Multiple sequence alignment - TraesCS6D01G379600

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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 TraesCS6D01G379600 chr6D 100.000 4622 0 0 1 4622 461333945 461329324 0.000000e+00 8536
1 TraesCS6D01G379600 chr6A 95.484 4252 159 12 1 4222 607932069 607927821 0.000000e+00 6758
2 TraesCS6D01G379600 chr6A 94.901 353 12 5 4263 4613 607927823 607927475 8.740000e-152 547
3 TraesCS6D01G379600 chr6B 95.010 4289 156 20 1 4257 702816086 702811824 0.000000e+00 6682
4 TraesCS6D01G379600 chr6B 90.647 278 12 4 4347 4619 702811778 702811510 1.580000e-94 357


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 TraesCS6D01G379600 chr6D 461329324 461333945 4621 True 8536.0 8536 100.0000 1 4622 1 chr6D.!!$R1 4621
1 TraesCS6D01G379600 chr6A 607927475 607932069 4594 True 3652.5 6758 95.1925 1 4613 2 chr6A.!!$R1 4612
2 TraesCS6D01G379600 chr6B 702811510 702816086 4576 True 3519.5 6682 92.8285 1 4619 2 chr6B.!!$R1 4618

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
370 387 0.850100 TACCCCCATAAGGCCACATG 59.150 55.000 5.01 7.63 0.00 3.21 F
1103 1144 1.677633 TGGAGGAGCATGACGTCGA 60.678 57.895 11.62 0.26 0.00 4.20 F
2148 2189 0.517316 GGTGCATTCAGAACGGTGAC 59.483 55.000 0.00 0.00 0.00 3.67 F
2307 2348 0.679002 ACCAGCATGCACCATCTGTC 60.679 55.000 21.98 0.00 31.97 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1585 1626 0.463116 GTGAACGGGTTCGGCCATAT 60.463 55.000 2.24 0.0 42.28 1.78 R
2974 3015 0.603975 GGCATGCCTCCGATAAGGTC 60.604 60.000 29.98 0.0 41.99 3.85 R
3348 3389 1.569493 CACAAAGCTCGTGTTCGGG 59.431 57.895 7.85 0.0 40.98 5.14 R
4257 4312 1.069022 CACGAAAACTGGCATGGTCTG 60.069 52.381 0.00 0.0 0.00 3.51 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
144 145 1.798813 CGGGAAAACGAGTCTTCCAAG 59.201 52.381 10.15 0.75 42.56 3.61
193 210 1.471684 CAGAGTTTAGACGCCGGTACT 59.528 52.381 1.90 2.70 0.00 2.73
202 219 1.226030 ACGCCGGTACTGAAACAAGC 61.226 55.000 1.90 0.00 0.00 4.01
369 386 1.149101 CTACCCCCATAAGGCCACAT 58.851 55.000 5.01 0.00 0.00 3.21
370 387 0.850100 TACCCCCATAAGGCCACATG 59.150 55.000 5.01 7.63 0.00 3.21
450 467 2.598565 TCATCCTGTCCTAATCGGGAG 58.401 52.381 0.00 0.00 42.63 4.30
873 912 2.040009 AACCCATATCGACCCAGGCG 62.040 60.000 0.00 0.00 0.00 5.52
987 1028 4.457496 CCATGTGCTCCGGCGACT 62.457 66.667 9.30 0.00 42.25 4.18
1097 1138 3.083349 CCGGGTGGAGGAGCATGA 61.083 66.667 0.00 0.00 37.49 3.07
1100 1141 2.660064 GGGTGGAGGAGCATGACGT 61.660 63.158 0.00 0.00 0.00 4.34
1103 1144 1.677633 TGGAGGAGCATGACGTCGA 60.678 57.895 11.62 0.26 0.00 4.20
1527 1568 2.357760 TTGCTCACCGGTTACGCC 60.358 61.111 2.97 0.00 39.22 5.68
1532 1573 4.770874 CACCGGTTACGCCCAGGG 62.771 72.222 2.97 0.00 39.22 4.45
1704 1745 2.125512 GGATGCCGCTCGACAGTT 60.126 61.111 0.00 0.00 0.00 3.16
1713 1754 0.928229 GCTCGACAGTTTTCGTGTGT 59.072 50.000 0.00 0.00 40.07 3.72
1836 1877 0.823356 TGGCAGGCCTTCTGTTGAAC 60.823 55.000 0.00 0.00 45.08 3.18
1858 1899 3.721706 GTGAGGTGGAGGCCCTGG 61.722 72.222 0.00 0.00 30.60 4.45
1948 1989 3.004734 GCTATGTGCAAACCTCAAACAGT 59.995 43.478 0.00 0.00 42.31 3.55
2080 2121 7.123098 TGGATGATGCTTTCAACATATTCTTGT 59.877 33.333 0.00 0.00 36.09 3.16
2148 2189 0.517316 GGTGCATTCAGAACGGTGAC 59.483 55.000 0.00 0.00 0.00 3.67
2307 2348 0.679002 ACCAGCATGCACCATCTGTC 60.679 55.000 21.98 0.00 31.97 3.51
2547 2588 4.840005 GCTAGTCCCACCGCTGGC 62.840 72.222 0.00 0.00 36.00 4.85
2805 2846 2.797278 GGGCGTCGAGATGGATGGT 61.797 63.158 0.00 0.00 0.00 3.55
2974 3015 3.007182 AGGCAAGTTGGATGAAACAATGG 59.993 43.478 4.75 0.00 32.21 3.16
3270 3311 4.020128 GTCCATTCCTTTATAGCCTCCGAT 60.020 45.833 0.00 0.00 0.00 4.18
3453 3494 1.335142 GCCTTCGGTCTGATAGCTACG 60.335 57.143 0.00 0.00 0.00 3.51
3736 3780 2.107378 TGTGTTGTCTGAAGCCCCAATA 59.893 45.455 0.00 0.00 0.00 1.90
3754 3798 7.106239 CCCCAATATCAGCTATACAAAGGTAG 58.894 42.308 0.00 0.00 31.88 3.18
3879 3929 2.164624 GAGCGTGGATCTTACACTGACT 59.835 50.000 0.00 0.00 36.71 3.41
3886 3936 6.456501 GTGGATCTTACACTGACTGTTTAGT 58.543 40.000 0.00 0.00 36.51 2.24
3892 3942 9.862371 ATCTTACACTGACTGTTTAGTTGATAG 57.138 33.333 0.00 0.00 37.25 2.08
3937 3988 6.192234 ACATACGTGTTTGTGTTTTTACCA 57.808 33.333 0.00 0.00 34.01 3.25
4092 4143 3.058160 GCGAGTGCAGCACCCAAT 61.058 61.111 22.41 2.91 42.15 3.16
4129 4181 3.200605 TGTTCATCCTGGTGCATATCTGT 59.799 43.478 0.00 0.00 0.00 3.41
4152 4204 2.672961 TTGGCTCTGTTATGGACTCG 57.327 50.000 0.00 0.00 0.00 4.18
4188 4243 7.560262 GGCCTGGTAAGTAAAGAAATCCTATTT 59.440 37.037 0.00 0.00 0.00 1.40
4189 4244 8.967918 GCCTGGTAAGTAAAGAAATCCTATTTT 58.032 33.333 0.00 0.00 0.00 1.82
4230 4285 9.612066 TTCAACATGAGTATGCATATCAACTTA 57.388 29.630 10.16 1.87 37.85 2.24
4257 4312 5.295045 CCATTCTTTATTTGCAAATCCCAGC 59.705 40.000 27.28 0.00 0.00 4.85
4258 4313 5.480642 TTCTTTATTTGCAAATCCCAGCA 57.519 34.783 27.28 10.08 39.32 4.41
4259 4314 5.075858 TCTTTATTTGCAAATCCCAGCAG 57.924 39.130 27.28 14.55 42.39 4.24
4261 4316 4.454728 TTATTTGCAAATCCCAGCAGAC 57.545 40.909 27.28 0.00 42.39 3.51
4263 4318 0.178967 TTGCAAATCCCAGCAGACCA 60.179 50.000 0.00 0.00 42.39 4.02
4321 4376 4.772100 ACCATTTGGGATTGGTTCTAACTG 59.228 41.667 0.96 0.00 43.73 3.16
4322 4377 4.381932 CCATTTGGGATTGGTTCTAACTGC 60.382 45.833 0.00 0.00 40.01 4.40
4332 4387 1.871039 GTTCTAACTGCCAGCGTTTGA 59.129 47.619 0.00 6.38 0.00 2.69
4349 4404 1.548081 TGACATGGCCTGTGGATTTG 58.452 50.000 11.89 0.00 38.54 2.32
4353 4409 3.505386 ACATGGCCTGTGGATTTGTTTA 58.495 40.909 3.32 0.00 36.48 2.01
4389 4445 2.660572 TGCCTACTTTTTGCCAGAACA 58.339 42.857 0.00 0.00 0.00 3.18
4420 4477 7.010091 GGTGACCAAACTTTTTGTGAAGTAATG 59.990 37.037 0.00 0.00 38.86 1.90
4432 4489 6.235231 TGTGAAGTAATGATCCCCTCTTAC 57.765 41.667 0.00 0.00 0.00 2.34
4565 4625 6.878923 TGATCATGAGTAACAAGGGTAAAGTG 59.121 38.462 0.09 0.00 0.00 3.16
4619 4680 5.198965 CCTTTTGTTCTCATCCATCCAGAT 58.801 41.667 0.00 0.00 0.00 2.90
4620 4681 6.069440 ACCTTTTGTTCTCATCCATCCAGATA 60.069 38.462 0.00 0.00 0.00 1.98
4621 4682 7.002879 CCTTTTGTTCTCATCCATCCAGATAT 58.997 38.462 0.00 0.00 0.00 1.63
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
34 35 3.561725 CAGTGTTTCTTCTCCTGGTTCAC 59.438 47.826 0.00 0.00 0.00 3.18
144 145 5.242434 TCTTGGTGGTTGTGTGATGTATAC 58.758 41.667 0.00 0.00 0.00 1.47
193 210 1.346395 TCCTTCTAGCGGCTTGTTTCA 59.654 47.619 8.26 0.00 0.00 2.69
202 219 0.872021 GTGTGCGATCCTTCTAGCGG 60.872 60.000 0.00 0.00 0.00 5.52
369 386 0.874390 GCTTCAATGCTTCACGGTCA 59.126 50.000 0.00 0.00 0.00 4.02
370 387 0.169009 GGCTTCAATGCTTCACGGTC 59.831 55.000 0.00 0.00 0.00 4.79
450 467 7.689446 AGGTTTCCTCTGAATTTTAACTAGC 57.311 36.000 0.00 0.00 0.00 3.42
549 582 2.364186 TGGAGCTGGAGCCGATCA 60.364 61.111 0.00 0.00 43.38 2.92
850 889 0.622154 TGGGTCGATATGGGTTGGGT 60.622 55.000 0.00 0.00 0.00 4.51
877 916 1.005394 TCGGTTTGACTTCGGCTCC 60.005 57.895 0.00 0.00 0.00 4.70
907 947 2.363018 TGAGGAGAGTCGGGGCTG 60.363 66.667 0.00 0.00 0.00 4.85
975 1016 4.492160 CGCTTAGTCGCCGGAGCA 62.492 66.667 5.05 0.00 39.83 4.26
987 1028 1.067416 CGCCATGCTACCTCGCTTA 59.933 57.895 0.00 0.00 0.00 3.09
1084 1125 1.517257 CGACGTCATGCTCCTCCAC 60.517 63.158 17.16 0.00 0.00 4.02
1097 1138 3.687102 TGTTGGGGCGATCGACGT 61.687 61.111 21.57 0.00 44.60 4.34
1100 1141 4.090588 GGGTGTTGGGGCGATCGA 62.091 66.667 21.57 0.00 0.00 3.59
1129 1170 4.712425 ACTTCCGTCGAACGCCCG 62.712 66.667 0.00 0.00 40.91 6.13
1416 1457 4.429561 GTGTACACGTCGACGAGG 57.570 61.111 41.52 32.06 43.02 4.63
1427 1468 2.731721 CGCCGCACTTCGTGTACA 60.732 61.111 0.00 0.00 35.75 2.90
1455 1496 3.535629 CTCGAACACCAGCCTGGCA 62.536 63.158 22.65 0.00 42.67 4.92
1457 1498 2.046892 CCTCGAACACCAGCCTGG 60.047 66.667 9.83 9.83 45.02 4.45
1585 1626 0.463116 GTGAACGGGTTCGGCCATAT 60.463 55.000 2.24 0.00 42.28 1.78
1701 1742 4.710324 TCAGGGAATTACACACGAAAACT 58.290 39.130 0.00 0.00 0.00 2.66
1704 1745 4.900684 TCATCAGGGAATTACACACGAAA 58.099 39.130 0.00 0.00 0.00 3.46
1713 1754 4.814234 GCGTACATGTTCATCAGGGAATTA 59.186 41.667 2.30 0.00 31.56 1.40
1746 1787 1.986882 CCTTGGCTTCTTCAACCAGT 58.013 50.000 0.00 0.00 34.28 4.00
1836 1877 4.394712 GCCTCCACCTCACACCCG 62.395 72.222 0.00 0.00 0.00 5.28
2043 2084 1.815421 ATCATCCAGTTCGCCGCAC 60.815 57.895 0.00 0.00 0.00 5.34
2080 2121 1.827344 ACTCTGCGATCCTGACATCAA 59.173 47.619 0.00 0.00 0.00 2.57
2086 2127 0.960861 ACGACACTCTGCGATCCTGA 60.961 55.000 0.00 0.00 0.00 3.86
2148 2189 1.093159 GTGAGGCAGCAAGAGGAATG 58.907 55.000 0.00 0.00 0.00 2.67
2547 2588 1.079127 CTGCCTACCCTGGTCAACG 60.079 63.158 0.00 0.00 0.00 4.10
2974 3015 0.603975 GGCATGCCTCCGATAAGGTC 60.604 60.000 29.98 0.00 41.99 3.85
3270 3311 3.429043 GGACAGACGGTGCGATTTA 57.571 52.632 0.00 0.00 0.00 1.40
3348 3389 1.569493 CACAAAGCTCGTGTTCGGG 59.431 57.895 7.85 0.00 40.98 5.14
3382 3423 1.743958 CATGGCTTCCTTCTGCTCTTG 59.256 52.381 0.00 0.00 0.00 3.02
3736 3780 6.739331 AGCTTCTACCTTTGTATAGCTGAT 57.261 37.500 0.00 0.00 40.49 2.90
3754 3798 5.524281 GCAAGAACCACTACCTATAAGCTTC 59.476 44.000 0.00 0.00 0.00 3.86
3879 3929 9.781834 CTTGTTGTGTTTTCTATCAACTAAACA 57.218 29.630 0.00 0.00 40.20 2.83
3886 3936 6.321181 AGCTTCCTTGTTGTGTTTTCTATCAA 59.679 34.615 0.00 0.00 0.00 2.57
3892 3942 6.096695 TGTTTAGCTTCCTTGTTGTGTTTTC 58.903 36.000 0.00 0.00 0.00 2.29
3937 3988 2.907458 AGGTTTAGATGCCCAAAGCT 57.093 45.000 0.00 0.00 44.23 3.74
4092 4143 8.588472 CCAGGATGAACAAGATCATATACTACA 58.412 37.037 0.00 0.00 40.08 2.74
4136 4188 2.941453 TGACGAGTCCATAACAGAGC 57.059 50.000 0.34 0.00 0.00 4.09
4152 4204 7.338449 TCTTTACTTACCAGGCCAATAAATGAC 59.662 37.037 5.01 0.00 0.00 3.06
4188 4243 6.931281 TCATGTTGAACACAAGGAAACAAAAA 59.069 30.769 0.00 0.00 39.50 1.94
4189 4244 6.459066 TCATGTTGAACACAAGGAAACAAAA 58.541 32.000 0.00 0.00 39.50 2.44
4230 4285 8.088463 TGGGATTTGCAAATAAAGAATGGTAT 57.912 30.769 24.15 0.00 0.00 2.73
4238 4293 4.866486 GTCTGCTGGGATTTGCAAATAAAG 59.134 41.667 24.15 20.23 38.81 1.85
4257 4312 1.069022 CACGAAAACTGGCATGGTCTG 60.069 52.381 0.00 0.00 0.00 3.51
4258 4313 1.202758 TCACGAAAACTGGCATGGTCT 60.203 47.619 0.00 0.00 0.00 3.85
4259 4314 1.234821 TCACGAAAACTGGCATGGTC 58.765 50.000 0.00 0.00 0.00 4.02
4261 4316 3.009723 AGTATCACGAAAACTGGCATGG 58.990 45.455 0.00 0.00 0.00 3.66
4263 4318 3.937814 TGAGTATCACGAAAACTGGCAT 58.062 40.909 0.00 0.00 42.56 4.40
4321 4376 2.126346 GCCATGTCAAACGCTGGC 60.126 61.111 7.47 7.47 40.62 4.85
4322 4377 1.973281 AGGCCATGTCAAACGCTGG 60.973 57.895 5.01 0.00 0.00 4.85
4332 4387 2.014010 AACAAATCCACAGGCCATGT 57.986 45.000 5.01 3.39 45.43 3.21
4349 4404 5.469760 AGGCAACAATCCTGCAAAAATAAAC 59.530 36.000 0.00 0.00 41.78 2.01
4353 4409 3.775261 AGGCAACAATCCTGCAAAAAT 57.225 38.095 0.00 0.00 41.78 1.82
4389 4445 2.499693 CAAAAAGTTTGGTCACCCACCT 59.500 45.455 0.00 0.00 46.98 4.00
4415 4472 7.560368 CCATAGATGTAAGAGGGGATCATTAC 58.440 42.308 0.00 0.00 0.00 1.89
4420 4477 3.840666 TGCCATAGATGTAAGAGGGGATC 59.159 47.826 0.00 0.00 0.00 3.36
4432 4489 2.501261 CTGTCCCACATGCCATAGATG 58.499 52.381 0.00 0.00 0.00 2.90
4532 4589 6.294120 CCTTGTTACTCATGATCAAAGTGCAA 60.294 38.462 19.25 19.52 0.00 4.08
4565 4625 3.709653 TGGATTCCTAGTCATACACCACC 59.290 47.826 3.95 0.00 0.00 4.61


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

AutoCloner maintained by Alex Coulton.