Multiple sequence alignment - TraesCS3B01G010800

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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 TraesCS3B01G010800 chr3B 100.000 2670 0 0 1 2670 5068564 5071233 0.000000e+00 4931
1 TraesCS3B01G010800 chr3B 97.494 1756 36 7 918 2670 4214040 4215790 0.000000e+00 2992
2 TraesCS3B01G010800 chr3B 85.326 184 20 5 685 865 4212459 4212638 1.630000e-42 183
3 TraesCS3B01G010800 chr3D 93.250 1037 60 8 917 1949 1882841 1883871 0.000000e+00 1519
4 TraesCS3B01G010800 chr3D 92.683 861 37 7 1 861 1881869 1882703 0.000000e+00 1218
5 TraesCS3B01G010800 chr3D 88.206 407 42 5 2255 2660 1883999 1884400 5.170000e-132 481
6 TraesCS3B01G010800 chr3D 86.891 267 34 1 2405 2670 14178406 14178140 5.590000e-77 298
7 TraesCS3B01G010800 chr3D 81.268 347 47 9 178 510 42399131 42399473 5.670000e-67 265
8 TraesCS3B01G010800 chr3D 89.241 158 12 3 2255 2412 445344301 445344453 2.710000e-45 193
9 TraesCS3B01G010800 chr3D 90.123 81 6 1 856 934 1882756 1882836 1.310000e-18 104
10 TraesCS3B01G010800 chr3A 95.232 839 39 1 1 839 7142007 7141170 0.000000e+00 1327
11 TraesCS3B01G010800 chr3A 92.111 862 53 7 859 1709 7131776 7130919 0.000000e+00 1201
12 TraesCS3B01G010800 chr3A 86.777 363 39 4 156 510 712196855 712197216 1.930000e-106 396
13 TraesCS3B01G010800 chr3A 86.590 261 32 3 2405 2663 277489647 277489906 4.350000e-73 285
14 TraesCS3B01G010800 chr3A 86.111 180 22 3 1986 2162 80542242 80542063 9.760000e-45 191
15 TraesCS3B01G010800 chr3A 87.179 156 14 2 2257 2412 725145353 725145502 3.530000e-39 172
16 TraesCS3B01G010800 chr7D 88.390 267 30 1 2405 2670 515488448 515488182 1.190000e-83 320
17 TraesCS3B01G010800 chr7D 80.442 317 42 9 177 478 231338637 231338326 9.620000e-55 224
18 TraesCS3B01G010800 chr7D 79.143 350 46 14 146 478 116632868 116633207 1.610000e-52 217
19 TraesCS3B01G010800 chr7D 85.987 157 19 3 2007 2162 404072772 404072618 5.910000e-37 165
20 TraesCS3B01G010800 chr1D 88.015 267 31 1 2405 2670 365879125 365879391 5.550000e-82 315
21 TraesCS3B01G010800 chr2D 87.640 267 31 2 2405 2670 571949182 571948917 2.580000e-80 309
22 TraesCS3B01G010800 chr6D 87.266 267 33 1 2405 2670 454623480 454623746 1.200000e-78 303
23 TraesCS3B01G010800 chr6D 87.059 170 20 2 1995 2162 429004852 429004683 9.760000e-45 191
24 TraesCS3B01G010800 chr2B 87.500 264 32 1 2405 2667 685264102 685263839 1.200000e-78 303
25 TraesCS3B01G010800 chr1A 89.503 181 17 1 1986 2164 182077309 182077489 7.440000e-56 228
26 TraesCS3B01G010800 chr1A 97.938 97 2 0 1986 2082 536873466 536873562 4.570000e-38 169
27 TraesCS3B01G010800 chr1B 79.341 334 54 5 159 478 17394185 17393853 1.240000e-53 220
28 TraesCS3B01G010800 chr1B 87.845 181 18 3 302 478 17467036 17466856 2.690000e-50 209
29 TraesCS3B01G010800 chr1B 88.050 159 13 3 2255 2412 14186159 14186006 1.630000e-42 183
30 TraesCS3B01G010800 chr1B 86.076 158 16 4 2255 2412 56324363 56324514 5.910000e-37 165
31 TraesCS3B01G010800 chr7A 80.449 312 40 10 178 473 244477557 244477251 4.480000e-53 219
32 TraesCS3B01G010800 chr7A 79.422 277 39 13 186 452 324921762 324921494 2.110000e-41 180
33 TraesCS3B01G010800 chr7A 84.810 158 17 5 2007 2162 463001039 463000887 4.600000e-33 152
34 TraesCS3B01G010800 chr2A 86.139 202 26 2 159 360 603861491 603861292 1.610000e-52 217
35 TraesCS3B01G010800 chrUn 87.640 178 20 2 1987 2162 93879933 93879756 3.480000e-49 206
36 TraesCS3B01G010800 chr6A 85.294 204 25 5 159 360 510797515 510797315 3.480000e-49 206
37 TraesCS3B01G010800 chr4D 88.535 157 14 2 2257 2412 432460817 432460664 1.260000e-43 187
38 TraesCS3B01G010800 chr4D 86.164 159 15 4 2255 2412 91235939 91236091 5.910000e-37 165
39 TraesCS3B01G010800 chr4D 75.211 355 64 11 156 490 308948533 308948883 2.140000e-31 147
40 TraesCS3B01G010800 chr7B 83.251 203 25 8 538 735 711656040 711655842 7.600000e-41 178
41 TraesCS3B01G010800 chr7B 88.652 141 15 1 551 690 711655382 711655242 1.270000e-38 171
42 TraesCS3B01G010800 chr5D 86.076 158 17 2 2255 2412 60258631 60258479 5.910000e-37 165
43 TraesCS3B01G010800 chr5D 83.516 182 24 6 1984 2162 432157162 432157340 5.910000e-37 165
44 TraesCS3B01G010800 chr4A 96.939 98 3 0 1985 2082 714217401 714217498 5.910000e-37 165
45 TraesCS3B01G010800 chr4A 82.418 182 28 3 1987 2165 740542751 740542931 3.560000e-34 156


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 TraesCS3B01G010800 chr3B 5068564 5071233 2669 False 4931.0 4931 100.0000 1 2670 1 chr3B.!!$F1 2669
1 TraesCS3B01G010800 chr3B 4212459 4215790 3331 False 1587.5 2992 91.4100 685 2670 2 chr3B.!!$F2 1985
2 TraesCS3B01G010800 chr3D 1881869 1884400 2531 False 830.5 1519 91.0655 1 2660 4 chr3D.!!$F3 2659
3 TraesCS3B01G010800 chr3A 7141170 7142007 837 True 1327.0 1327 95.2320 1 839 1 chr3A.!!$R2 838
4 TraesCS3B01G010800 chr3A 7130919 7131776 857 True 1201.0 1201 92.1110 859 1709 1 chr3A.!!$R1 850

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
814 816 0.096454 CTGCATGTGCGTCTGTGATG 59.904 55.0 0.01 0.0 45.83 3.07 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2511 3898 1.372087 GGTGAAGCAAGAGGATGGCG 61.372 60.0 0.0 0.0 0.0 5.69 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
133 134 6.374613 CACGATGCTATACCTAGTTAGATCCA 59.625 42.308 0.00 0.00 0.00 3.41
183 184 2.057137 ATATGCCCGTCTGTTGCAAT 57.943 45.000 0.59 0.00 38.69 3.56
234 235 5.292589 ACACACTCGACGACTTTAACAAATT 59.707 36.000 0.00 0.00 0.00 1.82
528 529 8.637986 TGTTTGCAGAAAAGTATTAATTGAGGT 58.362 29.630 0.00 0.00 0.00 3.85
625 626 9.725019 TCTGAGCGATTTCCATTTATAATATGT 57.275 29.630 0.00 0.00 0.00 2.29
729 731 0.396060 TGGGCCAAAATTGCAAGACC 59.604 50.000 2.13 2.48 0.00 3.85
752 754 2.041620 TGCAGCTTAGGAATCAAACCCT 59.958 45.455 0.00 0.00 36.60 4.34
761 763 0.704664 AATCAAACCCTGGTCTCCCC 59.295 55.000 0.00 0.00 0.00 4.81
787 789 2.197283 AGAGTTCGGTCGGTTCTAGT 57.803 50.000 0.00 0.00 0.00 2.57
809 811 3.807538 GGGCTGCATGTGCGTCTG 61.808 66.667 0.50 0.00 45.83 3.51
814 816 0.096454 CTGCATGTGCGTCTGTGATG 59.904 55.000 0.01 0.00 45.83 3.07
857 920 1.159285 ATGATATGCAATGGTCGGCG 58.841 50.000 0.00 0.00 0.00 6.46
861 924 0.747852 TATGCAATGGTCGGCGACTA 59.252 50.000 35.42 31.85 32.47 2.59
983 2339 2.297033 AGCACAATTAAGGCAACCTGTG 59.703 45.455 0.00 0.00 36.80 3.66
984 2340 2.035832 GCACAATTAAGGCAACCTGTGT 59.964 45.455 0.00 0.00 36.41 3.72
996 2352 4.969196 CTGTGTCCTGCGTGGCGT 62.969 66.667 0.00 0.00 35.26 5.68
997 2353 4.961511 TGTGTCCTGCGTGGCGTC 62.962 66.667 0.00 0.00 35.26 5.19
1000 2356 2.260434 GTCCTGCGTGGCGTCTTA 59.740 61.111 0.00 0.00 35.26 2.10
1007 2363 4.460034 TCCTGCGTGGCGTCTTATATATAA 59.540 41.667 5.10 5.10 35.26 0.98
1032 2388 3.846360 AGAAAGCGTCGCCATATATACC 58.154 45.455 14.86 0.00 0.00 2.73
1094 2450 2.108514 CATCAATGGCGAGCACCGT 61.109 57.895 0.00 0.00 41.15 4.83
1157 2513 0.611062 TCTGACATCCTTCCCGTCGT 60.611 55.000 0.00 0.00 32.17 4.34
1328 2684 3.244112 ACTGTCTACAACAACACTAGGGC 60.244 47.826 0.00 0.00 37.45 5.19
1754 3113 3.051940 TCATCCCCTGCTTCTCTACAT 57.948 47.619 0.00 0.00 0.00 2.29
1783 3142 5.163045 ACATCTCTTCCCTCAAGTTCCTTTT 60.163 40.000 0.00 0.00 33.27 2.27
2511 3898 1.753073 CAAGTGATTCAAGCATCCCCC 59.247 52.381 0.00 0.00 0.00 5.40
2561 3948 2.637872 CAGTCTTTAGGTGTCTTCCCCA 59.362 50.000 0.00 0.00 0.00 4.96
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
41 42 2.168521 TCCCATGAGTGCTACTAGTTGC 59.831 50.000 20.53 20.53 0.00 4.17
202 203 1.135774 TCGTCGAGTGTGTGTATGAGC 60.136 52.381 0.00 0.00 0.00 4.26
251 252 6.533730 TCATGGTGTTTCTTGTATGTCTTCT 58.466 36.000 0.00 0.00 0.00 2.85
256 257 7.121168 CCACTTATCATGGTGTTTCTTGTATGT 59.879 37.037 0.00 0.00 32.08 2.29
270 271 5.710099 ACCTTTACAACACCACTTATCATGG 59.290 40.000 0.00 0.00 43.43 3.66
284 285 9.203421 CTTTAAAAATCATCCCACCTTTACAAC 57.797 33.333 0.00 0.00 0.00 3.32
729 731 2.159517 GGTTTGATTCCTAAGCTGCACG 60.160 50.000 1.02 0.00 0.00 5.34
761 763 1.344942 CCGACCGAACTCTTCTTGCG 61.345 60.000 0.00 0.00 0.00 4.85
787 789 2.674033 GCACATGCAGCCCACTCA 60.674 61.111 0.00 0.00 41.59 3.41
809 811 9.965902 ATATAAAGATATCCCCTCAAACATCAC 57.034 33.333 0.00 0.00 0.00 3.06
844 848 0.747852 TATAGTCGCCGACCATTGCA 59.252 50.000 14.60 0.00 32.18 4.08
849 853 0.820891 GTCCCTATAGTCGCCGACCA 60.821 60.000 14.60 0.00 32.18 4.02
857 920 6.761714 ACGTCATGAAAATTGTCCCTATAGTC 59.238 38.462 0.00 0.00 0.00 2.59
861 924 6.538742 CAGTACGTCATGAAAATTGTCCCTAT 59.461 38.462 0.00 0.00 0.00 2.57
983 2339 0.101759 TATAAGACGCCACGCAGGAC 59.898 55.000 0.00 0.00 41.22 3.85
984 2340 1.037493 ATATAAGACGCCACGCAGGA 58.963 50.000 0.00 0.00 41.22 3.86
996 2352 9.125906 GCGACGCTTTCTTCTTTATATATAAGA 57.874 33.333 13.73 0.00 0.00 2.10
997 2353 8.373992 GGCGACGCTTTCTTCTTTATATATAAG 58.626 37.037 20.77 0.00 0.00 1.73
1000 2356 6.220930 TGGCGACGCTTTCTTCTTTATATAT 58.779 36.000 20.77 0.00 0.00 0.86
1007 2363 2.380084 TATGGCGACGCTTTCTTCTT 57.620 45.000 20.77 2.64 0.00 2.52
1032 2388 1.593551 CGTTGCTGTTGTGTTGGTACG 60.594 52.381 0.00 0.00 0.00 3.67
1078 2434 1.153647 CTACGGTGCTCGCCATTGA 60.154 57.895 0.07 0.00 43.89 2.57
1094 2450 2.775351 GCCATTGCTACGGTTGCTA 58.225 52.632 15.15 8.51 33.53 3.49
1165 2521 2.187946 GGAGATGAGGCCGGTGTG 59.812 66.667 1.90 0.00 0.00 3.82
1168 2524 2.765807 CCTGGAGATGAGGCCGGT 60.766 66.667 1.90 0.00 0.00 5.28
1328 2684 2.157668 CCCTTGAACAAGTCGACGATTG 59.842 50.000 10.46 12.64 36.72 2.67
1435 2794 1.098712 AAAAAGTCGAGGGCAACGCA 61.099 50.000 0.00 0.00 37.60 5.24
1500 2859 1.134818 GCGTCCTCACACATATCACCA 60.135 52.381 0.00 0.00 0.00 4.17
1754 3113 3.578716 ACTTGAGGGAAGAGATGTTTCGA 59.421 43.478 0.00 0.00 35.42 3.71
1988 3348 3.934457 AATTCGGCCGAAATCTGTTTT 57.066 38.095 41.31 26.70 37.69 2.43
2511 3898 1.372087 GGTGAAGCAAGAGGATGGCG 61.372 60.000 0.00 0.00 0.00 5.69
2561 3948 3.901844 TGGAGTACTTAAGAGCACCAACT 59.098 43.478 10.09 1.03 0.00 3.16


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

AutoCloner maintained by Alex Coulton.