Multiple sequence alignment - TraesCS3B01G409800

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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 TraesCS3B01G409800 chr3B 100.000 3845 0 0 1 3845 646354833 646358677 0 7101
1 TraesCS3B01G409800 chr3B 96.365 3851 127 9 1 3845 656109231 656105388 0 6324
2 TraesCS3B01G409800 chr3B 93.831 3874 197 22 1 3845 664729687 664725827 0 5792
3 TraesCS3B01G409800 chr3B 93.146 1459 98 2 1 1458 420622505 420623962 0 2139
4 TraesCS3B01G409800 chr3B 91.413 1479 105 13 1 1458 545968850 545967373 0 2008
5 TraesCS3B01G409800 chr3B 90.965 1472 115 12 1 1458 151818821 151817354 0 1965
6 TraesCS3B01G409800 chr3B 92.625 678 46 4 1 674 300391203 300391880 0 972
7 TraesCS3B01G409800 chr1B 96.051 3849 137 9 1 3845 575067000 575063163 0 6252
8 TraesCS3B01G409800 chr1B 95.284 3817 144 13 39 3845 413055984 413059774 0 6019
9 TraesCS3B01G409800 chr1B 94.297 3875 186 21 1 3845 84522057 84518188 0 5899
10 TraesCS3B01G409800 chr5B 95.845 3851 148 10 1 3845 519961573 519957729 0 6215
11 TraesCS3B01G409800 chr4B 96.025 3824 137 11 1 3816 629506242 629510058 0 6205
12 TraesCS3B01G409800 chr2B 94.599 3851 163 29 1 3845 35778799 35774988 0 5917
13 TraesCS3B01G409800 chr6B 94.140 3874 184 27 1 3845 42180202 42176343 0 5856


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 TraesCS3B01G409800 chr3B 646354833 646358677 3844 False 7101 7101 100.000 1 3845 1 chr3B.!!$F3 3844
1 TraesCS3B01G409800 chr3B 656105388 656109231 3843 True 6324 6324 96.365 1 3845 1 chr3B.!!$R3 3844
2 TraesCS3B01G409800 chr3B 664725827 664729687 3860 True 5792 5792 93.831 1 3845 1 chr3B.!!$R4 3844
3 TraesCS3B01G409800 chr3B 420622505 420623962 1457 False 2139 2139 93.146 1 1458 1 chr3B.!!$F2 1457
4 TraesCS3B01G409800 chr3B 545967373 545968850 1477 True 2008 2008 91.413 1 1458 1 chr3B.!!$R2 1457
5 TraesCS3B01G409800 chr3B 151817354 151818821 1467 True 1965 1965 90.965 1 1458 1 chr3B.!!$R1 1457
6 TraesCS3B01G409800 chr3B 300391203 300391880 677 False 972 972 92.625 1 674 1 chr3B.!!$F1 673
7 TraesCS3B01G409800 chr1B 575063163 575067000 3837 True 6252 6252 96.051 1 3845 1 chr1B.!!$R2 3844
8 TraesCS3B01G409800 chr1B 413055984 413059774 3790 False 6019 6019 95.284 39 3845 1 chr1B.!!$F1 3806
9 TraesCS3B01G409800 chr1B 84518188 84522057 3869 True 5899 5899 94.297 1 3845 1 chr1B.!!$R1 3844
10 TraesCS3B01G409800 chr5B 519957729 519961573 3844 True 6215 6215 95.845 1 3845 1 chr5B.!!$R1 3844
11 TraesCS3B01G409800 chr4B 629506242 629510058 3816 False 6205 6205 96.025 1 3816 1 chr4B.!!$F1 3815
12 TraesCS3B01G409800 chr2B 35774988 35778799 3811 True 5917 5917 94.599 1 3845 1 chr2B.!!$R1 3844
13 TraesCS3B01G409800 chr6B 42176343 42180202 3859 True 5856 5856 94.140 1 3845 1 chr6B.!!$R1 3844

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
930 961 0.105760 TCCCACAAACCACCATTGCT 60.106 50.0 0.0 0.00 0.0 3.91 F
1050 1081 0.171455 ATGCCGAGACGTCAGAGAAC 59.829 55.0 19.5 2.39 0.0 3.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2691 2731 1.048601 ACGTGATGAGGTTGTCTGGT 58.951 50.000 0.00 0.0 0.0 4.00 R
3015 3055 1.069227 GCTAGCAAACTTGTTGGACGG 60.069 52.381 10.63 0.0 0.0 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
116 118 9.941325 ATGTTTGTCAATTATGCTAAATTTCCA 57.059 25.926 0.00 0.00 0.00 3.53
234 238 1.521906 TCCACACCACAACGAACGG 60.522 57.895 0.00 0.00 0.00 4.44
383 391 0.247185 ATTTCAAACCCATGCGCTGG 59.753 50.000 9.73 13.82 45.51 4.85
630 639 5.046878 ACAGATCCATACGTCACCTAAACAA 60.047 40.000 0.00 0.00 0.00 2.83
650 676 4.188462 CAATGCAAAATGCCATCATCACT 58.812 39.130 0.00 0.00 44.23 3.41
692 718 4.167892 TGGGATTTGGCAGGTCATAAGTAT 59.832 41.667 4.04 0.00 0.00 2.12
930 961 0.105760 TCCCACAAACCACCATTGCT 60.106 50.000 0.00 0.00 0.00 3.91
955 986 2.964464 TCCATTTCCACTGCACACAAAT 59.036 40.909 0.00 0.00 0.00 2.32
987 1018 1.071471 CTCCAAAGCCCACAGTCGT 59.929 57.895 0.00 0.00 0.00 4.34
994 1025 2.989824 CCCACAGTCGTCGGAGGT 60.990 66.667 0.00 0.00 0.00 3.85
1047 1078 0.383590 ATCATGCCGAGACGTCAGAG 59.616 55.000 19.50 8.11 0.00 3.35
1050 1081 0.171455 ATGCCGAGACGTCAGAGAAC 59.829 55.000 19.50 2.39 0.00 3.01
1080 1111 1.131883 CTCGTCGACATTAACGTCCCT 59.868 52.381 17.16 0.00 39.78 4.20
1130 1161 0.779997 AAAGGGGTTGAGCTCCATGT 59.220 50.000 12.15 0.00 41.40 3.21
1181 1212 3.530910 AACCAGACAAGGCCGACGG 62.531 63.158 10.29 10.29 0.00 4.79
1198 1229 1.301558 GGGATGATGAGCAGGCTCG 60.302 63.158 15.83 0.00 45.48 5.03
1357 1389 1.261989 CACAAAATGGCGAGCAATCG 58.738 50.000 0.00 0.00 0.00 3.34
1727 1761 8.072321 ACTACTGATCATTCATCTGTTGTACT 57.928 34.615 0.00 0.00 43.00 2.73
1840 1875 9.562583 TTTATTAAGTTACATGCATTTCCGAAC 57.437 29.630 0.00 0.00 0.00 3.95
1864 1899 4.214310 TGTGAAGTGGATTGTTTCACCAT 58.786 39.130 12.42 0.00 46.23 3.55
2254 2292 9.887406 AAAATAACACGGTGTAGTTGAATTTAG 57.113 29.630 15.11 0.00 0.00 1.85
2258 2296 7.324354 ACACGGTGTAGTTGAATTTAGTTTT 57.676 32.000 12.96 0.00 0.00 2.43
2494 2533 1.699083 TCAGCATTGGAGGTGACAAGA 59.301 47.619 0.00 0.00 40.73 3.02
2550 2589 3.119743 CCAACAACTTCATCGACATGCAT 60.120 43.478 0.00 0.00 0.00 3.96
2814 2854 1.133009 CAGGAGGCTGACCCCTACTAT 60.133 57.143 0.00 0.00 44.62 2.12
2819 2859 2.789992 AGGCTGACCCCTACTATCACTA 59.210 50.000 0.00 0.00 36.11 2.74
2873 2913 3.679502 GCATTTGTTATGTTGAACCAGCC 59.320 43.478 0.00 0.00 0.00 4.85
3015 3055 5.216566 TCAAGTACATCGTTTGCTTATGC 57.783 39.130 0.00 0.00 40.20 3.14
3285 3331 2.568623 AAGTTTCAGCCGAGGACAAT 57.431 45.000 0.00 0.00 0.00 2.71
3388 3434 6.886459 ACCAGTACGTATTTCCTAGTCACTAA 59.114 38.462 0.00 0.00 0.00 2.24
3404 3450 5.419471 AGTCACTAACATCCTAGGACTGAAC 59.581 44.000 15.42 4.89 32.65 3.18
3417 3463 3.130693 AGGACTGAACGTTCTGGTATAGC 59.869 47.826 30.70 16.55 27.35 2.97
3531 3577 6.892658 AACAGTGGCAATACAACTGAAATA 57.107 33.333 7.20 0.00 33.15 1.40
3561 3607 4.650754 ACTAAGTCTATACGGCAAGTGG 57.349 45.455 0.00 0.00 0.00 4.00
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
234 238 7.413767 GGGTTTGAGATTATTTTACGACCAGAC 60.414 40.741 0.00 0.00 0.00 3.51
309 316 8.812972 ACTGATCCTGTTGTTTTAGTACTGATA 58.187 33.333 5.39 0.00 0.00 2.15
383 391 8.627487 TGTGTGAACTGAATTGTAATTTCAAC 57.373 30.769 0.00 0.00 0.00 3.18
650 676 1.080772 CTTGCACGTCTCTGCGGTA 60.081 57.895 0.00 0.00 40.31 4.02
692 718 7.520451 TGAACTAACTAGTCTTGTCAAGCTA 57.480 36.000 7.78 11.01 34.99 3.32
791 817 2.644418 GCCGTTTGCAGTGCATCA 59.356 55.556 20.50 5.98 38.76 3.07
930 961 0.961019 GTGCAGTGGAAATGGAAGCA 59.039 50.000 0.00 0.00 31.16 3.91
955 986 0.038310 TTGGAGAGAGACGCTGGAGA 59.962 55.000 0.00 0.00 0.00 3.71
987 1018 3.161450 GCCATGGCCTACCTCCGA 61.161 66.667 27.24 0.00 36.63 4.55
994 1025 2.366301 TTCCTCCGCCATGGCCTA 60.366 61.111 30.79 17.66 37.80 3.93
1130 1161 1.685517 CGATCTCCAGCATCTCCTTGA 59.314 52.381 0.00 0.00 0.00 3.02
1181 1212 1.301558 CCGAGCCTGCTCATCATCC 60.302 63.158 18.45 0.00 42.86 3.51
1198 1229 4.570874 GCCGCCTCCCTTCATCCC 62.571 72.222 0.00 0.00 0.00 3.85
1298 1329 0.241213 CAAGCAGAGTTCCTCGACGA 59.759 55.000 0.00 0.00 35.36 4.20
1357 1389 3.254166 CCATATGCAGGGCAAATGAGTAC 59.746 47.826 0.00 0.00 43.62 2.73
1411 1443 6.549364 AGTTGGGAAACAAGTGTGATCAAATA 59.451 34.615 0.00 0.00 41.13 1.40
1416 1448 5.305585 TCTAGTTGGGAAACAAGTGTGATC 58.694 41.667 0.00 0.00 42.57 2.92
1840 1875 3.004734 GGTGAAACAATCCACTTCACAGG 59.995 47.826 14.18 0.00 46.98 4.00
2254 2292 9.322773 AGAAACTAGTACACAAAGTCCTAAAAC 57.677 33.333 0.00 0.00 0.00 2.43
2258 2296 7.828508 TCAGAAACTAGTACACAAAGTCCTA 57.171 36.000 0.00 0.00 0.00 2.94
2494 2533 1.202330 CCAGACTTCTCCAGCATCCT 58.798 55.000 0.00 0.00 0.00 3.24
2576 2615 3.195661 GCCAAGGAGTCGTAGTATTTGG 58.804 50.000 0.00 0.00 37.30 3.28
2691 2731 1.048601 ACGTGATGAGGTTGTCTGGT 58.951 50.000 0.00 0.00 0.00 4.00
2814 2854 1.542472 TCATCCGCGAAGTTGTAGTGA 59.458 47.619 8.23 0.00 0.00 3.41
2819 2859 2.002586 CATCTTCATCCGCGAAGTTGT 58.997 47.619 8.23 0.00 42.53 3.32
3015 3055 1.069227 GCTAGCAAACTTGTTGGACGG 60.069 52.381 10.63 0.00 0.00 4.79
3230 3276 9.010029 AGTGTTCTTCTGAAACTAAAAACTGAA 57.990 29.630 0.00 0.00 33.52 3.02
3285 3331 7.000575 GCACGATGCTTTTTAGTACTGAATA 57.999 36.000 5.39 0.00 40.96 1.75
3388 3434 3.193691 CAGAACGTTCAGTCCTAGGATGT 59.806 47.826 28.78 2.35 0.00 3.06
3404 3450 3.612860 GTGTGTTCAGCTATACCAGAACG 59.387 47.826 7.58 0.00 42.35 3.95
3417 3463 1.842720 TGAACGTACCGTGTGTTCAG 58.157 50.000 13.40 0.00 44.97 3.02
3462 3508 2.079925 GGAATGCGAACTGAAGCTTCT 58.920 47.619 26.09 7.23 0.00 2.85
3531 3577 6.544931 TGCCGTATAGACTTAGTTGTACTGAT 59.455 38.462 0.00 0.00 0.00 2.90
3561 3607 3.620488 TCCAGGCAATGTTTGATCCTAC 58.380 45.455 0.00 0.00 0.00 3.18


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

AutoCloner maintained by Alex Coulton.