Multiple sequence alignment - TraesCS6D01G065200

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 TraesCS6D01G065200 chr6D 100.000 5657 0 0 1 5657 31772197 31766541 0.000000e+00 10447.0
1 TraesCS6D01G065200 chr6D 99.188 5663 32 5 1 5657 23442074 23436420 0.000000e+00 10190.0
2 TraesCS6D01G065200 chr6D 84.388 1928 260 36 1628 3534 31754447 31752540 0.000000e+00 1855.0
3 TraesCS6D01G065200 chr6D 80.611 1145 198 18 3608 4745 31752436 31751309 0.000000e+00 863.0
4 TraesCS6D01G065200 chr6D 79.423 520 55 24 828 1314 23425591 23425091 2.540000e-83 320.0
5 TraesCS6D01G065200 chr6D 77.480 635 72 36 828 1423 31755579 31754977 1.180000e-81 315.0
6 TraesCS6D01G065200 chr6A 89.401 4359 335 61 455 4745 36254066 36249767 0.000000e+00 5373.0
7 TraesCS6D01G065200 chr6A 83.714 1928 269 33 1625 3536 36108985 36107087 0.000000e+00 1779.0
8 TraesCS6D01G065200 chr6A 85.034 147 22 0 1174 1320 36056389 36056243 3.530000e-32 150.0
9 TraesCS6D01G065200 chr6A 95.652 92 3 1 179 270 36254393 36254303 4.570000e-31 147.0
10 TraesCS6D01G065200 chr6B 89.772 2855 247 25 1897 4741 67410980 67408161 0.000000e+00 3613.0
11 TraesCS6D01G065200 chr6B 89.443 2908 227 45 701 3540 66992872 66989977 0.000000e+00 3596.0
12 TraesCS6D01G065200 chr6B 90.773 2265 138 26 805 3028 68748054 68750288 0.000000e+00 2959.0
13 TraesCS6D01G065200 chr6B 90.121 2308 154 31 811 3075 68784088 68781812 0.000000e+00 2931.0
14 TraesCS6D01G065200 chr6B 88.517 2064 149 47 701 2688 67259768 67257717 0.000000e+00 2418.0
15 TraesCS6D01G065200 chr6B 88.273 1697 156 20 3059 4745 68781015 68779352 0.000000e+00 1991.0
16 TraesCS6D01G065200 chr6B 87.740 1664 165 20 3089 4742 68750713 68752347 0.000000e+00 1906.0
17 TraesCS6D01G065200 chr6B 83.497 1933 267 40 1628 3540 67131087 67129187 0.000000e+00 1755.0
18 TraesCS6D01G065200 chr6B 83.316 1936 268 43 1628 3540 67323612 67321709 0.000000e+00 1735.0
19 TraesCS6D01G065200 chr6B 86.879 1410 102 35 475 1839 67412350 67410979 0.000000e+00 1502.0
20 TraesCS6D01G065200 chr6B 88.474 1206 127 8 3547 4745 66989936 66988736 0.000000e+00 1447.0
21 TraesCS6D01G065200 chr6B 90.319 847 79 2 2695 3540 67229122 67228278 0.000000e+00 1107.0
22 TraesCS6D01G065200 chr6B 81.627 1143 187 16 3608 4742 67129088 67127961 0.000000e+00 926.0
23 TraesCS6D01G065200 chr6B 80.840 1143 196 16 3608 4742 67321610 67320483 0.000000e+00 876.0
24 TraesCS6D01G065200 chr6B 84.656 378 27 11 455 814 68745646 68746010 1.170000e-91 348.0
25 TraesCS6D01G065200 chr6B 84.656 378 27 11 455 814 68786946 68786582 1.170000e-91 348.0
26 TraesCS6D01G065200 chr6B 83.978 362 22 14 65 396 68745187 68745542 1.180000e-81 315.0
27 TraesCS6D01G065200 chr6B 83.978 362 22 14 65 396 68787405 68787050 1.180000e-81 315.0
28 TraesCS6D01G065200 chr6B 81.004 279 38 10 1153 1423 67131875 67131604 2.070000e-49 207.0
29 TraesCS6D01G065200 chr6B 82.843 204 21 5 779 970 67261618 67261417 2.710000e-38 171.0
30 TraesCS6D01G065200 chr6B 79.817 218 28 8 955 1157 67132132 67131916 1.640000e-30 145.0
31 TraesCS6D01G065200 chr6B 92.683 82 6 0 119 200 67418636 67418555 9.960000e-23 119.0
32 TraesCS6D01G065200 chr6B 88.542 96 9 2 295 388 67418103 67418008 1.290000e-21 115.0
33 TraesCS6D01G065200 chr6B 96.154 52 2 0 65 116 67458863 67458812 1.010000e-12 86.1
34 TraesCS6D01G065200 chr5A 92.857 910 64 1 4748 5657 41459347 41460255 0.000000e+00 1319.0
35 TraesCS6D01G065200 chr2D 91.816 892 48 8 4777 5657 491188926 491189803 0.000000e+00 1219.0
36 TraesCS6D01G065200 chr2D 89.729 516 42 4 5152 5657 12139887 12140401 0.000000e+00 649.0
37 TraesCS6D01G065200 chr2D 83.669 447 58 12 3093 3534 579387985 579388421 1.900000e-109 407.0
38 TraesCS6D01G065200 chr4D 92.121 863 65 2 4746 5608 3627929 3627070 0.000000e+00 1214.0
39 TraesCS6D01G065200 chr1B 89.221 937 79 7 4738 5657 128021827 128022758 0.000000e+00 1151.0
40 TraesCS6D01G065200 chr3B 90.603 862 70 8 4748 5608 667116505 667115654 0.000000e+00 1133.0
41 TraesCS6D01G065200 chrUn 80.791 1213 190 35 1630 2825 323636793 323637979 0.000000e+00 909.0
42 TraesCS6D01G065200 chrUn 81.623 419 62 13 1630 2041 100620300 100620710 3.270000e-87 333.0
43 TraesCS6D01G065200 chrUn 83.750 160 24 2 1156 1314 323636211 323636369 3.530000e-32 150.0
44 TraesCS6D01G065200 chrUn 83.750 160 24 2 1156 1314 323668068 323668226 3.530000e-32 150.0
45 TraesCS6D01G065200 chrUn 83.750 160 24 2 1156 1314 329024279 329024437 3.530000e-32 150.0
46 TraesCS6D01G065200 chrUn 83.750 160 24 2 1156 1314 329103642 329103800 3.530000e-32 150.0
47 TraesCS6D01G065200 chrUn 83.750 160 24 2 1156 1314 361926293 361926451 3.530000e-32 150.0
48 TraesCS6D01G065200 chrUn 85.816 141 20 0 1174 1314 478140650 478140510 3.530000e-32 150.0
49 TraesCS6D01G065200 chrUn 83.125 160 25 2 1156 1314 100489821 100489979 1.640000e-30 145.0
50 TraesCS6D01G065200 chr2B 86.347 813 105 6 4731 5538 161895358 161896169 0.000000e+00 881.0
51 TraesCS6D01G065200 chr2B 85.276 815 109 10 4731 5538 161918784 161919594 0.000000e+00 830.0
52 TraesCS6D01G065200 chr5B 86.146 794 102 8 4749 5538 477959915 477959126 0.000000e+00 850.0
53 TraesCS6D01G065200 chr1A 85.967 791 103 6 4749 5537 555932264 555931480 0.000000e+00 839.0
54 TraesCS6D01G065200 chr2A 82.526 475 67 12 3066 3534 717138766 717139230 2.450000e-108 403.0
55 TraesCS6D01G065200 chr7A 95.918 49 2 0 5559 5607 566049199 566049151 4.700000e-11 80.5


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 TraesCS6D01G065200 chr6D 31766541 31772197 5656 True 10447.00 10447 100.000000 1 5657 1 chr6D.!!$R3 5656
1 TraesCS6D01G065200 chr6D 23436420 23442074 5654 True 10190.00 10190 99.188000 1 5657 1 chr6D.!!$R2 5656
2 TraesCS6D01G065200 chr6D 31751309 31755579 4270 True 1011.00 1855 80.826333 828 4745 3 chr6D.!!$R4 3917
3 TraesCS6D01G065200 chr6D 23425091 23425591 500 True 320.00 320 79.423000 828 1314 1 chr6D.!!$R1 486
4 TraesCS6D01G065200 chr6A 36249767 36254393 4626 True 2760.00 5373 92.526500 179 4745 2 chr6A.!!$R3 4566
5 TraesCS6D01G065200 chr6A 36107087 36108985 1898 True 1779.00 1779 83.714000 1625 3536 1 chr6A.!!$R2 1911
6 TraesCS6D01G065200 chr6B 67408161 67412350 4189 True 2557.50 3613 88.325500 475 4741 2 chr6B.!!$R7 4266
7 TraesCS6D01G065200 chr6B 66988736 66992872 4136 True 2521.50 3596 88.958500 701 4745 2 chr6B.!!$R3 4044
8 TraesCS6D01G065200 chr6B 68779352 68787405 8053 True 1396.25 2931 86.757000 65 4745 4 chr6B.!!$R9 4680
9 TraesCS6D01G065200 chr6B 68745187 68752347 7160 False 1382.00 2959 86.786750 65 4742 4 chr6B.!!$F1 4677
10 TraesCS6D01G065200 chr6B 67320483 67323612 3129 True 1305.50 1735 82.078000 1628 4742 2 chr6B.!!$R6 3114
11 TraesCS6D01G065200 chr6B 67257717 67261618 3901 True 1294.50 2418 85.680000 701 2688 2 chr6B.!!$R5 1987
12 TraesCS6D01G065200 chr6B 67228278 67229122 844 True 1107.00 1107 90.319000 2695 3540 1 chr6B.!!$R1 845
13 TraesCS6D01G065200 chr6B 67127961 67132132 4171 True 758.25 1755 81.486250 955 4742 4 chr6B.!!$R4 3787
14 TraesCS6D01G065200 chr5A 41459347 41460255 908 False 1319.00 1319 92.857000 4748 5657 1 chr5A.!!$F1 909
15 TraesCS6D01G065200 chr2D 491188926 491189803 877 False 1219.00 1219 91.816000 4777 5657 1 chr2D.!!$F2 880
16 TraesCS6D01G065200 chr2D 12139887 12140401 514 False 649.00 649 89.729000 5152 5657 1 chr2D.!!$F1 505
17 TraesCS6D01G065200 chr4D 3627070 3627929 859 True 1214.00 1214 92.121000 4746 5608 1 chr4D.!!$R1 862
18 TraesCS6D01G065200 chr1B 128021827 128022758 931 False 1151.00 1151 89.221000 4738 5657 1 chr1B.!!$F1 919
19 TraesCS6D01G065200 chr3B 667115654 667116505 851 True 1133.00 1133 90.603000 4748 5608 1 chr3B.!!$R1 860
20 TraesCS6D01G065200 chrUn 323636211 323637979 1768 False 529.50 909 82.270500 1156 2825 2 chrUn.!!$F7 1669
21 TraesCS6D01G065200 chr2B 161895358 161896169 811 False 881.00 881 86.347000 4731 5538 1 chr2B.!!$F1 807
22 TraesCS6D01G065200 chr2B 161918784 161919594 810 False 830.00 830 85.276000 4731 5538 1 chr2B.!!$F2 807
23 TraesCS6D01G065200 chr5B 477959126 477959915 789 True 850.00 850 86.146000 4749 5538 1 chr5B.!!$R1 789
24 TraesCS6D01G065200 chr1A 555931480 555932264 784 True 839.00 839 85.967000 4749 5537 1 chr1A.!!$R1 788

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
419 452 2.959030 TCTCTCTCTCTCTCTCTCTCCG 59.041 54.545 0.00 0.00 0.00 4.63 F
1202 5020 1.303236 CACCGGTGGCCAGAAATGA 60.303 57.895 27.57 0.00 0.00 2.57 F
4060 9239 0.318441 TTGTCACTTCAGGAGCTCCG 59.682 55.000 26.95 20.71 42.08 4.63 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
3563 8736 5.424252 AGATAGGAACATCACGGAACCTTAA 59.576 40.000 0.0 0.0 0.0 1.85 R
4149 9328 2.848694 TCCCAGAGCCTCATGATCTTTT 59.151 45.455 0.0 0.0 0.0 2.27 R
5298 10533 2.440247 CCTTGGGGGCGTCATTCC 60.440 66.667 0.0 0.0 0.0 3.01 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
397 430 3.885297 CCAACCATCTCTCTCTCTCTCTC 59.115 52.174 0.00 0.00 0.00 3.20
398 431 4.385643 CCAACCATCTCTCTCTCTCTCTCT 60.386 50.000 0.00 0.00 0.00 3.10
399 432 4.696479 ACCATCTCTCTCTCTCTCTCTC 57.304 50.000 0.00 0.00 0.00 3.20
400 433 4.302067 ACCATCTCTCTCTCTCTCTCTCT 58.698 47.826 0.00 0.00 0.00 3.10
401 434 4.346418 ACCATCTCTCTCTCTCTCTCTCTC 59.654 50.000 0.00 0.00 0.00 3.20
402 435 4.592351 CCATCTCTCTCTCTCTCTCTCTCT 59.408 50.000 0.00 0.00 0.00 3.10
419 452 2.959030 TCTCTCTCTCTCTCTCTCTCCG 59.041 54.545 0.00 0.00 0.00 4.63
1202 5020 1.303236 CACCGGTGGCCAGAAATGA 60.303 57.895 27.57 0.00 0.00 2.57
1842 6117 5.776716 TGTGCAGATCTCATCCATAGTGATA 59.223 40.000 0.00 0.00 0.00 2.15
4060 9239 0.318441 TTGTCACTTCAGGAGCTCCG 59.682 55.000 26.95 20.71 42.08 4.63
4149 9328 1.607801 CGTGTCATCTCCTGCCCTGA 61.608 60.000 0.00 0.00 0.00 3.86
4866 10085 4.141574 ACAACAGTAAGAGTAAAGCCACCA 60.142 41.667 0.00 0.00 0.00 4.17
5298 10533 1.467543 CGATCACGTGTGTACCTCCAG 60.468 57.143 16.51 0.00 34.56 3.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
397 430 3.005261 CGGAGAGAGAGAGAGAGAGAGAG 59.995 56.522 0.00 0.0 0.00 3.20
398 431 2.959030 CGGAGAGAGAGAGAGAGAGAGA 59.041 54.545 0.00 0.0 0.00 3.10
399 432 2.546795 GCGGAGAGAGAGAGAGAGAGAG 60.547 59.091 0.00 0.0 0.00 3.20
400 433 1.412710 GCGGAGAGAGAGAGAGAGAGA 59.587 57.143 0.00 0.0 0.00 3.10
401 434 1.869754 CGCGGAGAGAGAGAGAGAGAG 60.870 61.905 0.00 0.0 0.00 3.20
402 435 0.104120 CGCGGAGAGAGAGAGAGAGA 59.896 60.000 0.00 0.0 0.00 3.10
3563 8736 5.424252 AGATAGGAACATCACGGAACCTTAA 59.576 40.000 0.00 0.0 0.00 1.85
4060 9239 7.031372 TGAAGAAAAGATGCATGAATACAAGC 58.969 34.615 2.46 0.0 40.52 4.01
4149 9328 2.848694 TCCCAGAGCCTCATGATCTTTT 59.151 45.455 0.00 0.0 0.00 2.27
5298 10533 2.440247 CCTTGGGGGCGTCATTCC 60.440 66.667 0.00 0.0 0.00 3.01


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

AutoCloner maintained by Alex Coulton.