Multiple sequence alignment - TraesCS5D01G160900

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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 TraesCS5D01G160900 chr5D 100.000 4196 0 0 1 4196 250603498 250599303 0 7749
1 TraesCS5D01G160900 chr5A 97.038 2127 41 10 1278 3394 334012839 334010725 0 3559
2 TraesCS5D01G160900 chr5A 92.057 982 31 10 3247 4196 334010742 334009776 0 1338
3 TraesCS5D01G160900 chr5A 96.804 438 13 1 778 1214 334013656 334013219 0 730
4 TraesCS5D01G160900 chr5B 95.292 2124 59 6 1377 3476 283407355 283405249 0 3330
5 TraesCS5D01G160900 chr5B 93.084 723 28 6 3471 4188 283401663 283400958 0 1038
6 TraesCS5D01G160900 chr5B 93.640 566 15 3 816 1380 283416631 283416086 0 826
7 TraesCS5D01G160900 chr3D 95.437 767 35 0 1 767 612807342 612808108 0 1223
8 TraesCS5D01G160900 chr3D 95.176 767 34 3 1 767 561766118 561766881 0 1208
9 TraesCS5D01G160900 chr3D 94.531 768 40 1 1 766 496065186 496065953 0 1184
10 TraesCS5D01G160900 chr1D 95.312 768 35 1 1 767 442053935 442053168 0 1218
11 TraesCS5D01G160900 chr1D 94.785 767 37 3 1 767 201651679 201650916 0 1192
12 TraesCS5D01G160900 chr1D 94.560 772 38 3 1 772 441188520 441189287 0 1190
13 TraesCS5D01G160900 chr7D 94.935 770 34 5 1 767 153293480 153294247 0 1201
14 TraesCS5D01G160900 chr6D 94.682 771 37 3 1 767 121817187 121816417 0 1194
15 TraesCS5D01G160900 chr2D 94.654 767 41 0 1 767 6992360 6991594 0 1190


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 TraesCS5D01G160900 chr5D 250599303 250603498 4195 True 7749.000000 7749 100.000000 1 4196 1 chr5D.!!$R1 4195
1 TraesCS5D01G160900 chr5A 334009776 334013656 3880 True 1875.666667 3559 95.299667 778 4196 3 chr5A.!!$R1 3418
2 TraesCS5D01G160900 chr5B 283400958 283407355 6397 True 2184.000000 3330 94.188000 1377 4188 2 chr5B.!!$R2 2811
3 TraesCS5D01G160900 chr5B 283416086 283416631 545 True 826.000000 826 93.640000 816 1380 1 chr5B.!!$R1 564
4 TraesCS5D01G160900 chr3D 612807342 612808108 766 False 1223.000000 1223 95.437000 1 767 1 chr3D.!!$F3 766
5 TraesCS5D01G160900 chr3D 561766118 561766881 763 False 1208.000000 1208 95.176000 1 767 1 chr3D.!!$F2 766
6 TraesCS5D01G160900 chr3D 496065186 496065953 767 False 1184.000000 1184 94.531000 1 766 1 chr3D.!!$F1 765
7 TraesCS5D01G160900 chr1D 442053168 442053935 767 True 1218.000000 1218 95.312000 1 767 1 chr1D.!!$R2 766
8 TraesCS5D01G160900 chr1D 201650916 201651679 763 True 1192.000000 1192 94.785000 1 767 1 chr1D.!!$R1 766
9 TraesCS5D01G160900 chr1D 441188520 441189287 767 False 1190.000000 1190 94.560000 1 772 1 chr1D.!!$F1 771
10 TraesCS5D01G160900 chr7D 153293480 153294247 767 False 1201.000000 1201 94.935000 1 767 1 chr7D.!!$F1 766
11 TraesCS5D01G160900 chr6D 121816417 121817187 770 True 1194.000000 1194 94.682000 1 767 1 chr6D.!!$R1 766
12 TraesCS5D01G160900 chr2D 6991594 6992360 766 True 1190.000000 1190 94.654000 1 767 1 chr2D.!!$R1 766

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
773 784 0.319469 GGCCGACCCAAACAAACATG 60.319 55.000 0.0 0.0 0.0 3.21 F
775 786 0.673437 CCGACCCAAACAAACATGCT 59.327 50.000 0.0 0.0 0.0 3.79 F
776 787 1.335872 CCGACCCAAACAAACATGCTC 60.336 52.381 0.0 0.0 0.0 4.26 F
2721 3049 1.550524 CAGACGGTGGAGAGGATGAAA 59.449 52.381 0.0 0.0 0.0 2.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
3012 3346 0.684535 TGCTGGTGAACATCCTCGAA 59.315 50.000 0.0 0.0 0.00 3.71 R
3161 3495 2.501222 CGTCGTTGTCCTCGTCGG 60.501 66.667 0.0 0.0 36.58 4.79 R
3181 3518 3.465588 AGGGATCTCTACTCTAGCTGGTT 59.534 47.826 0.0 0.0 0.00 3.67 R
3745 7820 0.179179 GCAAAGCTCAAGATGTCGGC 60.179 55.000 0.0 0.0 0.00 5.54 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
113 117 3.042059 ACCTGGGTGACGGTATCTATT 57.958 47.619 0.00 0.00 0.00 1.73
448 455 5.776716 ACAGTTCACCCAATTTCATGAAGAT 59.223 36.000 8.41 3.09 31.94 2.40
450 457 7.094205 ACAGTTCACCCAATTTCATGAAGATAC 60.094 37.037 8.41 3.07 31.94 2.24
492 499 3.928375 GTGTAGCTGCAAAATGATTTGGG 59.072 43.478 5.91 0.00 44.93 4.12
533 540 7.286313 TCATGTTGGCAACCAATAGATGTATA 58.714 34.615 26.31 4.34 45.80 1.47
695 706 1.153188 CCACGCCAGCACATATGGA 60.153 57.895 7.80 0.00 40.51 3.41
697 708 1.311859 CACGCCAGCACATATGGATT 58.688 50.000 7.80 0.00 40.51 3.01
702 713 2.564771 CCAGCACATATGGATTGACGT 58.435 47.619 7.80 0.00 40.51 4.34
744 755 4.689345 CCAAATCTAAAAGAGAACGGACGT 59.311 41.667 0.00 0.00 37.85 4.34
772 783 1.801309 CGGCCGACCCAAACAAACAT 61.801 55.000 24.07 0.00 0.00 2.71
773 784 0.319469 GGCCGACCCAAACAAACATG 60.319 55.000 0.00 0.00 0.00 3.21
774 785 0.943835 GCCGACCCAAACAAACATGC 60.944 55.000 0.00 0.00 0.00 4.06
775 786 0.673437 CCGACCCAAACAAACATGCT 59.327 50.000 0.00 0.00 0.00 3.79
776 787 1.335872 CCGACCCAAACAAACATGCTC 60.336 52.381 0.00 0.00 0.00 4.26
785 796 5.697633 CCAAACAAACATGCTCTAAATGCTT 59.302 36.000 0.00 0.00 0.00 3.91
786 797 6.203338 CCAAACAAACATGCTCTAAATGCTTT 59.797 34.615 0.00 0.00 0.00 3.51
796 807 5.643777 TGCTCTAAATGCTTTTAGTGAGTCC 59.356 40.000 26.03 14.94 43.19 3.85
814 825 3.118112 AGTCCTTGGGCTGTGAATGATAG 60.118 47.826 0.00 0.00 0.00 2.08
832 844 4.893524 TGATAGTAGGCAAGTTAGCTAGCA 59.106 41.667 18.83 0.00 34.17 3.49
2250 2578 4.977126 GTATCGACCCTCGCGGCG 62.977 72.222 17.70 17.70 40.21 6.46
2721 3049 1.550524 CAGACGGTGGAGAGGATGAAA 59.449 52.381 0.00 0.00 0.00 2.69
3012 3346 5.981088 AGAAGATCTACATCGAGATGCAT 57.019 39.130 12.54 0.00 42.39 3.96
3181 3518 1.280746 GACGAGGACAACGACGACA 59.719 57.895 0.00 0.00 34.70 4.35
3231 3568 4.546570 CTCCCGGAAAAGTTTTGACAATC 58.453 43.478 0.73 0.00 0.00 2.67
3277 3733 8.458052 CCAGTACATAATGCTGTTGTTTTATCA 58.542 33.333 0.00 0.00 39.29 2.15
3517 7592 9.855021 AACAGTGTTGATTATACAATTTAAGCC 57.145 29.630 7.96 0.00 32.36 4.35
3549 7624 2.791383 TGGATTGGACAACAAAAGCG 57.209 45.000 0.00 0.00 43.46 4.68
3607 7682 2.167281 CAGTGGTAGATCACAGGAGTGG 59.833 54.545 0.00 0.00 45.91 4.00
3609 7684 1.273267 TGGTAGATCACAGGAGTGGCT 60.273 52.381 0.00 0.00 45.91 4.75
3664 7739 0.036952 CGTGTCTGCTCCCTGATGTT 60.037 55.000 0.00 0.00 0.00 2.71
3730 7805 4.241590 TCGAACGCTTTTGGAGTACTTA 57.758 40.909 0.00 0.00 0.00 2.24
3745 7820 6.070995 TGGAGTACTTAGTACAGTCAAATGGG 60.071 42.308 22.48 0.00 41.03 4.00
4037 8113 8.523915 AGATGAGTTCCATATTTGCAATTACA 57.476 30.769 0.00 0.00 35.17 2.41
4038 8114 9.139734 AGATGAGTTCCATATTTGCAATTACAT 57.860 29.630 0.00 0.00 35.17 2.29
4041 8117 9.183368 TGAGTTCCATATTTGCAATTACATACA 57.817 29.630 0.00 0.00 0.00 2.29
4078 8154 0.546988 GGACTGGGTTCTGGGGTAGT 60.547 60.000 0.00 0.00 0.00 2.73
4143 8219 7.979444 TCCAGAACTTCCTGTTAAAATGTAG 57.021 36.000 0.00 0.00 39.30 2.74
4144 8220 7.514721 TCCAGAACTTCCTGTTAAAATGTAGT 58.485 34.615 0.00 0.00 39.30 2.73
4145 8221 8.653191 TCCAGAACTTCCTGTTAAAATGTAGTA 58.347 33.333 0.00 0.00 39.30 1.82
4163 8239 5.813672 TGTAGTATTTCATTTACCCGTCAGC 59.186 40.000 0.00 0.00 0.00 4.26
4173 8249 6.207810 TCATTTACCCGTCAGCTAAAAACATT 59.792 34.615 0.00 0.00 0.00 2.71
4190 8266 7.935338 AAAACATTGTGCTGAAAATAGTGAG 57.065 32.000 0.00 0.00 0.00 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
113 117 3.506398 TGACAATAGTGGTCCACTGAGA 58.494 45.455 31.23 14.60 45.01 3.27
448 455 1.001068 TGAGTTTCCCAATCACGCGTA 59.999 47.619 13.44 0.28 0.00 4.42
450 457 0.165944 GTGAGTTTCCCAATCACGCG 59.834 55.000 3.53 3.53 34.55 6.01
684 695 3.266510 ACACGTCAATCCATATGTGCT 57.733 42.857 1.24 0.00 36.31 4.40
785 796 2.054799 ACAGCCCAAGGACTCACTAAA 58.945 47.619 0.00 0.00 0.00 1.85
786 797 1.347707 CACAGCCCAAGGACTCACTAA 59.652 52.381 0.00 0.00 0.00 2.24
796 807 4.384056 CCTACTATCATTCACAGCCCAAG 58.616 47.826 0.00 0.00 0.00 3.61
814 825 3.134458 CCATGCTAGCTAACTTGCCTAC 58.866 50.000 17.23 0.00 43.07 3.18
832 844 1.078426 GTGGCCGAAGCTGTACCAT 60.078 57.895 0.00 0.00 39.73 3.55
870 882 5.894807 TCCTTTCTTCTTTTGTTTCTGCAG 58.105 37.500 7.63 7.63 0.00 4.41
983 995 0.954449 CATGATGGATGCTCCGCTCC 60.954 60.000 0.00 0.00 40.17 4.70
1380 1708 2.637383 GGAGTTGGCGTCGAGGAGT 61.637 63.158 9.75 0.00 0.00 3.85
3012 3346 0.684535 TGCTGGTGAACATCCTCGAA 59.315 50.000 0.00 0.00 0.00 3.71
3161 3495 2.501222 CGTCGTTGTCCTCGTCGG 60.501 66.667 0.00 0.00 36.58 4.79
3181 3518 3.465588 AGGGATCTCTACTCTAGCTGGTT 59.534 47.826 0.00 0.00 0.00 3.67
3231 3568 2.578495 GCATCTCTTTGCGAGTTTGTG 58.422 47.619 0.00 0.00 40.75 3.33
3302 3758 7.838079 ATTTCCTTACTGCCATTATGCAATA 57.162 32.000 0.00 0.00 41.51 1.90
3421 3901 1.409790 TCTTCTGTTTCGTCCGAACCA 59.590 47.619 0.91 0.35 33.41 3.67
3517 7592 7.871973 TGTTGTCCAATCCAACAATCTTATTTG 59.128 33.333 3.67 0.00 46.62 2.32
3607 7682 1.226831 GCTCAGCTCGGAGTGTAGC 60.227 63.158 6.90 8.99 37.24 3.58
3609 7684 2.483441 GAGCTCAGCTCGGAGTGTA 58.517 57.895 11.89 0.00 45.85 2.90
3664 7739 4.503296 GCACTTCACCTTCTCTTGAGGTAA 60.503 45.833 0.00 0.00 31.36 2.85
3730 7805 0.981183 TCGGCCCATTTGACTGTACT 59.019 50.000 0.00 0.00 0.00 2.73
3745 7820 0.179179 GCAAAGCTCAAGATGTCGGC 60.179 55.000 0.00 0.00 0.00 5.54
4037 8113 3.667360 GTGGTCACCGGTAAGTTTGTAT 58.333 45.455 6.87 0.00 0.00 2.29
4038 8114 2.545532 CGTGGTCACCGGTAAGTTTGTA 60.546 50.000 6.87 0.00 0.00 2.41
4039 8115 1.807377 CGTGGTCACCGGTAAGTTTGT 60.807 52.381 6.87 0.00 0.00 2.83
4040 8116 0.863144 CGTGGTCACCGGTAAGTTTG 59.137 55.000 6.87 0.00 0.00 2.93
4041 8117 0.249996 CCGTGGTCACCGGTAAGTTT 60.250 55.000 6.87 0.00 40.59 2.66
4042 8118 1.114722 TCCGTGGTCACCGGTAAGTT 61.115 55.000 6.87 0.00 45.63 2.66
4043 8119 1.531365 TCCGTGGTCACCGGTAAGT 60.531 57.895 6.87 0.00 45.63 2.24
4044 8120 1.080298 GTCCGTGGTCACCGGTAAG 60.080 63.158 6.87 0.00 45.63 2.34
4045 8121 1.531365 AGTCCGTGGTCACCGGTAA 60.531 57.895 6.87 0.00 45.63 2.85
4078 8154 4.580995 TGCAAAATTCTCCTACGGACAAAA 59.419 37.500 0.00 0.00 0.00 2.44
4143 8219 6.913873 TTAGCTGACGGGTAAATGAAATAC 57.086 37.500 3.42 0.00 35.32 1.89
4144 8220 7.925043 TTTTAGCTGACGGGTAAATGAAATA 57.075 32.000 17.12 1.55 44.14 1.40
4145 8221 6.827586 TTTTAGCTGACGGGTAAATGAAAT 57.172 33.333 17.12 0.00 44.14 2.17
4163 8239 9.462174 TCACTATTTTCAGCACAATGTTTTTAG 57.538 29.630 0.00 0.00 0.00 1.85


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

AutoCloner maintained by Alex Coulton.