Multiple sequence alignment - TraesCS6B01G058800

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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 TraesCS6B01G058800 chr6B 100.000 2585 0 0 1 2585 38941070 38943654 0 4774
1 TraesCS6B01G058800 chr6B 94.389 802 33 5 1 791 38934824 38935624 0 1221
2 TraesCS6B01G058800 chr6B 94.382 801 34 9 1 791 120700852 120700053 0 1219
3 TraesCS6B01G058800 chr6B 94.271 803 37 9 3 797 161693804 161693003 0 1219
4 TraesCS6B01G058800 chr6B 94.375 800 35 9 1 791 688905166 688904368 0 1219
5 TraesCS6B01G058800 chr6B 95.362 733 29 4 1856 2585 217822377 217823107 0 1160
6 TraesCS6B01G058800 chr6B 94.945 732 35 2 1856 2585 617056191 617055460 0 1146
7 TraesCS6B01G058800 chr5B 92.138 954 64 7 916 1861 517572335 517571385 0 1336
8 TraesCS6B01G058800 chr5B 93.092 912 57 4 948 1858 297042230 297043136 0 1330
9 TraesCS6B01G058800 chr5B 92.787 915 59 5 948 1858 56361543 56362454 0 1317
10 TraesCS6B01G058800 chr5B 95.212 731 33 2 1856 2585 470226866 470227595 0 1155
11 TraesCS6B01G058800 chr3D 92.733 922 50 10 948 1864 486147185 486146276 0 1315
12 TraesCS6B01G058800 chr5D 92.857 896 58 4 966 1860 397098263 397099153 0 1295
13 TraesCS6B01G058800 chr5D 92.291 921 56 9 948 1863 432179390 432178480 0 1293
14 TraesCS6B01G058800 chr5D 89.980 998 71 17 873 1858 84452213 84453193 0 1262
15 TraesCS6B01G058800 chr5D 95.622 731 31 1 1856 2585 236187262 236187992 0 1171
16 TraesCS6B01G058800 chr7A 93.441 869 53 4 991 1858 700256754 700257619 0 1286
17 TraesCS6B01G058800 chr3B 95.113 798 31 8 1 791 637793832 637794628 0 1251
18 TraesCS6B01G058800 chr7D 91.575 914 57 12 956 1858 582089014 582089918 0 1243
19 TraesCS6B01G058800 chr7B 94.875 800 30 6 3 791 614266621 614265822 0 1240
20 TraesCS6B01G058800 chr7B 94.598 796 39 4 3 794 686629276 686630071 0 1229
21 TraesCS6B01G058800 chr4B 94.730 797 35 4 3 793 85070415 85071210 0 1232
22 TraesCS6B01G058800 chr4B 95.486 731 32 1 1856 2585 176318721 176317991 0 1166
23 TraesCS6B01G058800 chr1B 94.500 800 34 8 1 791 538909164 538909962 0 1225
24 TraesCS6B01G058800 chr1B 96.170 731 25 3 1856 2585 611793435 611794163 0 1192
25 TraesCS6B01G058800 chr1B 95.486 731 32 1 1856 2585 68065358 68064628 0 1166
26 TraesCS6B01G058800 chr4A 95.075 731 34 2 1856 2585 717720303 717719574 0 1149
27 TraesCS6B01G058800 chrUn 95.062 729 35 1 1858 2585 379625261 379625989 0 1146


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 TraesCS6B01G058800 chr6B 38941070 38943654 2584 False 4774 4774 100.000 1 2585 1 chr6B.!!$F2 2584
1 TraesCS6B01G058800 chr6B 38934824 38935624 800 False 1221 1221 94.389 1 791 1 chr6B.!!$F1 790
2 TraesCS6B01G058800 chr6B 120700053 120700852 799 True 1219 1219 94.382 1 791 1 chr6B.!!$R1 790
3 TraesCS6B01G058800 chr6B 161693003 161693804 801 True 1219 1219 94.271 3 797 1 chr6B.!!$R2 794
4 TraesCS6B01G058800 chr6B 688904368 688905166 798 True 1219 1219 94.375 1 791 1 chr6B.!!$R4 790
5 TraesCS6B01G058800 chr6B 217822377 217823107 730 False 1160 1160 95.362 1856 2585 1 chr6B.!!$F3 729
6 TraesCS6B01G058800 chr6B 617055460 617056191 731 True 1146 1146 94.945 1856 2585 1 chr6B.!!$R3 729
7 TraesCS6B01G058800 chr5B 517571385 517572335 950 True 1336 1336 92.138 916 1861 1 chr5B.!!$R1 945
8 TraesCS6B01G058800 chr5B 297042230 297043136 906 False 1330 1330 93.092 948 1858 1 chr5B.!!$F2 910
9 TraesCS6B01G058800 chr5B 56361543 56362454 911 False 1317 1317 92.787 948 1858 1 chr5B.!!$F1 910
10 TraesCS6B01G058800 chr5B 470226866 470227595 729 False 1155 1155 95.212 1856 2585 1 chr5B.!!$F3 729
11 TraesCS6B01G058800 chr3D 486146276 486147185 909 True 1315 1315 92.733 948 1864 1 chr3D.!!$R1 916
12 TraesCS6B01G058800 chr5D 397098263 397099153 890 False 1295 1295 92.857 966 1860 1 chr5D.!!$F3 894
13 TraesCS6B01G058800 chr5D 432178480 432179390 910 True 1293 1293 92.291 948 1863 1 chr5D.!!$R1 915
14 TraesCS6B01G058800 chr5D 84452213 84453193 980 False 1262 1262 89.980 873 1858 1 chr5D.!!$F1 985
15 TraesCS6B01G058800 chr5D 236187262 236187992 730 False 1171 1171 95.622 1856 2585 1 chr5D.!!$F2 729
16 TraesCS6B01G058800 chr7A 700256754 700257619 865 False 1286 1286 93.441 991 1858 1 chr7A.!!$F1 867
17 TraesCS6B01G058800 chr3B 637793832 637794628 796 False 1251 1251 95.113 1 791 1 chr3B.!!$F1 790
18 TraesCS6B01G058800 chr7D 582089014 582089918 904 False 1243 1243 91.575 956 1858 1 chr7D.!!$F1 902
19 TraesCS6B01G058800 chr7B 614265822 614266621 799 True 1240 1240 94.875 3 791 1 chr7B.!!$R1 788
20 TraesCS6B01G058800 chr7B 686629276 686630071 795 False 1229 1229 94.598 3 794 1 chr7B.!!$F1 791
21 TraesCS6B01G058800 chr4B 85070415 85071210 795 False 1232 1232 94.730 3 793 1 chr4B.!!$F1 790
22 TraesCS6B01G058800 chr4B 176317991 176318721 730 True 1166 1166 95.486 1856 2585 1 chr4B.!!$R1 729
23 TraesCS6B01G058800 chr1B 538909164 538909962 798 False 1225 1225 94.500 1 791 1 chr1B.!!$F1 790
24 TraesCS6B01G058800 chr1B 611793435 611794163 728 False 1192 1192 96.170 1856 2585 1 chr1B.!!$F2 729
25 TraesCS6B01G058800 chr1B 68064628 68065358 730 True 1166 1166 95.486 1856 2585 1 chr1B.!!$R1 729
26 TraesCS6B01G058800 chr4A 717719574 717720303 729 True 1149 1149 95.075 1856 2585 1 chr4A.!!$R1 729
27 TraesCS6B01G058800 chrUn 379625261 379625989 728 False 1146 1146 95.062 1858 2585 1 chrUn.!!$F1 727

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
451 456 0.531090 CGTTGGTTTCACGTCAGGGA 60.531 55.0 0.0 0.0 0.0 4.20 F
799 819 0.597637 GAGATGTATCACCCCGCACG 60.598 60.0 0.0 0.0 0.0 5.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1381 1426 0.038251 TCACGCTTCCAGTAGTGCTG 60.038 55.0 0.47 0.47 44.63 4.41 R
2561 2635 1.124780 TGGAAGTCCGGTCTTTGACA 58.875 50.0 15.23 11.71 39.43 3.58 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
113 114 5.694006 CGTAAAAGAGATGAGGATGGTGATC 59.306 44.000 0.00 0.00 0.00 2.92
200 201 2.558575 CCACCAAGAGAGAGGAGGAGAA 60.559 54.545 0.00 0.00 37.80 2.87
223 224 1.463214 TCCCCCTTGTGCTTCCTCA 60.463 57.895 0.00 0.00 0.00 3.86
235 236 2.241941 TGCTTCCTCATCCATGGCTTTA 59.758 45.455 6.96 0.00 0.00 1.85
258 260 1.839994 CTCTGGTCCTTGGCCTTCATA 59.160 52.381 3.32 0.00 0.00 2.15
282 284 1.535202 GATGGCCCCTCCGAGATCT 60.535 63.158 0.00 0.00 37.80 2.75
451 456 0.531090 CGTTGGTTTCACGTCAGGGA 60.531 55.000 0.00 0.00 0.00 4.20
631 647 8.117813 TCATTTGGTATCCCTTTTCTGTAAAC 57.882 34.615 0.00 0.00 0.00 2.01
794 814 1.485066 ACGTTGGAGATGTATCACCCC 59.515 52.381 5.98 0.02 36.82 4.95
795 815 1.538204 CGTTGGAGATGTATCACCCCG 60.538 57.143 5.98 5.00 36.82 5.73
797 817 0.689412 TGGAGATGTATCACCCCGCA 60.689 55.000 5.98 0.00 36.82 5.69
799 819 0.597637 GAGATGTATCACCCCGCACG 60.598 60.000 0.00 0.00 0.00 5.34
800 820 2.203015 ATGTATCACCCCGCACGC 60.203 61.111 0.00 0.00 0.00 5.34
801 821 3.750373 ATGTATCACCCCGCACGCC 62.750 63.158 0.00 0.00 0.00 5.68
872 892 3.869272 CGCAGCAATGCCCGTCTC 61.869 66.667 0.00 0.00 0.00 3.36
873 893 3.512516 GCAGCAATGCCCGTCTCC 61.513 66.667 0.00 0.00 0.00 3.71
874 894 3.197790 CAGCAATGCCCGTCTCCG 61.198 66.667 0.00 0.00 0.00 4.63
875 895 3.706373 AGCAATGCCCGTCTCCGT 61.706 61.111 0.00 0.00 0.00 4.69
876 896 3.195698 GCAATGCCCGTCTCCGTC 61.196 66.667 0.00 0.00 0.00 4.79
877 897 2.511600 CAATGCCCGTCTCCGTCC 60.512 66.667 0.00 0.00 0.00 4.79
878 898 4.143333 AATGCCCGTCTCCGTCCG 62.143 66.667 0.00 0.00 0.00 4.79
946 966 1.963855 CACCGACATCCCGCAACAA 60.964 57.895 0.00 0.00 0.00 2.83
960 985 2.563798 AACAACGCCCGACTCCGTA 61.564 57.895 0.00 0.00 36.56 4.02
1014 1055 3.564027 CCGATGGCGCCGAAGAAC 61.564 66.667 23.90 8.03 35.83 3.01
1073 1114 2.686106 GCCCTCCGGTAACTGGGA 60.686 66.667 18.19 0.00 40.35 4.37
1084 1125 2.304761 GGTAACTGGGATGTGGAGTTCA 59.695 50.000 0.00 0.00 32.27 3.18
1119 1160 0.748005 GTTGGTGGCTCGGCACATAT 60.748 55.000 22.48 0.00 0.00 1.78
1126 1167 1.758440 GCTCGGCACATATCCCTCCA 61.758 60.000 0.00 0.00 0.00 3.86
1226 1268 4.509737 GAGTCGGGTGGTAGCGGC 62.510 72.222 0.00 0.00 0.00 6.53
1267 1309 3.251479 TCAACATGAAGGAGATCACGG 57.749 47.619 0.00 0.00 30.82 4.94
1284 1329 1.340248 ACGGCGAAGAAGAAGAAGACA 59.660 47.619 16.62 0.00 0.00 3.41
1348 1393 2.690778 GCGATGGCGAGGTTTGCTT 61.691 57.895 0.00 0.00 40.82 3.91
1381 1426 1.141019 TACGTCCAAGCCGAGATGC 59.859 57.895 0.00 0.00 0.00 3.91
1447 1496 0.759436 GAAGGAGGATGAGGCCGGTA 60.759 60.000 1.90 0.00 0.00 4.02
1522 1592 1.293683 GGAGGAGGAGGAGGAGGAGT 61.294 65.000 0.00 0.00 0.00 3.85
1545 1615 2.758089 CGACGACCCGACGAAGGAT 61.758 63.158 5.42 0.00 46.01 3.24
1872 1944 7.038302 TGGAGATGCTCTTAGAAGGACTTAAAA 60.038 37.037 0.00 0.00 0.00 1.52
2240 2314 6.636562 ATCAATTCAATGAGAATGCTCTCC 57.363 37.500 1.43 0.00 46.09 3.71
2248 2322 4.338379 TGAGAATGCTCTCCTCATCATG 57.662 45.455 1.43 0.00 46.67 3.07
2306 2380 2.059786 CCCTTCGCCATGGCCAAAT 61.060 57.895 30.79 0.00 37.98 2.32
2553 2627 0.482446 TTCCACAAGGCCATGTCCTT 59.518 50.000 11.47 1.13 46.86 3.36
2561 2635 2.133520 AGGCCATGTCCTTCATCATCT 58.866 47.619 5.01 0.00 34.09 2.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
17 18 9.387257 TGCTTTATGCTACATATTATGATCCAG 57.613 33.333 10.62 3.62 43.37 3.86
113 114 5.503520 CGTCTTCATCAACATCACCATCATG 60.504 44.000 0.00 0.00 0.00 3.07
200 201 0.402121 GAAGCACAAGGGGGAGAACT 59.598 55.000 0.00 0.00 0.00 3.01
223 224 1.496429 CCAGAGGGTAAAGCCATGGAT 59.504 52.381 18.40 6.18 38.46 3.41
258 260 2.446848 CGGAGGGGCCATCATCACT 61.447 63.158 21.12 0.00 35.94 3.41
282 284 3.089874 CCGGAGGCCATGGAGGAA 61.090 66.667 18.40 0.00 46.14 3.36
631 647 5.719173 TCTGTTTTCTCCTTGTTTTTGTGG 58.281 37.500 0.00 0.00 0.00 4.17
933 953 3.361977 GGCGTTGTTGCGGGATGT 61.362 61.111 0.00 0.00 35.06 3.06
943 963 2.985282 TACGGAGTCGGGCGTTGT 60.985 61.111 2.48 0.00 43.93 3.32
984 1009 3.532155 ATCGGAGAGCGGTGGAGC 61.532 66.667 0.00 0.00 43.63 4.70
987 1012 4.899239 GCCATCGGAGAGCGGTGG 62.899 72.222 0.00 0.00 43.63 4.61
1108 1149 0.034059 GTGGAGGGATATGTGCCGAG 59.966 60.000 0.00 0.00 41.45 4.63
1116 1157 0.471971 CCTCGTGGGTGGAGGGATAT 60.472 60.000 0.00 0.00 45.97 1.63
1226 1268 2.483745 CCTGCAGCACAAGCATCG 59.516 61.111 8.66 0.00 45.49 3.84
1267 1309 5.659048 TTCTTTGTCTTCTTCTTCTTCGC 57.341 39.130 0.00 0.00 0.00 4.70
1284 1329 1.219522 CGACAACCGACGGCTTCTTT 61.220 55.000 15.39 0.00 41.76 2.52
1348 1393 2.125326 CGTACTCCGGATGCTCCCA 61.125 63.158 3.57 0.00 31.13 4.37
1381 1426 0.038251 TCACGCTTCCAGTAGTGCTG 60.038 55.000 0.47 0.47 44.63 4.41
1414 1460 1.078143 CCTTCTTCGGCCCCTTCTG 60.078 63.158 0.00 0.00 0.00 3.02
1454 1503 1.048724 GGACTCGATGGGGATCACCA 61.049 60.000 21.60 21.60 46.24 4.17
1545 1615 0.687354 GGAACTGCTCCCAGAACTCA 59.313 55.000 0.00 0.00 41.77 3.41
1607 1677 6.701340 TCATACATCAACTTCAACTACTGCT 58.299 36.000 0.00 0.00 0.00 4.24
1608 1678 6.968131 TCATACATCAACTTCAACTACTGC 57.032 37.500 0.00 0.00 0.00 4.40
1609 1679 8.993121 AGTTTCATACATCAACTTCAACTACTG 58.007 33.333 0.00 0.00 0.00 2.74
1645 1715 7.752239 GTCCATTCAACATAGTTCAAACATCAG 59.248 37.037 0.00 0.00 0.00 2.90
1872 1944 3.827302 ACTTTCATCGGCGAGGTAGATAT 59.173 43.478 21.57 0.00 0.00 1.63
2306 2380 1.242989 ACAACACAATGCCATGCGTA 58.757 45.000 0.00 0.00 0.00 4.42
2553 2627 2.831526 TCCGGTCTTTGACAGATGATGA 59.168 45.455 0.00 0.00 33.68 2.92
2561 2635 1.124780 TGGAAGTCCGGTCTTTGACA 58.875 50.000 15.23 11.71 39.43 3.58


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

AutoCloner maintained by Alex Coulton.