTTGCCCC 59.888 55.000 0.00 0.00 35.39 5.80
937 944 1.880027 CGGGTTGGGTTTCTTCTCTTG 59.120 52.381 0.00 0.00 0.00 3.02
1709 1722 1.144565 CGCCTCTGAACTCTCATGCG 61.145 60.000 0.00 0.00 37.51 4.73
1872 1885 1.337728 TGCCCACTGTGTTGATACGAG 60.338 52.381 7.08 0.00 0.00 4.18
2174 2189 8.677300 GTGATGTATCTTTAAGCCAATGAGAAA 58.323 33.333 0.00 0.00 0.00 2.52
2181 2196 9.797642 ATCATATGTGATGTATCTTTAAGCCAA 57.202 29.630 3.88 0.00 43.35 4.52
2196 2211 7.585579 TGGCACAACAAATATCATATGTGAT 57.414 32.000 10.05 10.05 41.65 3.06
2343 2359 5.380043 ACACTCAAAGAACTGGAATCATGT 58.620 37.500 0.00 0.00 0.00 3.21
2436 2462 0.036010 CGGCATCAAGGAGGACAAGT 60.036 55.000 0.00 0.00 0.00 3.16
2509 2536 9.432982 TTCCCTATTTCAGGCATAAATTGTATT 57.567 29.630 2.94 0.00 43.98 1.89
2729 2772 6.093771 GTCTGAATCGGTAGTTCTGAGTTCTA 59.906 42.308 0.00 0.00 35.25 2.10
2892 2936 4.016572 TGGTCCTATAGGCATAGCTGGATA 60.017 45.833 14.50 0.00 33.95 2.59
2898 2942 6.094186 GCTAATTTTGGTCCTATAGGCATAGC 59.906 42.308 14.50 12.31 33.95 2.97
2901 2945 6.183361 TGAGCTAATTTTGGTCCTATAGGCAT 60.183 38.462 14.50 0.00 34.44 4.40
3015 3063 2.535012 TGCACTACATTGTGGAACGA 57.465 45.000 7.20 0.00 42.39 3.85


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

AutoCloner maintained by Alex Coulton.