Multiple sequence alignment - TraesCS7A01G407900

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 TraesCS7A01G407900 chr7A 100.000 2228 0 0 1 2228 593463154 593465381 0.000000e+00 4115.0
1 TraesCS7A01G407900 chr7B 96.466 2179 58 7 1 2169 551952470 551954639 0.000000e+00 3579.0
2 TraesCS7A01G407900 chr7D 95.388 1496 53 8 634 2126 518641383 518642865 0.000000e+00 2366.0
3 TraesCS7A01G407900 chr7D 95.626 663 9 5 1 647 518640607 518641265 0.000000e+00 1046.0
4 TraesCS7A01G407900 chr7D 92.157 51 1 3 1953 2002 547267045 547267093 3.970000e-08 69.4
5 TraesCS7A01G407900 chr3D 87.854 247 27 3 1766 2012 644475 644232 1.010000e-73 287.0
6 TraesCS7A01G407900 chr3D 88.235 68 5 3 1950 2016 138080508 138080573 6.600000e-11 78.7
7 TraesCS7A01G407900 chr3A 79.556 225 34 10 1798 2016 153728987 153729205 1.380000e-32 150.0
8 TraesCS7A01G407900 chr3B 87.143 70 7 2 1955 2023 125999730 125999662 6.600000e-11 78.7
9 TraesCS7A01G407900 chr6B 95.833 48 1 1 1971 2018 51093807 51093853 2.370000e-10 76.8
10 TraesCS7A01G407900 chr6A 86.567 67 6 3 1954 2020 574693012 574692949 1.100000e-08 71.3


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 TraesCS7A01G407900 chr7A 593463154 593465381 2227 False 4115 4115 100.000 1 2228 1 chr7A.!!$F1 2227
1 TraesCS7A01G407900 chr7B 551952470 551954639 2169 False 3579 3579 96.466 1 2169 1 chr7B.!!$F1 2168
2 TraesCS7A01G407900 chr7D 518640607 518642865 2258 False 1706 2366 95.507 1 2126 2 chr7D.!!$F2 2125

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
127 129 1.908344 TGCAGCTATGAGCAACCAAA 58.092 45.0 0.64 0.0 45.56 3.28 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1890 2042 0.469892 AAAAAGCAGTGACCCCAGGG 60.47 55.0 0.0 0.0 42.03 4.45 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
120 122 6.873076 ACTCTTTTCTATATGCAGCTATGAGC 59.127 38.462 0.00 0.00 42.84 4.26
121 123 6.762333 TCTTTTCTATATGCAGCTATGAGCA 58.238 36.000 0.00 0.00 45.56 4.26
122 124 7.219322 TCTTTTCTATATGCAGCTATGAGCAA 58.781 34.615 0.07 0.00 45.56 3.91
123 125 6.791887 TTTCTATATGCAGCTATGAGCAAC 57.208 37.500 0.07 0.00 45.56 4.17
127 129 1.908344 TGCAGCTATGAGCAACCAAA 58.092 45.000 0.64 0.00 45.56 3.28
252 263 6.246420 ACATGTCACTTTGATAGTTCAAGC 57.754 37.500 0.00 0.00 42.60 4.01
291 308 2.204291 AGGCTTCCATGACCCCCA 60.204 61.111 0.00 0.00 0.00 4.96
398 415 3.443099 TGCTGGTGACTAGATGATTCG 57.557 47.619 0.00 0.00 0.00 3.34
407 424 4.202121 TGACTAGATGATTCGTAACTGCCC 60.202 45.833 0.00 0.00 0.00 5.36
800 952 5.501156 GAGATTGTTGTTATCACCTCCCTT 58.499 41.667 0.00 0.00 0.00 3.95
828 980 3.067461 CCCATCACTCGACTCCTCTAAAG 59.933 52.174 0.00 0.00 0.00 1.85
998 1150 6.092122 CCACTAGCTACTTCTCTCATCGATAG 59.908 46.154 0.00 0.00 0.00 2.08
1235 1387 0.967380 CCACCAAACTGAGATGGCCC 60.967 60.000 0.00 0.00 40.51 5.80
1409 1561 2.420628 TGTGCCTGCATTTTCTTTCG 57.579 45.000 0.00 0.00 0.00 3.46
1438 1590 3.061469 CGTGAAAAACTTTTGCTTACCGC 60.061 43.478 0.00 0.00 39.77 5.68
1445 1597 1.464997 CTTTTGCTTACCGCTGTCTCC 59.535 52.381 0.00 0.00 40.11 3.71
1476 1628 4.274459 GCCTATTGATCTGTAGCAGTTTGG 59.726 45.833 0.00 0.00 32.61 3.28
1536 1688 4.342378 TGAGGAGGTATATGTGAGCTTGTC 59.658 45.833 0.00 0.00 0.00 3.18
1718 1870 9.030452 TGTGTAAATTGGTCAAGGCTAAAATAT 57.970 29.630 0.00 0.00 0.00 1.28
1727 1879 9.303116 TGGTCAAGGCTAAAATATTTGTTAAGA 57.697 29.630 0.39 0.00 0.00 2.10
1793 1945 1.593196 TCTTCACAAACAAGGCCTCG 58.407 50.000 5.23 0.00 0.00 4.63
1821 1973 1.949525 CCTCTGTTGTTGGTGGTCTTG 59.050 52.381 0.00 0.00 0.00 3.02
1835 1987 3.076621 TGGTCTTGTCAATGATCTGCAC 58.923 45.455 0.00 0.00 0.00 4.57
1890 2042 0.107017 ACATCCATGTACAGGCAGCC 60.107 55.000 1.84 1.84 39.68 4.85
1907 2059 2.845345 CCCCTGGGGTCACTGCTTT 61.845 63.158 24.54 0.00 38.25 3.51
1964 2116 5.888724 TCCAATGTGTTTTCCTCTTGTACAA 59.111 36.000 8.28 8.28 0.00 2.41
2062 2214 4.799715 TGGTTTCTTACTTCCCTTGGAA 57.200 40.909 0.00 0.00 39.66 3.53
2074 2226 5.785940 ACTTCCCTTGGAACTCTATGTACTT 59.214 40.000 0.00 0.00 36.71 2.24
2177 2329 2.472049 GCTCGTTGCGAAGTGAGC 59.528 61.111 7.99 7.99 45.95 4.26
2178 2330 4.251760 CTCGTTGCGAAGTGAGCT 57.748 55.556 0.00 0.00 34.74 4.09
2179 2331 3.401577 CTCGTTGCGAAGTGAGCTA 57.598 52.632 0.00 0.00 34.74 3.32
2180 2332 1.698165 CTCGTTGCGAAGTGAGCTAA 58.302 50.000 0.00 0.00 34.74 3.09
2181 2333 2.263077 CTCGTTGCGAAGTGAGCTAAT 58.737 47.619 0.00 0.00 34.74 1.73
2182 2334 2.259618 TCGTTGCGAAGTGAGCTAATC 58.740 47.619 0.00 0.00 31.06 1.75
2183 2335 2.094700 TCGTTGCGAAGTGAGCTAATCT 60.095 45.455 0.00 0.00 31.06 2.40
2184 2336 2.028523 CGTTGCGAAGTGAGCTAATCTG 59.971 50.000 0.00 0.00 35.28 2.90
2185 2337 2.996621 GTTGCGAAGTGAGCTAATCTGT 59.003 45.455 0.00 0.00 35.28 3.41
2186 2338 2.881074 TGCGAAGTGAGCTAATCTGTC 58.119 47.619 0.00 0.00 35.28 3.51
2187 2339 2.197577 GCGAAGTGAGCTAATCTGTCC 58.802 52.381 0.00 0.00 0.00 4.02
2188 2340 2.417379 GCGAAGTGAGCTAATCTGTCCA 60.417 50.000 0.00 0.00 0.00 4.02
2189 2341 3.182967 CGAAGTGAGCTAATCTGTCCAC 58.817 50.000 0.00 0.00 0.00 4.02
2190 2342 3.367395 CGAAGTGAGCTAATCTGTCCACA 60.367 47.826 0.00 0.00 0.00 4.17
2191 2343 4.569943 GAAGTGAGCTAATCTGTCCACAA 58.430 43.478 0.00 0.00 0.00 3.33
2192 2344 4.833478 AGTGAGCTAATCTGTCCACAAT 57.167 40.909 0.00 0.00 0.00 2.71
2193 2345 5.171339 AGTGAGCTAATCTGTCCACAATT 57.829 39.130 0.00 0.00 0.00 2.32
2194 2346 6.299805 AGTGAGCTAATCTGTCCACAATTA 57.700 37.500 0.00 0.00 0.00 1.40
2195 2347 6.893583 AGTGAGCTAATCTGTCCACAATTAT 58.106 36.000 0.00 0.00 0.00 1.28
2196 2348 7.341805 AGTGAGCTAATCTGTCCACAATTATT 58.658 34.615 0.00 0.00 0.00 1.40
2197 2349 7.831193 AGTGAGCTAATCTGTCCACAATTATTT 59.169 33.333 0.00 0.00 0.00 1.40
2198 2350 8.462016 GTGAGCTAATCTGTCCACAATTATTTT 58.538 33.333 0.00 0.00 0.00 1.82
2199 2351 8.461222 TGAGCTAATCTGTCCACAATTATTTTG 58.539 33.333 0.00 0.00 0.00 2.44
2200 2352 7.260603 AGCTAATCTGTCCACAATTATTTTGC 58.739 34.615 0.00 0.00 0.00 3.68
2201 2353 6.476706 GCTAATCTGTCCACAATTATTTTGCC 59.523 38.462 0.00 0.00 0.00 4.52
2202 2354 6.610075 AATCTGTCCACAATTATTTTGCCT 57.390 33.333 0.00 0.00 0.00 4.75
2203 2355 5.643379 TCTGTCCACAATTATTTTGCCTC 57.357 39.130 0.00 0.00 0.00 4.70
2204 2356 5.076182 TCTGTCCACAATTATTTTGCCTCA 58.924 37.500 0.00 0.00 0.00 3.86
2205 2357 5.048083 TCTGTCCACAATTATTTTGCCTCAC 60.048 40.000 0.00 0.00 0.00 3.51
2206 2358 4.832266 TGTCCACAATTATTTTGCCTCACT 59.168 37.500 0.00 0.00 0.00 3.41
2207 2359 5.163513 GTCCACAATTATTTTGCCTCACTG 58.836 41.667 0.00 0.00 0.00 3.66
2208 2360 5.048083 GTCCACAATTATTTTGCCTCACTGA 60.048 40.000 0.00 0.00 0.00 3.41
2209 2361 5.183713 TCCACAATTATTTTGCCTCACTGAG 59.816 40.000 0.00 0.00 0.00 3.35
2210 2362 5.047802 CCACAATTATTTTGCCTCACTGAGT 60.048 40.000 5.32 0.00 0.00 3.41
2211 2363 5.860182 CACAATTATTTTGCCTCACTGAGTG 59.140 40.000 6.18 6.18 34.45 3.51
2212 2364 5.536161 ACAATTATTTTGCCTCACTGAGTGT 59.464 36.000 12.93 0.00 34.79 3.55
2213 2365 6.040842 ACAATTATTTTGCCTCACTGAGTGTT 59.959 34.615 12.93 0.00 34.79 3.32
2214 2366 6.655078 ATTATTTTGCCTCACTGAGTGTTT 57.345 33.333 12.93 0.00 34.79 2.83
2215 2367 6.463995 TTATTTTGCCTCACTGAGTGTTTT 57.536 33.333 12.93 0.00 34.79 2.43
2216 2368 4.370364 TTTTGCCTCACTGAGTGTTTTC 57.630 40.909 12.93 1.72 34.79 2.29
2217 2369 2.708216 TGCCTCACTGAGTGTTTTCA 57.292 45.000 12.93 4.26 34.79 2.69
2218 2370 3.213206 TGCCTCACTGAGTGTTTTCAT 57.787 42.857 12.93 0.00 34.79 2.57
2219 2371 3.554934 TGCCTCACTGAGTGTTTTCATT 58.445 40.909 12.93 0.00 34.79 2.57
2220 2372 3.953612 TGCCTCACTGAGTGTTTTCATTT 59.046 39.130 12.93 0.00 34.79 2.32
2221 2373 4.202040 TGCCTCACTGAGTGTTTTCATTTG 60.202 41.667 12.93 0.00 34.79 2.32
2222 2374 4.293415 CCTCACTGAGTGTTTTCATTTGC 58.707 43.478 12.93 0.00 34.79 3.68
2223 2375 4.202040 CCTCACTGAGTGTTTTCATTTGCA 60.202 41.667 12.93 0.00 34.79 4.08
2224 2376 4.923893 TCACTGAGTGTTTTCATTTGCAG 58.076 39.130 12.93 0.00 34.79 4.41
2225 2377 4.398988 TCACTGAGTGTTTTCATTTGCAGT 59.601 37.500 12.93 0.00 35.92 4.40
2226 2378 5.104374 CACTGAGTGTTTTCATTTGCAGTT 58.896 37.500 4.01 0.00 33.51 3.16
2227 2379 6.094742 TCACTGAGTGTTTTCATTTGCAGTTA 59.905 34.615 12.93 0.00 33.51 2.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
120 122 5.841810 TGGAGCTTCTAATTGTTTTGGTTG 58.158 37.500 0.00 0.00 0.00 3.77
121 123 6.098266 AGTTGGAGCTTCTAATTGTTTTGGTT 59.902 34.615 0.00 0.00 0.00 3.67
122 124 5.598417 AGTTGGAGCTTCTAATTGTTTTGGT 59.402 36.000 0.00 0.00 0.00 3.67
123 125 6.089249 AGTTGGAGCTTCTAATTGTTTTGG 57.911 37.500 0.00 0.00 0.00 3.28
127 129 4.829492 AGCAAGTTGGAGCTTCTAATTGTT 59.171 37.500 16.14 8.97 38.01 2.83
271 282 1.225704 GGGGTCATGGAAGCCTCAG 59.774 63.158 2.97 0.00 37.00 3.35
291 308 7.272978 CCAGTTGTACTAGTATGGCATACTTT 58.727 38.462 37.01 27.39 43.27 2.66
407 424 7.745620 ATTTAGTGTTACCAAAGACTGAAGG 57.254 36.000 0.00 0.00 39.41 3.46
448 465 4.809958 CCAGTGCATCAATCAAACAAACAA 59.190 37.500 0.00 0.00 0.00 2.83
800 952 0.039764 AGTCGAGTGATGGGAGGACA 59.960 55.000 0.00 0.00 0.00 4.02
864 1016 7.192628 AGAGCCAGCTCCCTTCTTTATATATA 58.807 38.462 15.87 0.00 43.70 0.86
998 1150 3.737266 CGTATTTGATGAAATGGCCATGC 59.263 43.478 21.63 15.36 33.63 4.06
1235 1387 1.258982 GTATGGAACGAAGCAGCATCG 59.741 52.381 18.14 18.14 45.47 3.84
1409 1561 5.034797 AGCAAAAGTTTTTCACGTAAGAGC 58.965 37.500 0.00 0.00 43.62 4.09
1438 1590 2.285889 TAGGCCCTCCTCGGAGACAG 62.286 65.000 14.45 1.85 44.53 3.51
1445 1597 1.274728 CAGATCAATAGGCCCTCCTCG 59.725 57.143 0.00 0.00 43.06 4.63
1522 1674 6.348540 GGAAAACTTTCGACAAGCTCACATAT 60.349 38.462 7.10 0.00 38.06 1.78
1536 1688 4.618489 GTCATCATTGCAGGAAAACTTTCG 59.382 41.667 0.00 0.00 38.06 3.46
1793 1945 0.947244 CAACAACAGAGGCTGGACAC 59.053 55.000 0.00 0.00 35.51 3.67
1821 1973 2.877168 GGATCAGGTGCAGATCATTGAC 59.123 50.000 14.35 0.00 42.84 3.18
1835 1987 1.875576 GCTACATTCAGCCGGATCAGG 60.876 57.143 5.05 7.64 35.40 3.86
1869 2021 2.094675 GCTGCCTGTACATGGATGTTT 58.905 47.619 13.57 0.00 41.97 2.83
1890 2042 0.469892 AAAAAGCAGTGACCCCAGGG 60.470 55.000 0.00 0.00 42.03 4.45
1899 2051 6.198966 AGCATAAGAAAAACGAAAAAGCAGTG 59.801 34.615 0.00 0.00 0.00 3.66
1907 2059 5.048294 GGGAGGAAGCATAAGAAAAACGAAA 60.048 40.000 0.00 0.00 0.00 3.46
2074 2226 6.636454 ACTGGTTAGGAAAATAGATGGTCA 57.364 37.500 0.00 0.00 0.00 4.02
2169 2321 4.193826 TGTGGACAGATTAGCTCACTTC 57.806 45.455 0.00 0.00 0.00 3.01
2170 2322 4.623932 TTGTGGACAGATTAGCTCACTT 57.376 40.909 0.00 0.00 0.00 3.16
2171 2323 4.833478 ATTGTGGACAGATTAGCTCACT 57.167 40.909 0.00 0.00 0.00 3.41
2172 2324 7.559590 AATAATTGTGGACAGATTAGCTCAC 57.440 36.000 0.00 0.00 0.00 3.51
2173 2325 8.461222 CAAAATAATTGTGGACAGATTAGCTCA 58.539 33.333 0.00 0.00 0.00 4.26
2174 2326 7.433425 GCAAAATAATTGTGGACAGATTAGCTC 59.567 37.037 0.00 0.00 0.00 4.09
2175 2327 7.260603 GCAAAATAATTGTGGACAGATTAGCT 58.739 34.615 0.00 0.00 0.00 3.32
2176 2328 6.476706 GGCAAAATAATTGTGGACAGATTAGC 59.523 38.462 0.00 0.00 0.00 3.09
2177 2329 7.775120 AGGCAAAATAATTGTGGACAGATTAG 58.225 34.615 0.00 0.00 0.00 1.73
2178 2330 7.395772 TGAGGCAAAATAATTGTGGACAGATTA 59.604 33.333 0.00 0.00 0.00 1.75
2179 2331 6.211184 TGAGGCAAAATAATTGTGGACAGATT 59.789 34.615 0.00 0.00 0.00 2.40
2180 2332 5.716228 TGAGGCAAAATAATTGTGGACAGAT 59.284 36.000 0.00 0.00 0.00 2.90
2181 2333 5.048083 GTGAGGCAAAATAATTGTGGACAGA 60.048 40.000 0.00 0.00 0.00 3.41
2182 2334 5.047802 AGTGAGGCAAAATAATTGTGGACAG 60.048 40.000 0.00 0.00 0.00 3.51
2183 2335 4.832266 AGTGAGGCAAAATAATTGTGGACA 59.168 37.500 0.00 0.00 0.00 4.02
2184 2336 5.048083 TCAGTGAGGCAAAATAATTGTGGAC 60.048 40.000 0.00 0.00 0.00 4.02
2185 2337 5.076182 TCAGTGAGGCAAAATAATTGTGGA 58.924 37.500 0.00 0.00 0.00 4.02
2186 2338 5.047802 ACTCAGTGAGGCAAAATAATTGTGG 60.048 40.000 23.79 0.00 33.35 4.17
2187 2339 5.860182 CACTCAGTGAGGCAAAATAATTGTG 59.140 40.000 23.79 5.60 35.23 3.33
2188 2340 5.536161 ACACTCAGTGAGGCAAAATAATTGT 59.464 36.000 23.79 11.70 36.96 2.71
2189 2341 6.017400 ACACTCAGTGAGGCAAAATAATTG 57.983 37.500 23.79 11.09 36.96 2.32
2190 2342 6.655078 AACACTCAGTGAGGCAAAATAATT 57.345 33.333 23.79 0.00 36.96 1.40
2191 2343 6.655078 AAACACTCAGTGAGGCAAAATAAT 57.345 33.333 23.79 0.00 36.96 1.28
2192 2344 6.096141 TGAAAACACTCAGTGAGGCAAAATAA 59.904 34.615 23.79 1.04 36.96 1.40
2193 2345 5.592282 TGAAAACACTCAGTGAGGCAAAATA 59.408 36.000 23.79 3.23 36.96 1.40
2194 2346 4.402155 TGAAAACACTCAGTGAGGCAAAAT 59.598 37.500 23.79 5.78 36.96 1.82
2195 2347 3.761218 TGAAAACACTCAGTGAGGCAAAA 59.239 39.130 23.79 1.06 36.96 2.44
2196 2348 3.351740 TGAAAACACTCAGTGAGGCAAA 58.648 40.909 23.79 0.56 36.96 3.68
2197 2349 2.997980 TGAAAACACTCAGTGAGGCAA 58.002 42.857 23.79 0.02 36.96 4.52
2198 2350 2.708216 TGAAAACACTCAGTGAGGCA 57.292 45.000 23.79 9.04 36.96 4.75
2199 2351 4.293415 CAAATGAAAACACTCAGTGAGGC 58.707 43.478 23.79 6.74 36.96 4.70
2200 2352 4.202040 TGCAAATGAAAACACTCAGTGAGG 60.202 41.667 23.79 14.71 36.96 3.86
2201 2353 4.923893 TGCAAATGAAAACACTCAGTGAG 58.076 39.130 18.83 18.83 36.96 3.51
2202 2354 4.398988 ACTGCAAATGAAAACACTCAGTGA 59.601 37.500 13.14 0.00 36.96 3.41
2203 2355 4.675510 ACTGCAAATGAAAACACTCAGTG 58.324 39.130 2.22 2.22 39.75 3.66
2204 2356 4.989279 ACTGCAAATGAAAACACTCAGT 57.011 36.364 0.00 0.00 0.00 3.41


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

AutoCloner maintained by Alex Coulton.