Multiple sequence alignment - TraesCS5A01G164500

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 TraesCS5A01G164500 chr5A 100.000 2129 0 0 1 2129 353169216 353171344 0.000000e+00 3932
1 TraesCS5A01G164500 chr5A 97.640 890 19 2 1165 2052 359742450 359741561 0.000000e+00 1526
2 TraesCS5A01G164500 chr4A 97.531 891 16 5 1165 2049 187761831 187762721 0.000000e+00 1519
3 TraesCS5A01G164500 chr4A 97.514 885 18 4 1165 2045 235946574 235947458 0.000000e+00 1509
4 TraesCS5A01G164500 chr4A 97.407 887 18 4 1165 2047 222023678 222022793 0.000000e+00 1506
5 TraesCS5A01G164500 chr2A 97.222 900 19 5 1158 2053 540565922 540566819 0.000000e+00 1519
6 TraesCS5A01G164500 chr2B 97.111 900 23 3 1160 2057 138809911 138810809 0.000000e+00 1515
7 TraesCS5A01G164500 chr2B 97.111 900 16 8 1159 2051 110926262 110925366 0.000000e+00 1509
8 TraesCS5A01G164500 chr2B 84.843 574 37 14 1 543 788687337 788686783 1.120000e-147 532
9 TraesCS5A01G164500 chr1B 97.520 887 18 4 1162 2046 313321322 313320438 0.000000e+00 1513
10 TraesCS5A01G164500 chr3B 96.792 904 23 5 1156 2056 327811336 327812236 0.000000e+00 1504
11 TraesCS5A01G164500 chr5D 95.271 571 25 1 596 1164 265662294 265662864 0.000000e+00 904
12 TraesCS5A01G164500 chr5D 87.624 606 37 15 1 588 557779420 557780005 0.000000e+00 669
13 TraesCS5A01G164500 chr5D 92.593 81 6 0 2046 2126 265662856 265662936 1.330000e-22 117
14 TraesCS5A01G164500 chr5B 96.731 520 15 1 647 1164 299015328 299015847 0.000000e+00 865
15 TraesCS5A01G164500 chr5B 95.062 81 4 0 2046 2126 299015839 299015919 6.170000e-26 128
16 TraesCS5A01G164500 chr3D 75.481 416 64 25 187 587 42988570 42988962 3.630000e-38 169
17 TraesCS5A01G164500 chr3D 88.000 100 8 3 286 384 42988580 42988676 4.800000e-22 115
18 TraesCS5A01G164500 chr6A 88.496 113 11 2 314 425 572870876 572870765 3.690000e-28 135
19 TraesCS5A01G164500 chr1D 85.849 106 10 3 452 554 426924350 426924247 8.030000e-20 108
20 TraesCS5A01G164500 chr6D 90.667 75 5 1 351 425 428229196 428229124 4.830000e-17 99


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 TraesCS5A01G164500 chr5A 353169216 353171344 2128 False 3932.0 3932 100.0000 1 2129 1 chr5A.!!$F1 2128
1 TraesCS5A01G164500 chr5A 359741561 359742450 889 True 1526.0 1526 97.6400 1165 2052 1 chr5A.!!$R1 887
2 TraesCS5A01G164500 chr4A 187761831 187762721 890 False 1519.0 1519 97.5310 1165 2049 1 chr4A.!!$F1 884
3 TraesCS5A01G164500 chr4A 235946574 235947458 884 False 1509.0 1509 97.5140 1165 2045 1 chr4A.!!$F2 880
4 TraesCS5A01G164500 chr4A 222022793 222023678 885 True 1506.0 1506 97.4070 1165 2047 1 chr4A.!!$R1 882
5 TraesCS5A01G164500 chr2A 540565922 540566819 897 False 1519.0 1519 97.2220 1158 2053 1 chr2A.!!$F1 895
6 TraesCS5A01G164500 chr2B 138809911 138810809 898 False 1515.0 1515 97.1110 1160 2057 1 chr2B.!!$F1 897
7 TraesCS5A01G164500 chr2B 110925366 110926262 896 True 1509.0 1509 97.1110 1159 2051 1 chr2B.!!$R1 892
8 TraesCS5A01G164500 chr2B 788686783 788687337 554 True 532.0 532 84.8430 1 543 1 chr2B.!!$R2 542
9 TraesCS5A01G164500 chr1B 313320438 313321322 884 True 1513.0 1513 97.5200 1162 2046 1 chr1B.!!$R1 884
10 TraesCS5A01G164500 chr3B 327811336 327812236 900 False 1504.0 1504 96.7920 1156 2056 1 chr3B.!!$F1 900
11 TraesCS5A01G164500 chr5D 557779420 557780005 585 False 669.0 669 87.6240 1 588 1 chr5D.!!$F1 587
12 TraesCS5A01G164500 chr5D 265662294 265662936 642 False 510.5 904 93.9320 596 2126 2 chr5D.!!$F2 1530
13 TraesCS5A01G164500 chr5B 299015328 299015919 591 False 496.5 865 95.8965 647 2126 2 chr5B.!!$F1 1479

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
589 635 0.096976 CGGTTGATTTGTAGCAGGCG 59.903 55.0 0.0 0.0 0.0 5.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2100 2164 2.859165 AGGAATGCACGAAAAGAGGA 57.141 45.0 0.0 0.0 0.0 3.71 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
121 134 3.240134 GAGCCTGCAACCCACTCGA 62.240 63.158 0.00 0.00 0.00 4.04
149 162 1.148273 ATGTTGTATGGGGCGCGAT 59.852 52.632 12.10 3.33 0.00 4.58
151 164 1.817941 GTTGTATGGGGCGCGATGT 60.818 57.895 12.10 0.00 0.00 3.06
163 176 1.805945 GCGATGTCGTCAGGTCACC 60.806 63.158 4.20 0.00 42.22 4.02
164 177 1.514228 CGATGTCGTCAGGTCACCG 60.514 63.158 0.00 0.00 34.11 4.94
165 178 1.153823 GATGTCGTCAGGTCACCGG 60.154 63.158 0.00 0.00 0.00 5.28
166 179 1.874345 GATGTCGTCAGGTCACCGGT 61.874 60.000 0.00 0.00 0.00 5.28
167 180 2.049433 GTCGTCAGGTCACCGGTG 60.049 66.667 29.26 29.26 0.00 4.94
168 181 3.986006 TCGTCAGGTCACCGGTGC 61.986 66.667 30.25 23.00 0.00 5.01
169 182 3.991051 CGTCAGGTCACCGGTGCT 61.991 66.667 30.25 19.00 0.00 4.40
170 183 2.357517 GTCAGGTCACCGGTGCTG 60.358 66.667 30.25 28.44 0.00 4.41
171 184 4.314440 TCAGGTCACCGGTGCTGC 62.314 66.667 30.25 20.32 0.00 5.25
174 187 4.760047 GGTCACCGGTGCTGCGAT 62.760 66.667 30.25 0.00 0.00 4.58
175 188 3.490759 GTCACCGGTGCTGCGATG 61.491 66.667 30.25 3.59 0.00 3.84
186 199 4.819761 TGCGATGCAGCCCTCGTC 62.820 66.667 14.04 8.40 37.23 4.20
281 314 1.269723 ACAATGAAGCTCTCGTCGTCA 59.730 47.619 0.00 0.00 0.00 4.35
311 344 2.464459 GCAATGAAGCCCTCGTCGG 61.464 63.158 0.00 0.00 0.00 4.79
539 585 1.625818 AGGGATGAATCGGATGGCTAC 59.374 52.381 0.00 0.00 0.00 3.58
550 596 1.673808 GATGGCTACGGACCCGACTT 61.674 60.000 16.07 0.00 42.83 3.01
556 602 2.100418 GCTACGGACCCGACTTATTTCT 59.900 50.000 16.07 0.00 42.83 2.52
558 604 2.173519 ACGGACCCGACTTATTTCTGA 58.826 47.619 16.07 0.00 42.83 3.27
580 626 6.908825 TGAAGGAAATAAGTCGGTTGATTTG 58.091 36.000 0.00 0.00 0.00 2.32
581 627 6.488683 TGAAGGAAATAAGTCGGTTGATTTGT 59.511 34.615 0.00 0.00 0.00 2.83
588 634 1.130561 GTCGGTTGATTTGTAGCAGGC 59.869 52.381 0.00 0.00 0.00 4.85
589 635 0.096976 CGGTTGATTTGTAGCAGGCG 59.903 55.000 0.00 0.00 0.00 5.52
590 636 1.165270 GGTTGATTTGTAGCAGGCGT 58.835 50.000 0.00 0.00 0.00 5.68
591 637 1.130561 GGTTGATTTGTAGCAGGCGTC 59.869 52.381 0.00 0.00 0.00 5.19
592 638 1.130561 GTTGATTTGTAGCAGGCGTCC 59.869 52.381 0.00 0.00 0.00 4.79
593 639 0.613260 TGATTTGTAGCAGGCGTCCT 59.387 50.000 0.00 0.00 0.00 3.85
594 640 1.828595 TGATTTGTAGCAGGCGTCCTA 59.171 47.619 0.00 0.00 29.64 2.94
620 666 3.904965 TGCATCCGTAATACTTATCCCCA 59.095 43.478 0.00 0.00 0.00 4.96
622 668 4.935808 GCATCCGTAATACTTATCCCCAAG 59.064 45.833 0.00 0.00 0.00 3.61
672 718 2.159156 CCCCACGTTGTCATAATCGAGA 60.159 50.000 0.00 0.00 0.00 4.04
801 847 2.184579 GCCGACCTGAGCTGGTAC 59.815 66.667 0.00 0.00 41.00 3.34
839 885 2.351726 GTGAATCATTGTACGCCTCCAC 59.648 50.000 0.00 0.00 0.00 4.02
889 935 2.448453 CCTACCTTCTCGTCACCTTCT 58.552 52.381 0.00 0.00 0.00 2.85
893 939 2.698797 ACCTTCTCGTCACCTTCTTCAA 59.301 45.455 0.00 0.00 0.00 2.69
939 987 6.183360 ATGAATACATACATGCACTTGGTGTG 60.183 38.462 9.52 7.49 41.06 3.82
1156 1204 5.715921 TGATGATCAGGATAACCAGAGGTA 58.284 41.667 0.09 0.00 35.26 3.08
1157 1205 5.540337 TGATGATCAGGATAACCAGAGGTAC 59.460 44.000 0.09 0.00 35.26 3.34
1285 1333 1.327303 AGAAATGCCCTTTTGCGACA 58.673 45.000 0.00 0.00 0.00 4.35
1399 1456 0.508213 GCAAGGCGTGTGCAAATTTC 59.492 50.000 1.69 0.00 45.35 2.17
1466 1523 7.536964 TCATAAATTTTGTACGCATGTGAACAG 59.463 33.333 14.43 0.00 0.00 3.16
1583 1643 2.145397 TTGGACATCGTAGGAGCTCT 57.855 50.000 14.64 2.18 0.00 4.09
2073 2137 3.745332 TTGTTGCGTGCATAGATTGAG 57.255 42.857 0.00 0.00 0.00 3.02
2096 2160 4.683320 GCCTTTCTTCTTCAAGCAATGTTC 59.317 41.667 0.00 0.00 0.00 3.18
2100 2164 5.499139 TCTTCTTCAAGCAATGTTCGTTT 57.501 34.783 0.00 0.00 0.00 3.60
2110 2174 3.664025 GCAATGTTCGTTTCCTCTTTTCG 59.336 43.478 0.00 0.00 0.00 3.46
2126 2190 1.459450 TTCGTGCATTCCTAAAGCCC 58.541 50.000 0.00 0.00 0.00 5.19
2127 2191 0.326595 TCGTGCATTCCTAAAGCCCA 59.673 50.000 0.00 0.00 0.00 5.36
2128 2192 1.173043 CGTGCATTCCTAAAGCCCAA 58.827 50.000 0.00 0.00 0.00 4.12
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
12 13 1.980772 GCCCCTGCTGCATTGAAGT 60.981 57.895 1.31 0.00 33.53 3.01
121 134 0.804364 CATACAACATGCAGCACCGT 59.196 50.000 0.00 0.00 0.00 4.83
149 162 2.520020 ACCGGTGACCTGACGACA 60.520 61.111 6.12 0.00 0.00 4.35
151 164 3.986006 GCACCGGTGACCTGACGA 61.986 66.667 38.30 0.00 0.00 4.20
169 182 4.819761 GACGAGGGCTGCATCGCA 62.820 66.667 21.45 0.00 42.61 5.10
190 203 4.760047 ATCGCAGCACCGGTGACC 62.760 66.667 38.30 21.09 32.22 4.02
191 204 3.490759 CATCGCAGCACCGGTGAC 61.491 66.667 38.30 26.95 41.67 3.67
192 205 3.233259 TTCATCGCAGCACCGGTGA 62.233 57.895 38.30 17.51 45.64 4.02
193 206 2.741985 TTCATCGCAGCACCGGTG 60.742 61.111 30.66 30.66 40.54 4.94
194 207 2.434884 CTTCATCGCAGCACCGGT 60.435 61.111 0.00 0.00 0.00 5.28
195 208 3.869272 GCTTCATCGCAGCACCGG 61.869 66.667 0.00 0.00 37.22 5.28
320 353 1.303799 CGAGGCTTCATTGCAGCACT 61.304 55.000 10.43 5.04 39.21 4.40
539 585 2.953466 TCAGAAATAAGTCGGGTCCG 57.047 50.000 2.52 2.52 41.35 4.79
556 602 6.488683 ACAAATCAACCGACTTATTTCCTTCA 59.511 34.615 0.00 0.00 0.00 3.02
558 604 6.894339 ACAAATCAACCGACTTATTTCCTT 57.106 33.333 0.00 0.00 0.00 3.36
566 612 3.074412 CCTGCTACAAATCAACCGACTT 58.926 45.455 0.00 0.00 0.00 3.01
580 626 1.937108 GCATGATAGGACGCCTGCTAC 60.937 57.143 8.44 0.00 34.61 3.58
581 627 0.318441 GCATGATAGGACGCCTGCTA 59.682 55.000 8.44 0.00 34.61 3.49
588 634 3.297830 TTACGGATGCATGATAGGACG 57.702 47.619 2.46 0.00 0.00 4.79
589 635 5.967088 AGTATTACGGATGCATGATAGGAC 58.033 41.667 2.46 0.00 0.00 3.85
590 636 6.605471 AAGTATTACGGATGCATGATAGGA 57.395 37.500 2.46 0.00 0.00 2.94
591 637 7.653713 GGATAAGTATTACGGATGCATGATAGG 59.346 40.741 2.46 0.00 30.46 2.57
592 638 7.653713 GGGATAAGTATTACGGATGCATGATAG 59.346 40.741 2.46 0.00 30.46 2.08
593 639 7.418597 GGGGATAAGTATTACGGATGCATGATA 60.419 40.741 2.46 0.00 30.46 2.15
594 640 6.349300 GGGATAAGTATTACGGATGCATGAT 58.651 40.000 2.46 0.00 30.46 2.45
628 674 4.093850 GTGGTGGTAACGTGGAATACATTC 59.906 45.833 0.00 0.00 42.51 2.67
672 718 1.063642 TCTGTGAGGTGGAGGATCGAT 60.064 52.381 0.00 0.00 34.37 3.59
788 834 2.968574 CTCATATGGTACCAGCTCAGGT 59.031 50.000 21.41 3.80 45.72 4.00
801 847 7.848223 TGATTCACACAACTAACTCATATGG 57.152 36.000 2.13 0.00 0.00 2.74
839 885 0.320683 TGTCGTGGACAGATGGCTTG 60.321 55.000 0.00 0.00 37.67 4.01
889 935 1.705337 GCTCGCGGCTGCTAATTGAA 61.705 55.000 17.03 0.00 39.65 2.69
893 939 2.125147 TTGCTCGCGGCTGCTAAT 60.125 55.556 17.03 0.00 42.39 1.73
939 987 2.094417 GCAGATAAACCAGCTCACGAAC 59.906 50.000 0.00 0.00 0.00 3.95
1011 1059 1.074775 GCACACCACCATCTCCCAA 59.925 57.895 0.00 0.00 0.00 4.12
1156 1204 8.796475 GCATAGATGTAAATGTCCCAATAATGT 58.204 33.333 0.00 0.00 0.00 2.71
1157 1205 8.246180 GGCATAGATGTAAATGTCCCAATAATG 58.754 37.037 0.00 0.00 0.00 1.90
1388 1445 0.743688 ACGGCACAGAAATTTGCACA 59.256 45.000 0.00 0.00 40.75 4.57
1399 1456 3.041940 GGTGTCCGAACGGCACAG 61.042 66.667 27.16 3.18 41.05 3.66
1514 1573 5.246203 TGTGCACCTAAGTATCTTCAGTTCT 59.754 40.000 15.69 0.00 0.00 3.01
1662 1723 7.124298 ACTGAAGATACTTAGGTGCACAAGATA 59.876 37.037 20.43 9.68 0.00 1.98
2073 2137 4.248691 ACATTGCTTGAAGAAGAAAGGC 57.751 40.909 0.00 0.00 32.50 4.35
2096 2160 2.969443 ATGCACGAAAAGAGGAAACG 57.031 45.000 0.00 0.00 0.00 3.60
2100 2164 2.859165 AGGAATGCACGAAAAGAGGA 57.141 45.000 0.00 0.00 0.00 3.71


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

AutoCloner maintained by Alex Coulton.