Multiple sequence alignment - TraesCS2D01G279200

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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 TraesCS2D01G279200 chr2D 100.000 3797 0 0 706 4502 350793166 350796962 0.000000e+00 7012
1 TraesCS2D01G279200 chr2D 100.000 273 0 0 1 273 350792461 350792733 5.200000e-139 505
2 TraesCS2D01G279200 chr2B 94.361 3848 138 35 706 4502 416871132 416874951 0.000000e+00 5830
3 TraesCS2D01G279200 chr2B 94.891 274 13 1 1 273 416870831 416871104 1.160000e-115 427
4 TraesCS2D01G279200 chr2A 93.304 2942 107 24 1607 4502 468495505 468498402 0.000000e+00 4259
5 TraesCS2D01G279200 chr2A 96.057 837 21 2 706 1542 468494681 468495505 0.000000e+00 1352
6 TraesCS2D01G279200 chr2A 96.337 273 10 0 1 273 468494379 468494651 2.470000e-122 449


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 TraesCS2D01G279200 chr2D 350792461 350796962 4501 False 3758.5 7012 100.000000 1 4502 2 chr2D.!!$F1 4501
1 TraesCS2D01G279200 chr2B 416870831 416874951 4120 False 3128.5 5830 94.626000 1 4502 2 chr2B.!!$F1 4501
2 TraesCS2D01G279200 chr2A 468494379 468498402 4023 False 2020.0 4259 95.232667 1 4502 3 chr2A.!!$F1 4501

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
249 250 0.685097 TCTCTCAAGAACCGTTGGGG 59.315 55.0 0.0 0.0 43.62 4.96 F
1096 1099 0.250770 GTGTCTTGGTCCCTTGGTCC 60.251 60.0 0.0 0.0 0.00 4.46 F
1681 1686 0.533085 GGGGAAATCCTCAGCGTAGC 60.533 60.0 0.0 0.0 46.34 3.58 F
2430 2457 1.354040 CTGACGATGAAGTGGCTGTC 58.646 55.0 0.0 0.0 0.00 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1956 1983 1.296715 GATGGGTTCAGCGGTGACT 59.703 57.895 18.42 0.00 30.10 3.41 R
2405 2432 0.742281 CACTTCATCGTCAGGCTGGG 60.742 60.000 15.73 7.41 0.00 4.45 R
2623 2650 1.210478 AGCAAACCGATGGTAGCAGAT 59.790 47.619 13.55 0.00 38.67 2.90 R
3969 4040 0.108520 TGGCGAGGGAACGAACATAC 60.109 55.000 0.00 0.00 35.09 2.39 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 3.813166 TGACCGACCAGAATTCTTGAAAC 59.187 43.478 13.19 4.00 0.00 2.78
187 188 4.750098 TGTTTGCTCAGTTCTACTAGTTGC 59.250 41.667 0.00 0.00 0.00 4.17
192 193 4.322049 GCTCAGTTCTACTAGTTGCAAGGA 60.322 45.833 0.00 0.00 0.00 3.36
245 246 2.484889 GTGCTTCTCTCAAGAACCGTT 58.515 47.619 0.00 0.00 36.59 4.44
249 250 0.685097 TCTCTCAAGAACCGTTGGGG 59.315 55.000 0.00 0.00 43.62 4.96
801 804 6.463995 AACCACAAGCTTTGACTTTCAATA 57.536 33.333 0.00 0.00 36.11 1.90
952 955 0.846693 AGGAGTGTGGCCTGTTTTCT 59.153 50.000 3.32 0.00 33.59 2.52
1094 1097 0.991355 TGGTGTCTTGGTCCCTTGGT 60.991 55.000 0.00 0.00 0.00 3.67
1096 1099 0.250770 GTGTCTTGGTCCCTTGGTCC 60.251 60.000 0.00 0.00 0.00 4.46
1098 1101 1.134438 GTCTTGGTCCCTTGGTCCCT 61.134 60.000 0.00 0.00 29.89 4.20
1182 1185 9.088512 CGTTAGCTAATTAATTAGGCATAGAGG 57.911 37.037 28.27 8.55 40.01 3.69
1474 1477 6.317857 CCAACTAGCTTATGCAAACTTCTTC 58.682 40.000 0.00 0.00 42.74 2.87
1475 1478 6.317857 CAACTAGCTTATGCAAACTTCTTCC 58.682 40.000 0.00 0.00 42.74 3.46
1496 1499 4.515191 TCCTAATGCAATTCGGTTAGCATC 59.485 41.667 0.00 0.00 46.10 3.91
1542 1545 8.969260 TTTTGTATGAGCATCTATCAGTTGAT 57.031 30.769 0.00 0.00 38.51 2.57
1681 1686 0.533085 GGGGAAATCCTCAGCGTAGC 60.533 60.000 0.00 0.00 46.34 3.58
1770 1797 2.695359 TGGTACTCCTGAAAACGATGC 58.305 47.619 0.00 0.00 34.23 3.91
1903 1930 3.377172 CACGGAAGAACAAGAAAACAGGT 59.623 43.478 0.00 0.00 0.00 4.00
1942 1969 2.996395 CCAGGACATCAGCAGCCT 59.004 61.111 0.00 0.00 0.00 4.58
1993 2020 2.397597 TCAGCATATACACCTGAGCCA 58.602 47.619 0.00 0.00 32.30 4.75
2064 2091 4.752879 CCATCACCGCGAACCCGT 62.753 66.667 8.23 0.00 38.24 5.28
2346 2373 8.980481 TTGTTTCTCTTCTTTCTTATTGGTCT 57.020 30.769 0.00 0.00 0.00 3.85
2389 2416 6.006449 ACTTTGGAGATAATGAGCTGTTTGT 58.994 36.000 0.00 0.00 0.00 2.83
2399 2426 4.861389 TGAGCTGTTTGTTTTTGCATTG 57.139 36.364 0.00 0.00 0.00 2.82
2405 2432 4.967437 TGTTTGTTTTTGCATTGCTGAAC 58.033 34.783 10.49 11.64 0.00 3.18
2430 2457 1.354040 CTGACGATGAAGTGGCTGTC 58.646 55.000 0.00 0.00 0.00 3.51
2678 2705 5.348724 TGACTTCAGAATTTCGACTGCATAC 59.651 40.000 0.00 0.00 34.57 2.39
2743 2770 6.243216 TCGTTAGGGAATTGGTAGCTTTAT 57.757 37.500 0.00 0.00 0.00 1.40
2744 2771 6.655930 TCGTTAGGGAATTGGTAGCTTTATT 58.344 36.000 0.00 0.00 0.00 1.40
2745 2772 7.794041 TCGTTAGGGAATTGGTAGCTTTATTA 58.206 34.615 0.00 0.00 0.00 0.98
2881 2908 1.730501 TGCAGCACATCTAGCAGAAC 58.269 50.000 0.00 0.00 32.48 3.01
2905 2932 6.417635 ACAAAAATGTCTACAAAATGTGCGAG 59.582 34.615 0.00 0.00 0.00 5.03
2910 2937 3.678072 GTCTACAAAATGTGCGAGTGCTA 59.322 43.478 0.00 0.00 43.34 3.49
2995 3022 6.228258 TCACTCTAAACAATGGGTACTTCAC 58.772 40.000 0.00 0.00 0.00 3.18
3377 3442 6.929049 TGTGTTTGTATCTTTCTAGTGGACAG 59.071 38.462 0.00 0.00 0.00 3.51
3424 3489 6.024552 TCTGTTTCTATTTCATTTGCCACC 57.975 37.500 0.00 0.00 0.00 4.61
3505 3570 3.503363 TCCTTGCTGCATACTTTGACAAG 59.497 43.478 1.84 0.00 34.57 3.16
3516 3581 4.927267 ACTTTGACAAGATGGGGATACA 57.073 40.909 0.00 0.00 33.63 2.29
3646 3716 8.774586 GCTTATTAGTCATTACTATTGGTGTGG 58.225 37.037 0.00 0.00 38.02 4.17
3669 3739 4.498009 GGTGTGTACCTATGATTGCATTGC 60.498 45.833 0.46 0.46 43.97 3.56
3800 3870 2.711899 ATACCCCTCCCTCGCTGGA 61.712 63.158 0.00 0.00 38.35 3.86
3897 3968 0.459899 ATCTGATCGGTTGCGCTGTA 59.540 50.000 9.73 0.00 0.00 2.74
3921 3992 6.977213 ACTTCATTACGGTTGCACTAAAATT 58.023 32.000 0.00 0.00 0.00 1.82
3969 4040 1.494716 AACCCCCTGAGTTAACCCCG 61.495 60.000 0.88 0.00 0.00 5.73
4394 4471 6.414732 TGCTTTACACATAAGCTAATCTGGT 58.585 36.000 8.78 0.00 46.30 4.00
4462 4539 8.861033 TTTGATTTCTGTTGAAGAATCTGTTG 57.139 30.769 0.00 0.00 44.46 3.33
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 3.237746 CTCCTGGGCATGAATCTCTCTA 58.762 50.000 0.00 0.00 0.00 2.43
119 120 4.556523 CCACGCAAAAACCAACAAAATTTG 59.443 37.500 3.89 3.89 34.84 2.32
249 250 1.134367 GAAACGAGGGGGCTAATTTGC 59.866 52.381 3.03 3.03 0.00 3.68
801 804 2.225117 CCAGTCCCAACTCCCAAGAATT 60.225 50.000 0.00 0.00 31.71 2.17
952 955 5.310594 TCCCTCCTTTCTCTCAAATTCTTGA 59.689 40.000 0.00 0.00 39.30 3.02
1094 1097 3.974719 TGCATTATGCTTTACCAAGGGA 58.025 40.909 18.44 0.00 45.31 4.20
1096 1099 6.817641 TGAAAATGCATTATGCTTTACCAAGG 59.182 34.615 18.44 0.00 45.31 3.61
1098 1101 8.789825 AATGAAAATGCATTATGCTTTACCAA 57.210 26.923 18.44 5.96 45.31 3.67
1223 1226 4.825085 TCCAACCTGAACAAGAAATGGTAC 59.175 41.667 0.00 0.00 0.00 3.34
1474 1477 4.320494 GGATGCTAACCGAATTGCATTAGG 60.320 45.833 9.70 5.81 44.80 2.69
1475 1478 4.275689 TGGATGCTAACCGAATTGCATTAG 59.724 41.667 9.70 0.00 44.80 1.73
1681 1686 2.969443 AATCTTTCCGAACGTTGCAG 57.031 45.000 5.00 0.00 0.00 4.41
1790 1817 5.752955 GTGGTTGCTGTTTAAACAACATGAT 59.247 36.000 21.59 0.00 44.27 2.45
1903 1930 4.462483 GGCTCATTTGGATTGGAGTAAACA 59.538 41.667 0.00 0.00 0.00 2.83
1956 1983 1.296715 GATGGGTTCAGCGGTGACT 59.703 57.895 18.42 0.00 30.10 3.41
1993 2020 2.286523 CCTGGGAGCCTGTTCTCGT 61.287 63.158 0.00 0.00 33.98 4.18
2044 2071 4.090588 GGTTCGCGGTGATGGGGA 62.091 66.667 6.13 0.00 0.00 4.81
2078 2105 2.584608 CTCCCGCGGAGGATTTGT 59.415 61.111 30.73 0.00 45.43 2.83
2346 2373 6.356556 CAAAGTCCAGACACATATATTCCCA 58.643 40.000 0.00 0.00 0.00 4.37
2389 2416 2.836262 CTGGGTTCAGCAATGCAAAAA 58.164 42.857 8.35 0.00 33.86 1.94
2405 2432 0.742281 CACTTCATCGTCAGGCTGGG 60.742 60.000 15.73 7.41 0.00 4.45
2623 2650 1.210478 AGCAAACCGATGGTAGCAGAT 59.790 47.619 13.55 0.00 38.67 2.90
2702 2729 8.729756 CCCTAACGAAAATGCATTCATGATATA 58.270 33.333 13.38 0.49 32.23 0.86
2787 2814 6.151144 GCCACAGAACTCTATTACCAAATTGT 59.849 38.462 0.00 0.00 0.00 2.71
2881 2908 6.417635 ACTCGCACATTTTGTAGACATTTTTG 59.582 34.615 0.00 0.00 0.00 2.44
2995 3022 7.079475 TGAATCATCATTGCAATACTTATGCG 58.921 34.615 12.53 0.00 46.76 4.73
3045 3072 2.350057 TCATCTGCTAGCGACCTAGT 57.650 50.000 10.77 0.00 42.51 2.57
3127 3154 6.321821 TGCTAACAACACTATTTATCCCCT 57.678 37.500 0.00 0.00 0.00 4.79
3447 3512 2.698797 AGAGGGAAAGTTCAGTCAACGA 59.301 45.455 0.00 0.00 40.32 3.85
3505 3570 4.346418 ACTCTCTGTGATTGTATCCCCATC 59.654 45.833 0.00 0.00 0.00 3.51
3646 3716 4.498009 GCAATGCAATCATAGGTACACACC 60.498 45.833 0.00 0.00 37.19 4.16
3800 3870 5.579047 TCATTGTGGTAATGGAACCTGATT 58.421 37.500 0.00 0.00 40.44 2.57
3897 3968 6.569179 ATTTTAGTGCAACCGTAATGAAGT 57.431 33.333 0.00 0.00 37.80 3.01
3941 4012 6.151648 GGTTAACTCAGGGGGTTTAATACAAC 59.848 42.308 5.42 0.00 0.00 3.32
3969 4040 0.108520 TGGCGAGGGAACGAACATAC 60.109 55.000 0.00 0.00 35.09 2.39
4099 4170 9.294030 GATGGTATTCAGCAAGTTTAAAATCAG 57.706 33.333 0.00 0.00 35.40 2.90
4192 4263 9.430623 GTAAAATGCTAACCATACCAAATGTTT 57.569 29.630 0.00 0.00 32.67 2.83
4298 4375 5.487488 ACAACTGTTCCCATTATACTCTGGA 59.513 40.000 0.00 0.00 34.24 3.86
4394 4471 1.240641 CCCACTGGCGCAACATGTTA 61.241 55.000 11.53 0.00 0.00 2.41
4436 4513 9.472361 CAACAGATTCTTCAACAGAAATCAAAT 57.528 29.630 0.00 0.00 45.06 2.32
4451 4528 5.355350 GCAATACCTACAGCAACAGATTCTT 59.645 40.000 0.00 0.00 0.00 2.52


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

AutoCloner maintained by Alex Coulton.