Multiple sequence alignment - TraesCS3D01G328600

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 TraesCS3D01G328600 chr3D 100.000 2442 0 0 1 2442 441245259 441247700 0.000000e+00 4510
1 TraesCS3D01G328600 chr7B 94.721 1326 51 8 1134 2442 33930073 33928750 0.000000e+00 2043
2 TraesCS3D01G328600 chr7B 94.741 1217 45 7 831 2031 33936090 33934877 0.000000e+00 1875
3 TraesCS3D01G328600 chr7B 94.940 1166 43 7 1290 2442 13771757 13772919 0.000000e+00 1812
4 TraesCS3D01G328600 chr7B 92.339 992 52 10 314 1296 13770758 13771734 0.000000e+00 1389
5 TraesCS3D01G328600 chr7B 89.451 474 32 12 303 768 33936557 33936094 1.260000e-162 582
6 TraesCS3D01G328600 chr7B 86.246 349 31 10 1 343 33936808 33936471 1.780000e-96 363
7 TraesCS3D01G328600 chr7D 89.050 1242 58 25 1 1237 528781910 528780742 0.000000e+00 1469
8 TraesCS3D01G328600 chr7D 93.023 731 28 8 1717 2442 528762812 528762100 0.000000e+00 1046
9 TraesCS3D01G328600 chr7D 88.517 627 60 7 780 1400 90761369 90760749 0.000000e+00 749
10 TraesCS3D01G328600 chr7D 88.517 627 60 7 780 1400 93793007 93793627 0.000000e+00 749
11 TraesCS3D01G328600 chr7D 87.584 596 36 23 1398 1960 90760713 90760123 0.000000e+00 656
12 TraesCS3D01G328600 chr7D 87.584 596 36 23 1398 1960 93793663 93794253 0.000000e+00 656
13 TraesCS3D01G328600 chr7D 80.226 354 42 14 241 581 90761861 90761523 8.730000e-60 241
14 TraesCS3D01G328600 chr7D 80.055 361 43 15 235 581 93792508 93792853 8.730000e-60 241
15 TraesCS3D01G328600 chr1A 93.054 691 27 7 1756 2442 543028232 543028905 0.000000e+00 990
16 TraesCS3D01G328600 chr2A 88.517 627 60 7 780 1400 22185146 22184526 0.000000e+00 749
17 TraesCS3D01G328600 chr2A 86.913 596 40 23 1398 1960 22184490 22183900 3.430000e-178 634
18 TraesCS3D01G328600 chr2A 89.759 498 33 12 1960 2442 150921544 150922038 2.670000e-174 621
19 TraesCS3D01G328600 chr2A 85.643 599 47 14 1398 1960 150920904 150921499 5.810000e-166 593
20 TraesCS3D01G328600 chr2A 88.032 376 40 3 1029 1400 150920494 150920868 8.020000e-120 440
21 TraesCS3D01G328600 chr2A 77.229 628 77 40 1 581 22185909 22185301 8.480000e-80 307
22 TraesCS3D01G328600 chr2A 88.333 120 12 2 1 119 150924750 150924632 2.530000e-30 143
23 TraesCS3D01G328600 chr2A 90.196 102 7 3 615 714 150920061 150920161 1.970000e-26 130
24 TraesCS3D01G328600 chr7A 87.400 627 65 9 780 1400 727614023 727613405 0.000000e+00 708
25 TraesCS3D01G328600 chr7A 89.940 497 33 9 1960 2442 85909796 85909303 2.060000e-175 625
26 TraesCS3D01G328600 chr7A 89.222 501 32 9 1960 2442 727612750 727612254 7.470000e-170 606
27 TraesCS3D01G328600 chr7A 85.522 594 36 27 1398 1960 727613369 727612795 2.110000e-160 575
28 TraesCS3D01G328600 chr7A 84.925 597 53 11 1398 1960 85910434 85909841 9.800000e-159 569
29 TraesCS3D01G328600 chr7A 88.032 376 40 3 1029 1400 85910844 85910470 8.020000e-120 440
30 TraesCS3D01G328600 chr7A 86.996 223 22 4 766 987 85911047 85910831 6.740000e-61 244
31 TraesCS3D01G328600 chr7A 75.573 393 56 23 1 379 85911829 85911463 9.040000e-35 158
32 TraesCS3D01G328600 chr7A 77.570 321 29 14 293 581 727614485 727614176 1.170000e-33 154
33 TraesCS3D01G328600 chr7A 90.196 102 7 3 615 714 85911277 85911177 1.970000e-26 130
34 TraesCS3D01G328600 chr4A 89.738 497 33 11 1960 2442 45369050 45369542 9.590000e-174 619
35 TraesCS3D01G328600 chr4A 89.738 497 34 10 1960 2442 608588109 608588602 9.590000e-174 619
36 TraesCS3D01G328600 chr4A 85.643 599 46 17 1398 1960 45368411 45369005 5.810000e-166 593
37 TraesCS3D01G328600 chr4A 85.619 598 49 12 1398 1960 608587469 608588064 5.810000e-166 593
38 TraesCS3D01G328600 chr4A 86.996 223 22 4 766 987 45367798 45368014 6.740000e-61 244
39 TraesCS3D01G328600 chr4A 88.333 120 12 2 1 119 45372254 45372136 2.530000e-30 143
40 TraesCS3D01G328600 chr4A 85.000 140 17 4 1 138 608586132 608586269 3.270000e-29 139
41 TraesCS3D01G328600 chr4A 91.089 101 6 3 615 713 45367568 45367667 1.520000e-27 134
42 TraesCS3D01G328600 chr4A 90.196 102 7 3 615 714 608586626 608586726 1.970000e-26 130


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 TraesCS3D01G328600 chr3D 441245259 441247700 2441 False 4510.000000 4510 100.000000 1 2442 1 chr3D.!!$F1 2441
1 TraesCS3D01G328600 chr7B 33928750 33930073 1323 True 2043.000000 2043 94.721000 1134 2442 1 chr7B.!!$R1 1308
2 TraesCS3D01G328600 chr7B 13770758 13772919 2161 False 1600.500000 1812 93.639500 314 2442 2 chr7B.!!$F1 2128
3 TraesCS3D01G328600 chr7B 33934877 33936808 1931 True 940.000000 1875 90.146000 1 2031 3 chr7B.!!$R2 2030
4 TraesCS3D01G328600 chr7D 528780742 528781910 1168 True 1469.000000 1469 89.050000 1 1237 1 chr7D.!!$R2 1236
5 TraesCS3D01G328600 chr7D 528762100 528762812 712 True 1046.000000 1046 93.023000 1717 2442 1 chr7D.!!$R1 725
6 TraesCS3D01G328600 chr7D 90760123 90761861 1738 True 548.666667 749 85.442333 241 1960 3 chr7D.!!$R3 1719
7 TraesCS3D01G328600 chr7D 93792508 93794253 1745 False 548.666667 749 85.385333 235 1960 3 chr7D.!!$F1 1725
8 TraesCS3D01G328600 chr1A 543028232 543028905 673 False 990.000000 990 93.054000 1756 2442 1 chr1A.!!$F1 686
9 TraesCS3D01G328600 chr2A 22183900 22185909 2009 True 563.333333 749 84.219667 1 1960 3 chr2A.!!$R2 1959
10 TraesCS3D01G328600 chr2A 150920061 150922038 1977 False 446.000000 621 88.407500 615 2442 4 chr2A.!!$F1 1827
11 TraesCS3D01G328600 chr7A 727612254 727614485 2231 True 510.750000 708 84.928500 293 2442 4 chr7A.!!$R2 2149
12 TraesCS3D01G328600 chr7A 85909303 85911829 2526 True 361.000000 625 85.943667 1 2442 6 chr7A.!!$R1 2441
13 TraesCS3D01G328600 chr4A 45367568 45369542 1974 False 397.500000 619 88.366500 615 2442 4 chr4A.!!$F1 1827
14 TraesCS3D01G328600 chr4A 608586132 608588602 2470 False 370.250000 619 87.638250 1 2442 4 chr4A.!!$F2 2441

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
41 42 0.968901 AACCCGGACGTCATCTGCTA 60.969 55.0 18.91 0.0 31.52 3.49 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1801 2300 0.994247 AGGATGCCACATTGTCCTCA 59.006 50.0 0.0 0.0 36.36 3.86 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
41 42 0.968901 AACCCGGACGTCATCTGCTA 60.969 55.000 18.91 0.00 31.52 3.49
202 232 1.506493 CACACAGAACAGAGCAGTCC 58.494 55.000 0.00 0.00 0.00 3.85
270 303 4.189188 CGTCGGGAATCGCCTCGT 62.189 66.667 0.00 0.00 39.05 4.18
290 323 2.202960 CCGCCGGGATTCGCTTTA 60.203 61.111 2.18 0.00 37.59 1.85
291 324 2.244651 CCGCCGGGATTCGCTTTAG 61.245 63.158 2.18 0.00 37.59 1.85
611 809 1.745141 CGGGAGAGAAGCAAATGGAGG 60.745 57.143 0.00 0.00 0.00 4.30
627 825 3.909732 TGGAGGTGGATGAACTTTGTTT 58.090 40.909 0.00 0.00 0.00 2.83
700 972 9.730705 AATGATTAACAAATCTCTCAAGTCTGA 57.269 29.630 0.35 0.00 0.00 3.27
731 1003 6.181908 AGAGATATGTATCGGTCCCTTAGTC 58.818 44.000 0.00 0.00 37.76 2.59
737 1009 3.666345 ATCGGTCCCTTAGTCAGTACT 57.334 47.619 0.00 0.00 39.91 2.73
738 1010 4.785346 ATCGGTCCCTTAGTCAGTACTA 57.215 45.455 0.00 0.00 37.15 1.82
739 1011 3.878778 TCGGTCCCTTAGTCAGTACTAC 58.121 50.000 0.00 0.00 37.94 2.73
846 1224 9.762381 TTCAACCTTACCTTGTATGGATAATTT 57.238 29.630 11.77 0.00 0.00 1.82
893 1271 8.316946 TCTGATTAATCCAGGTAGCATTATCTG 58.683 37.037 12.90 0.00 37.69 2.90
1024 1404 5.914898 TTAAAAAGGCATAAGCTTCTCCC 57.085 39.130 0.00 1.21 41.70 4.30
1065 1446 1.202794 TCAGTCAAGATGGCACTGCAA 60.203 47.619 2.82 0.00 37.95 4.08
1213 1600 0.527817 GCGCAATAGCTACACTCCGT 60.528 55.000 0.30 0.00 39.10 4.69
1539 2017 3.281727 AACTTCAGTGTGAGGCTCAAA 57.718 42.857 20.62 11.93 0.00 2.69
1640 2118 9.454859 AATTCTATAACTTCTTTAGCAGCTTGT 57.545 29.630 0.00 0.00 0.00 3.16
1710 2206 5.420739 TCCAGTGTGCTACAGTACATCAATA 59.579 40.000 3.44 0.00 42.31 1.90
1715 2211 7.659799 AGTGTGCTACAGTACATCAATAACAAA 59.340 33.333 3.44 0.00 42.31 2.83
1754 2250 7.969536 AATTACATCCAAAGGATCATACTCG 57.030 36.000 0.00 0.00 40.98 4.18
1979 2527 5.462398 GCCATACTAGAAACGTCAATGGTAG 59.538 44.000 0.00 0.00 35.81 3.18
2148 2702 6.848069 TCTTTTGGGTCTCCTATTTTCAGAA 58.152 36.000 0.00 0.00 0.00 3.02
2151 2705 7.906199 TTTGGGTCTCCTATTTTCAGAAAAA 57.094 32.000 12.38 0.00 38.66 1.94
2152 2706 8.491045 TTTGGGTCTCCTATTTTCAGAAAAAT 57.509 30.769 12.38 6.37 45.02 1.82
2364 2928 6.204108 CCTTTTAGTGTGTCGGTAGTTGAAAT 59.796 38.462 0.00 0.00 0.00 2.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
41 42 1.366366 GTCCAGCTGTACACGTGGT 59.634 57.895 21.57 8.16 0.00 4.16
91 94 4.443266 GGAGCCGAGCTGCGTCTT 62.443 66.667 2.98 0.00 39.88 3.01
202 232 2.818132 GCAGGATCTGGAGTCGGG 59.182 66.667 0.00 0.00 31.21 5.14
255 288 3.884350 CGACGAGGCGATTCCCGA 61.884 66.667 0.00 0.00 41.76 5.14
285 318 4.166011 CAGTGGCGGCGCTAAAGC 62.166 66.667 32.30 14.23 37.78 3.51
286 319 3.499737 CCAGTGGCGGCGCTAAAG 61.500 66.667 32.30 20.35 0.00 1.85
299 332 4.162690 GGCGAGGCGATTCCCAGT 62.163 66.667 0.00 0.00 34.51 4.00
636 834 8.798859 AATCAAACTACAAAGCATCAGATACT 57.201 30.769 0.00 0.00 0.00 2.12
700 972 7.071321 AGGGACCGATACATATCTCTTTTCTTT 59.929 37.037 0.00 0.00 0.00 2.52
703 975 6.347859 AGGGACCGATACATATCTCTTTTC 57.652 41.667 0.00 0.00 0.00 2.29
720 992 4.248174 AGGTAGTACTGACTAAGGGACC 57.752 50.000 5.39 1.33 39.91 4.46
760 1138 3.334691 GAGGCACATGCTTACACAGTTA 58.665 45.455 3.48 0.00 41.70 2.24
761 1139 2.154462 GAGGCACATGCTTACACAGTT 58.846 47.619 3.48 0.00 41.70 3.16
762 1140 1.611673 GGAGGCACATGCTTACACAGT 60.612 52.381 3.48 0.00 41.70 3.55
763 1141 1.089920 GGAGGCACATGCTTACACAG 58.910 55.000 3.48 0.00 41.70 3.66
764 1142 0.692476 AGGAGGCACATGCTTACACA 59.308 50.000 3.48 0.00 41.70 3.72
765 1143 1.826385 AAGGAGGCACATGCTTACAC 58.174 50.000 3.48 0.00 41.70 2.90
766 1144 2.161855 CAAAGGAGGCACATGCTTACA 58.838 47.619 3.48 0.00 41.70 2.41
767 1145 2.095059 CACAAAGGAGGCACATGCTTAC 60.095 50.000 3.48 0.00 41.70 2.34
815 1193 6.834451 TCCATACAAGGTAAGGTTGAAAAACA 59.166 34.615 0.00 0.00 34.45 2.83
816 1194 7.279750 TCCATACAAGGTAAGGTTGAAAAAC 57.720 36.000 0.00 0.00 0.00 2.43
852 1230 3.641434 ATCAGAAGTCCAAGACCATGG 57.359 47.619 11.19 11.19 42.12 3.66
893 1271 5.470098 TCCACTTCTTCAGATTGTAGCAAAC 59.530 40.000 0.00 0.00 0.00 2.93
1024 1404 2.490165 CTCTTCAAGCATGCAGGGG 58.510 57.895 21.98 6.01 0.00 4.79
1085 1466 1.972872 CCTGTACAAGGCATCATCCC 58.027 55.000 0.00 0.00 39.93 3.85
1213 1600 1.822990 AGCCTTTGGATAGAACGACGA 59.177 47.619 0.00 0.00 0.00 4.20
1299 1718 4.873010 TCCTAGTCTAAGTCTGCTCCATT 58.127 43.478 0.00 0.00 0.00 3.16
1449 1910 9.165287 TGCATAGCAAATCAGAGAAACACTCAC 62.165 40.741 0.00 0.00 40.95 3.51
1450 1911 7.242269 TGCATAGCAAATCAGAGAAACACTCA 61.242 38.462 0.00 0.00 40.95 3.41
1451 1912 5.122869 TGCATAGCAAATCAGAGAAACACTC 59.877 40.000 0.00 0.00 39.74 3.51
1452 1913 5.005740 TGCATAGCAAATCAGAGAAACACT 58.994 37.500 0.00 0.00 34.76 3.55
1453 1914 5.091431 GTGCATAGCAAATCAGAGAAACAC 58.909 41.667 0.00 0.00 41.47 3.32
1640 2118 6.912203 TGAGTTTTTGATGAGTTTGTACGA 57.088 33.333 0.00 0.00 0.00 3.43
1710 2206 8.432805 TGTAATTTGGTTTACCCATGATTTGTT 58.567 29.630 0.00 0.00 44.74 2.83
1715 2211 6.900186 TGGATGTAATTTGGTTTACCCATGAT 59.100 34.615 0.00 0.00 44.74 2.45
1754 2250 4.573201 TGAATAGTATTTGGCGCAACCTAC 59.427 41.667 10.83 5.52 40.22 3.18
1801 2300 0.994247 AGGATGCCACATTGTCCTCA 59.006 50.000 0.00 0.00 36.36 3.86
2058 2606 8.821686 TTGATGGTAAAACATATGACTTGGAT 57.178 30.769 10.38 0.00 0.00 3.41
2327 2882 8.714179 CGACACACTAAAAGGTACAATATCAAA 58.286 33.333 0.00 0.00 0.00 2.69
2364 2928 5.975693 AAAATCAAATGAGGTTCCGCTAA 57.024 34.783 0.00 0.00 0.00 3.09


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

AutoCloner maintained by Alex Coulton.