Multiple sequence alignment - TraesCS3B01G233400

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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 TraesCS3B01G233400 chr3B 100.000 2897 0 0 1 2897 361553205 361556101 0.000000e+00 5350.0
1 TraesCS3B01G233400 chr3B 92.840 2905 169 20 17 2897 284887288 284884399 0.000000e+00 4176.0
2 TraesCS3B01G233400 chr3B 92.473 2750 163 22 11 2737 291334189 291336917 0.000000e+00 3892.0
3 TraesCS3B01G233400 chr3B 83.696 92 6 8 2 89 261626921 261627007 8.610000e-11 78.7
4 TraesCS3B01G233400 chr4B 97.028 2826 61 8 89 2897 451473306 451476125 0.000000e+00 4732.0
5 TraesCS3B01G233400 chr4B 92.987 2923 138 39 1 2897 379118206 379115325 0.000000e+00 4200.0
6 TraesCS3B01G233400 chr4B 92.960 2912 154 28 20 2897 422726239 422723345 0.000000e+00 4194.0
7 TraesCS3B01G233400 chr4B 92.326 2919 148 44 17 2897 411556109 411558989 0.000000e+00 4080.0
8 TraesCS3B01G233400 chr4B 91.121 2917 206 28 13 2897 162547899 162550794 0.000000e+00 3903.0
9 TraesCS3B01G233400 chr7B 96.410 2841 82 7 75 2897 161598416 161601254 0.000000e+00 4663.0
10 TraesCS3B01G233400 chr7B 89.320 2912 238 42 15 2897 595538711 595541578 0.000000e+00 3587.0
11 TraesCS3B01G233400 chr7B 84.992 1186 129 31 1717 2897 182945410 182944269 0.000000e+00 1158.0
12 TraesCS3B01G233400 chr1B 93.685 2898 151 14 18 2896 230373429 230370545 0.000000e+00 4309.0
13 TraesCS3B01G233400 chr2B 92.451 2901 165 22 18 2896 272450357 272453225 0.000000e+00 4095.0
14 TraesCS3B01G233400 chr5B 90.000 2930 200 55 15 2897 293193064 293190181 0.000000e+00 3701.0
15 TraesCS3B01G233400 chr3A 81.963 2944 381 96 17 2897 417633955 417631099 0.000000e+00 2357.0
16 TraesCS3B01G233400 chr4A 84.243 971 94 32 1943 2897 344967767 344966840 0.000000e+00 891.0
17 TraesCS3B01G233400 chr6B 96.970 297 9 0 2601 2897 680657606 680657902 1.550000e-137 499.0


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 TraesCS3B01G233400 chr3B 361553205 361556101 2896 False 5350 5350 100.000 1 2897 1 chr3B.!!$F3 2896
1 TraesCS3B01G233400 chr3B 284884399 284887288 2889 True 4176 4176 92.840 17 2897 1 chr3B.!!$R1 2880
2 TraesCS3B01G233400 chr3B 291334189 291336917 2728 False 3892 3892 92.473 11 2737 1 chr3B.!!$F2 2726
3 TraesCS3B01G233400 chr4B 451473306 451476125 2819 False 4732 4732 97.028 89 2897 1 chr4B.!!$F3 2808
4 TraesCS3B01G233400 chr4B 379115325 379118206 2881 True 4200 4200 92.987 1 2897 1 chr4B.!!$R1 2896
5 TraesCS3B01G233400 chr4B 422723345 422726239 2894 True 4194 4194 92.960 20 2897 1 chr4B.!!$R2 2877
6 TraesCS3B01G233400 chr4B 411556109 411558989 2880 False 4080 4080 92.326 17 2897 1 chr4B.!!$F2 2880
7 TraesCS3B01G233400 chr4B 162547899 162550794 2895 False 3903 3903 91.121 13 2897 1 chr4B.!!$F1 2884
8 TraesCS3B01G233400 chr7B 161598416 161601254 2838 False 4663 4663 96.410 75 2897 1 chr7B.!!$F1 2822
9 TraesCS3B01G233400 chr7B 595538711 595541578 2867 False 3587 3587 89.320 15 2897 1 chr7B.!!$F2 2882
10 TraesCS3B01G233400 chr7B 182944269 182945410 1141 True 1158 1158 84.992 1717 2897 1 chr7B.!!$R1 1180
11 TraesCS3B01G233400 chr1B 230370545 230373429 2884 True 4309 4309 93.685 18 2896 1 chr1B.!!$R1 2878
12 TraesCS3B01G233400 chr2B 272450357 272453225 2868 False 4095 4095 92.451 18 2896 1 chr2B.!!$F1 2878
13 TraesCS3B01G233400 chr5B 293190181 293193064 2883 True 3701 3701 90.000 15 2897 1 chr5B.!!$R1 2882
14 TraesCS3B01G233400 chr3A 417631099 417633955 2856 True 2357 2357 81.963 17 2897 1 chr3A.!!$R1 2880
15 TraesCS3B01G233400 chr4A 344966840 344967767 927 True 891 891 84.243 1943 2897 1 chr4A.!!$R1 954

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
832 898 1.032014 ACACAAGCAGTCCGCAATTT 58.968 45.0 0.0 0.0 46.13 1.82 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2584 2707 3.132289 ACATGGTATACACCTGGTTCGAG 59.868 47.826 5.01 0.0 45.98 4.04 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
94 128 8.084073 TCATTTTCTTTGTTGATGATCCTTGTC 58.916 33.333 0.00 0.00 0.00 3.18
148 187 4.288626 TCATTTGGGTCACCTAGCTTTAGT 59.711 41.667 0.00 0.00 37.76 2.24
271 315 2.102553 GGGACTAGTGTCGAGCGC 59.897 66.667 0.00 0.00 43.79 5.92
404 455 5.834169 GGATACTAACCTTCTGACTAGTGC 58.166 45.833 0.00 0.00 0.00 4.40
413 464 5.164954 CCTTCTGACTAGTGCTTACTGTTC 58.835 45.833 0.00 0.00 0.00 3.18
447 498 8.271458 TGTGTAGGGAATCATAAATCTTTGCTA 58.729 33.333 0.00 0.00 0.00 3.49
631 682 1.267574 GGACTGCCCACTGAGGATCA 61.268 60.000 0.00 0.00 41.22 2.92
699 750 4.785376 AGTACCATGGAGTTCCTCAAGATT 59.215 41.667 21.47 0.00 36.82 2.40
721 772 5.868043 TCTATCAAGTGCATGTTGTTCTG 57.132 39.130 10.56 2.43 0.00 3.02
741 792 3.577848 CTGATTCTCTCTCCGGGATGATT 59.422 47.826 0.00 0.00 0.00 2.57
759 811 2.273370 TTCTCGTGCTTGGTATCGAC 57.727 50.000 0.00 0.00 0.00 4.20
832 898 1.032014 ACACAAGCAGTCCGCAATTT 58.968 45.000 0.00 0.00 46.13 1.82
858 924 2.562738 TGAGATCCTCAGCTTCGTTCAA 59.437 45.455 0.00 0.00 35.39 2.69
954 1020 2.159184 CGAGAGATGGTTAGAGCTGCAA 60.159 50.000 1.02 0.00 0.00 4.08
1108 1174 4.347000 GGTACAATGATAAGCCCACCTCTA 59.653 45.833 0.00 0.00 0.00 2.43
1435 1501 3.457610 TCGATGATGTCAGCTGCATTA 57.542 42.857 19.92 17.21 0.00 1.90
1819 1891 4.638865 AGTGTTCTTTCAGGTTTACGCTTT 59.361 37.500 0.00 0.00 0.00 3.51
2413 2511 0.249120 TCGGTAGCATGTGAACCAGG 59.751 55.000 11.98 0.00 32.55 4.45
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
37 39 8.497745 AGCAAAGGGAGATGAAGATTATCTTTA 58.502 33.333 8.99 5.39 36.73 1.85
38 40 7.352738 AGCAAAGGGAGATGAAGATTATCTTT 58.647 34.615 8.99 0.00 36.73 2.52
94 128 9.796120 TGAAAACAGAAAATAAACCTAACACTG 57.204 29.630 0.00 0.00 0.00 3.66
126 165 4.589908 ACTAAAGCTAGGTGACCCAAATG 58.410 43.478 0.00 0.00 0.00 2.32
148 187 2.431260 GGCGGCAACTACGTTCGA 60.431 61.111 3.07 0.00 0.00 3.71
164 205 2.363795 TCCACAGGGACTAGGCGG 60.364 66.667 0.00 0.00 38.64 6.13
262 306 0.666274 CCTAACACAAGCGCTCGACA 60.666 55.000 12.06 0.00 0.00 4.35
404 455 5.635280 CCTACACACACTCATGAACAGTAAG 59.365 44.000 0.00 0.00 0.00 2.34
413 464 4.206477 TGATTCCCTACACACACTCATG 57.794 45.455 0.00 0.00 0.00 3.07
631 682 5.131067 TGACTCGGTATAAGTGCTCATAGT 58.869 41.667 0.00 0.00 0.00 2.12
699 750 5.550290 TCAGAACAACATGCACTTGATAGA 58.450 37.500 11.95 1.49 0.00 1.98
721 772 3.831911 AGAATCATCCCGGAGAGAGAATC 59.168 47.826 0.73 4.36 0.00 2.52
741 792 0.454600 GGTCGATACCAAGCACGAGA 59.545 55.000 0.00 0.00 45.98 4.04
832 898 2.622470 CGAAGCTGAGGATCTCATCTCA 59.378 50.000 2.37 0.00 39.92 3.27
858 924 0.322975 ACAAGCTCTCGCCTTCATGT 59.677 50.000 0.00 0.00 36.60 3.21
954 1020 9.621239 TCCCAAGTCAATCCTCTATAGAATATT 57.379 33.333 3.57 3.95 0.00 1.28
1108 1174 4.197750 TGTTGCAAGCAAACCAATGAATT 58.802 34.783 9.32 0.00 37.70 2.17
2279 2376 6.832384 TGATCTAGGTGTATCGAGGTAAAAGT 59.168 38.462 0.00 0.00 0.00 2.66
2413 2511 3.564644 CAGGAATCATCACTTCTCCATGC 59.435 47.826 0.00 0.00 0.00 4.06
2531 2645 5.192927 CCCAAGCTAACCTGATTTCACATA 58.807 41.667 0.00 0.00 0.00 2.29
2584 2707 3.132289 ACATGGTATACACCTGGTTCGAG 59.868 47.826 5.01 0.00 45.98 4.04


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

AutoCloner maintained by Alex Coulton.