Multiple sequence alignment - TraesCS7B01G424700

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 TraesCS7B01G424700 chr7B 100.000 2910 0 0 1 2910 693617465 693620374 0.000000e+00 5374
1 TraesCS7B01G424700 chr7B 93.763 2902 117 26 49 2910 698649994 698652871 0.000000e+00 4298
2 TraesCS7B01G424700 chr7B 92.417 2954 141 33 1 2910 699136596 699139510 0.000000e+00 4137
3 TraesCS7B01G424700 chr7B 96.801 2188 49 10 1 2173 694359342 694361523 0.000000e+00 3633
4 TraesCS7B01G424700 chr7B 93.067 2250 124 18 52 2280 699177492 699179730 0.000000e+00 3262
5 TraesCS7B01G424700 chr7B 90.264 1325 87 15 49 1341 696140168 696141482 0.000000e+00 1694
6 TraesCS7B01G424700 chr7B 95.524 715 5 3 2210 2910 694361517 694362218 0.000000e+00 1118
7 TraesCS7B01G424700 chr7B 84.797 1059 144 14 1046 2094 697027536 697026485 0.000000e+00 1048
8 TraesCS7B01G424700 chr7B 98.889 450 4 1 2461 2910 699142733 699143181 0.000000e+00 802
9 TraesCS7B01G424700 chr7B 90.821 414 21 2 2513 2910 699180016 699180428 3.300000e-149 538
10 TraesCS7B01G424700 chr7B 86.920 474 53 6 2353 2823 696142414 696142881 9.240000e-145 523
11 TraesCS7B01G424700 chr7B 90.123 162 15 1 2281 2442 699179861 699180021 2.940000e-50 209
12 TraesCS7B01G424700 chr4A 90.375 2930 190 31 33 2910 661819450 661822339 0.000000e+00 3764
13 TraesCS7B01G424700 chr7D 93.658 1561 82 8 546 2101 608194801 608196349 0.000000e+00 2318
14 TraesCS7B01G424700 chr7D 90.680 1309 86 14 59 1341 514744254 514745552 0.000000e+00 1709
15 TraesCS7B01G424700 chr7D 90.128 1327 89 21 52 1341 600237982 600236661 0.000000e+00 1687
16 TraesCS7B01G424700 chr7D 82.217 1389 196 31 1046 2405 609651375 609650009 0.000000e+00 1149
17 TraesCS7B01G424700 chr7D 90.057 875 59 9 237 1084 79325957 79326830 0.000000e+00 1109
18 TraesCS7B01G424700 chr7D 85.005 1067 139 17 1043 2094 609333457 609334517 0.000000e+00 1064
19 TraesCS7B01G424700 chr7D 88.395 517 37 8 2409 2903 514746522 514747037 4.150000e-168 601
20 TraesCS7B01G424700 chr7D 86.679 563 27 17 2278 2823 610535273 610534742 5.410000e-162 580
21 TraesCS7B01G424700 chr7D 88.557 402 28 4 2526 2910 608196747 608197147 3.390000e-129 472
22 TraesCS7B01G424700 chr7D 90.099 303 13 2 2537 2823 600235579 600235278 7.610000e-101 377
23 TraesCS7B01G424700 chr7D 92.537 201 14 1 2278 2478 600235784 600235585 1.320000e-73 287
24 TraesCS7B01G424700 chr7D 91.589 107 5 2 2278 2384 514746433 514746535 8.400000e-31 145
25 TraesCS7B01G424700 chr7A 89.228 1801 147 26 434 2204 700508867 700507084 0.000000e+00 2207
26 TraesCS7B01G424700 chr7A 88.664 1579 128 21 1370 2909 700205612 700207178 0.000000e+00 1877
27 TraesCS7B01G424700 chr7A 89.370 1270 93 21 107 1341 700204351 700205613 0.000000e+00 1559
28 TraesCS7B01G424700 chr7A 89.059 393 25 6 52 437 700509518 700509137 3.390000e-129 472
29 TraesCS7B01G424700 chr7A 89.744 312 29 3 2278 2589 700507033 700506725 2.100000e-106 396
30 TraesCS7B01G424700 chr1D 91.101 854 52 9 237 1084 16257678 16258513 0.000000e+00 1134
31 TraesCS7B01G424700 chr5D 90.149 873 60 11 237 1084 385871469 385870598 0.000000e+00 1112
32 TraesCS7B01G424700 chr4D 85.217 460 35 7 2476 2910 461482980 461482529 2.660000e-120 442


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 TraesCS7B01G424700 chr7B 693617465 693620374 2909 False 5374.000000 5374 100.000000 1 2910 1 chr7B.!!$F1 2909
1 TraesCS7B01G424700 chr7B 698649994 698652871 2877 False 4298.000000 4298 93.763000 49 2910 1 chr7B.!!$F2 2861
2 TraesCS7B01G424700 chr7B 699136596 699143181 6585 False 2469.500000 4137 95.653000 1 2910 2 chr7B.!!$F5 2909
3 TraesCS7B01G424700 chr7B 694359342 694362218 2876 False 2375.500000 3633 96.162500 1 2910 2 chr7B.!!$F3 2909
4 TraesCS7B01G424700 chr7B 699177492 699180428 2936 False 1336.333333 3262 91.337000 52 2910 3 chr7B.!!$F6 2858
5 TraesCS7B01G424700 chr7B 696140168 696142881 2713 False 1108.500000 1694 88.592000 49 2823 2 chr7B.!!$F4 2774
6 TraesCS7B01G424700 chr7B 697026485 697027536 1051 True 1048.000000 1048 84.797000 1046 2094 1 chr7B.!!$R1 1048
7 TraesCS7B01G424700 chr4A 661819450 661822339 2889 False 3764.000000 3764 90.375000 33 2910 1 chr4A.!!$F1 2877
8 TraesCS7B01G424700 chr7D 608194801 608197147 2346 False 1395.000000 2318 91.107500 546 2910 2 chr7D.!!$F4 2364
9 TraesCS7B01G424700 chr7D 609650009 609651375 1366 True 1149.000000 1149 82.217000 1046 2405 1 chr7D.!!$R1 1359
10 TraesCS7B01G424700 chr7D 79325957 79326830 873 False 1109.000000 1109 90.057000 237 1084 1 chr7D.!!$F1 847
11 TraesCS7B01G424700 chr7D 609333457 609334517 1060 False 1064.000000 1064 85.005000 1043 2094 1 chr7D.!!$F2 1051
12 TraesCS7B01G424700 chr7D 514744254 514747037 2783 False 818.333333 1709 90.221333 59 2903 3 chr7D.!!$F3 2844
13 TraesCS7B01G424700 chr7D 600235278 600237982 2704 True 783.666667 1687 90.921333 52 2823 3 chr7D.!!$R3 2771
14 TraesCS7B01G424700 chr7D 610534742 610535273 531 True 580.000000 580 86.679000 2278 2823 1 chr7D.!!$R2 545
15 TraesCS7B01G424700 chr7A 700204351 700207178 2827 False 1718.000000 1877 89.017000 107 2909 2 chr7A.!!$F1 2802
16 TraesCS7B01G424700 chr7A 700506725 700509518 2793 True 1025.000000 2207 89.343667 52 2589 3 chr7A.!!$R1 2537
17 TraesCS7B01G424700 chr1D 16257678 16258513 835 False 1134.000000 1134 91.101000 237 1084 1 chr1D.!!$F1 847
18 TraesCS7B01G424700 chr5D 385870598 385871469 871 True 1112.000000 1112 90.149000 237 1084 1 chr5D.!!$R1 847

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
559 883 0.966179 TAGAGTTCGCAACAGGCTCA 59.034 50.0 0.0 0.0 41.67 4.26 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1963 2409 1.344114 GAATTCTTGTTGCTGGGCCAA 59.656 47.619 8.04 0.0 0.0 4.52 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
508 831 5.663106 AGCATAGTTCATATACGATCCCCAT 59.337 40.000 0.00 0.00 0.00 4.00
559 883 0.966179 TAGAGTTCGCAACAGGCTCA 59.034 50.000 0.00 0.00 41.67 4.26
569 893 2.416747 CAACAGGCTCAGTCGAAATCA 58.583 47.619 0.00 0.00 0.00 2.57
613 938 7.649533 ATTTCATTGTTCTTGATGATAGGCA 57.350 32.000 0.00 0.00 32.73 4.75
619 944 5.851720 TGTTCTTGATGATAGGCAGAGATC 58.148 41.667 0.00 0.00 0.00 2.75
734 1071 6.894828 ACGATGTTTAATTGTTGTGGTCTAC 58.105 36.000 0.00 0.00 0.00 2.59
1015 1410 2.766263 ACACATATGCCCGAGAAAGAGA 59.234 45.455 1.58 0.00 0.00 3.10
1227 1646 9.817809 GTACCATTTGTCATTATCTCAAGTAGA 57.182 33.333 0.00 0.00 39.02 2.59
1387 1809 0.320683 GGCCAAAAACATGGGAGCAC 60.321 55.000 0.00 0.00 41.01 4.40
1585 2014 2.021355 ACATGCTCTCACTGCTTAGC 57.979 50.000 0.00 0.00 35.51 3.09
1963 2409 6.707290 TCATACAGTACTTTTGGTGTAGCAT 58.293 36.000 0.00 0.00 0.00 3.79
1980 2432 0.680618 CATTGGCCCAGCAACAAGAA 59.319 50.000 0.00 0.00 0.00 2.52
2140 2627 2.192861 CGACCTGTTGGCTTGCCAA 61.193 57.895 21.59 21.59 36.63 4.52
2297 3012 3.525268 TGCAGTTGATAGCTCGAATCA 57.475 42.857 0.00 0.00 0.00 2.57
2502 6941 1.133513 AGGTTTGTTGTGCATCCTGGA 60.134 47.619 0.00 0.00 33.04 3.86
2633 7104 9.535170 TCTTCTCTAGAAAGGAATTCAGTCTTA 57.465 33.333 7.93 0.00 40.72 2.10
2780 7252 6.761099 TGTTCAGGTGTAAAACTTTTGCTA 57.239 33.333 4.28 0.00 0.00 3.49
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
613 938 8.099537 ACATATGTTGAGTGAACTTTGATCTCT 58.900 33.333 1.41 0.00 35.37 3.10
619 944 6.558771 TCCACATATGTTGAGTGAACTTTG 57.441 37.500 5.37 0.00 35.33 2.77
1387 1809 5.199024 TGTCCAATGGTCATTGTTTCTTG 57.801 39.130 18.70 6.14 44.97 3.02
1963 2409 1.344114 GAATTCTTGTTGCTGGGCCAA 59.656 47.619 8.04 0.00 0.00 4.52
2297 3012 4.626081 GGCGTGTCACAGGTGCCT 62.626 66.667 11.21 0.00 42.44 4.75
2502 6941 8.950210 GGATATCGTCATCAACCAATATGATTT 58.050 33.333 0.00 0.00 35.38 2.17
2780 7252 3.795688 TTTCTTCAGGTTCAGGCATCT 57.204 42.857 0.00 0.00 0.00 2.90


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

AutoCloner maintained by Alex Coulton.