Multiple sequence alignment - TraesCS2B01G208500

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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 TraesCS2B01G208500 chr2B 100.000 2747 0 0 1 2747 189746820 189744074 0.000000e+00 5073
1 TraesCS2B01G208500 chr2A 93.439 2774 137 23 4 2747 141284423 141281665 0.000000e+00 4072
2 TraesCS2B01G208500 chr2D 92.825 2676 124 26 5 2637 133273997 133271347 0.000000e+00 3816
3 TraesCS2B01G208500 chr2D 92.857 112 8 0 2636 2747 133271196 133271085 2.190000e-36 163


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 TraesCS2B01G208500 chr2B 189744074 189746820 2746 True 5073.0 5073 100.000 1 2747 1 chr2B.!!$R1 2746
1 TraesCS2B01G208500 chr2A 141281665 141284423 2758 True 4072.0 4072 93.439 4 2747 1 chr2A.!!$R1 2743
2 TraesCS2B01G208500 chr2D 133271085 133273997 2912 True 1989.5 3816 92.841 5 2747 2 chr2D.!!$R1 2742

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
389 417 0.035915 GAAAGCCAGTCTCCACTCCC 60.036 60.0 0.0 0.00 0.00 4.30 F
794 823 0.664767 GCGCATCACCTAGATCCGTC 60.665 60.0 0.3 0.00 40.08 4.79 F
1620 1658 0.327259 ATGCTGATATGATGCCGGCT 59.673 50.0 29.7 13.55 33.59 5.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1341 1379 0.307760 GCGTCCTGAACACAAAGTGG 59.692 55.000 1.93 0.0 37.94 4.00 R
1701 1739 1.076677 TCCGAGAGAGGTAACAGGGTT 59.923 52.381 0.00 0.0 41.41 4.11 R
2439 2488 5.011840 TGGGCAAATGAAATTCTGTGATTCA 59.988 36.000 0.00 0.0 33.67 2.57 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
36 37 6.604735 AAGACGTGTGCTTCATTATATTCC 57.395 37.500 0.00 0.00 0.00 3.01
47 48 9.791801 TGCTTCATTATATTCCTACTTAATGCA 57.208 29.630 0.00 0.00 33.88 3.96
80 89 7.722728 TCTTTAGGGATAGAGTTTGCGATAGTA 59.277 37.037 0.00 0.00 39.35 1.82
91 100 3.974871 TGCGATAGTAGCGTGAATGTA 57.025 42.857 9.85 0.00 37.44 2.29
93 102 3.314357 TGCGATAGTAGCGTGAATGTAGT 59.686 43.478 9.85 0.00 37.44 2.73
119 128 3.057315 AGAAAATTGTTCACGGGCTGATG 60.057 43.478 0.00 0.00 0.00 3.07
122 131 1.522668 TTGTTCACGGGCTGATGAAG 58.477 50.000 0.00 0.00 35.55 3.02
138 147 4.460731 TGATGAAGCTATATCTGGGAGTCG 59.539 45.833 10.42 0.00 0.00 4.18
144 153 3.957497 GCTATATCTGGGAGTCGGATGAT 59.043 47.826 0.00 0.00 41.35 2.45
148 157 2.437413 TCTGGGAGTCGGATGATATCG 58.563 52.381 0.00 0.00 0.00 2.92
149 158 2.039879 TCTGGGAGTCGGATGATATCGA 59.960 50.000 0.00 0.00 0.00 3.59
150 159 2.421775 CTGGGAGTCGGATGATATCGAG 59.578 54.545 0.00 0.00 36.00 4.04
157 166 5.290386 AGTCGGATGATATCGAGGAAAAAC 58.710 41.667 0.00 0.00 36.00 2.43
158 167 4.448060 GTCGGATGATATCGAGGAAAAACC 59.552 45.833 0.00 0.00 36.00 3.27
159 168 4.100344 TCGGATGATATCGAGGAAAAACCA 59.900 41.667 0.00 0.00 42.04 3.67
160 169 4.211374 CGGATGATATCGAGGAAAAACCAC 59.789 45.833 0.00 0.00 42.04 4.16
161 170 5.368989 GGATGATATCGAGGAAAAACCACT 58.631 41.667 0.00 0.00 42.04 4.00
162 171 6.522054 GGATGATATCGAGGAAAAACCACTA 58.478 40.000 0.00 0.00 42.04 2.74
163 172 6.990349 GGATGATATCGAGGAAAAACCACTAA 59.010 38.462 0.00 0.00 42.04 2.24
165 174 5.815740 TGATATCGAGGAAAAACCACTAAGC 59.184 40.000 0.00 0.00 42.04 3.09
166 175 3.764237 TCGAGGAAAAACCACTAAGCT 57.236 42.857 0.00 0.00 42.04 3.74
167 176 3.399330 TCGAGGAAAAACCACTAAGCTG 58.601 45.455 0.00 0.00 42.04 4.24
176 186 7.923878 GGAAAAACCACTAAGCTGTTTTTATGA 59.076 33.333 18.94 0.00 46.45 2.15
265 292 3.794028 TGAAAACGGCGAAAGAAAACATG 59.206 39.130 16.62 0.00 0.00 3.21
268 295 1.066303 ACGGCGAAAGAAAACATGCAA 59.934 42.857 16.62 0.00 0.00 4.08
327 354 2.362120 TTCCTCTCGGGTCGGTCC 60.362 66.667 0.00 0.00 36.25 4.46
386 414 0.318762 GTCGAAAGCCAGTCTCCACT 59.681 55.000 0.00 0.00 0.00 4.00
389 417 0.035915 GAAAGCCAGTCTCCACTCCC 60.036 60.000 0.00 0.00 0.00 4.30
668 697 4.373116 TCGCGTCCCTGCTGTTCC 62.373 66.667 5.77 0.00 0.00 3.62
712 741 2.362717 GGTAGCTTTCGAGGTATGAGCT 59.637 50.000 0.00 1.58 45.01 4.09
726 755 4.278669 GGTATGAGCTTTCTAGTCATCCGA 59.721 45.833 0.00 0.00 33.05 4.55
732 761 4.586421 AGCTTTCTAGTCATCCGATGATCA 59.414 41.667 14.15 0.00 42.04 2.92
733 762 4.683781 GCTTTCTAGTCATCCGATGATCAC 59.316 45.833 14.15 2.76 42.04 3.06
734 763 4.855715 TTCTAGTCATCCGATGATCACC 57.144 45.455 14.15 1.84 42.04 4.02
747 776 4.815533 ATGATCACCTCATCGGGATTAG 57.184 45.455 0.00 0.00 40.77 1.73
767 796 1.804748 GCTTCGAGAAATTTCGGGTGT 59.195 47.619 12.42 0.00 40.83 4.16
772 801 1.443702 GAAATTTCGGGTGTGCGCC 60.444 57.895 4.18 0.00 0.00 6.53
793 822 1.364171 GCGCATCACCTAGATCCGT 59.636 57.895 0.30 0.00 40.08 4.69
794 823 0.664767 GCGCATCACCTAGATCCGTC 60.665 60.000 0.30 0.00 40.08 4.79
797 826 0.969894 CATCACCTAGATCCGTCCCC 59.030 60.000 0.00 0.00 33.72 4.81
871 902 9.237187 CCTCTATCTGATCTGTTATAGCAGTTA 57.763 37.037 15.27 0.00 37.70 2.24
877 908 9.409918 TCTGATCTGTTATAGCAGTTAGTAAGT 57.590 33.333 15.27 0.00 37.70 2.24
905 936 3.065786 GCGATTGAATGGAATGCTCTTCA 59.934 43.478 0.00 0.00 0.00 3.02
927 958 5.945191 TCATGTGACTGAATTGCTAAATCCA 59.055 36.000 0.00 0.00 0.00 3.41
947 978 2.757077 CAGGAAAAGAGGCGGGGT 59.243 61.111 0.00 0.00 0.00 4.95
973 1010 2.821366 GAGGTAGGCGTCGGTCGA 60.821 66.667 0.00 0.00 42.86 4.20
975 1012 0.882042 GAGGTAGGCGTCGGTCGATA 60.882 60.000 0.00 0.00 42.86 2.92
1089 1127 2.048127 GAGGACGCGCTGTTCCTT 60.048 61.111 19.55 7.19 31.03 3.36
1221 1259 1.227943 GGCGCCCAAGATGATGCTA 60.228 57.895 18.11 0.00 0.00 3.49
1275 1313 3.311110 AACTGGAAGGCGCTCGGA 61.311 61.111 7.64 0.00 39.30 4.55
1341 1379 1.823899 GAACATCCATGTCCCCGGC 60.824 63.158 0.00 0.00 40.80 6.13
1365 1403 1.092921 TTGTGTTCAGGACGCGCTTT 61.093 50.000 5.73 0.00 41.73 3.51
1556 1594 1.133668 GCAGGCTAGGTTCCATCCAAT 60.134 52.381 0.00 0.00 0.00 3.16
1620 1658 0.327259 ATGCTGATATGATGCCGGCT 59.673 50.000 29.70 13.55 33.59 5.52
1689 1727 3.544684 TGTATGCCTGAATGGACATGTC 58.455 45.455 17.91 17.91 38.35 3.06
1701 1739 2.311243 TGGACATGTCATTGGATTGGGA 59.689 45.455 26.47 0.00 0.00 4.37
1813 1851 9.626045 CTTGGTTCCTGTCATTAGTTTAATTTC 57.374 33.333 0.00 0.00 0.00 2.17
1819 1857 9.362151 TCCTGTCATTAGTTTAATTTCCAAAGT 57.638 29.630 0.00 0.00 0.00 2.66
1846 1884 7.025963 CAGCTTAGCTTTATCTTCAAAGGTTG 58.974 38.462 3.00 2.27 42.08 3.77
2000 2038 3.002759 GCCGGCAGATTAACTCTTCAATC 59.997 47.826 24.80 0.00 29.16 2.67
2007 2045 8.608317 GGCAGATTAACTCTTCAATCTCTTTAC 58.392 37.037 0.00 0.00 39.02 2.01
2016 2054 6.390721 TCTTCAATCTCTTTACGAAGACCAG 58.609 40.000 0.00 0.00 37.70 4.00
2047 2085 4.262164 GGGCTGACAATTTGAATGAACAGT 60.262 41.667 2.79 0.00 32.78 3.55
2052 2092 7.972277 GCTGACAATTTGAATGAACAGTGATAT 59.028 33.333 2.79 0.00 32.78 1.63
2301 2341 9.857656 ATTTGGTCTCATACATTTACATCATCT 57.142 29.630 0.00 0.00 0.00 2.90
2335 2375 3.275143 TGTTCAAACAACGATCAGTGGT 58.725 40.909 0.00 0.00 39.07 4.16
2363 2403 8.718102 TGTTTATATCAGTAAGAAAGCTCACC 57.282 34.615 0.00 0.00 0.00 4.02
2381 2421 4.416601 AGGCCGGCTCTACCCCTT 62.417 66.667 28.56 0.00 33.26 3.95
2396 2436 8.959548 GCTCTACCCCTTATCTACTAATCTTAC 58.040 40.741 0.00 0.00 0.00 2.34
2402 2442 9.256228 CCCCTTATCTACTAATCTTACTGCATA 57.744 37.037 0.00 0.00 0.00 3.14
2414 2463 8.696043 AATCTTACTGCATATAAATGAAGCCA 57.304 30.769 0.00 0.00 41.99 4.75
2439 2488 6.891908 AGGATCATGGCTGTAACTAAATTTGT 59.108 34.615 0.00 0.00 0.00 2.83
2621 2671 8.338259 GTGTTATGTATCAACCTCATAGCTTTG 58.662 37.037 0.00 0.00 0.00 2.77
2693 2895 7.470563 GCCAGTTAGAATAAGGCAGCATAAATT 60.471 37.037 0.00 0.00 44.59 1.82
2699 2901 7.436933 AGAATAAGGCAGCATAAATTTAAGCC 58.563 34.615 18.99 18.89 40.85 4.35
2723 2925 6.425114 CCTACTTATGTGATGATAGTGCAACC 59.575 42.308 0.00 0.00 37.80 3.77
2737 2939 3.838317 AGTGCAACCTATCAGTAACCAGA 59.162 43.478 0.00 0.00 37.80 3.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 7.295952 AGCACACGTCTTTGATAAGAAATAG 57.704 36.000 0.00 0.00 41.86 1.73
2 3 6.204688 TGAAGCACACGTCTTTGATAAGAAAT 59.795 34.615 0.00 0.00 41.86 2.17
21 22 9.791801 TGCATTAAGTAGGAATATAATGAAGCA 57.208 29.630 8.18 0.00 37.75 3.91
47 48 9.785982 GCAAACTCTATCCCTAAAGATAAATCT 57.214 33.333 0.00 0.00 39.22 2.40
59 60 4.218852 GCTACTATCGCAAACTCTATCCCT 59.781 45.833 0.00 0.00 0.00 4.20
63 64 4.275196 TCACGCTACTATCGCAAACTCTAT 59.725 41.667 0.00 0.00 0.00 1.98
64 65 3.624410 TCACGCTACTATCGCAAACTCTA 59.376 43.478 0.00 0.00 0.00 2.43
80 89 8.349983 ACAATTTTCTTTAACTACATTCACGCT 58.650 29.630 0.00 0.00 0.00 5.07
91 100 5.068591 AGCCCGTGAACAATTTTCTTTAACT 59.931 36.000 0.00 0.00 0.00 2.24
93 102 5.067936 TCAGCCCGTGAACAATTTTCTTTAA 59.932 36.000 0.00 0.00 29.64 1.52
119 128 3.422796 TCCGACTCCCAGATATAGCTTC 58.577 50.000 0.00 0.00 0.00 3.86
122 131 3.357203 TCATCCGACTCCCAGATATAGC 58.643 50.000 0.00 0.00 0.00 2.97
131 140 1.746220 CCTCGATATCATCCGACTCCC 59.254 57.143 3.12 0.00 0.00 4.30
132 141 2.712709 TCCTCGATATCATCCGACTCC 58.287 52.381 3.12 0.00 0.00 3.85
138 147 5.368989 AGTGGTTTTTCCTCGATATCATCC 58.631 41.667 3.12 0.00 37.07 3.51
144 153 5.175859 CAGCTTAGTGGTTTTTCCTCGATA 58.824 41.667 0.00 0.00 37.07 2.92
148 157 5.515797 AAACAGCTTAGTGGTTTTTCCTC 57.484 39.130 0.00 0.00 37.07 3.71
149 158 5.932619 AAAACAGCTTAGTGGTTTTTCCT 57.067 34.783 6.13 0.00 40.67 3.36
150 159 7.923878 TCATAAAAACAGCTTAGTGGTTTTTCC 59.076 33.333 21.17 0.00 43.34 3.13
157 166 6.373779 CACACTCATAAAAACAGCTTAGTGG 58.626 40.000 0.00 0.00 37.89 4.00
158 167 6.204688 TCCACACTCATAAAAACAGCTTAGTG 59.795 38.462 0.00 0.00 39.14 2.74
159 168 6.296026 TCCACACTCATAAAAACAGCTTAGT 58.704 36.000 0.00 0.00 0.00 2.24
160 169 6.801539 TCCACACTCATAAAAACAGCTTAG 57.198 37.500 0.00 0.00 0.00 2.18
161 170 7.575414 TTTCCACACTCATAAAAACAGCTTA 57.425 32.000 0.00 0.00 0.00 3.09
162 171 6.463995 TTTCCACACTCATAAAAACAGCTT 57.536 33.333 0.00 0.00 0.00 3.74
163 172 6.655078 ATTTCCACACTCATAAAAACAGCT 57.345 33.333 0.00 0.00 0.00 4.24
165 174 8.356657 TGGTAATTTCCACACTCATAAAAACAG 58.643 33.333 0.00 0.00 31.96 3.16
166 175 8.239038 TGGTAATTTCCACACTCATAAAAACA 57.761 30.769 0.00 0.00 31.96 2.83
167 176 9.191995 CTTGGTAATTTCCACACTCATAAAAAC 57.808 33.333 2.84 0.00 37.20 2.43
176 186 8.644374 TTTATTAGCTTGGTAATTTCCACACT 57.356 30.769 2.84 6.78 37.20 3.55
207 221 3.756082 TTCTGCAGGGGGTTCATTTAT 57.244 42.857 15.13 0.00 0.00 1.40
265 292 1.685148 GGGGATGGATGAGTTCTTGC 58.315 55.000 0.00 0.00 0.00 4.01
268 295 1.879575 TTCGGGGATGGATGAGTTCT 58.120 50.000 0.00 0.00 0.00 3.01
327 354 0.841961 TGGATGGAGGGCTGAGATTG 59.158 55.000 0.00 0.00 0.00 2.67
428 457 1.134371 GGGATGAAGAGGAAAGGGACG 60.134 57.143 0.00 0.00 0.00 4.79
686 715 2.577059 CTCGAAAGCTACCGCCCA 59.423 61.111 3.12 0.00 36.60 5.36
689 718 1.066605 TCATACCTCGAAAGCTACCGC 59.933 52.381 3.12 0.00 0.00 5.68
691 720 2.362717 AGCTCATACCTCGAAAGCTACC 59.637 50.000 0.00 0.00 41.32 3.18
694 723 3.196685 AGAAAGCTCATACCTCGAAAGCT 59.803 43.478 0.00 0.00 44.84 3.74
696 725 5.897050 ACTAGAAAGCTCATACCTCGAAAG 58.103 41.667 0.00 0.00 0.00 2.62
712 741 4.895889 AGGTGATCATCGGATGACTAGAAA 59.104 41.667 22.09 0.00 43.01 2.52
732 761 1.341531 CGAAGCTAATCCCGATGAGGT 59.658 52.381 0.00 0.00 38.74 3.85
733 762 1.613925 TCGAAGCTAATCCCGATGAGG 59.386 52.381 0.00 0.00 40.63 3.86
734 763 2.554462 TCTCGAAGCTAATCCCGATGAG 59.446 50.000 0.00 0.00 0.00 2.90
740 769 4.024809 CCGAAATTTCTCGAAGCTAATCCC 60.025 45.833 15.92 0.00 41.44 3.85
747 776 1.804748 ACACCCGAAATTTCTCGAAGC 59.195 47.619 15.92 0.00 41.44 3.86
772 801 1.373497 GATCTAGGTGATGCGCGGG 60.373 63.158 8.83 0.00 35.14 6.13
774 803 4.251760 GGATCTAGGTGATGCGCG 57.748 61.111 0.00 0.00 35.14 6.86
871 902 7.108841 TCCATTCAATCGCTACTTACTTACT 57.891 36.000 0.00 0.00 0.00 2.24
877 908 5.368145 AGCATTCCATTCAATCGCTACTTA 58.632 37.500 0.00 0.00 0.00 2.24
881 912 4.077300 AGAGCATTCCATTCAATCGCTA 57.923 40.909 0.00 0.00 0.00 4.26
905 936 6.626623 GCTTGGATTTAGCAATTCAGTCACAT 60.627 38.462 0.00 0.00 38.51 3.21
927 958 1.303643 CCCGCCTCTTTTCCTGCTT 60.304 57.895 0.00 0.00 0.00 3.91
947 978 3.161450 GCCTACCTCCCCATGCGA 61.161 66.667 0.00 0.00 0.00 5.10
973 1010 3.019564 GCAGCCAAAATCACTCCAGTAT 58.980 45.455 0.00 0.00 0.00 2.12
975 1012 1.251251 GCAGCCAAAATCACTCCAGT 58.749 50.000 0.00 0.00 0.00 4.00
1221 1259 1.227380 GCCGTCGGAATGCAGATCT 60.227 57.895 17.49 0.00 0.00 2.75
1275 1313 2.775911 TGCAGTAGATCAGCAGCTTT 57.224 45.000 0.00 0.00 33.75 3.51
1323 1361 1.823899 GCCGGGGACATGGATGTTC 60.824 63.158 2.18 0.00 41.95 3.18
1341 1379 0.307760 GCGTCCTGAACACAAAGTGG 59.692 55.000 1.93 0.00 37.94 4.00
1365 1403 1.600636 CTTGCCTGCGGTCCTTGAA 60.601 57.895 0.00 0.00 0.00 2.69
1556 1594 0.324275 GCAATAGGGGCAAACCTCCA 60.324 55.000 0.00 0.00 42.09 3.86
1689 1727 2.236489 ACAGGGTTCCCAATCCAATG 57.764 50.000 10.73 0.47 0.00 2.82
1701 1739 1.076677 TCCGAGAGAGGTAACAGGGTT 59.923 52.381 0.00 0.00 41.41 4.11
1813 1851 4.397417 AGATAAAGCTAAGCTGCACTTTGG 59.603 41.667 14.92 1.03 39.62 3.28
1819 1857 5.124457 CCTTTGAAGATAAAGCTAAGCTGCA 59.876 40.000 1.02 0.00 39.62 4.41
2000 2038 6.531948 CCATAGAAACTGGTCTTCGTAAAGAG 59.468 42.308 0.00 0.00 42.14 2.85
2007 2045 2.093447 AGCCCATAGAAACTGGTCTTCG 60.093 50.000 0.00 0.00 31.44 3.79
2016 2054 5.643379 TCAAATTGTCAGCCCATAGAAAC 57.357 39.130 0.00 0.00 0.00 2.78
2276 2316 9.685276 AAGATGATGTAAATGTATGAGACCAAA 57.315 29.630 0.00 0.00 0.00 3.28
2396 2436 5.708697 TGATCCTGGCTTCATTTATATGCAG 59.291 40.000 0.00 0.00 0.00 4.41
2414 2463 6.891908 ACAAATTTAGTTACAGCCATGATCCT 59.108 34.615 0.00 0.00 0.00 3.24
2439 2488 5.011840 TGGGCAAATGAAATTCTGTGATTCA 59.988 36.000 0.00 0.00 33.67 2.57
2693 2895 7.872993 GCACTATCATCACATAAGTAGGCTTAA 59.127 37.037 0.00 0.00 40.22 1.85
2699 2901 7.212976 AGGTTGCACTATCATCACATAAGTAG 58.787 38.462 0.00 0.00 0.00 2.57


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

AutoCloner maintained by Alex Coulton.