Multiple sequence alignment - TraesCS3B01G459000

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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 TraesCS3B01G459000 chr3B 100.000 3871 0 0 1 3871 702692963 702689093 0.000000e+00 7149.0
1 TraesCS3B01G459000 chr3B 88.679 212 18 6 24 232 40247532 40247324 1.790000e-63 254.0
2 TraesCS3B01G459000 chr3B 94.231 52 1 2 3261 3310 750356587 750356536 1.150000e-10 78.7
3 TraesCS3B01G459000 chr3D 97.423 3880 82 6 3 3871 531368196 531364324 0.000000e+00 6595.0
4 TraesCS3B01G459000 chr3D 96.482 3468 85 14 171 3618 426440081 426443531 0.000000e+00 5694.0
5 TraesCS3B01G459000 chr3D 97.287 258 7 0 3614 3871 426444828 426445085 4.590000e-119 438.0
6 TraesCS3B01G459000 chr3D 87.556 225 23 5 1 223 23088363 23088142 4.960000e-64 255.0
7 TraesCS3B01G459000 chr3A 97.951 2977 49 5 332 3307 665967211 665964246 0.000000e+00 5149.0
8 TraesCS3B01G459000 chr3A 93.322 569 13 2 3303 3871 665963988 665963445 0.000000e+00 817.0
9 TraesCS3B01G459000 chr3A 89.905 317 29 2 3 317 665967574 665967259 4.660000e-109 405.0
10 TraesCS3B01G459000 chr1D 93.061 3084 177 15 364 3437 391317203 391320259 0.000000e+00 4475.0
11 TraesCS3B01G459000 chr1D 88.889 198 16 5 24 218 483524064 483523870 5.000000e-59 239.0
12 TraesCS3B01G459000 chr1A 92.937 3030 165 23 371 3392 493823624 493820636 0.000000e+00 4364.0
13 TraesCS3B01G459000 chr1B 95.088 2565 120 1 368 2932 531206272 531203714 0.000000e+00 4034.0
14 TraesCS3B01G459000 chr1B 83.619 525 46 16 2929 3437 531203604 531203104 1.270000e-124 457.0
15 TraesCS3B01G459000 chr4D 88.649 881 69 11 2976 3853 12419949 12420801 0.000000e+00 1044.0
16 TraesCS3B01G459000 chr4D 85.588 451 32 21 610 1052 12419533 12419958 3.550000e-120 442.0
17 TraesCS3B01G459000 chr4A 90.988 688 51 4 375 1052 590255595 590254909 0.000000e+00 917.0
18 TraesCS3B01G459000 chr4A 87.313 536 43 3 3337 3871 590254592 590254081 1.200000e-164 590.0
19 TraesCS3B01G459000 chr4A 86.364 330 34 5 2979 3298 590254915 590254587 2.210000e-92 350.0
20 TraesCS3B01G459000 chrUn 100.000 386 0 0 2588 2973 480559231 480559616 0.000000e+00 713.0
21 TraesCS3B01G459000 chr4B 88.132 514 53 6 2976 3486 22753569 22754077 4.280000e-169 604.0
22 TraesCS3B01G459000 chr4B 91.150 339 26 3 3504 3842 22804991 22805325 1.270000e-124 457.0
23 TraesCS3B01G459000 chr5D 84.848 297 38 6 12 307 531475372 531475082 3.780000e-75 292.0
24 TraesCS3B01G459000 chr5D 81.672 311 46 10 2 307 531470874 531470570 8.310000e-62 248.0
25 TraesCS3B01G459000 chr5B 84.768 302 33 12 12 307 669485885 669485591 1.360000e-74 291.0
26 TraesCS3B01G459000 chr5A 89.573 211 17 5 12 220 658600634 658600427 2.970000e-66 263.0
27 TraesCS3B01G459000 chr5A 81.208 149 21 5 160 307 658486623 658486765 3.160000e-21 113.0


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 TraesCS3B01G459000 chr3B 702689093 702692963 3870 True 7149.000000 7149 100.000000 1 3871 1 chr3B.!!$R2 3870
1 TraesCS3B01G459000 chr3D 531364324 531368196 3872 True 6595.000000 6595 97.423000 3 3871 1 chr3D.!!$R2 3868
2 TraesCS3B01G459000 chr3D 426440081 426445085 5004 False 3066.000000 5694 96.884500 171 3871 2 chr3D.!!$F1 3700
3 TraesCS3B01G459000 chr3A 665963445 665967574 4129 True 2123.666667 5149 93.726000 3 3871 3 chr3A.!!$R1 3868
4 TraesCS3B01G459000 chr1D 391317203 391320259 3056 False 4475.000000 4475 93.061000 364 3437 1 chr1D.!!$F1 3073
5 TraesCS3B01G459000 chr1A 493820636 493823624 2988 True 4364.000000 4364 92.937000 371 3392 1 chr1A.!!$R1 3021
6 TraesCS3B01G459000 chr1B 531203104 531206272 3168 True 2245.500000 4034 89.353500 368 3437 2 chr1B.!!$R1 3069
7 TraesCS3B01G459000 chr4D 12419533 12420801 1268 False 743.000000 1044 87.118500 610 3853 2 chr4D.!!$F1 3243
8 TraesCS3B01G459000 chr4A 590254081 590255595 1514 True 619.000000 917 88.221667 375 3871 3 chr4A.!!$R1 3496
9 TraesCS3B01G459000 chr4B 22753569 22754077 508 False 604.000000 604 88.132000 2976 3486 1 chr4B.!!$F1 510


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
243 245 0.885196 GGTTTGTTGCCATTCGCCTA 59.115 50.000 0.00 0.00 36.24 3.93 F
1091 1151 0.177141 CTGAGAATAACCGCCCGGAA 59.823 55.000 14.44 1.32 38.96 4.30 F
1252 1313 2.569059 GCTTTATGATGCTGAGCCTCA 58.431 47.619 14.56 14.56 37.56 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1289 1350 1.073199 GGCATCCTCAATACCCCCG 59.927 63.158 0.0 0.0 0.00 5.73 R
2186 2247 1.592223 GCCAGCACGTCCTAGAAGT 59.408 57.895 0.0 0.0 0.00 3.01 R
3245 3447 3.431233 GCCTTTTGCATTTTCTCTGAAGC 59.569 43.478 0.0 0.0 40.77 3.86 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
237 239 1.112315 TCAGCGGGTTTGTTGCCATT 61.112 50.000 0.00 0.00 0.00 3.16
243 245 0.885196 GGTTTGTTGCCATTCGCCTA 59.115 50.000 0.00 0.00 36.24 3.93
300 304 1.146263 CTTCCGCGGCCCTAATTCT 59.854 57.895 23.51 0.00 0.00 2.40
1091 1151 0.177141 CTGAGAATAACCGCCCGGAA 59.823 55.000 14.44 1.32 38.96 4.30
1252 1313 2.569059 GCTTTATGATGCTGAGCCTCA 58.431 47.619 14.56 14.56 37.56 3.86
1289 1350 4.873817 TGCTTGATATGTATGCCAAATGC 58.126 39.130 0.00 0.00 41.77 3.56
2186 2247 5.123820 GGAGCATTACACTTGCATTGTTAGA 59.876 40.000 6.78 0.00 42.62 2.10
2244 2305 9.094578 CTCTGAACTTTATTGGAGATATCCCTA 57.905 37.037 3.38 0.00 0.00 3.53
2245 2306 9.447279 TCTGAACTTTATTGGAGATATCCCTAA 57.553 33.333 3.38 0.00 0.00 2.69
2288 2349 0.100146 GTGCATTGCTTAGCTCCTGC 59.900 55.000 10.49 15.43 40.05 4.85
2586 2647 4.569015 GGCTAAACCTGAAAACCCATAGGA 60.569 45.833 0.00 0.00 33.89 2.94
2968 3142 7.924412 GCTGGTTGAAATGATTATGTTGATGAT 59.076 33.333 0.00 0.00 0.00 2.45
2969 3143 9.811995 CTGGTTGAAATGATTATGTTGATGATT 57.188 29.630 0.00 0.00 0.00 2.57
2972 3146 9.910511 GTTGAAATGATTATGTTGATGATTTGC 57.089 29.630 0.00 0.00 0.00 3.68
2973 3147 9.654663 TTGAAATGATTATGTTGATGATTTGCA 57.345 25.926 0.00 0.00 0.00 4.08
2974 3148 9.825109 TGAAATGATTATGTTGATGATTTGCAT 57.175 25.926 0.00 0.00 40.77 3.96
2997 3171 2.436417 TGCTGGACATAAAAGAGCACC 58.564 47.619 0.00 0.00 34.78 5.01
3112 3301 3.643199 TGTGCTAGGTTGGCATCAATA 57.357 42.857 0.00 0.00 41.86 1.90
3188 3387 6.186957 AGGTAAACATGCAATAGATCCAACA 58.813 36.000 0.00 0.00 0.00 3.33
3245 3447 4.651778 TGTACCCTCTCCAGAATGTTTTG 58.348 43.478 0.00 0.00 0.00 2.44
3249 3451 3.192212 CCCTCTCCAGAATGTTTTGCTTC 59.808 47.826 0.00 0.00 0.00 3.86
3271 3478 4.099881 TCAGAGAAAATGCAAAAGGCTTGT 59.900 37.500 0.00 0.00 45.15 3.16
3347 3822 5.353394 ACAACACACACTAGAAAAGGAGA 57.647 39.130 0.00 0.00 0.00 3.71
3348 3823 5.360591 ACAACACACACTAGAAAAGGAGAG 58.639 41.667 0.00 0.00 0.00 3.20
3403 3878 1.092348 GGGATTAGAACACGCAACCC 58.908 55.000 0.00 0.00 0.00 4.11
3454 3929 3.372025 GCCTCATCCCTGATTAAACCTGT 60.372 47.826 0.00 0.00 0.00 4.00
3487 3962 8.548025 TCTCCAGAATGTTACATTGAAGGATAA 58.452 33.333 15.83 7.84 0.00 1.75
3488 3963 8.737168 TCCAGAATGTTACATTGAAGGATAAG 57.263 34.615 15.83 0.00 0.00 1.73
3489 3964 7.775093 TCCAGAATGTTACATTGAAGGATAAGG 59.225 37.037 15.83 4.22 0.00 2.69
3490 3965 7.775093 CCAGAATGTTACATTGAAGGATAAGGA 59.225 37.037 15.83 0.00 0.00 3.36
3491 3966 9.177608 CAGAATGTTACATTGAAGGATAAGGAA 57.822 33.333 15.83 0.00 0.00 3.36
3492 3967 9.753674 AGAATGTTACATTGAAGGATAAGGAAA 57.246 29.630 15.83 0.00 0.00 3.13
3495 3970 8.698973 TGTTACATTGAAGGATAAGGAAAACA 57.301 30.769 0.00 0.00 0.00 2.83
3496 3971 9.308000 TGTTACATTGAAGGATAAGGAAAACAT 57.692 29.630 0.00 0.00 0.00 2.71
3497 3972 9.788960 GTTACATTGAAGGATAAGGAAAACATC 57.211 33.333 0.00 0.00 0.00 3.06
3498 3973 9.527157 TTACATTGAAGGATAAGGAAAACATCA 57.473 29.630 0.00 0.00 0.00 3.07
3499 3974 8.421249 ACATTGAAGGATAAGGAAAACATCAA 57.579 30.769 0.00 0.00 0.00 2.57
3500 3975 9.039165 ACATTGAAGGATAAGGAAAACATCAAT 57.961 29.630 0.00 0.00 35.90 2.57
3501 3976 9.880157 CATTGAAGGATAAGGAAAACATCAATT 57.120 29.630 0.00 0.00 33.93 2.32
3502 3977 9.880157 ATTGAAGGATAAGGAAAACATCAATTG 57.120 29.630 0.00 0.00 32.70 2.32
3503 3978 8.648698 TGAAGGATAAGGAAAACATCAATTGA 57.351 30.769 11.26 11.26 0.00 2.57
3504 3979 9.087871 TGAAGGATAAGGAAAACATCAATTGAA 57.912 29.630 13.09 0.00 0.00 2.69
3505 3980 9.578439 GAAGGATAAGGAAAACATCAATTGAAG 57.422 33.333 13.09 10.92 0.00 3.02
3506 3981 8.071177 AGGATAAGGAAAACATCAATTGAAGG 57.929 34.615 13.09 10.37 0.00 3.46
3507 3982 7.895429 AGGATAAGGAAAACATCAATTGAAGGA 59.105 33.333 13.09 0.00 0.00 3.36
3508 3983 8.699130 GGATAAGGAAAACATCAATTGAAGGAT 58.301 33.333 13.09 0.00 0.00 3.24
3818 5640 5.633182 GTGCTGAAGTTTTGAAAAGTTGACA 59.367 36.000 14.83 7.30 0.00 3.58
3835 5657 5.240623 AGTTGACAAGGTGCGAATATTGAAA 59.759 36.000 0.00 0.00 0.00 2.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 3.070018 CAGGTCACTTTTCTTCTCGCAT 58.930 45.455 0.00 0.00 0.00 4.73
10 11 1.457303 CGCAGGTCACTTTTCTTCTCG 59.543 52.381 0.00 0.00 0.00 4.04
21 22 4.719616 GTTTCGCGCGCAGGTCAC 62.720 66.667 32.61 15.51 0.00 3.67
164 165 1.808891 CGACCCAGCTTATAAACCCGG 60.809 57.143 0.00 0.00 0.00 5.73
237 239 4.435970 TGGAGACCGGCTAGGCGA 62.436 66.667 37.12 15.61 46.52 5.54
281 285 1.153229 GAATTAGGGCCGCGGAAGT 60.153 57.895 33.48 14.01 0.00 3.01
300 304 1.717038 TTTTTGGGCCCCCGTCTACA 61.717 55.000 22.27 0.00 39.42 2.74
1091 1151 1.228657 GGAAAACCTGAAGCGCGTCT 61.229 55.000 23.50 1.94 0.00 4.18
1252 1313 4.250431 GCAGCGCACCACAAACGT 62.250 61.111 11.47 0.00 0.00 3.99
1289 1350 1.073199 GGCATCCTCAATACCCCCG 59.927 63.158 0.00 0.00 0.00 5.73
1336 1397 8.946085 TCATAAAACTCCAAAGTATCACATCAC 58.054 33.333 0.00 0.00 33.48 3.06
2186 2247 1.592223 GCCAGCACGTCCTAGAAGT 59.408 57.895 0.00 0.00 0.00 3.01
2288 2349 7.143340 CCAGATCCACATTTTTATGCACTATG 58.857 38.462 0.00 0.00 0.00 2.23
2971 3145 4.328169 GCTCTTTTATGTCCAGCAAAATGC 59.672 41.667 0.00 0.00 45.46 3.56
2972 3146 5.346822 GTGCTCTTTTATGTCCAGCAAAATG 59.653 40.000 0.00 0.00 41.63 2.32
2973 3147 5.473039 GTGCTCTTTTATGTCCAGCAAAAT 58.527 37.500 0.00 0.00 41.63 1.82
2974 3148 4.261994 GGTGCTCTTTTATGTCCAGCAAAA 60.262 41.667 0.00 0.00 41.63 2.44
2997 3171 5.106157 GGTACATGATTCACCTGAACAAAGG 60.106 44.000 0.00 0.00 43.57 3.11
3112 3301 8.449251 TTTTCTTTTTGCAAATTATCCTGCTT 57.551 26.923 13.65 0.00 39.38 3.91
3245 3447 3.431233 GCCTTTTGCATTTTCTCTGAAGC 59.569 43.478 0.00 0.00 40.77 3.86
3249 3451 4.210537 CACAAGCCTTTTGCATTTTCTCTG 59.789 41.667 0.00 0.00 44.83 3.35
3271 3478 9.567776 TTTCTACCTTTTCAATACATCAAGACA 57.432 29.630 0.00 0.00 0.00 3.41
3347 3822 5.714333 TGTGCACTAATCTTTCTCTCTCTCT 59.286 40.000 19.41 0.00 0.00 3.10
3348 3823 5.960113 TGTGCACTAATCTTTCTCTCTCTC 58.040 41.667 19.41 0.00 0.00 3.20
3403 3878 3.052082 CTTGTGCCGGTGCTCTGG 61.052 66.667 9.38 9.38 42.72 3.86
3454 3929 4.101114 TGTAACATTCTGGAGAGGGCTAA 58.899 43.478 0.00 0.00 0.00 3.09
3487 3962 7.890127 TCTGTATCCTTCAATTGATGTTTTCCT 59.110 33.333 9.40 0.00 0.00 3.36
3488 3963 8.055279 TCTGTATCCTTCAATTGATGTTTTCC 57.945 34.615 9.40 0.00 0.00 3.13
3489 3964 9.912634 TTTCTGTATCCTTCAATTGATGTTTTC 57.087 29.630 9.40 3.58 0.00 2.29
3491 3966 9.696917 GTTTTCTGTATCCTTCAATTGATGTTT 57.303 29.630 9.40 4.07 0.00 2.83
3492 3967 9.082313 AGTTTTCTGTATCCTTCAATTGATGTT 57.918 29.630 9.40 4.41 0.00 2.71
3493 3968 8.641498 AGTTTTCTGTATCCTTCAATTGATGT 57.359 30.769 9.40 0.00 0.00 3.06
3494 3969 9.565213 GAAGTTTTCTGTATCCTTCAATTGATG 57.435 33.333 9.40 11.57 33.43 3.07
3495 3970 9.300681 TGAAGTTTTCTGTATCCTTCAATTGAT 57.699 29.630 9.40 0.00 38.74 2.57
3496 3971 8.690203 TGAAGTTTTCTGTATCCTTCAATTGA 57.310 30.769 3.38 3.38 38.74 2.57
3497 3972 8.025445 CCTGAAGTTTTCTGTATCCTTCAATTG 58.975 37.037 0.00 0.00 40.50 2.32
3498 3973 7.725844 ACCTGAAGTTTTCTGTATCCTTCAATT 59.274 33.333 0.00 0.00 40.50 2.32
3499 3974 7.234355 ACCTGAAGTTTTCTGTATCCTTCAAT 58.766 34.615 0.00 0.00 40.50 2.57
3500 3975 6.601332 ACCTGAAGTTTTCTGTATCCTTCAA 58.399 36.000 0.00 0.00 40.50 2.69
3501 3976 6.187727 ACCTGAAGTTTTCTGTATCCTTCA 57.812 37.500 0.00 0.00 39.21 3.02
3502 3977 7.511959 AAACCTGAAGTTTTCTGTATCCTTC 57.488 36.000 0.00 0.00 46.79 3.46
3627 5449 6.889198 TCCGGAGAAAGATGAAATGTTCTAT 58.111 36.000 0.00 0.00 29.89 1.98
3818 5640 5.003804 AGTGAGTTTCAATATTCGCACCTT 58.996 37.500 5.51 0.00 32.68 3.50
3835 5657 9.099454 GTTTCATCGATCCTAAATTTAGTGAGT 57.901 33.333 20.99 6.55 0.00 3.41



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

AutoCloner maintained by Alex Coulton.