Multiple sequence alignment - TraesCS6B01G094700

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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 TraesCS6B01G094700 chr6B 100.000 3895 0 0 936 4830 71148011 71151905 0.000000e+00 7193.0
1 TraesCS6B01G094700 chr6B 100.000 256 0 0 1 256 71147076 71147331 1.570000e-129 473.0
2 TraesCS6B01G094700 chr6D 95.575 3819 109 36 936 4722 34394916 34398706 0.000000e+00 6061.0
3 TraesCS6B01G094700 chr6D 93.452 168 2 5 1 161 34394434 34394599 1.740000e-59 241.0
4 TraesCS6B01G094700 chr6D 93.220 59 4 0 2092 2150 34396144 34396202 2.390000e-13 87.9
5 TraesCS6B01G094700 chr6D 100.000 40 0 0 141 180 34394597 34394636 1.860000e-09 75.0
6 TraesCS6B01G094700 chr6A 94.683 3912 149 39 936 4830 38550516 38554385 0.000000e+00 6017.0
7 TraesCS6B01G094700 chr6A 95.436 241 8 3 1 240 38549922 38550160 9.810000e-102 381.0
8 TraesCS6B01G094700 chr2B 81.720 558 60 22 2906 3452 378049768 378049242 1.240000e-115 427.0
9 TraesCS6B01G094700 chr1B 91.262 103 9 0 1000 1102 564165507 564165405 1.810000e-29 141.0
10 TraesCS6B01G094700 chr1A 91.262 103 9 0 1000 1102 514553874 514553772 1.810000e-29 141.0


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 TraesCS6B01G094700 chr6B 71147076 71151905 4829 False 3833.000 7193 100.00000 1 4830 2 chr6B.!!$F1 4829
1 TraesCS6B01G094700 chr6D 34394434 34398706 4272 False 1616.225 6061 95.56175 1 4722 4 chr6D.!!$F1 4721
2 TraesCS6B01G094700 chr6A 38549922 38554385 4463 False 3199.000 6017 95.05950 1 4830 2 chr6A.!!$F1 4829
3 TraesCS6B01G094700 chr2B 378049242 378049768 526 True 427.000 427 81.72000 2906 3452 1 chr2B.!!$R1 546

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
962 986 2.184631 TCCTCCCCTCCCCTGTCTT 61.185 63.158 0.00 0.00 0.00 3.01 F
1316 1350 0.108585 TGATCTAGATTTGGGCCGGC 59.891 55.000 21.18 21.18 0.00 6.13 F
1934 1974 0.842635 AGATTAGCTTGGAGCCCTGG 59.157 55.000 0.00 0.00 43.77 4.45 F
3325 3386 1.944024 CGTGCTTGTGTTCTTTACCCA 59.056 47.619 0.00 0.00 0.00 4.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2436 2478 0.109342 CCTCCTGACCTGTTGCAGTT 59.891 55.000 0.00 0.0 0.00 3.16 R
3068 3122 1.545614 CCAACGTCACTTCCGTCGTG 61.546 60.000 0.00 0.0 37.61 4.35 R
3500 3563 3.885901 AGGGAAAGAGCAAGAAAGACAAC 59.114 43.478 0.00 0.0 0.00 3.32 R
4671 4744 0.322816 TGGCTGGCCATCTTCTGAAC 60.323 55.000 5.51 0.0 41.89 3.18 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
119 120 4.194497 TCCACCTCCACCCACCCA 62.194 66.667 0.00 0.00 0.00 4.51
199 223 2.512515 CAGGCTAAGCGGAGGCAC 60.513 66.667 15.18 0.00 44.29 5.01
202 226 4.096003 GCTAAGCGGAGGCACCCA 62.096 66.667 0.00 0.00 43.41 4.51
203 227 2.187946 CTAAGCGGAGGCACCCAG 59.812 66.667 0.00 0.00 43.41 4.45
204 228 4.096003 TAAGCGGAGGCACCCAGC 62.096 66.667 0.00 0.00 43.41 4.85
253 277 3.866582 CACCCCCGCATCCCTCTC 61.867 72.222 0.00 0.00 0.00 3.20
255 279 4.888325 CCCCCGCATCCCTCTCCT 62.888 72.222 0.00 0.00 0.00 3.69
962 986 2.184631 TCCTCCCCTCCCCTGTCTT 61.185 63.158 0.00 0.00 0.00 3.01
1116 1140 0.814812 CCGTACGTCCCTCTCTCTCC 60.815 65.000 15.21 0.00 0.00 3.71
1132 1160 7.125659 CCTCTCTCTCCTCCTTTCTTTTCTTAT 59.874 40.741 0.00 0.00 0.00 1.73
1134 1162 9.548631 TCTCTCTCCTCCTTTCTTTTCTTATTA 57.451 33.333 0.00 0.00 0.00 0.98
1137 1165 9.377312 CTCTCCTCCTTTCTTTTCTTATTACTG 57.623 37.037 0.00 0.00 0.00 2.74
1138 1166 7.824779 TCTCCTCCTTTCTTTTCTTATTACTGC 59.175 37.037 0.00 0.00 0.00 4.40
1139 1167 7.690256 TCCTCCTTTCTTTTCTTATTACTGCT 58.310 34.615 0.00 0.00 0.00 4.24
1179 1207 4.096984 CAGGTTGCTTCTTGTTCTTGTTCT 59.903 41.667 0.00 0.00 0.00 3.01
1180 1208 4.706962 AGGTTGCTTCTTGTTCTTGTTCTT 59.293 37.500 0.00 0.00 0.00 2.52
1181 1209 4.800471 GGTTGCTTCTTGTTCTTGTTCTTG 59.200 41.667 0.00 0.00 0.00 3.02
1182 1210 5.402398 GTTGCTTCTTGTTCTTGTTCTTGT 58.598 37.500 0.00 0.00 0.00 3.16
1183 1211 5.643379 TGCTTCTTGTTCTTGTTCTTGTT 57.357 34.783 0.00 0.00 0.00 2.83
1184 1212 5.640732 TGCTTCTTGTTCTTGTTCTTGTTC 58.359 37.500 0.00 0.00 0.00 3.18
1226 1254 0.803380 CTGCTTGCGCCTTTTATGCC 60.803 55.000 4.18 0.00 34.43 4.40
1248 1282 5.723295 CCGGATTGGTTGATTGATTCTTTT 58.277 37.500 0.00 0.00 0.00 2.27
1312 1346 4.526970 TGGTTCTTGATCTAGATTTGGGC 58.473 43.478 6.70 0.00 0.00 5.36
1315 1349 2.104792 TCTTGATCTAGATTTGGGCCGG 59.895 50.000 6.70 0.00 0.00 6.13
1316 1350 0.108585 TGATCTAGATTTGGGCCGGC 59.891 55.000 21.18 21.18 0.00 6.13
1427 1461 1.801242 TCCTCAGCGAAATGGGGATA 58.199 50.000 0.54 0.00 45.23 2.59
1434 1468 5.200483 TCAGCGAAATGGGGATATTTTCTT 58.800 37.500 0.00 0.00 30.78 2.52
1442 1476 8.712228 AAATGGGGATATTTTCTTCTGATACC 57.288 34.615 0.00 0.00 0.00 2.73
1583 1622 2.277084 GGCTCGTGATTTCGTACCAAT 58.723 47.619 0.00 0.00 0.00 3.16
1595 1634 2.159382 CGTACCAATTTGGCTCCACTT 58.841 47.619 15.49 0.00 42.67 3.16
1857 1897 4.979335 AGGAGAGGAAGAAAGAAACCTTG 58.021 43.478 0.00 0.00 32.53 3.61
1908 1948 2.375174 TGATGGGGTTACTCTGCTTTGT 59.625 45.455 0.00 0.00 0.00 2.83
1934 1974 0.842635 AGATTAGCTTGGAGCCCTGG 59.157 55.000 0.00 0.00 43.77 4.45
2202 2243 8.760980 TTCTTGGACTTGGAAGAAAGAATTTA 57.239 30.769 0.00 0.00 39.27 1.40
2397 2439 2.682856 TGTTTGTTCTGTCTGCTTGGTC 59.317 45.455 0.00 0.00 0.00 4.02
2427 2469 4.749976 TGGTGCCAAGTTGTAAAAGTTTC 58.250 39.130 1.45 0.00 0.00 2.78
2436 2478 8.032451 CCAAGTTGTAAAAGTTTCTTCTTTGGA 58.968 33.333 1.45 0.00 37.65 3.53
2568 2610 5.588648 TGTTTCAAAGAAGGTAACAGTCTGG 59.411 40.000 4.53 0.00 41.41 3.86
2666 2716 7.654568 TCATTTCACCATCATTTCTATGCATC 58.345 34.615 0.19 0.00 0.00 3.91
2722 2772 6.492254 CATGTATGTCATGTTTGATGAGTGG 58.508 40.000 0.00 0.00 46.18 4.00
2726 2776 5.437289 TGTCATGTTTGATGAGTGGTTTC 57.563 39.130 0.00 0.00 33.56 2.78
2739 2791 4.640201 TGAGTGGTTTCTTTTCTTCAGTGG 59.360 41.667 0.00 0.00 0.00 4.00
2779 2831 6.934048 AGAAATAGGCTTTAATGCACTCTC 57.066 37.500 14.56 5.07 34.04 3.20
2815 2867 5.048083 CCAGTAGTCTCCTATTCATCAGAGC 60.048 48.000 0.00 0.00 0.00 4.09
3021 3073 4.280929 GTGGGAACAAAGCTTGGTAAGAAT 59.719 41.667 6.98 0.00 46.06 2.40
3068 3122 7.692088 CAGAAATCTGATATCCTGTTGTGTTC 58.308 38.462 4.37 0.00 46.59 3.18
3325 3386 1.944024 CGTGCTTGTGTTCTTTACCCA 59.056 47.619 0.00 0.00 0.00 4.51
3537 3600 1.821332 CCCTTGAAGGAGGCGATGC 60.821 63.158 13.97 0.00 37.67 3.91
4263 4330 9.944376 GTTATGGTATCTATTCCTGCATTTAGA 57.056 33.333 0.00 0.00 0.00 2.10
4304 4371 6.820470 TGAATTGTGATTCGGTTTTGTTTC 57.180 33.333 0.00 0.00 43.75 2.78
4305 4372 5.457148 TGAATTGTGATTCGGTTTTGTTTCG 59.543 36.000 0.00 0.00 43.75 3.46
4306 4373 2.722071 TGTGATTCGGTTTTGTTTCGC 58.278 42.857 0.00 0.00 0.00 4.70
4346 4417 1.601419 AATGGAGCATGTGCAGTGCC 61.601 55.000 13.72 4.57 43.50 5.01
4406 4477 4.588528 GTGGGTTGTGGCATATAATTGGAT 59.411 41.667 0.00 0.00 0.00 3.41
4453 4524 6.863126 GCAGGGTATGTTTTGTATGATATTGC 59.137 38.462 0.00 0.00 0.00 3.56
4455 4526 9.283768 CAGGGTATGTTTTGTATGATATTGCTA 57.716 33.333 0.00 0.00 0.00 3.49
4461 4532 7.432869 TGTTTTGTATGATATTGCTATTGGCC 58.567 34.615 0.00 0.00 40.92 5.36
4462 4533 7.287466 TGTTTTGTATGATATTGCTATTGGCCT 59.713 33.333 3.32 0.00 40.92 5.19
4463 4534 8.792633 GTTTTGTATGATATTGCTATTGGCCTA 58.207 33.333 3.32 0.00 40.92 3.93
4635 4708 0.534412 CTTGTTTGTTGGCCACCACA 59.466 50.000 3.88 5.26 30.78 4.17
4671 4744 2.169789 CGCCGCCTGTCTGAATCAG 61.170 63.158 3.38 3.38 0.00 2.90
4723 4796 2.476619 CTGACGCTGTAACTCAAACAGG 59.523 50.000 5.47 0.00 43.71 4.00
4745 4818 5.357032 AGGGTTATTGCTTTAGAACGATTGG 59.643 40.000 0.00 0.00 0.00 3.16
4759 4832 2.094752 ACGATTGGTTATTTGTGGCTGC 60.095 45.455 0.00 0.00 0.00 5.25
4760 4833 2.094803 CGATTGGTTATTTGTGGCTGCA 60.095 45.455 0.50 0.00 0.00 4.41
4762 4835 4.506758 GATTGGTTATTTGTGGCTGCATT 58.493 39.130 0.50 0.00 0.00 3.56
4766 4839 3.928375 GGTTATTTGTGGCTGCATTTCAG 59.072 43.478 0.50 0.00 45.62 3.02
4775 4848 1.881973 GCTGCATTTCAGTCAGTTGGA 59.118 47.619 0.00 0.00 44.66 3.53
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1116 1140 8.787852 ACAAGCAGTAATAAGAAAAGAAAGGAG 58.212 33.333 0.00 0.00 0.00 3.69
1132 1160 4.217550 GCATTACCCAAGAACAAGCAGTAA 59.782 41.667 0.00 0.00 0.00 2.24
1134 1162 2.558359 GCATTACCCAAGAACAAGCAGT 59.442 45.455 0.00 0.00 0.00 4.40
1137 1165 1.892474 TGGCATTACCCAAGAACAAGC 59.108 47.619 0.00 0.00 37.83 4.01
1138 1166 2.493278 CCTGGCATTACCCAAGAACAAG 59.507 50.000 0.00 0.00 37.83 3.16
1139 1167 2.158385 ACCTGGCATTACCCAAGAACAA 60.158 45.455 0.00 0.00 37.83 2.83
1179 1207 1.689813 TGTCCGCCTCTACAAGAACAA 59.310 47.619 0.00 0.00 0.00 2.83
1180 1208 1.334160 TGTCCGCCTCTACAAGAACA 58.666 50.000 0.00 0.00 0.00 3.18
1181 1209 2.450609 TTGTCCGCCTCTACAAGAAC 57.549 50.000 0.00 0.00 32.11 3.01
1182 1210 3.244422 ACATTTGTCCGCCTCTACAAGAA 60.244 43.478 0.00 0.00 36.96 2.52
1183 1211 2.301870 ACATTTGTCCGCCTCTACAAGA 59.698 45.455 0.00 0.00 36.96 3.02
1184 1212 2.699954 ACATTTGTCCGCCTCTACAAG 58.300 47.619 0.00 0.00 36.96 3.16
1226 1254 6.646240 ACAAAAAGAATCAATCAACCAATCCG 59.354 34.615 0.00 0.00 0.00 4.18
1248 1282 5.067273 CCCTAATTAGGAACACACACACAA 58.933 41.667 29.75 0.00 46.63 3.33
1284 1318 3.034635 TCTAGATCAAGAACCAGCCTCC 58.965 50.000 0.00 0.00 0.00 4.30
1315 1349 1.012889 CGAATCGAGCGCAGAAAGC 60.013 57.895 11.47 1.89 40.87 3.51
1342 1376 0.407528 TGTGCCCAAATTAGGAGCCA 59.592 50.000 0.00 0.00 0.00 4.75
1427 1461 6.502138 TGATTTGGGGGTATCAGAAGAAAAT 58.498 36.000 0.00 0.00 0.00 1.82
1434 1468 1.494721 GGCTGATTTGGGGGTATCAGA 59.505 52.381 14.42 0.00 46.86 3.27
1442 1476 1.288188 AATTTGGGGCTGATTTGGGG 58.712 50.000 0.00 0.00 0.00 4.96
1550 1587 2.203029 GAGCCGACGAAATCCCCC 60.203 66.667 0.00 0.00 0.00 5.40
1551 1588 2.585247 CGAGCCGACGAAATCCCC 60.585 66.667 0.00 0.00 35.09 4.81
1583 1622 4.500265 GCTGGAAGTGGAGCCAAA 57.500 55.556 0.00 0.00 35.30 3.28
1595 1634 4.738998 CCCACATTGCCGGCTGGA 62.739 66.667 28.91 15.88 37.49 3.86
1842 1882 5.823045 TCTTGTCTCCAAGGTTTCTTTCTTC 59.177 40.000 2.88 0.00 46.65 2.87
1857 1897 6.049790 GGTGGTATTATCTTGTCTTGTCTCC 58.950 44.000 0.00 0.00 0.00 3.71
1908 1948 2.700897 GCTCCAAGCTAATCTACCCTCA 59.299 50.000 0.00 0.00 38.45 3.86
1954 1994 0.534412 CTACTGCTGCTGCTACCACT 59.466 55.000 17.00 0.00 40.48 4.00
2183 2224 6.089476 GCAGCTAAATTCTTTCTTCCAAGTC 58.911 40.000 0.00 0.00 0.00 3.01
2202 2243 2.787994 AGATAAACAGCAAGTGCAGCT 58.212 42.857 6.00 0.00 45.16 4.24
2258 2299 2.418628 ACTGAAGTTGTCAAACACCGTG 59.581 45.455 0.00 0.00 38.88 4.94
2354 2395 5.241506 ACATGTAACCATCACAAACCAAGAG 59.758 40.000 0.00 0.00 0.00 2.85
2397 2439 3.333804 ACAACTTGGCACCAAAAACAAG 58.666 40.909 3.29 0.00 44.32 3.16
2427 2469 2.689983 ACCTGTTGCAGTTCCAAAGAAG 59.310 45.455 0.00 0.00 30.91 2.85
2436 2478 0.109342 CCTCCTGACCTGTTGCAGTT 59.891 55.000 0.00 0.00 0.00 3.16
2610 2652 3.716872 AGAGAACTTCTGGAACCAGGAAA 59.283 43.478 18.99 7.69 43.75 3.13
2722 2772 9.764363 AATAATTTCCCACTGAAGAAAAGAAAC 57.236 29.630 0.00 0.00 35.72 2.78
2779 2831 5.800239 AGGAGACTACTGGAAAAACCATTCG 60.800 44.000 0.00 0.00 44.06 3.34
2815 2867 9.853177 AACAGAAATTAGGGGAAACTATATCAG 57.147 33.333 0.00 0.00 0.00 2.90
3021 3073 4.100035 TGAAAAACAATGTGGCCATGTACA 59.900 37.500 9.72 1.34 0.00 2.90
3054 3108 2.608506 CCGTCGTGAACACAACAGGATA 60.609 50.000 5.80 0.00 35.28 2.59
3068 3122 1.545614 CCAACGTCACTTCCGTCGTG 61.546 60.000 0.00 0.00 37.61 4.35
3500 3563 3.885901 AGGGAAAGAGCAAGAAAGACAAC 59.114 43.478 0.00 0.00 0.00 3.32
3537 3600 7.667043 TTGGCATCTAAAGTTAGTAACACAG 57.333 36.000 15.28 8.58 32.61 3.66
3937 4000 1.798626 GGTAACCTAGGGTGGGGTAG 58.201 60.000 10.48 0.00 35.34 3.18
4245 4308 7.684937 GCATCTTCTAAATGCAGGAATAGAT 57.315 36.000 3.35 0.00 46.93 1.98
4263 4330 6.183361 ACAATTCATAGGGTAGGATGCATCTT 60.183 38.462 25.28 20.86 0.00 2.40
4264 4331 5.311649 ACAATTCATAGGGTAGGATGCATCT 59.688 40.000 25.28 14.04 0.00 2.90
4265 4332 5.413833 CACAATTCATAGGGTAGGATGCATC 59.586 44.000 18.81 18.81 0.00 3.91
4276 4343 5.835113 AAACCGAATCACAATTCATAGGG 57.165 39.130 0.00 0.00 41.22 3.53
4305 4372 2.591715 AGCAATCATACGCCGGGC 60.592 61.111 9.54 9.54 0.00 6.13
4306 4373 2.253758 CCAGCAATCATACGCCGGG 61.254 63.158 2.18 0.00 0.00 5.73
4346 4417 4.074970 AGTATCAAAACAGGCAGGTCAAG 58.925 43.478 0.00 0.00 0.00 3.02
4453 4524 4.511527 CAGCAGATACCATAGGCCAATAG 58.488 47.826 5.01 0.00 0.00 1.73
4455 4526 2.553904 GCAGCAGATACCATAGGCCAAT 60.554 50.000 5.01 0.00 0.00 3.16
4460 4531 4.223700 TCCTATTGCAGCAGATACCATAGG 59.776 45.833 17.57 17.57 0.00 2.57
4461 4532 5.411831 TCCTATTGCAGCAGATACCATAG 57.588 43.478 0.00 0.00 0.00 2.23
4462 4533 7.681259 ATATCCTATTGCAGCAGATACCATA 57.319 36.000 4.61 0.00 0.00 2.74
4463 4534 4.923516 ATCCTATTGCAGCAGATACCAT 57.076 40.909 0.00 0.00 0.00 3.55
4554 4627 4.640201 ACAATGGCATGTGTATCCAAGTAC 59.360 41.667 0.00 0.00 33.04 2.73
4555 4628 4.639755 CACAATGGCATGTGTATCCAAGTA 59.360 41.667 16.78 0.00 44.46 2.24
4671 4744 0.322816 TGGCTGGCCATCTTCTGAAC 60.323 55.000 5.51 0.00 41.89 3.18
4723 4796 6.190954 ACCAATCGTTCTAAAGCAATAACC 57.809 37.500 0.00 0.00 0.00 2.85
4724 4797 9.783256 AATAACCAATCGTTCTAAAGCAATAAC 57.217 29.630 0.00 0.00 35.79 1.89
4759 4832 5.005740 TCCTTGATCCAACTGACTGAAATG 58.994 41.667 0.00 0.00 0.00 2.32
4760 4833 5.246981 TCCTTGATCCAACTGACTGAAAT 57.753 39.130 0.00 0.00 0.00 2.17
4762 4835 3.008375 CCTCCTTGATCCAACTGACTGAA 59.992 47.826 0.00 0.00 0.00 3.02
4766 4839 2.093235 CCTCCTCCTTGATCCAACTGAC 60.093 54.545 0.00 0.00 0.00 3.51
4775 4848 0.618968 AGTTCGCCCTCCTCCTTGAT 60.619 55.000 0.00 0.00 0.00 2.57


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

AutoCloner maintained by Alex Coulton.