Multiple sequence alignment - TraesCS2B01G351900

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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 TraesCS2B01G351900 chr2B 100.000 2768 0 0 1 2768 500839387 500836620 0.000000e+00 5112
1 TraesCS2B01G351900 chr2D 92.757 2775 136 35 32 2768 425495498 425492751 0.000000e+00 3951
2 TraesCS2B01G351900 chr2A 91.485 1832 102 19 32 1846 562680402 562682196 0.000000e+00 2470
3 TraesCS2B01G351900 chr2A 87.150 786 38 19 1919 2675 562685939 562686690 0.000000e+00 833
4 TraesCS2B01G351900 chr2A 92.405 79 3 1 1838 1916 562685808 562685883 2.910000e-20 110


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 TraesCS2B01G351900 chr2B 500836620 500839387 2767 True 5112.000000 5112 100.000000 1 2768 1 chr2B.!!$R1 2767
1 TraesCS2B01G351900 chr2D 425492751 425495498 2747 True 3951.000000 3951 92.757000 32 2768 1 chr2D.!!$R1 2736
2 TraesCS2B01G351900 chr2A 562680402 562686690 6288 False 1137.666667 2470 90.346667 32 2675 3 chr2A.!!$F1 2643

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
163 164 0.250770 GCCGGGGAGAAGAGTTTGTT 60.251 55.0 2.18 0.0 0.00 2.83 F
832 839 0.811616 AGCATAGCTAACACCAGCGC 60.812 55.0 0.00 0.0 46.52 5.92 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1356 1382 0.033405 AGGCCGAGAGCTGGTAGTAA 60.033 55.0 0.0 0.0 43.05 2.24 R
2023 5724 0.599204 GGTGTCAAAAGACGGAGCGA 60.599 55.0 0.0 0.0 0.00 4.93 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
18 19 4.736896 GCGACACGGGAGGGACAC 62.737 72.222 0.00 0.00 36.77 3.67
24 25 2.361357 CGGGAGGGACACGTCTCT 60.361 66.667 0.00 0.00 44.55 3.10
29 30 3.989782 AGGGACACGTCTCTCTCAT 57.010 52.632 0.00 0.00 34.85 2.90
30 31 1.468985 AGGGACACGTCTCTCTCATG 58.531 55.000 0.00 0.00 34.85 3.07
163 164 0.250770 GCCGGGGAGAAGAGTTTGTT 60.251 55.000 2.18 0.00 0.00 2.83
166 167 2.143925 CGGGGAGAAGAGTTTGTTCAC 58.856 52.381 0.00 0.00 0.00 3.18
167 168 2.505405 GGGGAGAAGAGTTTGTTCACC 58.495 52.381 0.00 0.00 34.80 4.02
168 169 2.106684 GGGGAGAAGAGTTTGTTCACCT 59.893 50.000 3.29 0.00 35.60 4.00
169 170 3.142174 GGGAGAAGAGTTTGTTCACCTG 58.858 50.000 3.29 0.00 35.60 4.00
170 171 2.550180 GGAGAAGAGTTTGTTCACCTGC 59.450 50.000 0.00 0.00 33.29 4.85
171 172 3.206150 GAGAAGAGTTTGTTCACCTGCA 58.794 45.455 0.00 0.00 0.00 4.41
172 173 3.209410 AGAAGAGTTTGTTCACCTGCAG 58.791 45.455 6.78 6.78 0.00 4.41
202 203 2.604373 GCAGCAAAACTACGTGCATCAA 60.604 45.455 0.00 0.00 43.42 2.57
324 331 4.034742 ACACAGCACTAGTTTGTTTAACGG 59.965 41.667 6.98 0.00 41.78 4.44
329 336 7.095355 ACAGCACTAGTTTGTTTAACGGATAAG 60.095 37.037 0.00 0.00 41.78 1.73
353 360 3.173151 TCAGTTGGCATGTCCTCTAGAA 58.827 45.455 0.00 0.00 35.26 2.10
395 402 6.121776 TCTGCATTTTTGTAGAGGGTTCTA 57.878 37.500 0.00 0.00 34.79 2.10
602 609 5.174035 GTGCTCAACTATCATCACGACATAC 59.826 44.000 0.00 0.00 0.00 2.39
653 660 4.280677 TGTAAAATCACAGCCCCAGAAAAG 59.719 41.667 0.00 0.00 0.00 2.27
673 680 1.068541 GTTTACTGAAGCCAAAGCGGG 60.069 52.381 0.00 0.00 46.67 6.13
689 696 0.951558 CGGGTCCTGTTTGTTCCAAG 59.048 55.000 0.00 0.00 0.00 3.61
700 707 1.429930 TGTTCCAAGGTACCTGCAGA 58.570 50.000 17.14 9.94 0.00 4.26
701 708 1.347707 TGTTCCAAGGTACCTGCAGAG 59.652 52.381 17.14 8.04 0.00 3.35
702 709 1.623811 GTTCCAAGGTACCTGCAGAGA 59.376 52.381 17.14 5.36 0.00 3.10
778 785 2.507886 ACATTCCCGAACCATATCACCA 59.492 45.455 0.00 0.00 0.00 4.17
790 797 5.862845 ACCATATCACCATGTTCAGATCTC 58.137 41.667 0.00 0.00 0.00 2.75
832 839 0.811616 AGCATAGCTAACACCAGCGC 60.812 55.000 0.00 0.00 46.52 5.92
910 917 7.368833 AGTACCATGTGCTATAAATACGTCTC 58.631 38.462 0.00 0.00 0.00 3.36
931 938 2.796383 CGCCTTCGTAGAGATTCACCAG 60.796 54.545 0.00 0.00 38.43 4.00
938 945 1.494960 AGAGATTCACCAGAGCCTCC 58.505 55.000 0.00 0.00 0.00 4.30
968 994 2.493278 GGTGCATTTGTAGCAAGTCCAT 59.507 45.455 0.00 0.00 44.64 3.41
969 995 3.428045 GGTGCATTTGTAGCAAGTCCATC 60.428 47.826 0.00 0.00 44.64 3.51
971 997 3.019564 GCATTTGTAGCAAGTCCATCCT 58.980 45.455 0.00 0.00 0.00 3.24
972 998 3.181493 GCATTTGTAGCAAGTCCATCCTG 60.181 47.826 0.00 0.00 0.00 3.86
973 999 3.788227 TTTGTAGCAAGTCCATCCTGT 57.212 42.857 0.00 0.00 0.00 4.00
974 1000 4.901197 TTTGTAGCAAGTCCATCCTGTA 57.099 40.909 0.00 0.00 0.00 2.74
976 1002 5.435686 TTGTAGCAAGTCCATCCTGTAAT 57.564 39.130 0.00 0.00 0.00 1.89
979 1005 5.423931 TGTAGCAAGTCCATCCTGTAATACA 59.576 40.000 0.00 0.00 0.00 2.29
980 1006 4.770795 AGCAAGTCCATCCTGTAATACAC 58.229 43.478 0.00 0.00 0.00 2.90
981 1007 4.225042 AGCAAGTCCATCCTGTAATACACA 59.775 41.667 0.00 0.00 35.30 3.72
982 1008 4.332819 GCAAGTCCATCCTGTAATACACAC 59.667 45.833 0.00 0.00 32.33 3.82
983 1009 4.386867 AGTCCATCCTGTAATACACACG 57.613 45.455 0.00 0.00 32.33 4.49
984 1010 3.132289 AGTCCATCCTGTAATACACACGG 59.868 47.826 0.00 0.00 32.33 4.94
987 1013 2.925578 TCCTGTAATACACACGGTCG 57.074 50.000 0.00 0.00 32.33 4.79
996 1022 1.278637 CACACGGTCGAGTTTTGCC 59.721 57.895 0.00 0.00 0.00 4.52
1023 1049 2.747855 CCCAAGGCGGCTGTTCTC 60.748 66.667 14.21 0.00 0.00 2.87
1190 1216 1.975680 GTTCCTGGAGTACCTCACCAA 59.024 52.381 0.00 0.00 36.43 3.67
1233 1259 4.988598 AGCCAGGCCAACGACACG 62.989 66.667 8.22 0.00 0.00 4.49
1311 1337 1.069765 CGTGCTGTCCAACCTCACT 59.930 57.895 0.00 0.00 0.00 3.41
1413 1439 0.606401 CGAGCCAGGTGTCCATGTTT 60.606 55.000 0.00 0.00 0.00 2.83
1753 1779 2.203788 TTCTGCTGGTCTCCGGGT 60.204 61.111 0.00 0.00 0.00 5.28
1883 5529 8.126700 GGTGTACTACAACATAATGTAAATGGC 58.873 37.037 0.00 0.00 35.45 4.40
1992 5693 4.203828 CGTGAATCAACGTCTCTGTTTTG 58.796 43.478 0.00 0.00 38.74 2.44
2023 5724 3.007723 TCTGAAGAACAAGAGCTCTGCAT 59.992 43.478 19.06 6.02 25.38 3.96
2070 5782 0.744874 TCGATCCTCTTAACCGCCTG 59.255 55.000 0.00 0.00 0.00 4.85
2071 5783 0.249489 CGATCCTCTTAACCGCCTGG 60.249 60.000 0.00 0.00 42.84 4.45
2075 5787 1.002773 TCCTCTTAACCGCCTGGAAAC 59.997 52.381 0.00 0.00 39.21 2.78
2079 5791 2.235402 TCTTAACCGCCTGGAAACTAGG 59.765 50.000 0.00 0.00 39.21 3.02
2080 5792 1.941377 TAACCGCCTGGAAACTAGGA 58.059 50.000 0.00 0.00 37.52 2.94
2081 5793 1.061546 AACCGCCTGGAAACTAGGAA 58.938 50.000 0.00 0.00 37.52 3.36
2082 5794 0.613777 ACCGCCTGGAAACTAGGAAG 59.386 55.000 0.00 0.00 37.52 3.46
2083 5795 0.744771 CCGCCTGGAAACTAGGAAGC 60.745 60.000 0.00 0.00 37.52 3.86
2084 5796 0.250513 CGCCTGGAAACTAGGAAGCT 59.749 55.000 0.00 0.00 37.52 3.74
2085 5797 1.480954 CGCCTGGAAACTAGGAAGCTA 59.519 52.381 0.00 0.00 37.52 3.32
2086 5798 2.482142 CGCCTGGAAACTAGGAAGCTAG 60.482 54.545 0.00 0.00 37.52 3.42
2087 5799 2.743510 GCCTGGAAACTAGGAAGCTAGC 60.744 54.545 6.62 6.62 37.52 3.42
2088 5800 2.158885 CCTGGAAACTAGGAAGCTAGCC 60.159 54.545 12.13 0.00 37.52 3.93
2197 5920 4.849310 GCCGCCGCAATGTCCCTA 62.849 66.667 0.00 0.00 34.03 3.53
2344 6067 0.596577 TCGTGGAGGTGTTCGAGAAG 59.403 55.000 0.00 0.00 0.00 2.85
2427 6150 0.668401 GTCCACCCGTCGGTAACTTG 60.668 60.000 11.06 0.00 42.04 3.16
2475 6198 7.758613 TCATACTATCGTCTCGATCTGATAC 57.241 40.000 7.90 0.00 43.45 2.24
2485 6214 2.360801 TCGATCTGATACGATGTTGGCA 59.639 45.455 7.70 0.00 33.62 4.92
2687 6419 2.671070 CTGTCGAGGTGGGCCAAT 59.329 61.111 8.40 0.00 37.19 3.16
2706 6438 2.190578 CCAAGATCCTCGGCACCC 59.809 66.667 0.00 0.00 0.00 4.61
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 4.736896 GTGTCCCTCCCGTGTCGC 62.737 72.222 0.00 0.00 0.00 5.19
2 3 4.415332 CGTGTCCCTCCCGTGTCG 62.415 72.222 0.00 0.00 0.00 4.35
3 4 3.278592 GACGTGTCCCTCCCGTGTC 62.279 68.421 0.00 0.00 34.51 3.67
4 5 3.300765 GACGTGTCCCTCCCGTGT 61.301 66.667 0.00 0.00 34.51 4.49
5 6 2.989824 AGACGTGTCCCTCCCGTG 60.990 66.667 0.00 0.00 34.51 4.94
6 7 2.675772 GAGACGTGTCCCTCCCGT 60.676 66.667 0.17 0.00 37.56 5.28
7 8 2.361357 AGAGACGTGTCCCTCCCG 60.361 66.667 9.40 0.00 0.00 5.14
8 9 1.000646 AGAGAGACGTGTCCCTCCC 60.001 63.158 9.40 0.00 35.36 4.30
9 10 0.322636 TGAGAGAGACGTGTCCCTCC 60.323 60.000 19.38 4.66 35.36 4.30
10 11 1.403679 CATGAGAGAGACGTGTCCCTC 59.596 57.143 16.10 16.10 35.04 4.30
11 12 1.468985 CATGAGAGAGACGTGTCCCT 58.531 55.000 9.40 1.97 0.00 4.20
12 13 0.457851 CCATGAGAGAGACGTGTCCC 59.542 60.000 9.40 0.00 0.00 4.46
13 14 0.179124 GCCATGAGAGAGACGTGTCC 60.179 60.000 9.40 1.07 0.00 4.02
14 15 0.179124 GGCCATGAGAGAGACGTGTC 60.179 60.000 4.17 4.17 0.00 3.67
15 16 0.900182 TGGCCATGAGAGAGACGTGT 60.900 55.000 0.00 0.00 0.00 4.49
16 17 0.463204 ATGGCCATGAGAGAGACGTG 59.537 55.000 20.04 0.00 0.00 4.49
17 18 1.198713 AATGGCCATGAGAGAGACGT 58.801 50.000 21.63 0.00 0.00 4.34
18 19 3.257873 AGATAATGGCCATGAGAGAGACG 59.742 47.826 21.63 0.00 0.00 4.18
19 20 4.563168 CCAGATAATGGCCATGAGAGAGAC 60.563 50.000 21.63 5.49 43.83 3.36
20 21 3.581770 CCAGATAATGGCCATGAGAGAGA 59.418 47.826 21.63 0.00 43.83 3.10
21 22 3.940319 CCAGATAATGGCCATGAGAGAG 58.060 50.000 21.63 8.13 43.83 3.20
68 69 2.200370 ACCCCGTGTCTCACCAGA 59.800 61.111 0.00 0.00 0.00 3.86
93 94 4.208686 GTCTCGGCGCTACTGGGG 62.209 72.222 7.64 0.00 0.00 4.96
121 122 4.363990 CTGGAGACGTGCACGCCT 62.364 66.667 37.35 33.09 44.43 5.52
152 153 2.287248 GCTGCAGGTGAACAAACTCTTC 60.287 50.000 17.12 0.00 0.00 2.87
180 181 0.240945 ATGCACGTAGTTTTGCTGCC 59.759 50.000 0.00 0.00 41.61 4.85
187 188 5.700832 TCTGAATCTTTGATGCACGTAGTTT 59.299 36.000 0.00 0.00 41.61 2.66
245 251 9.585369 TGAATGATCAAATAATAATGTAGGCCA 57.415 29.630 5.01 0.00 30.99 5.36
324 331 5.615289 AGGACATGCCAACTGATACTTATC 58.385 41.667 8.58 0.00 40.02 1.75
329 336 3.550437 AGAGGACATGCCAACTGATAC 57.450 47.619 8.58 0.00 40.02 2.24
353 360 4.213482 GCAGAATAGACGTGGAAACTGTTT 59.787 41.667 5.29 5.29 0.00 2.83
395 402 0.810031 GCACCGACGGAATGCATAGT 60.810 55.000 23.38 0.11 39.23 2.12
398 405 2.824041 GGCACCGACGGAATGCAT 60.824 61.111 25.38 0.00 41.27 3.96
556 563 1.142870 TGTGCTTAGCCCTTCAGTTGT 59.857 47.619 0.29 0.00 0.00 3.32
596 603 5.793030 ACCTTCAGGCATAGTAGTATGTC 57.207 43.478 13.35 13.35 41.00 3.06
602 609 5.122396 GTGTCAAAACCTTCAGGCATAGTAG 59.878 44.000 0.00 0.00 39.32 2.57
653 660 1.068541 CCCGCTTTGGCTTCAGTAAAC 60.069 52.381 0.00 0.00 35.87 2.01
689 696 1.205893 CAGGAACTCTCTGCAGGTACC 59.794 57.143 15.13 2.73 34.60 3.34
700 707 5.188555 TGTTCTTCTGATATGCAGGAACTCT 59.811 40.000 16.02 0.00 44.98 3.24
701 708 5.423015 TGTTCTTCTGATATGCAGGAACTC 58.577 41.667 16.02 0.00 44.98 3.01
702 709 5.426689 TGTTCTTCTGATATGCAGGAACT 57.573 39.130 16.02 0.00 44.98 3.01
778 785 3.584406 TGGTCAACTGGAGATCTGAACAT 59.416 43.478 0.00 0.00 30.69 2.71
910 917 1.134367 TGGTGAATCTCTACGAAGGCG 59.866 52.381 0.00 0.00 44.79 5.52
931 938 0.033228 CACCTGATCGATGGAGGCTC 59.967 60.000 16.75 5.78 0.00 4.70
938 945 3.303593 GCTACAAATGCACCTGATCGATG 60.304 47.826 0.54 0.00 0.00 3.84
968 994 2.421073 CTCGACCGTGTGTATTACAGGA 59.579 50.000 7.41 0.00 45.61 3.86
969 995 2.163010 ACTCGACCGTGTGTATTACAGG 59.837 50.000 0.00 0.00 40.69 4.00
971 997 3.921119 AACTCGACCGTGTGTATTACA 57.079 42.857 0.00 0.00 36.82 2.41
972 998 4.664891 GCAAAACTCGACCGTGTGTATTAC 60.665 45.833 0.00 0.00 0.00 1.89
973 999 3.429543 GCAAAACTCGACCGTGTGTATTA 59.570 43.478 0.00 0.00 0.00 0.98
974 1000 2.222445 GCAAAACTCGACCGTGTGTATT 59.778 45.455 0.00 0.00 0.00 1.89
976 1002 1.210870 GCAAAACTCGACCGTGTGTA 58.789 50.000 0.00 0.00 0.00 2.90
979 1005 2.241880 CGGCAAAACTCGACCGTGT 61.242 57.895 1.98 0.00 40.77 4.49
980 1006 1.492319 TTCGGCAAAACTCGACCGTG 61.492 55.000 9.38 0.00 45.76 4.94
981 1007 0.810823 TTTCGGCAAAACTCGACCGT 60.811 50.000 9.38 0.00 45.76 4.83
982 1008 0.515564 ATTTCGGCAAAACTCGACCG 59.484 50.000 3.66 3.66 46.97 4.79
983 1009 1.401018 CCATTTCGGCAAAACTCGACC 60.401 52.381 0.00 0.00 34.99 4.79
984 1010 1.533731 TCCATTTCGGCAAAACTCGAC 59.466 47.619 0.00 0.00 34.99 4.20
987 1013 1.402852 GGCTCCATTTCGGCAAAACTC 60.403 52.381 0.00 0.00 33.14 3.01
996 1022 3.200522 GCCTTGGGCTCCATTTCG 58.799 61.111 0.80 0.00 46.69 3.46
1083 1109 3.593794 GGGGTCTCGACGATCGGG 61.594 72.222 20.98 11.07 42.83 5.14
1190 1216 0.168348 CGTCTTGATCACGTCGGTCT 59.832 55.000 10.25 0.00 32.41 3.85
1233 1259 2.045926 ACGGTGATGCCCTGCTTC 60.046 61.111 0.00 0.00 34.04 3.86
1356 1382 0.033405 AGGCCGAGAGCTGGTAGTAA 60.033 55.000 0.00 0.00 43.05 2.24
1400 1426 1.202710 TGTACGCAAACATGGACACCT 60.203 47.619 0.00 0.00 0.00 4.00
1413 1439 0.102663 TGACGTTCACCTTGTACGCA 59.897 50.000 5.39 2.85 43.43 5.24
1753 1779 7.827236 AGAATTATCCGACTACACCATCAAAAA 59.173 33.333 0.00 0.00 0.00 1.94
1864 5510 5.123979 TGTGCGCCATTTACATTATGTTGTA 59.876 36.000 4.18 0.00 0.00 2.41
1865 5511 4.082517 TGTGCGCCATTTACATTATGTTGT 60.083 37.500 4.18 0.00 0.00 3.32
1866 5512 4.419280 TGTGCGCCATTTACATTATGTTG 58.581 39.130 4.18 0.00 0.00 3.33
1883 5529 4.460505 CAGTGCATACATTATGATGTGCG 58.539 43.478 13.08 5.26 45.80 5.34
2023 5724 0.599204 GGTGTCAAAAGACGGAGCGA 60.599 55.000 0.00 0.00 0.00 4.93
2043 5755 3.007398 GGTTAAGAGGATCGATGCAGGAT 59.993 47.826 19.67 2.90 42.67 3.24
2070 5782 1.755380 TCGGCTAGCTTCCTAGTTTCC 59.245 52.381 15.72 0.00 42.51 3.13
2071 5783 3.449632 CTTCGGCTAGCTTCCTAGTTTC 58.550 50.000 15.72 0.00 42.51 2.78
2075 5787 3.579066 GCTTCGGCTAGCTTCCTAG 57.421 57.895 15.72 6.60 43.23 3.02
2098 5810 0.884704 TCCGTTCTTTGTGCAGAGGC 60.885 55.000 0.00 0.00 41.68 4.70
2135 5858 3.730761 GCAACTGCCGCAGTGAGG 61.731 66.667 26.37 18.71 44.62 3.86
2136 5859 2.974148 TGCAACTGCCGCAGTGAG 60.974 61.111 26.37 21.30 44.62 3.51
2137 5860 3.279116 GTGCAACTGCCGCAGTGA 61.279 61.111 26.37 11.01 44.62 3.41
2371 6094 4.796495 GCGGGGGCGAAGATGGTT 62.796 66.667 0.00 0.00 0.00 3.67
2475 6198 4.531708 CAACGGTTGCCAACATCG 57.468 55.556 10.18 7.27 0.00 3.84
2485 6214 2.124320 ACAGCACCTGCAACGGTT 60.124 55.556 0.00 0.00 45.16 4.44
2667 6399 4.329545 GGCCCACCTCGACAGCAA 62.330 66.667 0.00 0.00 0.00 3.91


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

AutoCloner maintained by Alex Coulton.