Multiple sequence alignment - TraesCS7B01G113900

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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 TraesCS7B01G113900 chr7B 100.000 2648 0 0 1 2648 131954034 131951387 0.000000e+00 4891
1 TraesCS7B01G113900 chr7A 91.083 2714 137 28 12 2644 169034796 169032107 0.000000e+00 3574
2 TraesCS7B01G113900 chr7D 92.285 1672 80 14 1011 2644 167536074 167534414 0.000000e+00 2327
3 TraesCS7B01G113900 chr7D 86.621 1024 89 11 1 986 167546843 167545830 0.000000e+00 1088
4 TraesCS7B01G113900 chr1D 71.869 487 121 16 1100 1578 467438379 467437901 2.770000e-25 126


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 TraesCS7B01G113900 chr7B 131951387 131954034 2647 True 4891 4891 100.000 1 2648 1 chr7B.!!$R1 2647
1 TraesCS7B01G113900 chr7A 169032107 169034796 2689 True 3574 3574 91.083 12 2644 1 chr7A.!!$R1 2632
2 TraesCS7B01G113900 chr7D 167534414 167536074 1660 True 2327 2327 92.285 1011 2644 1 chr7D.!!$R1 1633
3 TraesCS7B01G113900 chr7D 167545830 167546843 1013 True 1088 1088 86.621 1 986 1 chr7D.!!$R2 985

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
68 84 0.119358 AGTTAGGGTCCCAAGAGGCT 59.881 55.0 11.55 0.0 34.51 4.58 F
965 1012 0.255890 CGGAGACCATTGGACCCAAT 59.744 55.0 10.37 8.4 46.35 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1137 1201 0.326595 TTGACAGATTGGCGCCCTTA 59.673 50.0 26.77 10.04 0.0 2.69 R
2344 2453 1.098050 GGCATTCCTCAAGCACGAAT 58.902 50.0 0.00 0.00 0.0 3.34 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
40 41 2.401017 TCGATGTGCTACGATGTAGC 57.599 50.000 19.33 19.33 40.76 3.58
68 84 0.119358 AGTTAGGGTCCCAAGAGGCT 59.881 55.000 11.55 0.00 34.51 4.58
79 95 3.706594 TCCCAAGAGGCTATGACAGTTAG 59.293 47.826 1.56 0.00 34.51 2.34
80 96 3.181461 CCCAAGAGGCTATGACAGTTAGG 60.181 52.174 1.56 0.00 0.00 2.69
88 104 4.003648 GCTATGACAGTTAGGCAGTTGTT 58.996 43.478 0.00 0.00 39.86 2.83
110 126 7.337938 TGTTCTATGGTTGATTTGATAGCTCA 58.662 34.615 0.00 0.00 0.00 4.26
119 135 7.268586 GTTGATTTGATAGCTCAAGGAGAGTA 58.731 38.462 0.00 0.00 46.47 2.59
173 189 6.500589 ACATTAACCCACTATAGCATCACT 57.499 37.500 0.00 0.00 0.00 3.41
211 227 2.289694 ACGATCTCCCACAAGTTTCCTG 60.290 50.000 0.00 0.00 0.00 3.86
246 265 3.838244 ACACTACACCATCACACAACT 57.162 42.857 0.00 0.00 0.00 3.16
305 326 2.945447 GCATTTAGCTGCCAACATCA 57.055 45.000 0.00 0.00 41.15 3.07
316 337 2.158711 TGCCAACATCATCCTCCATCTC 60.159 50.000 0.00 0.00 0.00 2.75
340 361 3.364441 GCCATGACACTTGCGGCA 61.364 61.111 0.00 0.00 42.50 5.69
357 378 1.661498 GCAGCCTGGCTCCTAAAAGC 61.661 60.000 20.49 13.76 36.40 3.51
368 389 3.084039 CTCCTAAAAGCTGCACAATGGA 58.916 45.455 1.02 3.10 0.00 3.41
407 428 1.447489 CTTCGTGCTCTCTGGCCAG 60.447 63.158 27.87 27.87 0.00 4.85
409 430 1.758440 TTCGTGCTCTCTGGCCAGTT 61.758 55.000 31.58 0.00 0.00 3.16
419 440 1.203187 TCTGGCCAGTTCACCTACTCT 60.203 52.381 31.58 0.00 0.00 3.24
498 519 4.225042 AGCCACATACCTTGTTGACTATGA 59.775 41.667 0.00 0.00 36.00 2.15
529 550 3.368531 GGCCTAGCCCTAACTATCGATTG 60.369 52.174 1.71 3.78 44.06 2.67
592 613 5.105567 TCCTTGCCGATTCTACCATTAAA 57.894 39.130 0.00 0.00 0.00 1.52
599 620 8.684386 TGCCGATTCTACCATTAAATTCATAA 57.316 30.769 0.00 0.00 0.00 1.90
631 652 1.192146 AGCACTCCGGCCTTAGTGAA 61.192 55.000 28.87 0.00 44.79 3.18
649 670 2.771943 TGAAGAGACTTGTGTTCCACCT 59.228 45.455 0.00 0.00 32.73 4.00
671 692 3.888323 TGCACTTTCTTACATTGAGCCAA 59.112 39.130 0.00 0.00 0.00 4.52
709 730 2.475466 CCGCGCCGAGGTAGAACTA 61.475 63.158 0.00 0.00 0.00 2.24
713 734 1.376543 CGCCGAGGTAGAACTAGTCA 58.623 55.000 0.00 0.00 0.00 3.41
727 748 7.333528 AGAACTAGTCATCTTCTCAGTGATC 57.666 40.000 0.00 0.00 0.00 2.92
755 776 4.142790 CCTACTGGCTAAGACGAGGATTA 58.857 47.826 0.00 0.00 0.00 1.75
772 793 3.997021 GGATTAACCTTGATGCGATCGAT 59.003 43.478 21.57 9.56 35.41 3.59
779 800 6.025749 ACCTTGATGCGATCGATATTCTAA 57.974 37.500 21.57 8.17 0.00 2.10
801 822 3.088532 TCACCAACTGCAGTGTCTTTTT 58.911 40.909 22.49 0.00 35.45 1.94
805 826 3.380004 CCAACTGCAGTGTCTTTTTACCA 59.620 43.478 22.49 0.00 0.00 3.25
884 931 3.120889 CGTCATCAACAGTAACTGCAGTG 60.121 47.826 22.49 10.52 34.37 3.66
890 937 0.674895 CAGTAACTGCAGTGGGGCTC 60.675 60.000 22.49 7.52 34.04 4.70
944 991 1.131771 CATATGCGCTAGTGGTGTCG 58.868 55.000 9.73 0.00 0.00 4.35
965 1012 0.255890 CGGAGACCATTGGACCCAAT 59.744 55.000 10.37 8.40 46.35 3.16
971 1018 3.054361 AGACCATTGGACCCAATCACTAC 60.054 47.826 10.37 3.09 43.92 2.73
1005 1069 2.365582 GTTATCTTGTTCCGCATGGGT 58.634 47.619 9.14 0.00 37.00 4.51
1052 1116 1.068352 AGGTCCAAAGCCAGGTTCCT 61.068 55.000 0.00 0.00 0.00 3.36
1104 1168 0.389426 GTGACGACAATGCCTACCGT 60.389 55.000 0.00 0.00 36.08 4.83
1125 1189 3.746045 TGTGTGTACCAAGAGGAAGAC 57.254 47.619 0.00 0.00 38.69 3.01
1128 1192 3.056749 GTGTGTACCAAGAGGAAGACGAT 60.057 47.826 0.00 0.00 38.69 3.73
1137 1201 3.379452 AGAGGAAGACGATGAGGGAATT 58.621 45.455 0.00 0.00 0.00 2.17
1254 1318 5.477510 TCAGAGCTGATCAAGTTTCTTCTC 58.522 41.667 0.00 0.00 34.14 2.87
1266 1330 1.338107 TTCTTCTCGTCTCCTTGGCA 58.662 50.000 0.00 0.00 0.00 4.92
1378 1442 1.202417 CGGTGATCAGCTCGGTACAAT 60.202 52.381 21.73 0.00 0.00 2.71
1449 1513 3.063861 TGCATCAATTCGGAAATCAGTCG 59.936 43.478 0.00 0.00 0.00 4.18
1682 1752 7.782168 TGACTATACTCTCACCAAGAAGATCAT 59.218 37.037 0.00 0.00 32.23 2.45
1683 1753 8.177119 ACTATACTCTCACCAAGAAGATCATC 57.823 38.462 0.00 0.00 32.23 2.92
1685 1755 3.122297 CTCTCACCAAGAAGATCATCGC 58.878 50.000 0.00 0.00 32.23 4.58
1689 1759 2.353889 CACCAAGAAGATCATCGCCAAG 59.646 50.000 0.00 0.00 0.00 3.61
2120 2224 6.349300 ACGATGCAAGATGAGGTTATTTACT 58.651 36.000 0.00 0.00 0.00 2.24
2240 2347 5.839063 AGAAAGTCCATATACATCTTCCCGA 59.161 40.000 0.00 0.00 0.00 5.14
2408 2518 7.878036 TGTAATTTCTTTGTAACTTGGCTACC 58.122 34.615 0.00 0.00 0.00 3.18
2453 2563 6.656693 ACTCTCTTAAACAAATGGGATGACAG 59.343 38.462 0.00 0.00 0.00 3.51
2640 2750 8.587950 CGTTTAGATTGAACTCACTATCTTGTC 58.412 37.037 0.00 0.00 35.06 3.18
2644 2754 7.319646 AGATTGAACTCACTATCTTGTCACTC 58.680 38.462 0.00 0.00 30.83 3.51
2645 2755 5.392767 TGAACTCACTATCTTGTCACTCC 57.607 43.478 0.00 0.00 0.00 3.85
2646 2756 4.220821 TGAACTCACTATCTTGTCACTCCC 59.779 45.833 0.00 0.00 0.00 4.30
2647 2757 4.054359 ACTCACTATCTTGTCACTCCCT 57.946 45.455 0.00 0.00 0.00 4.20
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
9 10 3.115554 AGCACATCGAAACAAAAACAGC 58.884 40.909 0.00 0.00 0.00 4.40
10 11 4.375698 CGTAGCACATCGAAACAAAAACAG 59.624 41.667 0.00 0.00 0.00 3.16
40 41 3.349022 TGGGACCCTAACTTTTATTGCG 58.651 45.455 13.00 0.00 0.00 4.85
68 84 5.483685 AGAACAACTGCCTAACTGTCATA 57.516 39.130 0.00 0.00 0.00 2.15
79 95 5.048083 TCAAATCAACCATAGAACAACTGCC 60.048 40.000 0.00 0.00 0.00 4.85
80 96 6.012658 TCAAATCAACCATAGAACAACTGC 57.987 37.500 0.00 0.00 0.00 4.40
88 104 6.994496 CCTTGAGCTATCAAATCAACCATAGA 59.006 38.462 0.00 0.00 44.68 1.98
110 126 9.836864 AAAAAGATTTGCAAAAATACTCTCCTT 57.163 25.926 17.19 8.23 0.00 3.36
119 135 7.987649 TCTTGCTCAAAAAGATTTGCAAAAAT 58.012 26.923 17.19 4.74 44.52 1.82
173 189 6.342819 AGATCGTTATATAGGGGATCAGGA 57.657 41.667 15.95 0.23 36.76 3.86
286 307 2.945447 TGATGTTGGCAGCTAAATGC 57.055 45.000 2.28 0.00 45.74 3.56
305 326 1.970639 CGATGGCGAGATGGAGGAT 59.029 57.895 0.00 0.00 40.82 3.24
316 337 2.108514 AAGTGTCATGGCGATGGCG 61.109 57.895 8.84 0.00 36.95 5.69
340 361 0.034670 CAGCTTTTAGGAGCCAGGCT 60.035 55.000 16.12 16.12 43.74 4.58
346 367 2.416431 CCATTGTGCAGCTTTTAGGAGC 60.416 50.000 0.00 0.00 43.02 4.70
357 378 1.140161 CCGGCAATCCATTGTGCAG 59.860 57.895 0.00 0.00 42.74 4.41
397 418 1.203187 AGTAGGTGAACTGGCCAGAGA 60.203 52.381 39.19 18.58 0.00 3.10
407 428 2.749621 CAATGGGCAAGAGTAGGTGAAC 59.250 50.000 0.00 0.00 0.00 3.18
409 430 1.985159 ACAATGGGCAAGAGTAGGTGA 59.015 47.619 0.00 0.00 0.00 4.02
419 440 1.691434 GGTTGGAAGAACAATGGGCAA 59.309 47.619 0.00 0.00 32.24 4.52
498 519 2.193248 GGCTAGGCCGGAAGCAAT 59.807 61.111 23.51 0.00 46.50 3.56
592 613 5.120830 GTGCTCAAGAACTCGTGTTATGAAT 59.879 40.000 15.08 0.00 36.39 2.57
599 620 2.141535 GAGTGCTCAAGAACTCGTGT 57.858 50.000 2.38 0.00 40.60 4.49
649 670 3.485394 TGGCTCAATGTAAGAAAGTGCA 58.515 40.909 0.00 0.00 0.00 4.57
671 692 3.682718 CGGGCTTCATCCAGACTACAATT 60.683 47.826 0.00 0.00 0.00 2.32
709 730 4.886489 TCATCGATCACTGAGAAGATGACT 59.114 41.667 16.34 0.00 43.36 3.41
713 734 4.214310 AGGTCATCGATCACTGAGAAGAT 58.786 43.478 0.00 0.00 0.00 2.40
727 748 2.287069 CGTCTTAGCCAGTAGGTCATCG 60.287 54.545 0.00 0.00 37.19 3.84
755 776 4.887748 AGAATATCGATCGCATCAAGGTT 58.112 39.130 11.09 0.00 0.00 3.50
769 790 5.755375 ACTGCAGTTGGTGATTAGAATATCG 59.245 40.000 15.25 0.00 0.00 2.92
772 793 5.804639 ACACTGCAGTTGGTGATTAGAATA 58.195 37.500 18.94 0.00 37.22 1.75
779 800 2.645838 AAGACACTGCAGTTGGTGAT 57.354 45.000 18.94 1.25 37.22 3.06
801 822 1.816074 GGCAATTGACGGAACTGGTA 58.184 50.000 10.34 0.00 0.00 3.25
838 859 0.320421 GGTCACCTCGCAGCTTGTAA 60.320 55.000 0.00 0.00 0.00 2.41
884 931 2.044946 ATGTTCCTTGCGAGCCCC 60.045 61.111 0.00 0.00 0.00 5.80
890 937 1.089920 CCTCCAAGATGTTCCTTGCG 58.910 55.000 0.00 0.00 41.53 4.85
926 973 1.029681 TCGACACCACTAGCGCATAT 58.970 50.000 11.47 0.00 0.00 1.78
927 974 0.099968 GTCGACACCACTAGCGCATA 59.900 55.000 11.47 0.00 0.00 3.14
929 976 2.257371 GTCGACACCACTAGCGCA 59.743 61.111 11.47 0.00 0.00 6.09
944 991 1.221021 GGGTCCAATGGTCTCCGTC 59.779 63.158 0.00 0.00 0.00 4.79
956 1003 1.216977 CGCGTAGTGATTGGGTCCA 59.783 57.895 0.00 0.00 43.07 4.02
965 1012 0.038343 GGTTGTTACCCGCGTAGTGA 60.038 55.000 4.92 0.00 38.60 3.41
986 1033 2.364632 CACCCATGCGGAACAAGATAA 58.635 47.619 7.17 0.00 34.64 1.75
1018 1082 6.540438 TTTGGACCTAGAACTCGATAACAT 57.460 37.500 0.00 0.00 0.00 2.71
1104 1168 3.491964 CGTCTTCCTCTTGGTACACACAA 60.492 47.826 0.00 0.00 39.29 3.33
1107 1171 2.589720 TCGTCTTCCTCTTGGTACACA 58.410 47.619 0.00 0.00 39.29 3.72
1125 1189 1.512926 CGCCCTTAATTCCCTCATCG 58.487 55.000 0.00 0.00 0.00 3.84
1128 1192 1.226262 GGCGCCCTTAATTCCCTCA 59.774 57.895 18.11 0.00 0.00 3.86
1137 1201 0.326595 TTGACAGATTGGCGCCCTTA 59.673 50.000 26.77 10.04 0.00 2.69
1378 1442 5.512060 GCTCATCTGATAGATTAAGGCCACA 60.512 44.000 5.01 0.00 31.32 4.17
1449 1513 1.067846 TCGTACCACACAGATGCACTC 60.068 52.381 0.00 0.00 0.00 3.51
1682 1752 4.500035 GGTTTCAATTTTGTACCTTGGCGA 60.500 41.667 0.00 0.00 33.93 5.54
1683 1753 3.738791 GGTTTCAATTTTGTACCTTGGCG 59.261 43.478 0.00 0.00 33.93 5.69
1685 1755 5.931724 GGATGGTTTCAATTTTGTACCTTGG 59.068 40.000 14.08 0.00 36.03 3.61
1689 1759 6.128309 GCAATGGATGGTTTCAATTTTGTACC 60.128 38.462 9.11 9.11 35.79 3.34
2120 2224 5.877012 GGATGATCTGCACTAGAGACAAAAA 59.123 40.000 0.00 0.00 39.20 1.94
2344 2453 1.098050 GGCATTCCTCAAGCACGAAT 58.902 50.000 0.00 0.00 0.00 3.34
2408 2518 8.196771 AGAGAGTATGACTAGCATTTCTTGAAG 58.803 37.037 5.22 0.00 38.44 3.02


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

AutoCloner maintained by Alex Coulton.