Multiple sequence alignment - TraesCS4B01G007000

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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 TraesCS4B01G007000 chr4B 100.000 5326 0 0 1 5326 4716915 4722240 0.000000e+00 9836
1 TraesCS4B01G007000 chr4B 82.567 2587 397 38 1555 4103 4998681 4996111 0.000000e+00 2230
2 TraesCS4B01G007000 chr4B 82.663 1765 282 20 2353 4105 5196807 5195055 0.000000e+00 1543
3 TraesCS4B01G007000 chr4B 81.594 1782 286 34 2353 4105 5015708 5013940 0.000000e+00 1435
4 TraesCS4B01G007000 chr4B 82.016 1101 170 19 2970 4061 5245911 5244830 0.000000e+00 911
5 TraesCS4B01G007000 chr4B 80.359 1171 193 18 1188 2346 5198031 5196886 0.000000e+00 854
6 TraesCS4B01G007000 chr4B 79.900 1199 178 36 1188 2346 5016962 5015787 0.000000e+00 821
7 TraesCS4B01G007000 chr4B 77.953 1202 185 41 1037 2175 5259287 5258103 0.000000e+00 678
8 TraesCS4B01G007000 chr4B 79.452 949 161 17 1404 2346 5082105 5081185 4.500000e-180 641
9 TraesCS4B01G007000 chr4B 83.359 643 102 3 2353 2994 5081106 5080468 1.650000e-164 590
10 TraesCS4B01G007000 chr4B 81.990 583 99 6 2343 2922 5178331 5177752 1.720000e-134 490
11 TraesCS4B01G007000 chr4B 79.924 523 102 3 1795 2317 5178948 5178429 1.080000e-101 381
12 TraesCS4B01G007000 chr4B 84.539 304 39 7 1219 1517 4998992 4998692 1.450000e-75 294
13 TraesCS4B01G007000 chr4B 85.268 224 29 3 1188 1407 5087689 5087466 1.490000e-55 228
14 TraesCS4B01G007000 chr4B 88.095 84 9 1 4112 4195 5013892 5013810 1.220000e-16 99
15 TraesCS4B01G007000 chr4A 93.849 3918 200 17 672 4562 600915405 600911502 0.000000e+00 5862
16 TraesCS4B01G007000 chr4A 83.871 1767 264 19 2348 4105 601016845 601015091 0.000000e+00 1664
17 TraesCS4B01G007000 chr4A 82.946 1765 277 21 2353 4105 600975487 600973735 0.000000e+00 1570
18 TraesCS4B01G007000 chr4A 80.747 1766 305 22 2353 4105 600930804 600929061 0.000000e+00 1345
19 TraesCS4B01G007000 chr4A 91.134 767 54 12 4569 5326 699257405 699256644 0.000000e+00 1027
20 TraesCS4B01G007000 chr4A 82.409 1154 167 22 1212 2346 600976702 600975566 0.000000e+00 974
21 TraesCS4B01G007000 chr4A 81.581 1189 173 26 1188 2346 601018091 601016919 0.000000e+00 941
22 TraesCS4B01G007000 chr4A 82.793 1017 167 6 2351 3365 601008109 601007099 0.000000e+00 902
23 TraesCS4B01G007000 chr4A 79.951 1222 217 22 1135 2346 601009389 601008186 0.000000e+00 874
24 TraesCS4B01G007000 chr4A 84.562 719 109 2 3387 4105 601007046 601006330 0.000000e+00 712
25 TraesCS4B01G007000 chr4D 91.674 2222 155 10 2353 4562 3840751 3838548 0.000000e+00 3051
26 TraesCS4B01G007000 chr4D 82.485 1787 268 29 2353 4105 3693121 3694896 0.000000e+00 1524
27 TraesCS4B01G007000 chr4D 81.393 1177 167 34 1212 2346 3841996 3840830 0.000000e+00 913
28 TraesCS4B01G007000 chr4D 81.385 1112 179 22 1214 2304 3691896 3693000 0.000000e+00 881
29 TraesCS4B01G007000 chr4D 87.129 303 28 8 269 566 3843497 3843201 3.070000e-87 333
30 TraesCS4B01G007000 chr5A 82.500 1600 248 20 1232 2826 549187624 549189196 0.000000e+00 1375
31 TraesCS4B01G007000 chr6B 92.593 756 43 8 4582 5326 66678228 66678981 0.000000e+00 1074
32 TraesCS4B01G007000 chr6B 91.432 782 45 10 4566 5326 666389785 666389005 0.000000e+00 1053
33 TraesCS4B01G007000 chr6B 90.613 767 52 14 4569 5326 547575292 547574537 0.000000e+00 1000
34 TraesCS4B01G007000 chr6B 90.415 772 52 15 4565 5326 515553596 515554355 0.000000e+00 996
35 TraesCS4B01G007000 chr5B 91.741 787 39 14 4563 5326 491431447 491432230 0.000000e+00 1070
36 TraesCS4B01G007000 chr5B 92.198 769 33 14 4582 5326 437125441 437126206 0.000000e+00 1062
37 TraesCS4B01G007000 chr7B 91.635 789 33 15 4567 5326 646399365 646398581 0.000000e+00 1061
38 TraesCS4B01G007000 chr1B 91.406 768 47 12 4563 5325 668038248 668039001 0.000000e+00 1035
39 TraesCS4B01G007000 chr6A 89.080 174 19 0 1344 1517 609573407 609573580 3.230000e-52 217


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 TraesCS4B01G007000 chr4B 4716915 4722240 5325 False 9836.000000 9836 100.000000 1 5326 1 chr4B.!!$F1 5325
1 TraesCS4B01G007000 chr4B 4996111 4998992 2881 True 1262.000000 2230 83.553000 1219 4103 2 chr4B.!!$R4 2884
2 TraesCS4B01G007000 chr4B 5195055 5198031 2976 True 1198.500000 1543 81.511000 1188 4105 2 chr4B.!!$R8 2917
3 TraesCS4B01G007000 chr4B 5244830 5245911 1081 True 911.000000 911 82.016000 2970 4061 1 chr4B.!!$R2 1091
4 TraesCS4B01G007000 chr4B 5013810 5016962 3152 True 785.000000 1435 83.196333 1188 4195 3 chr4B.!!$R5 3007
5 TraesCS4B01G007000 chr4B 5258103 5259287 1184 True 678.000000 678 77.953000 1037 2175 1 chr4B.!!$R3 1138
6 TraesCS4B01G007000 chr4B 5080468 5082105 1637 True 615.500000 641 81.405500 1404 2994 2 chr4B.!!$R6 1590
7 TraesCS4B01G007000 chr4B 5177752 5178948 1196 True 435.500000 490 80.957000 1795 2922 2 chr4B.!!$R7 1127
8 TraesCS4B01G007000 chr4A 600911502 600915405 3903 True 5862.000000 5862 93.849000 672 4562 1 chr4A.!!$R1 3890
9 TraesCS4B01G007000 chr4A 600929061 600930804 1743 True 1345.000000 1345 80.747000 2353 4105 1 chr4A.!!$R2 1752
10 TraesCS4B01G007000 chr4A 601015091 601018091 3000 True 1302.500000 1664 82.726000 1188 4105 2 chr4A.!!$R6 2917
11 TraesCS4B01G007000 chr4A 600973735 600976702 2967 True 1272.000000 1570 82.677500 1212 4105 2 chr4A.!!$R4 2893
12 TraesCS4B01G007000 chr4A 699256644 699257405 761 True 1027.000000 1027 91.134000 4569 5326 1 chr4A.!!$R3 757
13 TraesCS4B01G007000 chr4A 601006330 601009389 3059 True 829.333333 902 82.435333 1135 4105 3 chr4A.!!$R5 2970
14 TraesCS4B01G007000 chr4D 3838548 3843497 4949 True 1432.333333 3051 86.732000 269 4562 3 chr4D.!!$R1 4293
15 TraesCS4B01G007000 chr4D 3691896 3694896 3000 False 1202.500000 1524 81.935000 1214 4105 2 chr4D.!!$F1 2891
16 TraesCS4B01G007000 chr5A 549187624 549189196 1572 False 1375.000000 1375 82.500000 1232 2826 1 chr5A.!!$F1 1594
17 TraesCS4B01G007000 chr6B 66678228 66678981 753 False 1074.000000 1074 92.593000 4582 5326 1 chr6B.!!$F1 744
18 TraesCS4B01G007000 chr6B 666389005 666389785 780 True 1053.000000 1053 91.432000 4566 5326 1 chr6B.!!$R2 760
19 TraesCS4B01G007000 chr6B 547574537 547575292 755 True 1000.000000 1000 90.613000 4569 5326 1 chr6B.!!$R1 757
20 TraesCS4B01G007000 chr6B 515553596 515554355 759 False 996.000000 996 90.415000 4565 5326 1 chr6B.!!$F2 761
21 TraesCS4B01G007000 chr5B 491431447 491432230 783 False 1070.000000 1070 91.741000 4563 5326 1 chr5B.!!$F2 763
22 TraesCS4B01G007000 chr5B 437125441 437126206 765 False 1062.000000 1062 92.198000 4582 5326 1 chr5B.!!$F1 744
23 TraesCS4B01G007000 chr7B 646398581 646399365 784 True 1061.000000 1061 91.635000 4567 5326 1 chr7B.!!$R1 759
24 TraesCS4B01G007000 chr1B 668038248 668039001 753 False 1035.000000 1035 91.406000 4563 5325 1 chr1B.!!$F1 762


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
143 144 0.027979 CTGGTGTGTGTTTGTGCGAG 59.972 55.0 0.00 0.0 0.00 5.03 F
193 194 0.036765 CGGTTAGTGGCTGGCTGTTA 60.037 55.0 2.00 0.0 0.00 2.41 F
319 320 0.173481 ATGATGCGACGCTGTACTGT 59.827 50.0 22.08 0.0 0.00 3.55 F
474 478 0.251916 TTCCCGTCACATGGCTTAGG 59.748 55.0 0.00 0.0 0.00 2.69 F
647 651 0.321346 TGCATGACGGTGTGATGAGT 59.679 50.0 0.00 0.0 28.91 3.41 F
648 652 0.723414 GCATGACGGTGTGATGAGTG 59.277 55.0 0.00 0.0 28.91 3.51 F
2590 3840 0.026803 GCTTAGATGGCAAACTCGCG 59.973 55.0 0.00 0.0 0.00 5.87 F
2794 4052 0.831307 AGTTCCACGGCTATTCCCTC 59.169 55.0 0.00 0.0 0.00 4.30 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1155 1176 0.252881 AGCAGATCCCACTCCAGGAA 60.253 55.000 0.00 0.00 36.85 3.36 R
1185 1227 1.063717 AGGGAACGGCAATGGAATGAT 60.064 47.619 0.00 0.00 0.00 2.45 R
1304 2342 1.227089 CCGGAATCAGACGGCTCTG 60.227 63.158 0.00 0.00 43.96 3.35 R
2406 3656 1.300620 TTCCTTCACGAGCACACCG 60.301 57.895 0.00 0.00 0.00 4.94 R
2498 3748 4.302559 AGTCTAAATGGAGGAACCCAAC 57.697 45.455 0.00 0.00 40.04 3.77 R
2794 4052 9.995003 AGAGAGATCCAAGCTTGTTATATTTAG 57.005 33.333 24.35 6.47 0.00 1.85 R
3829 5128 0.464036 TGGACGACACTTTGCTCTGT 59.536 50.000 0.00 0.00 0.00 3.41 R
4879 6275 0.180406 CAGCGCACCCCCTTTAGTAT 59.820 55.000 11.47 0.00 0.00 2.12 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)



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AutoCloner maintained by Alex Coulton.