Multiple sequence alignment - TraesCS5D01G085600

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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 TraesCS5D01G085600 chr5D 100.000 2733 0 0 1 2733 90688377 90685645 0.000000e+00 5048.0
1 TraesCS5D01G085600 chr5D 95.556 45 2 0 1040 1084 473486587 473486543 3.780000e-09 73.1
2 TraesCS5D01G085600 chr5B 93.920 2714 79 31 51 2733 96020475 96017817 0.000000e+00 4019.0
3 TraesCS5D01G085600 chr5A 91.837 2450 73 44 1 2391 84152311 84149930 0.000000e+00 3299.0
4 TraesCS5D01G085600 chr5A 97.778 45 1 0 1040 1084 593241858 593241814 8.110000e-11 78.7
5 TraesCS5D01G085600 chr4A 92.208 77 6 0 1008 1084 546485392 546485316 2.880000e-20 110.0
6 TraesCS5D01G085600 chr4D 92.424 66 5 0 1019 1084 50327262 50327327 8.060000e-16 95.3


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 TraesCS5D01G085600 chr5D 90685645 90688377 2732 True 5048 5048 100.000 1 2733 1 chr5D.!!$R1 2732
1 TraesCS5D01G085600 chr5B 96017817 96020475 2658 True 4019 4019 93.920 51 2733 1 chr5B.!!$R1 2682
2 TraesCS5D01G085600 chr5A 84149930 84152311 2381 True 3299 3299 91.837 1 2391 1 chr5A.!!$R1 2390

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
244 248 0.599558 CCATATCCTGCATTTGGGCG 59.4 55.0 0.0 0.0 36.28 6.13 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2093 2145 0.675083 CCTGTGAACCTTTGCATGCA 59.325 50.0 18.46 18.46 0.0 3.96 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
244 248 0.599558 CCATATCCTGCATTTGGGCG 59.400 55.000 0.00 0.00 36.28 6.13
257 261 0.897401 TTGGGCGTGCCAATGATCAA 60.897 50.000 13.76 3.63 37.98 2.57
366 370 3.060611 ACTCCTCCTCCTGAGCTAGTAT 58.939 50.000 0.00 0.00 39.98 2.12
372 376 2.961741 CCTCCTGAGCTAGTATGAGCAA 59.038 50.000 0.00 0.00 45.43 3.91
374 378 4.769488 CCTCCTGAGCTAGTATGAGCAATA 59.231 45.833 0.00 0.00 45.43 1.90
380 384 9.664332 CCTGAGCTAGTATGAGCAATATTAATT 57.336 33.333 0.00 0.00 45.43 1.40
542 546 0.762082 TGGCATGCCAAAAAGGTGGA 60.762 50.000 36.95 9.68 44.12 4.02
719 723 2.981859 TTCCTCCGTTCTATCTTGCC 57.018 50.000 0.00 0.00 0.00 4.52
912 947 2.550830 TGACCAGAGTTGCTTCCTTC 57.449 50.000 0.00 0.00 0.00 3.46
989 1025 2.746362 CAGGCTTAGAGCAAGTTTGAGG 59.254 50.000 2.04 0.00 44.75 3.86
1101 1137 6.047231 ACAGGTACGTAGCAATTAATCTTCC 58.953 40.000 25.28 4.84 0.00 3.46
1104 1140 5.695363 GGTACGTAGCAATTAATCTTCCTCC 59.305 44.000 19.43 0.00 0.00 4.30
1119 1155 2.257207 TCCTCCGTTCTTCTTCACCAT 58.743 47.619 0.00 0.00 0.00 3.55
1145 1181 2.967459 CAAACTGTTGCGTGCTATGA 57.033 45.000 0.00 0.00 0.00 2.15
1146 1182 3.266541 CAAACTGTTGCGTGCTATGAA 57.733 42.857 0.00 0.00 0.00 2.57
1147 1183 3.228749 CAAACTGTTGCGTGCTATGAAG 58.771 45.455 0.00 0.00 0.00 3.02
1148 1184 2.169832 ACTGTTGCGTGCTATGAAGT 57.830 45.000 0.00 0.00 0.00 3.01
1149 1185 3.313012 ACTGTTGCGTGCTATGAAGTA 57.687 42.857 0.00 0.00 0.00 2.24
1150 1186 3.861840 ACTGTTGCGTGCTATGAAGTAT 58.138 40.909 0.00 0.00 0.00 2.12
1151 1187 3.618594 ACTGTTGCGTGCTATGAAGTATG 59.381 43.478 0.00 0.00 0.00 2.39
1177 1213 6.258160 ACTGCTAATCATTTGCGTTGATAAC 58.742 36.000 0.00 0.00 33.52 1.89
1815 1860 2.254459 GGCATGATCGCATCGTACTAG 58.746 52.381 0.00 0.00 30.68 2.57
1816 1861 1.651138 GCATGATCGCATCGTACTAGC 59.349 52.381 0.00 0.00 30.68 3.42
1850 1895 3.333029 TGCATTGTAGAAGCAGTAGCA 57.667 42.857 0.00 0.00 45.49 3.49
1861 1906 5.749462 AGAAGCAGTAGCAATGGAGTATTT 58.251 37.500 0.00 0.00 45.49 1.40
1868 1913 7.659390 GCAGTAGCAATGGAGTATTTCTTATCT 59.341 37.037 0.00 0.00 41.58 1.98
1869 1914 9.553064 CAGTAGCAATGGAGTATTTCTTATCTT 57.447 33.333 0.00 0.00 0.00 2.40
1938 1983 1.152610 CGGGGAGGATCGGGTTCTA 60.153 63.158 0.00 0.00 34.37 2.10
1940 1985 1.049402 GGGGAGGATCGGGTTCTAAG 58.951 60.000 0.00 0.00 34.37 2.18
1943 1988 3.303049 GGGAGGATCGGGTTCTAAGTTA 58.697 50.000 0.00 0.00 34.37 2.24
1952 1997 3.455327 GGGTTCTAAGTTACGATCCTGC 58.545 50.000 0.00 0.00 0.00 4.85
2023 2071 6.456795 TGATTAGTCATCGATGTTCAGAGT 57.543 37.500 24.09 10.47 34.08 3.24
2076 2128 7.703621 CCATGTTCATGATTTGTACTCCATTTC 59.296 37.037 13.51 0.00 0.00 2.17
2168 2224 1.345741 TCAGAGGAACAGAAGTGCAGG 59.654 52.381 0.00 0.00 0.00 4.85
2178 2234 3.070018 CAGAAGTGCAGGGAAACTAGTG 58.930 50.000 0.00 0.00 0.00 2.74
2283 2352 4.019051 ACAATGGATGTGGTCATGAAGAGA 60.019 41.667 0.00 0.00 41.93 3.10
2466 2535 3.227614 GCCAAAAAGTTACAGGGAGGAA 58.772 45.455 0.00 0.00 0.00 3.36
2493 2562 4.358851 TCAAGTTCCAGCACAAAATTTCG 58.641 39.130 0.00 0.00 0.00 3.46
2606 2675 7.713764 AATTTTCCTCCAAAATGACGAAAAG 57.286 32.000 0.00 0.00 42.86 2.27
2612 2681 5.470098 CCTCCAAAATGACGAAAAGAAGAGA 59.530 40.000 0.00 0.00 0.00 3.10
2670 2739 9.785982 GGAGCATTCCTAATTAAATAGAGAAGT 57.214 33.333 0.00 0.00 40.58 3.01
2689 2758 1.757118 GTATGTGAGAGCTAGGCACCA 59.243 52.381 9.70 1.14 0.00 4.17
2712 2781 3.256631 GCCCAAAGCTGAAGAAATCTCAA 59.743 43.478 0.00 0.00 38.99 3.02
2721 2790 6.772716 AGCTGAAGAAATCTCAAGTAAAACCA 59.227 34.615 0.00 0.00 0.00 3.67
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
174 178 4.896482 CCTCCAGCTCCATTTAGTACTACT 59.104 45.833 0.91 0.00 0.00 2.57
175 179 4.501743 GCCTCCAGCTCCATTTAGTACTAC 60.502 50.000 0.91 0.00 38.99 2.73
176 180 3.641906 GCCTCCAGCTCCATTTAGTACTA 59.358 47.826 0.00 0.00 38.99 1.82
257 261 0.540133 TGACATGCATGGTGTTGCCT 60.540 50.000 29.41 6.76 42.06 4.75
326 330 2.035066 AGTGCATTTCAAACAGTGAGCC 59.965 45.455 0.00 0.00 37.61 4.70
328 332 3.567164 AGGAGTGCATTTCAAACAGTGAG 59.433 43.478 0.00 0.00 37.61 3.51
329 333 3.554934 AGGAGTGCATTTCAAACAGTGA 58.445 40.909 0.00 0.00 0.00 3.41
401 405 1.378762 GCCCCACCTGCAGAAACTA 59.621 57.895 17.39 0.00 0.00 2.24
619 623 4.332819 AGGTGCTCATTTATAAACGCAGAC 59.667 41.667 15.08 12.21 0.00 3.51
719 723 2.033801 CACTCAAACTTGCAAGGGACAG 59.966 50.000 29.18 20.20 0.00 3.51
912 947 6.680810 TCAAAAACTTGTAAGCATCCATCTG 58.319 36.000 0.00 0.00 0.00 2.90
989 1025 2.016096 GCTTGCCCATCTCTCCTCAAC 61.016 57.143 0.00 0.00 0.00 3.18
1101 1137 6.809196 GCTATATATGGTGAAGAAGAACGGAG 59.191 42.308 0.00 0.00 0.00 4.63
1104 1140 7.946655 TTGCTATATATGGTGAAGAAGAACG 57.053 36.000 0.00 0.00 0.00 3.95
1145 1181 6.094048 ACGCAAATGATTAGCAGTTCATACTT 59.906 34.615 0.00 0.00 31.43 2.24
1146 1182 5.586243 ACGCAAATGATTAGCAGTTCATACT 59.414 36.000 0.00 0.00 31.43 2.12
1147 1183 5.810525 ACGCAAATGATTAGCAGTTCATAC 58.189 37.500 0.00 0.00 31.43 2.39
1148 1184 6.093357 TCAACGCAAATGATTAGCAGTTCATA 59.907 34.615 0.00 0.00 31.43 2.15
1149 1185 4.970662 ACGCAAATGATTAGCAGTTCAT 57.029 36.364 0.00 0.00 31.43 2.57
1150 1186 4.215185 TCAACGCAAATGATTAGCAGTTCA 59.785 37.500 0.00 0.00 31.43 3.18
1151 1187 4.722194 TCAACGCAAATGATTAGCAGTTC 58.278 39.130 0.00 0.00 31.43 3.01
1479 1515 2.245438 GAAGGGTGAGGAGAAGCCGG 62.245 65.000 0.00 0.00 43.43 6.13
1789 1834 1.228459 ATGCGATCATGCCATGGCT 60.228 52.632 35.53 17.44 42.51 4.75
1815 1860 3.189287 ACAATGCAACACAAGCTACTAGC 59.811 43.478 0.00 0.00 42.84 3.42
1816 1861 5.869344 TCTACAATGCAACACAAGCTACTAG 59.131 40.000 0.00 0.00 0.00 2.57
1938 1983 1.568504 TGGGAGCAGGATCGTAACTT 58.431 50.000 0.00 0.00 0.00 2.66
1940 1985 1.941325 CTTGGGAGCAGGATCGTAAC 58.059 55.000 0.00 0.00 0.00 2.50
2093 2145 0.675083 CCTGTGAACCTTTGCATGCA 59.325 50.000 18.46 18.46 0.00 3.96
2094 2146 0.961019 TCCTGTGAACCTTTGCATGC 59.039 50.000 11.82 11.82 0.00 4.06
2095 2147 3.731652 TTTCCTGTGAACCTTTGCATG 57.268 42.857 0.00 0.00 0.00 4.06
2096 2148 4.443315 CCTTTTTCCTGTGAACCTTTGCAT 60.443 41.667 0.00 0.00 0.00 3.96
2137 2193 6.627087 TCTGTTCCTCTGATTATCACCTTT 57.373 37.500 0.00 0.00 0.00 3.11
2168 2224 7.435068 TTTCATGCTTTCTACACTAGTTTCC 57.565 36.000 0.00 0.00 0.00 3.13
2178 2234 7.965107 CCACTATTCACTTTTCATGCTTTCTAC 59.035 37.037 0.00 0.00 0.00 2.59
2209 2265 1.757682 ACGTAGCCTCCTTCTCTCTG 58.242 55.000 0.00 0.00 0.00 3.35
2211 2267 3.442977 TGTAAACGTAGCCTCCTTCTCTC 59.557 47.826 0.00 0.00 0.00 3.20
2212 2268 3.428532 TGTAAACGTAGCCTCCTTCTCT 58.571 45.455 0.00 0.00 0.00 3.10
2283 2352 8.262227 ACATCTGAATTCCATGTTAATTTGCAT 58.738 29.630 12.32 0.00 0.00 3.96
2315 2384 7.174413 TCATCTCCACCATTTTGTAATTCTGA 58.826 34.615 0.00 0.00 0.00 3.27
2368 2437 6.149973 GGATATCAGTCATGAGAGAGAGACAG 59.850 46.154 4.83 0.00 39.29 3.51
2466 2535 7.472334 AATTTTGTGCTGGAACTTGATCTAT 57.528 32.000 0.00 0.00 0.00 1.98
2493 2562 7.985634 TTGCACAAAATCTGTAACTTCTTTC 57.014 32.000 0.00 0.00 36.10 2.62
2545 2614 7.814264 ACATAATCTCTTGGGCTTTGAATAG 57.186 36.000 0.00 0.00 0.00 1.73
2592 2661 8.841444 TTTTCTCTCTTCTTTTCGTCATTTTG 57.159 30.769 0.00 0.00 0.00 2.44
2641 2710 9.615660 TCTCTATTTAATTAGGAATGCTCCCTA 57.384 33.333 4.91 0.00 43.64 3.53
2642 2711 8.511748 TCTCTATTTAATTAGGAATGCTCCCT 57.488 34.615 4.91 0.00 43.64 4.20
2659 2728 7.255801 GCCTAGCTCTCACATACTTCTCTATTT 60.256 40.741 0.00 0.00 0.00 1.40
2662 2731 5.067273 GCCTAGCTCTCACATACTTCTCTA 58.933 45.833 0.00 0.00 0.00 2.43
2670 2739 2.034878 CTGGTGCCTAGCTCTCACATA 58.965 52.381 12.86 3.45 32.69 2.29


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

AutoCloner maintained by Alex Coulton.