Multiple sequence alignment - TraesCS6A01G115500

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 TraesCS6A01G115500 chr6A 100.000 2451 0 0 1 2451 85409412 85406962 0.000000e+00 4527.0
1 TraesCS6A01G115500 chr6A 95.750 1247 52 1 1 1246 85371992 85370746 0.000000e+00 2008.0
2 TraesCS6A01G115500 chr6A 94.864 1285 64 2 1167 2451 85434782 85433500 0.000000e+00 2006.0
3 TraesCS6A01G115500 chr6A 93.100 1116 65 2 1 1115 85435908 85434804 0.000000e+00 1624.0
4 TraesCS6A01G115500 chr6A 96.344 930 22 1 1522 2451 85370742 85369825 0.000000e+00 1519.0
5 TraesCS6A01G115500 chr6A 82.974 881 124 24 1 871 356815714 356814850 0.000000e+00 773.0
6 TraesCS6A01G115500 chr6A 94.974 378 19 0 2074 2451 378279401 378279024 5.840000e-166 593.0
7 TraesCS6A01G115500 chr6A 95.430 372 16 1 2080 2451 223236106 223236476 2.100000e-165 592.0
8 TraesCS6A01G115500 chr6A 95.161 372 16 2 2080 2451 566257095 566256726 9.760000e-164 586.0
9 TraesCS6A01G115500 chr6A 94.652 374 18 2 2078 2451 221619290 221619661 1.630000e-161 579.0
10 TraesCS6A01G115500 chr6A 94.355 372 19 2 2080 2451 566249109 566248740 9.830000e-159 569.0
11 TraesCS6A01G115500 chr6A 89.474 437 43 3 1467 1900 262374273 262373837 1.280000e-152 549.0
12 TraesCS6A01G115500 chr6A 91.235 251 22 0 832 1082 396400105 396400355 2.330000e-90 342.0
13 TraesCS6A01G115500 chr6A 88.800 250 25 3 1075 1323 209758007 209757760 1.100000e-78 303.0
14 TraesCS6A01G115500 chr6A 87.500 128 12 4 1618 1744 20005544 20005668 7.060000e-31 145.0
15 TraesCS6A01G115500 chr6A 90.000 50 5 0 1983 2032 259788839 259788790 5.660000e-07 65.8
16 TraesCS6A01G115500 chr6A 86.000 50 7 0 1983 2032 259804411 259804362 1.000000e-03 54.7
17 TraesCS6A01G115500 chr7A 85.303 1946 211 43 1 1937 312270583 312268704 0.000000e+00 1940.0
18 TraesCS6A01G115500 chr7A 89.990 1039 94 7 832 1869 366607183 366608212 0.000000e+00 1334.0
19 TraesCS6A01G115500 chr7A 90.229 829 69 5 832 1659 366616573 366617390 0.000000e+00 1072.0
20 TraesCS6A01G115500 chr7A 92.473 186 12 2 1362 1547 508738824 508738641 5.200000e-67 265.0
21 TraesCS6A01G115500 chr7A 90.860 186 16 1 1362 1547 508719517 508719333 5.230000e-62 248.0
22 TraesCS6A01G115500 chr7A 93.407 91 5 1 1960 2049 327820886 327820796 1.530000e-27 134.0
23 TraesCS6A01G115500 chr1A 89.531 1366 122 18 1 1356 204673655 204675009 0.000000e+00 1711.0
24 TraesCS6A01G115500 chr1A 94.892 372 17 2 2080 2451 142117978 142117609 4.540000e-162 580.0
25 TraesCS6A01G115500 chr1A 94.624 372 18 2 2080 2451 142140124 142139755 2.110000e-160 575.0
26 TraesCS6A01G115500 chr1A 92.533 375 23 4 2080 2451 379464700 379465072 1.290000e-147 532.0
27 TraesCS6A01G115500 chr1A 90.099 404 33 6 2050 2451 351713756 351714154 3.610000e-143 518.0
28 TraesCS6A01G115500 chr1A 89.409 406 35 5 2050 2451 351722489 351722890 2.810000e-139 505.0
29 TraesCS6A01G115500 chr1A 90.228 307 28 2 2074 2380 244251717 244252021 1.370000e-107 399.0
30 TraesCS6A01G115500 chr1A 89.902 307 29 2 2074 2380 244259696 244260000 6.350000e-106 394.0
31 TraesCS6A01G115500 chr1A 96.444 225 8 0 2227 2451 284856456 284856232 2.980000e-99 372.0
32 TraesCS6A01G115500 chr1A 89.655 261 26 1 822 1082 401295879 401295620 5.050000e-87 331.0
33 TraesCS6A01G115500 chr1A 88.346 266 30 1 1035 1300 95243317 95243581 3.930000e-83 318.0
34 TraesCS6A01G115500 chr1A 88.583 254 24 5 1075 1326 44437574 44437824 1.100000e-78 303.0
35 TraesCS6A01G115500 chr1A 93.122 189 12 1 1359 1547 95243572 95243759 2.400000e-70 276.0
36 TraesCS6A01G115500 chr1A 91.515 165 12 2 1618 1782 168535948 168535786 2.450000e-55 226.0
37 TraesCS6A01G115500 chr1A 92.593 108 8 0 1307 1414 168536365 168536258 3.260000e-34 156.0
38 TraesCS6A01G115500 chr1A 92.771 83 6 0 1362 1444 119032493 119032411 1.190000e-23 121.0
39 TraesCS6A01G115500 chr1A 95.588 68 2 1 1398 1465 348757424 348757358 9.270000e-20 108.0
40 TraesCS6A01G115500 chr1A 91.781 73 6 0 1495 1567 269344286 269344358 4.310000e-18 102.0
41 TraesCS6A01G115500 chr4A 89.559 680 64 7 1 676 278302381 278301705 0.000000e+00 856.0
42 TraesCS6A01G115500 chr4A 89.069 677 69 5 4 677 278311308 278310634 0.000000e+00 835.0
43 TraesCS6A01G115500 chr4A 94.715 492 24 1 1960 2451 333085793 333085304 0.000000e+00 763.0
44 TraesCS6A01G115500 chr4A 96.543 376 12 1 2076 2451 491982566 491982940 2.680000e-174 621.0
45 TraesCS6A01G115500 chr4A 91.111 180 13 3 1618 1797 557070424 557070248 8.760000e-60 241.0
46 TraesCS6A01G115500 chr4A 92.593 108 8 0 1307 1414 557057096 557056989 3.260000e-34 156.0
47 TraesCS6A01G115500 chr4A 91.150 113 9 1 1381 1493 262187124 262187235 4.220000e-33 152.0
48 TraesCS6A01G115500 chr4A 91.071 112 9 1 1381 1492 262139584 262139694 1.520000e-32 150.0
49 TraesCS6A01G115500 chr3A 84.174 872 116 18 1 858 144422370 144421507 0.000000e+00 826.0
50 TraesCS6A01G115500 chr3A 95.758 495 20 1 1957 2451 557448420 557448913 0.000000e+00 797.0
51 TraesCS6A01G115500 chr3A 83.276 873 123 17 1 858 144364862 144363998 0.000000e+00 782.0
52 TraesCS6A01G115500 chr3A 96.414 474 16 1 1978 2451 557429912 557430384 0.000000e+00 780.0
53 TraesCS6A01G115500 chr3A 94.694 490 24 1 1962 2451 260337527 260337040 0.000000e+00 760.0
54 TraesCS6A01G115500 chr3A 94.709 378 20 0 2074 2451 489495769 489495392 2.710000e-164 588.0
55 TraesCS6A01G115500 chr3A 88.057 494 50 5 1304 1797 189837993 189838477 5.880000e-161 577.0
56 TraesCS6A01G115500 chr3A 89.500 400 33 4 1398 1797 734275485 734275875 4.710000e-137 497.0
57 TraesCS6A01G115500 chr3A 88.015 267 29 3 1485 1749 182038082 182038347 1.830000e-81 313.0
58 TraesCS6A01G115500 chr3A 87.336 229 27 2 1569 1797 189883634 189883860 6.720000e-66 261.0
59 TraesCS6A01G115500 chr3A 84.252 254 33 6 1041 1290 113693921 113693671 8.760000e-60 241.0
60 TraesCS6A01G115500 chr3A 90.323 62 4 2 1966 2026 352851662 352851602 2.020000e-11 80.5
61 TraesCS6A01G115500 chr3A 88.710 62 5 2 1966 2026 352843460 352843400 9.400000e-10 75.0
62 TraesCS6A01G115500 chr3A 80.460 87 12 4 1898 1982 207407307 207407224 7.320000e-06 62.1
63 TraesCS6A01G115500 chr3A 92.500 40 2 1 1899 1938 283920535 283920497 3.400000e-04 56.5
64 TraesCS6A01G115500 chr5A 95.893 487 16 4 1966 2451 450361424 450360941 0.000000e+00 785.0
65 TraesCS6A01G115500 chr5A 82.201 927 125 34 1 904 636361860 636362769 0.000000e+00 761.0
66 TraesCS6A01G115500 chr5A 96.000 450 17 1 2002 2451 450323600 450323152 0.000000e+00 730.0
67 TraesCS6A01G115500 chr2A 93.103 261 17 1 822 1082 299299558 299299817 4.950000e-102 381.0
68 TraesCS6A01G115500 chr2A 91.011 267 18 5 605 868 570206389 570206126 3.000000e-94 355.0
69 TraesCS6A01G115500 chr2A 86.885 122 8 5 1930 2049 222524308 222524423 1.980000e-26 130.0
70 TraesCS6A01G115500 chr2A 86.066 122 9 5 1930 2049 222531937 222532052 9.200000e-25 124.0
71 TraesCS6A01G115500 chr2A 83.117 77 8 4 1878 1950 470691433 470691358 5.660000e-07 65.8
72 TraesCS6A01G115500 chr4D 93.289 149 10 0 2207 2355 164096043 164096191 1.140000e-53 220.0
73 TraesCS6A01G115500 chr7D 87.952 83 8 2 1668 1749 178266087 178266168 2.010000e-16 97.1
74 TraesCS6A01G115500 chr1B 87.952 83 8 2 1668 1749 493178472 493178553 2.010000e-16 97.1
75 TraesCS6A01G115500 chr5B 85.366 82 10 2 1668 1748 659020666 659020746 1.560000e-12 84.2


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 TraesCS6A01G115500 chr6A 85406962 85409412 2450 True 4527.0 4527 100.000 1 2451 1 chr6A.!!$R1 2450
1 TraesCS6A01G115500 chr6A 85433500 85435908 2408 True 1815.0 2006 93.982 1 2451 2 chr6A.!!$R11 2450
2 TraesCS6A01G115500 chr6A 85369825 85371992 2167 True 1763.5 2008 96.047 1 2451 2 chr6A.!!$R10 2450
3 TraesCS6A01G115500 chr6A 356814850 356815714 864 True 773.0 773 82.974 1 871 1 chr6A.!!$R6 870
4 TraesCS6A01G115500 chr7A 312268704 312270583 1879 True 1940.0 1940 85.303 1 1937 1 chr7A.!!$R1 1936
5 TraesCS6A01G115500 chr7A 366607183 366608212 1029 False 1334.0 1334 89.990 832 1869 1 chr7A.!!$F1 1037
6 TraesCS6A01G115500 chr7A 366616573 366617390 817 False 1072.0 1072 90.229 832 1659 1 chr7A.!!$F2 827
7 TraesCS6A01G115500 chr1A 204673655 204675009 1354 False 1711.0 1711 89.531 1 1356 1 chr1A.!!$F2 1355
8 TraesCS6A01G115500 chr4A 278301705 278302381 676 True 856.0 856 89.559 1 676 1 chr4A.!!$R1 675
9 TraesCS6A01G115500 chr4A 278310634 278311308 674 True 835.0 835 89.069 4 677 1 chr4A.!!$R2 673
10 TraesCS6A01G115500 chr3A 144421507 144422370 863 True 826.0 826 84.174 1 858 1 chr3A.!!$R3 857
11 TraesCS6A01G115500 chr3A 144363998 144364862 864 True 782.0 782 83.276 1 858 1 chr3A.!!$R2 857
12 TraesCS6A01G115500 chr5A 636361860 636362769 909 False 761.0 761 82.201 1 904 1 chr5A.!!$F1 903

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
568 596 0.03601 ATGGCAACGAGGAGGAACAG 60.036 55.0 0.0 0.0 42.51 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2126 2198 0.180406 CCATCCCTACTTCAACCCCG 59.82 60.0 0.0 0.0 0.0 5.73 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
136 141 3.618351 TCTCTCCCGTTTAGGTACTCAG 58.382 50.000 0.00 0.00 41.75 3.35
334 346 5.863397 CGGATGACATGTGCAAGTTTTATTT 59.137 36.000 1.15 0.00 0.00 1.40
459 477 2.037144 ACATATCGGTTCCGGTAGCTT 58.963 47.619 11.37 0.00 0.00 3.74
568 596 0.036010 ATGGCAACGAGGAGGAACAG 60.036 55.000 0.00 0.00 42.51 3.16
603 631 3.440872 GGCGAATACAACAACCAACCATA 59.559 43.478 0.00 0.00 0.00 2.74
682 712 4.054455 GCGTGCGTTTCGAAGCGA 62.054 61.111 33.87 18.02 34.38 4.93
699 732 2.959707 AGCGAATCGGTTCTAGAGGAAT 59.040 45.455 6.88 0.00 36.24 3.01
923 985 1.067212 GGTAGTCGAACATGGCGATCT 59.933 52.381 14.56 14.48 40.19 2.75
1128 1190 2.626266 TCTTGCGAAGAGGTACTTGACA 59.374 45.455 0.00 0.00 41.55 3.58
1169 1238 1.592400 GAGGGTCGTCGTGTCATGGA 61.592 60.000 0.00 0.00 0.00 3.41
1202 1271 1.478510 TCTCGGAGAAGATGCTTGACC 59.521 52.381 4.96 0.00 34.09 4.02
1246 1315 4.633565 GTGTTGTTCTTGCCAATCCAAAAA 59.366 37.500 0.00 0.00 0.00 1.94
1251 1320 5.115480 GTTCTTGCCAATCCAAAAACTCAA 58.885 37.500 0.00 0.00 0.00 3.02
1253 1322 4.161189 TCTTGCCAATCCAAAAACTCAACA 59.839 37.500 0.00 0.00 0.00 3.33
1357 1427 2.347490 GTGGTGCTCGGACATGGT 59.653 61.111 0.00 0.00 0.00 3.55
1608 1680 1.000396 GCTGCTGGGTCCATTCCTT 60.000 57.895 0.00 0.00 0.00 3.36
1833 1905 3.319198 GGGGACGCTGGGAGAACA 61.319 66.667 0.00 0.00 0.00 3.18
2173 2245 7.545615 GGGACATATTTCTGGAAAACATGAAAC 59.454 37.037 18.91 12.74 34.06 2.78
2289 2362 6.074648 ACCTAACCAAACTGAATCCAAATGA 58.925 36.000 0.00 0.00 0.00 2.57
2360 2433 7.603784 GGGCAAAAGATGAACATTTATTTGAGT 59.396 33.333 16.83 0.00 0.00 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
371 384 1.501292 CGCCACGATGACAAATGCA 59.499 52.632 0.00 0.00 0.00 3.96
477 496 1.079750 GCTCCCGTCACACTTCCTC 60.080 63.158 0.00 0.00 0.00 3.71
568 596 1.076332 ATTCGCCTGTGAACGTTAGC 58.924 50.000 0.00 0.00 0.00 3.09
603 631 5.163824 CGAATGCTTGTGTTGTATGAGATGT 60.164 40.000 0.00 0.00 0.00 3.06
682 712 7.184067 ACAACTAATTCCTCTAGAACCGATT 57.816 36.000 0.00 0.00 37.29 3.34
699 732 1.600164 CGACGACCCGTGAACAACTAA 60.600 52.381 0.00 0.00 41.37 2.24
844 904 5.313506 AGAACCTCTACTTCCCCTTCAAAAT 59.686 40.000 0.00 0.00 0.00 1.82
923 985 0.627451 TCCGGCAAGTACCCTCTCTA 59.373 55.000 0.00 0.00 0.00 2.43
1004 1066 0.602905 GCACTTCGCCAAGTACCACT 60.603 55.000 0.00 0.00 41.24 4.00
1128 1190 2.351157 GGACGCGTCAAGTAACACTACT 60.351 50.000 37.26 0.00 40.25 2.57
1169 1238 3.486383 TCTCCGAGAATTTTGCCAAGTT 58.514 40.909 0.00 0.00 0.00 2.66
1246 1315 2.031870 GGCCCTTTTGTCTTGTTGAGT 58.968 47.619 0.00 0.00 0.00 3.41
1251 1320 1.479389 CCTGAGGCCCTTTTGTCTTGT 60.479 52.381 0.00 0.00 0.00 3.16
1253 1322 0.540597 GCCTGAGGCCCTTTTGTCTT 60.541 55.000 13.77 0.00 44.06 3.01
1440 1510 2.348998 CTGCTGGTCACCTCCACC 59.651 66.667 0.00 0.00 33.55 4.61
1709 1781 2.483889 CCGCTCCCTCCTTGATTTAGTC 60.484 54.545 0.00 0.00 0.00 2.59
1713 1785 0.914417 TCCCGCTCCCTCCTTGATTT 60.914 55.000 0.00 0.00 0.00 2.17
1784 1856 2.396955 CGTCCTCCAGCTACGTCGT 61.397 63.158 2.21 2.21 32.16 4.34
1833 1905 1.969240 GCTCCATCTCCTCACCCTCTT 60.969 57.143 0.00 0.00 0.00 2.85
1909 1981 2.682494 ATACTCCCACACCGCCGT 60.682 61.111 0.00 0.00 0.00 5.68
2126 2198 0.180406 CCATCCCTACTTCAACCCCG 59.820 60.000 0.00 0.00 0.00 5.73
2173 2245 8.647143 AAACTAATTTGATTAAATCGGGCATG 57.353 30.769 0.00 0.00 35.50 4.06
2389 2462 3.005897 GCCACTTCCTTCTTTCCCTTTTC 59.994 47.826 0.00 0.00 0.00 2.29


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

AutoCloner maintained by Alex Coulton.