Multiple sequence alignment - TraesCS3B01G371100

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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 TraesCS3B01G371100 chr3B 100.000 3572 0 0 1 3572 583387217 583390788 0.000000e+00 6597
1 TraesCS3B01G371100 chr3D 93.148 3065 145 38 3 3025 445032093 445035134 0.000000e+00 4436
2 TraesCS3B01G371100 chr3D 92.640 394 23 2 3179 3572 445035738 445036125 2.410000e-156 562
3 TraesCS3B01G371100 chr3D 87.209 172 8 8 3024 3181 445035249 445035420 2.190000e-42 183
4 TraesCS3B01G371100 chr3A 94.064 2611 134 13 978 3572 586418361 586420966 0.000000e+00 3943
5 TraesCS3B01G371100 chr3A 91.357 995 53 25 3 977 586417349 586418330 0.000000e+00 1330


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 TraesCS3B01G371100 chr3B 583387217 583390788 3571 False 6597.0 6597 100.0000 1 3572 1 chr3B.!!$F1 3571
1 TraesCS3B01G371100 chr3D 445032093 445036125 4032 False 1727.0 4436 90.9990 3 3572 3 chr3D.!!$F1 3569
2 TraesCS3B01G371100 chr3A 586417349 586420966 3617 False 2636.5 3943 92.7105 3 3572 2 chr3A.!!$F1 3569

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
861 887 0.101579 GTCTAGCGAGAAGGTGGAGC 59.898 60.0 0.0 0.0 38.51 4.7 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2606 2672 0.101579 CCAAAACAACACCCGTGTCC 59.898 55.0 0.04 0.0 44.13 4.02 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
73 74 4.183865 CAGTTATCTCGCTTGGATCAACA 58.816 43.478 0.00 0.00 0.00 3.33
105 106 0.745845 ATGCGGCGAAAGAGAGCAAT 60.746 50.000 12.98 0.00 39.05 3.56
190 191 0.326595 TACAGGGCATCCGCTCAAAA 59.673 50.000 0.00 0.00 43.19 2.44
265 266 3.666902 CGTTCCAAGTAACCGCATTCTTG 60.667 47.826 0.00 0.00 37.57 3.02
286 287 3.607987 GGCATCTCGTCGAACGCG 61.608 66.667 3.53 3.53 42.21 6.01
297 298 2.230940 CGAACGCGATCCGAGCATT 61.231 57.895 15.93 0.00 40.82 3.56
325 326 2.125713 CCGCACACGACATAGGCA 60.126 61.111 0.00 0.00 43.93 4.75
331 332 1.324435 CACACGACATAGGCATTGACG 59.676 52.381 9.20 9.20 38.04 4.35
370 371 3.228499 GTGGAACTCGAACCCCTTC 57.772 57.895 0.00 0.00 0.00 3.46
499 500 1.254284 CGTCCCTGAAGAGGCTCAGT 61.254 60.000 18.26 3.53 41.15 3.41
631 632 3.227276 CGCCTCTCCGCCTGGTAT 61.227 66.667 0.00 0.00 36.30 2.73
646 647 0.834261 GGTATCTCAGGAGGAGGGCC 60.834 65.000 0.00 0.00 44.19 5.80
744 750 2.801631 CCATGAGGGGCTCCGTCTC 61.802 68.421 0.00 0.00 38.97 3.36
751 757 2.043852 GGCTCCGTCTCCTCCAGA 60.044 66.667 0.00 0.00 0.00 3.86
778 784 1.153939 CCAACGCCTCTCTCGTCTG 60.154 63.158 0.00 0.00 39.48 3.51
786 792 2.360801 GCCTCTCTCGTCTGCTTAGAAT 59.639 50.000 0.00 0.00 0.00 2.40
787 793 3.181480 GCCTCTCTCGTCTGCTTAGAATT 60.181 47.826 0.00 0.00 0.00 2.17
788 794 4.036971 GCCTCTCTCGTCTGCTTAGAATTA 59.963 45.833 0.00 0.00 0.00 1.40
789 795 5.278758 GCCTCTCTCGTCTGCTTAGAATTAT 60.279 44.000 0.00 0.00 0.00 1.28
815 839 2.775960 TCATGGTGCAATGGAGAGAGAT 59.224 45.455 0.00 0.00 0.00 2.75
826 852 5.768980 ATGGAGAGAGATAGAGAGAGAGG 57.231 47.826 0.00 0.00 0.00 3.69
836 862 2.427872 AGAGAGAGAGGGAGAGGCATA 58.572 52.381 0.00 0.00 0.00 3.14
837 863 2.108250 AGAGAGAGAGGGAGAGGCATAC 59.892 54.545 0.00 0.00 0.00 2.39
846 872 2.679082 GGAGAGGCATACCCTTGTCTA 58.321 52.381 0.00 0.00 46.60 2.59
848 874 2.036604 GAGAGGCATACCCTTGTCTAGC 59.963 54.545 0.00 0.00 46.60 3.42
858 884 2.285827 CTTGTCTAGCGAGAAGGTGG 57.714 55.000 0.00 0.00 37.01 4.61
859 885 1.819288 CTTGTCTAGCGAGAAGGTGGA 59.181 52.381 0.00 0.00 37.01 4.02
860 886 1.464734 TGTCTAGCGAGAAGGTGGAG 58.535 55.000 0.00 0.00 38.51 3.86
861 887 0.101579 GTCTAGCGAGAAGGTGGAGC 59.898 60.000 0.00 0.00 38.51 4.70
862 888 0.323451 TCTAGCGAGAAGGTGGAGCA 60.323 55.000 0.00 0.00 32.83 4.26
951 978 2.021355 TTGTGTTTTGCTTGCCCTTG 57.979 45.000 0.00 0.00 0.00 3.61
973 1000 0.525029 GGGCGTACTACGTTGCTCTC 60.525 60.000 10.23 0.00 44.73 3.20
986 1043 1.261480 TGCTCTCTTGTCCTCACTCC 58.739 55.000 0.00 0.00 0.00 3.85
999 1056 2.124693 CACTCCTCGCTCCTCCTCC 61.125 68.421 0.00 0.00 0.00 4.30
1008 1065 1.599047 CTCCTCCTCCATGTTGCGT 59.401 57.895 0.00 0.00 0.00 5.24
1014 1071 0.035439 CCTCCATGTTGCGTAGGGTT 60.035 55.000 0.00 0.00 0.00 4.11
1062 1119 2.189521 CCCGGATTCTCCAACCCG 59.810 66.667 0.73 0.00 41.47 5.28
1065 1122 2.674754 GGATTCTCCAACCCGCCA 59.325 61.111 0.00 0.00 36.28 5.69
1086 1143 1.985116 GAGGAGTCGGCCTGTCCTT 60.985 63.158 16.30 3.58 41.00 3.36
1088 1145 1.985116 GGAGTCGGCCTGTCCTTCT 60.985 63.158 0.00 0.00 0.00 2.85
1094 1151 2.679716 GCCTGTCCTTCTGCCCAT 59.320 61.111 0.00 0.00 0.00 4.00
1095 1152 1.000396 GCCTGTCCTTCTGCCCATT 60.000 57.895 0.00 0.00 0.00 3.16
1152 1215 2.520741 GAGAGCGAGGGGGAGGAG 60.521 72.222 0.00 0.00 0.00 3.69
1545 1611 2.201022 GCTCCTCCTAATCCGGCGA 61.201 63.158 9.30 0.00 0.00 5.54
1704 1770 1.739562 CCTGCTTCTGTCCAGCGAC 60.740 63.158 0.00 0.00 40.45 5.19
1749 1815 1.470098 GGCTTCAACATCGTGCTCAAT 59.530 47.619 0.00 0.00 0.00 2.57
1866 1932 3.316588 GGAGTATGATCTCGTGCTTCTCA 59.683 47.826 0.00 0.00 35.52 3.27
1914 1980 3.818210 TGAAGCTCTTTAACCGCATGAAA 59.182 39.130 0.00 0.00 0.00 2.69
2089 2155 0.392706 TCTTTGCAAGGCTCGTCAGA 59.607 50.000 3.19 0.00 0.00 3.27
2103 2169 1.198713 GTCAGATCCAGGAGGCAAGA 58.801 55.000 0.00 0.00 33.74 3.02
2205 2271 2.093235 CCCCACTGAGGTCTTTGATCTC 60.093 54.545 1.21 1.21 39.98 2.75
2232 2298 6.058183 GGATAAGATGAAGGCACTACATTGT 58.942 40.000 0.00 0.00 38.49 2.71
2377 2443 5.726688 GCGTACATTGTGTTCATACATGGAC 60.727 44.000 0.00 0.00 36.50 4.02
2395 2461 2.040412 GGACTGTTCCTGAATGGGAAGT 59.960 50.000 0.00 0.00 44.83 3.01
2606 2672 6.301169 ACTTGGAAGTGGTCTATAAAGAGG 57.699 41.667 0.00 0.00 37.98 3.69
2715 2781 8.539770 TCAAGTGATCTTCATCTACTTTGTTC 57.460 34.615 0.00 0.00 32.52 3.18
2743 2809 3.423154 GGTCAAGGAAGCCACGCG 61.423 66.667 3.53 3.53 0.00 6.01
2939 3006 4.749099 CACTAGATTGCTTGGCTGTAGATC 59.251 45.833 0.00 0.00 0.00 2.75
2944 3011 1.134699 TGCTTGGCTGTAGATCGGAAG 60.135 52.381 0.00 0.00 0.00 3.46
2969 3036 5.641155 AGAAAGTGCAACCTAGGGTTTATT 58.359 37.500 14.81 0.00 44.33 1.40
2977 3044 6.657541 TGCAACCTAGGGTTTATTCTGTTTAG 59.342 38.462 14.81 0.00 44.33 1.85
3045 3228 7.455058 TCATAGTTTGTACTGGGTACATGTTT 58.545 34.615 2.30 2.21 46.36 2.83
3046 3229 7.389330 TCATAGTTTGTACTGGGTACATGTTTG 59.611 37.037 2.30 6.64 46.36 2.93
3072 3255 9.888878 GATGATTGGTTCACAACATATAATGAG 57.111 33.333 0.00 0.00 42.94 2.90
3116 3299 3.635373 TCCGACTCCTATACTTTCGCATT 59.365 43.478 0.00 0.00 0.00 3.56
3244 3761 6.873076 TCATTTTCATGCTTACAACAATTCCC 59.127 34.615 0.00 0.00 0.00 3.97
3250 3767 5.957842 TGCTTACAACAATTCCCTTAGTG 57.042 39.130 0.00 0.00 0.00 2.74
3251 3768 4.217550 TGCTTACAACAATTCCCTTAGTGC 59.782 41.667 0.00 0.00 0.00 4.40
3289 3806 7.780008 TTCACATATAACCATTTAGTGACCG 57.220 36.000 0.00 0.00 34.64 4.79
3299 3816 1.496060 TTAGTGACCGCTCATCCCAT 58.504 50.000 0.00 0.00 0.00 4.00
3315 3832 3.211963 ATTGCAGAATCGGCCGCC 61.212 61.111 23.51 12.26 0.00 6.13
3332 3849 1.600485 CGCCGTGTGAAGTTTTAGGTT 59.400 47.619 0.00 0.00 0.00 3.50
3524 4041 2.224281 TGTTGATTCTGAGGTGAGCGTT 60.224 45.455 0.00 0.00 0.00 4.84
3532 4049 1.272490 TGAGGTGAGCGTTTACCAGAG 59.728 52.381 15.48 0.00 39.46 3.35
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 6.796785 ATATTGGAAGGATTCTTTTGGGTG 57.203 37.500 0.00 0.00 46.56 4.61
1 2 8.343787 TCTAATATTGGAAGGATTCTTTTGGGT 58.656 33.333 0.00 0.00 46.56 4.51
73 74 1.452651 CCGCATGATGGCAGAAGGT 60.453 57.895 0.00 0.00 0.00 3.50
105 106 3.138798 GTCGCTCGGTAGAGGCCA 61.139 66.667 5.01 0.00 44.51 5.36
190 191 2.154798 TTGAGTACGCGAGGCTGCTT 62.155 55.000 15.93 0.00 0.00 3.91
265 266 4.508128 TTCGACGAGATGCCGGCC 62.508 66.667 26.77 9.73 33.11 6.13
286 287 1.958205 CCTGGCGAATGCTCGGATC 60.958 63.158 0.00 0.00 45.55 3.36
325 326 2.047274 CACACCGCCCTCGTCAAT 60.047 61.111 0.00 0.00 0.00 2.57
331 332 4.367023 TACGTGCACACCGCCCTC 62.367 66.667 18.64 0.00 41.33 4.30
630 631 1.383803 GTGGCCCTCCTCCTGAGAT 60.384 63.158 0.00 0.00 44.42 2.75
631 632 2.039624 GTGGCCCTCCTCCTGAGA 59.960 66.667 0.00 0.00 44.42 3.27
704 708 2.266055 GTTCCCGGCTGACCTCTG 59.734 66.667 0.00 0.00 0.00 3.35
744 750 2.108970 GTTGGGTAGTAGGTCTGGAGG 58.891 57.143 0.00 0.00 0.00 4.30
751 757 0.040794 AGAGGCGTTGGGTAGTAGGT 59.959 55.000 0.00 0.00 0.00 3.08
753 759 1.677052 GAGAGAGGCGTTGGGTAGTAG 59.323 57.143 0.00 0.00 0.00 2.57
754 760 1.760192 GAGAGAGGCGTTGGGTAGTA 58.240 55.000 0.00 0.00 0.00 1.82
755 761 1.313812 CGAGAGAGGCGTTGGGTAGT 61.314 60.000 0.00 0.00 0.00 2.73
778 784 7.874940 TGCACCATGACATAATAATTCTAAGC 58.125 34.615 0.00 0.00 0.00 3.09
786 792 6.363882 TCTCCATTGCACCATGACATAATAA 58.636 36.000 0.00 0.00 0.00 1.40
787 793 5.939447 TCTCCATTGCACCATGACATAATA 58.061 37.500 0.00 0.00 0.00 0.98
788 794 4.795469 TCTCCATTGCACCATGACATAAT 58.205 39.130 0.00 0.00 0.00 1.28
789 795 4.080413 TCTCTCCATTGCACCATGACATAA 60.080 41.667 0.00 0.00 0.00 1.90
815 839 1.900254 TGCCTCTCCCTCTCTCTCTA 58.100 55.000 0.00 0.00 0.00 2.43
826 852 1.501582 AGACAAGGGTATGCCTCTCC 58.498 55.000 0.00 0.00 34.45 3.71
836 862 1.187087 CCTTCTCGCTAGACAAGGGT 58.813 55.000 0.00 0.00 38.43 4.34
837 863 1.134965 CACCTTCTCGCTAGACAAGGG 60.135 57.143 9.99 3.52 43.99 3.95
846 872 1.910772 ACTGCTCCACCTTCTCGCT 60.911 57.895 0.00 0.00 0.00 4.93
848 874 1.079543 CCACTGCTCCACCTTCTCG 60.080 63.158 0.00 0.00 0.00 4.04
855 881 2.985456 CCTCCTCCACTGCTCCAC 59.015 66.667 0.00 0.00 0.00 4.02
856 882 3.005539 GCCTCCTCCACTGCTCCA 61.006 66.667 0.00 0.00 0.00 3.86
857 883 2.686835 AGCCTCCTCCACTGCTCC 60.687 66.667 0.00 0.00 0.00 4.70
858 884 2.583520 CAGCCTCCTCCACTGCTC 59.416 66.667 0.00 0.00 30.08 4.26
859 885 3.007920 CCAGCCTCCTCCACTGCT 61.008 66.667 0.00 0.00 33.52 4.24
860 886 3.005539 TCCAGCCTCCTCCACTGC 61.006 66.667 0.00 0.00 0.00 4.40
861 887 1.611851 AGTCCAGCCTCCTCCACTG 60.612 63.158 0.00 0.00 0.00 3.66
862 888 1.305718 GAGTCCAGCCTCCTCCACT 60.306 63.158 0.00 0.00 0.00 4.00
973 1000 0.172352 GAGCGAGGAGTGAGGACAAG 59.828 60.000 0.00 0.00 0.00 3.16
986 1043 0.179089 CAACATGGAGGAGGAGCGAG 60.179 60.000 0.00 0.00 0.00 5.03
999 1056 0.999406 CGAGAACCCTACGCAACATG 59.001 55.000 0.00 0.00 0.00 3.21
1008 1065 3.145551 GCTCCCGCGAGAACCCTA 61.146 66.667 8.23 0.00 38.52 3.53
1074 1131 3.706373 GGCAGAAGGACAGGCCGA 61.706 66.667 0.00 0.00 43.43 5.54
1136 1193 4.150454 CCTCCTCCCCCTCGCTCT 62.150 72.222 0.00 0.00 0.00 4.09
1137 1194 4.144727 TCCTCCTCCCCCTCGCTC 62.145 72.222 0.00 0.00 0.00 5.03
1152 1215 1.214853 GAAGGAGAACGGGTCGTCC 59.785 63.158 4.06 4.06 39.99 4.79
1560 1626 1.586564 GATCGCGCTAGCAACGTCT 60.587 57.895 22.11 13.41 45.49 4.18
1704 1770 0.601558 TCTCGAACGGGAACTCCTTG 59.398 55.000 0.00 0.00 35.95 3.61
1749 1815 1.902918 GACCATGTTGCACCAGCCA 60.903 57.895 0.00 0.00 41.13 4.75
1839 1905 3.761218 AGCACGAGATCATACTCCCATAG 59.239 47.826 0.00 0.00 33.83 2.23
1866 1932 2.155197 AATCCAAGCTCCCGGCCTTT 62.155 55.000 0.00 0.00 43.05 3.11
1977 2043 3.127533 GCCTCATCCACACACCGC 61.128 66.667 0.00 0.00 0.00 5.68
2089 2155 2.048601 CATCTCTCTTGCCTCCTGGAT 58.951 52.381 0.00 0.00 34.57 3.41
2103 2169 5.901853 TCCTACCATCTCATCAAACATCTCT 59.098 40.000 0.00 0.00 0.00 3.10
2205 2271 5.674525 TGTAGTGCCTTCATCTTATCCAAG 58.325 41.667 0.00 0.00 0.00 3.61
2232 2298 1.649321 AAGTGTCCATCTCTGGCTCA 58.351 50.000 0.00 0.00 42.80 4.26
2377 2443 5.165961 TCTAACTTCCCATTCAGGAACAG 57.834 43.478 0.00 0.00 41.08 3.16
2395 2461 4.844349 AATACTTTGCAGCCTCCTCTAA 57.156 40.909 0.00 0.00 0.00 2.10
2594 2660 3.029570 ACCCGTGTCCCTCTTTATAGAC 58.970 50.000 0.00 0.00 0.00 2.59
2601 2667 1.342672 ACAACACCCGTGTCCCTCTT 61.343 55.000 0.04 0.00 44.13 2.85
2603 2669 0.464916 AAACAACACCCGTGTCCCTC 60.465 55.000 0.04 0.00 44.13 4.30
2606 2672 0.101579 CCAAAACAACACCCGTGTCC 59.898 55.000 0.04 0.00 44.13 4.02
2715 2781 2.268076 CCTTGACCAAACCGGCCAG 61.268 63.158 0.00 0.00 39.03 4.85
2939 3006 2.767505 AGGTTGCACTTTCTACTTCCG 58.232 47.619 0.00 0.00 0.00 4.30
2944 3011 3.697619 ACCCTAGGTTGCACTTTCTAC 57.302 47.619 8.29 0.00 27.29 2.59
2969 3036 5.425217 TGATGCCTATCCAAGTCTAAACAGA 59.575 40.000 0.00 0.00 32.09 3.41
2977 3044 3.065925 GCAAAGTGATGCCTATCCAAGTC 59.934 47.826 0.00 0.00 40.49 3.01
3045 3228 9.406113 TCATTATATGTTGTGAACCAATCATCA 57.594 29.630 0.00 0.00 40.97 3.07
3046 3229 9.888878 CTCATTATATGTTGTGAACCAATCATC 57.111 33.333 0.00 0.00 40.97 2.92
3072 3255 5.036117 ACCAGTATGAATATGGTGGACAC 57.964 43.478 0.00 0.00 45.53 3.67
3219 3736 6.873076 GGGAATTGTTGTAAGCATGAAAATGA 59.127 34.615 0.00 0.00 0.00 2.57
3250 3767 9.559958 GTTATATGTGAATAAATATGCCAGTGC 57.440 33.333 0.00 0.00 38.26 4.40
3289 3806 1.266175 CGATTCTGCAATGGGATGAGC 59.734 52.381 0.00 0.00 0.00 4.26
3524 4041 8.783660 ATCAGATATAACTGGAACTCTGGTAA 57.216 34.615 9.85 0.00 38.31 2.85
3532 4049 8.643324 ACCTAACTGATCAGATATAACTGGAAC 58.357 37.037 29.27 3.50 38.31 3.62


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

AutoCloner maintained by Alex Coulton.