Multiple sequence alignment - TraesCS1D01G308700

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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 TraesCS1D01G308700 chr1D 100.000 2477 0 0 1 2477 404654631 404657107 0.000000e+00 4575.0
1 TraesCS1D01G308700 chr1A 94.778 2068 67 18 437 2477 500285229 500287282 0.000000e+00 3182.0
2 TraesCS1D01G308700 chr1B 95.383 1018 25 6 610 1617 544491577 544492582 0.000000e+00 1600.0
3 TraesCS1D01G308700 chr1B 91.762 874 49 12 1616 2477 544492665 544493527 0.000000e+00 1194.0
4 TraesCS1D01G308700 chr1B 85.522 297 17 9 2 298 544490866 544491136 1.120000e-73 287.0
5 TraesCS1D01G308700 chr1B 92.105 152 8 3 436 584 544491428 544491578 6.940000e-51 211.0
6 TraesCS1D01G308700 chr1B 95.556 45 2 0 1760 1804 544492847 544492803 3.420000e-09 73.1
7 TraesCS1D01G308700 chr1B 89.286 56 4 2 203 257 600981491 600981437 4.420000e-08 69.4
8 TraesCS1D01G308700 chr3B 86.131 137 15 3 1082 1214 577490356 577490492 7.140000e-31 145.0
9 TraesCS1D01G308700 chr3B 78.761 113 17 6 148 257 715069786 715069678 4.420000e-08 69.4
10 TraesCS1D01G308700 chr3A 86.131 137 15 3 1082 1214 580608678 580608814 7.140000e-31 145.0
11 TraesCS1D01G308700 chr5B 94.545 55 1 2 203 256 47093449 47093396 1.580000e-12 84.2
12 TraesCS1D01G308700 chr5B 78.641 103 18 3 156 257 404079029 404079128 5.720000e-07 65.8
13 TraesCS1D01G308700 chr2B 92.857 56 2 2 203 257 678557090 678557144 2.040000e-11 80.5
14 TraesCS1D01G308700 chr2B 89.831 59 5 1 200 257 90015524 90015582 9.500000e-10 75.0
15 TraesCS1D01G308700 chr5A 90.909 55 4 1 203 257 634019219 634019166 3.420000e-09 73.1
16 TraesCS1D01G308700 chr3D 89.655 58 4 2 200 256 525019645 525019701 3.420000e-09 73.1
17 TraesCS1D01G308700 chr7B 89.286 56 4 2 203 257 705725606 705725552 4.420000e-08 69.4


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 TraesCS1D01G308700 chr1D 404654631 404657107 2476 False 4575 4575 100.000 1 2477 1 chr1D.!!$F1 2476
1 TraesCS1D01G308700 chr1A 500285229 500287282 2053 False 3182 3182 94.778 437 2477 1 chr1A.!!$F1 2040
2 TraesCS1D01G308700 chr1B 544490866 544493527 2661 False 823 1600 91.193 2 2477 4 chr1B.!!$F1 2475

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
159 160 0.179227 CACACACACACACACACACG 60.179 55.0 0.0 0.0 0.0 4.49 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1886 2165 0.388006 TGTGTACATGTGTCGCTCCG 60.388 55.0 9.11 0.0 0.0 4.63 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
97 98 6.595772 AATTTCATAGCAAGACTAGAAGCG 57.404 37.500 0.00 0.00 33.29 4.68
155 156 1.548269 TCTCTCACACACACACACACA 59.452 47.619 0.00 0.00 0.00 3.72
156 157 1.660607 CTCTCACACACACACACACAC 59.339 52.381 0.00 0.00 0.00 3.82
157 158 1.001406 TCTCACACACACACACACACA 59.999 47.619 0.00 0.00 0.00 3.72
158 159 1.128507 CTCACACACACACACACACAC 59.871 52.381 0.00 0.00 0.00 3.82
159 160 0.179227 CACACACACACACACACACG 60.179 55.000 0.00 0.00 0.00 4.49
160 161 1.225991 CACACACACACACACACGC 60.226 57.895 0.00 0.00 0.00 5.34
161 162 1.669437 ACACACACACACACACGCA 60.669 52.632 0.00 0.00 0.00 5.24
162 163 1.225991 CACACACACACACACGCAC 60.226 57.895 0.00 0.00 0.00 5.34
163 164 2.021243 CACACACACACACGCACG 59.979 61.111 0.00 0.00 0.00 5.34
164 165 3.860125 ACACACACACACGCACGC 61.860 61.111 0.00 0.00 0.00 5.34
165 166 3.858989 CACACACACACGCACGCA 61.859 61.111 0.00 0.00 0.00 5.24
166 167 3.860125 ACACACACACGCACGCAC 61.860 61.111 0.00 0.00 0.00 5.34
167 168 3.858989 CACACACACGCACGCACA 61.859 61.111 0.00 0.00 0.00 4.57
168 169 3.860125 ACACACACGCACGCACAC 61.860 61.111 0.00 0.00 0.00 3.82
169 170 3.858989 CACACACGCACGCACACA 61.859 61.111 0.00 0.00 0.00 3.72
170 171 3.860125 ACACACGCACGCACACAC 61.860 61.111 0.00 0.00 0.00 3.82
171 172 3.858989 CACACGCACGCACACACA 61.859 61.111 0.00 0.00 0.00 3.72
172 173 3.860125 ACACGCACGCACACACAC 61.860 61.111 0.00 0.00 0.00 3.82
173 174 3.858989 CACGCACGCACACACACA 61.859 61.111 0.00 0.00 0.00 3.72
174 175 3.860125 ACGCACGCACACACACAC 61.860 61.111 0.00 0.00 0.00 3.82
175 176 3.858989 CGCACGCACACACACACA 61.859 61.111 0.00 0.00 0.00 3.72
176 177 2.277247 GCACGCACACACACACAC 60.277 61.111 0.00 0.00 0.00 3.82
177 178 2.021243 CACGCACACACACACACG 59.979 61.111 0.00 0.00 0.00 4.49
178 179 3.860125 ACGCACACACACACACGC 61.860 61.111 0.00 0.00 0.00 5.34
179 180 4.918060 CGCACACACACACACGCG 62.918 66.667 3.53 3.53 36.47 6.01
221 222 1.557832 ACACACACACACAACCCTACT 59.442 47.619 0.00 0.00 0.00 2.57
231 232 3.195825 ACACAACCCTACTCTATGAGCAC 59.804 47.826 0.00 0.00 32.04 4.40
240 241 2.948979 ACTCTATGAGCACCTTCGAGAG 59.051 50.000 0.00 0.00 36.55 3.20
249 250 2.405594 CTTCGAGAGACCGAGCCG 59.594 66.667 0.00 0.00 41.84 5.52
260 261 1.442857 CCGAGCCGACATATCTCGC 60.443 63.158 5.46 0.00 45.78 5.03
261 262 1.794003 CGAGCCGACATATCTCGCG 60.794 63.158 0.00 0.00 42.28 5.87
298 299 1.876799 CGACGGGCATGCCATAAAATA 59.123 47.619 36.56 0.00 37.98 1.40
299 300 2.292016 CGACGGGCATGCCATAAAATAA 59.708 45.455 36.56 0.00 37.98 1.40
300 301 3.057596 CGACGGGCATGCCATAAAATAAT 60.058 43.478 36.56 11.34 37.98 1.28
301 302 4.558496 CGACGGGCATGCCATAAAATAATT 60.558 41.667 36.56 8.56 37.98 1.40
302 303 4.881920 ACGGGCATGCCATAAAATAATTC 58.118 39.130 36.56 14.46 37.98 2.17
303 304 4.588528 ACGGGCATGCCATAAAATAATTCT 59.411 37.500 36.56 3.64 37.98 2.40
304 305 4.925054 CGGGCATGCCATAAAATAATTCTG 59.075 41.667 36.56 7.59 37.98 3.02
338 368 2.550830 ACACATGTCAAGTCCAGGAC 57.449 50.000 12.25 12.25 34.63 3.85
349 379 0.605589 GTCCAGGACTTGAAACCGGG 60.606 60.000 12.94 0.00 41.60 5.73
350 380 1.971695 CCAGGACTTGAAACCGGGC 60.972 63.158 6.32 0.00 35.09 6.13
351 381 1.228124 CAGGACTTGAAACCGGGCA 60.228 57.895 6.32 0.00 0.00 5.36
381 411 5.762179 TCCATCACAAGGAATCTAACTGT 57.238 39.130 0.00 0.00 30.71 3.55
391 421 9.220767 ACAAGGAATCTAACTGTTTAAGCTAAG 57.779 33.333 0.00 0.00 0.00 2.18
412 442 3.619038 AGCTTAATTCGCACTAGAAGCAC 59.381 43.478 10.16 0.00 41.34 4.40
422 452 4.554526 CGCACTAGAAGCACAATTGACAAA 60.555 41.667 13.59 0.00 0.00 2.83
531 696 6.537660 GGTCGTATGCCCCATATTAAAGATAC 59.462 42.308 0.00 0.00 0.00 2.24
535 700 8.450964 CGTATGCCCCATATTAAAGATACTTTG 58.549 37.037 6.95 0.00 0.00 2.77
541 708 7.998964 CCCCATATTAAAGATACTTTGGTGTCT 59.001 37.037 6.95 0.00 44.00 3.41
608 775 3.198417 GTGCATTTGGGGATTTCCTGATT 59.802 43.478 0.00 0.00 35.95 2.57
613 780 6.013984 GCATTTGGGGATTTCCTGATTATCAT 60.014 38.462 0.00 0.00 35.95 2.45
663 830 2.158564 CCCACCTGACCATGCATTATCT 60.159 50.000 0.00 0.00 0.00 1.98
675 842 2.072298 GCATTATCTAAGGCGCCTCTG 58.928 52.381 32.93 24.68 33.17 3.35
694 861 1.896183 CACCCACATTGCACACCGA 60.896 57.895 0.00 0.00 0.00 4.69
981 1148 1.227674 CCTCCGCAGCCCATACTTC 60.228 63.158 0.00 0.00 0.00 3.01
1502 1679 2.158711 TCTGTGATCCATCCATCCAAGC 60.159 50.000 0.00 0.00 0.00 4.01
1598 1775 0.521242 GTGCATGTGCGTTCGATTCC 60.521 55.000 0.00 0.00 45.83 3.01
1790 2062 4.679654 CGATGATGATTTGCAATGTGGATG 59.320 41.667 0.00 0.00 0.00 3.51
1886 2165 2.157474 GGTTTTTGATTTCATGCACGGC 59.843 45.455 0.00 0.00 0.00 5.68
2149 2435 4.096732 AGATGCGCATGGTTTAGTTTTC 57.903 40.909 30.76 9.57 0.00 2.29
2152 2438 1.613270 CGCATGGTTTAGTTTTCGGC 58.387 50.000 0.00 0.00 0.00 5.54
2158 2444 2.030363 TGGTTTAGTTTTCGGCATGCTG 60.030 45.455 21.02 21.02 0.00 4.41
2166 2452 4.158394 AGTTTTCGGCATGCTGATAACATT 59.842 37.500 40.00 28.33 42.03 2.71
2300 2587 8.621286 TGACATTTTCTAGAACTTCCAAAGAAC 58.379 33.333 4.18 0.00 0.00 3.01
2381 2668 0.676466 CCATTAGGCCACGCAGTTGA 60.676 55.000 5.01 0.00 41.61 3.18
2382 2669 0.447801 CATTAGGCCACGCAGTTGAC 59.552 55.000 5.01 0.00 41.61 3.18
2383 2670 0.676782 ATTAGGCCACGCAGTTGACC 60.677 55.000 5.01 0.00 41.61 4.02
2384 2671 1.764571 TTAGGCCACGCAGTTGACCT 61.765 55.000 5.01 0.00 41.61 3.85
2385 2672 2.449031 TAGGCCACGCAGTTGACCTG 62.449 60.000 5.01 0.00 41.61 4.00
2386 2673 2.591715 GCCACGCAGTTGACCTGT 60.592 61.111 0.00 0.00 41.61 4.00
2387 2674 2.186826 GCCACGCAGTTGACCTGTT 61.187 57.895 0.00 0.00 41.61 3.16
2388 2675 1.648720 CCACGCAGTTGACCTGTTG 59.351 57.895 0.00 0.00 41.61 3.33
2439 2726 0.327259 GTGGTAAAGAGGACCCACCC 59.673 60.000 0.00 0.00 41.20 4.61
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
110 111 1.003233 GAGAGGGGATCCACGTGTTTT 59.997 52.381 15.23 0.00 34.83 2.43
114 115 0.396417 AGAGAGAGGGGATCCACGTG 60.396 60.000 15.23 9.08 34.83 4.49
118 119 1.780309 GAGAGAGAGAGAGGGGATCCA 59.220 57.143 15.23 0.00 34.83 3.41
125 126 3.009723 GTGTGTGAGAGAGAGAGAGAGG 58.990 54.545 0.00 0.00 0.00 3.69
155 156 3.860125 GTGTGTGTGCGTGCGTGT 61.860 61.111 0.00 0.00 0.00 4.49
156 157 3.858989 TGTGTGTGTGCGTGCGTG 61.859 61.111 0.00 0.00 0.00 5.34
157 158 3.860125 GTGTGTGTGTGCGTGCGT 61.860 61.111 0.00 0.00 0.00 5.24
158 159 3.858989 TGTGTGTGTGTGCGTGCG 61.859 61.111 0.00 0.00 0.00 5.34
159 160 2.277247 GTGTGTGTGTGTGCGTGC 60.277 61.111 0.00 0.00 0.00 5.34
160 161 2.021243 CGTGTGTGTGTGTGCGTG 59.979 61.111 0.00 0.00 0.00 5.34
161 162 3.860125 GCGTGTGTGTGTGTGCGT 61.860 61.111 0.00 0.00 0.00 5.24
162 163 4.918060 CGCGTGTGTGTGTGTGCG 62.918 66.667 0.00 0.00 39.57 5.34
164 165 3.858989 TGCGCGTGTGTGTGTGTG 61.859 61.111 8.43 0.00 0.00 3.82
165 166 3.860125 GTGCGCGTGTGTGTGTGT 61.860 61.111 8.43 0.00 0.00 3.72
166 167 3.858989 TGTGCGCGTGTGTGTGTG 61.859 61.111 8.43 0.00 0.00 3.82
167 168 3.860125 GTGTGCGCGTGTGTGTGT 61.860 61.111 8.43 0.00 0.00 3.72
168 169 3.858989 TGTGTGCGCGTGTGTGTG 61.859 61.111 8.43 0.00 0.00 3.82
169 170 3.860125 GTGTGTGCGCGTGTGTGT 61.860 61.111 8.43 0.00 0.00 3.72
170 171 3.858989 TGTGTGTGCGCGTGTGTG 61.859 61.111 8.43 0.00 0.00 3.82
171 172 3.860125 GTGTGTGTGCGCGTGTGT 61.860 61.111 8.43 0.00 0.00 3.72
172 173 3.858989 TGTGTGTGTGCGCGTGTG 61.859 61.111 8.43 0.00 0.00 3.82
173 174 3.860125 GTGTGTGTGTGCGCGTGT 61.860 61.111 8.43 0.00 0.00 4.49
174 175 3.858989 TGTGTGTGTGTGCGCGTG 61.859 61.111 8.43 0.00 0.00 5.34
175 176 3.860125 GTGTGTGTGTGTGCGCGT 61.860 61.111 8.43 0.00 0.00 6.01
176 177 3.858989 TGTGTGTGTGTGTGCGCG 61.859 61.111 0.00 0.00 0.00 6.86
177 178 2.277247 GTGTGTGTGTGTGTGCGC 60.277 61.111 0.00 0.00 0.00 6.09
178 179 1.225991 GTGTGTGTGTGTGTGTGCG 60.226 57.895 0.00 0.00 0.00 5.34
179 180 0.454285 GTGTGTGTGTGTGTGTGTGC 60.454 55.000 0.00 0.00 0.00 4.57
180 181 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
221 222 2.946329 GTCTCTCGAAGGTGCTCATAGA 59.054 50.000 0.00 0.00 0.00 1.98
231 232 2.802106 GGCTCGGTCTCTCGAAGG 59.198 66.667 0.00 0.00 38.77 3.46
240 241 0.110147 CGAGATATGTCGGCTCGGTC 60.110 60.000 14.15 0.00 45.54 4.79
249 250 1.518929 GTGCTTGTCGCGAGATATGTC 59.481 52.381 10.24 0.00 45.19 3.06
272 273 2.183300 GCATGCCCGTCGACTACA 59.817 61.111 14.70 9.15 0.00 2.74
298 299 7.865706 GTGTACTCACATATTTCCCAGAATT 57.134 36.000 0.00 0.00 43.37 2.17
313 343 3.990092 TGGACTTGACATGTGTACTCAC 58.010 45.455 1.15 0.00 44.08 3.51
331 361 1.758592 CCCGGTTTCAAGTCCTGGA 59.241 57.895 0.00 0.00 31.15 3.86
333 363 1.228124 TGCCCGGTTTCAAGTCCTG 60.228 57.895 0.00 0.00 0.00 3.86
360 390 6.824305 AAACAGTTAGATTCCTTGTGATGG 57.176 37.500 0.00 0.00 0.00 3.51
391 421 3.370978 TGTGCTTCTAGTGCGAATTAAGC 59.629 43.478 0.00 0.00 39.73 3.09
412 442 8.137437 AGTACAAGAAGATTGGTTTGTCAATTG 58.863 33.333 0.00 0.00 37.47 2.32
422 452 7.112122 TGATATTGCAGTACAAGAAGATTGGT 58.888 34.615 0.00 0.00 42.87 3.67
567 734 3.002791 CACTCATGCGGTTATGTGTCTT 58.997 45.455 0.00 0.00 33.81 3.01
598 765 4.763793 CCCAGCGAATGATAATCAGGAAAT 59.236 41.667 0.00 0.00 0.00 2.17
608 775 2.304092 ACGTCTACCCAGCGAATGATA 58.696 47.619 0.00 0.00 0.00 2.15
613 780 1.246649 TGTTACGTCTACCCAGCGAA 58.753 50.000 0.00 0.00 0.00 4.70
675 842 2.339712 GGTGTGCAATGTGGGTGC 59.660 61.111 0.00 0.00 42.55 5.01
694 861 1.623811 ACATACGCTGTGAGAAAGGGT 59.376 47.619 0.00 0.00 42.72 4.34
981 1148 3.240884 CATGACCAAGATCGATCTAGCG 58.759 50.000 27.52 18.81 35.76 4.26
1091 1258 3.323758 TTGATCGGCTTGTCCCCGG 62.324 63.158 0.00 0.00 45.60 5.73
1230 1403 4.838486 CTGCTCTCGCCGACGTCC 62.838 72.222 10.58 0.00 41.18 4.79
1761 2033 7.114388 CCACATTGCAAATCATCATCGATTAAG 59.886 37.037 1.71 0.00 34.49 1.85
1767 2039 4.295857 TCCACATTGCAAATCATCATCG 57.704 40.909 1.71 0.00 0.00 3.84
1768 2040 4.447724 GCATCCACATTGCAAATCATCATC 59.552 41.667 1.71 0.00 39.90 2.92
1790 2062 3.003897 TGTCTCAAACACCCGTTATTTGC 59.996 43.478 0.00 0.00 33.99 3.68
1798 2075 0.951558 CCCTTTGTCTCAAACACCCG 59.048 55.000 0.00 0.00 37.70 5.28
1840 2118 4.503741 AAATCGGTGTTGAAACTGATGG 57.496 40.909 0.00 0.00 43.83 3.51
1886 2165 0.388006 TGTGTACATGTGTCGCTCCG 60.388 55.000 9.11 0.00 0.00 4.63
2149 2435 3.561310 ACACTAATGTTATCAGCATGCCG 59.439 43.478 15.66 3.71 34.46 5.69
2245 2532 8.724229 GTGGTTATTTCGTTCTATAGTTTTGGT 58.276 33.333 0.00 0.00 0.00 3.67
2252 2539 9.093970 TGTCAATGTGGTTATTTCGTTCTATAG 57.906 33.333 0.00 0.00 0.00 1.31
2300 2587 1.638388 CTGCACAGCACGTACCCATG 61.638 60.000 0.00 0.00 33.79 3.66
2384 2671 3.379057 CCATTAGATCATGCTGCACAACA 59.621 43.478 3.57 0.00 0.00 3.33
2385 2672 3.243301 CCCATTAGATCATGCTGCACAAC 60.243 47.826 3.57 0.00 0.00 3.32
2386 2673 2.953648 CCCATTAGATCATGCTGCACAA 59.046 45.455 3.57 0.00 0.00 3.33
2387 2674 2.578786 CCCATTAGATCATGCTGCACA 58.421 47.619 3.57 0.00 0.00 4.57
2388 2675 1.268899 GCCCATTAGATCATGCTGCAC 59.731 52.381 3.57 0.00 0.00 4.57
2439 2726 4.047627 AGGAAAACCTCCCCACTAATTG 57.952 45.455 0.00 0.00 46.81 2.32


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

AutoCloner maintained by Alex Coulton.