Multiple sequence alignment - TraesCS5A01G092300

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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 TraesCS5A01G092300 chr5A 100.000 4428 0 0 1 4428 127574669 127570242 0 8178
1 TraesCS5A01G092300 chr5B 96.525 3568 98 7 866 4420 128811169 128814723 0 5879
2 TraesCS5A01G092300 chr5D 92.015 3632 180 40 866 4426 118051496 118047904 0 5000
3 TraesCS5A01G092300 chr2A 92.922 876 51 6 1 868 281748069 281747197 0 1264
4 TraesCS5A01G092300 chr1D 92.563 874 63 2 1 872 30313045 30312172 0 1253
5 TraesCS5A01G092300 chr1D 91.190 874 71 4 1 868 460247044 460246171 0 1182
6 TraesCS5A01G092300 chr7A 91.264 870 73 3 1 869 119886201 119885334 0 1182
7 TraesCS5A01G092300 chr7A 90.868 876 69 8 1 868 615044444 615045316 0 1164
8 TraesCS5A01G092300 chr7A 90.400 875 73 6 3 868 149413225 149414097 0 1140
9 TraesCS5A01G092300 chr6A 91.126 879 66 9 1 868 183269774 183268897 0 1181
10 TraesCS5A01G092300 chr6B 91.043 882 65 8 1 868 123489071 123488190 0 1179
11 TraesCS5A01G092300 chr2B 90.503 874 75 5 1 869 2284182 2285052 0 1147


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 TraesCS5A01G092300 chr5A 127570242 127574669 4427 True 8178 8178 100.000 1 4428 1 chr5A.!!$R1 4427
1 TraesCS5A01G092300 chr5B 128811169 128814723 3554 False 5879 5879 96.525 866 4420 1 chr5B.!!$F1 3554
2 TraesCS5A01G092300 chr5D 118047904 118051496 3592 True 5000 5000 92.015 866 4426 1 chr5D.!!$R1 3560
3 TraesCS5A01G092300 chr2A 281747197 281748069 872 True 1264 1264 92.922 1 868 1 chr2A.!!$R1 867
4 TraesCS5A01G092300 chr1D 30312172 30313045 873 True 1253 1253 92.563 1 872 1 chr1D.!!$R1 871
5 TraesCS5A01G092300 chr1D 460246171 460247044 873 True 1182 1182 91.190 1 868 1 chr1D.!!$R2 867
6 TraesCS5A01G092300 chr7A 119885334 119886201 867 True 1182 1182 91.264 1 869 1 chr7A.!!$R1 868
7 TraesCS5A01G092300 chr7A 615044444 615045316 872 False 1164 1164 90.868 1 868 1 chr7A.!!$F2 867
8 TraesCS5A01G092300 chr7A 149413225 149414097 872 False 1140 1140 90.400 3 868 1 chr7A.!!$F1 865
9 TraesCS5A01G092300 chr6A 183268897 183269774 877 True 1181 1181 91.126 1 868 1 chr6A.!!$R1 867
10 TraesCS5A01G092300 chr6B 123488190 123489071 881 True 1179 1179 91.043 1 868 1 chr6B.!!$R1 867
11 TraesCS5A01G092300 chr2B 2284182 2285052 870 False 1147 1147 90.503 1 869 1 chr2B.!!$F1 868

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
597 609 0.179100 GCTCGAGGACAAGCTGCATA 60.179 55.0 15.58 0.0 35.60 3.14 F
1559 1588 0.247974 GCACTCGATGATTGCACAGC 60.248 55.0 4.51 0.0 37.98 4.40 F
1654 1683 0.469705 AGGAGATCATGGAGCTCGCT 60.470 55.0 7.83 0.0 44.84 4.93 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1654 1683 0.253044 GCTTCACCACTATCCTGGCA 59.747 55.000 0.00 0.0 34.20 4.92 R
3155 3210 3.429207 GTCCAGAAGTTCTCGTGCTTTAC 59.571 47.826 1.26 0.0 0.00 2.01 R
3474 3533 3.937706 CTGCTACCACAGATTTCTTCAGG 59.062 47.826 0.00 0.0 40.25 3.86 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
108 109 1.227383 GTCGGGGATCTTGGGCATT 59.773 57.895 0.00 0.00 0.00 3.56
143 144 1.151668 GCAGCGACATCAAAGTCTGT 58.848 50.000 0.00 0.00 36.38 3.41
192 200 4.124970 CTCTCATCATTCTCCATCGCAAA 58.875 43.478 0.00 0.00 0.00 3.68
231 239 4.030452 GTGCAGACCAACAGCCGC 62.030 66.667 0.00 0.00 0.00 6.53
467 479 2.041216 AGGGGTCCAAAATAAAGCGTCT 59.959 45.455 0.00 0.00 0.00 4.18
520 532 1.202188 GCCGAGATGTAAAAGGCTTGC 60.202 52.381 0.00 0.00 44.06 4.01
526 538 6.378582 CGAGATGTAAAAGGCTTGCTTTTAA 58.621 36.000 0.00 1.77 37.80 1.52
597 609 0.179100 GCTCGAGGACAAGCTGCATA 60.179 55.000 15.58 0.00 35.60 3.14
614 626 1.072331 CATATCCAGGTGGGGTGTAGC 59.928 57.143 0.00 0.00 37.22 3.58
632 645 4.875536 TGTAGCGTTAGAGTACGTAATGGA 59.124 41.667 0.00 0.00 43.22 3.41
666 688 5.068636 CAGTATAGCCCGTTAGTCTTAGGA 58.931 45.833 0.00 0.00 0.00 2.94
795 817 8.874156 AGCAAGAATTAAGAAGAAAATCCCTTT 58.126 29.630 0.00 0.00 0.00 3.11
805 827 4.681484 AGAAAATCCCTTTCATCTTGCCT 58.319 39.130 0.52 0.00 45.15 4.75
831 855 4.986708 GCAAAAGGTCCCCGGCCA 62.987 66.667 2.24 0.00 0.00 5.36
851 875 2.282446 CCTCTCGCCCCCTCCTTA 59.718 66.667 0.00 0.00 0.00 2.69
914 938 2.766263 TGCAGGGTCTTCGATGTATCTT 59.234 45.455 0.00 0.00 0.00 2.40
920 944 5.046591 AGGGTCTTCGATGTATCTTTGAACA 60.047 40.000 0.00 0.00 0.00 3.18
955 979 1.022735 TCAGGAGATCGTACTTCGGC 58.977 55.000 0.00 0.00 40.32 5.54
966 990 1.812686 TACTTCGGCTTCCTGCGTGT 61.813 55.000 0.00 0.00 44.05 4.49
1159 1183 0.541998 TGATCACCGGCGGGATATCT 60.542 55.000 31.78 4.41 36.97 1.98
1202 1226 1.952102 TTACGGCGAGGTGGATGGAC 61.952 60.000 16.62 0.00 0.00 4.02
1234 1258 2.434428 CAGCCTGCTCTGAATGTCTTT 58.566 47.619 0.00 0.00 36.19 2.52
1349 1373 3.515602 ACAAGCTGGACAAAGAAGGAT 57.484 42.857 0.00 0.00 0.00 3.24
1494 1518 2.042843 CAGCTACCTCTCCGGGGT 60.043 66.667 0.00 3.14 40.53 4.95
1527 1551 1.849976 GCACTCTTGGCACAGTCAGC 61.850 60.000 0.00 0.00 42.39 4.26
1528 1552 0.250209 CACTCTTGGCACAGTCAGCT 60.250 55.000 0.00 0.00 42.39 4.24
1558 1587 1.062148 CAGCACTCGATGATTGCACAG 59.938 52.381 11.02 0.00 40.03 3.66
1559 1588 0.247974 GCACTCGATGATTGCACAGC 60.248 55.000 4.51 0.00 37.98 4.40
1560 1589 1.366679 CACTCGATGATTGCACAGCT 58.633 50.000 0.00 0.00 0.00 4.24
1561 1590 1.326852 CACTCGATGATTGCACAGCTC 59.673 52.381 0.00 0.00 0.00 4.09
1562 1591 1.066645 ACTCGATGATTGCACAGCTCA 60.067 47.619 0.00 0.00 0.00 4.26
1627 1656 0.802222 CGCTCGATTCAAGAAGCCGA 60.802 55.000 8.88 8.88 0.00 5.54
1654 1683 0.469705 AGGAGATCATGGAGCTCGCT 60.470 55.000 7.83 0.00 44.84 4.93
1819 1848 2.907458 AGCAAGGCCTTGTTATCCTT 57.093 45.000 38.87 17.72 42.31 3.36
1850 1879 2.227388 GCTGCTGACAAACATAACTGCT 59.773 45.455 0.00 0.00 0.00 4.24
1937 1966 3.310774 CCACCTCATTGATCATGACGAAC 59.689 47.826 0.00 0.00 36.94 3.95
2069 2098 3.028969 GCATGGAGCGGATTCTGC 58.971 61.111 9.56 9.56 0.00 4.26
2133 2162 9.125026 AGTCATCAAAATTCTCACAAAACTACT 57.875 29.630 0.00 0.00 0.00 2.57
2318 2355 2.829120 TGGTGGTGTTGTCGATGATCTA 59.171 45.455 0.00 0.00 0.00 1.98
2349 2386 3.476552 CTCTTTAAGGCTGACCACAACA 58.523 45.455 0.00 0.00 39.06 3.33
2618 2670 4.164843 ACAAGGAAGGAAGTACAAGCAA 57.835 40.909 0.00 0.00 0.00 3.91
2680 2732 4.378774 CTGACTTAGAAGATGGCCATGAG 58.621 47.826 26.56 8.38 0.00 2.90
3396 3455 2.221169 TGTGGGCAGAATCATATTCGC 58.779 47.619 0.00 0.00 0.00 4.70
3474 3533 3.119101 TGGCTTCGATGGAGAGTACTTTC 60.119 47.826 4.83 4.83 0.00 2.62
3501 3560 4.026744 AGAAATCTGTGGTAGCAGCTAGA 58.973 43.478 1.02 0.00 36.49 2.43
3569 3628 5.030936 GCTCAAAAGTTGTCTTCACTTGTC 58.969 41.667 0.00 0.00 32.90 3.18
3675 3734 4.450976 TCAGCACGCCATTCTTAATATGT 58.549 39.130 0.00 0.00 0.00 2.29
3743 3802 9.165035 TCTTTCAGAATTTTGTTCAAAATTGCT 57.835 25.926 28.84 22.92 41.06 3.91
3888 3976 9.295825 TCAAATGGAAAATTAGCTAACTCAAGA 57.704 29.630 8.70 0.00 0.00 3.02
3923 4011 0.777446 AGCTAAGAACAAAGGCCCCA 59.223 50.000 0.00 0.00 0.00 4.96
3962 4050 2.832838 TCCTCAACTCCTAGATGCCAA 58.167 47.619 0.00 0.00 0.00 4.52
4011 4099 4.316823 TCCGGTGGAGGCAGGAGT 62.317 66.667 0.00 0.00 0.00 3.85
4096 4185 0.397941 CTTTGGGCCAGTCAGACTCA 59.602 55.000 6.23 0.00 0.00 3.41
4314 4414 8.948631 AATTTTCTCAGCTACGAAGATTATCA 57.051 30.769 9.71 0.00 0.00 2.15
4375 4475 5.241949 GTCACCTTCTATCGGATGTACATCT 59.758 44.000 29.87 16.43 37.92 2.90
4391 4491 1.203441 ATCTCCAGCTGGCTTCCACA 61.203 55.000 28.91 7.95 34.44 4.17
4401 4501 0.035056 GGCTTCCACATACTGCAGGT 60.035 55.000 19.93 3.12 0.00 4.00
4420 4520 1.610522 GTGCTCTGCATTCTTTGTGGT 59.389 47.619 0.00 0.00 41.91 4.16
4426 4526 0.320683 GCATTCTTTGTGGTTGGGCC 60.321 55.000 0.00 0.00 37.90 5.80
4427 4527 0.038343 CATTCTTTGTGGTTGGGCCG 60.038 55.000 0.00 0.00 41.21 6.13
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
132 133 2.350522 GCCGATGTCACAGACTTTGAT 58.649 47.619 0.00 0.00 33.15 2.57
143 144 4.402528 CCCCAACCGCCGATGTCA 62.403 66.667 0.00 0.00 0.00 3.58
168 175 2.298446 GCGATGGAGAATGATGAGAGGA 59.702 50.000 0.00 0.00 0.00 3.71
192 200 1.638529 CACAGAGAAGAGTGGAGGGT 58.361 55.000 0.00 0.00 32.24 4.34
467 479 3.648067 ACTCTCAACCTGAAATGGACTGA 59.352 43.478 0.00 0.00 0.00 3.41
520 532 6.020995 CGCAACACAAACCTAACACTTAAAAG 60.021 38.462 0.00 0.00 0.00 2.27
526 538 2.353579 GACGCAACACAAACCTAACACT 59.646 45.455 0.00 0.00 0.00 3.55
597 609 2.367202 CGCTACACCCCACCTGGAT 61.367 63.158 0.00 0.00 37.39 3.41
632 645 1.700042 GCTATACTGCCAGCCCAGGT 61.700 60.000 0.00 0.00 37.16 4.00
666 688 8.001292 AGCAAGCAACCCTTATCTCTAATTAAT 58.999 33.333 0.00 0.00 31.00 1.40
685 707 0.771127 ACTTGACCCCTAAGCAAGCA 59.229 50.000 0.00 0.00 41.97 3.91
785 807 3.516700 CCAGGCAAGATGAAAGGGATTTT 59.483 43.478 0.00 0.00 0.00 1.82
795 817 2.046023 CACGGCCAGGCAAGATGA 60.046 61.111 15.19 0.00 0.00 2.92
842 866 1.004440 GCGCTGCTATAAGGAGGGG 60.004 63.158 13.02 0.00 44.69 4.79
851 875 1.875514 CATGTGTTATGGCGCTGCTAT 59.124 47.619 7.64 4.98 33.54 2.97
943 967 0.179108 GCAGGAAGCCGAAGTACGAT 60.179 55.000 0.00 0.00 45.77 3.73
955 979 4.152402 GTGGCATATATAACACGCAGGAAG 59.848 45.833 0.00 0.00 0.00 3.46
966 990 4.218852 TGTCGATCACCGTGGCATATATAA 59.781 41.667 0.00 0.00 39.75 0.98
999 1023 3.766051 GGCATTTCTCCTTTTCCTGATGT 59.234 43.478 0.00 0.00 0.00 3.06
1159 1183 2.494445 CGTATCAGGCGCCACAGA 59.506 61.111 31.54 23.21 0.00 3.41
1234 1258 2.325484 TGGAACAGAGCCAGTGAGTAA 58.675 47.619 0.00 0.00 0.00 2.24
1379 1403 1.545428 GCACCCATTTCTGGTCTGACA 60.545 52.381 10.38 0.00 41.37 3.58
1494 1518 3.695830 AGAGTGCGTCCAAAATCCTTA 57.304 42.857 0.00 0.00 0.00 2.69
1527 1551 0.458197 CGAGTGCTGCTCCTTGAGAG 60.458 60.000 0.00 0.00 46.29 3.20
1528 1552 0.895559 TCGAGTGCTGCTCCTTGAGA 60.896 55.000 0.00 0.00 41.10 3.27
1558 1587 2.189499 GGATGCCGACCCAATGAGC 61.189 63.158 0.00 0.00 0.00 4.26
1559 1588 0.816825 CAGGATGCCGACCCAATGAG 60.817 60.000 0.00 0.00 0.00 2.90
1560 1589 1.224315 CAGGATGCCGACCCAATGA 59.776 57.895 0.00 0.00 0.00 2.57
1561 1590 3.831883 CAGGATGCCGACCCAATG 58.168 61.111 0.00 0.00 0.00 2.82
1627 1656 3.370315 GCTCCATGATCTCCTTGTCTTGT 60.370 47.826 0.00 0.00 0.00 3.16
1654 1683 0.253044 GCTTCACCACTATCCTGGCA 59.747 55.000 0.00 0.00 34.20 4.92
1850 1879 3.023832 TCTGGTCTTCGCATATGAGACA 58.976 45.455 19.26 10.07 0.00 3.41
1937 1966 1.868997 CTGCAGCTACACCAAACCG 59.131 57.895 0.00 0.00 0.00 4.44
2069 2098 6.939627 TGTGTTTACGACAGATTTTACAGTG 58.060 36.000 0.00 0.00 39.39 3.66
2149 2178 1.531602 GCTTTTGGTGCCCACTCCT 60.532 57.895 0.00 0.00 30.78 3.69
2318 2355 4.471386 TCAGCCTTAAAGAGCATCCTACTT 59.529 41.667 0.00 0.00 33.66 2.24
2349 2386 5.089970 TCAGCTGCAGTTATTCTGTATGT 57.910 39.130 16.64 0.00 45.23 2.29
2411 2448 7.587037 TTTCATGAGTTCCTTGAAACAATCT 57.413 32.000 0.00 0.00 41.25 2.40
2486 2523 8.842358 AAGAAACGGTAATAATTCAAGTGAGA 57.158 30.769 0.00 0.00 0.00 3.27
3022 3077 4.319177 AGTATCAAGCTGTCAAACCTGTC 58.681 43.478 0.00 0.00 0.00 3.51
3023 3078 4.357918 AGTATCAAGCTGTCAAACCTGT 57.642 40.909 0.00 0.00 0.00 4.00
3024 3079 6.344500 AGATAGTATCAAGCTGTCAAACCTG 58.656 40.000 12.66 0.00 0.00 4.00
3025 3080 6.382570 AGAGATAGTATCAAGCTGTCAAACCT 59.617 38.462 12.66 0.00 0.00 3.50
3026 3081 6.478344 CAGAGATAGTATCAAGCTGTCAAACC 59.522 42.308 12.66 0.00 0.00 3.27
3155 3210 3.429207 GTCCAGAAGTTCTCGTGCTTTAC 59.571 47.826 1.26 0.00 0.00 2.01
3203 3258 3.945285 CACGGAAGGTGCTGGTATAATTT 59.055 43.478 0.00 0.00 40.33 1.82
3474 3533 3.937706 CTGCTACCACAGATTTCTTCAGG 59.062 47.826 0.00 0.00 40.25 3.86
3501 3560 4.969359 ACCATAGCCTATACACTTGACCTT 59.031 41.667 0.00 0.00 0.00 3.50
3569 3628 8.777865 TTACTCAAGAAATCTCCAGTAACATG 57.222 34.615 8.85 0.00 30.91 3.21
3675 3734 7.122055 ACAAGAAGATTGTGTAAACCAAGAACA 59.878 33.333 0.00 0.00 0.00 3.18
3743 3802 6.238842 GCAGATGCAGCTTAAATCTGGAATTA 60.239 38.462 22.42 0.00 44.87 1.40
3745 3804 4.037684 GCAGATGCAGCTTAAATCTGGAAT 59.962 41.667 22.42 0.00 44.87 3.01
3746 3805 3.379372 GCAGATGCAGCTTAAATCTGGAA 59.621 43.478 22.42 0.00 44.87 3.53
3837 3925 5.200454 CACGAAGTCAATTTTCTGTGTGAG 58.800 41.667 0.00 0.00 41.61 3.51
3888 3976 2.191128 AGCTCGCCATTTGAAGAAGT 57.809 45.000 0.00 0.00 0.00 3.01
3923 4011 3.425162 GAAGTCAGGTGAGTTCCCAAT 57.575 47.619 14.31 0.00 44.63 3.16
3962 4050 0.904649 TGGCATCGATGTGGAGAAGT 59.095 50.000 25.47 0.00 0.00 3.01
4004 4092 2.134287 TCTGGGCGGATACTCCTGC 61.134 63.158 0.00 0.00 42.75 4.85
4096 4185 4.910585 GTTCCCCGCCGCATCGAT 62.911 66.667 0.00 0.00 0.00 3.59
4149 4238 1.620819 AGCCGAATGAGCTATTCCGAT 59.379 47.619 0.00 0.00 41.78 4.18
4174 4263 4.336889 TCTTTCTCCTCGTGTTTGTCAT 57.663 40.909 0.00 0.00 0.00 3.06
4177 4266 6.037786 TCATATCTTTCTCCTCGTGTTTGT 57.962 37.500 0.00 0.00 0.00 2.83
4250 4350 1.749258 GTTTCTCCCGCCCCATCAC 60.749 63.158 0.00 0.00 0.00 3.06
4314 4414 1.289160 TCCAGCACAGCCCTATCTTT 58.711 50.000 0.00 0.00 0.00 2.52
4375 4475 0.253044 GTATGTGGAAGCCAGCTGGA 59.747 55.000 37.21 14.16 37.39 3.86
4401 4501 1.985473 ACCACAAAGAATGCAGAGCA 58.015 45.000 0.00 0.00 44.86 4.26


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

AutoCloner maintained by Alex Coulton.