Multiple sequence alignment - TraesCS4A01G134800

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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 TraesCS4A01G134800 chr4A 100.000 7525 0 0 1 7525 183969579 183977103 0.000000e+00 13897
1 TraesCS4A01G134800 chr4A 78.439 974 134 35 5131 6056 94765911 94766856 3.940000e-157 566
2 TraesCS4A01G134800 chr4D 96.879 7626 113 41 1 7525 299778780 299771179 0.000000e+00 12648
3 TraesCS4A01G134800 chr4B 96.708 7624 136 43 1 7525 372909639 372902032 0.000000e+00 12582
4 TraesCS4A01G134800 chr6D 78.651 993 143 32 5131 6080 161151665 161152631 5.030000e-166 595
5 TraesCS4A01G134800 chr5D 78.636 997 142 31 5128 6080 435152511 435153480 5.030000e-166 595
6 TraesCS4A01G134800 chr7A 78.147 993 139 37 5131 6078 8739568 8740527 1.830000e-155 560
7 TraesCS4A01G134800 chr6A 77.823 974 140 35 5131 6056 77892857 77893802 4.000000e-147 532
8 TraesCS4A01G134800 chr5A 77.977 949 136 33 5174 6078 154491792 154490873 1.860000e-145 527
9 TraesCS4A01G134800 chr3A 82.883 444 48 12 5510 5933 725058453 725058888 2.560000e-99 374
10 TraesCS4A01G134800 chrUn 82.658 444 49 12 5510 5933 45785436 45785871 1.190000e-97 368
11 TraesCS4A01G134800 chr3D 82.658 444 49 12 5510 5933 594480526 594480961 1.190000e-97 368


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 TraesCS4A01G134800 chr4A 183969579 183977103 7524 False 13897 13897 100.000 1 7525 1 chr4A.!!$F2 7524
1 TraesCS4A01G134800 chr4A 94765911 94766856 945 False 566 566 78.439 5131 6056 1 chr4A.!!$F1 925
2 TraesCS4A01G134800 chr4D 299771179 299778780 7601 True 12648 12648 96.879 1 7525 1 chr4D.!!$R1 7524
3 TraesCS4A01G134800 chr4B 372902032 372909639 7607 True 12582 12582 96.708 1 7525 1 chr4B.!!$R1 7524
4 TraesCS4A01G134800 chr6D 161151665 161152631 966 False 595 595 78.651 5131 6080 1 chr6D.!!$F1 949
5 TraesCS4A01G134800 chr5D 435152511 435153480 969 False 595 595 78.636 5128 6080 1 chr5D.!!$F1 952
6 TraesCS4A01G134800 chr7A 8739568 8740527 959 False 560 560 78.147 5131 6078 1 chr7A.!!$F1 947
7 TraesCS4A01G134800 chr6A 77892857 77893802 945 False 532 532 77.823 5131 6056 1 chr6A.!!$F1 925
8 TraesCS4A01G134800 chr5A 154490873 154491792 919 True 527 527 77.977 5174 6078 1 chr5A.!!$R1 904

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
181 186 0.818040 GAGTTCCCACACCACACACC 60.818 60.000 0.00 0.00 0.00 4.16 F
590 622 1.006102 CTCCGCGACCAAAGTCTGT 60.006 57.895 8.23 0.00 41.16 3.41 F
1425 1474 1.376466 GGGCAGGAACAAGAGCTCA 59.624 57.895 17.77 0.00 0.00 4.26 F
1806 1855 3.481453 TCAACATGGTGATTTTCGGTCA 58.519 40.909 10.05 0.00 0.00 4.02 F
2873 2922 2.016318 TGATTGGTGATCGATTGGCAC 58.984 47.619 0.00 3.05 37.60 5.01 F
3285 3334 1.136891 GGTGCAATTGATTACCAGGGC 59.863 52.381 10.34 0.00 33.42 5.19 F
4680 4730 1.475682 CCTCTGCAAAAGGCTGGAATC 59.524 52.381 2.03 0.00 45.15 2.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1668 1717 1.003118 AGTAGCGGGAACAATGAAGCA 59.997 47.619 0.00 0.0 0.00 3.91 R
2208 2257 2.771089 AGATTGCTGCTCTTTGAACGA 58.229 42.857 0.00 0.0 0.00 3.85 R
2873 2922 0.034896 AAGGTGGGTCTAGTTGCACG 59.965 55.000 0.00 0.0 0.00 5.34 R
3061 3110 0.969149 TGTTGGCTCGATGACTCTGT 59.031 50.000 0.00 0.0 0.00 3.41 R
3690 3739 2.100584 AGTTTTGGCGTGCAAAGAATCA 59.899 40.909 0.00 0.0 0.00 2.57 R
5152 5206 0.400594 GGGTTAAGCTGACTGGGTGT 59.599 55.000 4.41 0.0 0.00 4.16 R
6669 6767 1.864711 GTGCTCTTGCGTGTGTCTAAA 59.135 47.619 0.00 0.0 43.34 1.85 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
181 186 0.818040 GAGTTCCCACACCACACACC 60.818 60.000 0.00 0.00 0.00 4.16
590 622 1.006102 CTCCGCGACCAAAGTCTGT 60.006 57.895 8.23 0.00 41.16 3.41
862 911 5.059161 TGACTGAAGAAATCTGTGGTCTTG 58.941 41.667 0.00 0.00 39.98 3.02
1425 1474 1.376466 GGGCAGGAACAAGAGCTCA 59.624 57.895 17.77 0.00 0.00 4.26
1492 1541 6.856757 AGGCTAATTTACATCAATGATCCCT 58.143 36.000 0.00 0.00 0.00 4.20
1493 1542 6.718454 AGGCTAATTTACATCAATGATCCCTG 59.282 38.462 0.00 0.00 0.00 4.45
1668 1717 3.857157 TTAGCTGTGTTTGGAAGGACT 57.143 42.857 0.00 0.00 0.00 3.85
1806 1855 3.481453 TCAACATGGTGATTTTCGGTCA 58.519 40.909 10.05 0.00 0.00 4.02
2383 2432 4.134563 GAGAAAGTACTTCACCTTTGGCA 58.865 43.478 8.95 0.00 36.40 4.92
2682 2731 3.498927 AAGATGGAATTTCAGCAAGCG 57.501 42.857 4.50 0.00 0.00 4.68
2873 2922 2.016318 TGATTGGTGATCGATTGGCAC 58.984 47.619 0.00 3.05 37.60 5.01
2973 3022 6.522054 AGTTCAAGTTTCTAGTTCCGATGAA 58.478 36.000 0.00 0.00 0.00 2.57
3285 3334 1.136891 GGTGCAATTGATTACCAGGGC 59.863 52.381 10.34 0.00 33.42 5.19
3466 3515 3.502123 ATTTCTTCCCGAGTTGACCAA 57.498 42.857 0.00 0.00 0.00 3.67
3501 3550 6.413783 TGTACCTGTTGACAATCTTCTACA 57.586 37.500 0.00 0.00 31.64 2.74
3690 3739 3.834231 CCAGGAACCATGATGGACTTTTT 59.166 43.478 20.11 0.50 40.96 1.94
3894 3943 1.679898 GGCAGCCCTTGTAGAGTGT 59.320 57.895 0.00 0.00 0.00 3.55
4071 4120 8.773645 CGATTATTAACTCAAGGTATGCATTCA 58.226 33.333 3.54 0.00 0.00 2.57
4293 4342 7.364522 TGCTAATGACAAGTCAGTAAACATC 57.635 36.000 10.96 1.25 43.61 3.06
4401 4450 8.812513 TTGAATCAGAGGTTTGTGATCATATT 57.187 30.769 0.00 0.00 36.39 1.28
4680 4730 1.475682 CCTCTGCAAAAGGCTGGAATC 59.524 52.381 2.03 0.00 45.15 2.52
4748 4798 4.636249 GGTGATGGTGAGATTCTGTATCC 58.364 47.826 0.00 0.00 33.45 2.59
4781 4831 7.336679 TGTTGCTATGTTGTTAGTGAGCATATT 59.663 33.333 0.00 0.00 39.50 1.28
4782 4832 7.864108 TGCTATGTTGTTAGTGAGCATATTT 57.136 32.000 0.00 0.00 35.12 1.40
4784 4834 8.739039 TGCTATGTTGTTAGTGAGCATATTTTT 58.261 29.630 0.00 0.00 35.12 1.94
5094 5148 4.320608 TCTCGTGCATTGCATATCTGTA 57.679 40.909 15.49 0.00 41.91 2.74
5136 5190 7.886629 ATACACTGGTAAGAGTTTATACGGA 57.113 36.000 0.00 0.00 32.19 4.69
5162 5216 8.693120 TTTATACAATAACAAACACCCAGTCA 57.307 30.769 0.00 0.00 0.00 3.41
5278 5332 5.986741 TCTGTTTTCGCTGTACATCAAACTA 59.013 36.000 11.58 1.75 0.00 2.24
5283 5339 5.128992 TCGCTGTACATCAAACTAGTCAA 57.871 39.130 0.00 0.00 0.00 3.18
5366 5430 7.434013 ACGTTCATATTGACAGTTTGGTTTTTC 59.566 33.333 0.00 0.00 0.00 2.29
5462 5528 0.784778 GTCAAGAAGGTCGTCAAGCG 59.215 55.000 0.00 0.00 43.01 4.68
5543 5609 3.979911 ACATGGGCACTGGAATTATCAA 58.020 40.909 0.00 0.00 0.00 2.57
5617 5683 6.367422 GTGCTAATGCTCTTCTGGTACATATC 59.633 42.308 0.00 0.00 37.75 1.63
5714 5802 6.730038 AGAATATACAGAAGCATCATCCTCCT 59.270 38.462 0.00 0.00 0.00 3.69
5762 5851 7.558161 TCTTGTAATGCAGGTTGATCTAATG 57.442 36.000 0.00 0.00 0.00 1.90
5812 5905 0.726827 ACACTGCATATTCCGCAACG 59.273 50.000 0.00 0.00 39.30 4.10
6073 6171 3.255888 TCAGTACGATGGACATATGGAGC 59.744 47.826 7.80 0.00 0.00 4.70
6528 6626 6.457528 GCCTGAAAGTGATATCAGCTAACAAC 60.458 42.308 5.42 0.00 41.36 3.32
6529 6627 6.595326 CCTGAAAGTGATATCAGCTAACAACA 59.405 38.462 5.42 0.00 41.36 3.33
6530 6628 7.119699 CCTGAAAGTGATATCAGCTAACAACAA 59.880 37.037 5.42 0.00 41.36 2.83
6531 6629 8.565896 TGAAAGTGATATCAGCTAACAACAAT 57.434 30.769 5.42 0.00 0.00 2.71
6532 6630 8.453320 TGAAAGTGATATCAGCTAACAACAATG 58.547 33.333 5.42 0.00 0.00 2.82
6533 6631 6.932356 AGTGATATCAGCTAACAACAATGG 57.068 37.500 5.42 0.00 0.00 3.16
6534 6632 6.418101 AGTGATATCAGCTAACAACAATGGT 58.582 36.000 5.42 0.00 0.00 3.55
6593 6691 4.682860 GTGTTGATTCATTTGTTGAGCTGG 59.317 41.667 0.00 0.00 35.27 4.85
6691 6789 0.461870 AGACACACGCAAGAGCACAA 60.462 50.000 0.00 0.00 42.27 3.33
6863 6983 4.599047 TTTTTAGGCACAAACATCCCAG 57.401 40.909 0.00 0.00 0.00 4.45
6877 6997 1.059098 TCCCAGTCTGTGACTTGCAT 58.941 50.000 0.00 0.00 41.37 3.96
6890 7010 9.448438 TCTGTGACTTGCATTTTTATACTGTAT 57.552 29.630 5.53 5.53 0.00 2.29
6958 7078 2.167398 TAGTGCTGACCTGCCGGTTC 62.167 60.000 1.90 0.00 45.73 3.62
7033 7153 1.742268 GCAAGGACAAGAGATTCTGGC 59.258 52.381 0.00 0.00 0.00 4.85
7116 7236 3.508762 GCATCAAACAGCTTCATCCTTG 58.491 45.455 0.00 0.00 0.00 3.61
7136 7257 1.345715 GGGGGTGGGGACTAGTGATG 61.346 65.000 0.00 0.00 0.00 3.07
7355 7478 5.010617 GTGGTGTGTCTGGTTGGAATTTTAT 59.989 40.000 0.00 0.00 0.00 1.40
7520 7675 2.166870 TGCTTGCCTTGCTGATTATTGG 59.833 45.455 0.00 0.00 0.00 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
18 19 4.602340 TTATTCGCCCAATCTACCTCTC 57.398 45.455 0.00 0.00 0.00 3.20
590 622 6.425721 CCCTCAACAACTAATACGAAACAGAA 59.574 38.462 0.00 0.00 0.00 3.02
730 762 7.338710 ACAAGCTAATATTACTGAAAGCTGGA 58.661 34.615 14.36 0.00 40.06 3.86
842 891 4.645535 TCCAAGACCACAGATTTCTTCAG 58.354 43.478 0.00 0.00 0.00 3.02
843 892 4.505566 CCTCCAAGACCACAGATTTCTTCA 60.506 45.833 0.00 0.00 0.00 3.02
844 893 4.006319 CCTCCAAGACCACAGATTTCTTC 58.994 47.826 0.00 0.00 0.00 2.87
845 894 3.395941 ACCTCCAAGACCACAGATTTCTT 59.604 43.478 0.00 0.00 0.00 2.52
862 911 1.377725 CTGCACCATGGACACCTCC 60.378 63.158 21.47 0.00 37.04 4.30
1149 1198 4.757657 TCCGCAAAATTAACAGAAGCAGTA 59.242 37.500 0.00 0.00 0.00 2.74
1216 1265 2.752358 CTCTGCCACCCTGCTCAA 59.248 61.111 0.00 0.00 0.00 3.02
1425 1474 7.068593 TCAGATGAAAACAGGTCTTCAAAATGT 59.931 33.333 0.00 0.00 35.31 2.71
1492 1541 2.442212 TATCGGTCGTTTGTTCTGCA 57.558 45.000 0.00 0.00 0.00 4.41
1493 1542 2.927477 TCATATCGGTCGTTTGTTCTGC 59.073 45.455 0.00 0.00 0.00 4.26
1668 1717 1.003118 AGTAGCGGGAACAATGAAGCA 59.997 47.619 0.00 0.00 0.00 3.91
2208 2257 2.771089 AGATTGCTGCTCTTTGAACGA 58.229 42.857 0.00 0.00 0.00 3.85
2383 2432 5.899547 ACTCAAAATCCTTTCTGTTTTCCCT 59.100 36.000 0.00 0.00 0.00 4.20
2682 2731 5.435291 CCATAATTCCTCCCATAGATGCTC 58.565 45.833 0.00 0.00 0.00 4.26
2873 2922 0.034896 AAGGTGGGTCTAGTTGCACG 59.965 55.000 0.00 0.00 0.00 5.34
3061 3110 0.969149 TGTTGGCTCGATGACTCTGT 59.031 50.000 0.00 0.00 0.00 3.41
3466 3515 6.183360 TGTCAACAGGTACAAAATGCATTTCT 60.183 34.615 24.28 13.88 0.00 2.52
3690 3739 2.100584 AGTTTTGGCGTGCAAAGAATCA 59.899 40.909 0.00 0.00 0.00 2.57
3894 3943 2.106338 TGCACCCAGAAGAGTCAAATCA 59.894 45.455 0.00 0.00 0.00 2.57
4071 4120 7.745717 TCTCGGAGGAACCATTTATGATAATT 58.254 34.615 4.96 0.00 38.90 1.40
4263 4312 6.743575 ACTGACTTGTCATTAGCAATAACC 57.256 37.500 3.79 0.00 0.00 2.85
4293 4342 5.953183 TCATCAAAATTTGGTGATTCCTCG 58.047 37.500 16.84 0.00 45.34 4.63
4600 4650 5.587289 TGCCAAGTCAAATAACTGTCAAAC 58.413 37.500 0.00 0.00 0.00 2.93
4680 4730 4.026475 GTCCTGCTTTTAATCAGATCGACG 60.026 45.833 0.00 0.00 32.26 5.12
4748 4798 6.684131 CACTAACAACATAGCAACATGAATCG 59.316 38.462 0.00 0.00 0.00 3.34
4784 4834 9.547753 GCCAATTGATACAGAAGACTAAGATAA 57.452 33.333 7.12 0.00 0.00 1.75
4788 4838 7.335422 ACAAGCCAATTGATACAGAAGACTAAG 59.665 37.037 7.12 0.00 41.83 2.18
4975 5029 3.069016 ACCGGTATTCGCACTATCATTCA 59.931 43.478 4.49 0.00 37.59 2.57
5094 5148 6.093219 CAGTGTATAGCTGAATTGCACTCTTT 59.907 38.462 0.00 0.00 36.12 2.52
5136 5190 9.303116 TGACTGGGTGTTTGTTATTGTATAAAT 57.697 29.630 0.00 0.00 0.00 1.40
5152 5206 0.400594 GGGTTAAGCTGACTGGGTGT 59.599 55.000 4.41 0.00 0.00 4.16
5162 5216 5.186409 TCTGTACTAATTGTCGGGTTAAGCT 59.814 40.000 4.41 0.00 0.00 3.74
5242 5296 3.740321 GCGAAAACAGAAATTGGCATCAA 59.260 39.130 0.00 0.00 37.28 2.57
5366 5430 7.260603 CCCCTGCAAATAGAAAACAAGATTAG 58.739 38.462 0.00 0.00 0.00 1.73
5462 5528 2.494870 AGCAAAATCTGAAGCCATCACC 59.505 45.455 0.00 0.00 33.47 4.02
5543 5609 5.474578 AGAGAATCATGTATGCCATACGT 57.525 39.130 10.12 7.04 36.56 3.57
5617 5683 2.105649 GGAGAAAAGCATAGAGGAGGGG 59.894 54.545 0.00 0.00 0.00 4.79
6073 6171 5.111293 GCAATTGTCCATAAACTTCCCATG 58.889 41.667 7.40 0.00 0.00 3.66
6528 6626 4.853196 CGAACTAACTGCATGAAACCATTG 59.147 41.667 0.00 0.00 0.00 2.82
6529 6627 4.518970 ACGAACTAACTGCATGAAACCATT 59.481 37.500 0.00 0.00 0.00 3.16
6530 6628 4.072131 ACGAACTAACTGCATGAAACCAT 58.928 39.130 0.00 0.00 0.00 3.55
6531 6629 3.472652 ACGAACTAACTGCATGAAACCA 58.527 40.909 0.00 0.00 0.00 3.67
6532 6630 3.496884 TGACGAACTAACTGCATGAAACC 59.503 43.478 0.00 0.00 0.00 3.27
6533 6631 4.455124 GTGACGAACTAACTGCATGAAAC 58.545 43.478 0.00 0.00 0.00 2.78
6534 6632 3.496884 GGTGACGAACTAACTGCATGAAA 59.503 43.478 0.00 0.00 0.00 2.69
6613 6711 4.946784 ATGGCAGTCGTGAATAAAACTC 57.053 40.909 0.00 0.00 0.00 3.01
6669 6767 1.864711 GTGCTCTTGCGTGTGTCTAAA 59.135 47.619 0.00 0.00 43.34 1.85
6738 6836 7.603404 AGCTCATGATTGCTTCTTATGATCTAC 59.397 37.037 3.70 0.00 35.86 2.59
6742 6840 6.372103 GCTAGCTCATGATTGCTTCTTATGAT 59.628 38.462 14.01 0.00 40.35 2.45
6743 6841 5.699915 GCTAGCTCATGATTGCTTCTTATGA 59.300 40.000 14.01 0.00 40.35 2.15
6744 6842 5.469084 TGCTAGCTCATGATTGCTTCTTATG 59.531 40.000 17.23 1.77 40.35 1.90
6747 6845 3.878103 CTGCTAGCTCATGATTGCTTCTT 59.122 43.478 17.23 0.00 40.35 2.52
6749 6847 3.002451 CACTGCTAGCTCATGATTGCTTC 59.998 47.826 17.23 7.96 40.35 3.86
6863 6983 7.584987 ACAGTATAAAAATGCAAGTCACAGAC 58.415 34.615 0.00 0.00 0.00 3.51
6890 7010 9.330063 CTATGCTACAGGAAGAACAATATCAAA 57.670 33.333 0.00 0.00 0.00 2.69
6921 7041 5.009010 AGCACTAGTCCACAATGAAAACTTG 59.991 40.000 0.00 0.00 0.00 3.16
6932 7052 0.969149 CAGGTCAGCACTAGTCCACA 59.031 55.000 0.00 0.00 0.00 4.17
6958 7078 6.019640 CAGTAATTTCACAAAACAACAGGCAG 60.020 38.462 0.00 0.00 0.00 4.85
7033 7153 4.456911 TGCATTTTTCAGCCTCTTCTACAG 59.543 41.667 0.00 0.00 0.00 2.74
7124 7245 5.069648 TGTCATCTGATTCATCACTAGTCCC 59.930 44.000 0.00 0.00 32.50 4.46
7355 7478 8.658840 AATTTATCCTGTACCCTTTTAAAGCA 57.341 30.769 0.00 0.00 0.00 3.91
7448 7600 3.306641 GGGCAATTCAGCAATAAACCACA 60.307 43.478 0.00 0.00 35.83 4.17


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

AutoCloner maintained by Alex Coulton.