Multiple sequence alignment - TraesCS4A01G303100

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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 TraesCS4A01G303100 chr4A 100.000 5883 0 0 1 5883 599224173 599218291 0.000000e+00 10864.0
1 TraesCS4A01G303100 chr4A 99.577 4970 20 1 1 4969 599180746 599175777 0.000000e+00 9060.0
2 TraesCS4A01G303100 chr4A 98.794 4893 47 2 1 4881 599103367 599098475 0.000000e+00 8698.0
3 TraesCS4A01G303100 chr4A 94.504 2784 143 9 2177 4955 599246791 599244013 0.000000e+00 4285.0
4 TraesCS4A01G303100 chr4A 94.365 2786 144 11 2177 4955 599157712 599154933 0.000000e+00 4263.0
5 TraesCS4A01G303100 chr4A 94.287 2783 150 8 2177 4955 599124753 599121976 0.000000e+00 4250.0
6 TraesCS4A01G303100 chr4A 98.557 2357 29 3 1 2356 599147583 599145231 0.000000e+00 4159.0
7 TraesCS4A01G303100 chr4A 95.997 2523 96 5 2437 4955 599083271 599080750 0.000000e+00 4095.0
8 TraesCS4A01G303100 chr4A 96.346 2381 82 5 1 2378 599085644 599083266 0.000000e+00 3910.0
9 TraesCS4A01G303100 chr4A 98.972 2043 20 1 2358 4400 599144528 599142487 0.000000e+00 3655.0
10 TraesCS4A01G303100 chr4A 93.434 2117 116 17 1 2101 599126860 599124751 0.000000e+00 3118.0
11 TraesCS4A01G303100 chr4A 93.296 2118 119 16 1 2101 599159821 599157710 0.000000e+00 3103.0
12 TraesCS4A01G303100 chr4A 93.245 2117 122 15 1 2101 599248900 599246789 0.000000e+00 3097.0
13 TraesCS4A01G303100 chr4A 98.998 898 8 1 4986 5883 599175794 599174898 0.000000e+00 1607.0
14 TraesCS4A01G303100 chr4A 97.971 887 11 3 5003 5883 599097632 599096747 0.000000e+00 1531.0
15 TraesCS4A01G303100 chr4A 96.655 837 21 5 5050 5883 599080720 599079888 0.000000e+00 1384.0
16 TraesCS4A01G303100 chr4A 93.720 844 48 5 5014 5854 599121971 599121130 0.000000e+00 1260.0
17 TraesCS4A01G303100 chr4A 86.644 1168 101 28 738 1882 598816175 598815040 0.000000e+00 1242.0
18 TraesCS4A01G303100 chr4A 92.536 844 45 7 5014 5854 599244008 599243180 0.000000e+00 1194.0
19 TraesCS4A01G303100 chr4A 93.997 683 35 3 4238 4914 599125750 599125068 0.000000e+00 1029.0
20 TraesCS4A01G303100 chr4A 93.997 683 35 3 4238 4914 599247789 599247107 0.000000e+00 1029.0
21 TraesCS4A01G303100 chr4A 98.540 548 4 3 5048 5594 599098187 599097643 0.000000e+00 965.0
22 TraesCS4A01G303100 chr4A 98.540 548 4 3 5048 5594 599141988 599141444 0.000000e+00 965.0
23 TraesCS4A01G303100 chr4A 95.556 45 0 2 4912 4955 599314959 599314916 2.940000e-08 71.3
24 TraesCS4A01G303100 chr4A 97.143 35 1 0 5849 5883 599297129 599297095 6.370000e-05 60.2
25 TraesCS4A01G303100 chrUn 94.397 2784 146 9 2177 4955 216674910 216672132 0.000000e+00 4268.0
26 TraesCS4A01G303100 chrUn 98.486 1982 25 3 376 2356 360633605 360631628 0.000000e+00 3489.0
27 TraesCS4A01G303100 chrUn 100.000 1276 0 0 1 1276 216653054 216651779 0.000000e+00 2357.0
28 TraesCS4A01G303100 chrUn 92.891 844 42 7 5014 5854 216672127 216671299 0.000000e+00 1210.0
29 TraesCS4A01G303100 chrUn 99.306 288 2 0 5596 5883 291673858 291674145 6.760000e-144 521.0
30 TraesCS4A01G303100 chr4D 91.196 2976 191 36 589 3532 4416666 4419602 0.000000e+00 3978.0
31 TraesCS4A01G303100 chr4D 94.893 607 23 5 5014 5613 4377653 4378258 0.000000e+00 942.0
32 TraesCS4A01G303100 chr4D 93.506 231 15 0 5624 5854 4381939 4382169 1.570000e-90 344.0
33 TraesCS4A01G303100 chr4D 97.143 35 1 0 5849 5883 4382176 4382210 6.370000e-05 60.2
34 TraesCS4A01G303100 chr6A 93.440 2439 117 19 746 3177 593027288 593024886 0.000000e+00 3578.0
35 TraesCS4A01G303100 chr6A 94.165 1748 92 5 3218 4955 593024889 593023142 0.000000e+00 2654.0
36 TraesCS4A01G303100 chr6A 93.107 885 42 7 5014 5883 593023137 593022257 0.000000e+00 1279.0
37 TraesCS4A01G303100 chr4B 87.823 271 21 3 5624 5882 7154780 7155050 2.060000e-79 307.0
38 TraesCS4A01G303100 chr3D 88.742 151 17 0 5220 5370 434949462 434949612 1.010000e-42 185.0


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 TraesCS4A01G303100 chr4A 599218291 599224173 5882 True 10864.000000 10864 100.000000 1 5883 1 chr4A.!!$R2 5882
1 TraesCS4A01G303100 chr4A 599174898 599180746 5848 True 5333.500000 9060 99.287500 1 5883 2 chr4A.!!$R10 5882
2 TraesCS4A01G303100 chr4A 599096747 599103367 6620 True 3731.333333 8698 98.435000 1 5883 3 chr4A.!!$R6 5882
3 TraesCS4A01G303100 chr4A 599154933 599159821 4888 True 3683.000000 4263 93.830500 1 4955 2 chr4A.!!$R9 4954
4 TraesCS4A01G303100 chr4A 599079888 599085644 5756 True 3129.666667 4095 96.332667 1 5883 3 chr4A.!!$R5 5882
5 TraesCS4A01G303100 chr4A 599141444 599147583 6139 True 2926.333333 4159 98.689667 1 5594 3 chr4A.!!$R8 5593
6 TraesCS4A01G303100 chr4A 599121130 599126860 5730 True 2414.250000 4250 93.859500 1 5854 4 chr4A.!!$R7 5853
7 TraesCS4A01G303100 chr4A 599243180 599248900 5720 True 2401.250000 4285 93.570500 1 5854 4 chr4A.!!$R11 5853
8 TraesCS4A01G303100 chr4A 598815040 598816175 1135 True 1242.000000 1242 86.644000 738 1882 1 chr4A.!!$R1 1144
9 TraesCS4A01G303100 chrUn 360631628 360633605 1977 True 3489.000000 3489 98.486000 376 2356 1 chrUn.!!$R2 1980
10 TraesCS4A01G303100 chrUn 216671299 216674910 3611 True 2739.000000 4268 93.644000 2177 5854 2 chrUn.!!$R3 3677
11 TraesCS4A01G303100 chrUn 216651779 216653054 1275 True 2357.000000 2357 100.000000 1 1276 1 chrUn.!!$R1 1275
12 TraesCS4A01G303100 chr4D 4416666 4419602 2936 False 3978.000000 3978 91.196000 589 3532 1 chr4D.!!$F1 2943
13 TraesCS4A01G303100 chr4D 4377653 4382210 4557 False 448.733333 942 95.180667 5014 5883 3 chr4D.!!$F2 869
14 TraesCS4A01G303100 chr6A 593022257 593027288 5031 True 2503.666667 3578 93.570667 746 5883 3 chr6A.!!$R1 5137

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
2102 2172 9.463443 GTTTTGCAAATGTTTGTTCTACTATCT 57.537 29.63 13.65 0.0 40.24 1.98 F
3819 4678 0.884704 GTGTCGTGGATGTGTTGCCT 60.885 55.00 0.00 0.0 0.00 4.75 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
4027 4886 1.801913 CTACTGCTCGTGGTGTCGC 60.802 63.158 0.0 0.0 0.0 5.19 R
4968 5857 5.960811 AGAGAGAGAGAGAGAGAGAAAGAGA 59.039 44.000 0.0 0.0 0.0 3.10 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
2102 2172 9.463443 GTTTTGCAAATGTTTGTTCTACTATCT 57.537 29.630 13.65 0.0 40.24 1.98
2788 3643 6.525121 TCATGTTGTCTTTTCTGTCGTTAG 57.475 37.500 0.00 0.0 0.00 2.34
2849 3704 6.725246 ACCTGATTTACTTTTTCACTTCGTG 58.275 36.000 0.00 0.0 34.45 4.35
2918 3773 7.119699 TGCTACATTTTGATGGTTCTCTTGTAG 59.880 37.037 0.00 0.0 37.90 2.74
3819 4678 0.884704 GTGTCGTGGATGTGTTGCCT 60.885 55.000 0.00 0.0 0.00 4.75
4027 4886 3.005578 GTGGCCTCCTTATAAGAGTACGG 59.994 52.174 14.28 7.4 0.00 4.02
4877 5764 8.578448 TCAATGATGAGGATAAATTGTTGTCA 57.422 30.769 0.00 0.0 31.63 3.58
4968 5857 6.386927 TCCAAATACTCTCTCTCTCTCTCTCT 59.613 42.308 0.00 0.0 0.00 3.10
4969 5858 6.708054 CCAAATACTCTCTCTCTCTCTCTCTC 59.292 46.154 0.00 0.0 0.00 3.20
4970 5859 7.419518 CCAAATACTCTCTCTCTCTCTCTCTCT 60.420 44.444 0.00 0.0 0.00 3.10
4971 5860 6.909550 ATACTCTCTCTCTCTCTCTCTCTC 57.090 45.833 0.00 0.0 0.00 3.20
4972 5861 4.877773 ACTCTCTCTCTCTCTCTCTCTCT 58.122 47.826 0.00 0.0 0.00 3.10
4973 5862 5.276440 ACTCTCTCTCTCTCTCTCTCTCTT 58.724 45.833 0.00 0.0 0.00 2.85
4974 5863 5.723887 ACTCTCTCTCTCTCTCTCTCTCTTT 59.276 44.000 0.00 0.0 0.00 2.52
4975 5864 6.127196 ACTCTCTCTCTCTCTCTCTCTCTTTC 60.127 46.154 0.00 0.0 0.00 2.62
4976 5865 5.960811 TCTCTCTCTCTCTCTCTCTCTTTCT 59.039 44.000 0.00 0.0 0.00 2.52
4977 5866 6.097554 TCTCTCTCTCTCTCTCTCTCTTTCTC 59.902 46.154 0.00 0.0 0.00 2.87
4978 5867 5.960811 TCTCTCTCTCTCTCTCTCTTTCTCT 59.039 44.000 0.00 0.0 0.00 3.10
4979 5868 6.097554 TCTCTCTCTCTCTCTCTCTTTCTCTC 59.902 46.154 0.00 0.0 0.00 3.20
4980 5869 5.960811 TCTCTCTCTCTCTCTCTTTCTCTCT 59.039 44.000 0.00 0.0 0.00 3.10
4981 5870 6.097554 TCTCTCTCTCTCTCTCTTTCTCTCTC 59.902 46.154 0.00 0.0 0.00 3.20
4982 5871 5.960811 TCTCTCTCTCTCTCTTTCTCTCTCT 59.039 44.000 0.00 0.0 0.00 3.10
4983 5872 6.097554 TCTCTCTCTCTCTCTTTCTCTCTCTC 59.902 46.154 0.00 0.0 0.00 3.20
4984 5873 5.960811 TCTCTCTCTCTCTTTCTCTCTCTCT 59.039 44.000 0.00 0.0 0.00 3.10
4985 5874 6.097554 TCTCTCTCTCTCTTTCTCTCTCTCTC 59.902 46.154 0.00 0.0 0.00 3.20
4986 5875 5.960811 TCTCTCTCTCTTTCTCTCTCTCTCT 59.039 44.000 0.00 0.0 0.00 3.10
4987 5876 6.097554 TCTCTCTCTCTTTCTCTCTCTCTCTC 59.902 46.154 0.00 0.0 0.00 3.20
4988 5877 5.960811 TCTCTCTCTTTCTCTCTCTCTCTCT 59.039 44.000 0.00 0.0 0.00 3.10
4989 5878 6.097554 TCTCTCTCTTTCTCTCTCTCTCTCTC 59.902 46.154 0.00 0.0 0.00 3.20
4990 5879 5.960811 TCTCTCTTTCTCTCTCTCTCTCTCT 59.039 44.000 0.00 0.0 0.00 3.10
4991 5880 6.097554 TCTCTCTTTCTCTCTCTCTCTCTCTC 59.902 46.154 0.00 0.0 0.00 3.20
4992 5881 5.960811 TCTCTTTCTCTCTCTCTCTCTCTCT 59.039 44.000 0.00 0.0 0.00 3.10
4993 5882 6.097554 TCTCTTTCTCTCTCTCTCTCTCTCTC 59.902 46.154 0.00 0.0 0.00 3.20
4994 5883 5.960811 TCTTTCTCTCTCTCTCTCTCTCTCT 59.039 44.000 0.00 0.0 0.00 3.10
4995 5884 7.126061 TCTTTCTCTCTCTCTCTCTCTCTCTA 58.874 42.308 0.00 0.0 0.00 2.43
4996 5885 7.786943 TCTTTCTCTCTCTCTCTCTCTCTCTAT 59.213 40.741 0.00 0.0 0.00 1.98
4997 5886 9.083422 CTTTCTCTCTCTCTCTCTCTCTCTATA 57.917 40.741 0.00 0.0 0.00 1.31
4998 5887 9.607333 TTTCTCTCTCTCTCTCTCTCTCTATAT 57.393 37.037 0.00 0.0 0.00 0.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2102 2172 1.879380 CATTGCCCGAAGAACAGACAA 59.121 47.619 0.00 0.00 0.00 3.18
2788 3643 5.581085 ACGTTAGATTGGTATGAGCTGAAAC 59.419 40.000 0.00 0.00 0.00 2.78
2849 3704 8.183536 TGAGTAATATCAACAATGTGATTGCAC 58.816 33.333 0.00 0.00 43.98 4.57
2918 3773 5.845391 ACAGAAGTCTAGAGCCAATAGAC 57.155 43.478 10.95 10.95 46.28 2.59
4027 4886 1.801913 CTACTGCTCGTGGTGTCGC 60.802 63.158 0.00 0.00 0.00 5.19
4234 5094 1.074405 GATATGGGCATTGAGCTGGGA 59.926 52.381 0.00 0.00 44.79 4.37
4968 5857 5.960811 AGAGAGAGAGAGAGAGAGAAAGAGA 59.039 44.000 0.00 0.00 0.00 3.10
4969 5858 6.098124 AGAGAGAGAGAGAGAGAGAGAAAGAG 59.902 46.154 0.00 0.00 0.00 2.85
4970 5859 5.960811 AGAGAGAGAGAGAGAGAGAGAAAGA 59.039 44.000 0.00 0.00 0.00 2.52
4971 5860 6.232581 AGAGAGAGAGAGAGAGAGAGAAAG 57.767 45.833 0.00 0.00 0.00 2.62
4972 5861 7.921041 ATAGAGAGAGAGAGAGAGAGAGAAA 57.079 40.000 0.00 0.00 0.00 2.52


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

AutoCloner maintained by Alex Coulton.