Multiple sequence alignment - TraesCS1B01G469000

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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 TraesCS1B01G469000 chr1B 100.000 2832 0 0 1 2832 678205116 678207947 0.000000e+00 5230.0
1 TraesCS1B01G469000 chr1B 85.784 408 53 3 1507 1913 681876247 681875844 7.250000e-116 427.0
2 TraesCS1B01G469000 chr1B 84.422 398 57 5 1518 1913 678213415 678213809 1.230000e-103 387.0
3 TraesCS1B01G469000 chr1B 79.559 499 76 17 674 1151 678212919 678213412 1.630000e-87 333.0
4 TraesCS1B01G469000 chr1B 92.437 119 9 0 1912 2030 681875874 681875756 1.350000e-38 171.0
5 TraesCS1B01G469000 chr1B 92.079 101 8 0 1912 2012 678213779 678213879 2.940000e-30 143.0
6 TraesCS1B01G469000 chr1B 88.571 70 5 2 2766 2832 681875486 681875417 6.500000e-12 82.4
7 TraesCS1B01G469000 chr1B 90.000 60 5 1 1948 2007 678251140 678251198 3.030000e-10 76.8
8 TraesCS1B01G469000 chr1D 96.214 2034 46 10 1 2030 487022706 487024712 0.000000e+00 3301.0
9 TraesCS1B01G469000 chr1D 94.521 803 32 8 2031 2832 487024912 487025703 0.000000e+00 1229.0
10 TraesCS1B01G469000 chr1D 90.982 499 44 1 1 498 106292609 106293107 0.000000e+00 671.0
11 TraesCS1B01G469000 chr1D 90.278 504 42 4 1 500 325966585 325966085 0.000000e+00 652.0
12 TraesCS1B01G469000 chr1D 85.831 614 70 13 2156 2767 472291907 472292505 1.110000e-178 636.0
13 TraesCS1B01G469000 chr1D 84.712 399 56 5 1518 1913 487030583 487030979 7.350000e-106 394.0
14 TraesCS1B01G469000 chr1D 80.285 492 78 14 674 1151 487030093 487030579 1.250000e-93 353.0
15 TraesCS1B01G469000 chr1D 93.069 101 7 0 1912 2012 487030949 487031049 6.320000e-32 148.0
16 TraesCS1B01G469000 chr1A 92.052 2076 77 22 1 2030 584525757 584527790 0.000000e+00 2839.0
17 TraesCS1B01G469000 chr1A 88.746 702 37 9 1331 2030 584519187 584519848 0.000000e+00 821.0
18 TraesCS1B01G469000 chr1A 90.928 485 31 8 2351 2832 584529968 584530442 8.550000e-180 640.0
19 TraesCS1B01G469000 chr1A 80.645 651 97 20 2115 2758 471711064 471710436 7.100000e-131 477.0
20 TraesCS1B01G469000 chr1A 90.634 331 31 0 2031 2361 584528003 584528333 9.310000e-120 440.0
21 TraesCS1B01G469000 chr1A 84.712 399 55 5 1518 1913 584534899 584535294 7.350000e-106 394.0
22 TraesCS1B01G469000 chr1A 91.489 94 5 1 1919 2012 584535271 584535361 2.960000e-25 126.0
23 TraesCS1B01G469000 chr7D 91.434 502 39 4 1 500 82608263 82607764 0.000000e+00 686.0
24 TraesCS1B01G469000 chr2D 91.036 502 43 2 1 501 650950403 650949903 0.000000e+00 676.0
25 TraesCS1B01G469000 chr2D 84.155 669 75 24 2115 2767 572048829 572048176 1.110000e-173 619.0
26 TraesCS1B01G469000 chr2D 84.118 170 20 6 1153 1320 558789852 558790016 1.050000e-34 158.0
27 TraesCS1B01G469000 chr2D 84.706 85 9 3 1375 1458 558790088 558790169 6.500000e-12 82.4
28 TraesCS1B01G469000 chr2D 100.000 30 0 0 1375 1404 539423661 539423690 3.940000e-04 56.5
29 TraesCS1B01G469000 chr6A 85.782 633 77 8 2137 2767 497996921 497996300 0.000000e+00 658.0
30 TraesCS1B01G469000 chr6A 90.419 501 42 5 1 498 602618953 602619450 0.000000e+00 654.0
31 TraesCS1B01G469000 chr5D 84.940 664 76 15 2115 2769 498464493 498465141 0.000000e+00 651.0
32 TraesCS1B01G469000 chr4D 90.361 498 43 3 1 497 447333695 447334188 0.000000e+00 649.0
33 TraesCS1B01G469000 chr4B 89.921 506 45 2 1 501 526721491 526721995 0.000000e+00 647.0
34 TraesCS1B01G469000 chr4B 83.491 636 74 17 2115 2744 77660216 77659606 5.300000e-157 564.0
35 TraesCS1B01G469000 chr4B 78.218 303 53 8 1585 1887 588551038 588551327 6.230000e-42 182.0
36 TraesCS1B01G469000 chr4B 77.888 303 54 8 1585 1887 588582864 588583153 2.900000e-40 176.0
37 TraesCS1B01G469000 chr4A 84.756 656 76 6 2115 2767 578106100 578106734 1.110000e-178 636.0
38 TraesCS1B01G469000 chr7A 83.756 671 83 16 2115 2773 510900608 510901264 1.860000e-171 612.0
39 TraesCS1B01G469000 chr7A 83.562 657 87 15 2115 2768 729559663 729559025 1.880000e-166 595.0
40 TraesCS1B01G469000 chr7A 78.808 302 29 14 1203 1479 96155871 96155580 1.350000e-38 171.0
41 TraesCS1B01G469000 chr5B 83.994 656 81 16 2115 2767 679666169 679666803 2.410000e-170 608.0
42 TraesCS1B01G469000 chr5A 83.648 636 90 11 2134 2767 635280915 635281538 1.130000e-163 586.0
43 TraesCS1B01G469000 chr3A 83.053 655 95 11 2118 2767 576201785 576202428 5.260000e-162 580.0
44 TraesCS1B01G469000 chr2B 81.982 666 91 22 2111 2767 39792771 39792126 3.210000e-149 538.0
45 TraesCS1B01G469000 chr2B 78.644 295 31 13 1206 1479 57671864 57671581 1.750000e-37 167.0
46 TraesCS1B01G469000 chr3B 86.871 457 47 11 2311 2765 581074011 581073566 1.510000e-137 499.0
47 TraesCS1B01G469000 chr3B 77.348 181 31 7 1145 1321 786267027 786267201 6.460000e-17 99.0
48 TraesCS1B01G469000 chr6D 76.420 352 43 18 1153 1479 291388452 291388116 1.360000e-33 154.0
49 TraesCS1B01G469000 chr6D 75.163 306 42 15 1206 1479 307044 307347 2.310000e-21 113.0
50 TraesCS1B01G469000 chr3D 83.333 174 20 5 979 1149 519690143 519689976 4.890000e-33 152.0
51 TraesCS1B01G469000 chr2A 88.889 54 6 0 1001 1054 4384600 4384653 1.820000e-07 67.6
52 TraesCS1B01G469000 chr7B 80.952 84 14 2 1375 1456 63125132 63125049 6.550000e-07 65.8


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 TraesCS1B01G469000 chr1B 678205116 678207947 2831 False 5230.000000 5230 100.000000 1 2832 1 chr1B.!!$F1 2831
1 TraesCS1B01G469000 chr1B 678212919 678213879 960 False 287.666667 387 85.353333 674 2012 3 chr1B.!!$F3 1338
2 TraesCS1B01G469000 chr1B 681875417 681876247 830 True 226.800000 427 88.930667 1507 2832 3 chr1B.!!$R1 1325
3 TraesCS1B01G469000 chr1D 487022706 487025703 2997 False 2265.000000 3301 95.367500 1 2832 2 chr1D.!!$F3 2831
4 TraesCS1B01G469000 chr1D 325966085 325966585 500 True 652.000000 652 90.278000 1 500 1 chr1D.!!$R1 499
5 TraesCS1B01G469000 chr1D 472291907 472292505 598 False 636.000000 636 85.831000 2156 2767 1 chr1D.!!$F2 611
6 TraesCS1B01G469000 chr1D 487030093 487031049 956 False 298.333333 394 86.022000 674 2012 3 chr1D.!!$F4 1338
7 TraesCS1B01G469000 chr1A 584525757 584530442 4685 False 1306.333333 2839 91.204667 1 2832 3 chr1A.!!$F2 2831
8 TraesCS1B01G469000 chr1A 584519187 584519848 661 False 821.000000 821 88.746000 1331 2030 1 chr1A.!!$F1 699
9 TraesCS1B01G469000 chr1A 471710436 471711064 628 True 477.000000 477 80.645000 2115 2758 1 chr1A.!!$R1 643
10 TraesCS1B01G469000 chr2D 650949903 650950403 500 True 676.000000 676 91.036000 1 501 1 chr2D.!!$R2 500
11 TraesCS1B01G469000 chr2D 572048176 572048829 653 True 619.000000 619 84.155000 2115 2767 1 chr2D.!!$R1 652
12 TraesCS1B01G469000 chr6A 497996300 497996921 621 True 658.000000 658 85.782000 2137 2767 1 chr6A.!!$R1 630
13 TraesCS1B01G469000 chr5D 498464493 498465141 648 False 651.000000 651 84.940000 2115 2769 1 chr5D.!!$F1 654
14 TraesCS1B01G469000 chr4B 526721491 526721995 504 False 647.000000 647 89.921000 1 501 1 chr4B.!!$F1 500
15 TraesCS1B01G469000 chr4B 77659606 77660216 610 True 564.000000 564 83.491000 2115 2744 1 chr4B.!!$R1 629
16 TraesCS1B01G469000 chr4A 578106100 578106734 634 False 636.000000 636 84.756000 2115 2767 1 chr4A.!!$F1 652
17 TraesCS1B01G469000 chr7A 510900608 510901264 656 False 612.000000 612 83.756000 2115 2773 1 chr7A.!!$F1 658
18 TraesCS1B01G469000 chr7A 729559025 729559663 638 True 595.000000 595 83.562000 2115 2768 1 chr7A.!!$R2 653
19 TraesCS1B01G469000 chr5B 679666169 679666803 634 False 608.000000 608 83.994000 2115 2767 1 chr5B.!!$F1 652
20 TraesCS1B01G469000 chr5A 635280915 635281538 623 False 586.000000 586 83.648000 2134 2767 1 chr5A.!!$F1 633
21 TraesCS1B01G469000 chr3A 576201785 576202428 643 False 580.000000 580 83.053000 2118 2767 1 chr3A.!!$F1 649
22 TraesCS1B01G469000 chr2B 39792126 39792771 645 True 538.000000 538 81.982000 2111 2767 1 chr2B.!!$R1 656

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
169 170 0.87909 GATTTGGTCGGTGGTTGTCC 59.121 55.0 0.0 0.0 0.0 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2132 2432 0.174617 GACGGGAGGAGAAGAGCTTG 59.825 60.0 0.0 0.0 0.0 4.01 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
104 105 1.275291 CGTCCCAATGGTGTGTCTAGT 59.725 52.381 0.00 0.00 0.00 2.57
169 170 0.879090 GATTTGGTCGGTGGTTGTCC 59.121 55.000 0.00 0.00 0.00 4.02
225 236 3.138283 TGTGTCTTCAGGTTGGATCCTTT 59.862 43.478 14.23 0.00 35.37 3.11
246 257 9.672673 TCCTTTCGATCTAAAATTCTCTTCATT 57.327 29.630 0.00 0.00 0.00 2.57
302 313 1.336609 GGACCTTAGCACGACGACTTT 60.337 52.381 0.00 0.00 0.00 2.66
303 314 1.719780 GACCTTAGCACGACGACTTTG 59.280 52.381 0.00 0.00 0.00 2.77
405 416 1.667724 GCTTGTAGTCGTCGCTAGGTA 59.332 52.381 0.00 0.00 0.00 3.08
481 492 8.930527 ACCATGATTGAAAATGAATACATCCAT 58.069 29.630 0.00 0.00 35.50 3.41
891 907 6.650120 TCTTCTCTTAACCTCTCTCTCTCTC 58.350 44.000 0.00 0.00 0.00 3.20
892 908 6.443849 TCTTCTCTTAACCTCTCTCTCTCTCT 59.556 42.308 0.00 0.00 0.00 3.10
893 909 6.235231 TCTCTTAACCTCTCTCTCTCTCTC 57.765 45.833 0.00 0.00 0.00 3.20
894 910 5.964477 TCTCTTAACCTCTCTCTCTCTCTCT 59.036 44.000 0.00 0.00 0.00 3.10
895 911 6.098409 TCTCTTAACCTCTCTCTCTCTCTCTC 59.902 46.154 0.00 0.00 0.00 3.20
896 912 5.964477 TCTTAACCTCTCTCTCTCTCTCTCT 59.036 44.000 0.00 0.00 0.00 3.10
897 913 7.130099 TCTTAACCTCTCTCTCTCTCTCTCTA 58.870 42.308 0.00 0.00 0.00 2.43
898 914 7.789831 TCTTAACCTCTCTCTCTCTCTCTCTAT 59.210 40.741 0.00 0.00 0.00 1.98
899 915 9.090103 CTTAACCTCTCTCTCTCTCTCTCTATA 57.910 40.741 0.00 0.00 0.00 1.31
900 916 9.615660 TTAACCTCTCTCTCTCTCTCTCTATAT 57.384 37.037 0.00 0.00 0.00 0.86
902 918 9.790297 AACCTCTCTCTCTCTCTCTCTATATAT 57.210 37.037 0.00 0.00 0.00 0.86
1298 1353 6.992063 TTTTGATGCAAAAAGGTTAAGCAA 57.008 29.167 7.52 0.00 39.85 3.91
1500 1585 1.571773 AAGCGCCCCTCCCATAAAGT 61.572 55.000 2.29 0.00 0.00 2.66
1691 1777 3.520569 GGTCGGGTTTATTGTAGCGTTA 58.479 45.455 0.00 0.00 0.00 3.18
2002 2089 7.201600 GCAATTGTTGTTGAGTATTTGGTTTGT 60.202 33.333 7.40 0.00 0.00 2.83
2058 2358 7.996385 ACATAATTGTTAGCATAAACCTGACC 58.004 34.615 0.00 0.00 29.55 4.02
2065 2365 3.482436 AGCATAAACCTGACCGAACAAA 58.518 40.909 0.00 0.00 0.00 2.83
2132 2432 3.500299 GCTCCTCTTTTCTCCTTCACAAC 59.500 47.826 0.00 0.00 0.00 3.32
2318 2638 4.141801 TGTCCCTTGGTAGGAATAATGTCG 60.142 45.833 0.00 0.00 45.05 4.35
2320 2640 3.433031 CCCTTGGTAGGAATAATGTCGCA 60.433 47.826 0.00 0.00 45.05 5.10
2405 4370 0.880718 GTTGGATCTCGCGGGATTCC 60.881 60.000 24.46 23.51 0.00 3.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
104 105 2.438975 ACACGCCCTCCGACGATA 60.439 61.111 0.00 0.00 41.02 2.92
169 170 2.202932 CCGAGCGGATCCACCAAG 60.203 66.667 13.41 0.00 38.90 3.61
191 192 4.576053 CCTGAAGACACATGAACAAAGACA 59.424 41.667 0.00 0.00 0.00 3.41
225 236 6.018751 CGCCAATGAAGAGAATTTTAGATCGA 60.019 38.462 0.00 0.00 0.00 3.59
302 313 3.317149 ACTTGTTGTAGTAGACAGTCGCA 59.683 43.478 0.00 0.00 39.88 5.10
303 314 3.898529 ACTTGTTGTAGTAGACAGTCGC 58.101 45.455 0.00 0.00 39.88 5.19
496 507 1.603739 GCGGCCCTCTGTTCCTTTT 60.604 57.895 0.00 0.00 0.00 2.27
910 926 9.430623 CAACAAATGACATGACCCGTATATATA 57.569 33.333 0.00 0.00 0.00 0.86
931 947 5.053140 TGCGAAATATTTGCTAGCAACAA 57.947 34.783 29.33 19.86 35.46 2.83
1298 1353 0.392336 TTTCTTTGCGCAGGCCAATT 59.608 45.000 11.31 0.00 38.85 2.32
1323 1378 5.182487 GGGTGAAATTTGGTCTTTGTTTGT 58.818 37.500 0.00 0.00 0.00 2.83
1324 1379 4.574421 GGGGTGAAATTTGGTCTTTGTTTG 59.426 41.667 0.00 0.00 0.00 2.93
1327 1382 2.703536 GGGGGTGAAATTTGGTCTTTGT 59.296 45.455 0.00 0.00 0.00 2.83
1456 1541 0.981943 CCCGGGTGAATAGTATCCCC 59.018 60.000 14.18 2.20 36.84 4.81
1465 1550 2.938798 TTGGGCTCCCGGGTGAAT 60.939 61.111 26.61 0.00 39.42 2.57
1599 1685 1.802960 CAGACATGATTCGGCCTATGC 59.197 52.381 0.00 0.00 0.00 3.14
1691 1777 3.350219 ACAACAGTCGCAATATCCCTT 57.650 42.857 0.00 0.00 0.00 3.95
2002 2089 9.263538 GAATGCCTCATATTTATTGCAATTTGA 57.736 29.630 18.75 11.71 31.81 2.69
2091 2391 8.116026 AGAGGAGCCATATTTAAAAAGAAGGAA 58.884 33.333 0.00 0.00 0.00 3.36
2097 2397 9.794685 GAGAAAAGAGGAGCCATATTTAAAAAG 57.205 33.333 0.00 0.00 0.00 2.27
2106 2406 4.080863 GTGAAGGAGAAAAGAGGAGCCATA 60.081 45.833 0.00 0.00 0.00 2.74
2132 2432 0.174617 GACGGGAGGAGAAGAGCTTG 59.825 60.000 0.00 0.00 0.00 4.01
2200 2515 4.933064 GCCGAGATCCTCCGCACG 62.933 72.222 0.00 0.00 35.45 5.34
2318 2638 1.934463 CCGGCGATAGAACATGTGC 59.066 57.895 9.30 0.00 39.76 4.57
2320 2640 1.227556 GGCCGGCGATAGAACATGT 60.228 57.895 22.54 0.00 39.76 3.21
2349 2669 1.889573 GCCCTCCAACGATGCTAGC 60.890 63.158 8.10 8.10 0.00 3.42
2405 4370 2.805353 CGAAGACCAGCACCGACG 60.805 66.667 0.00 0.00 0.00 5.12
2441 4406 1.069364 GGACGAAGACGAACGAAGACT 60.069 52.381 0.14 0.00 42.66 3.24


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

AutoCloner maintained by Alex Coulton.