Multiple sequence alignment - TraesCS7D01G427700

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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 TraesCS7D01G427700 chr7D 100.000 2192 0 0 667 2858 548617098 548619289 0.000000e+00 4048.0
1 TraesCS7D01G427700 chr7D 94.449 1189 52 6 667 1848 548608924 548610105 0.000000e+00 1818.0
2 TraesCS7D01G427700 chr7D 81.723 1149 178 22 714 1849 581271645 581272774 0.000000e+00 929.0
3 TraesCS7D01G427700 chr7D 79.795 1168 175 30 714 1849 581284186 581285324 0.000000e+00 793.0
4 TraesCS7D01G427700 chr7D 77.643 1154 187 32 708 1849 581039864 581040958 1.120000e-178 636.0
5 TraesCS7D01G427700 chr7D 100.000 271 0 0 1 271 548616432 548616702 4.250000e-138 501.0
6 TraesCS7D01G427700 chr7D 77.621 496 91 11 713 1198 581080823 581081308 1.680000e-72 283.0
7 TraesCS7D01G427700 chr7D 91.011 89 3 3 183 271 548608678 548608761 6.470000e-22 115.0
8 TraesCS7D01G427700 chr7A 91.890 1270 100 2 667 1933 632518476 632519745 0.000000e+00 1772.0
9 TraesCS7D01G427700 chr7A 90.806 1055 85 4 667 1715 632383240 632384288 0.000000e+00 1400.0
10 TraesCS7D01G427700 chr7A 77.193 912 158 23 948 1849 673013263 673014134 1.190000e-133 486.0
11 TraesCS7D01G427700 chr7A 73.721 1153 201 58 738 1849 721024689 721023598 9.740000e-95 357.0
12 TraesCS7D01G427700 chr7A 95.679 162 6 1 2 163 632518087 632518247 2.820000e-65 259.0
13 TraesCS7D01G427700 chr7A 87.037 108 6 4 167 271 632518214 632518316 6.470000e-22 115.0
14 TraesCS7D01G427700 chr6D 96.976 926 8 2 1933 2858 345784797 345785702 0.000000e+00 1537.0
15 TraesCS7D01G427700 chr1D 96.112 926 14 2 1933 2858 492433494 492434397 0.000000e+00 1491.0
16 TraesCS7D01G427700 chr3B 94.327 758 39 4 2103 2858 741613848 741613093 0.000000e+00 1158.0
17 TraesCS7D01G427700 chr3B 85.580 957 105 11 1933 2858 811726007 811726961 0.000000e+00 972.0
18 TraesCS7D01G427700 chr3B 97.122 139 4 0 1969 2107 741623052 741622914 4.760000e-58 235.0
19 TraesCS7D01G427700 chr3B 84.874 238 27 9 2551 2783 478313332 478313565 6.160000e-57 231.0
20 TraesCS7D01G427700 chr3B 85.279 197 28 1 2358 2553 478313078 478313274 4.830000e-48 202.0
21 TraesCS7D01G427700 chr2A 86.994 938 88 21 1933 2858 68019357 68020272 0.000000e+00 1026.0
22 TraesCS7D01G427700 chr2A 83.932 473 46 18 1933 2392 558653159 558653614 2.630000e-115 425.0
23 TraesCS7D01G427700 chr2A 84.691 405 48 4 2466 2858 558653603 558654005 2.670000e-105 392.0
24 TraesCS7D01G427700 chr2A 79.271 439 71 14 2332 2761 576067107 576066680 3.600000e-74 289.0
25 TraesCS7D01G427700 chr5B 85.162 957 109 11 1933 2858 455803944 455802990 0.000000e+00 950.0
26 TraesCS7D01G427700 chr5B 82.080 452 55 19 2355 2783 51961407 51960959 2.090000e-96 363.0
27 TraesCS7D01G427700 chr5D 78.608 1178 181 36 714 1849 289687142 289688290 0.000000e+00 713.0
28 TraesCS7D01G427700 chr2B 87.643 526 60 5 2337 2858 398696761 398696237 8.760000e-170 606.0
29 TraesCS7D01G427700 chr2B 86.480 392 50 3 1932 2321 398697235 398696845 7.320000e-116 427.0
30 TraesCS7D01G427700 chr4D 76.043 1127 218 33 740 1849 379501325 379500234 3.240000e-149 538.0
31 TraesCS7D01G427700 chrUn 74.828 1160 228 39 713 1849 93228281 93229399 1.550000e-127 466.0
32 TraesCS7D01G427700 chrUn 73.037 1146 249 38 727 1848 286625880 286626989 1.630000e-92 350.0
33 TraesCS7D01G427700 chrUn 77.157 394 57 23 1461 1849 87735025 87735390 6.250000e-47 198.0
34 TraesCS7D01G427700 chr7B 74.697 1154 232 36 714 1849 649404119 649405230 2.590000e-125 459.0
35 TraesCS7D01G427700 chr7B 73.037 1146 249 38 727 1848 649448487 649449596 1.630000e-92 350.0
36 TraesCS7D01G427700 chr7B 72.727 1144 255 36 727 1848 649458052 649459160 5.900000e-87 331.0
37 TraesCS7D01G427700 chr7B 78.082 365 62 10 1492 1853 648905751 648906100 6.200000e-52 215.0
38 TraesCS7D01G427700 chr7B 80.916 131 21 4 2721 2849 667177667 667177539 1.810000e-17 100.0
39 TraesCS7D01G427700 chr7B 83.333 72 7 5 1924 1991 4799660 4799590 8.550000e-06 62.1
40 TraesCS7D01G427700 chr4A 79.954 439 82 2 734 1169 84934840 84935275 4.590000e-83 318.0


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 TraesCS7D01G427700 chr7D 548616432 548619289 2857 False 2274.500000 4048 100.000000 1 2858 2 chr7D.!!$F6 2857
1 TraesCS7D01G427700 chr7D 548608678 548610105 1427 False 966.500000 1818 92.730000 183 1848 2 chr7D.!!$F5 1665
2 TraesCS7D01G427700 chr7D 581271645 581272774 1129 False 929.000000 929 81.723000 714 1849 1 chr7D.!!$F3 1135
3 TraesCS7D01G427700 chr7D 581284186 581285324 1138 False 793.000000 793 79.795000 714 1849 1 chr7D.!!$F4 1135
4 TraesCS7D01G427700 chr7D 581039864 581040958 1094 False 636.000000 636 77.643000 708 1849 1 chr7D.!!$F1 1141
5 TraesCS7D01G427700 chr7A 632383240 632384288 1048 False 1400.000000 1400 90.806000 667 1715 1 chr7A.!!$F1 1048
6 TraesCS7D01G427700 chr7A 632518087 632519745 1658 False 715.333333 1772 91.535333 2 1933 3 chr7A.!!$F3 1931
7 TraesCS7D01G427700 chr7A 673013263 673014134 871 False 486.000000 486 77.193000 948 1849 1 chr7A.!!$F2 901
8 TraesCS7D01G427700 chr7A 721023598 721024689 1091 True 357.000000 357 73.721000 738 1849 1 chr7A.!!$R1 1111
9 TraesCS7D01G427700 chr6D 345784797 345785702 905 False 1537.000000 1537 96.976000 1933 2858 1 chr6D.!!$F1 925
10 TraesCS7D01G427700 chr1D 492433494 492434397 903 False 1491.000000 1491 96.112000 1933 2858 1 chr1D.!!$F1 925
11 TraesCS7D01G427700 chr3B 741613093 741613848 755 True 1158.000000 1158 94.327000 2103 2858 1 chr3B.!!$R1 755
12 TraesCS7D01G427700 chr3B 811726007 811726961 954 False 972.000000 972 85.580000 1933 2858 1 chr3B.!!$F1 925
13 TraesCS7D01G427700 chr2A 68019357 68020272 915 False 1026.000000 1026 86.994000 1933 2858 1 chr2A.!!$F1 925
14 TraesCS7D01G427700 chr2A 558653159 558654005 846 False 408.500000 425 84.311500 1933 2858 2 chr2A.!!$F2 925
15 TraesCS7D01G427700 chr5B 455802990 455803944 954 True 950.000000 950 85.162000 1933 2858 1 chr5B.!!$R2 925
16 TraesCS7D01G427700 chr5D 289687142 289688290 1148 False 713.000000 713 78.608000 714 1849 1 chr5D.!!$F1 1135
17 TraesCS7D01G427700 chr2B 398696237 398697235 998 True 516.500000 606 87.061500 1932 2858 2 chr2B.!!$R1 926
18 TraesCS7D01G427700 chr4D 379500234 379501325 1091 True 538.000000 538 76.043000 740 1849 1 chr4D.!!$R1 1109
19 TraesCS7D01G427700 chrUn 93228281 93229399 1118 False 466.000000 466 74.828000 713 1849 1 chrUn.!!$F2 1136
20 TraesCS7D01G427700 chrUn 286625880 286626989 1109 False 350.000000 350 73.037000 727 1848 1 chrUn.!!$F3 1121
21 TraesCS7D01G427700 chr7B 649404119 649405230 1111 False 459.000000 459 74.697000 714 1849 1 chr7B.!!$F2 1135
22 TraesCS7D01G427700 chr7B 649448487 649449596 1109 False 350.000000 350 73.037000 727 1848 1 chr7B.!!$F3 1121
23 TraesCS7D01G427700 chr7B 649458052 649459160 1108 False 331.000000 331 72.727000 727 1848 1 chr7B.!!$F4 1121

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
262 263 0.036010 GCTGAGCCCATGTGTACTGT 60.036 55.000 0.0 0.0 0.0 3.55 F
1000 1050 3.050354 AACCACAAGCCCGTCCACA 62.050 57.895 0.0 0.0 0.0 4.17 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1224 1280 1.133809 TGTCAGGGTCCCAGGGAAAG 61.134 60.000 10.89 0.11 31.38 2.62 R
2717 2960 6.017109 GCTGGTACAAGAAGAACAAATTCTGA 60.017 38.462 0.00 0.00 40.98 3.27 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
75 76 4.688879 TCAAAATCGTCGTGCAGTAGAATT 59.311 37.500 0.00 0.00 0.00 2.17
86 87 5.564651 CGTGCAGTAGAATTTCCCAAACAAT 60.565 40.000 0.00 0.00 0.00 2.71
89 90 6.267471 TGCAGTAGAATTTCCCAAACAATTCT 59.733 34.615 10.98 10.98 46.68 2.40
160 161 9.495572 TTTTTAGAAACAAAATGTCCTGTGTTT 57.504 25.926 0.54 0.54 44.61 2.83
161 162 8.472683 TTTAGAAACAAAATGTCCTGTGTTTG 57.527 30.769 5.43 0.00 42.61 2.93
162 163 6.036577 AGAAACAAAATGTCCTGTGTTTGT 57.963 33.333 5.43 0.00 42.61 2.83
166 167 7.503521 AACAAAATGTCCTGTGTTTGTTTTT 57.496 28.000 7.38 0.00 46.62 1.94
205 206 9.539825 AACATGTCTTTTTGTTTGTATATGCAA 57.460 25.926 0.00 1.68 32.28 4.08
224 225 5.569355 TGCAAGTCCTATTCTTCCAATTCA 58.431 37.500 0.00 0.00 0.00 2.57
225 226 5.649395 TGCAAGTCCTATTCTTCCAATTCAG 59.351 40.000 0.00 0.00 0.00 3.02
262 263 0.036010 GCTGAGCCCATGTGTACTGT 60.036 55.000 0.00 0.00 0.00 3.55
1000 1050 3.050354 AACCACAAGCCCGTCCACA 62.050 57.895 0.00 0.00 0.00 4.17
1209 1262 5.042463 TCCATGTGTTTGAGTTGGTAGAA 57.958 39.130 0.00 0.00 0.00 2.10
1224 1280 5.028549 TGGTAGAAGAGCAGGATTCAATC 57.971 43.478 0.00 0.00 0.00 2.67
1320 1382 7.979444 AAAGAGATGGAACGAACAAATTAGA 57.021 32.000 0.00 0.00 0.00 2.10
1333 1395 7.122650 ACGAACAAATTAGATCCATTGACCATT 59.877 33.333 0.00 0.00 0.00 3.16
1335 1397 7.722949 ACAAATTAGATCCATTGACCATTGT 57.277 32.000 0.00 0.00 0.00 2.71
1892 2035 3.667960 CGACAGGCATTAGTTCTTTGTGC 60.668 47.826 0.00 0.00 35.17 4.57
2221 2379 1.966451 GTGTGAAGGAAGGGGCACG 60.966 63.158 0.00 0.00 34.12 5.34
2520 2760 0.897863 CCCGGATTTTGCTGGAACCA 60.898 55.000 0.73 0.00 36.35 3.67
2717 2960 4.041938 ACCAACATCCAAAAATGCTTCCAT 59.958 37.500 0.00 0.00 0.00 3.41
2788 3043 2.223688 TGTTTTGCTGGAACCAACATCG 60.224 45.455 0.00 0.00 0.00 3.84
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
41 42 6.022484 GCACGACGATTTTGACTTAATTAAGC 60.022 38.462 22.45 15.96 36.79 3.09
75 76 3.895041 GGTGAAGGAGAATTGTTTGGGAA 59.105 43.478 0.00 0.00 0.00 3.97
86 87 4.350816 TCTGAAGGAAATGGTGAAGGAGAA 59.649 41.667 0.00 0.00 0.00 2.87
89 90 4.722526 TTCTGAAGGAAATGGTGAAGGA 57.277 40.909 0.00 0.00 0.00 3.36
179 180 9.539825 TTGCATATACAAACAAAAAGACATGTT 57.460 25.926 0.00 0.00 41.31 2.71
180 181 9.195411 CTTGCATATACAAACAAAAAGACATGT 57.805 29.630 0.00 0.00 0.00 3.21
181 182 9.195411 ACTTGCATATACAAACAAAAAGACATG 57.805 29.630 0.00 0.00 0.00 3.21
182 183 9.410556 GACTTGCATATACAAACAAAAAGACAT 57.589 29.630 0.00 0.00 0.00 3.06
183 184 7.865385 GGACTTGCATATACAAACAAAAAGACA 59.135 33.333 0.00 0.00 0.00 3.41
184 185 8.082242 AGGACTTGCATATACAAACAAAAAGAC 58.918 33.333 0.00 0.00 0.00 3.01
185 186 8.177119 AGGACTTGCATATACAAACAAAAAGA 57.823 30.769 0.00 0.00 0.00 2.52
190 191 9.461312 AAGAATAGGACTTGCATATACAAACAA 57.539 29.630 0.00 0.00 0.00 2.83
205 206 6.882768 ACTCTGAATTGGAAGAATAGGACT 57.117 37.500 0.00 0.00 0.00 3.85
224 225 2.102588 AGCCGTGTCACAACTAAACTCT 59.897 45.455 3.42 0.00 0.00 3.24
225 226 2.221055 CAGCCGTGTCACAACTAAACTC 59.779 50.000 3.42 0.00 0.00 3.01
963 1010 2.439156 GGCAGGAAGGCGCAAGAT 60.439 61.111 10.83 0.00 43.02 2.40
1000 1050 1.518056 CCGTTGCAGCAGTCCAACAT 61.518 55.000 0.24 0.00 40.93 2.71
1209 1262 3.526841 AGGGAAAGATTGAATCCTGCTCT 59.473 43.478 0.75 0.00 33.61 4.09
1224 1280 1.133809 TGTCAGGGTCCCAGGGAAAG 61.134 60.000 10.89 0.11 31.38 2.62
1320 1382 3.433343 TGCTGAACAATGGTCAATGGAT 58.567 40.909 1.49 0.00 0.00 3.41
1333 1395 5.833406 TCAAGAAAGACAAATGCTGAACA 57.167 34.783 0.00 0.00 0.00 3.18
1335 1397 5.775686 CCATCAAGAAAGACAAATGCTGAA 58.224 37.500 0.00 0.00 0.00 3.02
1892 2035 6.620678 CCCACTTCAAACAAACATACCATAG 58.379 40.000 0.00 0.00 0.00 2.23
2717 2960 6.017109 GCTGGTACAAGAAGAACAAATTCTGA 60.017 38.462 0.00 0.00 40.98 3.27
2788 3043 9.764363 AATTAAACTCTGGAGGAAACATTTTTC 57.236 29.630 2.58 0.00 40.54 2.29


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

AutoCloner maintained by Alex Coulton.