Multiple sequence alignment - TraesCS5D01G033400

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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 TraesCS5D01G033400 chr5D 100.000 2296 0 0 1 2296 31477719 31475424 0 4241
1 TraesCS5D01G033400 chrUn 95.794 2306 85 7 1 2296 245706061 245708364 0 3711
2 TraesCS5D01G033400 chrUn 95.750 2306 87 6 1 2296 291535433 291537737 0 3705
3 TraesCS5D01G033400 chrUn 95.709 2307 87 9 1 2296 274341289 274338984 0 3701
4 TraesCS5D01G033400 chrUn 95.707 2306 88 6 1 2296 199874817 199877121 0 3699
5 TraesCS5D01G033400 chrUn 95.707 2306 88 6 1 2296 229310234 229307930 0 3699
6 TraesCS5D01G033400 chrUn 95.267 1141 46 2 1 1133 400881399 400882539 0 1801
7 TraesCS5D01G033400 chrUn 94.479 634 28 1 1 627 421526121 421526754 0 970
8 TraesCS5D01G033400 chrUn 95.472 530 24 0 1 530 400726002 400726531 0 846
9 TraesCS5D01G033400 chr1B 95.707 2306 86 7 1 2296 544593690 544595992 0 3698
10 TraesCS5D01G033400 chr1B 91.433 677 50 5 1 670 111151342 111150667 0 922
11 TraesCS5D01G033400 chr4A 94.709 2306 109 7 1 2296 554939822 554942124 0 3570
12 TraesCS5D01G033400 chr6B 94.102 2306 124 7 1 2296 111715915 111713612 0 3494
13 TraesCS5D01G033400 chr1A 93.888 2307 129 8 1 2296 419652 421957 0 3469


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 TraesCS5D01G033400 chr5D 31475424 31477719 2295 True 4241 4241 100.000 1 2296 1 chr5D.!!$R1 2295
1 TraesCS5D01G033400 chrUn 245706061 245708364 2303 False 3711 3711 95.794 1 2296 1 chrUn.!!$F2 2295
2 TraesCS5D01G033400 chrUn 291535433 291537737 2304 False 3705 3705 95.750 1 2296 1 chrUn.!!$F3 2295
3 TraesCS5D01G033400 chrUn 274338984 274341289 2305 True 3701 3701 95.709 1 2296 1 chrUn.!!$R2 2295
4 TraesCS5D01G033400 chrUn 199874817 199877121 2304 False 3699 3699 95.707 1 2296 1 chrUn.!!$F1 2295
5 TraesCS5D01G033400 chrUn 229307930 229310234 2304 True 3699 3699 95.707 1 2296 1 chrUn.!!$R1 2295
6 TraesCS5D01G033400 chrUn 400881399 400882539 1140 False 1801 1801 95.267 1 1133 1 chrUn.!!$F5 1132
7 TraesCS5D01G033400 chrUn 421526121 421526754 633 False 970 970 94.479 1 627 1 chrUn.!!$F6 626
8 TraesCS5D01G033400 chrUn 400726002 400726531 529 False 846 846 95.472 1 530 1 chrUn.!!$F4 529
9 TraesCS5D01G033400 chr1B 544593690 544595992 2302 False 3698 3698 95.707 1 2296 1 chr1B.!!$F1 2295
10 TraesCS5D01G033400 chr1B 111150667 111151342 675 True 922 922 91.433 1 670 1 chr1B.!!$R1 669
11 TraesCS5D01G033400 chr4A 554939822 554942124 2302 False 3570 3570 94.709 1 2296 1 chr4A.!!$F1 2295
12 TraesCS5D01G033400 chr6B 111713612 111715915 2303 True 3494 3494 94.102 1 2296 1 chr6B.!!$R1 2295
13 TraesCS5D01G033400 chr1A 419652 421957 2305 False 3469 3469 93.888 1 2296 1 chr1A.!!$F1 2295

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
805 814 0.393448 GGCCTCGGGAAGAGTAATCC 59.607 60.0 0.0 0.0 45.44 3.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2205 2219 0.324943 ATCTGGCACACGGTAGCTTT 59.675 50.0 0.0 0.0 0.0 3.51 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
28 29 1.201704 CGTGCAAATCGTTCGTCTGAG 60.202 52.381 0.00 0.00 0.00 3.35
37 38 2.559668 TCGTTCGTCTGAGTTGGGTATT 59.440 45.455 0.00 0.00 0.00 1.89
88 89 2.445525 AGCTGGTTCCCTCCAAAGTTTA 59.554 45.455 0.00 0.00 37.01 2.01
89 90 3.117284 AGCTGGTTCCCTCCAAAGTTTAA 60.117 43.478 0.00 0.00 37.01 1.52
115 116 1.344763 GATAGCTGGAGCCCATTACGT 59.655 52.381 0.00 0.00 43.38 3.57
123 124 3.131396 GGAGCCCATTACGTGTTCTATG 58.869 50.000 0.00 0.00 0.00 2.23
263 265 2.970987 AGTGGGCCATTTTTGGTAAGT 58.029 42.857 10.70 0.00 0.00 2.24
421 423 4.512571 GTGTAACAACACACCTACCGAATT 59.487 41.667 3.86 0.00 42.46 2.17
431 433 3.387050 CACCTACCGAATTAACTAGCCCT 59.613 47.826 0.00 0.00 0.00 5.19
509 511 0.481567 CCCCGATGAGTAGGAGGGTA 59.518 60.000 0.00 0.00 40.44 3.69
517 519 4.133373 TAGGAGGGTACGGCGGCT 62.133 66.667 13.24 0.00 0.00 5.52
607 616 2.218603 TGAGAACTTTGAAGGCCGAAC 58.781 47.619 0.00 0.00 0.00 3.95
801 810 2.042230 GGGGCCTCGGGAAGAGTA 60.042 66.667 0.84 0.00 45.44 2.59
805 814 0.393448 GGCCTCGGGAAGAGTAATCC 59.607 60.000 0.00 0.00 45.44 3.01
821 830 2.789409 ATCCTTTCTGCTTAACGGCT 57.211 45.000 0.00 0.00 0.00 5.52
824 833 1.880027 CCTTTCTGCTTAACGGCTTGT 59.120 47.619 0.00 0.00 0.00 3.16
837 846 1.632589 GGCTTGTCAACCCTGGAAAT 58.367 50.000 0.00 0.00 0.00 2.17
877 886 2.925170 AGTGGCCGGAAGAGCACT 60.925 61.111 5.05 0.00 0.00 4.40
881 890 2.437359 GCCGGAAGAGCACTGCAT 60.437 61.111 5.05 0.00 0.00 3.96
923 932 1.616091 CCCAGCGGCCCATGAAAATT 61.616 55.000 0.00 0.00 0.00 1.82
995 1004 0.687354 TCCAAGGTGAACAGCCTCTC 59.313 55.000 0.29 0.00 34.81 3.20
1026 1035 2.375174 ACAATGTAGGCAAGGGAAGTCA 59.625 45.455 0.00 0.00 0.00 3.41
1071 1080 3.562176 GGAAAAGGATTGGCTCTGAGGAA 60.562 47.826 6.83 0.00 0.00 3.36
1110 1120 4.047059 GAACCCGTCGGCTGTCGA 62.047 66.667 13.90 0.00 46.77 4.20
1222 1233 1.651138 GAGCATGAAACAGTCGACTCG 59.349 52.381 16.96 13.78 0.00 4.18
1248 1259 0.906775 GTACGGACAAGGGGAATCCA 59.093 55.000 0.09 0.00 38.24 3.41
1329 1340 0.607217 TGCCCAGTGCTCTGAATGTG 60.607 55.000 17.19 0.00 43.76 3.21
1405 1416 3.265737 TCTTAAGGTAGCCAAATGCCTCA 59.734 43.478 1.85 0.00 42.71 3.86
1424 1435 5.532557 CCTCATCATCTAATTAGTGACGCA 58.467 41.667 12.19 0.00 0.00 5.24
1460 1471 1.630878 GAGATTCCCACTGTCCCTGTT 59.369 52.381 0.00 0.00 0.00 3.16
1491 1502 0.961753 GAAACCACAGCCAAGGGAAG 59.038 55.000 0.00 0.00 0.00 3.46
1501 1512 2.866015 AAGGGAAGGGGCTTGGCT 60.866 61.111 0.00 0.00 0.00 4.75
1555 1566 3.220110 TGACTCTAGTCCGACTTTGTGT 58.780 45.455 6.31 7.38 44.15 3.72
1612 1623 1.024579 CGGGCGCAACTGAAATACCT 61.025 55.000 10.83 0.00 0.00 3.08
1620 1632 5.106673 GCGCAACTGAAATACCTCTACTTTT 60.107 40.000 0.30 0.00 0.00 2.27
1648 1661 9.621629 ACGTTATTTTACTTATTCCATGGATCA 57.378 29.630 17.06 0.89 0.00 2.92
1736 1749 2.714250 ACATTGTCAGGTGGGGAGTTTA 59.286 45.455 0.00 0.00 0.00 2.01
1791 1804 4.036518 AGGTGTCCTAAGATGAGCTCAAT 58.963 43.478 22.50 12.60 28.47 2.57
1850 1863 4.946157 AGCTCGTTTGATTCTGATTTCCAT 59.054 37.500 0.00 0.00 0.00 3.41
1943 1956 6.884836 GTCAGAAAAGTTACCACAGGGATAAT 59.115 38.462 0.00 0.00 38.05 1.28
1975 1988 1.068588 AGCCAAGCGTTCATAGCGATA 59.931 47.619 0.00 0.00 40.04 2.92
1994 2007 5.207768 CGATATTGCTTTTTGATCCTTCGG 58.792 41.667 0.00 0.00 0.00 4.30
2013 2026 1.202428 GGTGTCGGCTCTTCCTATCAC 60.202 57.143 0.00 0.00 0.00 3.06
2061 2074 3.308832 GGATTGTTCACCCACCAATAGGA 60.309 47.826 0.00 0.00 38.69 2.94
2070 2083 3.333680 ACCCACCAATAGGAAACATGAGT 59.666 43.478 0.00 0.00 38.69 3.41
2221 2235 2.258013 GCAAAGCTACCGTGTGCCA 61.258 57.895 0.00 0.00 0.00 4.92
2271 2285 2.169789 CAAGCTAGCATGCGACGCT 61.170 57.895 22.08 20.58 43.62 5.07
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
28 29 0.815095 CTTTCGCCCCAATACCCAAC 59.185 55.000 0.00 0.00 0.00 3.77
37 38 1.187974 TCGATTAGTCTTTCGCCCCA 58.812 50.000 1.16 0.00 35.39 4.96
88 89 1.127343 GGCTCCAGCTATCCTGAGTT 58.873 55.000 0.00 0.00 44.64 3.01
89 90 0.762461 GGGCTCCAGCTATCCTGAGT 60.762 60.000 0.00 0.00 44.64 3.41
115 116 6.061022 TCATTGGCTTTACCTCATAGAACA 57.939 37.500 0.00 0.00 40.22 3.18
123 124 4.517075 GCCTCTAATCATTGGCTTTACCTC 59.483 45.833 0.00 0.00 41.92 3.85
190 192 4.529219 CAGCCGCGCCATCCTACA 62.529 66.667 0.00 0.00 0.00 2.74
263 265 1.399744 ATCCCGCATCGCCAGTTCTA 61.400 55.000 0.00 0.00 0.00 2.10
308 310 1.097232 TCTAGGTTAGCGCGCAGTTA 58.903 50.000 35.10 14.78 0.00 2.24
408 410 3.133542 GGGCTAGTTAATTCGGTAGGTGT 59.866 47.826 0.00 0.00 0.00 4.16
414 416 4.563140 TTTCAGGGCTAGTTAATTCGGT 57.437 40.909 0.00 0.00 0.00 4.69
421 423 4.792068 CCATCCATTTTCAGGGCTAGTTA 58.208 43.478 0.00 0.00 0.00 2.24
431 433 2.231964 GCTTCAGTGCCATCCATTTTCA 59.768 45.455 0.00 0.00 0.00 2.69
483 485 0.752658 CTACTCATCGGGGCATGTCA 59.247 55.000 0.00 0.00 0.00 3.58
485 487 0.398522 TCCTACTCATCGGGGCATGT 60.399 55.000 0.00 0.00 0.00 3.21
517 519 3.233231 GGCCTGGGTTTTGCAGCA 61.233 61.111 0.00 0.00 0.00 4.41
539 548 4.451150 GCACCGATGACCGCTCCA 62.451 66.667 0.00 0.00 36.84 3.86
547 556 0.904649 ACCAAGATCTGCACCGATGA 59.095 50.000 0.00 0.00 0.00 2.92
549 558 0.107508 CCACCAAGATCTGCACCGAT 60.108 55.000 0.00 0.00 0.00 4.18
607 616 3.423539 TCACATGGAACCTTTCTCCTG 57.576 47.619 0.00 0.00 33.77 3.86
759 768 0.745468 GCGTCTCCGGACTTCCTAAT 59.255 55.000 0.00 0.00 40.10 1.73
801 810 3.073274 AGCCGTTAAGCAGAAAGGATT 57.927 42.857 6.74 0.00 34.23 3.01
805 814 2.548057 TGACAAGCCGTTAAGCAGAAAG 59.452 45.455 0.00 0.00 34.23 2.62
821 830 2.765689 ACCATTTCCAGGGTTGACAA 57.234 45.000 0.00 0.00 32.12 3.18
824 833 2.875296 CTGAACCATTTCCAGGGTTGA 58.125 47.619 0.05 0.00 46.97 3.18
837 846 1.987855 CCTACCTCCGGCTGAACCA 60.988 63.158 0.00 0.00 39.03 3.67
907 916 1.666209 CCGAATTTTCATGGGCCGCT 61.666 55.000 0.00 0.00 0.00 5.52
995 1004 1.202290 GCCTACATTGTTCCATTGGCG 60.202 52.381 0.00 0.00 0.00 5.69
1048 1057 2.025510 CCTCAGAGCCAATCCTTTTCCT 60.026 50.000 0.00 0.00 0.00 3.36
1110 1120 2.510238 GCAGCTCGAGCAATCCGT 60.510 61.111 36.87 14.56 45.16 4.69
1193 1204 1.004161 TGTTTCATGCTCGGGGAATGA 59.996 47.619 0.00 0.00 38.17 2.57
1194 1205 1.402968 CTGTTTCATGCTCGGGGAATG 59.597 52.381 0.00 0.00 32.20 2.67
1195 1206 1.004745 ACTGTTTCATGCTCGGGGAAT 59.995 47.619 0.00 0.00 0.00 3.01
1222 1233 0.036671 CCCTTGTCCGTACCAGTTCC 60.037 60.000 0.00 0.00 0.00 3.62
1329 1340 5.173854 CGCTTGGTTGAATTTCTTCACTTTC 59.826 40.000 0.00 0.00 41.05 2.62
1405 1416 6.515832 TCATGTGCGTCACTAATTAGATGAT 58.484 36.000 19.38 0.00 35.11 2.45
1424 1435 5.765182 GGGAATCTCGTTAATCCATTCATGT 59.235 40.000 0.00 0.00 33.48 3.21
1460 1471 3.857052 CTGTGGTTTCGCTGGATAGTAA 58.143 45.455 0.00 0.00 0.00 2.24
1491 1502 3.930504 CTGATTCAGCCAAGCCCC 58.069 61.111 0.00 0.00 0.00 5.80
1501 1512 1.628340 TCTTCTTTCCCCGCTGATTCA 59.372 47.619 0.00 0.00 0.00 2.57
1555 1566 7.839705 ACTTATCCTACACCTCTCAAGTCATTA 59.160 37.037 0.00 0.00 0.00 1.90
1641 1654 1.713005 ATGCCCCGCTTCTGATCCAT 61.713 55.000 0.00 0.00 0.00 3.41
1645 1658 1.153086 GACATGCCCCGCTTCTGAT 60.153 57.895 0.00 0.00 0.00 2.90
1791 1804 3.320826 TCCACACGAGATTTCTGTTCTCA 59.679 43.478 0.00 0.00 39.69 3.27
1850 1863 3.364621 GCTTTCACGGTTCGTATTCGTAA 59.635 43.478 0.00 0.00 38.32 3.18
1896 1909 3.383185 CACCTCTAGCTTCCTACTCCAAG 59.617 52.174 0.00 0.00 0.00 3.61
1898 1911 2.312140 ACACCTCTAGCTTCCTACTCCA 59.688 50.000 0.00 0.00 0.00 3.86
1904 1917 2.909504 TCTGACACCTCTAGCTTCCT 57.090 50.000 0.00 0.00 0.00 3.36
1905 1918 3.963428 TTTCTGACACCTCTAGCTTCC 57.037 47.619 0.00 0.00 0.00 3.46
1994 2007 1.751924 AGTGATAGGAAGAGCCGACAC 59.248 52.381 0.00 0.00 43.43 3.67
2061 2074 4.457466 ACGGTCTAAACCAACTCATGTTT 58.543 39.130 0.00 0.00 46.86 2.83
2070 2083 1.955778 TCTCACGACGGTCTAAACCAA 59.044 47.619 6.57 0.00 46.86 3.67
2125 2139 8.848182 CCTCTCGTACTAGGTTGAATTACTATT 58.152 37.037 0.00 0.00 0.00 1.73
2205 2219 0.324943 ATCTGGCACACGGTAGCTTT 59.675 50.000 0.00 0.00 0.00 3.51
2221 2235 5.361285 ACTTAGAGGCGTTCAGTCATAATCT 59.639 40.000 0.00 0.00 0.00 2.40


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

AutoCloner maintained by Alex Coulton.