Multiple sequence alignment - TraesCS3B01G008300

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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 TraesCS3B01G008300 chr3B 100.000 2528 0 0 1 2528 4213230 4215757 0.000000e+00 4669.0
1 TraesCS3B01G008300 chr3B 97.446 1723 36 7 811 2528 5069481 5071200 0.000000e+00 2931.0
2 TraesCS3B01G008300 chr3B 88.703 779 68 12 2 771 582270966 582270199 0.000000e+00 933.0
3 TraesCS3B01G008300 chr3B 88.845 762 73 12 2 758 642312757 642313511 0.000000e+00 926.0
4 TraesCS3B01G008300 chr3D 93.097 1043 67 5 801 1841 1882832 1883871 0.000000e+00 1522.0
5 TraesCS3B01G008300 chr3D 87.760 384 41 5 2146 2528 1883999 1884377 6.420000e-121 444.0
6 TraesCS3B01G008300 chr3D 86.752 234 30 1 2296 2528 14178406 14178173 2.490000e-65 259.0
7 TraesCS3B01G008300 chr3D 84.615 234 35 1 2296 2528 26212264 26212031 5.440000e-57 231.0
8 TraesCS3B01G008300 chr3D 88.608 158 13 3 2146 2303 445344301 445344453 1.190000e-43 187.0
9 TraesCS3B01G008300 chr3A 93.358 798 49 2 807 1601 7131715 7130919 0.000000e+00 1177.0
10 TraesCS3B01G008300 chr3A 89.426 766 68 10 2 758 316742189 316742950 0.000000e+00 953.0
11 TraesCS3B01G008300 chr3A 89.398 764 69 11 2 758 316706201 316706959 0.000000e+00 952.0
12 TraesCS3B01G008300 chr3A 86.996 223 26 3 2296 2516 277489647 277489868 5.400000e-62 248.0
13 TraesCS3B01G008300 chr3A 86.111 180 22 3 1877 2053 80542242 80542063 9.230000e-45 191.0
14 TraesCS3B01G008300 chr3A 87.179 156 14 2 2148 2303 725145353 725145502 3.340000e-39 172.0
15 TraesCS3B01G008300 chr4B 88.805 795 64 15 2 787 273914582 273913804 0.000000e+00 952.0
16 TraesCS3B01G008300 chr1D 90.909 715 53 11 61 771 277874077 277873371 0.000000e+00 950.0
17 TraesCS3B01G008300 chr1B 89.203 778 61 13 2 774 233698735 233697976 0.000000e+00 950.0
18 TraesCS3B01G008300 chr1B 87.975 158 15 2 2146 2303 14186159 14186006 1.540000e-42 183.0
19 TraesCS3B01G008300 chr1B 76.923 182 29 11 652 828 640188799 640188972 9.630000e-15 91.6
20 TraesCS3B01G008300 chr2B 89.281 765 65 15 3 757 250727050 250726293 0.000000e+00 942.0
21 TraesCS3B01G008300 chr2B 93.407 91 6 0 668 758 137858141 137858231 4.390000e-28 135.0
22 TraesCS3B01G008300 chr6B 88.701 708 61 11 2 702 638476322 638475627 0.000000e+00 846.0
23 TraesCS3B01G008300 chr7D 87.179 234 29 1 2296 2528 515488448 515488215 5.360000e-67 265.0
24 TraesCS3B01G008300 chr7D 85.987 157 19 3 1898 2053 404072772 404072618 5.590000e-37 165.0
25 TraesCS3B01G008300 chr4A 85.043 234 34 1 2296 2528 33673364 33673131 1.170000e-58 237.0
26 TraesCS3B01G008300 chr4A 96.939 98 3 0 1876 1973 714217401 714217498 5.590000e-37 165.0
27 TraesCS3B01G008300 chr4A 82.418 182 28 3 1878 2056 740542751 740542931 3.370000e-34 156.0
28 TraesCS3B01G008300 chr1A 89.503 181 17 1 1877 2055 182077309 182077489 7.040000e-56 228.0
29 TraesCS3B01G008300 chr1A 97.938 97 2 0 1877 1973 536873466 536873562 4.330000e-38 169.0
30 TraesCS3B01G008300 chr4D 83.404 235 31 4 2296 2528 7907933 7907705 7.090000e-51 211.0
31 TraesCS3B01G008300 chr4D 88.535 157 14 3 2148 2303 432460817 432460664 1.190000e-43 187.0
32 TraesCS3B01G008300 chr4D 86.164 159 15 4 2146 2303 91235939 91236091 5.590000e-37 165.0
33 TraesCS3B01G008300 chr7B 82.833 233 39 1 2296 2527 546319020 546318788 9.170000e-50 207.0
34 TraesCS3B01G008300 chrUn 87.640 178 20 2 1878 2053 93879933 93879756 3.300000e-49 206.0
35 TraesCS3B01G008300 chr6D 87.059 170 20 2 1886 2053 429004852 429004683 9.230000e-45 191.0
36 TraesCS3B01G008300 chr5D 86.076 158 17 2 2146 2303 60258631 60258479 5.590000e-37 165.0
37 TraesCS3B01G008300 chr5D 83.516 182 24 6 1875 2053 432157162 432157340 5.590000e-37 165.0
38 TraesCS3B01G008300 chr5B 86.076 158 17 2 2146 2303 491604070 491604222 5.590000e-37 165.0
39 TraesCS3B01G008300 chr7A 84.810 158 17 5 1898 2053 463001039 463000887 4.360000e-33 152.0


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 TraesCS3B01G008300 chr3B 4213230 4215757 2527 False 4669 4669 100.0000 1 2528 1 chr3B.!!$F1 2527
1 TraesCS3B01G008300 chr3B 5069481 5071200 1719 False 2931 2931 97.4460 811 2528 1 chr3B.!!$F2 1717
2 TraesCS3B01G008300 chr3B 582270199 582270966 767 True 933 933 88.7030 2 771 1 chr3B.!!$R1 769
3 TraesCS3B01G008300 chr3B 642312757 642313511 754 False 926 926 88.8450 2 758 1 chr3B.!!$F3 756
4 TraesCS3B01G008300 chr3D 1882832 1884377 1545 False 983 1522 90.4285 801 2528 2 chr3D.!!$F2 1727
5 TraesCS3B01G008300 chr3A 7130919 7131715 796 True 1177 1177 93.3580 807 1601 1 chr3A.!!$R1 794
6 TraesCS3B01G008300 chr3A 316742189 316742950 761 False 953 953 89.4260 2 758 1 chr3A.!!$F3 756
7 TraesCS3B01G008300 chr3A 316706201 316706959 758 False 952 952 89.3980 2 758 1 chr3A.!!$F2 756
8 TraesCS3B01G008300 chr4B 273913804 273914582 778 True 952 952 88.8050 2 787 1 chr4B.!!$R1 785
9 TraesCS3B01G008300 chr1D 277873371 277874077 706 True 950 950 90.9090 61 771 1 chr1D.!!$R1 710
10 TraesCS3B01G008300 chr1B 233697976 233698735 759 True 950 950 89.2030 2 774 1 chr1B.!!$R2 772
11 TraesCS3B01G008300 chr2B 250726293 250727050 757 True 942 942 89.2810 3 757 1 chr2B.!!$R1 754
12 TraesCS3B01G008300 chr6B 638475627 638476322 695 True 846 846 88.7010 2 702 1 chr6B.!!$R1 700

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
897 932 0.370958 TCTTGCGCGGCGTTTTATAC 59.629 50.0 24.46 5.59 0.0 1.47 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2402 2469 1.034292 GGTGAAGCAAGAGGATGGCC 61.034 60.0 0.0 0.0 0.0 5.36 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
137 144 9.184523 AGATTCCCGAATATGTTTTGAATACAA 57.815 29.630 0.00 0.00 0.00 2.41
138 145 9.796120 GATTCCCGAATATGTTTTGAATACAAA 57.204 29.630 0.00 0.00 43.10 2.83
244 257 4.691860 TTTTTGCAAAACCACCAACATG 57.308 36.364 23.79 0.00 0.00 3.21
268 282 8.316640 TGTTTTGAACTGCAAACTTTTTATGT 57.683 26.923 0.00 0.00 45.64 2.29
551 578 3.691342 CGAACCCTGGTCTCGCCA 61.691 66.667 2.27 0.00 46.95 5.69
558 585 1.271163 CCCTGGTCTCGCCACTAAAAA 60.271 52.381 0.00 0.00 43.61 1.94
594 622 1.079819 TCTGCTGCTACCGTTCTGC 60.080 57.895 0.00 0.00 0.00 4.26
600 628 1.805945 GCTACCGTTCTGCGACCTG 60.806 63.158 0.00 0.00 44.77 4.00
627 656 2.030091 GTCGCGCCTCTATAAAACAACC 59.970 50.000 0.00 0.00 0.00 3.77
640 670 2.035237 AACAACCAAGGAGGCGTCGA 62.035 55.000 0.00 0.00 43.14 4.20
645 675 1.165270 CCAAGGAGGCGTCGATTTTT 58.835 50.000 0.00 0.00 0.00 1.94
647 677 0.521735 AAGGAGGCGTCGATTTTTGC 59.478 50.000 0.00 0.00 0.00 3.68
786 817 9.779951 ATAGGTAAAGAGGTAAAGAGGTAAAGA 57.220 33.333 0.00 0.00 0.00 2.52
787 818 8.682297 AGGTAAAGAGGTAAAGAGGTAAAGAT 57.318 34.615 0.00 0.00 0.00 2.40
788 819 9.779951 AGGTAAAGAGGTAAAGAGGTAAAGATA 57.220 33.333 0.00 0.00 0.00 1.98
880 913 2.558359 GCACAATTAAGGCAACCTGTCT 59.442 45.455 0.00 0.00 30.81 3.41
885 918 1.234615 TAAGGCAACCTGTCTTGCGC 61.235 55.000 0.00 0.00 43.00 6.09
897 932 0.370958 TCTTGCGCGGCGTTTTATAC 59.629 50.000 24.46 5.59 0.00 1.47
923 958 3.386768 AGAAAGCGTCGCCATGTATAT 57.613 42.857 14.86 0.00 0.00 0.86
937 972 6.403746 CGCCATGTATATTGTACCAACACAAA 60.404 38.462 0.00 0.00 41.50 2.83
944 979 4.521130 TTGTACCAACACAAAAGCAACA 57.479 36.364 0.00 0.00 35.53 3.33
1050 1085 4.790861 GACGTCCTTCCCGTCGCC 62.791 72.222 3.51 0.00 44.29 5.54
1091 1126 0.318441 TCCAGGACGTGCAAGAAGAG 59.682 55.000 10.52 0.00 0.00 2.85
1368 1406 4.578898 TATGCCGGCGCGTCGAAT 62.579 61.111 37.21 27.91 38.08 3.34
2362 2429 1.613437 CACCCCGCAAGACAATTCTTT 59.387 47.619 0.00 0.00 40.34 2.52
2402 2469 1.402968 CAAGTGATTCAAGCATCCCCG 59.597 52.381 0.00 0.00 0.00 5.73
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
244 257 9.605955 AAACATAAAAAGTTTGCAGTTCAAAAC 57.394 25.926 0.00 0.00 45.35 2.43
376 396 8.624776 TCTCATTCTGTTTTCTTTCTTCTTTCC 58.375 33.333 0.00 0.00 0.00 3.13
558 585 3.848353 AGTGGTTGGCCAGTTGATT 57.152 47.368 5.11 0.00 45.81 2.57
565 592 2.113774 CAGCAGAGTGGTTGGCCA 59.886 61.111 0.00 0.00 43.73 5.36
600 628 2.888513 TATAGAGGCGCGACGAATAC 57.111 50.000 12.10 0.00 0.00 1.89
627 656 1.729149 GCAAAAATCGACGCCTCCTTG 60.729 52.381 0.00 0.00 0.00 3.61
645 675 3.651803 AACGATTTGATTTTTCGGGCA 57.348 38.095 0.00 0.00 37.20 5.36
712 742 5.232626 TGGTCGTCCGTCATTAAAATTATCG 59.767 40.000 0.00 0.00 36.30 2.92
761 792 9.779951 ATCTTTACCTCTTTACCTCTTTACCTA 57.220 33.333 0.00 0.00 0.00 3.08
762 793 8.682297 ATCTTTACCTCTTTACCTCTTTACCT 57.318 34.615 0.00 0.00 0.00 3.08
768 799 8.983789 CCTCTTTATCTTTACCTCTTTACCTCT 58.016 37.037 0.00 0.00 0.00 3.69
769 800 8.760735 ACCTCTTTATCTTTACCTCTTTACCTC 58.239 37.037 0.00 0.00 0.00 3.85
770 801 8.682297 ACCTCTTTATCTTTACCTCTTTACCT 57.318 34.615 0.00 0.00 0.00 3.08
880 913 0.095589 CTGTATAAAACGCCGCGCAA 59.904 50.000 13.88 0.00 0.00 4.85
885 918 5.724223 GCTTTCTTCTCTGTATAAAACGCCG 60.724 44.000 0.00 0.00 0.00 6.46
897 932 0.667487 TGGCGACGCTTTCTTCTCTG 60.667 55.000 20.77 0.00 0.00 3.35
937 972 2.224523 TGCACTTAGCTAGGTGTTGCTT 60.225 45.455 29.90 0.00 45.94 3.91
944 979 2.859165 TGCTTTGCACTTAGCTAGGT 57.141 45.000 2.03 2.03 45.94 3.08
968 1003 4.201951 CGGTGCTCGCTATTGGTT 57.798 55.556 0.00 0.00 0.00 3.67
1061 1096 1.333636 CGTCCTGGAGAAGAGGCCAT 61.334 60.000 5.01 0.00 32.89 4.40
1062 1097 1.984570 CGTCCTGGAGAAGAGGCCA 60.985 63.158 5.01 0.00 0.00 5.36
1069 1104 0.756294 TTCTTGCACGTCCTGGAGAA 59.244 50.000 0.00 0.00 0.00 2.87
1091 1126 4.162690 AGATCGCGGGGGTCTTGC 62.163 66.667 6.13 0.00 0.00 4.01
1368 1406 0.737367 CCTTCGCGAGCAAGATGACA 60.737 55.000 9.59 0.00 0.00 3.58
2362 2429 5.129320 ACTTGACTATATGCACTGGACATGA 59.871 40.000 0.00 0.00 0.00 3.07
2402 2469 1.034292 GGTGAAGCAAGAGGATGGCC 61.034 60.000 0.00 0.00 0.00 5.36


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

AutoCloner maintained by Alex Coulton.