Multiple sequence alignment - TraesCS1D01G385400

Loading Multiple Alignment...

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 TraesCS1D01G385400 chr1D 100.000 2543 0 0 1 2543 458786346 458783804 0.000000e+00 4697.0
1 TraesCS1D01G385400 chr1B 92.372 2268 108 30 2 2223 630522644 630520396 0.000000e+00 3169.0
2 TraesCS1D01G385400 chr1B 89.124 331 31 5 2215 2543 630520211 630519884 8.470000e-110 407.0
3 TraesCS1D01G385400 chr1B 90.948 232 16 3 2 229 630561591 630561361 8.840000e-80 307.0
4 TraesCS1D01G385400 chr1B 100.000 29 0 0 202 230 630561439 630561411 1.000000e-03 54.7
5 TraesCS1D01G385400 chr1A 89.864 1618 60 44 308 1853 551214519 551212934 0.000000e+00 1984.0
6 TraesCS1D01G385400 chr1A 90.263 647 46 8 1902 2543 551212774 551212140 0.000000e+00 830.0
7 TraesCS1D01G385400 chr1A 91.429 210 13 3 2 207 551214728 551214520 1.490000e-72 283.0


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 TraesCS1D01G385400 chr1D 458783804 458786346 2542 True 4697.000000 4697 100.000000 1 2543 1 chr1D.!!$R1 2542
1 TraesCS1D01G385400 chr1B 630519884 630522644 2760 True 1788.000000 3169 90.748000 2 2543 2 chr1B.!!$R1 2541
2 TraesCS1D01G385400 chr1A 551212140 551214728 2588 True 1032.333333 1984 90.518667 2 2543 3 chr1A.!!$R1 2541

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
316 327 0.17907 TATATTTGGCGCCGCTGACA 60.179 50.0 23.9 4.7 0.0 3.58 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1692 1786 1.171308 GCAAAGCTGAGCTGATCCAA 58.829 50.0 8.16 0.0 39.62 3.53 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
41 42 5.079406 CGACATCCAACAAAAAGACATACG 58.921 41.667 0.00 0.00 0.00 3.06
57 58 5.414454 AGACATACGATATCTTGAGCTCCTC 59.586 44.000 12.15 0.00 0.00 3.71
63 64 4.092821 CGATATCTTGAGCTCCTCTACTCG 59.907 50.000 12.15 9.54 35.61 4.18
94 101 7.382110 TCTTCAGTCCATGACTAAAGAAGAAG 58.618 38.462 16.70 13.83 42.06 2.85
95 102 6.918067 TCAGTCCATGACTAAAGAAGAAGA 57.082 37.500 0.00 0.00 41.37 2.87
96 103 7.303182 TCAGTCCATGACTAAAGAAGAAGAA 57.697 36.000 0.00 0.00 41.37 2.52
116 123 1.402787 AACAAGGCAAGACCCAACAG 58.597 50.000 0.00 0.00 40.58 3.16
151 159 6.566753 GCTTTCTCACTGGAAGACATACAAAC 60.567 42.308 0.00 0.00 37.43 2.93
196 204 4.198530 CAAATGCTTTTGAAACCAACCCT 58.801 39.130 17.74 0.00 44.11 4.34
207 215 5.762279 TGAAACCAACCCTCCCTAATAATC 58.238 41.667 0.00 0.00 0.00 1.75
208 216 5.494706 TGAAACCAACCCTCCCTAATAATCT 59.505 40.000 0.00 0.00 0.00 2.40
209 217 5.648330 AACCAACCCTCCCTAATAATCTC 57.352 43.478 0.00 0.00 0.00 2.75
218 229 7.799583 ACCCTCCCTAATAATCTCAAGGATTTA 59.200 37.037 0.00 0.00 41.42 1.40
250 261 3.002038 ACGTACTTCCAAAACCAACCA 57.998 42.857 0.00 0.00 0.00 3.67
251 262 3.354467 ACGTACTTCCAAAACCAACCAA 58.646 40.909 0.00 0.00 0.00 3.67
252 263 3.379057 ACGTACTTCCAAAACCAACCAAG 59.621 43.478 0.00 0.00 0.00 3.61
253 264 2.979814 ACTTCCAAAACCAACCAAGC 57.020 45.000 0.00 0.00 0.00 4.01
316 327 0.179070 TATATTTGGCGCCGCTGACA 60.179 50.000 23.90 4.70 0.00 3.58
334 347 2.749621 GACACCCTTAGATGCACAAAGG 59.250 50.000 14.00 14.00 39.63 3.11
423 437 1.283793 CAGTTTGCAGGTCTTGGCG 59.716 57.895 0.00 0.00 0.00 5.69
539 554 1.828979 GGGGCGACACCATTTTTCTA 58.171 50.000 0.00 0.00 42.05 2.10
540 555 2.375146 GGGGCGACACCATTTTTCTAT 58.625 47.619 0.00 0.00 42.05 1.98
541 556 2.357952 GGGGCGACACCATTTTTCTATC 59.642 50.000 0.00 0.00 42.05 2.08
542 557 3.279434 GGGCGACACCATTTTTCTATCT 58.721 45.455 0.00 0.00 42.05 1.98
546 561 5.179555 GGCGACACCATTTTTCTATCTATCC 59.820 44.000 0.00 0.00 38.86 2.59
731 781 1.154225 GCACGCGTTTCCAATCCAG 60.154 57.895 10.22 0.00 0.00 3.86
738 788 1.393603 GTTTCCAATCCAGGCTAGCC 58.606 55.000 27.19 27.19 0.00 3.93
831 886 0.964860 CCACCGCAAACATCCATCCA 60.965 55.000 0.00 0.00 0.00 3.41
832 887 1.105457 CACCGCAAACATCCATCCAT 58.895 50.000 0.00 0.00 0.00 3.41
833 888 1.066002 CACCGCAAACATCCATCCATC 59.934 52.381 0.00 0.00 0.00 3.51
834 889 0.670162 CCGCAAACATCCATCCATCC 59.330 55.000 0.00 0.00 0.00 3.51
983 1055 2.439883 GGAGGAGCTCCCGTACGT 60.440 66.667 29.54 9.67 44.36 3.57
1701 1797 6.781138 TCAAAACGTATACATTTGGATCAGC 58.219 36.000 21.67 0.00 35.34 4.26
1732 1828 3.865684 GCCATTTGTTTGTTCATCCCTGG 60.866 47.826 0.00 0.00 0.00 4.45
1734 1830 4.559153 CATTTGTTTGTTCATCCCTGGTC 58.441 43.478 0.00 0.00 0.00 4.02
1798 1894 5.487131 CCTGGGAAAGGGGAAAATAATTCAA 59.513 40.000 0.00 0.00 43.15 2.69
1858 1957 7.984617 TGTTTCTTTCCAAAAGAAATACAAGGG 59.015 33.333 23.09 0.00 44.87 3.95
1859 1958 6.096673 TCTTTCCAAAAGAAATACAAGGGC 57.903 37.500 0.00 0.00 43.50 5.19
1864 1963 7.732222 TCCAAAAGAAATACAAGGGCATTAT 57.268 32.000 0.00 0.00 0.00 1.28
1879 1978 9.696917 CAAGGGCATTATCTTACATATTTTTCC 57.303 33.333 0.00 0.00 0.00 3.13
1984 2191 2.691984 AATTTTGGCCGTACACGTTC 57.308 45.000 0.00 0.00 37.74 3.95
2000 2207 7.096518 CGTACACGTTCTAGAATGTTTTGTACA 60.097 37.037 31.45 15.38 38.39 2.90
2039 2247 9.817809 TCATATCACTAGACAAGGTTAACAATC 57.182 33.333 8.10 0.00 0.00 2.67
2089 2299 5.234972 CCTTTTGTTTTCAAGAAGATGCACC 59.765 40.000 0.00 0.00 41.09 5.01
2111 2321 6.037062 CACCAGATTTGCGAGTCATTTGTATA 59.963 38.462 0.00 0.00 0.00 1.47
2117 2327 9.214953 GATTTGCGAGTCATTTGTATAAAGAAG 57.785 33.333 0.00 0.00 0.00 2.85
2193 2403 4.573607 TGAGATCTTGATTTGAAGATGGCG 59.426 41.667 0.00 0.00 41.78 5.69
2194 2404 4.774124 AGATCTTGATTTGAAGATGGCGA 58.226 39.130 0.00 0.00 41.78 5.54
2264 2669 5.888161 ACCGAGATGATTTTTATTTCTGCCT 59.112 36.000 0.00 0.00 0.00 4.75
2266 2671 6.038603 CCGAGATGATTTTTATTTCTGCCTCA 59.961 38.462 0.00 0.00 0.00 3.86
2289 2694 4.406648 AGGATAATTCTCGATGTGCACA 57.593 40.909 24.08 24.08 0.00 4.57
2374 2779 8.466798 GCCTTTGTACATTGACCTATTTAATGT 58.533 33.333 0.00 0.00 44.54 2.71
2394 2799 6.814076 ATGTTAGCTCTTCGTTTAGAATCG 57.186 37.500 0.00 0.00 38.34 3.34
2405 2810 6.222389 TTCGTTTAGAATCGGTTTAAGACCA 58.778 36.000 7.35 0.00 40.25 4.02
2432 2838 7.134612 CGCATTCGGAAGTATCGTATATTAC 57.865 40.000 0.00 0.00 0.00 1.89
2509 2918 6.235231 AGGTTGATTGTAGTGGGTAGTATG 57.765 41.667 0.00 0.00 0.00 2.39
2510 2919 5.962031 AGGTTGATTGTAGTGGGTAGTATGA 59.038 40.000 0.00 0.00 0.00 2.15
2517 2926 6.290294 TGTAGTGGGTAGTATGAAAGTTCC 57.710 41.667 0.00 0.00 0.00 3.62
2525 2934 0.248012 TATGAAAGTTCCGCTCGCCA 59.752 50.000 0.00 0.00 0.00 5.69
2526 2935 0.392998 ATGAAAGTTCCGCTCGCCAT 60.393 50.000 0.00 0.00 0.00 4.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.751924 TCGTTTTCTTGGGTTGGGTTG 59.248 47.619 0.00 0.00 0.00 3.77
41 42 4.142687 GCGAGTAGAGGAGCTCAAGATATC 60.143 50.000 17.19 5.64 32.06 1.63
57 58 3.129462 TGGACTGAAGAATGAGCGAGTAG 59.871 47.826 0.00 0.00 0.00 2.57
63 64 3.871485 AGTCATGGACTGAAGAATGAGC 58.129 45.455 0.00 0.00 41.76 4.26
94 101 2.167487 TGTTGGGTCTTGCCTTGTTTTC 59.833 45.455 0.00 0.00 37.43 2.29
95 102 2.168313 CTGTTGGGTCTTGCCTTGTTTT 59.832 45.455 0.00 0.00 37.43 2.43
96 103 1.756538 CTGTTGGGTCTTGCCTTGTTT 59.243 47.619 0.00 0.00 37.43 2.83
166 174 7.556844 TGGTTTCAAAAGCATTTGTTTAGGTA 58.443 30.769 13.61 0.00 45.02 3.08
196 204 8.814448 AGGTAAATCCTTGAGATTATTAGGGA 57.186 34.615 0.00 0.00 44.75 4.20
207 215 8.943002 ACGTATTTGTTTAGGTAAATCCTTGAG 58.057 33.333 0.00 0.00 45.67 3.02
208 216 8.851541 ACGTATTTGTTTAGGTAAATCCTTGA 57.148 30.769 0.00 0.00 45.67 3.02
209 217 9.977762 GTACGTATTTGTTTAGGTAAATCCTTG 57.022 33.333 0.00 0.00 45.67 3.61
218 229 8.344831 GTTTTGGAAGTACGTATTTGTTTAGGT 58.655 33.333 8.17 0.00 0.00 3.08
250 261 1.628846 ACGAGAAACATAGGGTGGCTT 59.371 47.619 0.00 0.00 0.00 4.35
251 262 1.066143 CACGAGAAACATAGGGTGGCT 60.066 52.381 0.00 0.00 0.00 4.75
252 263 1.369625 CACGAGAAACATAGGGTGGC 58.630 55.000 0.00 0.00 0.00 5.01
253 264 1.406887 CCCACGAGAAACATAGGGTGG 60.407 57.143 1.14 1.14 43.44 4.61
316 327 1.075374 TGCCTTTGTGCATCTAAGGGT 59.925 47.619 21.31 0.00 44.92 4.34
334 347 7.063308 TCAGTCTTTTCACATTCTTTTTGTTGC 59.937 33.333 0.00 0.00 0.00 4.17
423 437 2.087646 GCTTCAGATTCAGACCCAACC 58.912 52.381 0.00 0.00 0.00 3.77
453 468 0.378962 TTTCCGGCTGTCAAACAACG 59.621 50.000 0.00 0.00 0.00 4.10
458 473 2.343101 CGTCTATTTCCGGCTGTCAAA 58.657 47.619 0.00 0.00 0.00 2.69
481 496 1.747367 CGGCTTTTATCCGTGGGCA 60.747 57.895 0.00 0.00 41.85 5.36
539 554 3.045634 TGGGTCGGAATGTTGGATAGAT 58.954 45.455 0.00 0.00 0.00 1.98
540 555 2.169769 GTGGGTCGGAATGTTGGATAGA 59.830 50.000 0.00 0.00 0.00 1.98
541 556 2.561569 GTGGGTCGGAATGTTGGATAG 58.438 52.381 0.00 0.00 0.00 2.08
542 557 1.210967 GGTGGGTCGGAATGTTGGATA 59.789 52.381 0.00 0.00 0.00 2.59
546 561 0.960364 CTGGGTGGGTCGGAATGTTG 60.960 60.000 0.00 0.00 0.00 3.33
1244 1316 2.434884 CCAGCTTCGTGCCGATGT 60.435 61.111 10.54 0.00 44.23 3.06
1692 1786 1.171308 GCAAAGCTGAGCTGATCCAA 58.829 50.000 8.16 0.00 39.62 3.53
1701 1797 3.460103 ACAAACAAATGGCAAAGCTGAG 58.540 40.909 0.00 0.00 0.00 3.35
1732 1828 8.696175 CGAATTTTAACATGTTTTTGTAGGGAC 58.304 33.333 17.78 0.00 0.00 4.46
1734 1830 8.804688 TCGAATTTTAACATGTTTTTGTAGGG 57.195 30.769 17.78 1.27 0.00 3.53
1798 1894 7.197901 TGATATTGGCCCAAGATTCAAATTT 57.802 32.000 4.86 0.00 0.00 1.82
1949 2156 7.161404 GGCCAAAATTTCCTATCTTTGACTTT 58.839 34.615 0.00 0.00 31.77 2.66
2000 2207 9.509956 GTCTAGTGATATGACCTAGTATCTTGT 57.490 37.037 0.00 0.00 32.01 3.16
2089 2299 8.390354 TCTTTATACAAATGACTCGCAAATCTG 58.610 33.333 0.00 0.00 0.00 2.90
2111 2321 5.164954 CGGTCTCGAATCTTCTTCTTCTTT 58.835 41.667 0.00 0.00 39.00 2.52
2117 2327 4.352600 TGTACGGTCTCGAATCTTCTTC 57.647 45.455 0.00 0.00 40.11 2.87
2233 2638 4.425577 AAAAATCATCTCGGTGTGCTTC 57.574 40.909 0.00 0.00 0.00 3.86
2264 2669 6.159293 GTGCACATCGAGAATTATCCTATGA 58.841 40.000 13.17 0.00 0.00 2.15
2266 2671 6.015095 TCTGTGCACATCGAGAATTATCCTAT 60.015 38.462 22.00 0.00 0.00 2.57
2374 2779 5.320549 ACCGATTCTAAACGAAGAGCTAA 57.679 39.130 0.00 0.00 34.56 3.09
2476 2882 7.208080 CCACTACAATCAACCTACTATACACC 58.792 42.308 0.00 0.00 0.00 4.16
2480 2886 8.284435 ACTACCCACTACAATCAACCTACTATA 58.716 37.037 0.00 0.00 0.00 1.31
2482 2888 6.496743 ACTACCCACTACAATCAACCTACTA 58.503 40.000 0.00 0.00 0.00 1.82
2483 2889 5.339477 ACTACCCACTACAATCAACCTACT 58.661 41.667 0.00 0.00 0.00 2.57
2484 2890 5.672421 ACTACCCACTACAATCAACCTAC 57.328 43.478 0.00 0.00 0.00 3.18
2489 2898 7.913789 ACTTTCATACTACCCACTACAATCAA 58.086 34.615 0.00 0.00 0.00 2.57
2509 2918 1.425428 CATGGCGAGCGGAACTTTC 59.575 57.895 0.00 0.00 0.00 2.62
2510 2919 2.040544 CCATGGCGAGCGGAACTTT 61.041 57.895 0.00 0.00 0.00 2.66
2517 2926 2.504681 GTTTTGCCATGGCGAGCG 60.505 61.111 30.87 0.00 45.51 5.03


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

AutoCloner maintained by Alex Coulton.