Multiple sequence alignment - TraesCS7D01G461100

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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 TraesCS7D01G461100 chr7D 100.000 2447 0 0 1 2447 577512074 577509628 0.000000e+00 4519.0
1 TraesCS7D01G461100 chr7D 98.417 1137 13 2 657 1793 577538079 577536948 0.000000e+00 1995.0
2 TraesCS7D01G461100 chr7D 97.533 608 14 1 1840 2447 577536954 577536348 0.000000e+00 1038.0
3 TraesCS7D01G461100 chr7D 90.031 321 21 5 1731 2049 571867938 571867627 2.930000e-109 405.0
4 TraesCS7D01G461100 chr7D 95.181 166 6 2 2046 2210 194552534 194552370 6.710000e-66 261.0
5 TraesCS7D01G461100 chr7D 92.308 182 10 4 2037 2217 270556980 270557158 3.120000e-64 255.0
6 TraesCS7D01G461100 chr7D 72.080 548 138 11 882 1423 576656704 576657242 1.520000e-32 150.0
7 TraesCS7D01G461100 chr7D 96.629 89 3 0 1 89 577538196 577538108 5.450000e-32 148.0
8 TraesCS7D01G461100 chr7D 70.641 562 153 10 869 1427 576703958 576703406 1.990000e-21 113.0
9 TraesCS7D01G461100 chr7B 93.893 1490 60 17 90 1574 640865899 640864436 0.000000e+00 2218.0
10 TraesCS7D01G461100 chr7B 94.332 247 11 2 2204 2447 640848079 640847833 2.300000e-100 375.0
11 TraesCS7D01G461100 chr7B 94.979 239 10 1 2204 2440 640864004 640863766 8.260000e-100 374.0
12 TraesCS7D01G461100 chr7B 92.481 133 5 4 1529 1656 640848203 640848071 4.160000e-43 185.0
13 TraesCS7D01G461100 chr7B 92.523 107 8 0 1637 1743 169360163 169360269 1.170000e-33 154.0
14 TraesCS7D01G461100 chr7B 81.283 187 23 3 1824 2010 419046934 419046760 9.120000e-30 141.0
15 TraesCS7D01G461100 chr7B 72.506 451 110 12 882 1328 639278409 639278849 1.530000e-27 134.0
16 TraesCS7D01G461100 chr7B 93.258 89 6 0 1 89 640866019 640865931 5.490000e-27 132.0
17 TraesCS7D01G461100 chr7B 70.973 565 146 14 869 1427 639393336 639393888 4.270000e-23 119.0
18 TraesCS7D01G461100 chr7B 90.361 83 5 3 1577 1656 640864078 640863996 3.330000e-19 106.0
19 TraesCS7D01G461100 chr7B 74.603 252 51 8 866 1112 644299849 644300092 5.570000e-17 99.0
20 TraesCS7D01G461100 chr7B 72.176 363 86 12 866 1219 639676756 639677112 2.000000e-16 97.1
21 TraesCS7D01G461100 chr7B 92.453 53 4 0 1063 1115 639657589 639657641 2.610000e-10 76.8
22 TraesCS7D01G461100 chr7A 91.165 1064 59 12 132 1189 669640069 669639035 0.000000e+00 1411.0
23 TraesCS7D01G461100 chr7A 94.030 67 4 0 1 67 669640225 669640159 4.300000e-18 102.0
24 TraesCS7D01G461100 chr7A 77.160 162 31 5 1061 1219 668990823 668990981 3.350000e-14 89.8
25 TraesCS7D01G461100 chr7A 82.667 75 11 2 1169 1242 27462899 27462972 5.650000e-07 65.8
26 TraesCS7D01G461100 chr2D 93.226 310 20 1 1736 2044 39308072 39307763 2.870000e-124 455.0
27 TraesCS7D01G461100 chr2D 92.532 308 17 2 1737 2043 125459217 125458915 1.040000e-118 436.0
28 TraesCS7D01G461100 chr2D 95.210 167 7 1 2043 2209 200212318 200212153 1.870000e-66 263.0
29 TraesCS7D01G461100 chr2D 93.805 113 4 3 1633 1743 319689431 319689320 1.510000e-37 167.0
30 TraesCS7D01G461100 chr4D 92.982 285 17 3 1761 2043 365096245 365095962 1.750000e-111 412.0
31 TraesCS7D01G461100 chr4D 93.396 106 5 2 1640 1743 59938832 59938937 3.260000e-34 156.0
32 TraesCS7D01G461100 chr4D 93.396 106 5 2 1640 1743 220549972 220549867 3.260000e-34 156.0
33 TraesCS7D01G461100 chr4D 96.970 33 1 0 1079 1111 509141162 509141130 3.400000e-04 56.5
34 TraesCS7D01G461100 chr4D 96.970 33 1 0 1079 1111 509165305 509165273 3.400000e-04 56.5
35 TraesCS7D01G461100 chr3D 90.968 310 21 5 1736 2043 607818763 607819067 6.300000e-111 411.0
36 TraesCS7D01G461100 chr3D 91.919 297 16 5 1755 2043 355719325 355719029 2.260000e-110 409.0
37 TraesCS7D01G461100 chr3D 90.291 309 21 5 1737 2043 296183581 296183280 1.760000e-106 396.0
38 TraesCS7D01G461100 chr3D 93.396 106 6 1 1639 1743 464851553 464851448 3.260000e-34 156.0
39 TraesCS7D01G461100 chr6D 91.986 287 21 2 1761 2045 176471113 176471399 3.790000e-108 401.0
40 TraesCS7D01G461100 chr6D 92.727 110 7 1 1635 1743 71970079 71970188 9.060000e-35 158.0
41 TraesCS7D01G461100 chr1D 89.711 311 21 6 1735 2043 472320531 472320230 1.060000e-103 387.0
42 TraesCS7D01G461100 chr1D 94.767 172 6 3 2037 2207 254094954 254095123 5.190000e-67 265.0
43 TraesCS7D01G461100 chr5D 96.296 162 5 1 2046 2207 85141157 85140997 5.190000e-67 265.0
44 TraesCS7D01G461100 chr5D 92.350 183 8 6 2037 2217 223855787 223855965 3.120000e-64 255.0
45 TraesCS7D01G461100 chr5D 92.308 182 10 4 2037 2217 518248306 518248484 3.120000e-64 255.0
46 TraesCS7D01G461100 chr5D 94.340 106 4 2 1640 1743 380462024 380462129 7.000000e-36 161.0
47 TraesCS7D01G461100 chr4B 93.785 177 7 4 2039 2214 162174391 162174218 1.870000e-66 263.0
48 TraesCS7D01G461100 chr4B 96.970 33 1 0 1079 1111 658002785 658002817 3.400000e-04 56.5
49 TraesCS7D01G461100 chr5B 95.283 106 3 2 1640 1743 317831479 317831374 1.510000e-37 167.0
50 TraesCS7D01G461100 chrUn 82.667 75 11 2 1169 1242 50429502 50429575 5.650000e-07 65.8
51 TraesCS7D01G461100 chr4A 82.667 75 11 2 1169 1242 703442343 703442416 5.650000e-07 65.8


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 TraesCS7D01G461100 chr7D 577509628 577512074 2446 True 4519.000000 4519 100.000000 1 2447 1 chr7D.!!$R4 2446
1 TraesCS7D01G461100 chr7D 577536348 577538196 1848 True 1060.333333 1995 97.526333 1 2447 3 chr7D.!!$R5 2446
2 TraesCS7D01G461100 chr7B 640863766 640866019 2253 True 707.500000 2218 93.122750 1 2440 4 chr7B.!!$R3 2439
3 TraesCS7D01G461100 chr7A 669639035 669640225 1190 True 756.500000 1411 92.597500 1 1189 2 chr7A.!!$R1 1188

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
181 225 1.008767 CTTCTCGGATCGTACCCGC 60.009 63.158 4.35 0.0 46.1 6.13 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1797 2220 0.180406 GGCTCAAAATCTAGGCCCGA 59.82 55.0 0.0 0.0 37.12 5.14 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
28 29 1.709147 GCAATCGCGCCAAGATGTCT 61.709 55.000 0.00 0.00 0.00 3.41
120 164 1.990563 GGAACAAATCGATCGACGTGT 59.009 47.619 22.06 22.71 43.13 4.49
121 165 2.222508 GGAACAAATCGATCGACGTGTG 60.223 50.000 27.10 18.25 43.13 3.82
143 187 2.613506 CGTTTCCGTGTTGAGCCCC 61.614 63.158 0.00 0.00 0.00 5.80
151 195 2.631062 CCGTGTTGAGCCCCTACATATA 59.369 50.000 0.00 0.00 33.41 0.86
152 196 3.260884 CCGTGTTGAGCCCCTACATATAT 59.739 47.826 0.00 0.00 33.41 0.86
153 197 4.464951 CCGTGTTGAGCCCCTACATATATA 59.535 45.833 0.00 0.00 33.41 0.86
154 198 5.128827 CCGTGTTGAGCCCCTACATATATAT 59.871 44.000 0.00 0.00 33.41 0.86
163 207 8.770010 AGCCCCTACATATATATGAGTACTTC 57.230 38.462 26.05 10.95 37.15 3.01
178 222 3.876320 AGTACTTCTTCTCGGATCGTACC 59.124 47.826 0.00 0.00 0.00 3.34
181 225 1.008767 CTTCTCGGATCGTACCCGC 60.009 63.158 4.35 0.00 46.10 6.13
270 330 3.900703 GTGTTTTCTCTTGCGATCGAAAC 59.099 43.478 21.57 17.71 0.00 2.78
1813 2236 3.780624 GCTCGGGCCTAGATTTTGA 57.219 52.632 9.63 0.00 0.00 2.69
1814 2237 1.587547 GCTCGGGCCTAGATTTTGAG 58.412 55.000 9.63 2.79 0.00 3.02
1815 2238 1.587547 CTCGGGCCTAGATTTTGAGC 58.412 55.000 0.84 0.00 0.00 4.26
1816 2239 0.180406 TCGGGCCTAGATTTTGAGCC 59.820 55.000 0.84 0.00 43.09 4.70
1818 2241 3.903208 GGCCTAGATTTTGAGCCCA 57.097 52.632 0.00 0.00 37.66 5.36
1819 2242 2.143876 GGCCTAGATTTTGAGCCCAA 57.856 50.000 0.00 0.00 37.66 4.12
1820 2243 2.456577 GGCCTAGATTTTGAGCCCAAA 58.543 47.619 0.00 0.00 40.24 3.28
1821 2244 2.428530 GGCCTAGATTTTGAGCCCAAAG 59.571 50.000 0.00 0.00 42.55 2.77
1822 2245 3.356290 GCCTAGATTTTGAGCCCAAAGA 58.644 45.455 0.00 0.00 42.55 2.52
1823 2246 3.129462 GCCTAGATTTTGAGCCCAAAGAC 59.871 47.826 0.00 0.00 42.55 3.01
1824 2247 3.696548 CCTAGATTTTGAGCCCAAAGACC 59.303 47.826 0.00 0.00 42.55 3.85
1825 2248 2.162681 AGATTTTGAGCCCAAAGACCG 58.837 47.619 0.00 0.00 42.55 4.79
1826 2249 1.202348 GATTTTGAGCCCAAAGACCGG 59.798 52.381 0.00 0.00 42.55 5.28
1876 2299 1.589803 CGTTTTTCTGAAGGACGGGT 58.410 50.000 15.42 0.00 0.00 5.28
1913 2336 1.193874 CAGACGGGCTTTTACGTGTTC 59.806 52.381 0.00 0.00 44.24 3.18
1917 2340 1.208358 GGCTTTTACGTGTTCGGGC 59.792 57.895 0.00 0.00 41.85 6.13
2062 2485 7.010771 GGTATAATGAGGGAAGGCCTTATTTT 58.989 38.462 20.54 11.50 0.00 1.82
2081 2504 3.517296 TTGCAAATGTGAAGAGGGGTA 57.483 42.857 0.00 0.00 0.00 3.69
2190 2613 4.279169 CACCATCATCACCAACTCTGTTTT 59.721 41.667 0.00 0.00 0.00 2.43
2254 2677 3.111853 CTGCTTACAGTTGGTCAGACA 57.888 47.619 2.17 0.00 39.22 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
28 29 1.482182 CTCCCAGACCATGTCATCGAA 59.518 52.381 0.00 0.00 34.60 3.71
151 195 5.998981 ACGATCCGAGAAGAAGTACTCATAT 59.001 40.000 0.00 0.00 33.86 1.78
152 196 5.366460 ACGATCCGAGAAGAAGTACTCATA 58.634 41.667 0.00 0.00 33.86 2.15
153 197 4.200874 ACGATCCGAGAAGAAGTACTCAT 58.799 43.478 0.00 0.00 33.86 2.90
154 198 3.607741 ACGATCCGAGAAGAAGTACTCA 58.392 45.455 0.00 0.00 33.86 3.41
286 346 3.412879 GAGAGTACTCGGCCCGTGC 62.413 68.421 17.07 0.00 33.32 5.34
291 351 1.063764 CTTACGTGAGAGTACTCGGCC 59.936 57.143 17.07 10.89 45.25 6.13
1675 2098 8.959548 ACTCATACAAATGCATCTTGATGTTAA 58.040 29.630 20.96 0.22 32.76 2.01
1795 2218 1.587547 CTCAAAATCTAGGCCCGAGC 58.412 55.000 0.00 0.00 38.76 5.03
1796 2219 1.587547 GCTCAAAATCTAGGCCCGAG 58.412 55.000 0.00 0.00 0.00 4.63
1797 2220 0.180406 GGCTCAAAATCTAGGCCCGA 59.820 55.000 0.00 0.00 37.12 5.14
1798 2221 2.707902 GGCTCAAAATCTAGGCCCG 58.292 57.895 0.00 0.00 37.12 6.13
1801 2224 3.129462 GTCTTTGGGCTCAAAATCTAGGC 59.871 47.826 13.82 0.00 41.70 3.93
1802 2225 3.696548 GGTCTTTGGGCTCAAAATCTAGG 59.303 47.826 13.82 0.00 41.70 3.02
1803 2226 3.375299 CGGTCTTTGGGCTCAAAATCTAG 59.625 47.826 13.82 0.39 41.70 2.43
1804 2227 3.343617 CGGTCTTTGGGCTCAAAATCTA 58.656 45.455 13.82 0.00 41.70 1.98
1805 2228 2.162681 CGGTCTTTGGGCTCAAAATCT 58.837 47.619 13.82 0.00 41.70 2.40
1806 2229 1.202348 CCGGTCTTTGGGCTCAAAATC 59.798 52.381 13.82 8.71 41.70 2.17
1807 2230 1.256812 CCGGTCTTTGGGCTCAAAAT 58.743 50.000 13.82 0.00 41.70 1.82
1808 2231 0.825840 CCCGGTCTTTGGGCTCAAAA 60.826 55.000 13.82 1.56 41.70 2.44
1809 2232 1.228429 CCCGGTCTTTGGGCTCAAA 60.228 57.895 12.09 12.09 40.47 2.69
1810 2233 2.434331 CCCGGTCTTTGGGCTCAA 59.566 61.111 0.00 0.00 40.47 3.02
1838 2261 3.138128 GAAAACGATGGGCCCGGG 61.138 66.667 19.09 19.09 0.00 5.73
1894 2317 1.505425 GAACACGTAAAAGCCCGTCT 58.495 50.000 0.00 0.00 34.59 4.18
1917 2340 1.810755 GTTTTCTTTACCCGAGCCCAG 59.189 52.381 0.00 0.00 0.00 4.45
1929 2352 1.170290 CCGTCGGGCCTGTTTTCTTT 61.170 55.000 12.43 0.00 0.00 2.52
1930 2353 1.599797 CCGTCGGGCCTGTTTTCTT 60.600 57.895 12.43 0.00 0.00 2.52
2062 2485 3.355378 CATACCCCTCTTCACATTTGCA 58.645 45.455 0.00 0.00 0.00 4.08
2254 2677 1.980765 TGGAGCACCAGTGAGAGAAAT 59.019 47.619 0.00 0.00 41.77 2.17


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

AutoCloner maintained by Alex Coulton.