Multiple sequence alignment - TraesCS2D01G309700

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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 TraesCS2D01G309700 chr2D 100.000 2339 0 0 1 2339 397901248 397898910 0.000000e+00 4320.0
1 TraesCS2D01G309700 chr2D 91.867 996 69 6 571 1555 446921477 446920483 0.000000e+00 1380.0
2 TraesCS2D01G309700 chr2B 94.506 1802 64 13 328 2102 470392781 470390988 0.000000e+00 2747.0
3 TraesCS2D01G309700 chr2B 89.329 984 77 4 571 1549 526755103 526756063 0.000000e+00 1210.0
4 TraesCS2D01G309700 chr2B 94.839 310 14 2 1 309 470393075 470392767 1.260000e-132 483.0
5 TraesCS2D01G309700 chr2B 86.561 253 29 4 1935 2182 42029559 42029811 8.230000e-70 274.0
6 TraesCS2D01G309700 chr2B 92.241 116 8 1 2160 2275 470390982 470390868 1.860000e-36 163.0
7 TraesCS2D01G309700 chr2B 95.082 61 3 0 2279 2339 69249617 69249557 1.910000e-16 97.1
8 TraesCS2D01G309700 chr2A 94.746 1713 54 8 328 2006 535147590 535145880 0.000000e+00 2632.0
9 TraesCS2D01G309700 chr2A 91.775 997 68 6 571 1554 590983850 590984845 0.000000e+00 1375.0
10 TraesCS2D01G309700 chr2A 91.640 311 14 4 1 309 535147876 535147576 1.000000e-113 420.0
11 TraesCS2D01G309700 chr2A 95.614 228 7 1 1988 2212 535144172 535143945 1.710000e-96 363.0
12 TraesCS2D01G309700 chr2A 86.853 251 29 3 1936 2182 66802949 66802699 6.370000e-71 278.0
13 TraesCS2D01G309700 chr7A 88.048 251 25 3 1936 2181 540721280 540721530 2.270000e-75 292.0
14 TraesCS2D01G309700 chr4A 87.500 256 27 3 1936 2186 138433246 138432991 8.180000e-75 291.0
15 TraesCS2D01G309700 chr1D 87.649 251 26 4 1937 2182 370611158 370610908 1.060000e-73 287.0
16 TraesCS2D01G309700 chr5B 87.251 251 28 2 1936 2182 250927395 250927145 1.370000e-72 283.0
17 TraesCS2D01G309700 chr1A 86.853 251 28 4 1937 2182 333879566 333879316 2.290000e-70 276.0
18 TraesCS2D01G309700 chr5D 98.305 59 1 0 2279 2337 528582861 528582919 1.140000e-18 104.0
19 TraesCS2D01G309700 chr5D 96.721 61 2 0 2277 2337 524450277 524450217 4.110000e-18 102.0
20 TraesCS2D01G309700 chr5D 100.000 28 0 0 2202 2229 56472049 56472076 4.000000e-03 52.8
21 TraesCS2D01G309700 chr4D 96.667 60 1 1 2279 2338 17843377 17843319 5.320000e-17 99.0


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 TraesCS2D01G309700 chr2D 397898910 397901248 2338 True 4320.000000 4320 100.000 1 2339 1 chr2D.!!$R1 2338
1 TraesCS2D01G309700 chr2D 446920483 446921477 994 True 1380.000000 1380 91.867 571 1555 1 chr2D.!!$R2 984
2 TraesCS2D01G309700 chr2B 526755103 526756063 960 False 1210.000000 1210 89.329 571 1549 1 chr2B.!!$F2 978
3 TraesCS2D01G309700 chr2B 470390868 470393075 2207 True 1131.000000 2747 93.862 1 2275 3 chr2B.!!$R2 2274
4 TraesCS2D01G309700 chr2A 590983850 590984845 995 False 1375.000000 1375 91.775 571 1554 1 chr2A.!!$F1 983
5 TraesCS2D01G309700 chr2A 535143945 535147876 3931 True 1138.333333 2632 94.000 1 2212 3 chr2A.!!$R2 2211

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
311 313 0.034477 CATCAGGTAGGCCGGGTTTT 60.034 55.0 2.18 0.0 40.5 2.43 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2306 4099 0.107703 TCAAGCCAAGTATGCGGGAG 60.108 55.0 0.0 0.0 0.0 4.3 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
129 130 2.809601 CACGCCGCTACGAGCTTT 60.810 61.111 2.02 0.00 39.60 3.51
159 160 2.661566 CGCTCCTGTGCTGTTGTCG 61.662 63.158 0.00 0.00 0.00 4.35
202 203 2.674380 CCCAGCACCTGTCTTGCC 60.674 66.667 0.00 0.00 41.18 4.52
206 207 2.743928 GCACCTGTCTTGCCCGAG 60.744 66.667 0.00 0.00 33.58 4.63
272 274 2.600470 TTGCTTGCAAACTCCCTTTG 57.400 45.000 5.49 0.00 42.12 2.77
273 275 0.752054 TGCTTGCAAACTCCCTTTGG 59.248 50.000 0.00 0.00 39.89 3.28
286 288 9.119418 CAAACTCCCTTTGGTTTTTGATAATTT 57.881 29.630 0.00 0.00 36.97 1.82
305 307 2.122783 TTTTTCCATCAGGTAGGCCG 57.877 50.000 0.00 0.00 40.50 6.13
306 308 0.254747 TTTTCCATCAGGTAGGCCGG 59.745 55.000 0.00 0.00 40.50 6.13
307 309 1.632018 TTTCCATCAGGTAGGCCGGG 61.632 60.000 2.18 0.00 40.50 5.73
308 310 2.768344 CCATCAGGTAGGCCGGGT 60.768 66.667 2.18 0.00 40.50 5.28
309 311 2.375345 CCATCAGGTAGGCCGGGTT 61.375 63.158 2.18 0.00 40.50 4.11
310 312 1.607612 CATCAGGTAGGCCGGGTTT 59.392 57.895 2.18 0.00 40.50 3.27
311 313 0.034477 CATCAGGTAGGCCGGGTTTT 60.034 55.000 2.18 0.00 40.50 2.43
312 314 0.702316 ATCAGGTAGGCCGGGTTTTT 59.298 50.000 2.18 0.00 40.50 1.94
451 459 4.664677 GTGCCCTGTCGCTCGTGT 62.665 66.667 0.00 0.00 0.00 4.49
458 466 1.278172 CTGTCGCTCGTGTTGTCCTG 61.278 60.000 0.00 0.00 0.00 3.86
464 472 1.502231 CTCGTGTTGTCCTGTTCCAG 58.498 55.000 0.00 0.00 0.00 3.86
608 646 4.344102 TGCCCTACAGATATCACTAACACC 59.656 45.833 5.32 0.00 0.00 4.16
640 678 1.133025 GGCAGTTGTCCATTCGATTGG 59.867 52.381 18.34 18.34 38.18 3.16
827 868 4.081420 TGAGGACCAGATCTTGCTAACTTC 60.081 45.833 0.00 0.00 0.00 3.01
897 939 2.500098 TCATCTAACCCTACACAGGCAC 59.500 50.000 0.00 0.00 41.08 5.01
930 972 2.496070 TGAGGTATCTTTGTCCTGACCG 59.504 50.000 0.00 0.00 32.04 4.79
939 981 2.604686 TCCTGACCGCTGGCTCTT 60.605 61.111 0.00 0.00 33.46 2.85
1274 1327 3.494332 AGGCAAACTTTGAAGAGAGCAT 58.506 40.909 5.65 0.00 0.00 3.79
1335 1388 5.300969 TGGCTGAGAAAGAAAATGAATCG 57.699 39.130 0.00 0.00 0.00 3.34
1347 1400 5.869888 AGAAAATGAATCGTAGCTTCGAACT 59.130 36.000 19.51 9.75 42.99 3.01
1745 1807 3.098377 TGTATAGGCACCGTCCTGTAAA 58.902 45.455 0.00 0.00 37.01 2.01
1939 2002 9.295825 TCATTATTGTCCAGTTTGTTTGATACT 57.704 29.630 0.00 0.00 0.00 2.12
1945 2009 4.597507 TCCAGTTTGTTTGATACTCCCTCT 59.402 41.667 0.00 0.00 0.00 3.69
1976 2040 8.324163 AGAATATAAGGTGTATTGATTTCCGC 57.676 34.615 0.00 0.00 0.00 5.54
2105 3898 9.528018 GGTATAATTTTGTATTGTGGATGTTGG 57.472 33.333 0.00 0.00 0.00 3.77
2144 3937 1.195448 CAGTCGAACATGCACTTGTCC 59.805 52.381 0.00 0.00 0.00 4.02
2153 3946 0.380378 TGCACTTGTCCGACTTTTGC 59.620 50.000 0.00 6.06 0.00 3.68
2259 4052 2.781681 ACCTCCCTATGGTGTTTTCG 57.218 50.000 0.00 0.00 36.30 3.46
2262 4055 2.290705 CCTCCCTATGGTGTTTTCGGTT 60.291 50.000 0.00 0.00 0.00 4.44
2292 4085 4.070552 GCCGGACGAGACTTGCCT 62.071 66.667 5.05 0.00 0.00 4.75
2293 4086 2.125912 CCGGACGAGACTTGCCTG 60.126 66.667 0.00 0.00 0.00 4.85
2294 4087 2.811317 CGGACGAGACTTGCCTGC 60.811 66.667 0.00 0.00 0.00 4.85
2295 4088 2.659610 GGACGAGACTTGCCTGCT 59.340 61.111 0.00 0.00 0.00 4.24
2296 4089 1.446966 GGACGAGACTTGCCTGCTC 60.447 63.158 0.00 0.00 0.00 4.26
2297 4090 1.446966 GACGAGACTTGCCTGCTCC 60.447 63.158 0.00 0.00 0.00 4.70
2298 4091 2.125350 CGAGACTTGCCTGCTCCC 60.125 66.667 0.00 0.00 0.00 4.30
2299 4092 2.947532 CGAGACTTGCCTGCTCCCA 61.948 63.158 0.00 0.00 0.00 4.37
2300 4093 1.606531 GAGACTTGCCTGCTCCCAT 59.393 57.895 0.00 0.00 0.00 4.00
2301 4094 0.463474 GAGACTTGCCTGCTCCCATC 60.463 60.000 0.00 0.00 0.00 3.51
2302 4095 1.452833 GACTTGCCTGCTCCCATCC 60.453 63.158 0.00 0.00 0.00 3.51
2303 4096 2.515523 CTTGCCTGCTCCCATCCG 60.516 66.667 0.00 0.00 0.00 4.18
2304 4097 3.329889 TTGCCTGCTCCCATCCGT 61.330 61.111 0.00 0.00 0.00 4.69
2305 4098 3.626996 TTGCCTGCTCCCATCCGTG 62.627 63.158 0.00 0.00 0.00 4.94
2307 4100 3.790437 CCTGCTCCCATCCGTGCT 61.790 66.667 0.00 0.00 0.00 4.40
2308 4101 2.202987 CTGCTCCCATCCGTGCTC 60.203 66.667 0.00 0.00 0.00 4.26
2309 4102 3.746949 CTGCTCCCATCCGTGCTCC 62.747 68.421 0.00 0.00 0.00 4.70
2310 4103 4.554036 GCTCCCATCCGTGCTCCC 62.554 72.222 0.00 0.00 0.00 4.30
2311 4104 4.227134 CTCCCATCCGTGCTCCCG 62.227 72.222 0.00 0.00 0.00 5.14
2321 4114 2.124736 TGCTCCCGCATACTTGGC 60.125 61.111 0.00 0.00 42.25 4.52
2322 4115 2.190578 GCTCCCGCATACTTGGCT 59.809 61.111 0.00 0.00 35.78 4.75
2323 4116 1.452108 GCTCCCGCATACTTGGCTT 60.452 57.895 0.00 0.00 35.78 4.35
2324 4117 1.718757 GCTCCCGCATACTTGGCTTG 61.719 60.000 0.00 0.00 35.78 4.01
2325 4118 0.107703 CTCCCGCATACTTGGCTTGA 60.108 55.000 0.00 0.00 0.00 3.02
2326 4119 0.546122 TCCCGCATACTTGGCTTGAT 59.454 50.000 0.00 0.00 0.00 2.57
2327 4120 1.064758 TCCCGCATACTTGGCTTGATT 60.065 47.619 0.00 0.00 0.00 2.57
2328 4121 1.750778 CCCGCATACTTGGCTTGATTT 59.249 47.619 0.00 0.00 0.00 2.17
2329 4122 2.480073 CCCGCATACTTGGCTTGATTTG 60.480 50.000 0.00 0.00 0.00 2.32
2330 4123 2.423185 CCGCATACTTGGCTTGATTTGA 59.577 45.455 0.00 0.00 0.00 2.69
2331 4124 3.067180 CCGCATACTTGGCTTGATTTGAT 59.933 43.478 0.00 0.00 0.00 2.57
2332 4125 4.440525 CCGCATACTTGGCTTGATTTGATT 60.441 41.667 0.00 0.00 0.00 2.57
2333 4126 4.501559 CGCATACTTGGCTTGATTTGATTG 59.498 41.667 0.00 0.00 0.00 2.67
2334 4127 4.807304 GCATACTTGGCTTGATTTGATTGG 59.193 41.667 0.00 0.00 0.00 3.16
2335 4128 5.394443 GCATACTTGGCTTGATTTGATTGGA 60.394 40.000 0.00 0.00 0.00 3.53
2336 4129 6.632909 CATACTTGGCTTGATTTGATTGGAA 58.367 36.000 0.00 0.00 0.00 3.53
2337 4130 5.549742 ACTTGGCTTGATTTGATTGGAAA 57.450 34.783 0.00 0.00 0.00 3.13
2338 4131 5.927819 ACTTGGCTTGATTTGATTGGAAAA 58.072 33.333 0.00 0.00 0.00 2.29
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
261 263 9.693739 AAAATTATCAAAAACCAAAGGGAGTTT 57.306 25.926 0.00 0.0 37.80 2.66
286 288 1.340600 CCGGCCTACCTGATGGAAAAA 60.341 52.381 0.00 0.0 37.04 1.94
291 293 1.921869 AAACCCGGCCTACCTGATGG 61.922 60.000 0.00 0.0 39.83 3.51
293 295 0.702316 AAAAACCCGGCCTACCTGAT 59.298 50.000 0.00 0.0 0.00 2.90
294 296 2.156920 AAAAACCCGGCCTACCTGA 58.843 52.632 0.00 0.0 0.00 3.86
295 297 4.834911 AAAAACCCGGCCTACCTG 57.165 55.556 0.00 0.0 0.00 4.00
335 337 3.001406 GGGCTAGACACACCCGGT 61.001 66.667 0.00 0.0 32.92 5.28
384 386 4.578871 AGCATGGGCCTTTTACATTTTTC 58.421 39.130 4.53 0.0 42.56 2.29
458 466 1.085091 TAGCTCGACTCGACTGGAAC 58.915 55.000 0.00 0.0 0.00 3.62
804 845 3.445008 AGTTAGCAAGATCTGGTCCTCA 58.555 45.455 0.00 0.0 36.95 3.86
810 851 1.936547 GCCGAAGTTAGCAAGATCTGG 59.063 52.381 0.00 0.0 0.00 3.86
827 868 0.314935 AACCTGCATGAAAGTTGCCG 59.685 50.000 0.00 0.0 39.39 5.69
897 939 2.968574 AGATACCTCAGCACACATAGGG 59.031 50.000 0.00 0.0 33.16 3.53
930 972 1.532523 AAGCTTCAGAAAGAGCCAGC 58.467 50.000 0.00 0.0 34.14 4.85
939 981 6.127647 ACACTTGAAATGACAAAGCTTCAGAA 60.128 34.615 0.00 0.0 0.00 3.02
1274 1327 5.757808 GCCTGCAACCTTTCTTTAAATTTCA 59.242 36.000 0.00 0.0 0.00 2.69
1335 1388 3.246619 CTTGTCCTCAGTTCGAAGCTAC 58.753 50.000 0.00 0.0 0.00 3.58
1347 1400 2.972021 TCAGTGAATGTCCTTGTCCTCA 59.028 45.455 0.00 0.0 0.00 3.86
1939 2002 6.443849 ACACCTTATATTCTTGAACAGAGGGA 59.556 38.462 0.00 0.0 31.12 4.20
1973 2037 4.497473 TTCAAATGGTTGACTTAAGCGG 57.503 40.909 1.29 0.0 43.52 5.52
2166 3959 7.008941 ACGGCTCTAGGTTCCTTTATATAAGA 58.991 38.462 0.00 0.0 0.00 2.10
2183 3976 1.895238 CGGAGGGAAAACGGCTCTA 59.105 57.895 0.00 0.0 0.00 2.43
2275 4068 4.070552 AGGCAAGTCTCGTCCGGC 62.071 66.667 0.00 0.0 0.00 6.13
2276 4069 2.125912 CAGGCAAGTCTCGTCCGG 60.126 66.667 0.00 0.0 0.00 5.14
2277 4070 2.811317 GCAGGCAAGTCTCGTCCG 60.811 66.667 0.00 0.0 0.00 4.79
2278 4071 1.446966 GAGCAGGCAAGTCTCGTCC 60.447 63.158 0.00 0.0 0.00 4.79
2279 4072 1.446966 GGAGCAGGCAAGTCTCGTC 60.447 63.158 0.00 0.0 0.00 4.20
2280 4073 2.659610 GGAGCAGGCAAGTCTCGT 59.340 61.111 0.00 0.0 0.00 4.18
2281 4074 2.125350 GGGAGCAGGCAAGTCTCG 60.125 66.667 0.00 0.0 0.00 4.04
2282 4075 0.463474 GATGGGAGCAGGCAAGTCTC 60.463 60.000 0.00 0.0 0.00 3.36
2283 4076 1.606531 GATGGGAGCAGGCAAGTCT 59.393 57.895 0.00 0.0 0.00 3.24
2284 4077 1.452833 GGATGGGAGCAGGCAAGTC 60.453 63.158 0.00 0.0 0.00 3.01
2285 4078 2.679716 GGATGGGAGCAGGCAAGT 59.320 61.111 0.00 0.0 0.00 3.16
2286 4079 2.515523 CGGATGGGAGCAGGCAAG 60.516 66.667 0.00 0.0 0.00 4.01
2287 4080 3.329889 ACGGATGGGAGCAGGCAA 61.330 61.111 0.00 0.0 0.00 4.52
2288 4081 4.100084 CACGGATGGGAGCAGGCA 62.100 66.667 0.00 0.0 0.00 4.75
2290 4083 3.746949 GAGCACGGATGGGAGCAGG 62.747 68.421 0.00 0.0 0.00 4.85
2291 4084 2.202987 GAGCACGGATGGGAGCAG 60.203 66.667 0.00 0.0 0.00 4.24
2292 4085 3.785859 GGAGCACGGATGGGAGCA 61.786 66.667 0.00 0.0 0.00 4.26
2293 4086 4.554036 GGGAGCACGGATGGGAGC 62.554 72.222 0.00 0.0 0.00 4.70
2294 4087 4.227134 CGGGAGCACGGATGGGAG 62.227 72.222 0.00 0.0 0.00 4.30
2306 4099 0.107703 TCAAGCCAAGTATGCGGGAG 60.108 55.000 0.00 0.0 0.00 4.30
2307 4100 0.546122 ATCAAGCCAAGTATGCGGGA 59.454 50.000 0.00 0.0 0.00 5.14
2308 4101 1.392589 AATCAAGCCAAGTATGCGGG 58.607 50.000 0.00 0.0 0.00 6.13
2309 4102 2.423185 TCAAATCAAGCCAAGTATGCGG 59.577 45.455 0.00 0.0 0.00 5.69
2310 4103 3.763097 TCAAATCAAGCCAAGTATGCG 57.237 42.857 0.00 0.0 0.00 4.73
2311 4104 4.807304 CCAATCAAATCAAGCCAAGTATGC 59.193 41.667 0.00 0.0 0.00 3.14
2312 4105 6.211587 TCCAATCAAATCAAGCCAAGTATG 57.788 37.500 0.00 0.0 0.00 2.39
2313 4106 6.855763 TTCCAATCAAATCAAGCCAAGTAT 57.144 33.333 0.00 0.0 0.00 2.12
2314 4107 6.662865 TTTCCAATCAAATCAAGCCAAGTA 57.337 33.333 0.00 0.0 0.00 2.24
2315 4108 5.549742 TTTCCAATCAAATCAAGCCAAGT 57.450 34.783 0.00 0.0 0.00 3.16


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

AutoCloner maintained by Alex Coulton.