Multiple sequence alignment - TraesCS3B01G295800

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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 TraesCS3B01G295800 chr3B 100.000 2516 0 0 1 2516 474243712 474241197 0 4647
1 TraesCS3B01G295800 chr3B 94.800 2000 90 8 527 2516 19701224 19703219 0 3105
2 TraesCS3B01G295800 chr3B 94.962 1985 90 9 539 2516 108092313 108090332 0 3103
3 TraesCS3B01G295800 chr3B 94.914 1986 86 6 539 2516 46395681 46393703 0 3094
4 TraesCS3B01G295800 chr4A 95.336 1994 80 9 530 2516 705529262 705527275 0 3155
5 TraesCS3B01G295800 chr1B 95.135 1994 82 9 530 2516 561526120 561528105 0 3131
6 TraesCS3B01G295800 chr1B 95.131 1992 83 10 535 2516 581717566 581715579 0 3129
7 TraesCS3B01G295800 chr1B 94.992 1997 89 8 526 2516 585423169 585425160 0 3123
8 TraesCS3B01G295800 chr1B 94.965 1986 86 9 538 2516 671392208 671394186 0 3101
9 TraesCS3B01G295800 chr2B 95.111 1984 86 8 539 2516 692955896 692957874 0 3116
10 TraesCS3B01G295800 chr4D 95.749 541 22 1 1 540 350595637 350595097 0 870
11 TraesCS3B01G295800 chr2D 95.741 540 23 0 1 540 82782186 82781647 0 870
12 TraesCS3B01G295800 chr7D 95.572 542 22 2 1 540 200902049 200901508 0 867
13 TraesCS3B01G295800 chr7D 95.564 541 23 1 1 540 158862920 158862380 0 865
14 TraesCS3B01G295800 chr5D 95.564 541 23 1 1 540 245051364 245050824 0 865
15 TraesCS3B01G295800 chr3D 95.556 540 24 0 1 540 281555380 281555919 0 865
16 TraesCS3B01G295800 chr3D 95.564 541 22 2 1 540 310739916 310739377 0 865
17 TraesCS3B01G295800 chr3D 95.564 541 23 1 1 540 474090276 474090816 0 865
18 TraesCS3B01G295800 chr3D 95.564 541 23 1 1 540 501184099 501183559 0 865


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 TraesCS3B01G295800 chr3B 474241197 474243712 2515 True 4647 4647 100.000 1 2516 1 chr3B.!!$R3 2515
1 TraesCS3B01G295800 chr3B 19701224 19703219 1995 False 3105 3105 94.800 527 2516 1 chr3B.!!$F1 1989
2 TraesCS3B01G295800 chr3B 108090332 108092313 1981 True 3103 3103 94.962 539 2516 1 chr3B.!!$R2 1977
3 TraesCS3B01G295800 chr3B 46393703 46395681 1978 True 3094 3094 94.914 539 2516 1 chr3B.!!$R1 1977
4 TraesCS3B01G295800 chr4A 705527275 705529262 1987 True 3155 3155 95.336 530 2516 1 chr4A.!!$R1 1986
5 TraesCS3B01G295800 chr1B 561526120 561528105 1985 False 3131 3131 95.135 530 2516 1 chr1B.!!$F1 1986
6 TraesCS3B01G295800 chr1B 581715579 581717566 1987 True 3129 3129 95.131 535 2516 1 chr1B.!!$R1 1981
7 TraesCS3B01G295800 chr1B 585423169 585425160 1991 False 3123 3123 94.992 526 2516 1 chr1B.!!$F2 1990
8 TraesCS3B01G295800 chr1B 671392208 671394186 1978 False 3101 3101 94.965 538 2516 1 chr1B.!!$F3 1978
9 TraesCS3B01G295800 chr2B 692955896 692957874 1978 False 3116 3116 95.111 539 2516 1 chr2B.!!$F1 1977
10 TraesCS3B01G295800 chr4D 350595097 350595637 540 True 870 870 95.749 1 540 1 chr4D.!!$R1 539
11 TraesCS3B01G295800 chr2D 82781647 82782186 539 True 870 870 95.741 1 540 1 chr2D.!!$R1 539
12 TraesCS3B01G295800 chr7D 200901508 200902049 541 True 867 867 95.572 1 540 1 chr7D.!!$R2 539
13 TraesCS3B01G295800 chr7D 158862380 158862920 540 True 865 865 95.564 1 540 1 chr7D.!!$R1 539
14 TraesCS3B01G295800 chr5D 245050824 245051364 540 True 865 865 95.564 1 540 1 chr5D.!!$R1 539
15 TraesCS3B01G295800 chr3D 281555380 281555919 539 False 865 865 95.556 1 540 1 chr3D.!!$F1 539
16 TraesCS3B01G295800 chr3D 310739377 310739916 539 True 865 865 95.564 1 540 1 chr3D.!!$R1 539
17 TraesCS3B01G295800 chr3D 474090276 474090816 540 False 865 865 95.564 1 540 1 chr3D.!!$F2 539
18 TraesCS3B01G295800 chr3D 501183559 501184099 540 True 865 865 95.564 1 540 1 chr3D.!!$R2 539

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
629 633 0.250597 GTTTTGCCCCTAGTCCGTGT 60.251 55.0 0.0 0.0 0.0 4.49 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2006 2028 0.461548 CTTGCCATCTGTCCTAGCGA 59.538 55.0 0.0 0.0 0.0 4.93 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
30 31 5.863965 TCACATGGAAGATTTGTGTGTAGA 58.136 37.500 0.00 0.00 41.14 2.59
35 36 5.935945 TGGAAGATTTGTGTGTAGAAGGAA 58.064 37.500 0.00 0.00 0.00 3.36
37 38 7.004086 TGGAAGATTTGTGTGTAGAAGGAATT 58.996 34.615 0.00 0.00 0.00 2.17
123 124 2.218603 GTTCGTCAGGAAAAGGCTTGA 58.781 47.619 0.00 0.00 36.14 3.02
153 154 7.780008 ATGTTTGTCGGATAATGATTTACGA 57.220 32.000 0.00 0.00 0.00 3.43
368 371 7.269084 CACATTTTATTTTAGCTCACACGTCAG 59.731 37.037 0.00 0.00 0.00 3.51
393 396 7.284944 AGACACTTATACTATTACTCTTGCGGT 59.715 37.037 0.00 0.00 0.00 5.68
443 446 3.721625 TCACGAAGAGAAGCGATGG 57.278 52.632 0.00 0.00 0.00 3.51
459 462 0.528924 ATGGACGCACGCACTAGTTA 59.471 50.000 0.00 0.00 0.00 2.24
629 633 0.250597 GTTTTGCCCCTAGTCCGTGT 60.251 55.000 0.00 0.00 0.00 4.49
692 696 3.366052 ACATTTTGACTCGGCCCTTAT 57.634 42.857 0.00 0.00 0.00 1.73
845 851 3.295273 ACGGCGACAGAGAGCACA 61.295 61.111 16.62 0.00 34.54 4.57
1067 1081 2.203056 CCGGGCGAGCATTGATCA 60.203 61.111 2.47 0.00 0.00 2.92
1085 1099 2.398588 TCAGAGGGTTTCTCACACACT 58.601 47.619 0.00 0.00 44.81 3.55
1092 1106 3.496870 GGGTTTCTCACACACTGAGGAAT 60.497 47.826 0.00 0.00 44.95 3.01
1093 1107 3.499918 GGTTTCTCACACACTGAGGAATG 59.500 47.826 0.00 0.00 44.95 2.67
1110 1124 4.099573 AGGAATGACAATCGTCCGTTCTAT 59.900 41.667 0.00 0.00 41.85 1.98
1116 1130 3.250744 CAATCGTCCGTTCTATGTGTGT 58.749 45.455 0.00 0.00 0.00 3.72
1119 1133 3.076621 TCGTCCGTTCTATGTGTGTAGT 58.923 45.455 0.00 0.00 0.00 2.73
1350 1364 1.068434 GAAGAAGAGATGGAGGGCGAG 59.932 57.143 0.00 0.00 0.00 5.03
1443 1457 4.316025 AGCACTACCAATACCCATTTGT 57.684 40.909 0.00 0.00 0.00 2.83
1792 1813 8.287439 TCCAATTCAAATACACCGTGATTTAT 57.713 30.769 5.28 0.00 0.00 1.40
1826 1847 4.895668 AATGTCATGGAAAATGTGCCTT 57.104 36.364 0.00 0.00 0.00 4.35
1963 1985 2.125912 CAGCTGGGGACTCGAACG 60.126 66.667 5.57 0.00 0.00 3.95
2006 2028 0.254747 TTTAGGGCTGCGCTGGTAAT 59.745 50.000 27.01 4.38 0.00 1.89
2032 2054 2.107204 AGGACAGATGGCAAGAGTTTGT 59.893 45.455 0.00 0.00 36.65 2.83
2139 2163 0.971447 GTGGCTAGGGACTCGAACCT 60.971 60.000 7.94 7.94 41.75 3.50
2225 2249 4.733077 TTGACATGGGTAGGGAAGAAAA 57.267 40.909 0.00 0.00 0.00 2.29
2226 2250 4.028993 TGACATGGGTAGGGAAGAAAAC 57.971 45.455 0.00 0.00 0.00 2.43
2241 2265 9.440761 AGGGAAGAAAACTATACATAGTGAGAT 57.559 33.333 2.71 0.00 42.47 2.75
2255 2279 7.521529 ACATAGTGAGATTGTGAAATTTGTCG 58.478 34.615 0.00 0.00 0.00 4.35
2374 2400 0.829333 TGCACTGCCATGTGGTTTTT 59.171 45.000 0.00 0.00 38.31 1.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
11 12 6.126863 TCCTTCTACACACAAATCTTCCAT 57.873 37.500 0.00 0.00 0.00 3.41
30 31 7.147976 GTCATTTAACAGAACAGCAATTCCTT 58.852 34.615 0.00 0.00 0.00 3.36
35 36 6.392354 CCATGTCATTTAACAGAACAGCAAT 58.608 36.000 0.00 0.00 31.50 3.56
37 38 4.321156 GCCATGTCATTTAACAGAACAGCA 60.321 41.667 0.00 0.00 31.50 4.41
123 124 2.684001 TATCCGACAAACATTCGCCT 57.316 45.000 0.00 0.00 35.06 5.52
335 338 3.849145 GCTAAAATAAAATGTGCGCGACA 59.151 39.130 12.10 12.38 39.53 4.35
337 340 4.142795 TGAGCTAAAATAAAATGTGCGCGA 60.143 37.500 12.10 0.00 0.00 5.87
368 371 7.378995 CACCGCAAGAGTAATAGTATAAGTGTC 59.621 40.741 0.00 0.00 43.02 3.67
393 396 3.134574 ACTATGCCCAAAGAACGTTCA 57.865 42.857 28.78 8.52 0.00 3.18
440 443 0.528924 TAACTAGTGCGTGCGTCCAT 59.471 50.000 0.00 0.00 0.00 3.41
443 446 2.110226 GAGATAACTAGTGCGTGCGTC 58.890 52.381 0.00 0.00 0.00 5.19
459 462 2.573869 CGCGAGTGGGTGTGAGAT 59.426 61.111 0.00 0.00 0.00 2.75
505 509 4.339814 GGTGGAGTGATTTTGTTGTACCAA 59.660 41.667 0.00 0.00 0.00 3.67
629 633 1.299850 CACAGAACGAGTCGGTGCA 60.300 57.895 18.30 0.00 43.94 4.57
692 696 3.009115 GCTGCCTGGTCCCACCTA 61.009 66.667 0.00 0.00 39.58 3.08
717 721 4.279671 TGCAACGGTCTGAATAAAATTGGT 59.720 37.500 0.00 0.00 0.00 3.67
820 826 4.293648 CTGTCGCCGTGGTCACCA 62.294 66.667 0.00 0.00 0.00 4.17
845 851 2.050351 CTCGTCGTGGTCAGCGTT 60.050 61.111 0.00 0.00 0.00 4.84
886 892 1.142748 CCCTCCACAGCTAGCTTCG 59.857 63.158 16.46 7.60 0.00 3.79
912 918 0.835941 CTCCACAGCTAGCTTCCCAT 59.164 55.000 16.46 0.00 0.00 4.00
1013 1027 2.046988 CAGGCATCTCCACACGCA 60.047 61.111 0.00 0.00 37.29 5.24
1067 1081 2.398588 TCAGTGTGTGAGAAACCCTCT 58.601 47.619 0.00 0.00 42.44 3.69
1093 1107 3.303495 CACACATAGAACGGACGATTGTC 59.697 47.826 4.31 4.31 44.72 3.18
1110 1124 5.781306 TCTTACCCCATTCTTACTACACACA 59.219 40.000 0.00 0.00 0.00 3.72
1116 1130 5.306160 CCCGATTCTTACCCCATTCTTACTA 59.694 44.000 0.00 0.00 0.00 1.82
1119 1133 3.393278 CCCCGATTCTTACCCCATTCTTA 59.607 47.826 0.00 0.00 0.00 2.10
1350 1364 1.735920 CTCTCTGTCAGTGCGTGCC 60.736 63.158 0.00 0.00 0.00 5.01
1443 1457 7.784470 ACCTACAAATGCCCAAAAGTATTTA 57.216 32.000 0.00 0.00 37.28 1.40
1700 1720 8.927675 TTTCTAACCTTAATTGTTTGGCTCTA 57.072 30.769 0.00 0.00 0.00 2.43
1792 1813 7.773489 TTCCATGACATTTTGGTCTTTGATA 57.227 32.000 0.00 0.00 38.61 2.15
1826 1847 5.269991 AGGTGTAAACATCTACCAGAGCTA 58.730 41.667 0.00 0.00 35.13 3.32
1947 1969 4.070552 GCGTTCGAGTCCCCAGCT 62.071 66.667 0.00 0.00 0.00 4.24
2006 2028 0.461548 CTTGCCATCTGTCCTAGCGA 59.538 55.000 0.00 0.00 0.00 4.93
2032 2054 1.922447 ACATTGCTTCCCTACCCATGA 59.078 47.619 0.00 0.00 0.00 3.07
2121 2145 0.627451 TAGGTTCGAGTCCCTAGCCA 59.373 55.000 5.32 0.00 32.08 4.75
2126 2150 1.849977 GGTCTTAGGTTCGAGTCCCT 58.150 55.000 5.79 5.79 34.74 4.20
2374 2400 3.290948 AAACCAAGTGCCACTCTAACA 57.709 42.857 0.00 0.00 0.00 2.41


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

AutoCloner maintained by Alex Coulton.