Multiple sequence alignment - TraesCS2B01G181400

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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 TraesCS2B01G181400 chr2B 100.000 3152 0 0 1 3152 156049179 156046028 0.000000e+00 5821
1 TraesCS2B01G181400 chr6B 96.570 2799 88 8 1 2795 542977888 542980682 0.000000e+00 4630
2 TraesCS2B01G181400 chr6B 96.473 2807 88 6 1 2797 69097140 69094335 0.000000e+00 4625
3 TraesCS2B01G181400 chr3B 96.537 2801 85 8 1 2795 56691735 56688941 0.000000e+00 4625
4 TraesCS2B01G181400 chr3B 96.394 2801 90 7 1 2795 56573848 56571053 0.000000e+00 4602
5 TraesCS2B01G181400 chr3B 90.060 332 20 7 2513 2836 545636784 545637110 4.860000e-113 418
6 TraesCS2B01G181400 chr3B 82.720 353 41 16 2518 2854 281166734 281167082 2.380000e-76 296
7 TraesCS2B01G181400 chr3B 82.235 349 42 13 2503 2836 335821210 335820867 1.850000e-72 283
8 TraesCS2B01G181400 chr3B 84.118 170 21 5 2503 2668 335808502 335808335 3.250000e-35 159
9 TraesCS2B01G181400 chr5B 96.540 2370 76 5 390 2757 18178708 18181073 0.000000e+00 3917
10 TraesCS2B01G181400 chr5B 85.596 604 61 20 2559 3152 182677566 182678153 7.470000e-171 610
11 TraesCS2B01G181400 chr4A 90.938 2869 199 45 1 2845 618796110 618793279 0.000000e+00 3801
12 TraesCS2B01G181400 chr4A 90.938 2825 190 50 1 2802 618718129 618715348 0.000000e+00 3738
13 TraesCS2B01G181400 chr4A 85.324 586 58 14 2574 3149 573111402 573111969 5.860000e-162 580
14 TraesCS2B01G181400 chr4A 86.852 540 43 18 2616 3144 618810083 618809561 2.110000e-161 579
15 TraesCS2B01G181400 chr4A 85.445 584 49 23 2574 3144 618714658 618714098 2.730000e-160 575
16 TraesCS2B01G181400 chr4A 86.481 540 45 18 2616 3144 618793414 618792892 4.560000e-158 568
17 TraesCS2B01G181400 chr4A 87.841 477 40 12 2679 3144 543519755 543519286 7.690000e-151 544
18 TraesCS2B01G181400 chr1A 93.120 2558 153 17 1 2551 115062444 115064985 0.000000e+00 3727
19 TraesCS2B01G181400 chr1A 90.997 2788 197 41 1 2770 84817933 84820684 0.000000e+00 3709
20 TraesCS2B01G181400 chr1A 89.933 447 34 7 2704 3144 84820880 84821321 1.640000e-157 566
21 TraesCS2B01G181400 chr4D 88.296 487 41 9 2677 3152 478460227 478460708 1.270000e-158 569
22 TraesCS2B01G181400 chrUn 88.445 476 38 12 2680 3144 411827766 411828235 2.750000e-155 558


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 TraesCS2B01G181400 chr2B 156046028 156049179 3151 True 5821.0 5821 100.0000 1 3152 1 chr2B.!!$R1 3151
1 TraesCS2B01G181400 chr6B 542977888 542980682 2794 False 4630.0 4630 96.5700 1 2795 1 chr6B.!!$F1 2794
2 TraesCS2B01G181400 chr6B 69094335 69097140 2805 True 4625.0 4625 96.4730 1 2797 1 chr6B.!!$R1 2796
3 TraesCS2B01G181400 chr3B 56688941 56691735 2794 True 4625.0 4625 96.5370 1 2795 1 chr3B.!!$R2 2794
4 TraesCS2B01G181400 chr3B 56571053 56573848 2795 True 4602.0 4602 96.3940 1 2795 1 chr3B.!!$R1 2794
5 TraesCS2B01G181400 chr5B 18178708 18181073 2365 False 3917.0 3917 96.5400 390 2757 1 chr5B.!!$F1 2367
6 TraesCS2B01G181400 chr5B 182677566 182678153 587 False 610.0 610 85.5960 2559 3152 1 chr5B.!!$F2 593
7 TraesCS2B01G181400 chr4A 618792892 618796110 3218 True 2184.5 3801 88.7095 1 3144 2 chr4A.!!$R4 3143
8 TraesCS2B01G181400 chr4A 618714098 618718129 4031 True 2156.5 3738 88.1915 1 3144 2 chr4A.!!$R3 3143
9 TraesCS2B01G181400 chr4A 573111402 573111969 567 False 580.0 580 85.3240 2574 3149 1 chr4A.!!$F1 575
10 TraesCS2B01G181400 chr4A 618809561 618810083 522 True 579.0 579 86.8520 2616 3144 1 chr4A.!!$R2 528
11 TraesCS2B01G181400 chr1A 115062444 115064985 2541 False 3727.0 3727 93.1200 1 2551 1 chr1A.!!$F1 2550
12 TraesCS2B01G181400 chr1A 84817933 84821321 3388 False 2137.5 3709 90.4650 1 3144 2 chr1A.!!$F2 3143

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
453 454 0.934496 TTTATTGCGCTCGAATCCGG 59.066 50.000 9.73 0.0 36.24 5.14 F
583 585 1.519408 GTCAAGGTAACATGCACGGT 58.481 50.000 0.00 0.0 41.41 4.83 F
1546 1560 2.066262 ACGCTATCGACTTGTTGTTGG 58.934 47.619 0.00 0.0 39.41 3.77 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1592 1606 1.202336 CCTGAAAAATCTCATGGCGCC 60.202 52.381 22.73 22.73 0.0 6.53 R
1945 1960 2.032981 CTTGCTTGGCGGAACAGTT 58.967 52.632 0.00 0.00 0.0 3.16 R
2918 4315 0.170561 ATTCTAGCGGCGCGTATAGG 59.829 55.000 27.59 13.48 0.0 2.57 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
143 144 2.570415 TTCCACACGATTTTAGCCCA 57.430 45.000 0.00 0.00 0.00 5.36
453 454 0.934496 TTTATTGCGCTCGAATCCGG 59.066 50.000 9.73 0.00 36.24 5.14
481 482 6.540189 CAGACTCACTATATTCCCAACAAAGG 59.460 42.308 0.00 0.00 0.00 3.11
498 500 2.101640 AGGTTTGTGGGCAATTCCTT 57.898 45.000 0.00 0.00 36.58 3.36
583 585 1.519408 GTCAAGGTAACATGCACGGT 58.481 50.000 0.00 0.00 41.41 4.83
1138 1150 2.568623 TTCTCTTGGAGAAAGCCCAC 57.431 50.000 7.42 0.00 44.37 4.61
1485 1499 5.591877 GGGAATAATGACACAGATTTCAGCT 59.408 40.000 0.00 0.00 0.00 4.24
1516 1530 6.428083 TGGATATTTCCGCTATTACCAAGA 57.572 37.500 0.00 0.00 45.89 3.02
1546 1560 2.066262 ACGCTATCGACTTGTTGTTGG 58.934 47.619 0.00 0.00 39.41 3.77
1592 1606 4.058817 GCCCCTACATTAACAGATTCTCG 58.941 47.826 0.00 0.00 0.00 4.04
1811 1826 5.506317 CCATTGAAGCGTCTCTGAAAACTTT 60.506 40.000 0.31 0.00 0.00 2.66
1945 1960 2.972713 AGGGTCAAGCAACTAGAGTCAA 59.027 45.455 0.00 0.00 0.00 3.18
1948 1963 4.381411 GGTCAAGCAACTAGAGTCAAACT 58.619 43.478 0.00 0.00 0.00 2.66
2061 2076 0.965866 AGACATCGACGCTGGAGGAA 60.966 55.000 3.49 0.00 0.00 3.36
2186 2201 1.276421 ACTCAGACTTGCATAAGGCGT 59.724 47.619 0.00 0.00 46.99 5.68
2193 2208 6.673748 AGACTTGCATAAGGCGTCCAATCA 62.674 45.833 0.00 0.00 46.99 2.57
2347 2362 3.201290 ACTCCGAGCTAATTGCATGAAG 58.799 45.455 0.00 0.00 45.94 3.02
2350 2365 4.765273 TCCGAGCTAATTGCATGAAGTAA 58.235 39.130 0.00 0.00 45.94 2.24
2838 4191 3.223435 CTCGTGAGGGTATGGAGTACAT 58.777 50.000 0.00 0.00 43.68 2.29
2839 4192 3.637229 CTCGTGAGGGTATGGAGTACATT 59.363 47.826 0.00 0.00 41.03 2.71
2901 4298 0.179145 CGGTGCCGACGAGTATTTCT 60.179 55.000 4.35 0.00 42.83 2.52
2918 4315 9.585099 GAGTATTTCTCATCTGGTGATATGATC 57.415 37.037 0.00 0.00 42.34 2.92
2999 4396 3.934457 AATTTTTCTTTCATCCGCCGT 57.066 38.095 0.00 0.00 0.00 5.68
3066 4463 5.182380 TGTTTGAACGACCTTCTTTTGACTT 59.818 36.000 0.00 0.00 0.00 3.01
3129 4526 6.108015 TCAAGATTTTGCAAAGCTTGAAGTT 58.892 32.000 33.78 13.63 37.77 2.66
3130 4527 6.594937 TCAAGATTTTGCAAAGCTTGAAGTTT 59.405 30.769 33.78 13.13 37.77 2.66
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
13 14 1.557832 TCTTCAGATAAACCCCCACCG 59.442 52.381 0.00 0.00 0.00 4.94
15 16 4.600062 ACATTCTTCAGATAAACCCCCAC 58.400 43.478 0.00 0.00 0.00 4.61
143 144 1.523758 AGAAATCGTGCGCCTTTTCT 58.476 45.000 4.18 11.17 34.46 2.52
453 454 6.640518 TGTTGGGAATATAGTGAGTCTGTTC 58.359 40.000 0.00 0.00 0.00 3.18
481 482 3.306019 CCACTAAGGAATTGCCCACAAAC 60.306 47.826 0.00 0.00 38.51 2.93
498 500 1.423541 ACCAGTTTGTCCATGCCACTA 59.576 47.619 0.00 0.00 0.00 2.74
583 585 4.651503 AGCCTTTCTTCATAGGAATCTCGA 59.348 41.667 0.00 0.00 33.13 4.04
1138 1150 2.144482 ACCAACTCGTCAAGGTTACG 57.856 50.000 0.00 0.00 41.64 3.18
1592 1606 1.202336 CCTGAAAAATCTCATGGCGCC 60.202 52.381 22.73 22.73 0.00 6.53
1811 1826 2.666317 TGGATGACATCTCTTCCGCTA 58.334 47.619 14.95 0.00 41.69 4.26
1945 1960 2.032981 CTTGCTTGGCGGAACAGTT 58.967 52.632 0.00 0.00 0.00 3.16
1948 1963 2.203337 AGCTTGCTTGGCGGAACA 60.203 55.556 0.00 0.00 34.52 3.18
2186 2201 3.903090 AGAAAATGGGTTTGCTGATTGGA 59.097 39.130 0.00 0.00 31.75 3.53
2193 2208 4.218312 AGACAAGAGAAAATGGGTTTGCT 58.782 39.130 0.00 0.00 35.84 3.91
2296 2311 8.559536 CATTCCACATAGAAACAAGCGTTATAT 58.440 33.333 0.00 0.00 33.99 0.86
2301 2316 3.440173 CCATTCCACATAGAAACAAGCGT 59.560 43.478 0.00 0.00 0.00 5.07
2347 2362 6.801718 AATAAATAAAGGGGCCCAAGTTAC 57.198 37.500 27.72 4.38 0.00 2.50
2350 2365 6.265304 TGTAAATAAATAAAGGGGCCCAAGT 58.735 36.000 27.72 11.85 0.00 3.16
2450 2477 6.051074 ACTGTTGTACAAAAGGGTAGTGTAC 58.949 40.000 26.01 4.84 45.08 2.90
2457 2484 5.655090 AGCTTAAACTGTTGTACAAAAGGGT 59.345 36.000 26.01 16.71 29.85 4.34
2789 4044 2.878406 CTGGGGCACAAATATTACTCCG 59.122 50.000 0.00 0.00 0.00 4.63
2798 4053 3.421844 GAGTCTAAACTGGGGCACAAAT 58.578 45.455 0.00 0.00 35.28 2.32
2845 4242 7.709269 TTCCTTAAGCGTTACTATGCATAAG 57.291 36.000 8.00 4.91 42.76 1.73
2901 4298 6.039829 GCGTATAGGATCATATCACCAGATGA 59.960 42.308 2.57 0.00 43.13 2.92
2918 4315 0.170561 ATTCTAGCGGCGCGTATAGG 59.829 55.000 27.59 13.48 0.00 2.57
2972 4369 5.107104 GCGGATGAAAGAAAAATTTGAACCC 60.107 40.000 0.00 0.00 0.00 4.11
2999 4396 5.056480 GTCATTCGTCCCATGAATATCACA 58.944 41.667 0.00 0.00 32.42 3.58


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

AutoCloner maintained by Alex Coulton.