Multiple sequence alignment - TraesCS2D01G499200

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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 TraesCS2D01G499200 chr2D 100.000 2603 0 0 1 2603 594448773 594451375 0 4807
1 TraesCS2D01G499200 chr2B 90.643 2052 87 43 95 2092 721714783 721716783 0 2628
2 TraesCS2D01G499200 chr2B 92.030 527 18 7 2088 2603 721716883 721717396 0 719
3 TraesCS2D01G499200 chr2A 91.351 1480 59 26 649 2092 728941091 728942537 0 1960
4 TraesCS2D01G499200 chr2A 92.829 516 24 5 2088 2603 728942597 728943099 0 736
5 TraesCS2D01G499200 chr2A 86.458 672 45 25 2 656 728930005 728930647 0 695


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 TraesCS2D01G499200 chr2D 594448773 594451375 2602 False 4807.0 4807 100.0000 1 2603 1 chr2D.!!$F1 2602
1 TraesCS2D01G499200 chr2B 721714783 721717396 2613 False 1673.5 2628 91.3365 95 2603 2 chr2B.!!$F1 2508
2 TraesCS2D01G499200 chr2A 728941091 728943099 2008 False 1348.0 1960 92.0900 649 2603 2 chr2A.!!$F2 1954
3 TraesCS2D01G499200 chr2A 728930005 728930647 642 False 695.0 695 86.4580 2 656 1 chr2A.!!$F1 654

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
538 567 0.107703 ACTACATCACATGCACCCCG 60.108 55.0 0.0 0.0 0.0 5.73 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2430 2638 0.178903 ACCACCCCTCAAGCACTCTA 60.179 55.0 0.0 0.0 0.0 2.43 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
22 23 1.743772 CGACGGATGCAAAGGGAAGAT 60.744 52.381 0.00 0.00 0.00 2.40
31 32 2.731572 CAAAGGGAAGATGGTGCTGAT 58.268 47.619 0.00 0.00 0.00 2.90
113 115 1.165270 CCTACGGTTCTTTGGCAAGG 58.835 55.000 2.45 2.45 0.00 3.61
114 116 1.271163 CCTACGGTTCTTTGGCAAGGA 60.271 52.381 8.09 8.09 0.00 3.36
115 117 2.076863 CTACGGTTCTTTGGCAAGGAG 58.923 52.381 12.03 2.31 0.00 3.69
148 150 4.644685 ACAGAAGTTGCACATGGTTTTAGT 59.355 37.500 0.00 0.00 0.00 2.24
180 182 1.741706 CCTCGTTGATTTGCATCAGCT 59.258 47.619 3.18 0.00 40.66 4.24
181 183 2.938451 CCTCGTTGATTTGCATCAGCTA 59.062 45.455 3.18 0.00 40.66 3.32
182 184 3.242543 CCTCGTTGATTTGCATCAGCTAC 60.243 47.826 3.18 0.00 40.66 3.58
183 185 2.677836 TCGTTGATTTGCATCAGCTACC 59.322 45.455 3.18 0.00 40.66 3.18
184 186 2.223340 CGTTGATTTGCATCAGCTACCC 60.223 50.000 3.18 0.00 40.66 3.69
253 263 0.392060 AGTTGCTCTCGATGCATGCA 60.392 50.000 25.04 25.04 40.34 3.96
254 264 0.661552 GTTGCTCTCGATGCATGCAT 59.338 50.000 32.66 32.66 40.34 3.96
255 265 0.661020 TTGCTCTCGATGCATGCATG 59.339 50.000 36.73 26.06 40.34 4.06
477 502 0.393537 CATTCCCTGCCCTGTGACTC 60.394 60.000 0.00 0.00 0.00 3.36
538 567 0.107703 ACTACATCACATGCACCCCG 60.108 55.000 0.00 0.00 0.00 5.73
540 569 2.884997 TACATCACATGCACCCCGCC 62.885 60.000 0.00 0.00 41.33 6.13
550 579 4.467107 ACCCCGCCCTCTCTCTCC 62.467 72.222 0.00 0.00 0.00 3.71
567 598 3.638627 CTCTCCCTCTACATGCATGTACA 59.361 47.826 31.03 22.13 41.97 2.90
568 599 4.226384 TCTCCCTCTACATGCATGTACAT 58.774 43.478 31.03 13.47 41.97 2.29
582 613 9.961265 CATGCATGTACATCAATTATTTCTCTT 57.039 29.630 18.91 0.00 0.00 2.85
632 663 1.815003 CACTCATTGGCTTTGTCCCTC 59.185 52.381 0.00 0.00 0.00 4.30
633 664 1.272147 ACTCATTGGCTTTGTCCCTCC 60.272 52.381 0.00 0.00 0.00 4.30
745 781 2.520020 AGCACAAAGGCAGCAGCA 60.520 55.556 2.65 0.00 44.61 4.41
816 856 2.499693 CCTCACCTTCTTCTTCCTCTCC 59.500 54.545 0.00 0.00 0.00 3.71
913 958 0.684805 TCCCGCCTTTCCTCTCTCTC 60.685 60.000 0.00 0.00 0.00 3.20
914 959 1.681486 CCCGCCTTTCCTCTCTCTCC 61.681 65.000 0.00 0.00 0.00 3.71
915 960 1.681486 CCGCCTTTCCTCTCTCTCCC 61.681 65.000 0.00 0.00 0.00 4.30
922 967 1.518367 TCCTCTCTCTCCCTCTCTCC 58.482 60.000 0.00 0.00 0.00 3.71
953 998 1.852965 CTCCTCCTCCTCCTCTTCTCT 59.147 57.143 0.00 0.00 0.00 3.10
982 1044 3.703001 TGAGGTGAGGTGAGGATTTTC 57.297 47.619 0.00 0.00 0.00 2.29
983 1045 2.305927 TGAGGTGAGGTGAGGATTTTCC 59.694 50.000 0.00 0.00 36.58 3.13
991 1053 0.682852 TGAGGATTTTCCGTGGACGT 59.317 50.000 0.00 0.00 42.75 4.34
1049 1111 2.086251 AACCCTAACCGCGTCGTTGA 62.086 55.000 4.92 0.00 0.00 3.18
1050 1112 1.804326 CCCTAACCGCGTCGTTGAG 60.804 63.158 4.92 0.00 0.00 3.02
1065 1127 2.353607 GAGAGCGTACCATCGGCG 60.354 66.667 0.00 0.00 0.00 6.46
1360 1425 3.667282 CAGCACCAGCACCAGCAC 61.667 66.667 0.00 0.00 45.49 4.40
1390 1461 4.812476 TCGGCGGACAAGCATCGG 62.812 66.667 7.21 0.00 39.27 4.18
1637 1717 3.596214 TCATCATCATCATGCATCCTCG 58.404 45.455 0.00 0.00 0.00 4.63
1639 1719 1.972795 TCATCATCATGCATCCTCGGA 59.027 47.619 0.00 0.00 0.00 4.55
1969 2052 0.961019 CACATTGGAACCACACCAGG 59.039 55.000 0.00 0.00 38.70 4.45
1970 2053 0.178964 ACATTGGAACCACACCAGGG 60.179 55.000 0.00 0.00 38.70 4.45
2044 2137 6.294361 AGGAGTTACATATGTGCAGTGTTA 57.706 37.500 18.81 0.00 0.00 2.41
2119 2316 6.780522 TGTAGGTTATGAGGCATATCTGTACA 59.219 38.462 0.00 0.00 0.00 2.90
2122 2319 6.015010 AGGTTATGAGGCATATCTGTACACTC 60.015 42.308 0.00 0.00 0.00 3.51
2124 2321 3.916035 TGAGGCATATCTGTACACTCCT 58.084 45.455 0.00 0.00 0.00 3.69
2176 2373 7.224362 GTCTATCTGTGAATTCTGATTGGTGAG 59.776 40.741 7.05 3.07 0.00 3.51
2252 2449 4.426416 TGCATGAAAGCATAGCAATGTTC 58.574 39.130 0.00 0.00 40.11 3.18
2257 2454 4.527816 TGAAAGCATAGCAATGTTCCCTTT 59.472 37.500 0.00 0.00 35.38 3.11
2298 2499 6.118170 ACAGATTGTATATTGCTGTTGAGCT 58.882 36.000 0.00 0.00 46.39 4.09
2299 2500 7.275183 ACAGATTGTATATTGCTGTTGAGCTA 58.725 34.615 0.00 0.00 46.39 3.32
2300 2501 7.440556 ACAGATTGTATATTGCTGTTGAGCTAG 59.559 37.037 0.00 0.00 46.39 3.42
2301 2502 5.991328 TTGTATATTGCTGTTGAGCTAGC 57.009 39.130 6.62 6.62 46.39 3.42
2302 2503 5.282055 TGTATATTGCTGTTGAGCTAGCT 57.718 39.130 19.45 19.45 46.39 3.32
2303 2504 6.405278 TGTATATTGCTGTTGAGCTAGCTA 57.595 37.500 19.38 0.00 46.39 3.32
2304 2505 6.450545 TGTATATTGCTGTTGAGCTAGCTAG 58.549 40.000 19.38 16.84 46.39 3.42
2388 2596 4.532314 TGTATAGCTGGATGATGCTCTG 57.468 45.455 0.00 0.00 40.35 3.35
2429 2637 4.088634 TGCCTTTTGCCTTGTGATTAGAT 58.911 39.130 0.00 0.00 40.16 1.98
2430 2638 4.527816 TGCCTTTTGCCTTGTGATTAGATT 59.472 37.500 0.00 0.00 40.16 2.40
2431 2639 5.714333 TGCCTTTTGCCTTGTGATTAGATTA 59.286 36.000 0.00 0.00 40.16 1.75
2432 2640 6.127647 TGCCTTTTGCCTTGTGATTAGATTAG 60.128 38.462 0.00 0.00 40.16 1.73
2433 2641 6.095440 GCCTTTTGCCTTGTGATTAGATTAGA 59.905 38.462 0.00 0.00 0.00 2.10
2456 2664 1.755179 CTTGAGGGGTGGTTATGCTG 58.245 55.000 0.00 0.00 0.00 4.41
2548 2756 6.200878 TGGAAGATAGGGGTTTGATAATCC 57.799 41.667 0.00 0.00 33.43 3.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.046314 CCCTTTGCATCCGTCGGT 60.046 61.111 11.88 0.00 0.00 4.69
22 23 8.447833 CGTAAGTTCTTAAATAAATCAGCACCA 58.552 33.333 0.00 0.00 0.00 4.17
69 70 9.247861 GGCCATACATTAGATCAAAATATTCCT 57.752 33.333 0.00 0.00 0.00 3.36
75 76 6.655003 CCGTAGGCCATACATTAGATCAAAAT 59.345 38.462 5.01 0.00 46.14 1.82
130 132 4.202111 GGTGAACTAAAACCATGTGCAACT 60.202 41.667 0.00 0.00 35.34 3.16
131 133 4.048504 GGTGAACTAAAACCATGTGCAAC 58.951 43.478 0.00 0.00 36.41 4.17
148 150 0.107831 CAACGAGGGACCAAGGTGAA 59.892 55.000 0.00 0.00 0.00 3.18
180 182 1.480954 GCAAGAGATGAACCTCGGGTA 59.519 52.381 0.00 0.00 38.19 3.69
181 183 0.250513 GCAAGAGATGAACCTCGGGT 59.749 55.000 0.00 0.00 38.19 5.28
182 184 0.539051 AGCAAGAGATGAACCTCGGG 59.461 55.000 0.00 0.00 38.19 5.14
183 185 2.005451 CAAGCAAGAGATGAACCTCGG 58.995 52.381 0.00 0.00 38.19 4.63
184 186 1.396301 GCAAGCAAGAGATGAACCTCG 59.604 52.381 0.00 0.00 38.19 4.63
254 264 1.533625 GTAACTCATGCCTTGGTGCA 58.466 50.000 0.00 0.00 46.94 4.57
255 265 0.811281 GGTAACTCATGCCTTGGTGC 59.189 55.000 0.00 0.00 0.00 5.01
425 444 1.000283 AGTGAACAACTCTCTCGCCTG 60.000 52.381 0.00 0.00 31.64 4.85
428 447 1.423395 CCAGTGAACAACTCTCTCGC 58.577 55.000 0.00 0.00 36.83 5.03
429 448 1.000283 AGCCAGTGAACAACTCTCTCG 60.000 52.381 0.00 0.00 36.83 4.04
538 567 0.553819 TGTAGAGGGAGAGAGAGGGC 59.446 60.000 0.00 0.00 0.00 5.19
540 569 2.238521 GCATGTAGAGGGAGAGAGAGG 58.761 57.143 0.00 0.00 0.00 3.69
546 575 3.642141 TGTACATGCATGTAGAGGGAGA 58.358 45.455 34.29 14.37 43.32 3.71
550 579 6.872628 AATTGATGTACATGCATGTAGAGG 57.127 37.500 34.29 8.80 43.32 3.69
595 626 7.255242 CCAATGAGTGTGTGTACATTTCTTTCT 60.255 37.037 0.00 0.00 39.39 2.52
596 627 6.857964 CCAATGAGTGTGTGTACATTTCTTTC 59.142 38.462 0.00 0.00 39.39 2.62
597 628 6.735694 GCCAATGAGTGTGTGTACATTTCTTT 60.736 38.462 0.00 0.00 39.39 2.52
598 629 5.278463 GCCAATGAGTGTGTGTACATTTCTT 60.278 40.000 0.00 0.00 39.39 2.52
632 663 7.280205 GTGTCTTATAATACCCAGTTGACAAGG 59.720 40.741 0.00 0.00 34.41 3.61
633 664 7.010183 CGTGTCTTATAATACCCAGTTGACAAG 59.990 40.741 0.00 0.00 34.41 3.16
768 808 3.731136 TGTCTGACACAAAGCGGC 58.269 55.556 6.36 0.00 29.30 6.53
816 856 2.386935 GGAGATTGGGTGGGGGAGG 61.387 68.421 0.00 0.00 0.00 4.30
913 958 2.520741 GAGGGCGAGGAGAGAGGG 60.521 72.222 0.00 0.00 0.00 4.30
914 959 1.528309 GAGAGGGCGAGGAGAGAGG 60.528 68.421 0.00 0.00 0.00 3.69
915 960 1.528309 GGAGAGGGCGAGGAGAGAG 60.528 68.421 0.00 0.00 0.00 3.20
922 967 2.520741 GGAGGAGGAGAGGGCGAG 60.521 72.222 0.00 0.00 0.00 5.03
953 998 1.688735 CACCTCACCTCAACTCACAGA 59.311 52.381 0.00 0.00 0.00 3.41
1008 1070 4.856607 CTCTCCGTCGCGCCCTTC 62.857 72.222 0.00 0.00 0.00 3.46
1049 1111 3.900892 CCGCCGATGGTACGCTCT 61.901 66.667 0.00 0.00 0.00 4.09
1188 1250 1.302033 CGCCATGGATGAGTAGGCC 60.302 63.158 18.40 0.00 42.28 5.19
1724 1804 3.616956 TGGATCGATATCATGGAAGCC 57.383 47.619 0.00 0.00 33.41 4.35
1725 1805 3.875727 CCATGGATCGATATCATGGAAGC 59.124 47.826 34.31 8.98 40.06 3.86
1726 1806 5.349061 TCCATGGATCGATATCATGGAAG 57.651 43.478 35.94 22.69 41.59 3.46
2021 2104 4.826274 ACACTGCACATATGTAACTCCT 57.174 40.909 8.32 0.00 0.00 3.69
2119 2316 6.327887 AGAGAAAAGGTAACAGAAAGAGGAGT 59.672 38.462 0.00 0.00 41.41 3.85
2122 2319 6.768381 ACAAGAGAAAAGGTAACAGAAAGAGG 59.232 38.462 0.00 0.00 41.41 3.69
2124 2321 7.931948 CCTACAAGAGAAAAGGTAACAGAAAGA 59.068 37.037 0.00 0.00 41.41 2.52
2176 2373 7.655521 AAGTTCCCCTAATTAATTACCTTGC 57.344 36.000 3.71 0.00 0.00 4.01
2300 2501 5.637006 ACATATGTGTCTAGCTAGCTAGC 57.363 43.478 36.81 33.96 44.10 3.42
2301 2502 7.208225 TCAACATATGTGTCTAGCTAGCTAG 57.792 40.000 36.20 36.20 45.38 3.42
2302 2503 7.767250 ATCAACATATGTGTCTAGCTAGCTA 57.233 36.000 22.85 22.85 37.67 3.32
2303 2504 6.662865 ATCAACATATGTGTCTAGCTAGCT 57.337 37.500 23.12 23.12 37.67 3.32
2304 2505 6.347240 GCAATCAACATATGTGTCTAGCTAGC 60.347 42.308 16.35 6.62 37.67 3.42
2305 2506 6.927936 AGCAATCAACATATGTGTCTAGCTAG 59.072 38.462 15.01 15.01 37.67 3.42
2315 2516 8.969260 TTGATTCTAGAGCAATCAACATATGT 57.031 30.769 12.36 1.41 42.64 2.29
2429 2637 0.984230 CCACCCCTCAAGCACTCTAA 59.016 55.000 0.00 0.00 0.00 2.10
2430 2638 0.178903 ACCACCCCTCAAGCACTCTA 60.179 55.000 0.00 0.00 0.00 2.43
2431 2639 1.062488 AACCACCCCTCAAGCACTCT 61.062 55.000 0.00 0.00 0.00 3.24
2432 2640 0.690762 TAACCACCCCTCAAGCACTC 59.309 55.000 0.00 0.00 0.00 3.51
2433 2641 1.004745 CATAACCACCCCTCAAGCACT 59.995 52.381 0.00 0.00 0.00 4.40
2456 2664 2.052782 ACACTCCACCAAACAACCTC 57.947 50.000 0.00 0.00 0.00 3.85
2548 2756 5.083533 AGTTATGTCTTCTCCAGCTCAAG 57.916 43.478 0.00 0.00 0.00 3.02


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

AutoCloner maintained by Alex Coulton.