Multiple sequence alignment - TraesCS5D01G352500

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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 TraesCS5D01G352500 chr5D 100.000 2664 0 0 1 2664 435262781 435265444 0.000000e+00 4920.0
1 TraesCS5D01G352500 chr5D 89.813 854 66 14 1790 2635 435270640 435271480 0.000000e+00 1075.0
2 TraesCS5D01G352500 chr5D 97.297 37 1 0 382 418 435263099 435263135 2.210000e-06 63.9
3 TraesCS5D01G352500 chr5D 97.297 37 1 0 319 355 435263162 435263198 2.210000e-06 63.9
4 TraesCS5D01G352500 chr5B 90.599 2319 157 30 361 2664 528574626 528576898 0.000000e+00 3018.0
5 TraesCS5D01G352500 chr5B 88.988 1008 97 11 1666 2664 528582642 528583644 0.000000e+00 1234.0
6 TraesCS5D01G352500 chr5B 89.489 333 17 3 1 324 528573915 528574238 3.190000e-109 405.0
7 TraesCS5D01G352500 chr5B 100.000 32 0 0 323 354 528574651 528574682 2.860000e-05 60.2
8 TraesCS5D01G352500 chr5A 92.900 1507 93 9 1162 2662 549201202 549202700 0.000000e+00 2178.0
9 TraesCS5D01G352500 chr5A 90.779 1399 103 12 465 1859 9386058 9384682 0.000000e+00 1845.0
10 TraesCS5D01G352500 chr5A 89.332 853 72 12 1790 2635 549211638 549212478 0.000000e+00 1053.0
11 TraesCS5D01G352500 chr5A 88.069 813 48 18 365 1173 549200415 549201182 0.000000e+00 918.0
12 TraesCS5D01G352500 chr5A 91.734 617 43 6 1847 2456 9383406 9382791 0.000000e+00 850.0
13 TraesCS5D01G352500 chr5A 86.214 457 46 11 1421 1872 549208584 549209028 1.860000e-131 479.0
14 TraesCS5D01G352500 chr5A 91.975 324 24 2 1 324 549200087 549200408 1.120000e-123 453.0
15 TraesCS5D01G352500 chr5A 94.040 151 6 2 2444 2594 9376033 9375886 2.670000e-55 226.0
16 TraesCS5D01G352500 chr5A 96.970 99 3 0 366 464 9386457 9386359 1.640000e-37 167.0
17 TraesCS5D01G352500 chr5A 87.387 111 2 4 256 354 9386516 9386406 1.680000e-22 117.0
18 TraesCS5D01G352500 chr3A 83.158 95 14 2 1816 1909 533643047 533643140 4.720000e-13 86.1
19 TraesCS5D01G352500 chr2B 89.583 48 3 2 1806 1853 182035646 182035691 2.860000e-05 60.2


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 TraesCS5D01G352500 chr5D 435262781 435265444 2663 False 1682.600000 4920 98.198000 1 2664 3 chr5D.!!$F2 2663
1 TraesCS5D01G352500 chr5D 435270640 435271480 840 False 1075.000000 1075 89.813000 1790 2635 1 chr5D.!!$F1 845
2 TraesCS5D01G352500 chr5B 528582642 528583644 1002 False 1234.000000 1234 88.988000 1666 2664 1 chr5B.!!$F1 998
3 TraesCS5D01G352500 chr5B 528573915 528576898 2983 False 1161.066667 3018 93.362667 1 2664 3 chr5B.!!$F2 2663
4 TraesCS5D01G352500 chr5A 549200087 549202700 2613 False 1183.000000 2178 90.981333 1 2662 3 chr5A.!!$F1 2661
5 TraesCS5D01G352500 chr5A 549208584 549212478 3894 False 766.000000 1053 87.773000 1421 2635 2 chr5A.!!$F2 1214
6 TraesCS5D01G352500 chr5A 9382791 9386516 3725 True 744.750000 1845 91.717500 256 2456 4 chr5A.!!$R2 2200

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
359 371 0.595825 GTTCAGCAACTTGCCACAGC 60.596 55.0 10.25 0.0 46.52 4.4 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1709 2410 0.038251 TGCCACGTAACTGAGCAGAG 60.038 55.0 4.21 0.0 0.0 3.35 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
78 90 5.723672 TTAGCAGTACAAACTACAGAGCT 57.276 39.130 0.00 0.00 33.48 4.09
141 153 9.023962 ACATATAAATTGAACAGCCTTGAAAGA 57.976 29.630 0.00 0.00 0.00 2.52
167 179 5.948992 AAATAAGACTTCACAGAAGGCAC 57.051 39.130 14.49 4.58 0.00 5.01
229 241 5.542635 AGACTAGTCCATACCTGTCAAACAA 59.457 40.000 19.38 0.00 33.40 2.83
263 275 4.794278 AATTTACGGGACCCATGTTTTC 57.206 40.909 12.15 0.00 0.00 2.29
324 336 2.019984 GAAGGCGCTGAGAAATGGATT 58.980 47.619 7.64 0.00 0.00 3.01
325 337 3.118261 AGAAGGCGCTGAGAAATGGATTA 60.118 43.478 7.64 0.00 0.00 1.75
327 339 3.144506 AGGCGCTGAGAAATGGATTATG 58.855 45.455 7.64 0.00 0.00 1.90
328 340 3.141398 GGCGCTGAGAAATGGATTATGA 58.859 45.455 7.64 0.00 0.00 2.15
329 341 3.188048 GGCGCTGAGAAATGGATTATGAG 59.812 47.826 7.64 0.00 0.00 2.90
330 342 3.812053 GCGCTGAGAAATGGATTATGAGT 59.188 43.478 0.00 0.00 0.00 3.41
332 344 5.466728 GCGCTGAGAAATGGATTATGAGTTA 59.533 40.000 0.00 0.00 0.00 2.24
333 345 6.148480 GCGCTGAGAAATGGATTATGAGTTAT 59.852 38.462 0.00 0.00 0.00 1.89
334 346 7.516481 CGCTGAGAAATGGATTATGAGTTATG 58.484 38.462 0.00 0.00 0.00 1.90
336 348 9.060347 GCTGAGAAATGGATTATGAGTTATGAA 57.940 33.333 0.00 0.00 0.00 2.57
345 357 9.166173 TGGATTATGAGTTATGAAACTGTTCAG 57.834 33.333 0.00 0.00 46.75 3.02
346 358 8.125448 GGATTATGAGTTATGAAACTGTTCAGC 58.875 37.037 0.00 0.00 46.75 4.26
347 359 7.977789 TTATGAGTTATGAAACTGTTCAGCA 57.022 32.000 0.00 0.00 46.75 4.41
348 360 6.882610 ATGAGTTATGAAACTGTTCAGCAA 57.117 33.333 0.00 0.00 46.75 3.91
349 361 6.060028 TGAGTTATGAAACTGTTCAGCAAC 57.940 37.500 0.00 7.91 46.75 4.17
350 362 5.822519 TGAGTTATGAAACTGTTCAGCAACT 59.177 36.000 14.33 14.33 46.75 3.16
352 364 6.498304 AGTTATGAAACTGTTCAGCAACTTG 58.502 36.000 10.90 0.00 46.75 3.16
353 365 3.149436 TGAAACTGTTCAGCAACTTGC 57.851 42.857 5.55 5.55 45.46 4.01
357 369 0.740149 CTGTTCAGCAACTTGCCACA 59.260 50.000 10.25 9.83 46.52 4.17
358 370 0.740149 TGTTCAGCAACTTGCCACAG 59.260 50.000 10.25 0.00 46.52 3.66
359 371 0.595825 GTTCAGCAACTTGCCACAGC 60.596 55.000 10.25 0.00 46.52 4.40
362 725 3.595758 GCAACTTGCCACAGCCGT 61.596 61.111 1.95 0.00 37.42 5.68
384 747 3.197766 TGTAGAAGTCAGGTAGGCCATTG 59.802 47.826 5.01 0.00 37.19 2.82
417 781 2.159254 TGAAACTGTTCAGCAACTTGCC 60.159 45.455 10.25 0.00 46.52 4.52
519 1183 1.676384 GCTAGCTAGCCCCATGAGG 59.324 63.158 31.67 0.00 43.39 3.86
765 1433 1.274167 CATTGCACAATGCTGGAACCT 59.726 47.619 10.22 0.00 45.31 3.50
890 1559 7.363181 CCAATAACATTTCCTTGATCTGCTTGA 60.363 37.037 0.00 0.00 0.00 3.02
891 1560 5.640189 AACATTTCCTTGATCTGCTTGAG 57.360 39.130 0.00 0.00 0.00 3.02
941 1610 3.288092 GTCCCCTTACCCAATCATCAAC 58.712 50.000 0.00 0.00 0.00 3.18
965 1634 3.679389 CACTTGACAGGGCTTGTATCTT 58.321 45.455 0.82 0.00 41.05 2.40
1173 1873 1.745232 TGACGGCAACAACAGAAGTT 58.255 45.000 0.00 0.00 38.88 2.66
1325 2025 0.869880 GTGTTTGGTTTCGCAGGCAC 60.870 55.000 0.00 0.00 0.00 5.01
1350 2050 2.832201 GGGATCAAGCTGCCCTGC 60.832 66.667 0.00 0.00 38.85 4.85
1431 2131 0.179062 AGGCAGCATTCCTTAGCTCG 60.179 55.000 0.00 0.00 39.50 5.03
1467 2167 0.987294 ACTATGCAGCTCCACCTGTT 59.013 50.000 0.00 0.00 35.28 3.16
1498 2198 3.940852 CCAGCATGTTATTGTCTGCAGTA 59.059 43.478 14.67 1.04 37.09 2.74
1512 2212 4.509600 GTCTGCAGTAGCTAATTGTCATCC 59.490 45.833 14.67 0.00 42.74 3.51
1521 2221 6.017400 AGCTAATTGTCATCCTGTTTTGTG 57.983 37.500 0.00 0.00 0.00 3.33
1564 2264 8.826765 AGTTCAATGTAGGAAATAGGAAAGAGA 58.173 33.333 0.00 0.00 0.00 3.10
1597 2297 6.572519 TGCAAAGAATTTTAGTTCTGCAACT 58.427 32.000 0.00 0.00 40.69 3.16
1709 2410 6.795399 TGAACAGAACAAGTCAAAGAATTCC 58.205 36.000 0.65 0.00 0.00 3.01
1715 2416 4.723309 ACAAGTCAAAGAATTCCTCTGCT 58.277 39.130 0.65 0.00 33.37 4.24
1728 2429 0.038251 CTCTGCTCAGTTACGTGGCA 60.038 55.000 0.00 0.00 0.00 4.92
1754 2456 9.883142 ATCAGACCAAAAATTTACAAAGAAACA 57.117 25.926 0.00 0.00 0.00 2.83
1791 2494 5.184671 GGAGAAATGTTCCTGAATGAGCTTT 59.815 40.000 0.00 0.00 0.00 3.51
1851 6539 4.325972 TCCGTCCAAATGGGTTTACTAAC 58.674 43.478 0.00 0.00 38.11 2.34
1881 6570 3.242413 CCGATCCAGTACAAAATTGAGCG 60.242 47.826 0.00 0.00 0.00 5.03
1895 6584 7.872483 ACAAAATTGAGCGTTTCATTAGGATTT 59.128 29.630 0.00 0.00 35.27 2.17
1902 6591 7.552687 TGAGCGTTTCATTAGGATTTTATGAGT 59.447 33.333 0.00 0.00 30.64 3.41
2000 6693 6.375377 CGCTGCTTAACAAAACAATACCTAA 58.625 36.000 0.00 0.00 0.00 2.69
2025 6718 2.749076 GCATTGCAGATGTAGACCACAA 59.251 45.455 3.15 0.00 41.55 3.33
2264 6963 4.401022 TCATCAGTGCTTGAGAATTTGGT 58.599 39.130 0.00 0.00 39.68 3.67
2340 7039 7.041916 GCAAACATCTTCCAAAATTCATCAACA 60.042 33.333 0.00 0.00 0.00 3.33
2358 7057 5.649557 TCAACAAAACCAATTGACTGACTG 58.350 37.500 7.12 0.00 34.38 3.51
2536 7236 5.076182 TGTTGCATTTCCTATTGTCCTGAA 58.924 37.500 0.00 0.00 0.00 3.02
2627 7328 0.821301 TGATGGCGGCAAACAACTCA 60.821 50.000 18.31 11.50 0.00 3.41
2628 7329 0.527565 GATGGCGGCAAACAACTCAT 59.472 50.000 18.31 0.00 0.00 2.90
2645 7346 1.409064 TCATACTGTAGCAAGGCCTCG 59.591 52.381 5.23 0.00 0.00 4.63
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
92 104 8.542497 TGTAACAGTTAGACATGACCAATTAC 57.458 34.615 0.00 0.00 0.00 1.89
109 121 8.807948 AGGCTGTTCAATTTATATGTAACAGT 57.192 30.769 12.88 0.00 43.49 3.55
141 153 8.515414 GTGCCTTCTGTGAAGTCTTATTTTATT 58.485 33.333 6.57 0.00 0.00 1.40
167 179 4.400567 CCCTTTGAGAATTTTCAGGCCTAG 59.599 45.833 3.98 0.00 0.00 3.02
181 193 2.297701 GTTGCACACTTCCCTTTGAGA 58.702 47.619 0.00 0.00 0.00 3.27
229 241 4.224370 TCCCGTAAATTTAGCTGGAAGTCT 59.776 41.667 11.01 0.00 35.30 3.24
289 301 1.301677 CCTTCTCCGCACTTTCCTGC 61.302 60.000 0.00 0.00 0.00 4.85
324 336 7.661437 AGTTGCTGAACAGTTTCATAACTCATA 59.339 33.333 3.77 0.00 42.67 2.15
325 337 6.488006 AGTTGCTGAACAGTTTCATAACTCAT 59.512 34.615 3.77 0.00 42.67 2.90
327 339 6.305693 AGTTGCTGAACAGTTTCATAACTC 57.694 37.500 3.77 0.00 42.67 3.01
328 340 6.498304 CAAGTTGCTGAACAGTTTCATAACT 58.502 36.000 3.77 9.57 43.67 2.24
329 341 5.173854 GCAAGTTGCTGAACAGTTTCATAAC 59.826 40.000 20.71 0.00 41.05 1.89
330 342 5.280945 GCAAGTTGCTGAACAGTTTCATAA 58.719 37.500 20.71 0.00 41.05 1.90
332 344 3.491447 GGCAAGTTGCTGAACAGTTTCAT 60.491 43.478 26.16 0.00 44.28 2.57
333 345 2.159254 GGCAAGTTGCTGAACAGTTTCA 60.159 45.455 26.16 0.00 44.28 2.69
334 346 2.159254 TGGCAAGTTGCTGAACAGTTTC 60.159 45.455 26.16 7.09 44.28 2.78
336 348 1.134946 GTGGCAAGTTGCTGAACAGTT 59.865 47.619 26.16 0.00 44.28 3.16
337 349 0.740737 GTGGCAAGTTGCTGAACAGT 59.259 50.000 26.16 0.00 44.28 3.55
338 350 0.740149 TGTGGCAAGTTGCTGAACAG 59.260 50.000 26.16 0.00 44.28 3.16
339 351 0.740149 CTGTGGCAAGTTGCTGAACA 59.260 50.000 26.16 23.50 44.28 3.18
340 352 0.595825 GCTGTGGCAAGTTGCTGAAC 60.596 55.000 26.16 20.71 44.28 3.18
342 354 2.195567 GGCTGTGGCAAGTTGCTGA 61.196 57.895 26.16 11.49 44.28 4.26
345 357 3.595758 ACGGCTGTGGCAAGTTGC 61.596 61.111 19.87 19.87 44.08 4.17
346 358 2.332514 CACGGCTGTGGCAAGTTG 59.667 61.111 18.43 0.00 42.59 3.16
357 369 2.093106 CTACCTGACTTCTACACGGCT 58.907 52.381 0.00 0.00 0.00 5.52
358 370 1.134560 CCTACCTGACTTCTACACGGC 59.865 57.143 0.00 0.00 0.00 5.68
359 371 1.134560 GCCTACCTGACTTCTACACGG 59.865 57.143 0.00 0.00 0.00 4.94
362 725 2.615986 TGGCCTACCTGACTTCTACA 57.384 50.000 3.32 0.00 36.63 2.74
384 747 8.668353 TGCTGAACAGTTTCATAACTCATAATC 58.332 33.333 3.77 0.00 42.67 1.75
417 781 3.829886 ACATTAACTGATGCAACACGG 57.170 42.857 0.00 0.00 0.00 4.94
765 1433 0.893270 CGAGGACCCCATGCAAACAA 60.893 55.000 0.00 0.00 0.00 2.83
871 1540 3.181489 GCCTCAAGCAGATCAAGGAAATG 60.181 47.826 0.00 0.00 42.97 2.32
890 1559 1.972795 AGGTTCATTTGTGCAATGCCT 59.027 42.857 1.53 0.00 42.06 4.75
891 1560 2.460757 AGGTTCATTTGTGCAATGCC 57.539 45.000 1.53 0.00 42.06 4.40
911 1580 1.218844 GGTAAGGGGACAAGGCCATA 58.781 55.000 5.01 0.00 0.00 2.74
941 1610 2.281761 AAGCCCTGTCAAGTGCCG 60.282 61.111 0.00 0.00 0.00 5.69
958 1627 9.547753 GACCAAGAATTTATAGCTCAAGATACA 57.452 33.333 0.00 0.00 0.00 2.29
959 1628 8.994170 GGACCAAGAATTTATAGCTCAAGATAC 58.006 37.037 0.00 0.00 0.00 2.24
965 1634 6.115446 CACTGGACCAAGAATTTATAGCTCA 58.885 40.000 0.00 0.00 0.00 4.26
1112 1781 2.586792 CTGCTACCCTCTGCCACC 59.413 66.667 0.00 0.00 0.00 4.61
1233 1933 2.629617 CAATGGCACCTCAAACCTTCTT 59.370 45.455 0.00 0.00 0.00 2.52
1237 1937 3.056213 CCAATGGCACCTCAAACCT 57.944 52.632 0.00 0.00 0.00 3.50
1325 2025 1.746516 GCAGCTTGATCCCTCCTTCAG 60.747 57.143 0.00 0.00 0.00 3.02
1350 2050 2.578163 ACTCCATCACCATGGCGTCG 62.578 60.000 13.04 0.00 43.53 5.12
1419 2119 3.805108 GCATCACCATCGAGCTAAGGAAT 60.805 47.826 0.00 0.00 0.00 3.01
1467 2167 5.321102 ACAATAACATGCTGGTTAACTCCA 58.679 37.500 5.42 1.02 36.86 3.86
1475 2175 2.751259 CTGCAGACAATAACATGCTGGT 59.249 45.455 8.42 0.00 39.42 4.00
1498 2198 5.565439 GCACAAAACAGGATGACAATTAGCT 60.565 40.000 0.00 0.00 39.69 3.32
1512 2212 5.715429 TTACATGCAAAAGCACAAAACAG 57.285 34.783 0.00 0.00 0.00 3.16
1521 2221 7.382218 ACATTGAACTACTTTACATGCAAAAGC 59.618 33.333 16.95 5.41 37.44 3.51
1590 2290 4.604843 TCGATTGCTTAATCAGTTGCAG 57.395 40.909 0.00 0.00 36.75 4.41
1597 2297 5.365403 ACCGTTTTTCGATTGCTTAATCA 57.635 34.783 0.00 0.00 42.86 2.57
1709 2410 0.038251 TGCCACGTAACTGAGCAGAG 60.038 55.000 4.21 0.00 0.00 3.35
1715 2416 1.067142 GGTCTGATGCCACGTAACTGA 60.067 52.381 0.00 0.00 0.00 3.41
1728 2429 9.883142 TGTTTCTTTGTAAATTTTTGGTCTGAT 57.117 25.926 0.00 0.00 0.00 2.90
1754 2456 2.978156 TTTCTCCTGCCCACTTGAAT 57.022 45.000 0.00 0.00 0.00 2.57
1791 2494 7.621683 AGGGGATATATTGTTTGGCAGTTTTTA 59.378 33.333 0.00 0.00 0.00 1.52
1851 6539 1.138859 TGTACTGGATCGGGCATTCTG 59.861 52.381 0.00 0.00 0.00 3.02
1895 6584 6.907961 TCTTAGTCCCAGCTACTACTCATAA 58.092 40.000 0.00 0.00 0.00 1.90
1902 6591 6.463049 GCATGATTTCTTAGTCCCAGCTACTA 60.463 42.308 0.00 0.00 0.00 1.82
2000 6693 3.452264 TGGTCTACATCTGCAATGCTAGT 59.548 43.478 6.82 2.39 0.00 2.57
2043 6736 5.801350 TGGAAAAAGAGATACGATTGCTG 57.199 39.130 0.00 0.00 0.00 4.41
2044 6737 8.682936 ATATTGGAAAAAGAGATACGATTGCT 57.317 30.769 0.00 0.00 0.00 3.91
2340 7039 3.030291 TGCCAGTCAGTCAATTGGTTTT 58.970 40.909 5.42 0.00 33.21 2.43
2627 7328 0.105039 GCGAGGCCTTGCTACAGTAT 59.895 55.000 34.14 0.00 37.03 2.12
2628 7329 1.515954 GCGAGGCCTTGCTACAGTA 59.484 57.895 34.14 0.00 37.03 2.74


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

AutoCloner maintained by Alex Coulton.