Multiple sequence alignment - TraesCS7D01G449100

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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 TraesCS7D01G449100 chr7D 100.000 3154 0 0 752 3905 568457400 568460553 0.000000e+00 5825.0
1 TraesCS7D01G449100 chr7D 100.000 457 0 0 1 457 568456649 568457105 0.000000e+00 845.0
2 TraesCS7D01G449100 chrUn 96.031 3200 69 15 752 3905 93957558 93960745 0.000000e+00 5153.0
3 TraesCS7D01G449100 chrUn 94.748 457 17 5 1 454 93956760 93957212 0.000000e+00 704.0
4 TraesCS7D01G449100 chr7A 94.067 3152 104 12 818 3905 727858383 727861515 0.000000e+00 4708.0
5 TraesCS7D01G449100 chr1D 96.069 2620 83 7 754 3358 66758734 66761348 0.000000e+00 4250.0
6 TraesCS7D01G449100 chr1D 91.517 1167 60 16 2736 3870 330030674 330029515 0.000000e+00 1570.0
7 TraesCS7D01G449100 chr1D 95.484 620 26 2 755 1374 370167780 370168397 0.000000e+00 989.0
8 TraesCS7D01G449100 chr1D 91.845 466 10 3 3467 3905 66761413 66761877 3.310000e-175 625.0
9 TraesCS7D01G449100 chr3D 95.995 2622 82 7 752 3358 21935224 21937837 0.000000e+00 4239.0
10 TraesCS7D01G449100 chr3D 92.248 1161 51 16 2736 3864 63802122 63803275 0.000000e+00 1609.0
11 TraesCS7D01G449100 chr3D 92.593 540 17 3 3386 3905 599650315 599650851 0.000000e+00 754.0
12 TraesCS7D01G449100 chr3D 91.202 466 14 2 3467 3905 21937902 21938367 3.340000e-170 608.0
13 TraesCS7D01G449100 chr2A 93.629 2527 136 3 755 3273 268560892 268558383 0.000000e+00 3751.0
14 TraesCS7D01G449100 chr2A 95.207 459 20 2 1 457 268561699 268561241 0.000000e+00 725.0
15 TraesCS7D01G449100 chr2A 92.637 421 18 7 1 419 469874821 469875230 9.340000e-166 593.0
16 TraesCS7D01G449100 chr2B 91.870 2337 100 33 1631 3905 71029553 71031861 0.000000e+00 3181.0
17 TraesCS7D01G449100 chr2B 92.694 1533 61 5 2422 3905 12732646 12734176 0.000000e+00 2163.0
18 TraesCS7D01G449100 chr2B 90.772 1463 62 16 2490 3905 398123759 398125195 0.000000e+00 1886.0
19 TraesCS7D01G449100 chr2B 95.727 866 32 3 1631 2495 398111910 398112771 0.000000e+00 1389.0
20 TraesCS7D01G449100 chr2B 90.909 418 26 5 1 416 12707117 12707524 5.700000e-153 551.0
21 TraesCS7D01G449100 chr2B 92.226 283 12 3 3037 3310 128580768 128580487 3.660000e-105 392.0
22 TraesCS7D01G449100 chr2B 97.468 79 1 1 1255 1333 12709209 12709286 2.450000e-27 134.0
23 TraesCS7D01G449100 chr2B 96.970 33 0 1 2985 3017 12733276 12733307 2.000000e-03 54.7
24 TraesCS7D01G449100 chr7B 94.660 1929 69 8 1574 3473 123397817 123399740 0.000000e+00 2961.0
25 TraesCS7D01G449100 chr7B 92.216 835 53 6 752 1580 123385722 123386550 0.000000e+00 1171.0
26 TraesCS7D01G449100 chr7B 91.164 464 20 2 3462 3905 123399759 123400221 9.280000e-171 610.0
27 TraesCS7D01G449100 chr7B 91.264 435 33 4 1 432 653340774 653341206 4.350000e-164 588.0
28 TraesCS7D01G449100 chr3B 91.497 1764 66 20 2138 3846 75640339 75638605 0.000000e+00 2350.0
29 TraesCS7D01G449100 chr3B 91.359 1759 70 16 2138 3847 484501178 484499453 0.000000e+00 2331.0
30 TraesCS7D01G449100 chr3B 90.351 456 30 9 5 456 807587036 807586591 1.560000e-163 586.0
31 TraesCS7D01G449100 chr3B 100.000 29 0 0 429 457 545652127 545652099 2.000000e-03 54.7
32 TraesCS7D01G449100 chr5D 91.574 1163 59 17 2736 3867 326030493 326031647 0.000000e+00 1568.0
33 TraesCS7D01G449100 chr6B 87.967 1230 77 20 2736 3905 608275483 608276701 0.000000e+00 1386.0
34 TraesCS7D01G449100 chr6B 88.514 801 30 19 3148 3905 577619226 577620007 0.000000e+00 913.0
35 TraesCS7D01G449100 chr5B 95.550 764 31 2 2230 2993 43858322 43857562 0.000000e+00 1219.0
36 TraesCS7D01G449100 chr5B 93.643 818 39 4 1345 2153 589128209 589127396 0.000000e+00 1210.0
37 TraesCS7D01G449100 chr5B 94.336 459 22 4 1 457 687950919 687950463 0.000000e+00 701.0
38 TraesCS7D01G449100 chr5A 87.563 788 50 20 1340 2106 599813663 599812903 0.000000e+00 869.0
39 TraesCS7D01G449100 chr4B 87.345 806 39 21 3148 3905 97762437 97761647 0.000000e+00 865.0
40 TraesCS7D01G449100 chr3A 85.283 761 73 19 3168 3905 569540645 569541389 0.000000e+00 749.0
41 TraesCS7D01G449100 chr3A 94.299 421 13 6 1 419 668636477 668636888 5.500000e-178 634.0
42 TraesCS7D01G449100 chr3A 91.924 421 19 7 1 419 718743690 718743283 3.380000e-160 575.0
43 TraesCS7D01G449100 chr3A 100.000 28 0 0 430 457 668636881 668636908 7.000000e-03 52.8
44 TraesCS7D01G449100 chr3A 100.000 28 0 0 430 457 718743290 718743263 7.000000e-03 52.8
45 TraesCS7D01G449100 chr1A 93.452 504 29 3 752 1251 343962564 343963067 0.000000e+00 745.0
46 TraesCS7D01G449100 chr6A 84.474 760 81 20 3168 3905 118183077 118183821 0.000000e+00 715.0


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 TraesCS7D01G449100 chr7D 568456649 568460553 3904 False 3335.00 5825 100.0000 1 3905 2 chr7D.!!$F1 3904
1 TraesCS7D01G449100 chrUn 93956760 93960745 3985 False 2928.50 5153 95.3895 1 3905 2 chrUn.!!$F1 3904
2 TraesCS7D01G449100 chr7A 727858383 727861515 3132 False 4708.00 4708 94.0670 818 3905 1 chr7A.!!$F1 3087
3 TraesCS7D01G449100 chr1D 66758734 66761877 3143 False 2437.50 4250 93.9570 754 3905 2 chr1D.!!$F2 3151
4 TraesCS7D01G449100 chr1D 330029515 330030674 1159 True 1570.00 1570 91.5170 2736 3870 1 chr1D.!!$R1 1134
5 TraesCS7D01G449100 chr1D 370167780 370168397 617 False 989.00 989 95.4840 755 1374 1 chr1D.!!$F1 619
6 TraesCS7D01G449100 chr3D 21935224 21938367 3143 False 2423.50 4239 93.5985 752 3905 2 chr3D.!!$F3 3153
7 TraesCS7D01G449100 chr3D 63802122 63803275 1153 False 1609.00 1609 92.2480 2736 3864 1 chr3D.!!$F1 1128
8 TraesCS7D01G449100 chr3D 599650315 599650851 536 False 754.00 754 92.5930 3386 3905 1 chr3D.!!$F2 519
9 TraesCS7D01G449100 chr2A 268558383 268561699 3316 True 2238.00 3751 94.4180 1 3273 2 chr2A.!!$R1 3272
10 TraesCS7D01G449100 chr2B 71029553 71031861 2308 False 3181.00 3181 91.8700 1631 3905 1 chr2B.!!$F1 2274
11 TraesCS7D01G449100 chr2B 398123759 398125195 1436 False 1886.00 1886 90.7720 2490 3905 1 chr2B.!!$F3 1415
12 TraesCS7D01G449100 chr2B 398111910 398112771 861 False 1389.00 1389 95.7270 1631 2495 1 chr2B.!!$F2 864
13 TraesCS7D01G449100 chr2B 12732646 12734176 1530 False 1108.85 2163 94.8320 2422 3905 2 chr2B.!!$F5 1483
14 TraesCS7D01G449100 chr2B 12707117 12709286 2169 False 342.50 551 94.1885 1 1333 2 chr2B.!!$F4 1332
15 TraesCS7D01G449100 chr7B 123397817 123400221 2404 False 1785.50 2961 92.9120 1574 3905 2 chr7B.!!$F3 2331
16 TraesCS7D01G449100 chr7B 123385722 123386550 828 False 1171.00 1171 92.2160 752 1580 1 chr7B.!!$F1 828
17 TraesCS7D01G449100 chr3B 75638605 75640339 1734 True 2350.00 2350 91.4970 2138 3846 1 chr3B.!!$R1 1708
18 TraesCS7D01G449100 chr3B 484499453 484501178 1725 True 2331.00 2331 91.3590 2138 3847 1 chr3B.!!$R2 1709
19 TraesCS7D01G449100 chr5D 326030493 326031647 1154 False 1568.00 1568 91.5740 2736 3867 1 chr5D.!!$F1 1131
20 TraesCS7D01G449100 chr6B 608275483 608276701 1218 False 1386.00 1386 87.9670 2736 3905 1 chr6B.!!$F2 1169
21 TraesCS7D01G449100 chr6B 577619226 577620007 781 False 913.00 913 88.5140 3148 3905 1 chr6B.!!$F1 757
22 TraesCS7D01G449100 chr5B 43857562 43858322 760 True 1219.00 1219 95.5500 2230 2993 1 chr5B.!!$R1 763
23 TraesCS7D01G449100 chr5B 589127396 589128209 813 True 1210.00 1210 93.6430 1345 2153 1 chr5B.!!$R2 808
24 TraesCS7D01G449100 chr5A 599812903 599813663 760 True 869.00 869 87.5630 1340 2106 1 chr5A.!!$R1 766
25 TraesCS7D01G449100 chr4B 97761647 97762437 790 True 865.00 865 87.3450 3148 3905 1 chr4B.!!$R1 757
26 TraesCS7D01G449100 chr3A 569540645 569541389 744 False 749.00 749 85.2830 3168 3905 1 chr3A.!!$F1 737
27 TraesCS7D01G449100 chr1A 343962564 343963067 503 False 745.00 745 93.4520 752 1251 1 chr1A.!!$F1 499
28 TraesCS7D01G449100 chr6A 118183077 118183821 744 False 715.00 715 84.4740 3168 3905 1 chr6A.!!$F1 737

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
812 1248 0.385751 GCGTCTTCCAGATCCATCGA 59.614 55.000 0.00 0.0 0.00 3.59 F
1270 2156 4.141869 TGCTCTGTTTCAGCATAGCATAGA 60.142 41.667 7.28 0.0 42.09 1.98 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2195 3107 3.063180 GGAGATGAAGACAAGATGCAACG 59.937 47.826 0.0 0.0 0.0 4.10 R
3019 3954 7.073265 GCAAGCAAAGTACGAACATTTTACTA 58.927 34.615 0.0 0.0 0.0 1.82 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
174 177 5.947663 TCCTTTCTTTCCAGTTTCCACATA 58.052 37.500 0.00 0.00 0.00 2.29
218 221 1.533469 CCCCGTCTCCTCGTTGTCTT 61.533 60.000 0.00 0.00 0.00 3.01
425 433 2.750237 GTCCCCCACGAATGGTGC 60.750 66.667 0.00 0.00 45.66 5.01
434 442 2.750237 GAATGGTGCCGTCCCCAC 60.750 66.667 0.00 0.00 32.49 4.61
812 1248 0.385751 GCGTCTTCCAGATCCATCGA 59.614 55.000 0.00 0.00 0.00 3.59
1238 1679 6.142817 CGTTCTTCCCATTTTACAGAGTTTG 58.857 40.000 0.00 0.00 0.00 2.93
1270 2156 4.141869 TGCTCTGTTTCAGCATAGCATAGA 60.142 41.667 7.28 0.00 42.09 1.98
2195 3107 5.998363 AGTTTGGTCCTTGTCTGATTTAGTC 59.002 40.000 0.00 0.00 0.00 2.59
2399 3328 3.411446 TGACATTACTGTTGCCTTGAGG 58.589 45.455 0.00 0.00 35.14 3.86
2486 3415 6.403309 GCAAGGCTTGAGTAATTTAGTGTACC 60.403 42.308 30.45 2.74 0.00 3.34
2509 3441 7.206687 ACCGCATCTTTAGTTTCAATTGAAAA 58.793 30.769 30.07 16.40 44.58 2.29
2578 3510 9.654663 ATGAAAGGAGTACTGTAGTTACAAATC 57.345 33.333 0.00 0.00 35.50 2.17
3019 3954 7.519032 TTTGGTAGTAGTTTGCTTTGCTATT 57.481 32.000 0.00 0.00 0.00 1.73
3482 4505 3.133901 AGTGTGTGTGTGTATCCAGTGAA 59.866 43.478 0.00 0.00 0.00 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
147 150 1.897560 AACTGGAAAGAAAGGAGGCG 58.102 50.000 0.00 0.00 0.00 5.52
174 177 2.039480 CTGGAATGGGATCGATGGATGT 59.961 50.000 0.54 0.00 31.51 3.06
218 221 2.042537 AGCTCTCTCCATCGGGCA 60.043 61.111 0.00 0.00 0.00 5.36
798 1234 2.034878 CCTCTGTCGATGGATCTGGAA 58.965 52.381 0.00 0.00 0.00 3.53
812 1248 2.043450 CGCCTCCTCCTCCTCTGT 60.043 66.667 0.00 0.00 0.00 3.41
856 1295 1.134936 GCGAGGAAGGAGAGAAGGTTC 60.135 57.143 0.00 0.00 0.00 3.62
1238 1679 3.556775 GCTGAAACAGAGCATCAGATCTC 59.443 47.826 6.21 3.02 38.74 2.75
1365 2251 0.890683 CAACTGAAGCCCCATGGAAC 59.109 55.000 15.22 4.34 0.00 3.62
1903 2811 7.442062 GTGTTGTTTCCAATTGATTCCAATTCT 59.558 33.333 7.12 0.00 46.83 2.40
2195 3107 3.063180 GGAGATGAAGACAAGATGCAACG 59.937 47.826 0.00 0.00 0.00 4.10
2578 3510 8.988064 ATAGATGTACATAATTTGTAGGCTCG 57.012 34.615 8.71 0.00 41.45 5.03
3019 3954 7.073265 GCAAGCAAAGTACGAACATTTTACTA 58.927 34.615 0.00 0.00 0.00 1.82


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

AutoCloner maintained by Alex Coulton.