Multiple sequence alignment - TraesCS3B01G239600

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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 TraesCS3B01G239600 chr3B 100.000 3224 0 0 1 3224 377914312 377911089 0.000000e+00 5954
1 TraesCS3B01G239600 chr3D 94.293 3259 93 29 1 3224 285728494 285731694 0.000000e+00 4902
2 TraesCS3B01G239600 chr3A 95.627 2241 59 15 634 2860 374317802 374320017 0.000000e+00 3559
3 TraesCS3B01G239600 chr3A 88.924 641 59 9 1 631 374314169 374314807 0.000000e+00 780
4 TraesCS3B01G239600 chr3A 93.562 233 11 2 2859 3090 374320186 374320415 8.560000e-91 344
5 TraesCS3B01G239600 chr5B 97.297 74 2 0 1986 2059 184778080 184778007 3.380000e-25 126
6 TraesCS3B01G239600 chr4A 95.946 74 3 0 1986 2059 362070976 362071049 1.570000e-23 121


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 TraesCS3B01G239600 chr3B 377911089 377914312 3223 True 5954 5954 100.000000 1 3224 1 chr3B.!!$R1 3223
1 TraesCS3B01G239600 chr3D 285728494 285731694 3200 False 4902 4902 94.293000 1 3224 1 chr3D.!!$F1 3223
2 TraesCS3B01G239600 chr3A 374314169 374320415 6246 False 1561 3559 92.704333 1 3090 3 chr3A.!!$F1 3089

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
963 3983 0.259938 TAACCGACCTACCTCCCTCC 59.740 60.000 0.0 0.0 0.0 4.30 F
974 3994 1.152139 CTCCCTCCCTCCCTCCATC 60.152 68.421 0.0 0.0 0.0 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1864 4884 0.611714 TTGAAGACCCGGAACCTAGC 59.388 55.0 0.73 0.0 0.0 3.42 R
2354 5374 0.675083 CACCAAATGCAGCAGGACAA 59.325 50.0 6.17 0.0 0.0 3.18 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
74 75 3.379452 ACGATCAAAGAGAGGAAGGGAT 58.621 45.455 0.00 0.00 0.00 3.85
117 118 2.889617 CGTGCCTCGTATGGGTCA 59.110 61.111 0.00 0.00 34.52 4.02
193 194 7.810658 ACATGATAAATATGAAGAATGGTCGC 58.189 34.615 0.00 0.00 0.00 5.19
199 200 1.452108 GAAGAATGGTCGCAGGGGG 60.452 63.158 0.00 0.00 0.00 5.40
215 216 2.024655 AGGGGGTACACACGAATCTCTA 60.025 50.000 0.00 0.00 0.00 2.43
223 224 1.067212 ACACGAATCTCTACGCCATCC 59.933 52.381 0.00 0.00 0.00 3.51
225 226 1.754803 ACGAATCTCTACGCCATCCAA 59.245 47.619 0.00 0.00 0.00 3.53
226 227 2.365617 ACGAATCTCTACGCCATCCAAT 59.634 45.455 0.00 0.00 0.00 3.16
323 324 3.679389 AGCTCAAACTTCATTCATCGGT 58.321 40.909 0.00 0.00 0.00 4.69
334 335 8.908786 ACTTCATTCATCGGTCAATATATTGT 57.091 30.769 21.89 2.94 38.84 2.71
358 359 4.237724 GCCATTGAAGTAGCTGGAAAAAC 58.762 43.478 0.00 0.00 0.00 2.43
612 629 7.203910 ACTCTTGTAAATGACCTATCGATCAC 58.796 38.462 0.00 0.00 0.00 3.06
616 633 6.978338 TGTAAATGACCTATCGATCACCTAC 58.022 40.000 0.00 1.14 0.00 3.18
939 3956 2.670019 TACCTCATCGGCCTAGCTAA 57.330 50.000 0.00 0.00 35.61 3.09
954 3971 0.740737 GCTAAGGCGTAACCGACCTA 59.259 55.000 0.00 0.00 45.85 3.08
961 3981 0.394899 CGTAACCGACCTACCTCCCT 60.395 60.000 0.00 0.00 35.63 4.20
962 3982 1.397672 GTAACCGACCTACCTCCCTC 58.602 60.000 0.00 0.00 0.00 4.30
963 3983 0.259938 TAACCGACCTACCTCCCTCC 59.740 60.000 0.00 0.00 0.00 4.30
964 3984 2.123382 CCGACCTACCTCCCTCCC 60.123 72.222 0.00 0.00 0.00 4.30
965 3985 2.702302 CCGACCTACCTCCCTCCCT 61.702 68.421 0.00 0.00 0.00 4.20
966 3986 1.152715 CGACCTACCTCCCTCCCTC 60.153 68.421 0.00 0.00 0.00 4.30
967 3987 1.233659 GACCTACCTCCCTCCCTCC 59.766 68.421 0.00 0.00 0.00 4.30
968 3988 2.315161 GACCTACCTCCCTCCCTCCC 62.315 70.000 0.00 0.00 0.00 4.30
969 3989 2.021652 CCTACCTCCCTCCCTCCCT 61.022 68.421 0.00 0.00 0.00 4.20
970 3990 1.544703 CTACCTCCCTCCCTCCCTC 59.455 68.421 0.00 0.00 0.00 4.30
971 3991 2.019272 TACCTCCCTCCCTCCCTCC 61.019 68.421 0.00 0.00 0.00 4.30
972 3992 2.836293 TACCTCCCTCCCTCCCTCCA 62.836 65.000 0.00 0.00 0.00 3.86
973 3993 2.731461 CCTCCCTCCCTCCCTCCAT 61.731 68.421 0.00 0.00 0.00 3.41
974 3994 1.152139 CTCCCTCCCTCCCTCCATC 60.152 68.421 0.00 0.00 0.00 3.51
975 3995 2.122189 CCCTCCCTCCCTCCATCC 60.122 72.222 0.00 0.00 0.00 3.51
976 3996 2.122189 CCTCCCTCCCTCCATCCC 60.122 72.222 0.00 0.00 0.00 3.85
977 3997 2.525381 CTCCCTCCCTCCATCCCG 60.525 72.222 0.00 0.00 0.00 5.14
1016 4036 4.181010 CATGGAGGTGGAGCCGGG 62.181 72.222 2.18 0.00 43.70 5.73
1260 4280 2.969238 GCCATCGACCGCATGAGG 60.969 66.667 14.66 14.66 37.30 3.86
1276 4296 4.477119 GGTACCCCCTCGGCCTCT 62.477 72.222 0.00 0.00 33.26 3.69
1608 4628 2.094494 GTCAGATGACGTGTGGATGAGT 60.094 50.000 0.00 0.00 35.12 3.41
1638 4658 1.890510 GGACGTCAAGTTTGCCGGT 60.891 57.895 18.91 0.00 33.31 5.28
1864 4884 1.071071 TCTACAACAACCAAGGGACGG 59.929 52.381 0.00 0.00 0.00 4.79
2034 5054 3.319198 GGGTTCGAGGGCTCCACA 61.319 66.667 0.00 0.00 0.00 4.17
2049 5069 1.829222 TCCACAATCTACTTCCCGGAC 59.171 52.381 0.73 0.00 0.00 4.79
2067 5087 2.822399 GACCGCTTCATCCCCGAT 59.178 61.111 0.00 0.00 0.00 4.18
2354 5374 3.334583 ACGTGGTGCTGAGATTGTATT 57.665 42.857 0.00 0.00 0.00 1.89
2451 5471 8.809468 TCCTACATATATACTCTAGCCACTTG 57.191 38.462 0.00 0.00 0.00 3.16
2456 5476 8.037758 ACATATATACTCTAGCCACTTGCAATC 58.962 37.037 0.00 0.00 44.83 2.67
2599 5619 1.135286 TGCTGTCTCGCATCAGTAGTG 60.135 52.381 0.00 0.00 34.44 2.74
2648 5670 9.454859 AACTGGAAATTCCTATTCAGTTTCTAG 57.545 33.333 13.78 2.57 36.31 2.43
2678 5711 2.675032 GCAAGCTATTTTTGGGTGCTCC 60.675 50.000 0.00 0.00 33.10 4.70
2689 5722 1.922447 TGGGTGCTCCTGGATATTGTT 59.078 47.619 4.53 0.00 36.20 2.83
2703 5737 8.153550 CCTGGATATTGTTTAGCTCTCATACTT 58.846 37.037 0.00 0.00 0.00 2.24
2710 5744 0.749649 AGCTCTCATACTTCCTGCCG 59.250 55.000 0.00 0.00 0.00 5.69
2717 5751 3.093814 TCATACTTCCTGCCGTCTGTTA 58.906 45.455 0.00 0.00 0.00 2.41
2732 5766 5.119743 CCGTCTGTTAAGGTTACTTTAGTGC 59.880 44.000 0.00 0.00 38.14 4.40
2743 5777 2.654863 ACTTTAGTGCCTTTGCTGTGT 58.345 42.857 0.00 0.00 38.71 3.72
2750 5784 1.134250 TGCCTTTGCTGTGTAGTGTGA 60.134 47.619 0.00 0.00 38.71 3.58
2753 5787 3.141398 CCTTTGCTGTGTAGTGTGATGT 58.859 45.455 0.00 0.00 0.00 3.06
2756 5790 1.872952 TGCTGTGTAGTGTGATGTTGC 59.127 47.619 0.00 0.00 0.00 4.17
2759 5793 2.481568 CTGTGTAGTGTGATGTTGCTGG 59.518 50.000 0.00 0.00 0.00 4.85
2810 5844 3.328382 ACGACCGAAAAATCTCCATGA 57.672 42.857 0.00 0.00 0.00 3.07
2811 5845 3.873910 ACGACCGAAAAATCTCCATGAT 58.126 40.909 0.00 0.00 36.89 2.45
2840 5874 2.733956 TCCACAAGCTCTTTGGTGTTT 58.266 42.857 7.81 0.00 41.25 2.83
2902 6106 3.320541 TGAATACACAAAAGCCTTGGTGG 59.679 43.478 7.48 0.00 35.62 4.61
2972 6177 7.352719 ACAGAGTAAATCAAACTCGAATGAC 57.647 36.000 0.00 0.00 46.46 3.06
2990 6195 5.622770 ATGACGTAGGTTCCAAATTCAAC 57.377 39.130 0.00 0.00 0.00 3.18
3039 6244 5.073311 TGTGTAGCTTCTTCTGATGGTAC 57.927 43.478 0.00 11.65 44.50 3.34
3048 6253 1.781786 TCTGATGGTACTCCTCCTGC 58.218 55.000 0.00 0.00 34.23 4.85
3055 6260 2.225293 TGGTACTCCTCCTGCAACTAGT 60.225 50.000 0.00 0.00 34.23 2.57
3056 6261 3.010920 TGGTACTCCTCCTGCAACTAGTA 59.989 47.826 0.00 0.00 34.23 1.82
3057 6262 3.380954 GGTACTCCTCCTGCAACTAGTAC 59.619 52.174 0.00 12.55 38.90 2.73
3069 6274 5.262009 TGCAACTAGTACTACAGTGGATCT 58.738 41.667 4.59 0.00 0.00 2.75
3093 6298 2.162681 GTGAATTGCCAGTGCTTACCT 58.837 47.619 0.00 0.00 38.71 3.08
3095 6300 3.756434 GTGAATTGCCAGTGCTTACCTTA 59.244 43.478 0.00 0.00 38.71 2.69
3098 6303 2.762535 TGCCAGTGCTTACCTTAGAC 57.237 50.000 0.00 0.00 38.71 2.59
3113 6320 2.751166 TAGACAGCAAGCTTCAGACC 57.249 50.000 0.00 0.00 0.00 3.85
3137 6347 7.557719 ACCCTTATTGACTGGATTGATAGTTTG 59.442 37.037 0.00 0.00 0.00 2.93
3154 6364 5.779529 AGTTTGCATGAAGTTCTCAATGT 57.220 34.783 4.17 0.00 37.67 2.71
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
74 75 1.039785 CATCAGACTCGGCTCTCCCA 61.040 60.000 0.00 0.00 0.00 4.37
117 118 9.159364 GTTCGGTATTCCAACTTTCTATAAGTT 57.841 33.333 0.00 0.00 40.80 2.66
193 194 0.902531 AGATTCGTGTGTACCCCCTG 59.097 55.000 0.00 0.00 0.00 4.45
199 200 2.159476 TGGCGTAGAGATTCGTGTGTAC 60.159 50.000 0.00 0.00 0.00 2.90
223 224 2.679450 TCGGTTAGTCGTGAACCATTG 58.321 47.619 13.60 1.79 45.70 2.82
225 226 3.949754 TCTATCGGTTAGTCGTGAACCAT 59.050 43.478 13.60 9.55 45.70 3.55
226 227 3.346315 TCTATCGGTTAGTCGTGAACCA 58.654 45.455 13.60 4.56 45.70 3.67
228 229 4.560427 GGTTTCTATCGGTTAGTCGTGAAC 59.440 45.833 0.00 0.00 0.00 3.18
230 231 3.181507 CGGTTTCTATCGGTTAGTCGTGA 60.182 47.826 0.00 0.00 0.00 4.35
231 232 3.103738 CGGTTTCTATCGGTTAGTCGTG 58.896 50.000 0.00 0.00 0.00 4.35
232 233 2.098117 CCGGTTTCTATCGGTTAGTCGT 59.902 50.000 0.00 0.00 41.23 4.34
334 335 2.877097 TCCAGCTACTTCAATGGCAA 57.123 45.000 0.00 0.00 32.63 4.52
358 359 2.205074 GTGTGGAATAGCGGTGATCTG 58.795 52.381 0.00 0.00 0.00 2.90
488 505 6.195613 CGTAAACAACTTCATTTGCTTTTCGA 59.804 34.615 0.00 0.00 30.90 3.71
492 509 6.096695 ACACGTAAACAACTTCATTTGCTTT 58.903 32.000 0.00 0.00 0.00 3.51
635 3644 4.621034 CGGCGCAGATTTTTCTTTGTAAAT 59.379 37.500 10.83 0.00 0.00 1.40
651 3660 2.504681 GGCAAAATGTCGGCGCAG 60.505 61.111 10.83 5.07 0.00 5.18
939 3956 1.000396 AGGTAGGTCGGTTACGCCT 60.000 57.895 7.87 7.87 44.66 5.52
954 3971 3.369388 GGAGGGAGGGAGGGAGGT 61.369 72.222 0.00 0.00 0.00 3.85
961 3981 3.364964 ACGGGATGGAGGGAGGGA 61.365 66.667 0.00 0.00 0.00 4.20
962 3982 2.844839 GACGGGATGGAGGGAGGG 60.845 72.222 0.00 0.00 0.00 4.30
963 3983 2.844839 GGACGGGATGGAGGGAGG 60.845 72.222 0.00 0.00 0.00 4.30
964 3984 2.844839 GGGACGGGATGGAGGGAG 60.845 72.222 0.00 0.00 0.00 4.30
1260 4280 2.838693 GAGAGGCCGAGGGGGTAC 60.839 72.222 0.00 0.00 38.44 3.34
1563 4583 3.261981 GACGTGATCCAGTTGGGTAAT 57.738 47.619 0.00 0.00 38.11 1.89
1590 4610 1.133216 CGACTCATCCACACGTCATCT 59.867 52.381 0.00 0.00 0.00 2.90
1638 4658 1.374252 GACGAAGAAGAAGGCGCCA 60.374 57.895 31.54 0.00 0.00 5.69
1864 4884 0.611714 TTGAAGACCCGGAACCTAGC 59.388 55.000 0.73 0.00 0.00 3.42
2034 5054 1.109609 GGTCGTCCGGGAAGTAGATT 58.890 55.000 9.80 0.00 0.00 2.40
2049 5069 3.151958 ATCGGGGATGAAGCGGTCG 62.152 63.158 0.00 0.00 0.00 4.79
2354 5374 0.675083 CACCAAATGCAGCAGGACAA 59.325 50.000 6.17 0.00 0.00 3.18
2451 5471 1.808411 TCGAACCTGAACTGGATTGC 58.192 50.000 4.82 0.00 0.00 3.56
2456 5476 1.338105 TGCAGATCGAACCTGAACTGG 60.338 52.381 18.67 0.00 38.70 4.00
2599 5619 1.474077 CAACTAGAACCTGCAATGCCC 59.526 52.381 1.53 0.00 0.00 5.36
2647 5669 4.796038 AAAATAGCTTGCAGCAACATCT 57.204 36.364 2.83 4.51 45.56 2.90
2648 5670 4.092383 CCAAAAATAGCTTGCAGCAACATC 59.908 41.667 2.83 0.00 45.56 3.06
2678 5711 9.202273 GAAGTATGAGAGCTAAACAATATCCAG 57.798 37.037 0.00 0.00 0.00 3.86
2689 5722 2.362397 CGGCAGGAAGTATGAGAGCTAA 59.638 50.000 0.00 0.00 0.00 3.09
2703 5737 1.053424 AACCTTAACAGACGGCAGGA 58.947 50.000 0.00 0.00 0.00 3.86
2710 5744 6.228995 AGGCACTAAAGTAACCTTAACAGAC 58.771 40.000 0.00 0.00 36.02 3.51
2717 5751 4.278419 CAGCAAAGGCACTAAAGTAACCTT 59.722 41.667 9.67 9.67 42.27 3.50
2732 5766 3.141398 ACATCACACTACACAGCAAAGG 58.859 45.455 0.00 0.00 0.00 3.11
2743 5777 1.419762 ACCACCAGCAACATCACACTA 59.580 47.619 0.00 0.00 0.00 2.74
2759 5793 2.200373 ACTGCCATTTCTGGTACCAC 57.800 50.000 11.60 0.00 45.10 4.16
2785 5819 5.327616 TGGAGATTTTTCGGTCGTATACA 57.672 39.130 3.32 0.00 0.00 2.29
2788 5822 5.018539 TCATGGAGATTTTTCGGTCGTAT 57.981 39.130 0.00 0.00 0.00 3.06
2792 5826 7.645340 CACAAATATCATGGAGATTTTTCGGTC 59.355 37.037 0.00 0.00 36.25 4.79
2840 5874 7.440198 TGAAATTAAATGGCATGTCTGACAAA 58.560 30.769 15.31 2.19 45.65 2.83
2902 6106 5.882557 CCCTACCTATCAATGCAATGATACC 59.117 44.000 18.52 0.00 40.44 2.73
2946 6151 8.922676 GTCATTCGAGTTTGATTTACTCTGTTA 58.077 33.333 0.00 0.00 39.86 2.41
2972 6177 5.880054 ATCTGTTGAATTTGGAACCTACG 57.120 39.130 0.00 0.00 0.00 3.51
2990 6195 3.374058 CGTGGGCTAGTTTTACCAATCTG 59.626 47.826 0.00 0.00 34.26 2.90
3039 6244 4.270834 TGTAGTACTAGTTGCAGGAGGAG 58.729 47.826 1.87 0.00 0.00 3.69
3048 6253 6.458478 CGGAAGATCCACTGTAGTACTAGTTG 60.458 46.154 1.87 0.86 35.91 3.16
3055 6260 3.959293 TCACGGAAGATCCACTGTAGTA 58.041 45.455 0.00 0.00 35.91 1.82
3056 6261 2.803956 TCACGGAAGATCCACTGTAGT 58.196 47.619 0.00 0.00 35.91 2.73
3057 6262 3.868757 TTCACGGAAGATCCACTGTAG 57.131 47.619 0.00 0.00 35.91 2.74
3069 6274 0.537143 AGCACTGGCAATTCACGGAA 60.537 50.000 0.00 0.00 44.61 4.30
3093 6298 2.289694 GGGTCTGAAGCTTGCTGTCTAA 60.290 50.000 2.10 0.00 0.00 2.10
3095 6300 0.036022 GGGTCTGAAGCTTGCTGTCT 59.964 55.000 2.10 0.00 0.00 3.41
3098 6303 2.479566 TAAGGGTCTGAAGCTTGCTG 57.520 50.000 2.10 0.00 0.00 4.41
3113 6320 7.067372 TGCAAACTATCAATCCAGTCAATAAGG 59.933 37.037 0.00 0.00 0.00 2.69
3137 6347 4.022068 TGGGAAACATTGAGAACTTCATGC 60.022 41.667 0.00 0.00 35.27 4.06
3154 6364 3.044894 AGCCAATTCCTTGTTTGGGAAA 58.955 40.909 4.05 0.00 44.64 3.13


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

AutoCloner maintained by Alex Coulton.