Multiple sequence alignment - TraesCS6B01G402800

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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 TraesCS6B01G402800 chr6B 100.000 2550 0 0 1 2550 678790158 678787609 0 4710
1 TraesCS6B01G402800 chr2D 96.157 2550 95 1 1 2550 591984631 591987177 0 4163
2 TraesCS6B01G402800 chr6D 96.118 2550 96 1 1 2550 389245800 389243254 0 4157
3 TraesCS6B01G402800 chr3A 96.118 2550 96 1 1 2550 66005111 66002565 0 4157
4 TraesCS6B01G402800 chr3A 95.216 2550 117 2 1 2550 695640409 695642953 0 4028
5 TraesCS6B01G402800 chr3D 96.078 2550 96 2 1 2550 589263504 589260959 0 4152
6 TraesCS6B01G402800 chr5D 96.039 2550 98 1 1 2550 503245294 503247840 0 4146
7 TraesCS6B01G402800 chr5D 96.000 2550 99 1 1 2550 503264754 503262208 0 4141
8 TraesCS6B01G402800 chr2A 96.039 2550 98 1 1 2550 726906433 726903887 0 4146
9 TraesCS6B01G402800 chr7B 95.765 2550 105 1 1 2550 663099403 663096857 0 4108


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 TraesCS6B01G402800 chr6B 678787609 678790158 2549 True 4710 4710 100.000 1 2550 1 chr6B.!!$R1 2549
1 TraesCS6B01G402800 chr2D 591984631 591987177 2546 False 4163 4163 96.157 1 2550 1 chr2D.!!$F1 2549
2 TraesCS6B01G402800 chr6D 389243254 389245800 2546 True 4157 4157 96.118 1 2550 1 chr6D.!!$R1 2549
3 TraesCS6B01G402800 chr3A 66002565 66005111 2546 True 4157 4157 96.118 1 2550 1 chr3A.!!$R1 2549
4 TraesCS6B01G402800 chr3A 695640409 695642953 2544 False 4028 4028 95.216 1 2550 1 chr3A.!!$F1 2549
5 TraesCS6B01G402800 chr3D 589260959 589263504 2545 True 4152 4152 96.078 1 2550 1 chr3D.!!$R1 2549
6 TraesCS6B01G402800 chr5D 503245294 503247840 2546 False 4146 4146 96.039 1 2550 1 chr5D.!!$F1 2549
7 TraesCS6B01G402800 chr5D 503262208 503264754 2546 True 4141 4141 96.000 1 2550 1 chr5D.!!$R1 2549
8 TraesCS6B01G402800 chr2A 726903887 726906433 2546 True 4146 4146 96.039 1 2550 1 chr2A.!!$R1 2549
9 TraesCS6B01G402800 chr7B 663096857 663099403 2546 True 4108 4108 95.765 1 2550 1 chr7B.!!$R1 2549

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
325 326 0.17576 GCATACTCCACTTGGCTCGA 59.824 55.0 0.0 0.0 34.44 4.04 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2265 2267 0.174845 CCTCGATTTGGTACCGCTCA 59.825 55.0 7.57 0.0 0.0 4.26 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
49 50 2.528564 CCTTCCTTTTTCTGCCCATCA 58.471 47.619 0.00 0.00 0.00 3.07
126 127 0.388134 GAAGAGCGCAGTACAACGGA 60.388 55.000 11.47 0.00 0.00 4.69
212 213 1.202099 TTGGTTGGATCGTAGGGGCA 61.202 55.000 0.00 0.00 0.00 5.36
283 284 2.301346 CTGCGCCAGGGAAAAGAATAT 58.699 47.619 4.18 0.00 0.00 1.28
293 294 7.448469 GCCAGGGAAAAGAATATAAGAAGCATA 59.552 37.037 0.00 0.00 0.00 3.14
325 326 0.175760 GCATACTCCACTTGGCTCGA 59.824 55.000 0.00 0.00 34.44 4.04
330 331 3.003173 CCACTTGGCTCGAGGGGA 61.003 66.667 15.58 0.00 40.84 4.81
390 391 1.091537 CGTTGCGATTATGGGTTGGT 58.908 50.000 0.00 0.00 0.00 3.67
403 404 3.142951 TGGGTTGGTTGTCTAATTGTCG 58.857 45.455 0.00 0.00 0.00 4.35
485 486 1.168714 GAGGACTGAAACATGCCACC 58.831 55.000 0.00 0.00 0.00 4.61
503 504 4.098196 GCCACCGAAAGACTCTACTAAGAT 59.902 45.833 0.00 0.00 0.00 2.40
544 545 2.803215 AGGTAGAGGAGGTAGGATGGA 58.197 52.381 0.00 0.00 0.00 3.41
656 657 0.899717 GGATCAAGTTGGCCCTTGCA 60.900 55.000 14.94 6.61 41.29 4.08
657 658 0.529378 GATCAAGTTGGCCCTTGCAG 59.471 55.000 14.94 0.00 41.29 4.41
810 811 1.740296 GGTTCACGGACCGACCATG 60.740 63.158 23.38 8.53 38.90 3.66
817 818 1.382146 GGACCGACCATGGACCCTA 60.382 63.158 21.47 0.00 37.81 3.53
871 872 1.765074 GGTTGGGCAGTAAGGGTCA 59.235 57.895 0.00 0.00 0.00 4.02
927 928 5.995565 TTCTTAAGATCAAAGAGTCGGGA 57.004 39.130 5.89 0.00 34.59 5.14
1003 1004 6.180472 GGAACCACAAGAATCCTTAGAATGA 58.820 40.000 0.00 0.00 0.00 2.57
1121 1122 4.100498 GGGGAGTTATTGTCTATCGTTGGA 59.900 45.833 0.00 0.00 0.00 3.53
1212 1213 1.382557 TCCGCTTATCTCCAGCCCA 60.383 57.895 0.00 0.00 33.29 5.36
1259 1260 3.551863 CGATAGCACCAAGTTTTGCCAAA 60.552 43.478 3.09 0.00 39.75 3.28
1299 1300 3.913548 TTTCACATTCATGGACGTTGG 57.086 42.857 0.00 0.00 0.00 3.77
1397 1398 1.400530 GCGGTGGATACCTAGGCACT 61.401 60.000 9.30 0.00 45.22 4.40
1461 1462 6.263168 CGGGGAGTTGAAAATAAGCATAGATT 59.737 38.462 0.00 0.00 0.00 2.40
1575 1577 4.442052 GCCAGAGGAAAAGAAAGCAAAAGT 60.442 41.667 0.00 0.00 0.00 2.66
1592 1594 2.048444 AGTGATTCCCGTAGTAGCGA 57.952 50.000 0.00 0.00 0.00 4.93
1671 1673 0.670546 GTTGTGCTGCTAGGCGAAGA 60.671 55.000 0.00 0.00 34.52 2.87
1681 1683 1.546476 CTAGGCGAAGAGGTTGAGTGT 59.454 52.381 0.00 0.00 0.00 3.55
1694 1696 2.426024 GTTGAGTGTCGCACCCTAGATA 59.574 50.000 6.39 0.00 34.49 1.98
1712 1714 4.547671 AGATAGCTAAAGTCCAGTAGCCA 58.452 43.478 0.00 0.00 43.13 4.75
1860 1862 1.611977 GAAAGGTGAAAAGAACCCCCG 59.388 52.381 0.00 0.00 38.57 5.73
1888 1890 6.657541 GGGTAGTGAAATAGAATGTGAAACCA 59.342 38.462 0.00 0.00 34.36 3.67
1935 1937 1.996191 GAAAGTGATCTCTGACCACGC 59.004 52.381 0.00 0.00 36.06 5.34
1957 1959 1.611673 CCTGTTGAAGAATGAGCCGGT 60.612 52.381 1.90 0.00 0.00 5.28
2015 2017 2.488355 CGGAGCCGTAGCGAAAGA 59.512 61.111 0.00 0.00 46.67 2.52
2030 2032 5.202004 AGCGAAAGAGAGTCTTAATAGGGA 58.798 41.667 0.00 0.00 35.27 4.20
2072 2074 1.000163 CGAACCTGGGTGATCTATCCG 60.000 57.143 0.00 0.00 0.00 4.18
2077 2079 2.311463 CTGGGTGATCTATCCGTGACT 58.689 52.381 0.00 0.00 0.00 3.41
2098 2100 6.011122 ACTAGGATGAAGCTTGGATGAAAT 57.989 37.500 2.10 0.00 0.00 2.17
2133 2135 3.120991 CGAACCGACTGATGTTGAAGAAC 60.121 47.826 0.00 0.00 0.00 3.01
2137 2139 3.393800 CGACTGATGTTGAAGAACCAGT 58.606 45.455 0.00 0.00 37.55 4.00
2185 2187 1.178276 CACTCGAACCCAGAGCTAGT 58.822 55.000 0.00 0.00 39.23 2.57
2197 2199 1.203313 AGAGCTAGTTGGTTCTCCCCA 60.203 52.381 0.00 0.00 0.00 4.96
2233 2235 3.308053 CGCAATAGTTGACTGGACATCTG 59.692 47.826 0.00 0.00 0.00 2.90
2234 2236 4.256920 GCAATAGTTGACTGGACATCTGT 58.743 43.478 0.00 0.00 0.00 3.41
2246 2248 1.732259 GACATCTGTGGGTAAAGCACG 59.268 52.381 0.00 0.00 0.00 5.34
2294 2296 1.470098 CCAAATCGAGGCAAACTCTGG 59.530 52.381 0.00 0.00 44.33 3.86
2330 2332 5.799827 CCCAAAAATAACAAGGGTCAAGA 57.200 39.130 0.00 0.00 34.75 3.02
2334 2336 4.965119 AAATAACAAGGGTCAAGATCGC 57.035 40.909 0.00 0.00 0.00 4.58
2354 2356 1.680522 CCAGTGAGACGATGGGGGAG 61.681 65.000 0.00 0.00 0.00 4.30
2402 2404 0.835941 CAGATCACCAGCTAAGGCCT 59.164 55.000 0.00 0.00 39.73 5.19
2448 2450 1.152756 GTGGGGGTGCAAAGACAGT 60.153 57.895 0.00 0.00 0.00 3.55
2472 2474 0.674895 AGGTTTGCCTAGAAGCAGCG 60.675 55.000 0.00 0.00 44.90 5.18
2500 2502 6.480320 CCTTTAAAGAGTGCGTAATAGCTCAT 59.520 38.462 16.98 0.00 38.13 2.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
12 13 1.476477 AGGCGTTAAGAGACCCTCTC 58.524 55.000 0.00 0.00 40.28 3.20
13 14 1.826096 GAAGGCGTTAAGAGACCCTCT 59.174 52.381 0.00 0.00 43.37 3.69
49 50 4.336280 GCAAGTCCTTGGGAAATAACTCT 58.664 43.478 8.97 0.00 40.74 3.24
126 127 1.350193 CGAACGCAGCATACAACTCT 58.650 50.000 0.00 0.00 0.00 3.24
212 213 2.936498 CTCGCCCGTGAAGTAAATCATT 59.064 45.455 0.00 0.00 0.00 2.57
283 284 7.049754 TGCATGAAAGAGTCATATGCTTCTTA 58.950 34.615 16.81 7.52 45.69 2.10
325 326 3.669949 ACCAACTGAGCTATATTCCCCT 58.330 45.455 0.00 0.00 0.00 4.79
352 353 1.611673 CGACCCAATTGCAAGAGAGGT 60.612 52.381 4.94 9.07 0.00 3.85
355 356 1.879380 CAACGACCCAATTGCAAGAGA 59.121 47.619 4.94 0.00 0.00 3.10
390 391 1.274167 ACCGCCTCGACAATTAGACAA 59.726 47.619 0.00 0.00 0.00 3.18
403 404 6.026947 ACAAGATACTATCATTACCGCCTC 57.973 41.667 0.00 0.00 0.00 4.70
435 436 7.606456 CCATTACTTAGAAAAAGTGAGCCACTA 59.394 37.037 8.07 0.00 44.62 2.74
503 504 7.189079 ACCTTTTTGACAACCCATCTTTTTA 57.811 32.000 0.00 0.00 0.00 1.52
544 545 5.519808 TCCATACTAGATCTGACCAACTGT 58.480 41.667 5.18 0.00 0.00 3.55
570 571 4.893524 TGACTCCAACTATCGTCCATGTAT 59.106 41.667 0.00 0.00 0.00 2.29
593 594 2.042435 AAGCCTAGGAGAGCCGCT 60.042 61.111 14.75 0.00 39.96 5.52
656 657 5.843421 AGGGAGATAGTGCATCAAGTTATCT 59.157 40.000 0.00 0.00 35.96 1.98
657 658 6.107901 AGGGAGATAGTGCATCAAGTTATC 57.892 41.667 0.00 0.00 35.96 1.75
762 763 2.372074 GGGCGTCCTTGGGGTGATA 61.372 63.158 0.00 0.00 0.00 2.15
810 811 5.589050 GTGTTCCACTTATTGAATAGGGTCC 59.411 44.000 0.00 0.00 0.00 4.46
817 818 7.606456 ACGACTAATGTGTTCCACTTATTGAAT 59.394 33.333 0.00 0.00 35.11 2.57
840 841 3.744719 CAACCGGAGAGCGGACGA 61.745 66.667 9.46 0.00 0.00 4.20
871 872 1.270907 ACGAGTGATTGCCCTTCTCT 58.729 50.000 0.00 0.00 0.00 3.10
927 928 0.995803 GGAGCTCTCCCCTTTTTCCT 59.004 55.000 14.64 0.00 43.94 3.36
1003 1004 3.515602 AAAGGTGCTGAGTTGGAATCT 57.484 42.857 0.00 0.00 0.00 2.40
1098 1099 4.100498 TCCAACGATAGACAATAACTCCCC 59.900 45.833 0.00 0.00 41.38 4.81
1099 1100 5.048507 GTCCAACGATAGACAATAACTCCC 58.951 45.833 0.00 0.00 41.38 4.30
1100 1101 5.903810 AGTCCAACGATAGACAATAACTCC 58.096 41.667 0.00 0.00 41.38 3.85
1121 1122 2.295885 CGACGGGTTCTACCATAGAGT 58.704 52.381 0.00 0.00 41.02 3.24
1175 1176 0.969149 ACTCGAACTGCTGACATCCA 59.031 50.000 0.00 0.00 0.00 3.41
1186 1187 1.677052 GGAGATAAGCGGACTCGAACT 59.323 52.381 0.00 0.00 39.00 3.01
1212 1213 7.484975 GCTATCATAGTATCCGCTAAGTTCAT 58.515 38.462 0.00 0.00 0.00 2.57
1249 1250 2.472488 CGAACTGCTGATTTGGCAAAAC 59.528 45.455 17.70 14.99 39.30 2.43
1259 1260 6.423302 GTGAAATCATAGATCGAACTGCTGAT 59.577 38.462 5.31 10.38 0.00 2.90
1299 1300 6.706716 GGTGCTACTAAATGGAAGGATCTTAC 59.293 42.308 0.00 0.00 0.00 2.34
1397 1398 2.046864 CGCCCTTCCTCGTCTCTGA 61.047 63.158 0.00 0.00 0.00 3.27
1424 1425 2.493278 CAACTCCCCGAAGCATTTCATT 59.507 45.455 0.00 0.00 32.67 2.57
1426 1427 1.073125 TCAACTCCCCGAAGCATTTCA 59.927 47.619 0.00 0.00 32.67 2.69
1461 1462 3.380393 TGACCTATTTGGGAATCTCCGA 58.620 45.455 0.00 0.00 37.43 4.55
1575 1577 0.659427 CGTCGCTACTACGGGAATCA 59.341 55.000 0.00 0.00 36.71 2.57
1592 1594 1.448540 CTGCTCCCATTTCGCTCGT 60.449 57.895 0.00 0.00 0.00 4.18
1671 1673 2.140792 AGGGTGCGACACTCAACCT 61.141 57.895 11.54 1.94 46.29 3.50
1681 1683 3.563223 ACTTTAGCTATCTAGGGTGCGA 58.437 45.455 0.00 0.00 0.00 5.10
1694 1696 4.327680 CTTTTGGCTACTGGACTTTAGCT 58.672 43.478 0.00 0.00 40.57 3.32
1807 1809 0.389391 CTTCGCTATCGGTCACCCAT 59.611 55.000 0.00 0.00 36.13 4.00
1860 1862 5.741011 TCACATTCTATTTCACTACCCACC 58.259 41.667 0.00 0.00 0.00 4.61
1935 1937 0.449388 GGCTCATTCTTCAACAGGCG 59.551 55.000 0.00 0.00 0.00 5.52
1957 1959 0.608130 AAGCCACTGCGTATGAGTCA 59.392 50.000 0.00 0.00 44.33 3.41
1966 1968 1.586154 CCCTTAACCAAGCCACTGCG 61.586 60.000 0.00 0.00 44.33 5.18
2015 2017 7.069331 CAGTGACAATCTCCCTATTAAGACTCT 59.931 40.741 0.00 0.00 0.00 3.24
2030 2032 3.370953 GGGTCCATAAGCAGTGACAATCT 60.371 47.826 0.00 0.00 0.00 2.40
2072 2074 3.895232 TCCAAGCTTCATCCTAGTCAC 57.105 47.619 0.00 0.00 0.00 3.67
2077 2079 7.013655 GCTTAATTTCATCCAAGCTTCATCCTA 59.986 37.037 0.00 0.00 40.16 2.94
2098 2100 0.245539 CGGTTCGGACCTCTGCTTAA 59.754 55.000 12.11 0.00 44.20 1.85
2133 2135 5.454755 CCCCTAACCACAACTCATATACTGG 60.455 48.000 0.00 0.00 0.00 4.00
2137 2139 5.282129 TCACCCCTAACCACAACTCATATA 58.718 41.667 0.00 0.00 0.00 0.86
2216 2218 2.567169 CCCACAGATGTCCAGTCAACTA 59.433 50.000 0.00 0.00 0.00 2.24
2233 2235 0.236449 CGAAACCGTGCTTTACCCAC 59.764 55.000 0.00 0.00 0.00 4.61
2234 2236 0.885596 CCGAAACCGTGCTTTACCCA 60.886 55.000 0.00 0.00 0.00 4.51
2265 2267 0.174845 CCTCGATTTGGTACCGCTCA 59.825 55.000 7.57 0.00 0.00 4.26
2321 2323 1.613630 ACTGGGCGATCTTGACCCT 60.614 57.895 10.28 0.00 44.56 4.34
2330 2332 1.439228 CATCGTCTCACTGGGCGAT 59.561 57.895 0.00 0.00 43.63 4.58
2354 2356 1.535015 CCCTCTCGACGATGAAGCTTC 60.535 57.143 19.89 19.89 0.00 3.86
2402 2404 5.592104 TTATCACTGAGCGGTCATTTAGA 57.408 39.130 18.98 13.34 30.18 2.10
2448 2450 1.279271 GCTTCTAGGCAAACCTCCTGA 59.721 52.381 0.00 0.00 46.34 3.86
2472 2474 5.006455 GCTATTACGCACTCTTTAAAGGGTC 59.994 44.000 18.05 11.67 37.74 4.46
2510 2512 0.036732 TTCATCTTCAGCGCAAGGGT 59.963 50.000 11.47 0.00 38.28 4.34


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

AutoCloner maintained by Alex Coulton.