Multiple sequence alignment - TraesCS7B01G389500

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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 TraesCS7B01G389500 chr7B 100.000 2489 0 0 1 2489 656273886 656276374 0.000000e+00 4597.0
1 TraesCS7B01G389500 chr7B 97.695 998 17 2 1 992 656239869 656240866 0.000000e+00 1711.0
2 TraesCS7B01G389500 chr7B 96.792 530 16 1 991 1520 656245148 656245676 0.000000e+00 883.0
3 TraesCS7B01G389500 chr7B 89.956 458 39 3 1159 1612 656287489 656287943 3.570000e-163 584.0
4 TraesCS7B01G389500 chr7A 93.426 1719 91 10 785 2489 682179744 682178034 0.000000e+00 2529.0
5 TraesCS7B01G389500 chr7A 91.855 1633 74 19 1 1608 682183644 682182046 0.000000e+00 2224.0
6 TraesCS7B01G389500 chr7A 92.518 1390 63 19 312 1694 676305306 676306661 0.000000e+00 1953.0
7 TraesCS7B01G389500 chr7A 91.707 627 36 6 772 1388 676307872 676308492 0.000000e+00 856.0
8 TraesCS7B01G389500 chr7A 86.864 609 70 8 1158 1757 676359963 676359356 0.000000e+00 673.0
9 TraesCS7B01G389500 chr7A 91.957 460 32 3 1696 2152 676346655 676347112 7.510000e-180 640.0
10 TraesCS7B01G389500 chr7A 90.372 457 27 7 1 440 676304565 676305021 3.570000e-163 584.0
11 TraesCS7B01G389500 chr7A 95.493 355 13 3 2136 2489 676364218 676363866 4.650000e-157 564.0
12 TraesCS7B01G389500 chr7A 83.554 529 49 19 668 1168 682176260 682175742 6.270000e-126 460.0
13 TraesCS7B01G389500 chr7A 83.051 531 52 18 668 1168 676361069 676360547 4.880000e-122 448.0
14 TraesCS7B01G389500 chr7A 84.422 398 40 15 19 396 677279979 677280374 3.020000e-99 372.0
15 TraesCS7B01G389500 chr7D 94.670 1182 47 8 520 1692 585656366 585657540 0.000000e+00 1820.0
16 TraesCS7B01G389500 chr7D 96.231 796 23 4 1696 2487 585662543 585663335 0.000000e+00 1297.0
17 TraesCS7B01G389500 chr7D 89.649 570 54 2 1155 1719 585667611 585668180 0.000000e+00 721.0
18 TraesCS7B01G389500 chr7D 90.782 499 22 14 48 527 585655790 585656283 0.000000e+00 645.0
19 TraesCS7B01G389500 chr7D 84.100 522 52 16 668 1168 585666474 585666985 2.240000e-130 475.0
20 TraesCS7B01G389500 chr7D 100.000 33 0 0 2113 2145 633507071 633507103 7.430000e-06 62.1
21 TraesCS7B01G389500 chr3D 90.110 273 27 0 1 273 55264901 55265173 3.040000e-94 355.0
22 TraesCS7B01G389500 chr3D 80.882 272 31 12 1950 2218 538338743 538338490 7.020000e-46 195.0
23 TraesCS7B01G389500 chr5D 86.842 114 13 2 2120 2232 276289607 276289719 2.600000e-25 126.0
24 TraesCS7B01G389500 chr2A 86.087 115 12 4 2120 2232 174230392 174230504 1.210000e-23 121.0
25 TraesCS7B01G389500 chr2A 88.119 101 11 1 2133 2232 174108846 174108946 4.350000e-23 119.0
26 TraesCS7B01G389500 chr2A 84.821 112 16 1 2120 2230 174030253 174030364 7.280000e-21 111.0
27 TraesCS7B01G389500 chr2A 91.111 45 2 2 2350 2393 31400273 31400316 2.670000e-05 60.2
28 TraesCS7B01G389500 chr2D 84.034 119 12 6 2119 2232 585743482 585743366 9.410000e-20 108.0
29 TraesCS7B01G389500 chr3A 97.368 38 1 0 2360 2397 638987355 638987318 5.750000e-07 65.8
30 TraesCS7B01G389500 chr4B 97.297 37 1 0 2360 2396 158268828 158268792 2.070000e-06 63.9
31 TraesCS7B01G389500 chr5A 89.583 48 5 0 2349 2396 622424505 622424458 7.430000e-06 62.1
32 TraesCS7B01G389500 chr5A 97.143 35 1 0 2362 2396 698325019 698324985 2.670000e-05 60.2
33 TraesCS7B01G389500 chr4A 94.737 38 1 1 377 414 204179673 204179637 9.620000e-05 58.4
34 TraesCS7B01G389500 chr6A 94.444 36 2 0 2362 2397 79346313 79346278 3.460000e-04 56.5


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 TraesCS7B01G389500 chr7B 656273886 656276374 2488 False 4597.000000 4597 100.000000 1 2489 1 chr7B.!!$F3 2488
1 TraesCS7B01G389500 chr7B 656239869 656240866 997 False 1711.000000 1711 97.695000 1 992 1 chr7B.!!$F1 991
2 TraesCS7B01G389500 chr7B 656245148 656245676 528 False 883.000000 883 96.792000 991 1520 1 chr7B.!!$F2 529
3 TraesCS7B01G389500 chr7A 682175742 682183644 7902 True 1737.666667 2529 89.611667 1 2489 3 chr7A.!!$R2 2488
4 TraesCS7B01G389500 chr7A 676304565 676308492 3927 False 1131.000000 1953 91.532333 1 1694 3 chr7A.!!$F3 1693
5 TraesCS7B01G389500 chr7A 676359356 676364218 4862 True 561.666667 673 88.469333 668 2489 3 chr7A.!!$R1 1821
6 TraesCS7B01G389500 chr7D 585655790 585657540 1750 False 1232.500000 1820 92.726000 48 1692 2 chr7D.!!$F2 1644
7 TraesCS7B01G389500 chr7D 585662543 585668180 5637 False 831.000000 1297 89.993333 668 2487 3 chr7D.!!$F3 1819

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
159 165 0.629058 TTTAATGGAGTGGGGAGGGC 59.371 55.000 0.0 0.0 0.0 5.19 F
245 256 1.288752 GGGGCATTGGTTTGTGTCG 59.711 57.895 0.0 0.0 0.0 4.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1383 9544 0.393077 CCTTCTCCACCACGTTGTCT 59.607 55.0 0.0 0.0 0.0 3.41 R
2024 11286 0.588730 CTTGCACACGGACAACAACG 60.589 55.0 0.0 0.0 0.0 4.10 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
43 44 8.726988 GCAAAACTAATAGTCACTTATTGTCCA 58.273 33.333 0.00 0.0 0.00 4.02
105 106 2.483014 ACACCGCAGCAAAGGTTATA 57.517 45.000 0.00 0.0 39.00 0.98
159 165 0.629058 TTTAATGGAGTGGGGAGGGC 59.371 55.000 0.00 0.0 0.00 5.19
245 256 1.288752 GGGGCATTGGTTTGTGTCG 59.711 57.895 0.00 0.0 0.00 4.35
325 349 3.439293 ACGTCTAGATTGCATCAAGTCG 58.561 45.455 0.00 0.0 0.00 4.18
1241 9402 1.960040 CTGGCAGCGGGAGTGATACA 61.960 60.000 0.00 0.0 0.00 2.29
1340 9501 2.359107 CAGCGGCTGGAAAGAGCA 60.359 61.111 22.11 0.0 41.08 4.26
1341 9502 1.748122 CAGCGGCTGGAAAGAGCAT 60.748 57.895 22.11 0.0 41.08 3.79
1383 9544 1.003839 GACGGACATGAAGTGGGCA 60.004 57.895 0.00 0.0 0.00 5.36
1388 9549 1.545428 GGACATGAAGTGGGCAGACAA 60.545 52.381 0.00 0.0 0.00 3.18
1526 9688 7.990886 ACGAACAATGGATAAATATGTACTGGT 59.009 33.333 0.00 0.0 0.00 4.00
1694 9866 5.672503 TGGCATTTCCATTGGTGAAATATG 58.327 37.500 1.86 0.0 39.71 1.78
1750 9922 9.482627 ACAGAAAAACTCATCTACAGTTTCTAG 57.517 33.333 0.00 0.0 42.14 2.43
1790 9962 1.530771 GGCCAGCCATCACAGATCT 59.469 57.895 3.12 0.0 35.81 2.75
1829 10002 0.253044 GACCATGCCTTCTGCCACTA 59.747 55.000 0.00 0.0 40.16 2.74
1887 10060 2.124236 AAACCGTTGCCCGTGGAA 60.124 55.556 0.00 0.0 33.66 3.53
1890 10063 4.636435 CCGTTGCCCGTGGAAGGT 62.636 66.667 0.00 0.0 33.66 3.50
1960 11222 5.991606 CCCTCATTGCGACTCTATCAAATTA 59.008 40.000 0.00 0.0 0.00 1.40
1978 11240 9.696917 ATCAAATTACTTTTGTGGATCTTCAAC 57.303 29.630 0.00 0.0 44.25 3.18
1979 11241 8.141268 TCAAATTACTTTTGTGGATCTTCAACC 58.859 33.333 0.00 0.0 44.25 3.77
1980 11242 7.839680 AATTACTTTTGTGGATCTTCAACCT 57.160 32.000 0.00 0.0 0.00 3.50
1985 11247 5.576563 TTTGTGGATCTTCAACCTTAGGA 57.423 39.130 4.77 0.0 0.00 2.94
2034 11296 0.165944 CGGAGCAATCGTTGTTGTCC 59.834 55.000 0.00 0.0 0.00 4.02
2045 11307 0.393132 TTGTTGTCCGTGTGCAAGGA 60.393 50.000 2.80 2.8 36.63 3.36
2059 11321 5.066505 GTGTGCAAGGAAGAAGAAAGAAGAA 59.933 40.000 0.00 0.0 0.00 2.52
2128 11392 4.070009 GTCGTTGGTTTGAGGGATTAAGT 58.930 43.478 0.00 0.0 0.00 2.24
2130 11394 5.009310 GTCGTTGGTTTGAGGGATTAAGTTT 59.991 40.000 0.00 0.0 0.00 2.66
2140 11404 5.369699 TGAGGGATTAAGTTTAGGGGATCTG 59.630 44.000 0.00 0.0 0.00 2.90
2142 11406 4.104897 GGGATTAAGTTTAGGGGATCTGCT 59.895 45.833 0.00 0.0 0.00 4.24
2143 11407 5.309806 GGGATTAAGTTTAGGGGATCTGCTA 59.690 44.000 0.00 0.0 0.00 3.49
2144 11408 6.468543 GGATTAAGTTTAGGGGATCTGCTAG 58.531 44.000 0.00 0.0 0.00 3.42
2145 11409 3.847671 AAGTTTAGGGGATCTGCTAGC 57.152 47.619 8.10 8.1 0.00 3.42
2197 11461 5.129368 TGAATTTTGGGGATAGGGAGAAG 57.871 43.478 0.00 0.0 0.00 2.85
2313 11577 3.904571 TGCATACGGACGTGGTATATTC 58.095 45.455 7.73 0.0 0.00 1.75
2340 11605 8.592809 TGCCACATTAACCTATTTTCTTTTGAT 58.407 29.630 0.00 0.0 0.00 2.57
2363 11628 7.867403 TGATTTTGCTTTGTACTTTCTTCATCC 59.133 33.333 0.00 0.0 0.00 3.51
2399 11664 9.658475 TGTCTTTGATTTAGTACAATTTTGACG 57.342 29.630 0.00 0.0 0.00 4.35
2417 11682 5.462530 TGACGTTTTCTCCTACTTCATCA 57.537 39.130 0.00 0.0 0.00 3.07
2424 11689 8.289618 CGTTTTCTCCTACTTCATCAATGAAAA 58.710 33.333 6.85 0.0 45.26 2.29
2433 11698 7.105241 ACTTCATCAATGAAAATTAGCTCCC 57.895 36.000 6.85 0.0 45.26 4.30
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
43 44 5.594317 GGCACTCCACAACCAATATTTAGAT 59.406 40.000 0.00 0.00 0.00 1.98
159 165 2.693864 ACCATGCCTCCTCCCCTG 60.694 66.667 0.00 0.00 0.00 4.45
245 256 1.709760 CACCATGCACACGATCGAC 59.290 57.895 24.34 8.61 0.00 4.20
325 349 7.500227 TGACAGGTTGATGAGATAATCCATTTC 59.500 37.037 0.00 0.00 0.00 2.17
385 409 9.897744 TCTCTACAAACTTGCTCAAATTTTATG 57.102 29.630 0.00 0.00 0.00 1.90
665 1198 4.330074 CACCTTGTTCACATCTATCGGAAC 59.670 45.833 0.00 0.00 39.93 3.62
666 1199 4.503910 CACCTTGTTCACATCTATCGGAA 58.496 43.478 0.00 0.00 0.00 4.30
668 1201 3.198068 CCACCTTGTTCACATCTATCGG 58.802 50.000 0.00 0.00 0.00 4.18
669 1202 2.609459 GCCACCTTGTTCACATCTATCG 59.391 50.000 0.00 0.00 0.00 2.92
671 1204 2.578021 AGGCCACCTTGTTCACATCTAT 59.422 45.455 5.01 0.00 0.00 1.98
1241 9402 1.415672 TTTCACTTCCTCGGTGCCCT 61.416 55.000 0.00 0.00 34.97 5.19
1288 9449 0.473755 TTCTCCAGCACAGCTTTGGA 59.526 50.000 1.35 4.15 36.40 3.53
1383 9544 0.393077 CCTTCTCCACCACGTTGTCT 59.607 55.000 0.00 0.00 0.00 3.41
1388 9549 1.071471 CTTGCCTTCTCCACCACGT 59.929 57.895 0.00 0.00 0.00 4.49
1526 9688 5.257082 TCACGCAGCTATGTATCTTTACA 57.743 39.130 0.00 0.00 42.35 2.41
1622 9793 6.127980 GCCAGATATGATGATTGACTTCATGG 60.128 42.308 0.00 0.00 41.39 3.66
1694 9866 4.453819 GCCATGAGTATTGTAATCTCTGGC 59.546 45.833 17.80 17.80 40.85 4.85
1750 9922 3.869246 CGACAACCATGGTTCTATGTACC 59.131 47.826 27.56 10.93 36.00 3.34
1781 9953 3.932710 GCAACGAATAACCAGATCTGTGA 59.067 43.478 21.11 6.45 0.00 3.58
1790 9962 4.551388 GTCCAAAATGCAACGAATAACCA 58.449 39.130 0.00 0.00 0.00 3.67
1829 10002 4.396357 TGAGTTCTTCTCCTCTTCTCCT 57.604 45.455 0.00 0.00 42.12 3.69
1887 10060 0.611714 AACGTAGGCGGAATTCACCT 59.388 50.000 19.71 19.71 43.45 4.00
1890 10063 1.468565 CGAGAACGTAGGCGGAATTCA 60.469 52.381 7.93 0.00 43.45 2.57
1960 11222 5.770162 CCTAAGGTTGAAGATCCACAAAAGT 59.230 40.000 4.17 0.00 0.00 2.66
1977 11239 3.232720 GAGCTAGCTAGGTCCTAAGGT 57.767 52.381 33.32 10.71 43.17 3.50
1985 11247 2.461300 TGTCCATGAGCTAGCTAGGT 57.539 50.000 24.94 24.94 36.62 3.08
2024 11286 0.588730 CTTGCACACGGACAACAACG 60.589 55.000 0.00 0.00 0.00 4.10
2034 11296 2.872245 TCTTTCTTCTTCCTTGCACACG 59.128 45.455 0.00 0.00 0.00 4.49
2045 11307 8.595362 TTCCTTTTTCCTTCTTCTTTCTTCTT 57.405 30.769 0.00 0.00 0.00 2.52
2059 11321 5.132816 TCTGTCTTCCTTCTTCCTTTTTCCT 59.867 40.000 0.00 0.00 0.00 3.36
2128 11392 2.968574 CTCAGCTAGCAGATCCCCTAAA 59.031 50.000 18.83 0.00 0.00 1.85
2130 11394 1.783365 TCTCAGCTAGCAGATCCCCTA 59.217 52.381 18.83 0.00 0.00 3.53
2140 11404 6.375736 AGGGATTAAACTTTTTCTCAGCTAGC 59.624 38.462 6.62 6.62 0.00 3.42
2142 11406 7.458397 TGAGGGATTAAACTTTTTCTCAGCTA 58.542 34.615 0.00 0.00 0.00 3.32
2143 11407 6.306987 TGAGGGATTAAACTTTTTCTCAGCT 58.693 36.000 0.00 0.00 0.00 4.24
2144 11408 6.575162 TGAGGGATTAAACTTTTTCTCAGC 57.425 37.500 0.00 0.00 0.00 4.26
2145 11409 9.987272 ATTTTGAGGGATTAAACTTTTTCTCAG 57.013 29.630 0.00 0.00 32.62 3.35
2232 11496 6.377912 AGTCTAACCATCAGAGCTAATACCT 58.622 40.000 0.00 0.00 0.00 3.08
2234 11498 7.278461 TGAGTCTAACCATCAGAGCTAATAC 57.722 40.000 0.00 0.00 0.00 1.89
2313 11577 8.087750 TCAAAAGAAAATAGGTTAATGTGGCAG 58.912 33.333 0.00 0.00 0.00 4.85
2340 11605 7.106439 TGGATGAAGAAAGTACAAAGCAAAA 57.894 32.000 0.00 0.00 0.00 2.44
2355 11620 9.130661 TCAAAGACACTTATTTTTGGATGAAGA 57.869 29.630 0.00 0.00 32.76 2.87
2389 11654 7.414436 TGAAGTAGGAGAAAACGTCAAAATTG 58.586 34.615 0.00 0.00 32.39 2.32
2417 11682 9.700831 ATAAGTAGTTGGGAGCTAATTTTCATT 57.299 29.630 0.00 0.00 30.77 2.57
2424 11689 8.268878 AGATGAATAAGTAGTTGGGAGCTAAT 57.731 34.615 0.00 0.00 0.00 1.73
2459 11724 8.041919 AGTTCCTTCATAGCTTAAGTCCTTTAC 58.958 37.037 4.02 0.00 0.00 2.01


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

AutoCloner maintained by Alex Coulton.