Multiple sequence alignment - TraesCS2D01G116900

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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 TraesCS2D01G116900 chr2D 100.000 2900 0 0 1 2900 65719011 65716112 0.000000e+00 5356
1 TraesCS2D01G116900 chr2D 84.213 1989 264 25 4 1970 66462792 66460832 0.000000e+00 1888
2 TraesCS2D01G116900 chr2A 92.475 2804 163 26 12 2786 68811443 68814227 0.000000e+00 3965
3 TraesCS2D01G116900 chr2A 83.611 1983 271 25 1 1960 68503872 68505823 0.000000e+00 1812
4 TraesCS2D01G116900 chr2A 95.000 120 6 0 2781 2900 68814305 68814424 3.810000e-44 189
5 TraesCS2D01G116900 chr2B 94.212 2436 106 19 1 2410 105372532 105374958 0.000000e+00 3685
6 TraesCS2D01G116900 chr2B 84.226 2035 261 35 1 2020 104894295 104896284 0.000000e+00 1925
7 TraesCS2D01G116900 chr2B 89.868 454 45 1 2431 2884 105379004 105379456 1.500000e-162 582


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 TraesCS2D01G116900 chr2D 65716112 65719011 2899 True 5356 5356 100.0000 1 2900 1 chr2D.!!$R1 2899
1 TraesCS2D01G116900 chr2D 66460832 66462792 1960 True 1888 1888 84.2130 4 1970 1 chr2D.!!$R2 1966
2 TraesCS2D01G116900 chr2A 68811443 68814424 2981 False 2077 3965 93.7375 12 2900 2 chr2A.!!$F2 2888
3 TraesCS2D01G116900 chr2A 68503872 68505823 1951 False 1812 1812 83.6110 1 1960 1 chr2A.!!$F1 1959
4 TraesCS2D01G116900 chr2B 105372532 105374958 2426 False 3685 3685 94.2120 1 2410 1 chr2B.!!$F2 2409
5 TraesCS2D01G116900 chr2B 104894295 104896284 1989 False 1925 1925 84.2260 1 2020 1 chr2B.!!$F1 2019

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
21 22 0.626916 AAGGGGCGGTATTTTAGGCA 59.373 50.0 0.0 0.0 0.00 4.75 F
1137 1193 0.537188 TGTCGGAGGATTTCTGGCTC 59.463 55.0 0.0 0.0 37.69 4.70 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1827 1901 0.098376 ACTCTTCGTCATCCGCGTAC 59.902 55.0 4.92 0.0 36.19 3.67 R
2038 2112 0.460109 TGCGCGACATGCAATCTACT 60.460 50.0 12.10 0.0 46.97 2.57 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
21 22 0.626916 AAGGGGCGGTATTTTAGGCA 59.373 50.000 0.00 0.00 0.00 4.75
37 38 6.808321 TTTAGGCATGGAGTTATGAGTAGT 57.192 37.500 0.00 0.00 0.00 2.73
46 47 5.647658 TGGAGTTATGAGTAGTGCAAAATGG 59.352 40.000 0.00 0.00 0.00 3.16
125 126 6.767902 ACAATATGAACAAATAGCGAGGACAT 59.232 34.615 0.00 0.00 0.00 3.06
128 130 3.270877 GAACAAATAGCGAGGACATGGT 58.729 45.455 0.00 0.00 0.00 3.55
151 153 7.383572 TGGTGACGACAAATAAATTTCAATTGG 59.616 33.333 5.42 0.00 0.00 3.16
285 288 2.568623 ACTGTTGAACCTAGCCCAAG 57.431 50.000 0.00 0.00 0.00 3.61
303 306 5.632902 GCCCAAGGGTGTTATTTATGGTCTA 60.633 44.000 7.05 0.00 37.65 2.59
518 539 4.017126 GGAAGGGTCCAAAATCTAGTTGG 58.983 47.826 4.56 4.56 45.89 3.77
706 729 5.529581 TCTCTCCATACATCGCAACAATA 57.470 39.130 0.00 0.00 0.00 1.90
762 788 3.228453 CATTCATTCATAGCCTTGGCCT 58.772 45.455 3.32 0.00 0.00 5.19
827 879 4.081531 ACATTATTTCACAACCATGGCCTG 60.082 41.667 13.04 12.38 0.00 4.85
882 934 4.453480 TCATCCCCCATATCCTCAAAAC 57.547 45.455 0.00 0.00 0.00 2.43
1137 1193 0.537188 TGTCGGAGGATTTCTGGCTC 59.463 55.000 0.00 0.00 37.69 4.70
1476 1532 4.595538 TTCGCGCACTTCACCCGT 62.596 61.111 8.75 0.00 0.00 5.28
1593 1649 1.676678 GCGCTCCATCCACTCCTGTA 61.677 60.000 0.00 0.00 0.00 2.74
1803 1868 3.423154 GCAAACGAGGACGGGCAG 61.423 66.667 0.00 0.00 44.46 4.85
2020 2094 1.356624 GTGCCTGTTGTGTCTGTGC 59.643 57.895 0.00 0.00 0.00 4.57
2025 2099 2.327940 GTTGTGTCTGTGCGTGCC 59.672 61.111 0.00 0.00 0.00 5.01
2028 2102 4.017877 GTGTCTGTGCGTGCCTGC 62.018 66.667 0.00 0.00 0.00 4.85
2029 2103 4.544047 TGTCTGTGCGTGCCTGCA 62.544 61.111 0.00 0.00 43.95 4.41
2036 2110 3.542046 TGCGTGCCTGCAGTATTTA 57.458 47.368 13.81 0.00 40.62 1.40
2037 2111 2.036958 TGCGTGCCTGCAGTATTTAT 57.963 45.000 13.81 0.00 40.62 1.40
2038 2112 3.186702 TGCGTGCCTGCAGTATTTATA 57.813 42.857 13.81 0.00 40.62 0.98
2039 2113 3.130633 TGCGTGCCTGCAGTATTTATAG 58.869 45.455 13.81 0.00 40.62 1.31
2043 2128 5.769367 CGTGCCTGCAGTATTTATAGTAGA 58.231 41.667 13.81 0.00 0.00 2.59
2054 2139 8.376203 CAGTATTTATAGTAGATTGCATGTCGC 58.624 37.037 0.00 0.00 42.89 5.19
2098 2183 1.671379 GGTCCTCAAGAACGTGCCC 60.671 63.158 0.00 0.00 0.00 5.36
2099 2184 1.671379 GTCCTCAAGAACGTGCCCC 60.671 63.158 0.00 0.00 0.00 5.80
2100 2185 2.359975 CCTCAAGAACGTGCCCCC 60.360 66.667 0.00 0.00 0.00 5.40
2143 2228 9.346005 TGGTCATAAATAAGTGTCGTCTCTATA 57.654 33.333 0.00 0.00 0.00 1.31
2301 2393 8.499403 TCCTTGGTTCTTTTTATTTTGTTTGG 57.501 30.769 0.00 0.00 0.00 3.28
2323 2419 5.818857 TGGTAAGCGAGGTGTATTTTTATCC 59.181 40.000 0.00 0.00 0.00 2.59
2498 2597 4.065789 AGACGAAAAAGGTTGGATCTGTC 58.934 43.478 0.00 0.00 0.00 3.51
2503 2602 5.221048 CGAAAAAGGTTGGATCTGTCTGTTT 60.221 40.000 0.00 0.00 0.00 2.83
2504 2603 6.017440 CGAAAAAGGTTGGATCTGTCTGTTTA 60.017 38.462 0.00 0.00 0.00 2.01
2507 2606 5.762179 AGGTTGGATCTGTCTGTTTATGA 57.238 39.130 0.00 0.00 0.00 2.15
2520 2619 8.032952 TGTCTGTTTATGAAAATACAGCTCAG 57.967 34.615 0.00 0.00 38.26 3.35
2556 2655 6.817765 ATGCGGTGAAATAAATTATCCGAT 57.182 33.333 12.99 3.79 38.68 4.18
2575 2674 3.854240 CGATCCGGTCTGATAAATCATCG 59.146 47.826 0.00 0.00 36.33 3.84
2631 2730 6.107901 TGCAAGCCAAAACCATTAAATACT 57.892 33.333 0.00 0.00 0.00 2.12
2634 2733 7.039363 TGCAAGCCAAAACCATTAAATACTACT 60.039 33.333 0.00 0.00 0.00 2.57
2658 2757 2.669240 GTGGAAACGCCTAGGCCT 59.331 61.111 28.09 14.23 37.98 5.19
2698 2797 3.486383 TCGAGGCCAAACAAAATCTCTT 58.514 40.909 5.01 0.00 0.00 2.85
2711 2810 5.163622 ACAAAATCTCTTTCATGCCATACCG 60.164 40.000 0.00 0.00 0.00 4.02
2713 2812 3.459232 TCTCTTTCATGCCATACCGAG 57.541 47.619 0.00 0.00 0.00 4.63
2717 2816 3.349006 CATGCCATACCGAGCGCC 61.349 66.667 2.29 0.00 0.00 6.53
2718 2817 3.550431 ATGCCATACCGAGCGCCT 61.550 61.111 2.29 0.00 0.00 5.52
2731 2830 3.303395 CCGAGCGCCTTAGATGAAAATTC 60.303 47.826 2.29 0.00 0.00 2.17
2734 2833 3.063997 AGCGCCTTAGATGAAAATTCGTG 59.936 43.478 2.29 0.00 0.00 4.35
2766 2865 5.211973 TGCCTATAGAAACCATGTCTCTCT 58.788 41.667 0.00 0.00 0.00 3.10
2840 3022 4.389772 GCAACATGCTCAATCCGC 57.610 55.556 0.00 0.00 40.96 5.54
2876 3058 7.125811 TCAACTGTAACCAAAGGATAGAGCTAT 59.874 37.037 0.00 0.00 27.13 2.97
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
21 22 6.319658 CCATTTTGCACTACTCATAACTCCAT 59.680 38.462 0.00 0.00 0.00 3.41
37 38 5.341872 ACAAATATAGCTGCCATTTTGCA 57.658 34.783 0.00 0.00 39.37 4.08
46 47 8.523464 CAATTCGTAAACAACAAATATAGCTGC 58.477 33.333 0.00 0.00 0.00 5.25
125 126 7.383572 CCAATTGAAATTTATTTGTCGTCACCA 59.616 33.333 7.12 0.00 0.00 4.17
128 130 6.367422 GGCCAATTGAAATTTATTTGTCGTCA 59.633 34.615 7.12 0.00 0.00 4.35
151 153 0.535102 CTCTCTCCTCTCCTCTCGGC 60.535 65.000 0.00 0.00 0.00 5.54
303 306 2.288030 CCTACACGAGTCGTTTGGTCTT 60.288 50.000 17.16 0.00 38.32 3.01
494 514 5.325239 CAACTAGATTTTGGACCCTTCCTT 58.675 41.667 0.00 0.00 43.31 3.36
518 539 3.297736 TCTAGCAAGGCTCCCTAACTAC 58.702 50.000 0.00 0.00 40.44 2.73
827 879 8.819643 AAAAACTCTCGAGATTATATGTAGCC 57.180 34.615 17.03 0.00 0.00 3.93
882 934 3.676873 GCTAGGCCATGGTTGTGAATTTG 60.677 47.826 14.67 0.00 0.00 2.32
1137 1193 1.789410 CGTCGCACCTTGTACTCGTAG 60.789 57.143 0.00 0.00 0.00 3.51
1476 1532 4.382541 TCCTCGCCCCTGAGCTCA 62.383 66.667 17.19 17.19 34.56 4.26
1604 1660 1.067060 GCTGTGGAGTTGAAACAACCC 59.933 52.381 10.38 11.32 0.00 4.11
1803 1868 2.101082 GACGGATTTAGTGTCCTCCTCC 59.899 54.545 0.00 0.00 33.46 4.30
1827 1901 0.098376 ACTCTTCGTCATCCGCGTAC 59.902 55.000 4.92 0.00 36.19 3.67
1845 1919 0.108756 GGTAGTCGTTCAGCAGGGAC 60.109 60.000 0.00 0.00 0.00 4.46
2020 2094 5.769367 TCTACTATAAATACTGCAGGCACG 58.231 41.667 19.93 0.00 0.00 5.34
2025 2099 9.212641 ACATGCAATCTACTATAAATACTGCAG 57.787 33.333 13.48 13.48 40.28 4.41
2028 2102 8.376203 GCGACATGCAATCTACTATAAATACTG 58.624 37.037 0.00 0.00 45.45 2.74
2029 2103 7.273598 CGCGACATGCAATCTACTATAAATACT 59.726 37.037 0.00 0.00 46.97 2.12
2030 2104 7.384124 CGCGACATGCAATCTACTATAAATAC 58.616 38.462 0.00 0.00 46.97 1.89
2031 2105 6.034577 GCGCGACATGCAATCTACTATAAATA 59.965 38.462 12.10 0.00 46.97 1.40
2032 2106 5.163953 GCGCGACATGCAATCTACTATAAAT 60.164 40.000 12.10 0.00 46.97 1.40
2034 2108 3.673338 GCGCGACATGCAATCTACTATAA 59.327 43.478 12.10 0.00 46.97 0.98
2036 2110 2.061773 GCGCGACATGCAATCTACTAT 58.938 47.619 12.10 0.00 46.97 2.12
2037 2111 1.202359 TGCGCGACATGCAATCTACTA 60.202 47.619 12.10 0.00 46.97 1.82
2038 2112 0.460109 TGCGCGACATGCAATCTACT 60.460 50.000 12.10 0.00 46.97 2.57
2039 2113 0.583438 ATGCGCGACATGCAATCTAC 59.417 50.000 12.10 0.00 46.87 2.59
2098 2183 3.181440 ACCAGGAATGCTATACACATGGG 60.181 47.826 0.00 0.00 0.00 4.00
2099 2184 4.067896 GACCAGGAATGCTATACACATGG 58.932 47.826 0.00 0.00 0.00 3.66
2100 2185 4.707105 TGACCAGGAATGCTATACACATG 58.293 43.478 0.00 0.00 0.00 3.21
2143 2228 8.745330 ACATCTCCATCAGATATATATCTCCCT 58.255 37.037 20.31 7.20 40.20 4.20
2205 2292 6.657541 ACACATTTACCCGACTGATAAAACAT 59.342 34.615 0.00 0.00 0.00 2.71
2301 2393 5.557703 GCGGATAAAAATACACCTCGCTTAC 60.558 44.000 0.00 0.00 37.98 2.34
2323 2419 3.116300 ACATCGTACTATTCTTGCTGCG 58.884 45.455 0.00 0.00 0.00 5.18
2484 2583 6.126863 TCATAAACAGACAGATCCAACCTT 57.873 37.500 0.00 0.00 0.00 3.50
2494 2593 8.032952 TGAGCTGTATTTTCATAAACAGACAG 57.967 34.615 5.55 0.00 36.18 3.51
2498 2597 7.185453 GCTCTGAGCTGTATTTTCATAAACAG 58.815 38.462 21.93 0.00 38.45 3.16
2520 2619 3.198068 TCACCGCATAGAAAATGAGCTC 58.802 45.455 6.82 6.82 0.00 4.09
2550 2649 3.832490 TGATTTATCAGACCGGATCGGAT 59.168 43.478 9.46 15.62 43.68 4.18
2556 2655 4.142038 TCTCGATGATTTATCAGACCGGA 58.858 43.478 9.46 0.00 40.64 5.14
2605 2704 0.469070 AATGGTTTTGGCTTGCAGCA 59.531 45.000 9.78 0.00 44.75 4.41
2658 2757 7.987458 GGCCTCGATTATTCATATGGAAATCTA 59.013 37.037 16.55 9.70 39.39 1.98
2698 2797 1.887242 GCGCTCGGTATGGCATGAA 60.887 57.895 10.98 0.00 0.00 2.57
2711 2810 3.309954 ACGAATTTTCATCTAAGGCGCTC 59.690 43.478 7.64 0.00 0.00 5.03
2713 2812 3.063452 TCACGAATTTTCATCTAAGGCGC 59.937 43.478 0.00 0.00 0.00 6.53
2788 2970 7.148755 GGTGACATGGAATTTCAAAGAAATTCG 60.149 37.037 26.21 19.35 43.80 3.34
2807 2989 2.225242 TGTTGCTATTTGGGGGTGACAT 60.225 45.455 0.00 0.00 0.00 3.06
2840 3022 7.308589 CCTTTGGTTACAGTTGACAAATAGAGG 60.309 40.741 0.00 0.00 31.51 3.69


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

AutoCloner maintained by Alex Coulton.