Multiple sequence alignment - TraesCS6D01G152900

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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 TraesCS6D01G152900 chr6D 100.000 2309 0 0 1 2309 126875691 126877999 0.000000e+00 4265.0
1 TraesCS6D01G152900 chr6D 81.944 72 13 0 27 98 428926035 428925964 6.890000e-06 62.1
2 TraesCS6D01G152900 chr6B 93.194 1719 70 18 621 2309 225875297 225876998 0.000000e+00 2483.0
3 TraesCS6D01G152900 chr6B 93.448 290 16 3 213 500 225872722 225873010 5.900000e-116 427.0
4 TraesCS6D01G152900 chr6B 93.488 215 13 1 1 214 225872426 225872640 3.700000e-83 318.0
5 TraesCS6D01G152900 chr6B 100.000 41 0 0 564 604 225875271 225875311 2.460000e-10 76.8
6 TraesCS6D01G152900 chr6A 93.668 1516 57 15 804 2309 152031521 152030035 0.000000e+00 2231.0
7 TraesCS6D01G152900 chr6A 93.488 215 9 4 1 214 152056904 152056694 4.790000e-82 315.0
8 TraesCS6D01G152900 chr6A 94.536 183 10 0 213 395 152056533 152056351 1.350000e-72 283.0
9 TraesCS6D01G152900 chr6A 91.837 196 12 3 621 816 152056190 152055999 1.050000e-68 270.0
10 TraesCS6D01G152900 chr6A 90.547 201 8 8 408 604 152056369 152056176 2.940000e-64 255.0
11 TraesCS6D01G152900 chr6A 95.652 46 2 0 51 96 88774789 88774744 8.850000e-10 75.0
12 TraesCS6D01G152900 chr6A 84.722 72 11 0 27 98 573510880 573510809 3.180000e-09 73.1
13 TraesCS6D01G152900 chr4A 89.041 73 4 1 27 95 227091290 227091218 1.140000e-13 87.9
14 TraesCS6D01G152900 chr5B 91.803 61 4 1 36 95 564511981 564512041 1.470000e-12 84.2
15 TraesCS6D01G152900 chr5B 93.750 48 3 0 34 81 473784920 473784873 3.180000e-09 73.1
16 TraesCS6D01G152900 chr1B 97.561 41 1 0 58 98 429763272 429763232 1.140000e-08 71.3
17 TraesCS6D01G152900 chr5D 100.000 29 0 0 28 56 325659067 325659039 1.000000e-03 54.7


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 TraesCS6D01G152900 chr6D 126875691 126877999 2308 False 4265.00 4265 100.0000 1 2309 1 chr6D.!!$F1 2308
1 TraesCS6D01G152900 chr6B 225872426 225876998 4572 False 826.20 2483 95.0325 1 2309 4 chr6B.!!$F1 2308
2 TraesCS6D01G152900 chr6A 152030035 152031521 1486 True 2231.00 2231 93.6680 804 2309 1 chr6A.!!$R2 1505
3 TraesCS6D01G152900 chr6A 152055999 152056904 905 True 280.75 315 92.6020 1 816 4 chr6A.!!$R4 815

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
272 436 2.078226 TTGCGACGACTAGCAATGC 58.922 52.632 0.0 0.0 46.83 3.56 F
545 861 2.203394 CACCACTGCCTGCCAAGT 60.203 61.111 0.0 0.0 0.00 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1164 3572 0.824109 AGCGGAAACCATCAGATCGA 59.176 50.000 0.0 0.0 0.00 3.59 R
1447 3855 1.002624 ACATACCGCAACACAGGGG 60.003 57.895 0.0 0.0 46.27 4.79 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
157 159 7.416154 AACAATAAGCAAATGATATGCATGC 57.584 32.000 11.82 11.82 46.22 4.06
180 182 8.109705 TGCTACTTGACAAAACATCAATACAT 57.890 30.769 0.00 0.00 35.57 2.29
191 193 7.475771 AAACATCAATACATTTGCGTTTGTT 57.524 28.000 0.00 0.00 0.00 2.83
219 383 8.898761 TCAATAGTGTTTTCTTTTCTAGTTGCA 58.101 29.630 0.00 0.00 0.00 4.08
240 404 5.163513 GCAATTTGTAACTGCTAGCAATGT 58.836 37.500 19.86 11.44 33.20 2.71
243 407 8.128582 GCAATTTGTAACTGCTAGCAATGTATA 58.871 33.333 19.86 6.60 33.20 1.47
272 436 2.078226 TTGCGACGACTAGCAATGC 58.922 52.632 0.00 0.00 46.83 3.56
314 478 8.352201 TCATGATCAAACTTTAAACTTGACCAG 58.648 33.333 0.00 3.26 32.19 4.00
316 480 7.479980 TGATCAAACTTTAAACTTGACCAGTG 58.520 34.615 9.20 0.00 35.12 3.66
374 538 5.939883 ACAAAGTGCAATCTGTATGCTCTAA 59.060 36.000 0.00 0.00 44.30 2.10
441 606 7.628101 ACCTAAGTTTCTCATAGGGAAATAGGT 59.372 37.037 14.53 14.53 40.29 3.08
544 860 3.677648 GCACCACTGCCTGCCAAG 61.678 66.667 0.00 0.00 37.45 3.61
545 861 2.203394 CACCACTGCCTGCCAAGT 60.203 61.111 0.00 0.00 0.00 3.16
547 863 2.203394 CCACTGCCTGCCAAGTGT 60.203 61.111 8.30 0.00 0.00 3.55
549 865 2.908940 ACTGCCTGCCAAGTGTGC 60.909 61.111 0.00 0.00 0.00 4.57
551 867 2.908428 TGCCTGCCAAGTGTGCTG 60.908 61.111 0.00 0.00 0.00 4.41
608 2986 8.753497 ACAATACTTATCTCCTTTTCAATCCC 57.247 34.615 0.00 0.00 0.00 3.85
609 2987 8.560903 ACAATACTTATCTCCTTTTCAATCCCT 58.439 33.333 0.00 0.00 0.00 4.20
610 2988 9.061435 CAATACTTATCTCCTTTTCAATCCCTC 57.939 37.037 0.00 0.00 0.00 4.30
611 2989 6.642733 ACTTATCTCCTTTTCAATCCCTCA 57.357 37.500 0.00 0.00 0.00 3.86
612 2990 7.032598 ACTTATCTCCTTTTCAATCCCTCAA 57.967 36.000 0.00 0.00 0.00 3.02
613 2991 7.470192 ACTTATCTCCTTTTCAATCCCTCAAA 58.530 34.615 0.00 0.00 0.00 2.69
614 2992 7.950124 ACTTATCTCCTTTTCAATCCCTCAAAA 59.050 33.333 0.00 0.00 0.00 2.44
615 2993 8.719645 TTATCTCCTTTTCAATCCCTCAAAAA 57.280 30.769 0.00 0.00 0.00 1.94
771 3150 5.472820 AGCAGAGGTTGAGAAGAGATTTTTG 59.527 40.000 0.00 0.00 0.00 2.44
780 3162 3.817647 AGAAGAGATTTTTGTTGAGCGCT 59.182 39.130 11.27 11.27 0.00 5.92
954 3361 2.404995 ACCGAGGACTAACCGAGCG 61.405 63.158 0.00 0.00 44.74 5.03
1164 3572 2.666862 TTGTTCCGTGCCGCGATT 60.667 55.556 8.23 0.00 44.77 3.34
1178 3586 1.860950 CGCGATTCGATCTGATGGTTT 59.139 47.619 10.88 0.00 41.67 3.27
1200 3608 0.890996 GCTGTGCAGGCCTGTACTTT 60.891 55.000 41.48 3.86 44.76 2.66
1307 3715 4.682334 TGGCGGGGAGGACGTGTA 62.682 66.667 0.00 0.00 0.00 2.90
1383 3791 5.297569 AGCCTGAGACAAGTTAGAGTTTT 57.702 39.130 0.00 0.00 0.00 2.43
1429 3837 7.325660 AGATTCACAGAATCGTTGCAATAAT 57.674 32.000 0.59 0.00 0.00 1.28
1447 3855 8.081633 TGCAATAATAATGTACTGCTAATTGCC 58.918 33.333 19.74 9.83 43.62 4.52
1459 3867 1.247419 TAATTGCCCCCTGTGTTGCG 61.247 55.000 0.00 0.00 0.00 4.85
1471 3879 1.198867 TGTGTTGCGGTATGTCAATGC 59.801 47.619 0.00 0.00 0.00 3.56
1474 3882 2.095314 TGTTGCGGTATGTCAATGCTTG 60.095 45.455 0.00 0.00 0.00 4.01
1503 3911 6.099579 CAAGAATTGTTATCTGACGACCTG 57.900 41.667 0.00 0.00 42.34 4.00
1508 3916 2.430694 TGTTATCTGACGACCTGGATGG 59.569 50.000 0.00 0.00 42.93 3.51
1524 3932 7.403312 CCTGGATGGTTTTATGTGTGAAATA 57.597 36.000 0.00 0.00 0.00 1.40
1559 3967 4.840401 TCAGATTATGCTTCGTTTCGTG 57.160 40.909 0.00 0.00 0.00 4.35
1565 3973 1.647346 TGCTTCGTTTCGTGACTGTT 58.353 45.000 0.00 0.00 0.00 3.16
1723 4131 8.723942 ATTTTCCATACTGTGATACTCTGTTC 57.276 34.615 0.00 0.00 0.00 3.18
1762 4170 4.761739 TGAGCCACTGTCTTTTAGGATTTG 59.238 41.667 0.00 0.00 0.00 2.32
1778 4186 6.121776 AGGATTTGTGTGTGTGTATTCCTA 57.878 37.500 0.00 0.00 29.52 2.94
1836 4244 9.807649 GATCAACTTAAAATGAACATAATGGCT 57.192 29.630 0.00 0.00 0.00 4.75
1892 4300 0.729116 CCAATACTTGCTGCACCTCG 59.271 55.000 0.00 0.00 0.00 4.63
1896 4304 0.108804 TACTTGCTGCACCTCGCTAC 60.109 55.000 0.00 0.00 43.06 3.58
1915 4323 6.376299 TCGCTACTTGACTACTTTTGATCCTA 59.624 38.462 0.00 0.00 0.00 2.94
1929 4337 0.846693 ATCCTAATGGGCACTGGGTC 59.153 55.000 0.00 0.00 34.39 4.46
1993 4401 1.065709 GTCCACCAACCCATCATACGT 60.066 52.381 0.00 0.00 0.00 3.57
2108 4516 6.016777 CCTTTTCTGTCTGCATTGTAGAGTTT 60.017 38.462 4.56 0.00 0.00 2.66
2155 4564 5.423931 TCCAGTGCCAGTGTATTAGATTGTA 59.576 40.000 0.00 0.00 0.00 2.41
2156 4565 6.099701 TCCAGTGCCAGTGTATTAGATTGTAT 59.900 38.462 0.00 0.00 0.00 2.29
2157 4566 6.767902 CCAGTGCCAGTGTATTAGATTGTATT 59.232 38.462 0.00 0.00 0.00 1.89
2158 4567 7.931407 CCAGTGCCAGTGTATTAGATTGTATTA 59.069 37.037 0.00 0.00 0.00 0.98
2159 4568 8.982685 CAGTGCCAGTGTATTAGATTGTATTAG 58.017 37.037 0.00 0.00 0.00 1.73
2160 4569 8.924303 AGTGCCAGTGTATTAGATTGTATTAGA 58.076 33.333 0.00 0.00 0.00 2.10
2161 4570 9.712305 GTGCCAGTGTATTAGATTGTATTAGAT 57.288 33.333 0.00 0.00 0.00 1.98
2206 4623 6.682423 TGGTAATCAACATAGTGCTGATTG 57.318 37.500 15.21 0.00 41.58 2.67
2212 4629 5.748402 TCAACATAGTGCTGATTGGATTCT 58.252 37.500 0.00 0.00 0.00 2.40
2262 4679 4.813697 GCCCAGTAGAAGATAAGCAGAAAG 59.186 45.833 0.00 0.00 0.00 2.62
2279 4696 5.232463 CAGAAAGCAGCCATAAATGTTTGT 58.768 37.500 0.00 0.00 0.00 2.83
2287 4704 6.644592 GCAGCCATAAATGTTTGTTTAAGTGA 59.355 34.615 0.00 0.00 0.00 3.41
2288 4705 7.170658 GCAGCCATAAATGTTTGTTTAAGTGAA 59.829 33.333 0.00 0.00 0.00 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
180 182 6.952935 AACACTATTGAAAACAAACGCAAA 57.047 29.167 0.00 0.00 0.00 3.68
219 383 9.396022 AGTATACATTGCTAGCAGTTACAAATT 57.604 29.630 18.45 0.00 0.00 1.82
240 404 5.693104 AGTCGTCGCAAACAAGAAAAGTATA 59.307 36.000 0.00 0.00 0.00 1.47
243 407 2.676342 AGTCGTCGCAAACAAGAAAAGT 59.324 40.909 0.00 0.00 0.00 2.66
314 478 7.062839 TGTTCAAAAGTACAAGCACATTTTCAC 59.937 33.333 0.00 0.00 0.00 3.18
316 480 7.518731 TGTTCAAAAGTACAAGCACATTTTC 57.481 32.000 0.00 0.00 0.00 2.29
441 606 1.810151 GCCTTATCGTTGCCAAGAACA 59.190 47.619 0.00 0.00 0.00 3.18
540 856 0.102844 CCAACAACCAGCACACTTGG 59.897 55.000 0.00 0.00 41.60 3.61
541 857 1.066002 CTCCAACAACCAGCACACTTG 59.934 52.381 0.00 0.00 0.00 3.16
542 858 1.392589 CTCCAACAACCAGCACACTT 58.607 50.000 0.00 0.00 0.00 3.16
543 859 0.466189 CCTCCAACAACCAGCACACT 60.466 55.000 0.00 0.00 0.00 3.55
544 860 0.751643 ACCTCCAACAACCAGCACAC 60.752 55.000 0.00 0.00 0.00 3.82
545 861 0.840617 TACCTCCAACAACCAGCACA 59.159 50.000 0.00 0.00 0.00 4.57
547 863 1.493022 ACTTACCTCCAACAACCAGCA 59.507 47.619 0.00 0.00 0.00 4.41
549 865 4.935808 GTGATACTTACCTCCAACAACCAG 59.064 45.833 0.00 0.00 0.00 4.00
551 867 4.259356 GGTGATACTTACCTCCAACAACC 58.741 47.826 0.00 0.00 35.30 3.77
669 3047 9.179909 TGATTTTGGATCTTAAACGCCTTATTA 57.820 29.630 0.00 0.00 0.00 0.98
672 3051 6.431543 TGTGATTTTGGATCTTAAACGCCTTA 59.568 34.615 0.00 0.00 0.00 2.69
674 3053 4.764823 TGTGATTTTGGATCTTAAACGCCT 59.235 37.500 0.00 0.00 0.00 5.52
675 3054 5.054390 TGTGATTTTGGATCTTAAACGCC 57.946 39.130 0.00 0.00 0.00 5.68
676 3055 5.516339 CCATGTGATTTTGGATCTTAAACGC 59.484 40.000 0.00 0.00 34.81 4.84
677 3056 6.620678 ACCATGTGATTTTGGATCTTAAACG 58.379 36.000 0.00 0.00 36.79 3.60
678 3057 8.087750 TCAACCATGTGATTTTGGATCTTAAAC 58.912 33.333 0.00 0.00 36.79 2.01
745 3124 5.596836 AATCTCTTCTCAACCTCTGCTAG 57.403 43.478 0.00 0.00 0.00 3.42
771 3150 0.514691 CTCAACCTCAAGCGCTCAAC 59.485 55.000 12.06 0.00 0.00 3.18
936 3343 2.404995 CGCTCGGTTAGTCCTCGGT 61.405 63.158 0.00 0.00 0.00 4.69
1088 3495 2.594131 AGTTTAGGGTTTGGTTCAGGC 58.406 47.619 0.00 0.00 0.00 4.85
1164 3572 0.824109 AGCGGAAACCATCAGATCGA 59.176 50.000 0.00 0.00 0.00 3.59
1383 3791 4.006780 TGTGAACAAGCAGCAGATAAGA 57.993 40.909 0.00 0.00 0.00 2.10
1447 3855 1.002624 ACATACCGCAACACAGGGG 60.003 57.895 0.00 0.00 46.27 4.79
1501 3909 8.685427 TCATATTTCACACATAAAACCATCCAG 58.315 33.333 0.00 0.00 0.00 3.86
1503 3911 8.686334 ACTCATATTTCACACATAAAACCATCC 58.314 33.333 0.00 0.00 0.00 3.51
1508 3916 9.906660 TTCCAACTCATATTTCACACATAAAAC 57.093 29.630 0.00 0.00 0.00 2.43
1513 3921 9.643693 GAATTTTCCAACTCATATTTCACACAT 57.356 29.630 0.00 0.00 0.00 3.21
1524 3932 8.302515 AGCATAATCTGAATTTTCCAACTCAT 57.697 30.769 0.00 0.00 0.00 2.90
1559 3967 4.855388 TCGATAAACTTACGAGCAACAGTC 59.145 41.667 0.00 0.00 0.00 3.51
1723 4131 9.113838 ACAGTGGCTCATTTTAGATAAATGTAG 57.886 33.333 9.33 7.36 38.44 2.74
1731 4139 7.337942 CCTAAAAGACAGTGGCTCATTTTAGAT 59.662 37.037 22.37 0.00 40.28 1.98
1762 4170 4.000988 CCAACCTAGGAATACACACACAC 58.999 47.826 17.98 0.00 0.00 3.82
1852 4260 4.202567 TGGTACTGAGGCAGGAAAAGAATT 60.203 41.667 0.00 0.00 35.51 2.17
1892 4300 8.821894 CATTAGGATCAAAAGTAGTCAAGTAGC 58.178 37.037 0.00 0.00 0.00 3.58
1896 4304 6.038714 GCCCATTAGGATCAAAAGTAGTCAAG 59.961 42.308 0.00 0.00 38.24 3.02
1915 4323 1.075482 CTGTGACCCAGTGCCCATT 59.925 57.895 0.00 0.00 36.37 3.16
1929 4337 7.500892 ACCTCATCAGTATTACTAGAGTCTGTG 59.499 40.741 1.86 0.00 0.00 3.66
2052 4460 2.779506 GCAAACCCTACTTGCAGTAGT 58.220 47.619 16.87 8.87 45.12 2.73
2108 4516 6.780522 GGATTATTCCATTTTACCCCTGCTAA 59.219 38.462 0.00 0.00 42.12 3.09
2194 4603 7.893124 AAATCAAGAATCCAATCAGCACTAT 57.107 32.000 0.00 0.00 0.00 2.12
2243 4660 5.115480 GCTGCTTTCTGCTTATCTTCTACT 58.885 41.667 0.00 0.00 43.37 2.57
2262 4679 6.644592 TCACTTAAACAAACATTTATGGCTGC 59.355 34.615 0.00 0.00 0.00 5.25


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

AutoCloner maintained by Alex Coulton.