Multiple sequence alignment - TraesCS3B01G055100

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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 TraesCS3B01G055100 chr3B 100.000 3089 0 0 1 3089 28519765 28516677 0.000000e+00 5705
1 TraesCS3B01G055100 chr3B 98.092 3093 53 4 1 3089 28531174 28528084 0.000000e+00 5380
2 TraesCS3B01G055100 chr3B 96.868 3097 87 7 1 3089 28410591 28407497 0.000000e+00 5173
3 TraesCS3B01G055100 chr3B 96.740 3098 90 7 1 3089 28457103 28454008 0.000000e+00 5151
4 TraesCS3B01G055100 chr3B 96.610 3097 96 6 1 3089 28423756 28420661 0.000000e+00 5129
5 TraesCS3B01G055100 chr3B 95.202 2751 105 13 359 3089 28564194 28561451 0.000000e+00 4325
6 TraesCS3B01G055100 chr3B 90.859 2899 186 25 256 3089 14024363 14021479 0.000000e+00 3812
7 TraesCS3B01G055100 chr3B 96.868 2267 60 7 831 3089 28492700 28490437 0.000000e+00 3783
8 TraesCS3B01G055100 chr3B 90.893 2833 202 18 305 3089 14106558 14103734 0.000000e+00 3751
9 TraesCS3B01G055100 chr3B 91.295 2780 191 16 256 2997 14066606 14063840 0.000000e+00 3746
10 TraesCS3B01G055100 chr3B 89.924 2878 223 30 256 3089 14113272 14110418 0.000000e+00 3646
11 TraesCS3B01G055100 chr3B 89.840 2874 228 36 256 3089 13994978 13992129 0.000000e+00 3631
12 TraesCS3B01G055100 chr3B 95.738 610 19 7 2484 3089 28468127 28467521 0.000000e+00 976
13 TraesCS3B01G055100 chr3B 96.825 252 8 0 1 252 28396320 28396069 3.680000e-114 422
14 TraesCS3B01G055100 chr3B 96.825 252 8 0 1 252 28442225 28441974 3.680000e-114 422
15 TraesCS3B01G055100 chr3B 94.841 252 12 1 1 252 416368482 416368232 2.890000e-105 392
16 TraesCS3B01G055100 chrUn 95.431 2495 96 12 606 3089 307487399 307489886 0.000000e+00 3960
17 TraesCS3B01G055100 chrUn 95.351 2495 98 12 606 3089 328827719 328830206 0.000000e+00 3949
18 TraesCS3B01G055100 chrUn 97.510 241 6 0 359 599 37979290 37979050 2.220000e-111 412
19 TraesCS3B01G055100 chr3D 83.913 2903 332 53 256 3089 9949189 9946353 0.000000e+00 2649
20 TraesCS3B01G055100 chr3D 86.097 597 65 15 256 844 5682515 5681929 7.270000e-176 627
21 TraesCS3B01G055100 chr2A 86.329 790 85 14 286 1070 19663943 19663172 0.000000e+00 839
22 TraesCS3B01G055100 chr4B 94.841 252 11 2 1 252 316079774 316080023 2.890000e-105 392
23 TraesCS3B01G055100 chr7D 94.444 252 14 0 1 252 361896431 361896180 3.740000e-104 388


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 TraesCS3B01G055100 chr3B 28516677 28519765 3088 True 5705.0 5705 100.0000 1 3089 1 chr3B.!!$R11 3088
1 TraesCS3B01G055100 chr3B 28528084 28531174 3090 True 5380.0 5380 98.0920 1 3089 1 chr3B.!!$R12 3088
2 TraesCS3B01G055100 chr3B 28407497 28410591 3094 True 5173.0 5173 96.8680 1 3089 1 chr3B.!!$R5 3088
3 TraesCS3B01G055100 chr3B 28454008 28457103 3095 True 5151.0 5151 96.7400 1 3089 1 chr3B.!!$R8 3088
4 TraesCS3B01G055100 chr3B 28420661 28423756 3095 True 5129.0 5129 96.6100 1 3089 1 chr3B.!!$R6 3088
5 TraesCS3B01G055100 chr3B 28561451 28564194 2743 True 4325.0 4325 95.2020 359 3089 1 chr3B.!!$R13 2730
6 TraesCS3B01G055100 chr3B 14021479 14024363 2884 True 3812.0 3812 90.8590 256 3089 1 chr3B.!!$R2 2833
7 TraesCS3B01G055100 chr3B 28490437 28492700 2263 True 3783.0 3783 96.8680 831 3089 1 chr3B.!!$R10 2258
8 TraesCS3B01G055100 chr3B 14063840 14066606 2766 True 3746.0 3746 91.2950 256 2997 1 chr3B.!!$R3 2741
9 TraesCS3B01G055100 chr3B 14103734 14113272 9538 True 3698.5 3751 90.4085 256 3089 2 chr3B.!!$R15 2833
10 TraesCS3B01G055100 chr3B 13992129 13994978 2849 True 3631.0 3631 89.8400 256 3089 1 chr3B.!!$R1 2833
11 TraesCS3B01G055100 chr3B 28467521 28468127 606 True 976.0 976 95.7380 2484 3089 1 chr3B.!!$R9 605
12 TraesCS3B01G055100 chrUn 307487399 307489886 2487 False 3960.0 3960 95.4310 606 3089 1 chrUn.!!$F1 2483
13 TraesCS3B01G055100 chrUn 328827719 328830206 2487 False 3949.0 3949 95.3510 606 3089 1 chrUn.!!$F2 2483
14 TraesCS3B01G055100 chr3D 9946353 9949189 2836 True 2649.0 2649 83.9130 256 3089 1 chr3D.!!$R2 2833
15 TraesCS3B01G055100 chr3D 5681929 5682515 586 True 627.0 627 86.0970 256 844 1 chr3D.!!$R1 588
16 TraesCS3B01G055100 chr2A 19663172 19663943 771 True 839.0 839 86.3290 286 1070 1 chr2A.!!$R1 784

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
599 7289 0.463116 GACTCCCACGTGTTTGGTGT 60.463 55.0 15.65 14.86 34.44 4.16 F
1731 8468 1.658686 GACTGGTGCTCCTCGACGAT 61.659 60.0 6.34 0.00 34.23 3.73 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2040 8783 0.792640 GCTTATCGATGCGGATGTGG 59.207 55.000 8.54 0.0 0.0 4.17 R
2928 9746 3.639094 AGCTAGCGTAGTCTTCATTCCAT 59.361 43.478 9.55 0.0 0.0 3.41 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
117 118 2.792947 GCATCGGCGAAGGGGTCTA 61.793 63.158 15.93 0.00 0.00 2.59
325 327 3.777465 ACTTCATGCAAGCAGCTAATG 57.223 42.857 0.00 0.56 45.94 1.90
413 7083 5.402270 GTGGTCATGTTGTTGTTATTTGCTC 59.598 40.000 0.00 0.00 0.00 4.26
480 7150 2.505819 AGTGAGGAAGGCGGAATGTATT 59.494 45.455 0.00 0.00 0.00 1.89
599 7289 0.463116 GACTCCCACGTGTTTGGTGT 60.463 55.000 15.65 14.86 34.44 4.16
1285 8007 3.600388 TCCTTCTTTCTTCCTCGATTGC 58.400 45.455 0.00 0.00 0.00 3.56
1713 8450 3.366915 TCGGTGTCGACCATGCGA 61.367 61.111 14.12 6.46 43.33 5.10
1727 8464 3.749064 GCGACTGGTGCTCCTCGA 61.749 66.667 17.61 0.00 34.63 4.04
1731 8468 1.658686 GACTGGTGCTCCTCGACGAT 61.659 60.000 6.34 0.00 34.23 3.73
2040 8783 1.752084 GCATCCATGGAAGTTCCCCTC 60.752 57.143 20.67 0.00 35.03 4.30
2120 8868 1.340889 GCTGCTGATGGGAAACAAACA 59.659 47.619 0.00 0.00 0.00 2.83
2911 9729 4.829968 AGATCTGACTCACTGACATTTGG 58.170 43.478 0.00 0.00 0.00 3.28
2912 9730 4.529769 AGATCTGACTCACTGACATTTGGA 59.470 41.667 0.00 0.00 0.00 3.53
2913 9731 3.995199 TCTGACTCACTGACATTTGGAC 58.005 45.455 0.00 0.00 0.00 4.02
2914 9732 3.387699 TCTGACTCACTGACATTTGGACA 59.612 43.478 0.00 0.00 0.00 4.02
2916 9734 3.876914 TGACTCACTGACATTTGGACAAC 59.123 43.478 0.00 0.00 0.00 3.32
2918 9736 4.130118 ACTCACTGACATTTGGACAACTC 58.870 43.478 0.00 0.00 0.00 3.01
2920 9738 4.380531 TCACTGACATTTGGACAACTCTC 58.619 43.478 0.00 0.00 0.00 3.20
2924 9742 6.483307 CACTGACATTTGGACAACTCTCTTTA 59.517 38.462 0.00 0.00 0.00 1.85
2925 9743 6.483640 ACTGACATTTGGACAACTCTCTTTAC 59.516 38.462 0.00 0.00 0.00 2.01
2926 9744 6.353323 TGACATTTGGACAACTCTCTTTACA 58.647 36.000 0.00 0.00 0.00 2.41
2927 9745 6.826231 TGACATTTGGACAACTCTCTTTACAA 59.174 34.615 0.00 0.00 0.00 2.41
2928 9746 7.338196 TGACATTTGGACAACTCTCTTTACAAA 59.662 33.333 0.00 0.00 0.00 2.83
2930 9748 8.511465 CATTTGGACAACTCTCTTTACAAATG 57.489 34.615 10.97 10.97 43.83 2.32
2931 9749 6.633500 TTGGACAACTCTCTTTACAAATGG 57.367 37.500 0.00 0.00 0.00 3.16
2933 9751 6.361433 TGGACAACTCTCTTTACAAATGGAA 58.639 36.000 0.00 0.00 0.00 3.53
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
117 118 1.213094 CGTGTGCGAGAAAACCGACT 61.213 55.000 0.00 0.0 41.33 4.18
196 197 3.189910 CGCATACTAGCCAAATCATGCAT 59.810 43.478 0.00 0.0 38.91 3.96
325 327 1.130561 CCCTCGACGCCAAAAATCTTC 59.869 52.381 0.00 0.0 0.00 2.87
413 7083 3.807538 GATGTGCTGGCTGCCACG 61.808 66.667 19.30 14.9 42.00 4.94
480 7150 5.527214 CACACAACTTTTCACCTAGATCACA 59.473 40.000 0.00 0.0 0.00 3.58
599 7289 5.163353 TGACTCCATCGCCAGATTATAACAA 60.163 40.000 0.00 0.0 34.23 2.83
1285 8007 2.230025 AGAATCGATCTATCACCGGCAG 59.770 50.000 0.00 0.0 36.32 4.85
1713 8450 1.679305 ATCGTCGAGGAGCACCAGT 60.679 57.895 13.85 0.0 38.94 4.00
1727 8464 2.158957 AGGAACACACAGTTGTCATCGT 60.159 45.455 0.00 0.0 41.51 3.73
1731 8468 3.118445 TCATGAGGAACACACAGTTGTCA 60.118 43.478 0.00 0.0 41.51 3.58
2040 8783 0.792640 GCTTATCGATGCGGATGTGG 59.207 55.000 8.54 0.0 0.00 4.17
2120 8868 0.877071 CGAACTGCCTTGAATGCACT 59.123 50.000 0.00 0.0 34.46 4.40
2911 9729 8.099364 TCATTCCATTTGTAAAGAGAGTTGTC 57.901 34.615 0.00 0.0 0.00 3.18
2912 9730 8.463930 TTCATTCCATTTGTAAAGAGAGTTGT 57.536 30.769 0.00 0.0 0.00 3.32
2913 9731 8.786898 TCTTCATTCCATTTGTAAAGAGAGTTG 58.213 33.333 0.00 0.0 0.00 3.16
2914 9732 8.787852 GTCTTCATTCCATTTGTAAAGAGAGTT 58.212 33.333 0.00 0.0 0.00 3.01
2916 9734 8.558973 AGTCTTCATTCCATTTGTAAAGAGAG 57.441 34.615 0.00 0.0 0.00 3.20
2918 9736 8.383619 CGTAGTCTTCATTCCATTTGTAAAGAG 58.616 37.037 0.00 0.0 0.00 2.85
2920 9738 6.961554 GCGTAGTCTTCATTCCATTTGTAAAG 59.038 38.462 0.00 0.0 0.00 1.85
2924 9742 4.579869 AGCGTAGTCTTCATTCCATTTGT 58.420 39.130 0.00 0.0 0.00 2.83
2925 9743 5.277058 GCTAGCGTAGTCTTCATTCCATTTG 60.277 44.000 0.00 0.0 0.00 2.32
2926 9744 4.811557 GCTAGCGTAGTCTTCATTCCATTT 59.188 41.667 0.00 0.0 0.00 2.32
2927 9745 4.100189 AGCTAGCGTAGTCTTCATTCCATT 59.900 41.667 9.55 0.0 0.00 3.16
2928 9746 3.639094 AGCTAGCGTAGTCTTCATTCCAT 59.361 43.478 9.55 0.0 0.00 3.41
2930 9748 3.719173 AGCTAGCGTAGTCTTCATTCC 57.281 47.619 9.55 0.0 0.00 3.01
2931 9749 5.631512 CCATTAGCTAGCGTAGTCTTCATTC 59.368 44.000 9.55 0.0 0.00 2.67
2933 9751 4.827835 TCCATTAGCTAGCGTAGTCTTCAT 59.172 41.667 9.55 0.0 0.00 2.57


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

AutoCloner maintained by Alex Coulton.