Multiple sequence alignment - TraesCS2B01G306100

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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 TraesCS2B01G306100 chr2B 100.000 4854 0 0 1 4854 436991082 436995935 0.000000e+00 8964
1 TraesCS2B01G306100 chr2D 96.120 4871 124 24 1 4854 367989640 367994462 0.000000e+00 7888
2 TraesCS2B01G306100 chr2A 96.639 3749 93 11 932 4668 498086212 498089939 0.000000e+00 6194
3 TraesCS2B01G306100 chr2A 93.908 952 33 13 1 947 498085267 498086198 0.000000e+00 1413
4 TraesCS2B01G306100 chr2A 98.113 212 2 1 4645 4854 498090115 498090326 7.680000e-98 368
5 TraesCS2B01G306100 chr2A 90.196 102 7 2 4754 4852 762011912 762011811 3.940000e-26 130
6 TraesCS2B01G306100 chr4A 85.116 430 64 0 1673 2102 5405427 5405856 1.600000e-119 440
7 TraesCS2B01G306100 chr4B 84.651 430 66 0 1673 2102 581537724 581537295 3.470000e-116 429
8 TraesCS2B01G306100 chr4B 73.950 357 55 26 2231 2563 518872403 518872745 5.140000e-20 110
9 TraesCS2B01G306100 chr4D 93.137 102 4 2 4755 4853 289339810 289339911 3.910000e-31 147
10 TraesCS2B01G306100 chr5A 92.784 97 4 2 4756 4849 110665086 110664990 2.360000e-28 137
11 TraesCS2B01G306100 chr3A 92.708 96 5 2 4756 4849 167879890 167879795 2.360000e-28 137
12 TraesCS2B01G306100 chr6B 91.837 98 5 2 4756 4850 684940398 684940301 3.050000e-27 134
13 TraesCS2B01G306100 chr5D 91.089 101 6 2 4752 4849 134782210 134782110 3.050000e-27 134
14 TraesCS2B01G306100 chr5B 87.826 115 9 4 4741 4852 698467298 698467186 3.940000e-26 130


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 TraesCS2B01G306100 chr2B 436991082 436995935 4853 False 8964.000000 8964 100.00 1 4854 1 chr2B.!!$F1 4853
1 TraesCS2B01G306100 chr2D 367989640 367994462 4822 False 7888.000000 7888 96.12 1 4854 1 chr2D.!!$F1 4853
2 TraesCS2B01G306100 chr2A 498085267 498090326 5059 False 2658.333333 6194 96.22 1 4854 3 chr2A.!!$F1 4853


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
72 73 0.881600 TCTGGAATCATCGCATGCCG 60.882 55.000 13.15 7.68 38.61 5.69 F
366 372 1.798813 GACTCTTAGTGGTTTGTGGCG 59.201 52.381 0.00 0.00 0.00 5.69 F
1847 1892 1.141657 TGGAAGCTCAAGCAGACAAGT 59.858 47.619 4.59 0.00 45.16 3.16 F
2453 2498 3.054139 TCCATGCAATCTAACCTCTTGCT 60.054 43.478 7.85 0.00 44.29 3.91 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1847 1892 1.080093 CTTCTTAGCGTCGGTGCCA 60.080 57.895 7.30 0.0 34.65 4.92 R
2326 2371 5.906772 ACCCTAATACTAAATCCCCTGTG 57.093 43.478 0.00 0.0 0.00 3.66 R
3025 3078 1.078918 TGCATCACAGAAGGCTCGG 60.079 57.895 0.00 0.0 0.00 4.63 R
4432 4486 0.976641 TAGTGACACCTGAAGCCCTG 59.023 55.000 0.84 0.0 0.00 4.45 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
37 38 2.126502 CCACGCGACCAAAATGCC 60.127 61.111 15.93 0.00 0.00 4.40
72 73 0.881600 TCTGGAATCATCGCATGCCG 60.882 55.000 13.15 7.68 38.61 5.69
104 105 5.481473 ACATACATTTCCATTCCAACAAGCT 59.519 36.000 0.00 0.00 0.00 3.74
107 108 2.673775 TTCCATTCCAACAAGCTCCA 57.326 45.000 0.00 0.00 0.00 3.86
112 113 3.305608 CCATTCCAACAAGCTCCAAGTTC 60.306 47.826 0.00 0.00 0.00 3.01
175 176 4.696479 ATTCCGGAGCTTCTGAACATAT 57.304 40.909 3.34 0.00 0.00 1.78
353 359 6.687081 AAAACCAACGAAATGTGACTCTTA 57.313 33.333 0.00 0.00 0.00 2.10
366 372 1.798813 GACTCTTAGTGGTTTGTGGCG 59.201 52.381 0.00 0.00 0.00 5.69
464 470 6.778559 TGCCAGGTAGTTAAGTAAAACCAATT 59.221 34.615 4.01 0.00 32.43 2.32
720 731 5.217400 AGTTTATACCCTCCCAGAGTAAGG 58.783 45.833 0.00 0.00 0.00 2.69
833 845 7.079700 TCCTAATGTTAATATGACCCTCCAGA 58.920 38.462 0.00 0.00 0.00 3.86
1258 1298 5.473162 TCAGTGTTTATGAGTTCAACCCATG 59.527 40.000 0.00 0.00 0.00 3.66
1465 1505 8.458573 TGAACAATCACTTGTAAACAACCTAT 57.541 30.769 0.00 0.00 44.83 2.57
1527 1571 1.929494 TGATTCACCCCAGGGCTAATT 59.071 47.619 0.00 0.00 39.32 1.40
1528 1572 3.127250 TGATTCACCCCAGGGCTAATTA 58.873 45.455 0.00 0.00 39.32 1.40
1529 1573 3.529734 TGATTCACCCCAGGGCTAATTAA 59.470 43.478 0.00 0.00 39.32 1.40
1530 1574 4.169856 TGATTCACCCCAGGGCTAATTAAT 59.830 41.667 0.00 0.00 39.32 1.40
1847 1892 1.141657 TGGAAGCTCAAGCAGACAAGT 59.858 47.619 4.59 0.00 45.16 3.16
2165 2210 5.888724 TGGAGTTGTCTGGTATTTCAACAAA 59.111 36.000 9.04 0.00 41.43 2.83
2201 2246 8.407832 CAGCTGGATTAATTGTTGATTATGACA 58.592 33.333 5.57 0.00 30.56 3.58
2263 2308 5.423015 TGGTTTGCAGTATTCAAAAAGCAA 58.577 33.333 0.00 0.00 31.99 3.91
2264 2309 5.523188 TGGTTTGCAGTATTCAAAAAGCAAG 59.477 36.000 0.00 0.00 42.11 4.01
2326 2371 8.816640 TTTCAAATCCTACAGAAATCAAAAGC 57.183 30.769 0.00 0.00 0.00 3.51
2345 2390 7.556275 TCAAAAGCACAGGGGATTTAGTATTAG 59.444 37.037 0.00 0.00 0.00 1.73
2421 2466 7.014326 GTGGATACCATAGTTGTCATAGACTCA 59.986 40.741 0.00 0.00 35.28 3.41
2453 2498 3.054139 TCCATGCAATCTAACCTCTTGCT 60.054 43.478 7.85 0.00 44.29 3.91
2469 2514 5.072329 CCTCTTGCTAGGAATCCTATGGAAA 59.928 44.000 9.80 0.00 39.15 3.13
2606 2651 4.261031 CCTTTGACCTAAAAGAACCGTGTG 60.261 45.833 0.00 0.00 39.12 3.82
2818 2864 8.684386 TCTTTGTTTCCAAGTGTTACATGATA 57.316 30.769 0.00 0.00 0.00 2.15
2851 2897 7.396540 AGTTGTTCTTGTTTCAGAGTGAATT 57.603 32.000 0.00 0.00 36.11 2.17
2865 2911 9.515020 TTCAGAGTGAATTTCAAACACAATAAC 57.485 29.630 0.00 0.00 37.05 1.89
2870 2916 7.069331 AGTGAATTTCAAACACAATAACCTGGA 59.931 33.333 0.00 0.00 37.05 3.86
2896 2942 8.581253 AATCCTAGTAGAAAAACATTTCCCTG 57.419 34.615 0.00 0.00 0.00 4.45
2973 3026 8.725405 TCTGAAATGCCGATATTTACAAACTA 57.275 30.769 0.00 0.00 30.78 2.24
2991 3044 7.127686 ACAAACTAACATTTCTTTCCGTTACG 58.872 34.615 0.00 0.00 0.00 3.18
3025 3078 2.175878 AGGACAGCTTCATCACACAC 57.824 50.000 0.00 0.00 0.00 3.82
3044 3097 1.364626 CCGAGCCTTCTGTGATGCAC 61.365 60.000 0.00 0.00 34.56 4.57
3323 3376 2.024176 TGGGAGTGAACCAAGCTCTA 57.976 50.000 0.00 0.00 34.44 2.43
3496 3549 1.008327 TCTTCTGGCATCCTAGGGACA 59.992 52.381 9.46 0.44 32.98 4.02
3505 3558 0.178970 TCCTAGGGACACCGATAGCC 60.179 60.000 9.46 0.00 43.47 3.93
3556 3609 2.926200 CAACAGCTCCTACATGAACTCG 59.074 50.000 0.00 0.00 0.00 4.18
3607 3660 2.825836 GCAGTGCCTTGGATCGGG 60.826 66.667 2.85 0.00 0.00 5.14
4144 4198 2.680312 TGCTGGAATAGAGAGTGCAC 57.320 50.000 9.40 9.40 0.00 4.57
4166 4220 7.493645 TGCACAACATGTATTTGATTGAACAAA 59.506 29.630 0.00 0.00 42.58 2.83
4251 4305 3.498774 ACAGAGTTGCCTCTCAAATGT 57.501 42.857 7.75 1.87 45.08 2.71
4252 4306 3.825328 ACAGAGTTGCCTCTCAAATGTT 58.175 40.909 7.75 0.00 45.08 2.71
4254 4308 5.564550 ACAGAGTTGCCTCTCAAATGTTAT 58.435 37.500 7.75 0.00 45.08 1.89
4255 4309 5.645497 ACAGAGTTGCCTCTCAAATGTTATC 59.355 40.000 7.75 0.00 45.08 1.75
4256 4310 5.065731 CAGAGTTGCCTCTCAAATGTTATCC 59.934 44.000 7.75 0.00 45.08 2.59
4257 4311 5.045286 AGAGTTGCCTCTCAAATGTTATCCT 60.045 40.000 7.75 0.00 45.08 3.24
4258 4312 5.574188 AGTTGCCTCTCAAATGTTATCCTT 58.426 37.500 0.00 0.00 36.26 3.36
4259 4313 5.649831 AGTTGCCTCTCAAATGTTATCCTTC 59.350 40.000 0.00 0.00 36.26 3.46
4260 4314 5.178096 TGCCTCTCAAATGTTATCCTTCA 57.822 39.130 0.00 0.00 0.00 3.02
4261 4315 5.188434 TGCCTCTCAAATGTTATCCTTCAG 58.812 41.667 0.00 0.00 0.00 3.02
4262 4316 5.189180 GCCTCTCAAATGTTATCCTTCAGT 58.811 41.667 0.00 0.00 0.00 3.41
4263 4317 5.295540 GCCTCTCAAATGTTATCCTTCAGTC 59.704 44.000 0.00 0.00 0.00 3.51
4383 4437 1.973515 AGAGGCTCAATGTCACTCACA 59.026 47.619 18.26 0.00 40.18 3.58
4432 4486 0.179001 ACAGTTTGTGGGCCAGTACC 60.179 55.000 6.40 0.00 0.00 3.34
4444 4498 1.201429 CCAGTACCAGGGCTTCAGGT 61.201 60.000 0.00 0.00 39.41 4.00
4530 4584 5.903010 TGATCCCTATTCTTAGGCTTGTACA 59.097 40.000 0.00 0.00 43.34 2.90
4617 4674 3.243535 TGCATGCGTTTACAAAATGTGGA 60.244 39.130 14.09 0.00 0.00 4.02
4716 4972 4.058721 TGATCTTCATGTACCATCACGG 57.941 45.455 0.00 0.00 42.50 4.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
37 38 0.674895 CAGAGAACCGAAAGCTGGGG 60.675 60.000 0.00 0.00 0.00 4.96
72 73 9.921637 TTGGAATGGAAATGTATGTTTAAACTC 57.078 29.630 18.72 9.99 0.00 3.01
175 176 5.479027 TCACTAGTGTAGCATACTTTGTGGA 59.521 40.000 21.99 0.00 43.54 4.02
292 298 7.193595 ACTTGCATTTGTGTTAACTGAGTTAC 58.806 34.615 4.23 0.00 0.00 2.50
353 359 0.110486 AGGATTCGCCACAAACCACT 59.890 50.000 0.00 0.00 40.02 4.00
366 372 4.555262 GCTGTGTAGCTCATCTAGGATTC 58.445 47.826 0.00 0.00 46.57 2.52
439 445 5.307544 TGGTTTTACTTAACTACCTGGCA 57.692 39.130 0.00 0.00 0.00 4.92
464 470 2.615391 TGAACCCTGTGTCCTGATACA 58.385 47.619 0.00 0.00 0.00 2.29
472 478 2.232941 TCCTTCGTATGAACCCTGTGTC 59.767 50.000 0.00 0.00 0.00 3.67
720 731 1.354506 GATCAAGCGCATCAGGCAC 59.645 57.895 11.47 0.00 45.17 5.01
833 845 4.536765 AGTTTTTGAGACCACTGGAACAT 58.463 39.130 0.71 0.00 38.20 2.71
895 907 9.398170 CAGCCAAATATATATTTTGTTTCCTCG 57.602 33.333 16.47 4.29 33.88 4.63
911 923 9.850198 ATTATTTGCCATTAAACAGCCAAATAT 57.150 25.926 0.00 0.00 0.00 1.28
912 924 9.107177 CATTATTTGCCATTAAACAGCCAAATA 57.893 29.630 0.00 0.00 0.00 1.40
1150 1190 1.453235 CATGGATGATGGGGTCGCT 59.547 57.895 0.00 0.00 0.00 4.93
1231 1271 6.549364 TGGGTTGAACTCATAAACACTGAAAT 59.451 34.615 0.00 0.00 0.00 2.17
1239 1279 5.391312 AAGCATGGGTTGAACTCATAAAC 57.609 39.130 10.82 3.80 37.15 2.01
1258 1298 2.360801 TGCCTTTGTGGTAGTTGAAAGC 59.639 45.455 0.00 0.00 38.35 3.51
1465 1505 9.296400 GTAAAAACAATAGTTCAGCAGTGAAAA 57.704 29.630 0.00 0.00 44.44 2.29
1530 1574 9.841295 AGAGCTATTTATTACCCGTGAAATAAA 57.159 29.630 0.00 7.88 40.15 1.40
1847 1892 1.080093 CTTCTTAGCGTCGGTGCCA 60.080 57.895 7.30 0.00 34.65 4.92
2180 2225 8.078596 GGAGCTGTCATAATCAACAATTAATCC 58.921 37.037 0.00 0.00 33.59 3.01
2201 2246 6.491403 GGGTATTGAATATCACATTTGGAGCT 59.509 38.462 0.00 0.00 0.00 4.09
2263 2308 8.840751 CCTATTCCTATGATTTTCCTATTCCCT 58.159 37.037 0.00 0.00 0.00 4.20
2264 2309 8.836735 TCCTATTCCTATGATTTTCCTATTCCC 58.163 37.037 0.00 0.00 0.00 3.97
2326 2371 5.906772 ACCCTAATACTAAATCCCCTGTG 57.093 43.478 0.00 0.00 0.00 3.66
2402 2447 6.878317 TCCTTTGAGTCTATGACAACTATGG 58.122 40.000 0.46 3.83 34.60 2.74
2453 2498 7.931015 ACACTACATTTCCATAGGATTCCTA 57.069 36.000 14.77 14.77 40.71 2.94
2469 2514 7.283127 CCTATGGATTGCTTTTGTACACTACAT 59.717 37.037 0.00 0.00 38.68 2.29
2519 2564 6.985188 TTTTCCTTTAGGTTCATCTGATCG 57.015 37.500 0.00 0.00 36.34 3.69
2520 2565 9.794685 GAAATTTTCCTTTAGGTTCATCTGATC 57.205 33.333 0.00 0.00 36.34 2.92
2576 2621 7.169140 CGGTTCTTTTAGGTCAAAGGATTTTTG 59.831 37.037 0.00 0.00 35.03 2.44
2579 2624 5.831525 ACGGTTCTTTTAGGTCAAAGGATTT 59.168 36.000 0.00 0.00 40.26 2.17
2606 2651 7.816640 TGTAATTGAATTTCTAGCCTGTGAAC 58.183 34.615 0.00 0.00 0.00 3.18
2729 2775 3.370103 GGTGAAACGGATGGTGGATCTAA 60.370 47.826 0.00 0.00 38.12 2.10
2803 2849 7.814107 ACTTGGCAAAATATCATGTAACACTTG 59.186 33.333 0.00 0.00 0.00 3.16
2851 2897 6.553100 AGGATTTCCAGGTTATTGTGTTTGAA 59.447 34.615 0.00 0.00 38.89 2.69
2865 2911 8.581253 AATGTTTTTCTACTAGGATTTCCAGG 57.419 34.615 0.00 0.00 38.89 4.45
2870 2916 9.025041 CAGGGAAATGTTTTTCTACTAGGATTT 57.975 33.333 0.00 0.00 40.91 2.17
2973 3026 8.036273 ACAATATCGTAACGGAAAGAAATGTT 57.964 30.769 0.00 0.00 0.00 2.71
2991 3044 7.334421 TGAAGCTGTCCTTTCTGTAACAATATC 59.666 37.037 0.00 0.00 32.78 1.63
3025 3078 1.078918 TGCATCACAGAAGGCTCGG 60.079 57.895 0.00 0.00 0.00 4.63
3044 3097 9.092876 GTTGATTCTGGAGTTATCTTCAGTTAG 57.907 37.037 8.65 0.00 45.11 2.34
3323 3376 3.133721 GGAGAGCTCATGGACATGTAAGT 59.866 47.826 17.77 0.00 39.72 2.24
3496 3549 6.493802 TCTTTCTATCACTATTGGCTATCGGT 59.506 38.462 0.00 0.00 0.00 4.69
3505 3558 7.978414 TCAGCAGTCTTCTTTCTATCACTATTG 59.022 37.037 0.00 0.00 0.00 1.90
3607 3660 1.202405 CCCATTGAAAATGGCGGTAGC 60.202 52.381 12.64 0.00 44.18 3.58
3622 3675 3.033909 GCTTCTATTTTCTGCCCCCATT 58.966 45.455 0.00 0.00 0.00 3.16
3991 4045 9.631257 TTTCATGAAATCATCTTCTAGCCATAA 57.369 29.630 16.91 0.00 33.61 1.90
4254 4308 9.098355 CAGATAAAAATGTATTCGACTGAAGGA 57.902 33.333 0.00 0.00 37.57 3.36
4255 4309 7.852945 GCAGATAAAAATGTATTCGACTGAAGG 59.147 37.037 0.00 0.00 37.57 3.46
4256 4310 8.607459 AGCAGATAAAAATGTATTCGACTGAAG 58.393 33.333 0.00 0.00 37.57 3.02
4257 4311 8.492673 AGCAGATAAAAATGTATTCGACTGAA 57.507 30.769 0.00 0.00 38.76 3.02
4258 4312 8.492673 AAGCAGATAAAAATGTATTCGACTGA 57.507 30.769 0.00 0.00 0.00 3.41
4259 4313 8.390354 TGAAGCAGATAAAAATGTATTCGACTG 58.610 33.333 0.00 0.00 0.00 3.51
4260 4314 8.492673 TGAAGCAGATAAAAATGTATTCGACT 57.507 30.769 0.00 0.00 0.00 4.18
4261 4315 8.391106 ACTGAAGCAGATAAAAATGTATTCGAC 58.609 33.333 0.82 0.00 35.18 4.20
4262 4316 8.492673 ACTGAAGCAGATAAAAATGTATTCGA 57.507 30.769 0.82 0.00 35.18 3.71
4383 4437 2.616376 TGTATTGTGTCGCAACAGCTTT 59.384 40.909 0.00 0.00 40.28 3.51
4432 4486 0.976641 TAGTGACACCTGAAGCCCTG 59.023 55.000 0.84 0.00 0.00 4.45
4444 4498 1.342074 AAGCTCTGCCAGTAGTGACA 58.658 50.000 0.00 0.00 0.00 3.58
4592 4649 5.333952 CCACATTTTGTAAACGCATGCATTT 60.334 36.000 16.71 16.71 0.00 2.32
4593 4650 4.152045 CCACATTTTGTAAACGCATGCATT 59.848 37.500 19.57 14.28 0.00 3.56
4594 4651 3.679025 CCACATTTTGTAAACGCATGCAT 59.321 39.130 19.57 0.00 0.00 3.96
4602 4659 6.366061 GCCATTTCTCTCCACATTTTGTAAAC 59.634 38.462 0.00 0.00 0.00 2.01
4617 4674 3.795688 TTGAAGAGGTGCCATTTCTCT 57.204 42.857 0.00 0.00 39.31 3.10
4716 4972 1.961793 TATTTATGTCCCAGCGGCAC 58.038 50.000 1.45 0.00 0.00 5.01



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

AutoCloner maintained by Alex Coulton.