Multiple sequence alignment - TraesCS1D01G218500

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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 TraesCS1D01G218500 chr1D 100.000 3219 0 0 1 3219 305230974 305227756 0.000000e+00 5945.0
1 TraesCS1D01G218500 chr1B 94.403 3252 104 31 1 3219 412242047 412245253 0.000000e+00 4926.0
2 TraesCS1D01G218500 chr1A 94.733 2525 67 19 720 3219 382253426 382250943 0.000000e+00 3866.0
3 TraesCS1D01G218500 chr1A 91.532 248 15 3 257 498 382253962 382253715 1.430000e-88 337.0
4 TraesCS1D01G218500 chr1A 94.737 57 3 0 1 57 382260840 382260784 4.420000e-14 89.8
5 TraesCS1D01G218500 chr2A 80.303 132 19 6 116 244 16333256 16333383 3.420000e-15 93.5


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 TraesCS1D01G218500 chr1D 305227756 305230974 3218 True 5945.0 5945 100.0000 1 3219 1 chr1D.!!$R1 3218
1 TraesCS1D01G218500 chr1B 412242047 412245253 3206 False 4926.0 4926 94.4030 1 3219 1 chr1B.!!$F1 3218
2 TraesCS1D01G218500 chr1A 382250943 382253962 3019 True 2101.5 3866 93.1325 257 3219 2 chr1A.!!$R2 2962

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
778 856 0.319469 CAAAAACCACCACCGCATCC 60.319 55.0 0.0 0.0 0.0 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2643 2725 1.000506 CAGCTTGCAACTTTCATGCCT 59.999 47.619 0.0 0.0 43.16 4.75 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
27 28 6.085573 TCATATGCGAGTTGTTTGATTTGTG 58.914 36.000 0.00 0.00 0.00 3.33
31 32 2.788786 CGAGTTGTTTGATTTGTGCACC 59.211 45.455 15.69 0.00 0.00 5.01
57 58 5.616866 GCGAAGGAAAACGAGATTCATTTCA 60.617 40.000 0.00 0.00 31.62 2.69
93 94 6.426587 AGACCTTGATAAGTGCCACATTTAT 58.573 36.000 0.00 0.00 30.82 1.40
107 108 5.531634 CCACATTTATGGCATGAACATACC 58.468 41.667 10.98 0.00 31.52 2.73
109 110 4.887071 ACATTTATGGCATGAACATACCGT 59.113 37.500 10.98 4.49 31.02 4.83
112 113 5.994887 TTATGGCATGAACATACCGTAAC 57.005 39.130 10.98 0.00 33.12 2.50
113 114 3.336138 TGGCATGAACATACCGTAACA 57.664 42.857 0.00 0.00 0.00 2.41
157 158 4.801330 TTAGTGACACGAGGATGACAAT 57.199 40.909 0.00 0.00 0.00 2.71
160 161 3.997021 AGTGACACGAGGATGACAATTTC 59.003 43.478 0.00 0.00 0.00 2.17
175 176 6.437928 TGACAATTTCAGTTGTAAGCATGAC 58.562 36.000 0.00 0.00 42.08 3.06
176 177 6.039159 TGACAATTTCAGTTGTAAGCATGACA 59.961 34.615 0.00 0.00 42.08 3.58
181 182 7.928908 TTTCAGTTGTAAGCATGACAATTTC 57.071 32.000 0.00 0.00 42.52 2.17
187 188 8.196771 AGTTGTAAGCATGACAATTTCTTTTCA 58.803 29.630 0.00 0.00 42.52 2.69
305 309 6.217294 TCACACGTGTGTCACTTATCATTTA 58.783 36.000 39.25 18.45 45.76 1.40
778 856 0.319469 CAAAAACCACCACCGCATCC 60.319 55.000 0.00 0.00 0.00 3.51
994 1072 4.090588 CCAAACCCTAGCCGCCGA 62.091 66.667 0.00 0.00 0.00 5.54
1938 2020 2.284258 AAGCTGGTCTCCTCCGCT 60.284 61.111 0.00 0.00 38.32 5.52
1944 2026 4.828925 GTCTCCTCCGCTGCTGCC 62.829 72.222 10.24 0.00 35.36 4.85
1961 2043 0.110104 GCCATGGAGGAGGATTGAGG 59.890 60.000 18.40 0.00 41.22 3.86
1965 2047 3.581101 CATGGAGGAGGATTGAGGACTA 58.419 50.000 0.00 0.00 0.00 2.59
1966 2048 3.320610 TGGAGGAGGATTGAGGACTAG 57.679 52.381 0.00 0.00 0.00 2.57
1967 2049 2.859404 TGGAGGAGGATTGAGGACTAGA 59.141 50.000 0.00 0.00 0.00 2.43
1968 2050 3.117322 TGGAGGAGGATTGAGGACTAGAG 60.117 52.174 0.00 0.00 0.00 2.43
1969 2051 3.496331 GAGGAGGATTGAGGACTAGAGG 58.504 54.545 0.00 0.00 0.00 3.69
1970 2052 1.967779 GGAGGATTGAGGACTAGAGGC 59.032 57.143 0.00 0.00 0.00 4.70
2057 2139 0.034476 CTGCTGCTCCTGTCAGTCAA 59.966 55.000 0.00 0.00 34.21 3.18
2125 2207 4.584327 TTTAAGAAGTGAAGGGCAAAGC 57.416 40.909 0.00 0.00 0.00 3.51
2419 2501 5.974108 TGCTTAACTATCAACTGGGTACTC 58.026 41.667 0.00 0.00 0.00 2.59
2553 2635 6.017440 TGCAGGAATTGAACTGTTTGTAGTAC 60.017 38.462 0.00 0.00 37.07 2.73
2643 2725 2.083774 GGACGGCTGAACATCAATGAA 58.916 47.619 0.00 0.00 0.00 2.57
2681 2763 1.588404 CTGCGGCTGTAACTAATGTCG 59.412 52.381 0.00 0.00 0.00 4.35
2936 3045 3.208747 TCAGGAGGGTTCAGAACAAAC 57.791 47.619 15.36 4.88 0.00 2.93
2937 3046 2.507886 TCAGGAGGGTTCAGAACAAACA 59.492 45.455 15.36 0.00 0.00 2.83
2938 3047 3.053991 TCAGGAGGGTTCAGAACAAACAA 60.054 43.478 15.36 0.00 0.00 2.83
2940 3049 4.159506 CAGGAGGGTTCAGAACAAACAAAA 59.840 41.667 15.36 0.00 0.00 2.44
2941 3050 4.402474 AGGAGGGTTCAGAACAAACAAAAG 59.598 41.667 15.36 0.00 0.00 2.27
2957 3067 5.489792 ACAAAAGTAGCCAGAAGATCAGA 57.510 39.130 0.00 0.00 0.00 3.27
2975 3085 5.152623 TCAGACTCATGGAAGAAACGAAT 57.847 39.130 0.00 0.00 0.00 3.34
2987 3097 1.266718 GAAACGAATCCTTGTGCTGCA 59.733 47.619 0.00 0.00 0.00 4.41
2995 3105 2.862541 TCCTTGTGCTGCATGTAAACT 58.137 42.857 5.27 0.00 0.00 2.66
3028 3140 4.697756 TACACCTGCAGCGGCCAC 62.698 66.667 8.66 0.00 40.13 5.01
3214 3336 5.416952 CAGATAATTCAGGTCCAACTGCTTT 59.583 40.000 0.00 0.00 38.36 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
27 28 1.082104 CGTTTTCCTTCGCTGGTGC 60.082 57.895 0.00 0.0 0.00 5.01
31 32 2.736721 TGAATCTCGTTTTCCTTCGCTG 59.263 45.455 0.00 0.0 0.00 5.18
93 94 3.004171 GTGTTACGGTATGTTCATGCCA 58.996 45.455 17.27 0.0 0.00 4.92
96 97 3.513662 TCGGTGTTACGGTATGTTCATG 58.486 45.455 0.00 0.0 0.00 3.07
128 129 2.479837 CTCGTGTCACTAAACTTGGCA 58.520 47.619 0.65 0.0 0.00 4.92
130 131 3.380479 TCCTCGTGTCACTAAACTTGG 57.620 47.619 0.65 0.0 0.00 3.61
143 144 4.214119 ACAACTGAAATTGTCATCCTCGTG 59.786 41.667 0.00 0.0 38.44 4.35
145 146 6.480524 TTACAACTGAAATTGTCATCCTCG 57.519 37.500 0.00 0.0 41.89 4.63
157 158 7.715657 AGAAATTGTCATGCTTACAACTGAAA 58.284 30.769 0.93 0.0 39.51 2.69
160 161 7.935338 AAAGAAATTGTCATGCTTACAACTG 57.065 32.000 0.93 0.0 39.51 3.16
175 176 8.861033 TGAACTTGTCATCTGAAAAGAAATTG 57.139 30.769 15.42 0.0 40.93 2.32
176 177 8.689972 ACTGAACTTGTCATCTGAAAAGAAATT 58.310 29.630 15.42 1.6 40.93 1.82
181 182 8.693542 AAAAACTGAACTTGTCATCTGAAAAG 57.306 30.769 8.30 8.3 43.40 2.27
187 188 8.463930 TCCAATAAAAACTGAACTTGTCATCT 57.536 30.769 0.00 0.0 35.07 2.90
271 275 1.860676 ACACGTGTGATACAAAGCGT 58.139 45.000 22.71 0.0 0.00 5.07
463 473 0.533032 CCGTCTCCTTTCCTGTCCTC 59.467 60.000 0.00 0.0 0.00 3.71
464 474 0.905337 CCCGTCTCCTTTCCTGTCCT 60.905 60.000 0.00 0.0 0.00 3.85
468 479 2.125512 CGCCCGTCTCCTTTCCTG 60.126 66.667 0.00 0.0 0.00 3.86
994 1072 0.684805 GAGGAGGAGGACATGGTCGT 60.685 60.000 0.00 0.0 32.65 4.34
1539 1621 3.756727 GACGAGGGGGACGACACC 61.757 72.222 0.00 0.0 39.23 4.16
1569 1651 4.704103 TGGAGGCTCCTGCTCCGT 62.704 66.667 32.28 0.0 38.48 4.69
1863 1945 1.211449 CTCGACGAAGAGCTGCTGT 59.789 57.895 7.01 0.0 0.00 4.40
1938 2020 1.284111 AATCCTCCTCCATGGCAGCA 61.284 55.000 6.96 0.0 35.26 4.41
1944 2026 2.406559 AGTCCTCAATCCTCCTCCATG 58.593 52.381 0.00 0.0 0.00 3.66
1961 2043 1.452145 CCGGAGCTCTGCCTCTAGTC 61.452 65.000 17.68 0.0 32.43 2.59
1987 2069 3.290776 AACACGGAGTTGAGCTGAC 57.709 52.632 0.00 0.0 41.61 3.51
2057 2139 6.763355 AGTAGAAACATCACAAGTCATCAGT 58.237 36.000 0.00 0.0 0.00 3.41
2125 2207 4.284490 ACAGCCATATCCTACACCTACATG 59.716 45.833 0.00 0.0 0.00 3.21
2372 2454 3.372025 GGGCCATCCATAACAAACTCTCT 60.372 47.826 4.39 0.0 35.00 3.10
2419 2501 3.305964 CTGCAGCAACTGTGAAATTCAG 58.694 45.455 0.00 0.0 38.68 3.02
2502 2584 1.064758 TGTGAAACTCAACAGTGCCCT 60.065 47.619 0.00 0.0 38.04 5.19
2573 2655 1.169661 TGTGGCGCCTTTTGATTCGT 61.170 50.000 29.70 0.0 0.00 3.85
2643 2725 1.000506 CAGCTTGCAACTTTCATGCCT 59.999 47.619 0.00 0.0 43.16 4.75
2681 2763 6.701841 TGAGAAGAACAAATATCGTATCCAGC 59.298 38.462 0.00 0.0 0.00 4.85
2936 3045 5.486526 AGTCTGATCTTCTGGCTACTTTTG 58.513 41.667 0.00 0.0 28.23 2.44
2937 3046 5.247110 TGAGTCTGATCTTCTGGCTACTTTT 59.753 40.000 0.00 0.0 30.26 2.27
2938 3047 4.774726 TGAGTCTGATCTTCTGGCTACTTT 59.225 41.667 0.00 0.0 30.26 2.66
2940 3049 3.974719 TGAGTCTGATCTTCTGGCTACT 58.025 45.455 0.00 0.0 30.26 2.57
2941 3050 4.501229 CCATGAGTCTGATCTTCTGGCTAC 60.501 50.000 0.00 0.0 30.26 3.58
2957 3067 4.559862 AGGATTCGTTTCTTCCATGAGT 57.440 40.909 0.00 0.0 31.65 3.41
2975 3085 2.862541 AGTTTACATGCAGCACAAGGA 58.137 42.857 0.00 0.0 0.00 3.36
2987 3097 4.277423 GGGTGTGTAGTTGCAAGTTTACAT 59.723 41.667 12.95 0.0 0.00 2.29
2995 3105 2.485835 GGTGTAGGGTGTGTAGTTGCAA 60.486 50.000 0.00 0.0 0.00 4.08
3028 3140 5.409520 TCAAATTTGATCTGTCGAGTCCTTG 59.590 40.000 16.91 0.0 31.01 3.61
3099 3212 2.432444 CGATGGACTGGTTGCCTTTAA 58.568 47.619 0.00 0.0 0.00 1.52
3100 3213 1.339631 CCGATGGACTGGTTGCCTTTA 60.340 52.381 0.00 0.0 0.00 1.85


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

AutoCloner maintained by Alex Coulton.