Multiple sequence alignment - TraesCS5A01G080500

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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 TraesCS5A01G080500 chr5A 100.000 2408 0 0 1 2408 101169752 101167345 0.000000e+00 4447
1 TraesCS5A01G080500 chr5A 92.928 2206 133 16 1 2197 444785844 444788035 0.000000e+00 3188
2 TraesCS5A01G080500 chr3A 93.443 2196 125 14 1 2190 211304965 211307147 0.000000e+00 3240
3 TraesCS5A01G080500 chr3A 89.615 2205 181 22 1 2196 46666764 46664599 0.000000e+00 2760
4 TraesCS5A01G080500 chr3A 84.205 975 109 30 1234 2197 296114439 296113499 0.000000e+00 905
5 TraesCS5A01G080500 chr3A 83.979 955 111 26 1253 2197 407010340 407009418 0.000000e+00 878
6 TraesCS5A01G080500 chr7A 93.200 2206 115 15 1 2197 592894924 592897103 0.000000e+00 3210
7 TraesCS5A01G080500 chr7A 93.055 2203 125 16 1 2197 404879864 404877684 0.000000e+00 3195
8 TraesCS5A01G080500 chr7A 90.950 2232 131 38 3 2197 385235957 385233760 0.000000e+00 2937
9 TraesCS5A01G080500 chr4A 91.308 2232 124 29 3 2197 344964760 344962562 0.000000e+00 2983
10 TraesCS5A01G080500 chr4A 91.092 2234 128 30 1 2197 344969269 344967070 0.000000e+00 2957
11 TraesCS5A01G080500 chr1A 89.588 2209 169 30 1 2197 313569431 313567272 0.000000e+00 2748
12 TraesCS5A01G080500 chr1A 86.969 1036 116 15 1162 2190 58160822 58159799 0.000000e+00 1147
13 TraesCS5A01G080500 chr7B 83.160 2209 276 54 1 2197 182946622 182944498 0.000000e+00 1930
14 TraesCS5A01G080500 chr7B 86.603 1045 95 33 1162 2197 172327928 172326920 0.000000e+00 1112
15 TraesCS5A01G080500 chr7B 83.301 1042 122 27 1162 2197 456123302 456124297 0.000000e+00 913
16 TraesCS5A01G080500 chr7B 82.871 1045 126 26 1162 2197 383864070 383865070 0.000000e+00 889
17 TraesCS5A01G080500 chr7B 82.871 1045 121 27 1162 2197 638610455 638609460 0.000000e+00 885
18 TraesCS5A01G080500 chr7B 81.790 972 113 40 1234 2197 595540432 595541347 0.000000e+00 756
19 TraesCS5A01G080500 chr7B 81.327 980 125 37 1233 2197 394022008 394021072 0.000000e+00 743
20 TraesCS5A01G080500 chr7B 94.872 273 13 1 2137 2408 172326900 172326628 2.210000e-115 425
21 TraesCS5A01G080500 chr2D 85.906 1043 101 24 1164 2197 286991507 286992512 0.000000e+00 1070
22 TraesCS5A01G080500 chr3B 82.775 1045 122 35 1162 2197 331026147 331027142 0.000000e+00 880
23 TraesCS5A01G080500 chr1B 82.314 1046 125 34 1162 2197 464916347 464917342 0.000000e+00 852
24 TraesCS5A01G080500 chr1B 80.534 1048 147 30 1162 2197 200996402 200997404 0.000000e+00 752
25 TraesCS5A01G080500 chr6B 81.167 977 133 35 1233 2197 182115537 182116474 0.000000e+00 737
26 TraesCS5A01G080500 chr6A 95.604 273 11 1 2137 2408 284425274 284425546 1.020000e-118 436
27 TraesCS5A01G080500 chr6D 89.964 279 22 6 2134 2408 318406488 318406212 2.940000e-94 355
28 TraesCS5A01G080500 chr4D 90.182 275 22 5 2137 2408 165542762 165543034 1.060000e-93 353
29 TraesCS5A01G080500 chr3D 90.217 276 20 7 2137 2408 213694511 213694239 1.060000e-93 353
30 TraesCS5A01G080500 chr3D 87.415 294 32 5 2118 2408 448146475 448146766 1.380000e-87 333
31 TraesCS5A01G080500 chr2B 88.316 291 28 6 2122 2408 114235441 114235153 6.370000e-91 344
32 TraesCS5A01G080500 chr1D 88.153 287 28 6 2126 2408 143120941 143120657 1.070000e-88 337
33 TraesCS5A01G080500 chr7D 87.075 294 33 5 2118 2408 149138982 149139273 6.420000e-86 327


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 TraesCS5A01G080500 chr5A 101167345 101169752 2407 True 4447.0 4447 100.0000 1 2408 1 chr5A.!!$R1 2407
1 TraesCS5A01G080500 chr5A 444785844 444788035 2191 False 3188.0 3188 92.9280 1 2197 1 chr5A.!!$F1 2196
2 TraesCS5A01G080500 chr3A 211304965 211307147 2182 False 3240.0 3240 93.4430 1 2190 1 chr3A.!!$F1 2189
3 TraesCS5A01G080500 chr3A 46664599 46666764 2165 True 2760.0 2760 89.6150 1 2196 1 chr3A.!!$R1 2195
4 TraesCS5A01G080500 chr3A 296113499 296114439 940 True 905.0 905 84.2050 1234 2197 1 chr3A.!!$R2 963
5 TraesCS5A01G080500 chr3A 407009418 407010340 922 True 878.0 878 83.9790 1253 2197 1 chr3A.!!$R3 944
6 TraesCS5A01G080500 chr7A 592894924 592897103 2179 False 3210.0 3210 93.2000 1 2197 1 chr7A.!!$F1 2196
7 TraesCS5A01G080500 chr7A 404877684 404879864 2180 True 3195.0 3195 93.0550 1 2197 1 chr7A.!!$R2 2196
8 TraesCS5A01G080500 chr7A 385233760 385235957 2197 True 2937.0 2937 90.9500 3 2197 1 chr7A.!!$R1 2194
9 TraesCS5A01G080500 chr4A 344962562 344969269 6707 True 2970.0 2983 91.2000 1 2197 2 chr4A.!!$R1 2196
10 TraesCS5A01G080500 chr1A 313567272 313569431 2159 True 2748.0 2748 89.5880 1 2197 1 chr1A.!!$R2 2196
11 TraesCS5A01G080500 chr1A 58159799 58160822 1023 True 1147.0 1147 86.9690 1162 2190 1 chr1A.!!$R1 1028
12 TraesCS5A01G080500 chr7B 182944498 182946622 2124 True 1930.0 1930 83.1600 1 2197 1 chr7B.!!$R1 2196
13 TraesCS5A01G080500 chr7B 456123302 456124297 995 False 913.0 913 83.3010 1162 2197 1 chr7B.!!$F2 1035
14 TraesCS5A01G080500 chr7B 383864070 383865070 1000 False 889.0 889 82.8710 1162 2197 1 chr7B.!!$F1 1035
15 TraesCS5A01G080500 chr7B 638609460 638610455 995 True 885.0 885 82.8710 1162 2197 1 chr7B.!!$R3 1035
16 TraesCS5A01G080500 chr7B 172326628 172327928 1300 True 768.5 1112 90.7375 1162 2408 2 chr7B.!!$R4 1246
17 TraesCS5A01G080500 chr7B 595540432 595541347 915 False 756.0 756 81.7900 1234 2197 1 chr7B.!!$F3 963
18 TraesCS5A01G080500 chr7B 394021072 394022008 936 True 743.0 743 81.3270 1233 2197 1 chr7B.!!$R2 964
19 TraesCS5A01G080500 chr2D 286991507 286992512 1005 False 1070.0 1070 85.9060 1164 2197 1 chr2D.!!$F1 1033
20 TraesCS5A01G080500 chr3B 331026147 331027142 995 False 880.0 880 82.7750 1162 2197 1 chr3B.!!$F1 1035
21 TraesCS5A01G080500 chr1B 464916347 464917342 995 False 852.0 852 82.3140 1162 2197 1 chr1B.!!$F2 1035
22 TraesCS5A01G080500 chr1B 200996402 200997404 1002 False 752.0 752 80.5340 1162 2197 1 chr1B.!!$F1 1035
23 TraesCS5A01G080500 chr6B 182115537 182116474 937 False 737.0 737 81.1670 1233 2197 1 chr6B.!!$F1 964

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
423 425 2.443255 ACCTCAACACCAGGAGATGTTT 59.557 45.455 0.00 0.0 36.92 2.83 F
691 693 2.686915 GCTGGCAGCACTATTTCTTCAT 59.313 45.455 33.33 0.0 41.89 2.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1385 5902 0.947244 CCATGCTCTAAATCCACCGC 59.053 55.000 0.00 0.00 0.0 5.68 R
2055 6685 1.672881 GGGAACATGACATGCTACTGC 59.327 52.381 15.49 3.29 40.2 4.40 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
97 98 5.660864 AGGCCTAGCTCTTATGATCCTTATC 59.339 44.000 1.29 0.0 0.00 1.75
122 123 3.776969 AGAGGTCATCCTTATGTTGCTCA 59.223 43.478 0.00 0.0 45.24 4.26
127 128 5.822519 GGTCATCCTTATGTTGCTCATACAA 59.177 40.000 2.59 0.0 38.55 2.41
150 151 3.960102 GCCATATTTGTGGATTTCAGGGA 59.040 43.478 0.00 0.0 42.02 4.20
423 425 2.443255 ACCTCAACACCAGGAGATGTTT 59.557 45.455 0.00 0.0 36.92 2.83
442 444 7.893302 AGATGTTTCCAATGGAGTTAAATGGTA 59.107 33.333 0.86 0.0 31.21 3.25
524 526 7.198390 CCCACACAAGATGAATTTGATGATAC 58.802 38.462 0.00 0.0 0.00 2.24
557 559 4.867047 CACATTGCTTAGTCTCGAGTTCAT 59.133 41.667 13.13 0.0 0.00 2.57
691 693 2.686915 GCTGGCAGCACTATTTCTTCAT 59.313 45.455 33.33 0.0 41.89 2.57
718 720 3.582647 TGAGCTGAGTGTTTCTGGGATTA 59.417 43.478 0.00 0.0 0.00 1.75
771 773 5.158141 TCATATCCAGCCAAGGAAGATAGT 58.842 41.667 0.00 0.0 41.92 2.12
932 934 6.672266 TCCTGTAGTTGAAGATGAAGAACT 57.328 37.500 0.00 0.0 33.32 3.01
957 959 3.996150 ATTCATTTGCCCATCGTCATC 57.004 42.857 0.00 0.0 0.00 2.92
1021 1023 5.581605 ACATGCGTCCATATGAATTGTTTC 58.418 37.500 3.65 0.0 0.00 2.78
1242 1244 4.452114 CGCCATGTTCTTTATAGCTATGCA 59.548 41.667 16.77 0.0 0.00 3.96
1385 5902 0.676782 GGTGACATTCCTTGGGACCG 60.677 60.000 0.00 0.0 0.00 4.79
1473 6066 1.339610 GTGCACGAGGATAGAGAGCAT 59.660 52.381 0.00 0.0 32.75 3.79
1514 6123 0.458543 GAGGAGTCGCGATGCAAGAA 60.459 55.000 14.06 0.0 0.00 2.52
1525 6135 3.059733 GCGATGCAAGAAGATGTGAGATC 60.060 47.826 0.00 0.0 0.00 2.75
1578 6194 5.376625 GTGAGCTATTTCATGACCCCAATA 58.623 41.667 0.00 0.0 0.00 1.90
1685 6304 2.238521 CACCTTTGGTATGGTGCTTGT 58.761 47.619 0.00 0.0 45.68 3.16
1809 6429 9.537852 TCAAATCCCTAGTACACTAGAAAACTA 57.462 33.333 16.34 0.0 46.80 2.24
1889 6509 1.168714 GTGCCAAGTGTCTTCCCATC 58.831 55.000 0.00 0.0 0.00 3.51
1894 6514 2.616510 CCAAGTGTCTTCCCATCCAGAC 60.617 54.545 0.00 0.0 40.03 3.51
1928 6548 6.874278 ACCACTATGGATTAGCATGCTATA 57.126 37.500 27.35 17.9 40.96 1.31
1940 6560 7.486407 TTAGCATGCTATATTCTCTGGATCA 57.514 36.000 27.35 5.1 0.00 2.92
1958 6578 4.507710 GATCAGTAGCATGTGAACCAGAA 58.492 43.478 0.00 0.0 0.00 3.02
2078 6708 2.840038 AGTAGCATGTCATGTTCCCTGA 59.160 45.455 14.26 0.0 0.00 3.86
2088 6718 2.106683 GTTCCCTGAATCGGTGGCG 61.107 63.158 0.00 0.0 0.00 5.69
2092 6722 1.671054 CCTGAATCGGTGGCGTGTT 60.671 57.895 0.00 0.0 0.00 3.32
2100 6731 1.267261 TCGGTGGCGTGTTAAATTTGG 59.733 47.619 0.00 0.0 0.00 3.28
2149 6790 7.903995 AAAAATGCAATATTTGTCGAACCAT 57.096 28.000 0.00 0.0 0.00 3.55
2190 6831 3.370103 GGATCGGTGGTATGTTCCTTTGA 60.370 47.826 0.00 0.0 0.00 2.69
2191 6832 3.992943 TCGGTGGTATGTTCCTTTGAT 57.007 42.857 0.00 0.0 0.00 2.57
2297 7018 3.657610 TCTGGGGATCATGCTCTCTTTA 58.342 45.455 0.00 0.0 0.00 1.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
122 123 7.201938 CCTGAAATCCACAAATATGGCTTGTAT 60.202 37.037 0.00 0.00 39.85 2.29
127 128 3.962718 CCCTGAAATCCACAAATATGGCT 59.037 43.478 0.00 0.00 39.85 4.75
150 151 3.758554 GCTGACATTTAGTGGGTGAATGT 59.241 43.478 1.00 1.00 45.54 2.71
163 164 3.244078 TGAGAGTAACCACGCTGACATTT 60.244 43.478 0.00 0.00 34.64 2.32
557 559 0.911769 ATCATCCTCGGCACTCCAAA 59.088 50.000 0.00 0.00 0.00 3.28
718 720 3.456277 GGAACCTCAGATGTATCAAGGGT 59.544 47.826 14.19 9.70 36.73 4.34
771 773 6.266558 GAGATATCTCTTCCTCAAGGCACTTA 59.733 42.308 23.06 0.00 42.94 2.24
932 934 4.946772 TGACGATGGGCAAATGAATTTCTA 59.053 37.500 0.00 0.00 0.00 2.10
957 959 2.036475 ACCTGCTATATCACGCTCTTGG 59.964 50.000 0.00 0.00 0.00 3.61
1021 1023 3.544684 TCATGCAATGCAAGGTAGTAGG 58.455 45.455 13.45 0.00 46.21 3.18
1385 5902 0.947244 CCATGCTCTAAATCCACCGC 59.053 55.000 0.00 0.00 0.00 5.68
1461 6054 5.754782 TCTCTATCCTCATGCTCTCTATCC 58.245 45.833 0.00 0.00 0.00 2.59
1473 6066 5.026121 TCTCCTTTTGCTTCTCTATCCTCA 58.974 41.667 0.00 0.00 0.00 3.86
1514 6123 2.225467 TCGCTCGATGATCTCACATCT 58.775 47.619 0.00 0.00 42.86 2.90
1525 6135 3.406728 TGAAGTAGAACTCGCTCGATG 57.593 47.619 0.00 0.00 0.00 3.84
1685 6304 8.164058 TCACAATTCAGTTCACATATTCACAA 57.836 30.769 0.00 0.00 0.00 3.33
1809 6429 7.669427 TCAAAGTAAATGCAGAAAATGATGGT 58.331 30.769 0.00 0.00 0.00 3.55
1889 6509 4.021102 AGTGGTTAAGTGATTGGTCTGG 57.979 45.455 0.00 0.00 0.00 3.86
1894 6514 7.041098 GCTAATCCATAGTGGTTAAGTGATTGG 60.041 40.741 0.00 0.00 39.03 3.16
1928 6548 4.652881 TCACATGCTACTGATCCAGAGAAT 59.347 41.667 0.45 0.00 35.18 2.40
1940 6560 4.012374 CCATTTCTGGTTCACATGCTACT 58.988 43.478 0.00 0.00 37.79 2.57
1958 6578 7.147949 GGAAACAAGAATCATCACTCATCCATT 60.148 37.037 0.00 0.00 0.00 3.16
2055 6685 1.672881 GGGAACATGACATGCTACTGC 59.327 52.381 15.49 3.29 40.20 4.40
2078 6708 3.570559 CAAATTTAACACGCCACCGATT 58.429 40.909 0.00 0.00 38.29 3.34
2088 6718 6.079424 TGTCCAAGCTACCAAATTTAACAC 57.921 37.500 0.00 0.00 0.00 3.32
2131 6768 4.732784 ACACATGGTTCGACAAATATTGC 58.267 39.130 0.00 0.00 0.00 3.56
2132 6769 8.067784 GGTATACACATGGTTCGACAAATATTG 58.932 37.037 5.01 0.00 0.00 1.90
2133 6770 7.771361 TGGTATACACATGGTTCGACAAATATT 59.229 33.333 5.01 0.00 0.00 1.28
2137 6774 4.895961 TGGTATACACATGGTTCGACAAA 58.104 39.130 5.01 0.00 0.00 2.83
2149 6790 3.367321 TCCCGAGAACATGGTATACACA 58.633 45.455 5.01 0.90 0.00 3.72
2248 6969 6.123651 ACTTGTTACCAGGAACACAACATTA 58.876 36.000 0.00 0.00 39.02 1.90
2278 6999 2.707791 CCTAAAGAGAGCATGATCCCCA 59.292 50.000 7.49 0.00 0.00 4.96
2279 7000 2.975489 TCCTAAAGAGAGCATGATCCCC 59.025 50.000 7.49 0.00 0.00 4.81
2280 7001 4.384940 GTTCCTAAAGAGAGCATGATCCC 58.615 47.826 7.49 0.00 0.00 3.85
2297 7018 2.629617 CAGATTGTGCCAAAAGGTTCCT 59.370 45.455 0.00 0.00 0.00 3.36
2317 7038 6.403866 AGTGGATCAACAAGTTTAAATGCA 57.596 33.333 2.34 0.00 0.00 3.96


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

AutoCloner maintained by Alex Coulton.