Multiple sequence alignment - TraesCS7A01G410500

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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 TraesCS7A01G410500 chr7A 100.000 2615 0 0 1 2615 597554934 597552320 0.000000e+00 4830.0
1 TraesCS7A01G410500 chr5A 97.459 1574 39 1 1043 2615 606329345 606330918 0.000000e+00 2684.0
2 TraesCS7A01G410500 chr2A 96.137 1372 51 2 1246 2615 659059441 659058070 0.000000e+00 2239.0
3 TraesCS7A01G410500 chr2A 92.233 412 16 6 855 1254 659088670 659088263 1.050000e-158 569.0
4 TraesCS7A01G410500 chr3D 93.897 1147 48 16 783 1915 134599598 134598460 0.000000e+00 1711.0
5 TraesCS7A01G410500 chr3D 93.636 1147 51 16 783 1915 365842307 365841169 0.000000e+00 1694.0
6 TraesCS7A01G410500 chr3D 92.554 1155 57 18 782 1915 593933533 593934679 0.000000e+00 1629.0
7 TraesCS7A01G410500 chr3D 95.475 906 32 4 1018 1915 535654891 535655795 0.000000e+00 1437.0
8 TraesCS7A01G410500 chr3D 96.884 706 20 1 1912 2615 134598432 134597727 0.000000e+00 1181.0
9 TraesCS7A01G410500 chr3D 96.761 710 20 2 1909 2615 535655820 535656529 0.000000e+00 1181.0
10 TraesCS7A01G410500 chr2D 93.328 1154 55 12 777 1915 472192678 472191532 0.000000e+00 1685.0
11 TraesCS7A01G410500 chr6D 95.622 868 31 2 1055 1915 466182370 466183237 0.000000e+00 1386.0
12 TraesCS7A01G410500 chr6D 96.897 709 20 1 1909 2615 466183262 466183970 0.000000e+00 1186.0
13 TraesCS7A01G410500 chr6D 96.756 709 21 1 1909 2615 47793896 47794604 0.000000e+00 1181.0
14 TraesCS7A01G410500 chr6D 82.730 359 38 9 36 393 15057904 15058239 5.470000e-77 298.0
15 TraesCS7A01G410500 chr6D 89.041 73 8 0 399 471 15058275 15058347 9.970000e-15 91.6
16 TraesCS7A01G410500 chr5D 96.301 811 23 2 1112 1915 100988722 100989532 0.000000e+00 1325.0
17 TraesCS7A01G410500 chr5D 96.610 708 23 1 1909 2615 100989557 100990264 0.000000e+00 1173.0
18 TraesCS7A01G410500 chr5D 87.209 344 24 17 778 1114 100987845 100988175 8.840000e-100 374.0
19 TraesCS7A01G410500 chr4B 96.733 704 23 0 1912 2615 592154294 592153591 0.000000e+00 1173.0
20 TraesCS7A01G410500 chr4B 91.036 357 18 6 782 1126 592032075 592031721 1.100000e-128 470.0
21 TraesCS7A01G410500 chr4B 91.200 125 6 4 780 901 409002304 409002182 5.790000e-37 165.0
22 TraesCS7A01G410500 chr3B 96.605 707 24 0 1909 2615 13053630 13054336 0.000000e+00 1173.0
23 TraesCS7A01G410500 chr3B 94.937 158 6 2 779 936 104276000 104276155 2.010000e-61 246.0
24 TraesCS7A01G410500 chr7B 90.465 818 50 13 782 1573 255252764 255251949 0.000000e+00 1053.0
25 TraesCS7A01G410500 chr7B 87.606 355 19 13 782 1117 699547030 699546682 3.160000e-104 388.0
26 TraesCS7A01G410500 chr7B 87.121 132 13 4 776 904 620567889 620568019 2.100000e-31 147.0
27 TraesCS7A01G410500 chr5B 90.978 787 31 11 1 753 410219443 410220223 0.000000e+00 1024.0
28 TraesCS7A01G410500 chr2B 90.421 783 23 9 1 753 160475848 160476608 0.000000e+00 983.0
29 TraesCS7A01G410500 chr2B 86.087 230 16 7 34 263 795582989 795582776 1.560000e-57 233.0
30 TraesCS7A01G410500 chr2B 84.018 219 20 6 34 252 795583475 795583272 2.050000e-46 196.0


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 TraesCS7A01G410500 chr7A 597552320 597554934 2614 True 4830.000000 4830 100.000000 1 2615 1 chr7A.!!$R1 2614
1 TraesCS7A01G410500 chr5A 606329345 606330918 1573 False 2684.000000 2684 97.459000 1043 2615 1 chr5A.!!$F1 1572
2 TraesCS7A01G410500 chr2A 659058070 659059441 1371 True 2239.000000 2239 96.137000 1246 2615 1 chr2A.!!$R1 1369
3 TraesCS7A01G410500 chr3D 365841169 365842307 1138 True 1694.000000 1694 93.636000 783 1915 1 chr3D.!!$R1 1132
4 TraesCS7A01G410500 chr3D 593933533 593934679 1146 False 1629.000000 1629 92.554000 782 1915 1 chr3D.!!$F1 1133
5 TraesCS7A01G410500 chr3D 134597727 134599598 1871 True 1446.000000 1711 95.390500 783 2615 2 chr3D.!!$R2 1832
6 TraesCS7A01G410500 chr3D 535654891 535656529 1638 False 1309.000000 1437 96.118000 1018 2615 2 chr3D.!!$F2 1597
7 TraesCS7A01G410500 chr2D 472191532 472192678 1146 True 1685.000000 1685 93.328000 777 1915 1 chr2D.!!$R1 1138
8 TraesCS7A01G410500 chr6D 466182370 466183970 1600 False 1286.000000 1386 96.259500 1055 2615 2 chr6D.!!$F3 1560
9 TraesCS7A01G410500 chr6D 47793896 47794604 708 False 1181.000000 1181 96.756000 1909 2615 1 chr6D.!!$F1 706
10 TraesCS7A01G410500 chr5D 100987845 100990264 2419 False 957.333333 1325 93.373333 778 2615 3 chr5D.!!$F1 1837
11 TraesCS7A01G410500 chr4B 592153591 592154294 703 True 1173.000000 1173 96.733000 1912 2615 1 chr4B.!!$R3 703
12 TraesCS7A01G410500 chr3B 13053630 13054336 706 False 1173.000000 1173 96.605000 1909 2615 1 chr3B.!!$F1 706
13 TraesCS7A01G410500 chr7B 255251949 255252764 815 True 1053.000000 1053 90.465000 782 1573 1 chr7B.!!$R1 791
14 TraesCS7A01G410500 chr5B 410219443 410220223 780 False 1024.000000 1024 90.978000 1 753 1 chr5B.!!$F1 752
15 TraesCS7A01G410500 chr2B 160475848 160476608 760 False 983.000000 983 90.421000 1 753 1 chr2B.!!$F1 752
16 TraesCS7A01G410500 chr2B 795582776 795583475 699 True 214.500000 233 85.052500 34 263 2 chr2B.!!$R1 229

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
625 1146 2.359214 TGTAAGCGTGCATGTTCCAAAA 59.641 40.909 7.93 0.0 0.0 2.44 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2447 3598 1.527034 ATGTCGCTGCATGTTTCAGT 58.473 45.0 0.0 0.0 34.21 3.41 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
120 121 8.915057 ATTCAATTAGAGAGAGAGAGAGAGAG 57.085 38.462 0.00 0.00 0.00 3.20
121 122 7.675161 TCAATTAGAGAGAGAGAGAGAGAGA 57.325 40.000 0.00 0.00 0.00 3.10
122 123 7.730084 TCAATTAGAGAGAGAGAGAGAGAGAG 58.270 42.308 0.00 0.00 0.00 3.20
123 124 5.537300 TTAGAGAGAGAGAGAGAGAGAGC 57.463 47.826 0.00 0.00 0.00 4.09
202 684 4.261801 TCGGCTTCCTCCTGAATAAAAAG 58.738 43.478 0.00 0.00 31.06 2.27
225 708 7.454260 AGTTCCACAGAAGTATTTTTCATCC 57.546 36.000 0.00 0.00 33.73 3.51
336 819 5.860941 ACTTCTCTACATGGTTGATCGAT 57.139 39.130 0.00 0.00 0.00 3.59
397 882 7.496529 TCAGACTCTTTATGGTTTCAGTTTG 57.503 36.000 0.00 0.00 0.00 2.93
482 989 4.098654 TGAACACGGACCAATGAAAACATT 59.901 37.500 0.00 0.00 0.00 2.71
603 1124 5.814705 CACCTGCACTAATTTGAACCAAAAA 59.185 36.000 0.00 0.00 36.90 1.94
625 1146 2.359214 TGTAAGCGTGCATGTTCCAAAA 59.641 40.909 7.93 0.00 0.00 2.44
767 1289 7.881775 AAAAATCAGGAGAAAGTGTAGTGTT 57.118 32.000 0.00 0.00 0.00 3.32
768 1290 8.974060 AAAAATCAGGAGAAAGTGTAGTGTTA 57.026 30.769 0.00 0.00 0.00 2.41
769 1291 9.574516 AAAAATCAGGAGAAAGTGTAGTGTTAT 57.425 29.630 0.00 0.00 0.00 1.89
773 1295 8.824756 TCAGGAGAAAGTGTAGTGTTATATCT 57.175 34.615 0.00 0.00 0.00 1.98
774 1296 8.904834 TCAGGAGAAAGTGTAGTGTTATATCTC 58.095 37.037 0.00 0.00 0.00 2.75
775 1297 8.908903 CAGGAGAAAGTGTAGTGTTATATCTCT 58.091 37.037 0.00 0.00 33.17 3.10
823 1345 3.752339 GGTAGGTCGCGTTCCGGT 61.752 66.667 5.77 0.00 37.59 5.28
845 1367 6.569994 CGGTTTTTATTTTCGTCCCACCATTA 60.570 38.462 0.00 0.00 0.00 1.90
1023 1584 1.066587 GGTCGAGATCAAGCTCCGG 59.933 63.158 0.00 0.00 0.00 5.14
1311 2424 3.782443 GCGGTCGACTCCCCCATT 61.782 66.667 16.46 0.00 0.00 3.16
1354 2467 2.044946 GCCTCGGCAGGGACAAAT 60.045 61.111 2.41 0.00 40.75 2.32
1367 2480 0.788391 GACAAATCGCCGTTCGTCTT 59.212 50.000 0.00 0.00 39.67 3.01
1376 2489 2.564975 GTTCGTCTTCCTCGGCGA 59.435 61.111 10.14 10.14 0.00 5.54
1852 2970 6.089417 GGTTTGCATTTCAATCCTCGTAAAAG 59.911 38.462 0.00 0.00 40.04 2.27
2274 3425 0.622665 CCCACCTTCCTGATGAGCTT 59.377 55.000 0.00 0.00 0.00 3.74
2433 3584 4.194640 GCCTGAGTTCATAGCTTGATTCA 58.805 43.478 0.00 3.07 33.34 2.57
2588 3740 5.055265 TGATGGTACTTTTTGGGAACAGA 57.945 39.130 0.00 0.00 44.54 3.41
2589 3741 5.450453 TGATGGTACTTTTTGGGAACAGAA 58.550 37.500 0.00 0.00 44.54 3.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
98 99 6.426328 GCTCTCTCTCTCTCTCTCTCTAATTG 59.574 46.154 0.00 0.00 0.00 2.32
99 100 6.529220 GCTCTCTCTCTCTCTCTCTCTAATT 58.471 44.000 0.00 0.00 0.00 1.40
118 119 7.090953 AGGTAAGATATATAAGTGCGCTCTC 57.909 40.000 13.07 0.90 0.00 3.20
119 120 7.316640 CAAGGTAAGATATATAAGTGCGCTCT 58.683 38.462 9.73 7.80 0.00 4.09
120 121 6.531948 CCAAGGTAAGATATATAAGTGCGCTC 59.468 42.308 9.73 4.74 0.00 5.03
121 122 6.398918 CCAAGGTAAGATATATAAGTGCGCT 58.601 40.000 9.73 0.00 0.00 5.92
122 123 5.063564 GCCAAGGTAAGATATATAAGTGCGC 59.936 44.000 0.00 0.00 0.00 6.09
123 124 6.163476 TGCCAAGGTAAGATATATAAGTGCG 58.837 40.000 0.00 0.00 0.00 5.34
202 684 6.208599 TGGGATGAAAAATACTTCTGTGGAAC 59.791 38.462 0.00 0.00 37.35 3.62
225 708 3.184178 GTGTGGCGATTGTTTGAAAATGG 59.816 43.478 0.00 0.00 0.00 3.16
482 989 4.521130 AGAACAGTATGAAGTCGAGCAA 57.479 40.909 0.00 0.00 39.69 3.91
603 1124 1.819928 TGGAACATGCACGCTTACAT 58.180 45.000 0.00 0.00 0.00 2.29
640 1161 2.372264 CTGATAATGGGCTGCACAACT 58.628 47.619 9.41 1.27 0.00 3.16
780 1302 9.295825 CAACTGAGACATTAGGAGTAGAGATAT 57.704 37.037 0.00 0.00 0.00 1.63
823 1345 7.094291 ACGATAATGGTGGGACGAAAATAAAAA 60.094 33.333 0.00 0.00 0.00 1.94
918 1464 1.141185 TCTAGGGATCGAGAGGAGCA 58.859 55.000 0.00 0.00 30.89 4.26
975 1536 4.858680 GGGTTGCGGCTAGGGCTC 62.859 72.222 0.00 0.00 38.73 4.70
1257 2370 2.596338 TCGACGCAGGTGAGGACA 60.596 61.111 0.00 0.00 0.00 4.02
1354 2467 2.564975 GAGGAAGACGAACGGCGA 59.435 61.111 16.62 0.00 44.57 5.54
1767 2884 8.956426 TCTTGGATGAAAGTTATCAAATACCAC 58.044 33.333 0.00 0.00 32.06 4.16
1852 2970 4.376146 GGATCATGCTCTAGGACAAGTTC 58.624 47.826 0.00 0.00 0.00 3.01
2274 3425 3.055819 GTGTATGCCTGAGACCAAGAAGA 60.056 47.826 0.00 0.00 0.00 2.87
2447 3598 1.527034 ATGTCGCTGCATGTTTCAGT 58.473 45.000 0.00 0.00 34.21 3.41
2574 3726 2.297315 GCCCTCTTCTGTTCCCAAAAAG 59.703 50.000 0.00 0.00 0.00 2.27
2588 3740 2.561478 ACAATAACACACGCCCTCTT 57.439 45.000 0.00 0.00 0.00 2.85
2589 3741 2.224426 TGAACAATAACACACGCCCTCT 60.224 45.455 0.00 0.00 0.00 3.69


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

AutoCloner maintained by Alex Coulton.