Multiple sequence alignment - TraesCS3B01G443400

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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 TraesCS3B01G443400 chr3B 100.000 2384 0 0 1 2384 683829404 683831787 0.000000e+00 4403
1 TraesCS3B01G443400 chr3B 93.276 2082 98 15 330 2384 683385117 683387183 0.000000e+00 3031
2 TraesCS3B01G443400 chr3B 89.480 2424 205 18 4 2384 786584292 786581876 0.000000e+00 3018
3 TraesCS3B01G443400 chr2D 91.243 2421 165 25 3 2384 549979724 549982136 0.000000e+00 3253
4 TraesCS3B01G443400 chr2D 91.096 2426 167 18 3 2384 549504267 549506687 0.000000e+00 3238
5 TraesCS3B01G443400 chr2D 91.654 671 37 4 1731 2384 367988025 367987357 0.000000e+00 911
6 TraesCS3B01G443400 chr2D 92.982 228 12 2 2157 2384 448520070 448519847 1.770000e-86 329
7 TraesCS3B01G443400 chr2B 89.667 2429 193 27 3 2384 250681506 250679089 0.000000e+00 3042
8 TraesCS3B01G443400 chr2B 90.805 2099 162 11 311 2384 642947694 642949786 0.000000e+00 2778
9 TraesCS3B01G443400 chr4B 89.550 2421 207 25 3 2384 595287929 595290342 0.000000e+00 3027
10 TraesCS3B01G443400 chr3D 89.631 2411 202 32 3 2384 429313626 429311235 0.000000e+00 3024
11 TraesCS3B01G443400 chr3D 88.005 2426 207 38 2 2384 522090006 522087622 0.000000e+00 2791
12 TraesCS3B01G443400 chr3D 93.074 231 11 3 2157 2384 402494983 402494755 1.370000e-87 333
13 TraesCS3B01G443400 chr4D 89.219 2421 209 23 3 2384 35486687 35489094 0.000000e+00 2977
14 TraesCS3B01G443400 chr1B 88.981 2414 226 11 3 2384 643811889 643809484 0.000000e+00 2948
15 TraesCS3B01G443400 chr1B 87.437 1186 138 8 5 1181 40438597 40439780 0.000000e+00 1354
16 TraesCS3B01G443400 chr5D 90.242 2193 177 20 223 2384 224764528 224762342 0.000000e+00 2830
17 TraesCS3B01G443400 chr7D 87.836 2417 239 35 3 2384 488804867 488802471 0.000000e+00 2784
18 TraesCS3B01G443400 chr7D 89.567 1984 179 12 3 1964 607550198 607548221 0.000000e+00 2492
19 TraesCS3B01G443400 chr5B 89.504 1372 128 6 3 1365 448296577 448295213 0.000000e+00 1722
20 TraesCS3B01G443400 chr5B 92.544 228 15 1 2157 2384 507077886 507077661 2.290000e-85 326
21 TraesCS3B01G443400 chr2A 89.427 454 40 7 1935 2384 7918432 7918881 1.240000e-157 566
22 TraesCS3B01G443400 chr7B 93.013 229 12 3 2157 2384 662648808 662648583 4.910000e-87 331
23 TraesCS3B01G443400 chr1D 92.174 230 14 2 2157 2384 236080045 236080272 2.960000e-84 322


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 TraesCS3B01G443400 chr3B 683829404 683831787 2383 False 4403 4403 100.000 1 2384 1 chr3B.!!$F2 2383
1 TraesCS3B01G443400 chr3B 683385117 683387183 2066 False 3031 3031 93.276 330 2384 1 chr3B.!!$F1 2054
2 TraesCS3B01G443400 chr3B 786581876 786584292 2416 True 3018 3018 89.480 4 2384 1 chr3B.!!$R1 2380
3 TraesCS3B01G443400 chr2D 549979724 549982136 2412 False 3253 3253 91.243 3 2384 1 chr2D.!!$F2 2381
4 TraesCS3B01G443400 chr2D 549504267 549506687 2420 False 3238 3238 91.096 3 2384 1 chr2D.!!$F1 2381
5 TraesCS3B01G443400 chr2D 367987357 367988025 668 True 911 911 91.654 1731 2384 1 chr2D.!!$R1 653
6 TraesCS3B01G443400 chr2B 250679089 250681506 2417 True 3042 3042 89.667 3 2384 1 chr2B.!!$R1 2381
7 TraesCS3B01G443400 chr2B 642947694 642949786 2092 False 2778 2778 90.805 311 2384 1 chr2B.!!$F1 2073
8 TraesCS3B01G443400 chr4B 595287929 595290342 2413 False 3027 3027 89.550 3 2384 1 chr4B.!!$F1 2381
9 TraesCS3B01G443400 chr3D 429311235 429313626 2391 True 3024 3024 89.631 3 2384 1 chr3D.!!$R2 2381
10 TraesCS3B01G443400 chr3D 522087622 522090006 2384 True 2791 2791 88.005 2 2384 1 chr3D.!!$R3 2382
11 TraesCS3B01G443400 chr4D 35486687 35489094 2407 False 2977 2977 89.219 3 2384 1 chr4D.!!$F1 2381
12 TraesCS3B01G443400 chr1B 643809484 643811889 2405 True 2948 2948 88.981 3 2384 1 chr1B.!!$R1 2381
13 TraesCS3B01G443400 chr1B 40438597 40439780 1183 False 1354 1354 87.437 5 1181 1 chr1B.!!$F1 1176
14 TraesCS3B01G443400 chr5D 224762342 224764528 2186 True 2830 2830 90.242 223 2384 1 chr5D.!!$R1 2161
15 TraesCS3B01G443400 chr7D 488802471 488804867 2396 True 2784 2784 87.836 3 2384 1 chr7D.!!$R1 2381
16 TraesCS3B01G443400 chr7D 607548221 607550198 1977 True 2492 2492 89.567 3 1964 1 chr7D.!!$R2 1961
17 TraesCS3B01G443400 chr5B 448295213 448296577 1364 True 1722 1722 89.504 3 1365 1 chr5B.!!$R1 1362

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
946 988 0.249868 CGAGACACAAAGCCAGGACA 60.25 55.0 0.0 0.0 0.0 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1779 1842 0.665835 TTGCGATCAAAGCGTTGGTT 59.334 45.0 12.54 0.67 37.44 3.67 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
20 21 4.403137 CGACCCAACGGACGCGTA 62.403 66.667 13.97 0.00 40.32 4.42
52 53 4.963878 GCATGACGACCCATTCCT 57.036 55.556 0.00 0.00 0.00 3.36
81 82 2.435938 GAGCCGGATTTGCGTCCA 60.436 61.111 5.05 0.00 38.21 4.02
85 86 2.405805 CCGGATTTGCGTCCATGCA 61.406 57.895 0.00 0.00 44.61 3.96
161 169 2.231380 AGCCACCACGATTTCCCCT 61.231 57.895 0.00 0.00 0.00 4.79
163 171 1.991230 CCACCACGATTTCCCCTCT 59.009 57.895 0.00 0.00 0.00 3.69
164 172 0.328258 CCACCACGATTTCCCCTCTT 59.672 55.000 0.00 0.00 0.00 2.85
165 173 1.271926 CCACCACGATTTCCCCTCTTT 60.272 52.381 0.00 0.00 0.00 2.52
243 258 3.718210 GACGCCATGGACCTCGACC 62.718 68.421 18.40 3.66 0.00 4.79
507 533 4.697756 CGGCGGCAACAAGGGAGA 62.698 66.667 10.53 0.00 0.00 3.71
749 784 0.613260 CCCATCGACCTCAACTCCAA 59.387 55.000 0.00 0.00 0.00 3.53
834 876 2.579201 CTCCCGGACACTCGCAAT 59.421 61.111 0.73 0.00 0.00 3.56
862 904 1.433053 CGAAATGTTATCCGCCGCCA 61.433 55.000 0.00 0.00 0.00 5.69
946 988 0.249868 CGAGACACAAAGCCAGGACA 60.250 55.000 0.00 0.00 0.00 4.02
949 991 0.536006 GACACAAAGCCAGGACAGCT 60.536 55.000 0.00 0.00 44.19 4.24
1096 1139 0.960861 AGAGGACGAGTGCGACATCA 60.961 55.000 0.00 0.00 43.29 3.07
1102 1147 1.001745 CGAGTGCGACATCAACGTGA 61.002 55.000 0.00 0.00 40.82 4.35
1636 1692 1.072173 TCCCATTGCTATCGGGTCATG 59.928 52.381 12.68 0.00 41.12 3.07
1900 1963 1.081174 TGGAGATCCAAAGGAGGAGGT 59.919 52.381 0.00 0.00 44.35 3.85
1915 1978 1.351017 GGAGGTTTGATCTGGACACCA 59.649 52.381 0.00 0.00 0.00 4.17
2127 2191 2.263077 GACATGCTCAAGTTCGACGAT 58.737 47.619 0.00 0.00 0.00 3.73
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
52 53 0.329931 TCCGGCTCAAAAATGGGCTA 59.670 50.000 0.00 0.00 0.00 3.93
53 54 0.324645 ATCCGGCTCAAAAATGGGCT 60.325 50.000 0.00 0.00 0.00 5.19
81 82 1.213013 GTCCGTCTCGTGTCTGCAT 59.787 57.895 0.00 0.00 0.00 3.96
85 86 4.086178 CGCGTCCGTCTCGTGTCT 62.086 66.667 0.00 0.00 34.71 3.41
105 112 2.442272 GGGAGAGGAGTAGGCGCA 60.442 66.667 10.83 0.00 0.00 6.09
210 225 2.100631 CGTCGTCCATGGCTGGTTC 61.101 63.158 6.96 0.00 43.61 3.62
258 273 4.816984 GGACGAGGCGAGGGAGGA 62.817 72.222 0.00 0.00 0.00 3.71
507 533 2.231529 CTACCCTAGCATGTAGAGCGT 58.768 52.381 0.00 0.00 37.26 5.07
677 711 4.069232 CTTCGGGCGAGCACTCCA 62.069 66.667 0.00 0.00 0.00 3.86
834 876 4.142988 GCGGATAACATTTCGTCAAACAGA 60.143 41.667 0.00 0.00 0.00 3.41
862 904 3.073062 AGGTTCTGCATGTAGTCCTTGTT 59.927 43.478 18.28 4.11 0.00 2.83
1026 1068 2.749044 TCGAGGGGGAAGTCGTCG 60.749 66.667 0.00 0.00 41.85 5.12
1031 1073 2.995574 CGTGGTCGAGGGGGAAGT 60.996 66.667 0.00 0.00 39.71 3.01
1096 1139 0.179067 TCGAACAAGGGCTTCACGTT 60.179 50.000 0.00 0.00 0.00 3.99
1102 1147 1.004918 CGTCCTCGAACAAGGGCTT 60.005 57.895 0.00 0.00 38.99 4.35
1184 1231 4.373116 GCTTGTCCTCGACCGCCA 62.373 66.667 0.00 0.00 0.00 5.69
1636 1692 4.394610 GCCTTGAACTTCTCCTCATTCTTC 59.605 45.833 0.00 0.00 0.00 2.87
1779 1842 0.665835 TTGCGATCAAAGCGTTGGTT 59.334 45.000 12.54 0.67 37.44 3.67
1900 1963 3.149196 GCTTCTTGGTGTCCAGATCAAA 58.851 45.455 0.00 0.00 33.81 2.69
1991 2055 2.930950 CCACTTCTTTCACCTTGGTCA 58.069 47.619 0.00 0.00 0.00 4.02
2127 2191 1.106944 TCGCCGCCATAGATCACTCA 61.107 55.000 0.00 0.00 0.00 3.41
2249 2354 5.412594 TCAGAAAATATCACCACAGTTCAGC 59.587 40.000 0.00 0.00 0.00 4.26


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

AutoCloner maintained by Alex Coulton.