Multiple sequence alignment - TraesCS3B01G008100

Loading Multiple Alignment...

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 TraesCS3B01G008100 chr3B 100.000 2210 0 0 1 2210 4201215 4203424 0.000000e+00 4045.0
1 TraesCS3B01G008100 chr3B 99.014 1116 10 1 729 1844 5058138 5059252 0.000000e+00 1999.0
2 TraesCS3B01G008100 chr3B 97.273 770 19 2 1 770 5057374 5058141 0.000000e+00 1304.0
3 TraesCS3B01G008100 chr3B 100.000 513 0 0 2495 3007 4203709 4204221 0.000000e+00 948.0
4 TraesCS3B01G008100 chr3B 97.856 513 2 1 2495 3007 5059758 5060261 0.000000e+00 878.0
5 TraesCS3B01G008100 chr3A 94.350 1292 38 15 869 2141 7201852 7200577 0.000000e+00 1951.0
6 TraesCS3B01G008100 chr3A 84.549 233 26 5 2503 2730 7199372 7199145 3.900000e-54 222.0
7 TraesCS3B01G008100 chr3D 92.632 1330 49 16 831 2141 1845153 1846452 0.000000e+00 1868.0
8 TraesCS3B01G008100 chr3D 84.681 235 30 4 2497 2730 1847963 1848192 2.330000e-56 230.0
9 TraesCS3B01G008100 chr4A 90.096 626 51 5 20 635 617049214 617049838 0.000000e+00 802.0
10 TraesCS3B01G008100 chr5A 90.132 608 60 0 1 608 662754515 662753908 0.000000e+00 791.0
11 TraesCS3B01G008100 chr5A 87.164 670 66 7 1 663 488439000 488438344 0.000000e+00 743.0
12 TraesCS3B01G008100 chr2A 87.776 679 63 10 1 663 155748734 155748060 0.000000e+00 776.0
13 TraesCS3B01G008100 chr1A 87.578 644 68 9 3 635 341176380 341177022 0.000000e+00 736.0
14 TraesCS3B01G008100 chr1A 88.342 609 62 4 1 608 490793243 490793843 0.000000e+00 723.0
15 TraesCS3B01G008100 chr7A 85.630 682 77 11 1 663 34137920 34137241 0.000000e+00 697.0
16 TraesCS3B01G008100 chr7A 93.846 65 2 2 777 839 508567141 508567205 2.470000e-16 97.1
17 TraesCS3B01G008100 chrUn 85.954 655 76 7 22 663 229263222 229262571 0.000000e+00 686.0
18 TraesCS3B01G008100 chr7D 88.732 213 14 5 626 835 638191782 638191987 4.980000e-63 252.0
19 TraesCS3B01G008100 chr7D 88.690 168 12 4 626 790 101553443 101553280 6.580000e-47 198.0
20 TraesCS3B01G008100 chr7D 81.818 110 13 6 727 835 623362077 623361974 5.340000e-13 86.1
21 TraesCS3B01G008100 chr5B 92.667 150 6 4 627 776 665716600 665716744 8.450000e-51 211.0
22 TraesCS3B01G008100 chr5B 83.178 107 17 1 729 835 132516016 132515911 2.470000e-16 97.1
23 TraesCS3B01G008100 chr7B 92.053 151 9 3 626 776 320118006 320118153 3.040000e-50 209.0
24 TraesCS3B01G008100 chr7B 89.333 75 7 1 767 841 26646409 26646336 3.190000e-15 93.5
25 TraesCS3B01G008100 chr2B 89.820 167 11 3 628 791 442534748 442534911 3.040000e-50 209.0
26 TraesCS3B01G008100 chr2D 90.323 155 7 5 626 776 61802719 61802869 2.360000e-46 196.0
27 TraesCS3B01G008100 chr5D 86.188 181 14 8 626 805 242951777 242951607 5.120000e-43 185.0
28 TraesCS3B01G008100 chr4B 89.032 155 8 7 626 775 639157565 639157715 1.840000e-42 183.0
29 TraesCS3B01G008100 chr6D 81.466 232 11 15 626 834 354544300 354544078 8.630000e-36 161.0
30 TraesCS3B01G008100 chr6B 91.304 69 5 1 767 835 148479644 148479577 3.190000e-15 93.5


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 TraesCS3B01G008100 chr3B 4201215 4204221 3006 False 2496.500000 4045 100.000000 1 3007 2 chr3B.!!$F1 3006
1 TraesCS3B01G008100 chr3B 5057374 5060261 2887 False 1393.666667 1999 98.047667 1 3007 3 chr3B.!!$F2 3006
2 TraesCS3B01G008100 chr3A 7199145 7201852 2707 True 1086.500000 1951 89.449500 869 2730 2 chr3A.!!$R1 1861
3 TraesCS3B01G008100 chr3D 1845153 1848192 3039 False 1049.000000 1868 88.656500 831 2730 2 chr3D.!!$F1 1899
4 TraesCS3B01G008100 chr4A 617049214 617049838 624 False 802.000000 802 90.096000 20 635 1 chr4A.!!$F1 615
5 TraesCS3B01G008100 chr5A 662753908 662754515 607 True 791.000000 791 90.132000 1 608 1 chr5A.!!$R2 607
6 TraesCS3B01G008100 chr5A 488438344 488439000 656 True 743.000000 743 87.164000 1 663 1 chr5A.!!$R1 662
7 TraesCS3B01G008100 chr2A 155748060 155748734 674 True 776.000000 776 87.776000 1 663 1 chr2A.!!$R1 662
8 TraesCS3B01G008100 chr1A 341176380 341177022 642 False 736.000000 736 87.578000 3 635 1 chr1A.!!$F1 632
9 TraesCS3B01G008100 chr1A 490793243 490793843 600 False 723.000000 723 88.342000 1 608 1 chr1A.!!$F2 607
10 TraesCS3B01G008100 chr7A 34137241 34137920 679 True 697.000000 697 85.630000 1 663 1 chr7A.!!$R1 662
11 TraesCS3B01G008100 chrUn 229262571 229263222 651 True 686.000000 686 85.954000 22 663 1 chrUn.!!$R1 641

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
757 799 0.038709 TGCATTTTTACCACGCCTGC 60.039 50.0 0.0 0.0 0.0 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2041 2147 1.135721 GAAAGGAGGCCATGCATGAAC 59.864 52.381 28.31 18.8 0.0 3.18 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
256 284 1.111116 ACTTCCCGGACGTCTTCACA 61.111 55.000 16.46 0.00 0.00 3.58
312 340 2.101415 GTCTCATCATCGACATGGACCA 59.899 50.000 0.00 0.00 0.00 4.02
619 656 4.299586 TGATGATGGTAGCAACTTGGAA 57.700 40.909 0.00 0.00 0.00 3.53
749 791 1.673700 GCGCGTGCTGCATTTTTACC 61.674 55.000 15.02 0.00 46.97 2.85
750 792 0.386605 CGCGTGCTGCATTTTTACCA 60.387 50.000 5.27 0.00 46.97 3.25
757 799 0.038709 TGCATTTTTACCACGCCTGC 60.039 50.000 0.00 0.00 0.00 4.85
760 802 1.539388 CATTTTTACCACGCCTGCTGA 59.461 47.619 0.00 0.00 0.00 4.26
1976 2079 2.966516 CCCCTACACCAAGATCCTAGTC 59.033 54.545 0.00 0.00 0.00 2.59
1998 2101 1.517242 CAACTGTGGAGTCCTTGAGC 58.483 55.000 11.33 0.00 0.00 4.26
1999 2102 1.131638 AACTGTGGAGTCCTTGAGCA 58.868 50.000 11.33 1.26 0.00 4.26
2000 2103 0.683973 ACTGTGGAGTCCTTGAGCAG 59.316 55.000 11.33 12.38 0.00 4.24
2054 2160 0.458669 CTTGAGGTTCATGCATGGCC 59.541 55.000 25.97 25.05 0.00 5.36
2159 2281 5.752712 TGTTGTTTTGTTGTTTGAAAAGGC 58.247 33.333 0.00 0.00 0.00 4.35
2163 3553 3.971245 TTGTTGTTTGAAAAGGCAGGT 57.029 38.095 0.00 0.00 0.00 4.00
2164 3554 3.971245 TGTTGTTTGAAAAGGCAGGTT 57.029 38.095 0.00 0.00 0.00 3.50
2189 3582 6.573434 ACTCCATGGTTTTCTTCTTTGTTTC 58.427 36.000 12.58 0.00 0.00 2.78
2193 3586 7.763985 TCCATGGTTTTCTTCTTTGTTTCTTTC 59.236 33.333 12.58 0.00 0.00 2.62
2194 3587 7.548780 CCATGGTTTTCTTCTTTGTTTCTTTCA 59.451 33.333 2.57 0.00 0.00 2.69
2208 3601 8.766000 TTGTTTCTTTCAAAAAGGAGGTTAAC 57.234 30.769 0.00 0.00 0.00 2.01
2775 4173 4.202451 TGAAGATCATTGTGTTGACCTCCA 60.202 41.667 0.00 0.00 0.00 3.86
2918 4316 3.141767 AGGGAACTGTAAAAGCACCTC 57.858 47.619 0.00 0.00 41.13 3.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
738 780 0.038709 GCAGGCGTGGTAAAAATGCA 60.039 50.000 8.72 0.00 32.58 3.96
749 791 2.459442 GCTAGCTTCAGCAGGCGTG 61.459 63.158 7.70 1.01 45.16 5.34
750 792 2.125350 GCTAGCTTCAGCAGGCGT 60.125 61.111 7.70 0.00 45.16 5.68
776 854 0.032815 TAAAAACTGCTTTGGGGCGC 59.967 50.000 0.00 0.00 34.52 6.53
780 858 1.418373 GCGCTAAAAACTGCTTTGGG 58.582 50.000 0.00 0.00 0.00 4.12
1867 1970 4.550422 TCACATTCATTCTCGATCGGATC 58.450 43.478 16.41 7.95 0.00 3.36
1868 1971 4.590850 TCACATTCATTCTCGATCGGAT 57.409 40.909 16.41 4.54 0.00 4.18
1869 1972 4.590850 ATCACATTCATTCTCGATCGGA 57.409 40.909 16.41 8.74 0.00 4.55
1870 1973 5.663795 AAATCACATTCATTCTCGATCGG 57.336 39.130 16.41 6.26 0.00 4.18
1998 2101 6.183360 TGCTTATTCCACTACTACTACTGCTG 60.183 42.308 0.00 0.00 0.00 4.41
1999 2102 5.892119 TGCTTATTCCACTACTACTACTGCT 59.108 40.000 0.00 0.00 0.00 4.24
2000 2103 6.145338 TGCTTATTCCACTACTACTACTGC 57.855 41.667 0.00 0.00 0.00 4.40
2041 2147 1.135721 GAAAGGAGGCCATGCATGAAC 59.864 52.381 28.31 18.80 0.00 3.18
2054 2160 7.230309 ACAGGAAAGAATGAAAAGAGAAAGGAG 59.770 37.037 0.00 0.00 0.00 3.69
2159 2281 5.316987 AGAAGAAAACCATGGAGTAACCTG 58.683 41.667 21.47 0.00 39.86 4.00
2163 3553 7.654022 AACAAAGAAGAAAACCATGGAGTAA 57.346 32.000 21.47 0.00 0.00 2.24
2164 3554 7.559897 AGAAACAAAGAAGAAAACCATGGAGTA 59.440 33.333 21.47 0.00 0.00 2.59
2775 4173 0.391661 CAGCAGTGTTCTATGGCGGT 60.392 55.000 0.00 0.00 0.00 5.68
2918 4316 2.205342 TCTAGGGGAGGTTGAAATGGG 58.795 52.381 0.00 0.00 0.00 4.00


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

AutoCloner maintained by Alex Coulton.