Multiple sequence alignment - TraesCS4B01G088900

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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 TraesCS4B01G088900 chr4B 100.000 2555 0 0 1 2555 89928092 89930646 0.000000e+00 4719.0
1 TraesCS4B01G088900 chr4D 92.715 2567 135 32 1 2555 62302774 62305300 0.000000e+00 3657.0
2 TraesCS4B01G088900 chr4D 78.469 209 35 7 23 229 67246830 67246630 7.420000e-26 128.0
3 TraesCS4B01G088900 chr4A 91.840 2598 144 24 1 2555 535818024 535820596 0.000000e+00 3561.0
4 TraesCS4B01G088900 chr4A 75.497 302 55 12 1 292 516357443 516357151 2.060000e-26 130.0
5 TraesCS4B01G088900 chr2A 77.670 309 51 14 1 303 711862055 711861759 3.380000e-39 172.0
6 TraesCS4B01G088900 chr2B 77.483 302 56 11 1 299 591605025 591605317 1.220000e-38 171.0
7 TraesCS4B01G088900 chr2B 81.356 177 28 5 126 300 512634013 512633840 3.430000e-29 139.0
8 TraesCS4B01G088900 chr7D 78.761 226 35 11 78 299 159412168 159411952 3.430000e-29 139.0
9 TraesCS4B01G088900 chr7D 77.083 240 44 8 1 238 27187232 27187002 7.420000e-26 128.0
10 TraesCS4B01G088900 chr1B 84.677 124 15 4 1 123 310393304 310393424 1.240000e-23 121.0
11 TraesCS4B01G088900 chrUn 82.258 124 18 3 1 122 77533036 77532915 1.250000e-18 104.0
12 TraesCS4B01G088900 chr3B 77.143 175 29 5 126 299 535542460 535542296 9.730000e-15 91.6
13 TraesCS4B01G088900 chr3B 82.075 106 12 7 215 320 628471144 628471046 1.630000e-12 84.2
14 TraesCS4B01G088900 chr3B 91.111 45 1 1 255 299 143149747 143149788 9.870000e-05 58.4


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 TraesCS4B01G088900 chr4B 89928092 89930646 2554 False 4719 4719 100.000 1 2555 1 chr4B.!!$F1 2554
1 TraesCS4B01G088900 chr4D 62302774 62305300 2526 False 3657 3657 92.715 1 2555 1 chr4D.!!$F1 2554
2 TraesCS4B01G088900 chr4A 535818024 535820596 2572 False 3561 3561 91.840 1 2555 1 chr4A.!!$F1 2554

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
211 213 0.320683 CAGACAGTGTTGGATGGCGA 60.321 55.0 0.0 0.0 0.0 5.54 F
747 761 0.543749 CATCACCTCCCTTGTCCTCC 59.456 60.0 0.0 0.0 0.0 4.30 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1077 1100 1.050988 CCCTGATCTCGGACACCCAT 61.051 60.0 3.53 0.0 0.0 4.00 R
2290 2333 0.036164 AATATCCTATGCGCCGCCAA 59.964 50.0 6.63 0.0 0.0 4.52 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
21 22 2.167693 TCAAGGGTATCCATGTCGTGAC 59.832 50.000 0.00 0.00 33.73 3.67
80 81 4.667519 ACCTTAGTCCGGTATAGCTTTG 57.332 45.455 0.00 0.00 31.69 2.77
89 90 7.336396 AGTCCGGTATAGCTTTGAGTTAAAAT 58.664 34.615 0.00 0.00 0.00 1.82
124 125 1.950472 CGAATGTCGTCTTGTTTGGC 58.050 50.000 0.00 0.00 34.72 4.52
150 151 4.458989 TGTATGAAATCCTCTGTGTTTGCC 59.541 41.667 0.00 0.00 0.00 4.52
193 195 8.386606 GTTCAAAAAGTTGTTGAAATGTATGCA 58.613 29.630 20.38 0.00 44.35 3.96
211 213 0.320683 CAGACAGTGTTGGATGGCGA 60.321 55.000 0.00 0.00 0.00 5.54
231 233 1.607801 CCTCCGGCATGAGTGTCTGA 61.608 60.000 0.00 0.00 0.00 3.27
233 235 0.900182 TCCGGCATGAGTGTCTGAGT 60.900 55.000 0.00 0.00 0.00 3.41
245 247 1.157513 TCTGAGTACTGGCCCACCA 59.842 57.895 0.00 0.00 46.51 4.17
301 303 3.168773 GCGTTGGAGATGCCCTTAA 57.831 52.632 0.00 0.00 34.03 1.85
365 377 6.302269 AGCTTCCATATATCCTTTTCCACAG 58.698 40.000 0.00 0.00 0.00 3.66
386 399 9.214957 CCACAGAAAAACAAGTAGTGACATATA 57.785 33.333 0.00 0.00 0.00 0.86
416 430 2.009051 TGGTTGAGCTATTGACATGCG 58.991 47.619 0.00 0.00 0.00 4.73
430 444 0.643310 CATGCGCACAACATTGATGC 59.357 50.000 14.90 4.22 34.29 3.91
493 507 6.264832 CAAGCCATTGAAGCGTGATAATAAA 58.735 36.000 0.00 0.00 41.49 1.40
502 516 5.160699 AGCGTGATAATAAACACATGCAG 57.839 39.130 0.00 0.00 44.45 4.41
542 556 5.381757 ACTAACTCCAAAACCATTGCACTA 58.618 37.500 0.00 0.00 0.00 2.74
639 653 6.421202 CGGTTTCTCTCTCTTTTTATATCCCG 59.579 42.308 0.00 0.00 0.00 5.14
719 733 2.575993 CTCCAGCTGTCTCCACCG 59.424 66.667 13.81 0.00 0.00 4.94
730 744 0.976641 TCTCCACCGAGCTCAAACAT 59.023 50.000 15.40 0.00 35.94 2.71
739 753 1.280421 GAGCTCAAACATCACCTCCCT 59.720 52.381 9.40 0.00 0.00 4.20
740 754 1.707427 AGCTCAAACATCACCTCCCTT 59.293 47.619 0.00 0.00 0.00 3.95
741 755 1.815003 GCTCAAACATCACCTCCCTTG 59.185 52.381 0.00 0.00 0.00 3.61
742 756 2.815589 GCTCAAACATCACCTCCCTTGT 60.816 50.000 0.00 0.00 0.00 3.16
743 757 3.077359 CTCAAACATCACCTCCCTTGTC 58.923 50.000 0.00 0.00 0.00 3.18
744 758 2.162681 CAAACATCACCTCCCTTGTCC 58.837 52.381 0.00 0.00 0.00 4.02
745 759 1.747444 AACATCACCTCCCTTGTCCT 58.253 50.000 0.00 0.00 0.00 3.85
746 760 1.280457 ACATCACCTCCCTTGTCCTC 58.720 55.000 0.00 0.00 0.00 3.71
747 761 0.543749 CATCACCTCCCTTGTCCTCC 59.456 60.000 0.00 0.00 0.00 4.30
748 762 0.621862 ATCACCTCCCTTGTCCTCCC 60.622 60.000 0.00 0.00 0.00 4.30
749 763 2.284699 ACCTCCCTTGTCCTCCCG 60.285 66.667 0.00 0.00 0.00 5.14
750 764 3.787001 CCTCCCTTGTCCTCCCGC 61.787 72.222 0.00 0.00 0.00 6.13
926 946 3.113260 ACACAACTTAGAGCTCACACC 57.887 47.619 17.77 0.00 0.00 4.16
928 948 1.687123 ACAACTTAGAGCTCACACCGT 59.313 47.619 17.77 2.64 0.00 4.83
971 991 0.713883 CTTGTACTTACACAGGCGCG 59.286 55.000 0.00 0.00 35.64 6.86
993 1013 4.610680 CGTCACATAGCTTCGATCGTCATA 60.611 45.833 15.94 4.91 0.00 2.15
1074 1097 1.201429 TGAGGAAGAGGAAGTGGGGC 61.201 60.000 0.00 0.00 0.00 5.80
1077 1100 0.112412 GGAAGAGGAAGTGGGGCAAA 59.888 55.000 0.00 0.00 0.00 3.68
1223 1246 4.016706 CAACTTCCCGGGCCTCGT 62.017 66.667 18.49 6.80 37.11 4.18
1308 1331 2.747686 GCCCAAGTCCGGTTCAGA 59.252 61.111 0.00 0.00 0.00 3.27
1390 1413 4.429212 TCGATGACGTGGCGTGGG 62.429 66.667 0.00 0.00 41.37 4.61
1674 1697 9.106070 ACAAATTTAAGTATCGGTAGCTTAAGG 57.894 33.333 4.29 0.00 36.47 2.69
1900 1923 3.244249 CCCCAAATAGAGAGGATCGAACC 60.244 52.174 2.97 2.97 42.67 3.62
1901 1924 3.553096 CCCAAATAGAGAGGATCGAACCG 60.553 52.174 6.02 0.00 42.67 4.44
1902 1925 3.068307 CCAAATAGAGAGGATCGAACCGT 59.932 47.826 6.02 0.00 42.67 4.83
1903 1926 4.441634 CCAAATAGAGAGGATCGAACCGTT 60.442 45.833 6.02 0.00 42.67 4.44
1904 1927 4.571372 AATAGAGAGGATCGAACCGTTC 57.429 45.455 6.02 8.07 42.67 3.95
2048 2082 6.917477 GTCAGAAAATTGTCATGCTACAACAA 59.083 34.615 2.34 1.15 41.89 2.83
2064 2098 3.181466 ACAACAAAGCTTTTCCATGGGTC 60.181 43.478 13.02 0.00 0.00 4.46
2099 2133 6.140786 CGTCATAATTGAAGCATGGAGATTG 58.859 40.000 0.00 0.00 32.48 2.67
2100 2134 6.017687 CGTCATAATTGAAGCATGGAGATTGA 60.018 38.462 0.00 0.00 32.48 2.57
2107 2141 0.106819 GCATGGAGATTGACCAGCCT 60.107 55.000 0.00 0.00 40.89 4.58
2111 2145 4.467769 CATGGAGATTGACCAGCCTAAAT 58.532 43.478 0.00 0.00 40.89 1.40
2140 2174 2.161855 TGATGAAAATTGCCACGCTCT 58.838 42.857 0.00 0.00 0.00 4.09
2154 2188 3.064958 CCACGCTCTAGATTTGTCGTCTA 59.935 47.826 0.00 0.00 0.00 2.59
2175 2210 7.431376 CGTCTAGCTACATCAACGAAAGAAATA 59.569 37.037 0.00 0.00 32.17 1.40
2225 2268 8.841444 ATAAATTGAAATGTGTTCGCTCATAC 57.159 30.769 0.00 0.00 31.81 2.39
2226 2269 5.878332 ATTGAAATGTGTTCGCTCATACA 57.122 34.783 0.00 0.00 31.81 2.29
2234 2277 2.760650 TGTTCGCTCATACAGTCATCCT 59.239 45.455 0.00 0.00 0.00 3.24
2239 2282 2.861750 GCTCATACAGTCATCCTGAGCG 60.862 54.545 7.04 0.00 46.35 5.03
2242 2285 2.941453 TACAGTCATCCTGAGCGAAC 57.059 50.000 0.00 0.00 44.49 3.95
2290 2333 0.541863 CTTAGAGGGTGCACGGGATT 59.458 55.000 11.45 0.00 0.00 3.01
2305 2348 1.891919 GATTTGGCGGCGCATAGGA 60.892 57.895 34.36 14.36 0.00 2.94
2333 2376 5.577945 TCGTGCGGAAAACCTATAAAACTAG 59.422 40.000 0.00 0.00 0.00 2.57
2345 2388 7.031975 ACCTATAAAACTAGCGTCAGTTGTAC 58.968 38.462 4.82 0.00 38.74 2.90
2352 2396 3.313012 AGCGTCAGTTGTACAGCATTA 57.687 42.857 12.54 0.00 0.00 1.90
2382 2426 2.373540 TTGCTGCCATGAGAATTTGC 57.626 45.000 0.00 0.00 0.00 3.68
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
21 22 1.575922 CGCCGGCACATATCCATTG 59.424 57.895 28.98 0.37 0.00 2.82
80 81 8.169268 CGTTACATTCTGGAGACATTTTAACTC 58.831 37.037 0.00 0.00 41.51 3.01
89 90 5.147330 ACATTCGTTACATTCTGGAGACA 57.853 39.130 0.00 0.00 39.59 3.41
117 118 5.774690 AGAGGATTTCATACAAAGCCAAACA 59.225 36.000 4.32 0.00 38.11 2.83
124 125 6.583806 GCAAACACAGAGGATTTCATACAAAG 59.416 38.462 0.00 0.00 0.00 2.77
150 151 4.735662 TGAACTAACCGGACAAAATTCG 57.264 40.909 9.46 0.00 0.00 3.34
193 195 0.320771 GTCGCCATCCAACACTGTCT 60.321 55.000 0.00 0.00 0.00 3.41
301 303 6.719370 TGAAAGCAAATATTGTGGGTAGAAGT 59.281 34.615 0.00 0.00 0.00 3.01
378 391 7.254761 GCTCAACCACGAATTTGATATATGTCA 60.255 37.037 0.00 0.00 31.41 3.58
386 399 5.647658 TCAATAGCTCAACCACGAATTTGAT 59.352 36.000 0.00 0.00 31.41 2.57
387 400 5.000591 TCAATAGCTCAACCACGAATTTGA 58.999 37.500 0.00 0.00 0.00 2.69
502 516 6.201806 GGAGTTAGTTATGATGTGATGCACTC 59.798 42.308 0.00 0.00 35.11 3.51
639 653 2.071778 AATGGCCATATGGGTGTGTC 57.928 50.000 21.15 5.10 39.65 3.67
672 686 1.946768 TGTCGCTTCCCTGTTTTTCTG 59.053 47.619 0.00 0.00 0.00 3.02
719 733 1.280421 AGGGAGGTGATGTTTGAGCTC 59.720 52.381 6.82 6.82 36.23 4.09
730 744 1.229529 GGGAGGACAAGGGAGGTGA 60.230 63.158 0.00 0.00 0.00 4.02
750 764 4.781616 TGGGTGCATGCATGGGGG 62.782 66.667 25.64 2.89 0.00 5.40
926 946 1.159713 TTTGCTGCAGGAGTGTCACG 61.160 55.000 17.12 0.00 0.00 4.35
928 948 0.469494 TCTTTGCTGCAGGAGTGTCA 59.531 50.000 17.12 0.00 0.00 3.58
971 991 3.066369 TGACGATCGAAGCTATGTGAC 57.934 47.619 24.34 0.00 0.00 3.67
993 1013 3.071206 ACGACCTCCATCGCAGCT 61.071 61.111 0.00 0.00 46.22 4.24
1074 1097 2.283298 CTGATCTCGGACACCCATTTG 58.717 52.381 0.00 0.00 0.00 2.32
1077 1100 1.050988 CCCTGATCTCGGACACCCAT 61.051 60.000 3.53 0.00 0.00 4.00
1203 1226 3.978571 GAGGCCCGGGAAGTTGAGC 62.979 68.421 29.31 5.40 0.00 4.26
1308 1331 2.282674 TGTAGCACGAGGTCGGGT 60.283 61.111 3.17 1.18 46.07 5.28
1473 1496 4.106925 CTGCCCTCCCAGACAGGC 62.107 72.222 0.00 0.00 45.96 4.85
1536 1559 2.797792 CGATCAGTAGCTCCAGCAAGAC 60.798 54.545 0.48 0.00 45.16 3.01
1860 1883 4.335416 TGGGGAATGATTGTTCTCTCAAC 58.665 43.478 0.00 0.00 0.00 3.18
1861 1884 4.656100 TGGGGAATGATTGTTCTCTCAA 57.344 40.909 0.00 0.00 0.00 3.02
2019 2053 7.660112 TGTAGCATGACAATTTTCTGACAATT 58.340 30.769 0.00 0.00 0.00 2.32
2048 2082 2.250924 CCAAGACCCATGGAAAAGCTT 58.749 47.619 15.22 6.04 40.56 3.74
2064 2098 4.013728 TCAATTATGACGGTTTCCCCAAG 58.986 43.478 0.00 0.00 0.00 3.61
2081 2115 4.346730 TGGTCAATCTCCATGCTTCAATT 58.653 39.130 0.00 0.00 0.00 2.32
2099 2133 8.686334 TCATCATTTCTTTTATTTAGGCTGGTC 58.314 33.333 0.00 0.00 0.00 4.02
2100 2134 8.593945 TCATCATTTCTTTTATTTAGGCTGGT 57.406 30.769 0.00 0.00 0.00 4.00
2111 2145 7.359933 GCGTGGCAATTTTCATCATTTCTTTTA 60.360 33.333 0.00 0.00 0.00 1.52
2135 2169 3.002862 AGCTAGACGACAAATCTAGAGCG 59.997 47.826 12.19 0.00 45.86 5.03
2140 2174 6.937436 TGATGTAGCTAGACGACAAATCTA 57.063 37.500 0.00 0.00 37.44 1.98
2154 2188 7.981789 TCTCATATTTCTTTCGTTGATGTAGCT 59.018 33.333 0.00 0.00 0.00 3.32
2175 2210 8.862325 TCTTTGTACAACATGGTAATTCTCAT 57.138 30.769 8.07 0.00 0.00 2.90
2225 2268 1.919918 GAGTTCGCTCAGGATGACTG 58.080 55.000 0.00 0.00 42.56 3.51
2235 2278 4.842139 ACGACAATATTTGAGTTCGCTC 57.158 40.909 0.00 0.00 44.33 5.03
2239 2282 7.672738 ACGTGATAACGACAATATTTGAGTTC 58.327 34.615 10.30 0.51 36.79 3.01
2242 2285 7.453034 ACAACGTGATAACGACAATATTTGAG 58.547 34.615 10.30 0.00 36.85 3.02
2250 2293 2.097299 GCGAACAACGTGATAACGACAA 60.097 45.455 10.30 0.00 44.60 3.18
2290 2333 0.036164 AATATCCTATGCGCCGCCAA 59.964 50.000 6.63 0.00 0.00 4.52
2305 2348 7.281549 AGTTTTATAGGTTTTCCGCACGAATAT 59.718 33.333 0.00 0.00 46.35 1.28
2333 2376 3.250744 TCTAATGCTGTACAACTGACGC 58.749 45.455 0.00 0.00 0.00 5.19
2352 2396 5.889853 TCTCATGGCAGCAAAATTTATCTCT 59.110 36.000 0.00 0.00 0.00 3.10
2382 2426 7.023575 CGAGGTTTGATTTTCAGTTAATCCTG 58.976 38.462 0.00 0.00 32.29 3.86


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

AutoCloner maintained by Alex Coulton.