Multiple sequence alignment - TraesCS7A01G004700

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 TraesCS7A01G004700 chr7A 100.000 2357 0 0 1 2357 2603148 2605504 0.000000e+00 4353.0
1 TraesCS7A01G004700 chr7A 94.633 1677 56 6 364 2008 2752626 2750952 0.000000e+00 2567.0
2 TraesCS7A01G004700 chr7A 92.368 511 33 3 1392 1896 2103338 2102828 0.000000e+00 723.0
3 TraesCS7A01G004700 chr7A 75.321 1090 228 26 502 1563 3204654 3205730 3.520000e-133 484.0
4 TraesCS7A01G004700 chr7A 91.086 359 29 2 1 356 2753413 2753055 1.270000e-132 483.0
5 TraesCS7A01G004700 chr7A 90.000 180 10 3 1935 2114 2102820 2102649 2.360000e-55 226.0
6 TraesCS7A01G004700 chr7A 89.773 176 13 4 2007 2182 2748587 2748417 1.100000e-53 220.0
7 TraesCS7A01G004700 chr7A 94.175 103 6 0 2209 2311 2102450 2102348 8.720000e-35 158.0
8 TraesCS7A01G004700 chr7A 92.079 101 4 1 2253 2349 2748297 2748197 3.160000e-29 139.0
9 TraesCS7A01G004700 chr7D 87.003 1785 146 22 437 2182 3598285 3596548 0.000000e+00 1932.0
10 TraesCS7A01G004700 chr7D 79.779 994 174 17 540 1518 9924704 9923723 0.000000e+00 697.0
11 TraesCS7A01G004700 chr7D 91.367 278 24 0 1 278 3569588 3569311 4.750000e-102 381.0
12 TraesCS7A01G004700 chr7D 96.094 128 5 0 2176 2303 3596401 3596274 2.370000e-50 209.0
13 TraesCS7A01G004700 chr7D 87.500 136 15 2 1 135 3600074 3599940 3.140000e-34 156.0
14 TraesCS7A01G004700 chr7D 100.000 35 0 0 294 328 3599054 3599020 5.440000e-07 65.8
15 TraesCS7A01G004700 chr7D 100.000 32 0 0 297 328 3569313 3569282 2.530000e-05 60.2
16 TraesCS7A01G004700 chr4A 94.286 1015 39 5 348 1343 742137945 742138959 0.000000e+00 1535.0
17 TraesCS7A01G004700 chr4A 83.397 1054 173 2 501 1553 10637235 10638287 0.000000e+00 976.0
18 TraesCS7A01G004700 chr4A 94.488 508 22 4 1398 1902 742138958 742139462 0.000000e+00 778.0
19 TraesCS7A01G004700 chr4A 75.788 1078 225 27 538 1588 741593746 741592678 1.620000e-141 512.0
20 TraesCS7A01G004700 chr4A 76.190 1029 198 34 582 1582 740015767 740016776 1.260000e-137 499.0
21 TraesCS7A01G004700 chr4A 75.872 1032 208 29 582 1588 740582390 740581375 2.720000e-134 488.0
22 TraesCS7A01G004700 chr4A 92.105 304 24 0 2 305 742137095 742137398 1.670000e-116 429.0
23 TraesCS7A01G004700 chr4D 83.563 1089 172 6 501 1587 458385124 458384041 0.000000e+00 1013.0
24 TraesCS7A01G004700 chr4B 83.932 1058 167 3 501 1556 572554543 572553487 0.000000e+00 1009.0


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 TraesCS7A01G004700 chr7A 2603148 2605504 2356 False 4353.00 4353 100.000000 1 2357 1 chr7A.!!$F1 2356
1 TraesCS7A01G004700 chr7A 2748197 2753413 5216 True 852.25 2567 91.892750 1 2349 4 chr7A.!!$R2 2348
2 TraesCS7A01G004700 chr7A 3204654 3205730 1076 False 484.00 484 75.321000 502 1563 1 chr7A.!!$F2 1061
3 TraesCS7A01G004700 chr7A 2102348 2103338 990 True 369.00 723 92.181000 1392 2311 3 chr7A.!!$R1 919
4 TraesCS7A01G004700 chr7D 9923723 9924704 981 True 697.00 697 79.779000 540 1518 1 chr7D.!!$R1 978
5 TraesCS7A01G004700 chr7D 3596274 3600074 3800 True 590.70 1932 92.649250 1 2303 4 chr7D.!!$R3 2302
6 TraesCS7A01G004700 chr4A 10637235 10638287 1052 False 976.00 976 83.397000 501 1553 1 chr4A.!!$F1 1052
7 TraesCS7A01G004700 chr4A 742137095 742139462 2367 False 914.00 1535 93.626333 2 1902 3 chr4A.!!$F3 1900
8 TraesCS7A01G004700 chr4A 741592678 741593746 1068 True 512.00 512 75.788000 538 1588 1 chr4A.!!$R2 1050
9 TraesCS7A01G004700 chr4A 740015767 740016776 1009 False 499.00 499 76.190000 582 1582 1 chr4A.!!$F2 1000
10 TraesCS7A01G004700 chr4A 740581375 740582390 1015 True 488.00 488 75.872000 582 1588 1 chr4A.!!$R1 1006
11 TraesCS7A01G004700 chr4D 458384041 458385124 1083 True 1013.00 1013 83.563000 501 1587 1 chr4D.!!$R1 1086
12 TraesCS7A01G004700 chr4B 572553487 572554543 1056 True 1009.00 1009 83.932000 501 1556 1 chr4B.!!$R1 1055

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
231 235 0.535102 AGTGGCTTGTCCTTCAACCG 60.535 55.0 0.0 0.0 33.27 4.44 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1601 3168 0.532573 GCCTTCTGGTCATCGTCTCA 59.467 55.0 0.0 0.0 35.27 3.27 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
61 62 2.158325 AGAATTTGAACAGCCTTGGGGA 60.158 45.455 0.00 0.0 33.58 4.81
62 63 2.397044 ATTTGAACAGCCTTGGGGAA 57.603 45.000 0.00 0.0 33.58 3.97
63 64 1.703411 TTTGAACAGCCTTGGGGAAG 58.297 50.000 0.00 0.0 33.58 3.46
91 92 3.185391 GCAAAGACTGAACCTCTTCTTCG 59.815 47.826 0.00 0.0 0.00 3.79
99 100 4.621991 TGAACCTCTTCTTCGTTCTCTTG 58.378 43.478 0.00 0.0 37.40 3.02
154 155 5.186996 ACTTAAAGTTGCAGGTCACAATG 57.813 39.130 0.00 0.0 0.00 2.82
168 172 4.348656 GTCACAATGCACATCATCATCAC 58.651 43.478 0.00 0.0 33.40 3.06
227 231 4.481195 GCAGTGGCTTGTCCTTCA 57.519 55.556 0.00 0.0 36.96 3.02
231 235 0.535102 AGTGGCTTGTCCTTCAACCG 60.535 55.000 0.00 0.0 33.27 4.44
330 1134 7.973048 TGATGTTCAGAAATACTAGTAGGGT 57.027 36.000 8.85 0.0 0.00 4.34
349 1153 8.772250 AGTAGGGTATTGAAGATGAAAGATCAA 58.228 33.333 0.00 0.0 39.49 2.57
523 1954 5.940192 TCATAAATATCCACCACATTCGC 57.060 39.130 0.00 0.0 0.00 4.70
560 1992 2.755469 GCAACCCATCACGGCCAT 60.755 61.111 2.24 0.0 0.00 4.40
639 2074 2.039480 CTGATCCGGGATCCATGAATGT 59.961 50.000 29.34 0.0 38.20 2.71
686 2124 2.838202 TCCTAGGACCTCCAATGACAAC 59.162 50.000 7.62 0.0 38.89 3.32
823 2273 5.187772 ACATCCTTGTCACTGTAATCAGCTA 59.812 40.000 0.00 0.0 44.77 3.32
899 2376 1.303317 GGCCCTCGGACATGTTGTT 60.303 57.895 0.00 0.0 0.00 2.83
920 2397 3.319198 GACCCTCCAAGACCGCCA 61.319 66.667 0.00 0.0 0.00 5.69
985 2465 3.298686 TGGTAACACCACCAATCACAA 57.701 42.857 0.00 0.0 44.79 3.33
1304 2803 3.151554 TGTCAGAGCACATGAAGCATTT 58.848 40.909 15.23 0.0 0.00 2.32
1601 3168 1.599047 CTCCATGAACCCAGTCGCT 59.401 57.895 0.00 0.0 0.00 4.93
1626 3193 1.307097 GATGACCAGAAGGCTCATGC 58.693 55.000 0.00 0.0 36.46 4.06
1662 3230 4.090057 GGCTTCAACGCGTGCCTC 62.090 66.667 25.97 10.0 41.92 4.70
1820 3399 6.211184 TCAACCTCTTTGGCATATTTTGACAT 59.789 34.615 0.00 0.0 44.92 3.06
1942 3524 4.828829 TCCTACTAGCTTGGTTTAACAGC 58.171 43.478 0.00 0.0 0.00 4.40
2073 6029 1.745115 GCCGCCTGCTAATCACACA 60.745 57.895 0.00 0.0 36.87 3.72
2100 6056 7.891498 ATTTCTCTCTAACCTAGAAGGAGAC 57.109 40.000 0.00 0.0 37.67 3.36
2175 6135 0.885196 GAAGAGCGTGGAGAGAGTGT 59.115 55.000 0.00 0.0 0.00 3.55
2178 6138 1.228583 AGCGTGGAGAGAGTGTGGA 60.229 57.895 0.00 0.0 0.00 4.02
2243 6421 3.923425 ACTCCTTCCTCCCCTGTTTAATT 59.077 43.478 0.00 0.0 0.00 1.40
2321 6503 4.019771 TGCAGGTATGACTACATGGTGAAA 60.020 41.667 0.00 0.0 39.46 2.69
2331 6513 1.004044 ACATGGTGAAAGAGGAGCTGG 59.996 52.381 0.00 0.0 0.00 4.85
2349 6531 0.961019 GGTGCACCTTGCTCAATGAA 59.039 50.000 29.12 0.0 45.31 2.57
2350 6532 1.068055 GGTGCACCTTGCTCAATGAAG 60.068 52.381 29.12 0.0 45.31 3.02
2351 6533 1.881973 GTGCACCTTGCTCAATGAAGA 59.118 47.619 5.22 0.0 45.31 2.87
2352 6534 2.095364 GTGCACCTTGCTCAATGAAGAG 60.095 50.000 5.22 0.0 45.31 2.85
2353 6535 2.224597 TGCACCTTGCTCAATGAAGAGA 60.225 45.455 0.00 0.0 45.31 3.10
2354 6536 2.816087 GCACCTTGCTCAATGAAGAGAA 59.184 45.455 0.00 0.0 40.96 2.87
2355 6537 3.365767 GCACCTTGCTCAATGAAGAGAAC 60.366 47.826 0.00 0.0 40.96 3.01
2356 6538 3.817084 CACCTTGCTCAATGAAGAGAACA 59.183 43.478 0.00 0.0 37.87 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
16 17 2.093447 AGAGATCAAATGGTCCACCGAC 60.093 50.000 0.00 0.00 39.43 4.79
61 62 2.282462 CAGTCTTTGCCGGCCCTT 60.282 61.111 26.77 0.00 0.00 3.95
62 63 2.829384 TTCAGTCTTTGCCGGCCCT 61.829 57.895 26.77 8.96 0.00 5.19
63 64 2.282180 TTCAGTCTTTGCCGGCCC 60.282 61.111 26.77 6.51 0.00 5.80
91 92 6.306837 CAGTTTCAGACTATCGTCAAGAGAAC 59.693 42.308 0.00 5.48 42.73 3.01
99 100 6.237332 CGAATTGACAGTTTCAGACTATCGTC 60.237 42.308 0.00 0.00 34.43 4.20
154 155 3.550275 GCATTGTTGTGATGATGATGTGC 59.450 43.478 0.00 0.00 0.00 4.57
195 199 4.478371 TGCTCTCCGCCTGGCATG 62.478 66.667 20.29 9.24 38.05 4.06
330 1134 7.989741 GGTCCTCTTGATCTTTCATCTTCAATA 59.010 37.037 0.00 0.00 0.00 1.90
349 1153 4.527038 TCAGTTTTAAGTCGATGGTCCTCT 59.473 41.667 0.00 0.00 0.00 3.69
391 1790 5.246981 TGTGATTCAAGATGGTCCTCTTT 57.753 39.130 0.00 0.00 33.18 2.52
445 1876 8.980143 TTTGTGTTATTAGCTTTAATTCTGGC 57.020 30.769 0.00 0.00 0.00 4.85
523 1954 2.863137 GCTGAGTCCGCTGAATAAAGAG 59.137 50.000 0.00 0.00 0.00 2.85
560 1992 6.312918 GTCATCCAAGAGCTTCGTTTATAACA 59.687 38.462 0.00 0.00 0.00 2.41
639 2074 0.108186 CTGGTGGCACGATTGAGCTA 60.108 55.000 12.17 0.00 31.76 3.32
686 2124 2.124983 CCTGTGGTGATCGGCTGG 60.125 66.667 0.00 0.00 0.00 4.85
899 2376 1.899437 GCGGTCTTGGAGGGTCATCA 61.899 60.000 0.00 0.00 0.00 3.07
920 2397 4.080863 GTGGTGAGGAATATGACTTGGAGT 60.081 45.833 0.00 0.00 0.00 3.85
985 2465 5.337009 GCACATTCATGGATGGAAAGTTCTT 60.337 40.000 18.42 0.00 0.00 2.52
1304 2803 0.618458 GCCCAAGATACCACCAGACA 59.382 55.000 0.00 0.00 0.00 3.41
1427 2994 0.757188 CCGCAGTGGGGAGATCTACT 60.757 60.000 21.34 0.00 37.91 2.57
1601 3168 0.532573 GCCTTCTGGTCATCGTCTCA 59.467 55.000 0.00 0.00 35.27 3.27
1662 3230 2.686470 TGAGGGCAGAGCAGGAGG 60.686 66.667 0.00 0.00 0.00 4.30
1705 3273 8.432110 AGAAATTTTACCGATTTGCAAAACTT 57.568 26.923 17.19 0.00 0.00 2.66
1820 3399 2.851263 ATGGAGCTAAACGGTTGTCA 57.149 45.000 0.00 0.00 0.00 3.58
1942 3524 6.674694 ACTACACTACTACTACCATGTTCG 57.325 41.667 0.00 0.00 0.00 3.95
2013 5969 1.737008 GGACGGAACTCAACTCGCC 60.737 63.158 0.00 0.00 0.00 5.54
2073 6029 7.896496 TCTCCTTCTAGGTTAGAGAGAAATTGT 59.104 37.037 0.00 0.00 34.87 2.71
2100 6056 2.483745 CAGCAGCCATGTCTTGCG 59.516 61.111 7.42 0.00 0.00 4.85
2175 6135 2.601240 TGGGTTCAGAATGCATTCCA 57.399 45.000 31.05 20.65 37.51 3.53
2178 6138 3.833650 TGTGATTGGGTTCAGAATGCATT 59.166 39.130 12.83 12.83 34.76 3.56
2243 6421 0.941542 GATTATTTGGCGGTAGCGCA 59.058 50.000 36.52 21.77 46.35 6.09
2264 6442 9.132521 CAATAACCTTTGAACAATCTGATTCAC 57.867 33.333 0.00 0.00 34.61 3.18
2293 6471 1.203758 TGTAGTCATACCTGCACACGG 59.796 52.381 0.00 0.00 0.00 4.94


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

AutoCloner maintained by Alex Coulton.