Multiple sequence alignment - TraesCS3B01G184500

Loading Multiple Alignment...

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 TraesCS3B01G184500 chr3B 100.000 3774 0 0 1 3774 199929681 199925908 0.000000e+00 6970.0
1 TraesCS3B01G184500 chr3B 98.868 2296 25 1 1 2296 199705294 199703000 0.000000e+00 4095.0
2 TraesCS3B01G184500 chr3B 95.797 1951 42 7 1112 3042 200365772 200367702 0.000000e+00 3112.0
3 TraesCS3B01G184500 chr3B 98.858 1488 10 3 2289 3774 199702520 199701038 0.000000e+00 2647.0
4 TraesCS3B01G184500 chr3B 91.138 1151 70 6 1 1126 200364614 200365757 0.000000e+00 1531.0
5 TraesCS3B01G184500 chr3B 95.045 444 21 1 3082 3524 200367712 200368155 0.000000e+00 697.0
6 TraesCS3B01G184500 chr3B 97.189 249 7 0 3526 3774 200368269 200368517 4.510000e-114 422.0
7 TraesCS3B01G184500 chr3B 93.309 269 18 0 1 269 199706872 199706604 7.600000e-107 398.0
8 TraesCS3B01G184500 chr3A 93.286 2949 124 29 864 3774 154742704 154739792 0.000000e+00 4281.0
9 TraesCS3B01G184500 chr3A 88.945 597 39 11 4 575 154793458 154792864 0.000000e+00 712.0
10 TraesCS3B01G184500 chr3A 88.591 298 25 3 570 867 154743408 154743120 1.670000e-93 353.0
11 TraesCS3B01G184500 chr3D 95.960 1584 52 5 913 2496 136776359 136774788 0.000000e+00 2560.0
12 TraesCS3B01G184500 chr3D 93.400 1303 42 15 2492 3774 136774621 136773343 0.000000e+00 1890.0
13 TraesCS3B01G184500 chr3D 89.426 889 52 8 6 867 136777756 136776883 0.000000e+00 1083.0
14 TraesCS3B01G184500 chr1B 89.275 1641 124 25 1064 2684 131789936 131788328 0.000000e+00 2008.0
15 TraesCS3B01G184500 chr1B 88.310 1651 120 31 1064 2684 131505321 131503714 0.000000e+00 1912.0
16 TraesCS3B01G184500 chr1B 87.211 563 44 14 3201 3738 130794052 130793493 1.930000e-172 616.0
17 TraesCS3B01G184500 chr1B 87.189 562 46 12 3201 3738 130859593 130859034 1.930000e-172 616.0
18 TraesCS3B01G184500 chr1B 86.477 562 50 11 3201 3738 131380122 131379563 9.030000e-166 593.0
19 TraesCS3B01G184500 chr1B 86.146 563 51 12 3201 3738 131583426 131582866 1.950000e-162 582.0
20 TraesCS3B01G184500 chr1B 83.992 531 56 8 1967 2497 131670724 131670223 2.040000e-132 483.0
21 TraesCS3B01G184500 chr1B 90.217 184 14 4 3524 3705 131502590 131502409 1.750000e-58 237.0
22 TraesCS3B01G184500 chr1B 90.164 122 7 3 3046 3166 229263159 229263276 1.820000e-33 154.0
23 TraesCS3B01G184500 chr1B 91.089 101 9 0 2950 3050 131787364 131787264 1.830000e-28 137.0
24 TraesCS3B01G184500 chr1B 86.239 109 7 2 2950 3050 131129883 131129775 1.110000e-20 111.0
25 TraesCS3B01G184500 chr1B 94.118 68 3 1 2616 2683 130795270 130795204 6.670000e-18 102.0
26 TraesCS3B01G184500 chr1D 87.731 1679 113 18 1031 2683 80006138 80004527 0.000000e+00 1873.0
27 TraesCS3B01G184500 chr1D 87.403 1675 125 26 1030 2684 79950163 79948555 0.000000e+00 1845.0
28 TraesCS3B01G184500 chr1D 86.177 463 36 11 3201 3636 80001947 80001486 3.410000e-130 475.0
29 TraesCS3B01G184500 chr1D 88.503 374 26 7 2686 3050 79948222 79947857 1.610000e-118 436.0
30 TraesCS3B01G184500 chr1D 88.187 364 40 3 3376 3738 79946739 79946378 7.490000e-117 431.0
31 TraesCS3B01G184500 chr1D 93.069 101 7 0 2950 3050 79947000 79946900 8.450000e-32 148.0
32 TraesCS3B01G184500 chr1D 88.073 109 5 2 2950 3050 80002122 80002014 5.120000e-24 122.0
33 TraesCS3B01G184500 chr1A 87.485 1614 116 21 1095 2684 98604580 98603029 0.000000e+00 1783.0
34 TraesCS3B01G184500 chr1A 89.157 249 20 2 3526 3774 98517548 98517307 1.700000e-78 303.0
35 TraesCS3B01G184500 chr1A 88.353 249 22 2 3526 3774 98602114 98601873 3.690000e-75 292.0
36 TraesCS3B01G184500 chr7B 92.982 114 5 1 3048 3161 15305768 15305658 3.020000e-36 163.0
37 TraesCS3B01G184500 chr7B 75.988 329 59 14 135 455 391962095 391961779 6.530000e-33 152.0
38 TraesCS3B01G184500 chr7B 85.294 68 7 3 513 578 217470618 217470684 2.430000e-07 67.6
39 TraesCS3B01G184500 chr6A 90.400 125 9 1 3038 3162 17663790 17663911 1.080000e-35 161.0
40 TraesCS3B01G184500 chr5D 91.597 119 6 2 3048 3166 501822823 501822709 1.080000e-35 161.0
41 TraesCS3B01G184500 chr5D 91.597 119 6 2 3048 3166 501862528 501862414 1.080000e-35 161.0
42 TraesCS3B01G184500 chr5B 92.174 115 5 2 3049 3163 511610849 511610739 3.900000e-35 159.0
43 TraesCS3B01G184500 chr5B 90.756 119 7 2 3048 3166 629852115 629852001 5.050000e-34 156.0


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 TraesCS3B01G184500 chr3B 199925908 199929681 3773 True 6970.000000 6970 100.000000 1 3774 1 chr3B.!!$R1 3773
1 TraesCS3B01G184500 chr3B 199701038 199706872 5834 True 2380.000000 4095 97.011667 1 3774 3 chr3B.!!$R2 3773
2 TraesCS3B01G184500 chr3B 200364614 200368517 3903 False 1440.500000 3112 94.792250 1 3774 4 chr3B.!!$F1 3773
3 TraesCS3B01G184500 chr3A 154739792 154743408 3616 True 2317.000000 4281 90.938500 570 3774 2 chr3A.!!$R2 3204
4 TraesCS3B01G184500 chr3A 154792864 154793458 594 True 712.000000 712 88.945000 4 575 1 chr3A.!!$R1 571
5 TraesCS3B01G184500 chr3D 136773343 136777756 4413 True 1844.333333 2560 92.928667 6 3774 3 chr3D.!!$R1 3768
6 TraesCS3B01G184500 chr1B 131502409 131505321 2912 True 1074.500000 1912 89.263500 1064 3705 2 chr1B.!!$R7 2641
7 TraesCS3B01G184500 chr1B 131787264 131789936 2672 True 1072.500000 2008 90.182000 1064 3050 2 chr1B.!!$R8 1986
8 TraesCS3B01G184500 chr1B 130859034 130859593 559 True 616.000000 616 87.189000 3201 3738 1 chr1B.!!$R1 537
9 TraesCS3B01G184500 chr1B 131379563 131380122 559 True 593.000000 593 86.477000 3201 3738 1 chr1B.!!$R3 537
10 TraesCS3B01G184500 chr1B 131582866 131583426 560 True 582.000000 582 86.146000 3201 3738 1 chr1B.!!$R4 537
11 TraesCS3B01G184500 chr1B 131670223 131670724 501 True 483.000000 483 83.992000 1967 2497 1 chr1B.!!$R5 530
12 TraesCS3B01G184500 chr1B 130793493 130795270 1777 True 359.000000 616 90.664500 2616 3738 2 chr1B.!!$R6 1122
13 TraesCS3B01G184500 chr1D 80001486 80006138 4652 True 823.333333 1873 87.327000 1031 3636 3 chr1D.!!$R2 2605
14 TraesCS3B01G184500 chr1D 79946378 79950163 3785 True 715.000000 1845 89.290500 1030 3738 4 chr1D.!!$R1 2708
15 TraesCS3B01G184500 chr1A 98601873 98604580 2707 True 1037.500000 1783 87.919000 1095 3774 2 chr1A.!!$R2 2679

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
984 3083 4.736896 GCGTTCGCCGGGACTTCT 62.737 66.667 2.18 0.0 36.94 2.85 F
1946 4103 0.603707 CAGAGCAAGAACCAGCGGAA 60.604 55.000 1.50 0.0 35.48 4.30 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2416 5090 0.663688 CCGATAGCTCGCTGTACTGT 59.336 55.000 0.85 0.0 43.66 3.55 R
3113 8168 5.439721 CTTGTCCCTCAAATGGATGTATCA 58.560 41.667 0.00 0.0 35.48 2.15 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
250 1830 6.360148 CCATTTCAACCATTTTGCGAAATTTG 59.640 34.615 9.31 12.21 34.84 2.32
385 1965 8.047310 GGGTTCATTCTACTTTCCTAAATCTCA 58.953 37.037 0.00 0.00 0.00 3.27
984 3083 4.736896 GCGTTCGCCGGGACTTCT 62.737 66.667 2.18 0.00 36.94 2.85
1062 3164 1.183549 AACGAACCGAGCTCACCTAT 58.816 50.000 15.40 0.00 0.00 2.57
1942 4099 1.303155 AGGCAGAGCAAGAACCAGC 60.303 57.895 0.00 0.00 0.00 4.85
1946 4103 0.603707 CAGAGCAAGAACCAGCGGAA 60.604 55.000 1.50 0.00 35.48 4.30
2156 4343 2.279069 CGTCTCACCAGCCACCTCT 61.279 63.158 0.00 0.00 0.00 3.69
2303 4977 1.336332 CCAGAGTCGTCACAAGTCAGG 60.336 57.143 0.00 0.00 0.00 3.86
2412 5086 1.132453 GCTATTGTTGGTCTTTCCCGC 59.868 52.381 0.00 0.00 34.77 6.13
2413 5087 2.432444 CTATTGTTGGTCTTTCCCGCA 58.568 47.619 0.00 0.00 34.77 5.69
2414 5088 1.247567 ATTGTTGGTCTTTCCCGCAG 58.752 50.000 0.00 0.00 34.77 5.18
2415 5089 0.106918 TTGTTGGTCTTTCCCGCAGT 60.107 50.000 0.00 0.00 34.77 4.40
2416 5090 0.759959 TGTTGGTCTTTCCCGCAGTA 59.240 50.000 0.00 0.00 34.77 2.74
2639 5525 2.877097 TGTAACTGGGATGCACACAT 57.123 45.000 0.00 0.00 39.98 3.21
3008 8051 5.250200 ACAATGGTTTTCCTTCTGCGTATA 58.750 37.500 0.00 0.00 41.38 1.47
3381 8579 5.769662 TGCCATCAATAGTCACTCTTTTTGT 59.230 36.000 0.00 0.00 0.00 2.83
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
250 1830 6.214819 TCCCATATAGTATTTAAGCCCCTGAC 59.785 42.308 0.00 0.00 0.00 3.51
677 2285 2.288091 CCTCGACATATCAGAGTGGCTG 60.288 54.545 0.00 0.00 46.31 4.85
798 2406 1.062581 CATCCCTTCTCCTCCTCCTCA 60.063 57.143 0.00 0.00 0.00 3.86
1062 3164 4.988716 ACGGGGAGAGCGGTGACA 62.989 66.667 0.00 0.00 0.00 3.58
1882 4030 1.351017 AGAACGCTTCTTGAATCCCCA 59.649 47.619 0.00 0.00 36.36 4.96
1942 4099 4.084888 GCGGTTCTTGCGGTTCCG 62.085 66.667 6.90 6.90 43.37 4.30
2070 4245 3.214123 CACTGGCATCGGCATGGG 61.214 66.667 0.00 0.00 43.71 4.00
2071 4246 1.105167 ATTCACTGGCATCGGCATGG 61.105 55.000 0.00 0.00 43.71 3.66
2072 4247 0.742505 AATTCACTGGCATCGGCATG 59.257 50.000 0.00 0.00 43.71 4.06
2073 4248 1.027357 GAATTCACTGGCATCGGCAT 58.973 50.000 0.00 0.00 43.71 4.40
2074 4249 1.368345 CGAATTCACTGGCATCGGCA 61.368 55.000 6.22 0.00 43.71 5.69
2075 4250 1.353103 CGAATTCACTGGCATCGGC 59.647 57.895 6.22 0.00 40.13 5.54
2078 4253 1.017387 GGTCCGAATTCACTGGCATC 58.983 55.000 6.22 0.00 0.00 3.91
2303 4977 3.838271 TCCAGCGTCGATGCCTCC 61.838 66.667 25.54 0.00 34.65 4.30
2412 5086 3.605002 CGATAGCTCGCTGTACTGTACTG 60.605 52.174 17.98 17.68 38.20 2.74
2413 5087 2.544686 CGATAGCTCGCTGTACTGTACT 59.455 50.000 17.98 0.00 38.20 2.73
2414 5088 2.349627 CCGATAGCTCGCTGTACTGTAC 60.350 54.545 10.98 10.98 43.66 2.90
2415 5089 1.871676 CCGATAGCTCGCTGTACTGTA 59.128 52.381 0.85 0.00 43.66 2.74
2416 5090 0.663688 CCGATAGCTCGCTGTACTGT 59.336 55.000 0.85 0.00 43.66 3.55
3008 8051 7.495055 AGAGCACTGAACTTTTTCATTTTCAT 58.505 30.769 0.00 0.00 41.05 2.57
3113 8168 5.439721 CTTGTCCCTCAAATGGATGTATCA 58.560 41.667 0.00 0.00 35.48 2.15


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

AutoCloner maintained by Alex Coulton.