Multiple sequence alignment - TraesCS5D01G239600

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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 TraesCS5D01G239600 chr5D 100.000 4053 0 0 1 4053 347443670 347447722 0.000000e+00 7485.0
1 TraesCS5D01G239600 chr5D 91.250 160 12 2 56 214 175300057 175299899 2.450000e-52 217.0
2 TraesCS5D01G239600 chr5D 90.741 162 13 1 56 217 528717428 528717269 8.820000e-52 215.0
3 TraesCS5D01G239600 chr5D 82.353 170 26 4 1019 1186 431781023 431781190 1.170000e-30 145.0
4 TraesCS5D01G239600 chr5D 81.421 183 28 6 1019 1198 433684738 433684559 1.170000e-30 145.0
5 TraesCS5D01G239600 chr5A 97.883 3779 73 4 280 4053 444533120 444529344 0.000000e+00 6529.0
6 TraesCS5D01G239600 chr5A 92.683 246 13 3 1 246 444533350 444533110 2.320000e-92 350.0
7 TraesCS5D01G239600 chr5A 90.741 162 13 1 56 217 656872435 656872276 8.820000e-52 215.0
8 TraesCS5D01G239600 chr5A 100.000 30 0 0 1799 1828 526395784 526395813 5.660000e-04 56.5
9 TraesCS5D01G239600 chr5A 94.286 35 1 1 1800 1834 447542596 447542629 7.000000e-03 52.8
10 TraesCS5D01G239600 chr5B 98.047 3482 55 6 581 4053 403708277 403704800 0.000000e+00 6041.0
11 TraesCS5D01G239600 chr5B 96.680 512 14 2 1 512 403708784 403708276 0.000000e+00 848.0
12 TraesCS5D01G239600 chr5B 91.358 162 12 1 56 217 665744619 665744460 1.900000e-53 220.0
13 TraesCS5D01G239600 chr5B 81.967 183 27 6 1019 1198 522408463 522408642 2.520000e-32 150.0
14 TraesCS5D01G239600 chr5B 81.421 183 28 6 1019 1198 522861648 522861469 1.170000e-30 145.0
15 TraesCS5D01G239600 chr3A 89.375 640 51 9 3424 4053 431819375 431818743 0.000000e+00 789.0
16 TraesCS5D01G239600 chr3A 94.798 173 9 0 3257 3429 431819683 431819511 1.860000e-68 270.0
17 TraesCS5D01G239600 chr3D 90.685 569 37 6 3495 4053 302933678 302934240 0.000000e+00 743.0
18 TraesCS5D01G239600 chr3D 91.213 239 15 4 3257 3493 302933276 302933510 1.820000e-83 320.0
19 TraesCS5D01G239600 chr3D 92.208 154 11 1 56 208 288550458 288550611 2.450000e-52 217.0
20 TraesCS5D01G239600 chr3D 91.195 159 12 2 56 214 73853088 73853244 8.820000e-52 215.0
21 TraesCS5D01G239600 chr3D 96.970 33 0 1 1799 1830 838149 838181 2.000000e-03 54.7
22 TraesCS5D01G239600 chr2D 91.824 159 12 1 55 212 79056320 79056162 1.900000e-53 220.0
23 TraesCS5D01G239600 chr2D 82.258 186 28 4 1001 1185 25338997 25339178 5.420000e-34 156.0
24 TraesCS5D01G239600 chr2B 82.778 180 29 2 1007 1185 41132697 41132875 4.190000e-35 159.0
25 TraesCS5D01G239600 chr2A 82.258 186 28 4 1001 1185 27952442 27952623 5.420000e-34 156.0
26 TraesCS5D01G239600 chr2A 87.500 48 3 3 1781 1825 444756502 444756549 7.000000e-03 52.8
27 TraesCS5D01G239600 chr1A 100.000 32 0 0 1796 1827 49259280 49259311 4.370000e-05 60.2
28 TraesCS5D01G239600 chr7B 94.444 36 2 0 1798 1833 164500712 164500747 5.660000e-04 56.5
29 TraesCS5D01G239600 chr3B 100.000 30 0 0 1799 1828 134272189 134272218 5.660000e-04 56.5


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 TraesCS5D01G239600 chr5D 347443670 347447722 4052 False 7485.0 7485 100.0000 1 4053 1 chr5D.!!$F1 4052
1 TraesCS5D01G239600 chr5A 444529344 444533350 4006 True 3439.5 6529 95.2830 1 4053 2 chr5A.!!$R2 4052
2 TraesCS5D01G239600 chr5B 403704800 403708784 3984 True 3444.5 6041 97.3635 1 4053 2 chr5B.!!$R3 4052
3 TraesCS5D01G239600 chr3A 431818743 431819683 940 True 529.5 789 92.0865 3257 4053 2 chr3A.!!$R1 796
4 TraesCS5D01G239600 chr3D 302933276 302934240 964 False 531.5 743 90.9490 3257 4053 2 chr3D.!!$F4 796

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
566 614 2.223876 TGCCGACTATCGTTTATGACCC 60.224 50.000 0.00 0.0 38.4 4.46 F
691 739 2.621338 ACACATGATACCTGCGTCTTG 58.379 47.619 0.00 0.0 0.0 3.02 F
913 965 2.731976 CGTGAGTTTGTCTTCACCTAGC 59.268 50.000 0.00 0.0 0.0 3.42 F
2735 2796 0.835276 CCAGAGGTCATCAGATGCCA 59.165 55.000 19.91 0.0 0.0 4.92 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1538 1598 3.058777 ACGAGTTCTCTCTCTTGTTCGTC 60.059 47.826 0.00 0.0 35.39 4.20 R
2392 2453 3.433598 GGGATAGTGCTCTTTGTGCCATA 60.434 47.826 0.00 0.0 0.00 2.74 R
2938 2999 4.041075 TCAAAGGGGAATTTTACTTTGGGC 59.959 41.667 20.10 0.0 45.90 5.36 R
3818 4200 1.130749 GCTGCTTGCAGAGTTCATGAG 59.869 52.381 24.67 0.0 42.31 2.90 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 6.906157 ATGGACTGAAATGAGTGAACAAAT 57.094 33.333 0.00 0.00 0.00 2.32
173 174 9.739276 TCTGTAGACATCCAATTCACTAAAAAT 57.261 29.630 0.00 0.00 0.00 1.82
235 283 5.690865 AGAAACTGTTCAAACCATACCTGA 58.309 37.500 0.00 0.00 36.09 3.86
238 286 6.976934 AACTGTTCAAACCATACCTGATTT 57.023 33.333 0.00 0.00 0.00 2.17
239 287 6.575162 ACTGTTCAAACCATACCTGATTTC 57.425 37.500 0.00 0.00 0.00 2.17
240 288 6.306987 ACTGTTCAAACCATACCTGATTTCT 58.693 36.000 0.00 0.00 0.00 2.52
241 289 7.458397 ACTGTTCAAACCATACCTGATTTCTA 58.542 34.615 0.00 0.00 0.00 2.10
242 290 8.109634 ACTGTTCAAACCATACCTGATTTCTAT 58.890 33.333 0.00 0.00 0.00 1.98
243 291 8.279970 TGTTCAAACCATACCTGATTTCTATG 57.720 34.615 0.00 0.00 0.00 2.23
244 292 8.106462 TGTTCAAACCATACCTGATTTCTATGA 58.894 33.333 0.00 0.00 0.00 2.15
245 293 8.956426 GTTCAAACCATACCTGATTTCTATGAA 58.044 33.333 0.00 0.00 0.00 2.57
246 294 9.527157 TTCAAACCATACCTGATTTCTATGAAA 57.473 29.630 0.00 0.00 0.00 2.69
247 295 8.956426 TCAAACCATACCTGATTTCTATGAAAC 58.044 33.333 0.00 0.00 0.00 2.78
248 296 8.960591 CAAACCATACCTGATTTCTATGAAACT 58.039 33.333 0.00 0.00 0.00 2.66
249 297 8.511604 AACCATACCTGATTTCTATGAAACTG 57.488 34.615 0.00 0.00 0.00 3.16
250 298 7.861629 ACCATACCTGATTTCTATGAAACTGA 58.138 34.615 0.00 0.00 0.00 3.41
251 299 7.770897 ACCATACCTGATTTCTATGAAACTGAC 59.229 37.037 0.00 0.00 0.00 3.51
252 300 7.770433 CCATACCTGATTTCTATGAAACTGACA 59.230 37.037 0.00 0.00 0.00 3.58
253 301 9.166173 CATACCTGATTTCTATGAAACTGACAA 57.834 33.333 0.00 0.00 0.00 3.18
254 302 9.739276 ATACCTGATTTCTATGAAACTGACAAA 57.261 29.630 0.00 0.00 0.00 2.83
255 303 8.641498 ACCTGATTTCTATGAAACTGACAAAT 57.359 30.769 0.00 0.00 0.00 2.32
256 304 9.739276 ACCTGATTTCTATGAAACTGACAAATA 57.261 29.630 0.00 0.00 0.00 1.40
283 331 8.863872 ATAAAAGAAATGGTGCTACTACTGTT 57.136 30.769 0.00 0.00 0.00 3.16
284 332 7.582667 AAAAGAAATGGTGCTACTACTGTTT 57.417 32.000 0.00 0.00 0.00 2.83
325 373 3.031736 TGCTTAGGGTGTCCTAGATCAC 58.968 50.000 0.00 0.00 45.60 3.06
372 420 8.877864 GGACAAATAATCCCCATATATGTTGA 57.122 34.615 11.73 7.75 0.00 3.18
375 423 9.827198 ACAAATAATCCCCATATATGTTGACAT 57.173 29.630 11.73 1.84 40.22 3.06
513 561 7.331026 TCTAGTCATGTTTAAGCAGCTGTAAT 58.669 34.615 16.64 4.42 0.00 1.89
566 614 2.223876 TGCCGACTATCGTTTATGACCC 60.224 50.000 0.00 0.00 38.40 4.46
684 732 5.812642 GTCCTCAAGTTACACATGATACCTG 59.187 44.000 0.00 0.00 0.00 4.00
691 739 2.621338 ACACATGATACCTGCGTCTTG 58.379 47.619 0.00 0.00 0.00 3.02
800 852 3.877508 ACTGTCAGTAAGAGTTTTGCCAC 59.122 43.478 2.87 0.00 0.00 5.01
913 965 2.731976 CGTGAGTTTGTCTTCACCTAGC 59.268 50.000 0.00 0.00 0.00 3.42
1323 1375 8.225107 GCCAGCATATACAATTTTGCATTTATG 58.775 33.333 0.00 0.00 37.56 1.90
1358 1410 7.911130 ATGAATGGAAGACATCTCTCTCTAA 57.089 36.000 0.00 0.00 39.40 2.10
1438 1490 3.795688 ATTCCACACTCACCATCTTGT 57.204 42.857 0.00 0.00 0.00 3.16
1487 1547 3.202151 TCATAGCCTCCTTACTTTTGGGG 59.798 47.826 0.00 0.00 0.00 4.96
1496 1556 3.756963 CCTTACTTTTGGGGAACTACAGC 59.243 47.826 0.00 0.00 0.00 4.40
1581 1641 4.692625 CGTGATTTCTGATCCACTTCAGTT 59.307 41.667 1.76 0.00 43.02 3.16
1612 1672 8.354426 GTTTTACTCTTAATACAAGTTGGGCAA 58.646 33.333 7.96 0.00 0.00 4.52
1684 1744 7.559335 AATAAGGCCATATCATACTCAGACA 57.441 36.000 5.01 0.00 0.00 3.41
1909 1969 6.709145 GCAAACATTACTTCATTGCATTGA 57.291 33.333 7.19 7.19 44.29 2.57
2199 2259 3.945921 CTGACTGGATGATGCATGAGTTT 59.054 43.478 2.46 0.00 0.00 2.66
2735 2796 0.835276 CCAGAGGTCATCAGATGCCA 59.165 55.000 19.91 0.00 0.00 4.92
2938 2999 2.158900 AGGCAATGAGTATGGAGTTCCG 60.159 50.000 0.00 0.00 39.43 4.30
2945 3006 1.065418 AGTATGGAGTTCCGCCCAAAG 60.065 52.381 0.00 0.00 39.43 2.77
3069 3132 4.096984 CCAATAGCTGCTCGAAGGAAAAAT 59.903 41.667 4.91 0.00 0.00 1.82
3458 3664 8.487176 GTTTAGAACAACTACCAATGCAAAATG 58.513 33.333 0.00 0.00 0.00 2.32
3818 4200 2.604046 ATCGTCCAAGTACAGCATCC 57.396 50.000 0.00 0.00 0.00 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
11 12 8.855110 ACTTTCAAATACATCAACACCACAATA 58.145 29.630 0.00 0.0 0.00 1.90
12 13 7.652909 CACTTTCAAATACATCAACACCACAAT 59.347 33.333 0.00 0.0 0.00 2.71
257 305 9.953565 AACAGTAGTAGCACCATTTCTTTTATA 57.046 29.630 0.00 0.0 0.00 0.98
258 306 8.863872 AACAGTAGTAGCACCATTTCTTTTAT 57.136 30.769 0.00 0.0 0.00 1.40
259 307 8.685838 AAACAGTAGTAGCACCATTTCTTTTA 57.314 30.769 0.00 0.0 0.00 1.52
260 308 7.582667 AAACAGTAGTAGCACCATTTCTTTT 57.417 32.000 0.00 0.0 0.00 2.27
261 309 8.730680 CATAAACAGTAGTAGCACCATTTCTTT 58.269 33.333 0.00 0.0 0.00 2.52
262 310 8.100791 TCATAAACAGTAGTAGCACCATTTCTT 58.899 33.333 0.00 0.0 0.00 2.52
263 311 7.620880 TCATAAACAGTAGTAGCACCATTTCT 58.379 34.615 0.00 0.0 0.00 2.52
264 312 7.843490 TCATAAACAGTAGTAGCACCATTTC 57.157 36.000 0.00 0.0 0.00 2.17
265 313 8.807948 ATTCATAAACAGTAGTAGCACCATTT 57.192 30.769 0.00 0.0 0.00 2.32
268 316 9.899661 AAATATTCATAAACAGTAGTAGCACCA 57.100 29.630 0.00 0.0 0.00 4.17
306 354 5.878406 ATTGTGATCTAGGACACCCTAAG 57.122 43.478 14.27 0.0 44.06 2.18
325 373 5.534654 TCCCTTTCACTTCACACCTAAATTG 59.465 40.000 0.00 0.0 0.00 2.32
372 420 6.413052 AGTATCTCAATGAAGACAAGCATGT 58.587 36.000 0.00 0.0 44.25 3.21
375 423 7.712639 GGATTAGTATCTCAATGAAGACAAGCA 59.287 37.037 0.00 0.0 0.00 3.91
466 514 2.328099 GGCCCACAACTCTGAAGCG 61.328 63.158 0.00 0.0 0.00 4.68
566 614 6.480320 GCTCCTATTATATGCCTTGTATTCCG 59.520 42.308 0.00 0.0 0.00 4.30
684 732 4.394920 TGGGAAAGAATGAATACAAGACGC 59.605 41.667 0.00 0.0 0.00 5.19
913 965 2.853705 TGGTTTTAGGGTCGAAGTTGG 58.146 47.619 0.00 0.0 0.00 3.77
1358 1410 7.120285 GCATAATATCTGGTGTCTGCATGTTAT 59.880 37.037 0.00 0.0 0.00 1.89
1487 1547 3.927142 ACTGTATCTTTGCGCTGTAGTTC 59.073 43.478 9.73 0.0 0.00 3.01
1538 1598 3.058777 ACGAGTTCTCTCTCTTGTTCGTC 60.059 47.826 0.00 0.0 35.39 4.20
1612 1672 9.745880 CATTGCTTGAAATATTGCTAGAAGATT 57.254 29.630 8.89 0.0 0.00 2.40
1684 1744 4.019501 ACAATCTTGGATCTTCTGTGCTCT 60.020 41.667 0.00 0.0 0.00 4.09
2199 2259 4.406003 GGATCAGTTAGTGAAGGAAGCCTA 59.594 45.833 0.00 0.0 39.19 3.93
2392 2453 3.433598 GGGATAGTGCTCTTTGTGCCATA 60.434 47.826 0.00 0.0 0.00 2.74
2938 2999 4.041075 TCAAAGGGGAATTTTACTTTGGGC 59.959 41.667 20.10 0.0 45.90 5.36
3319 3382 5.182760 CAGGCTCTTTGCTGAACTTAATTCT 59.817 40.000 0.00 0.0 42.39 2.40
3458 3664 3.066760 AGCCTTTTTACACTGTTCAGCAC 59.933 43.478 0.00 0.0 0.00 4.40
3461 3667 5.163663 TGTTGAGCCTTTTTACACTGTTCAG 60.164 40.000 0.00 0.0 0.00 3.02
3818 4200 1.130749 GCTGCTTGCAGAGTTCATGAG 59.869 52.381 24.67 0.0 42.31 2.90


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

AutoCloner maintained by Alex Coulton.