Multiple sequence alignment - TraesCS5D01G137300

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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 TraesCS5D01G137300 chr5D 100.000 3338 0 0 1 3338 218262390 218259053 0.000000e+00 6165.0
1 TraesCS5D01G137300 chr5D 91.111 45 4 0 2893 2937 57074216 57074172 1.000000e-05 62.1
2 TraesCS5D01G137300 chr5B 94.911 2751 106 15 605 3336 234904760 234902025 0.000000e+00 4274.0
3 TraesCS5D01G137300 chr5B 90.400 125 11 1 483 606 234904911 234904787 2.660000e-36 163.0
4 TraesCS5D01G137300 chr5A 95.115 2661 88 19 1 2623 291273409 291270753 0.000000e+00 4156.0
5 TraesCS5D01G137300 chrUn 100.000 401 0 0 1604 2004 478699349 478699749 0.000000e+00 741.0
6 TraesCS5D01G137300 chr6D 80.075 798 158 1 1415 2211 203748683 203747886 2.870000e-165 592.0
7 TraesCS5D01G137300 chr6A 80.075 798 158 1 1415 2211 289027066 289026269 2.870000e-165 592.0
8 TraesCS5D01G137300 chr6B 79.950 798 159 1 1415 2211 316460103 316459306 1.330000e-163 586.0
9 TraesCS5D01G137300 chr7A 73.557 745 170 24 1504 2233 645039047 645039779 3.300000e-65 259.0
10 TraesCS5D01G137300 chr7D 81.343 134 19 5 2810 2937 605785922 605785789 1.640000e-18 104.0
11 TraesCS5D01G137300 chr3D 80.000 140 16 7 2811 2945 551986590 551986458 3.550000e-15 93.5
12 TraesCS5D01G137300 chr3D 94.286 35 2 0 2912 2946 527207731 527207697 2.000000e-03 54.7
13 TraesCS5D01G137300 chr4B 79.231 130 23 3 2809 2937 659479774 659479900 1.650000e-13 87.9
14 TraesCS5D01G137300 chr4B 100.000 31 0 0 1107 1137 408975848 408975878 1.290000e-04 58.4
15 TraesCS5D01G137300 chr1D 76.812 138 25 5 2809 2939 411125633 411125770 1.660000e-08 71.3
16 TraesCS5D01G137300 chr4D 100.000 31 0 0 1107 1137 329133647 329133677 1.290000e-04 58.4
17 TraesCS5D01G137300 chr4A 100.000 31 0 0 1107 1137 140983359 140983329 1.290000e-04 58.4
18 TraesCS5D01G137300 chr1B 100.000 31 0 0 1107 1137 135826996 135826966 1.290000e-04 58.4


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 TraesCS5D01G137300 chr5D 218259053 218262390 3337 True 6165.0 6165 100.0000 1 3338 1 chr5D.!!$R2 3337
1 TraesCS5D01G137300 chr5B 234902025 234904911 2886 True 2218.5 4274 92.6555 483 3336 2 chr5B.!!$R1 2853
2 TraesCS5D01G137300 chr5A 291270753 291273409 2656 True 4156.0 4156 95.1150 1 2623 1 chr5A.!!$R1 2622
3 TraesCS5D01G137300 chr6D 203747886 203748683 797 True 592.0 592 80.0750 1415 2211 1 chr6D.!!$R1 796
4 TraesCS5D01G137300 chr6A 289026269 289027066 797 True 592.0 592 80.0750 1415 2211 1 chr6A.!!$R1 796
5 TraesCS5D01G137300 chr6B 316459306 316460103 797 True 586.0 586 79.9500 1415 2211 1 chr6B.!!$R1 796
6 TraesCS5D01G137300 chr7A 645039047 645039779 732 False 259.0 259 73.5570 1504 2233 1 chr7A.!!$F1 729

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
167 171 1.134491 GGTAGGGCTGCGTAGATTTGT 60.134 52.381 4.08 0.0 0.0 2.83 F
1119 1187 1.293924 GCTTCATCACCATCCTCGTG 58.706 55.000 0.00 0.0 0.0 4.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1265 1333 3.678717 AAGGACGCATCGACGACGG 62.679 63.158 7.55 3.72 40.21 4.79 R
2689 2766 0.958382 TAACCAAGCACCATGACGCC 60.958 55.000 0.00 0.00 0.00 5.68 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
46 49 2.147958 GCTACAACCGTTGATCACCAA 58.852 47.619 18.19 0.00 0.00 3.67
48 51 3.426159 GCTACAACCGTTGATCACCAATG 60.426 47.826 18.19 0.00 40.59 2.82
50 53 2.552315 ACAACCGTTGATCACCAATGTC 59.448 45.455 18.19 0.00 39.55 3.06
62 65 1.673920 ACCAATGTCGTGCGAGTTTTT 59.326 42.857 0.00 0.00 0.00 1.94
63 66 2.286772 ACCAATGTCGTGCGAGTTTTTC 60.287 45.455 0.00 0.00 0.00 2.29
65 68 1.878953 ATGTCGTGCGAGTTTTTCCT 58.121 45.000 0.00 0.00 0.00 3.36
94 98 1.346395 TCGTTTGCATAGTGTCCTGGT 59.654 47.619 0.00 0.00 0.00 4.00
103 107 2.071778 AGTGTCCTGGTGCAACAAAT 57.928 45.000 5.64 0.00 39.98 2.32
142 146 2.193536 GGAAACAAGCCGGTGTGCT 61.194 57.895 1.90 0.00 45.43 4.40
167 171 1.134491 GGTAGGGCTGCGTAGATTTGT 60.134 52.381 4.08 0.00 0.00 2.83
180 186 6.095021 TGCGTAGATTTGTGTGAGTAGACTAT 59.905 38.462 0.00 0.00 0.00 2.12
181 187 6.415280 GCGTAGATTTGTGTGAGTAGACTATG 59.585 42.308 0.00 0.00 0.00 2.23
197 203 8.482943 AGTAGACTATGTAATTATGTTGGTGCA 58.517 33.333 0.00 0.00 0.00 4.57
258 266 8.117370 GTCTCTTGTAAACAGTTGTTTCTCTTC 58.883 37.037 13.07 2.91 44.15 2.87
321 330 7.858052 AAAATCTTGTAAATCAAAGCGTGAG 57.142 32.000 0.00 0.00 40.43 3.51
322 331 6.801539 AATCTTGTAAATCAAAGCGTGAGA 57.198 33.333 0.00 0.00 40.43 3.27
354 380 3.821841 AGACGATTTTCACGGCATTTTC 58.178 40.909 0.00 0.00 41.61 2.29
358 384 4.214545 ACGATTTTCACGGCATTTTCAGTA 59.785 37.500 0.00 0.00 34.93 2.74
359 385 4.553429 CGATTTTCACGGCATTTTCAGTAC 59.447 41.667 0.00 0.00 0.00 2.73
360 386 4.902443 TTTTCACGGCATTTTCAGTACA 57.098 36.364 0.00 0.00 0.00 2.90
361 387 5.446143 TTTTCACGGCATTTTCAGTACAT 57.554 34.783 0.00 0.00 0.00 2.29
362 388 4.418013 TTCACGGCATTTTCAGTACATG 57.582 40.909 0.00 0.00 0.00 3.21
363 389 3.407698 TCACGGCATTTTCAGTACATGT 58.592 40.909 2.69 2.69 0.00 3.21
364 390 3.188254 TCACGGCATTTTCAGTACATGTG 59.812 43.478 9.11 0.00 0.00 3.21
367 393 2.825532 GGCATTTTCAGTACATGTGGGT 59.174 45.455 9.11 0.00 0.00 4.51
368 394 4.013728 GGCATTTTCAGTACATGTGGGTA 58.986 43.478 9.11 0.00 0.00 3.69
369 395 4.461081 GGCATTTTCAGTACATGTGGGTAA 59.539 41.667 9.11 0.00 0.00 2.85
370 396 5.399013 GCATTTTCAGTACATGTGGGTAAC 58.601 41.667 9.11 0.00 0.00 2.50
371 397 5.048364 GCATTTTCAGTACATGTGGGTAACA 60.048 40.000 9.11 0.00 44.79 2.41
372 398 6.611381 CATTTTCAGTACATGTGGGTAACAG 58.389 40.000 9.11 0.00 43.64 3.16
402 430 2.161855 AGCGACATGGCATTTTCTGAA 58.838 42.857 0.00 0.00 34.64 3.02
406 434 4.549458 CGACATGGCATTTTCTGAAAAGT 58.451 39.130 19.14 11.19 33.22 2.66
407 435 5.698832 CGACATGGCATTTTCTGAAAAGTA 58.301 37.500 19.14 7.42 33.22 2.24
416 444 5.682943 TTTTCTGAAAAGTATCACCCACG 57.317 39.130 11.33 0.00 0.00 4.94
418 446 4.345859 TCTGAAAAGTATCACCCACGTT 57.654 40.909 0.00 0.00 0.00 3.99
431 459 4.448395 TCACCCACGTTACGACTAAAAATG 59.552 41.667 13.03 0.00 0.00 2.32
453 481 3.561725 GTCATGAAAAGATAGGCCCTTCG 59.438 47.826 0.00 0.00 0.00 3.79
456 484 2.304761 TGAAAAGATAGGCCCTTCGTGT 59.695 45.455 0.00 0.00 0.00 4.49
546 574 2.094078 CGCCAAATGTCACCCAAATCAT 60.094 45.455 0.00 0.00 0.00 2.45
558 586 2.816087 CCCAAATCATAGATTCGGCCAG 59.184 50.000 2.24 0.00 0.00 4.85
627 684 2.026641 CCTTGTTTCCATGCATCCGAT 58.973 47.619 0.00 0.00 0.00 4.18
628 685 2.033801 CCTTGTTTCCATGCATCCGATC 59.966 50.000 0.00 0.00 0.00 3.69
633 690 1.708341 TCCATGCATCCGATCTCTCA 58.292 50.000 0.00 0.00 0.00 3.27
717 774 1.699054 ATCGAAGCTGGCCTGCCATA 61.699 55.000 28.96 13.96 46.15 2.74
900 967 5.339008 AACACTATACATCTCGGAGCAAA 57.661 39.130 0.00 0.00 0.00 3.68
901 968 4.683832 ACACTATACATCTCGGAGCAAAC 58.316 43.478 0.00 0.00 0.00 2.93
1119 1187 1.293924 GCTTCATCACCATCCTCGTG 58.706 55.000 0.00 0.00 0.00 4.35
1265 1333 4.477975 CGACGACGAGGACCAGCC 62.478 72.222 0.00 0.00 42.66 4.85
2352 2426 5.064834 CGAAACTTAAGTGGCTAATCCTTCC 59.935 44.000 9.34 0.00 35.26 3.46
2677 2754 7.657761 CCTGCACTAGATTAGGAACGAAAATAT 59.342 37.037 0.00 0.00 31.91 1.28
2696 2773 7.807977 AAATATGTTTTAGATCAGGCGTCAT 57.192 32.000 0.00 0.00 0.00 3.06
2708 2785 0.958382 GGCGTCATGGTGCTTGGTTA 60.958 55.000 9.44 0.00 0.00 2.85
2724 2801 6.202188 TGCTTGGTTAAAAACAAACAACGAAA 59.798 30.769 0.00 0.00 31.91 3.46
2792 2870 4.280929 AGTCCTGATTTTTAAAGGTGTGGC 59.719 41.667 0.00 0.00 32.59 5.01
2801 2879 2.969628 AAAGGTGTGGCTAGATCTCG 57.030 50.000 0.00 0.00 0.00 4.04
2802 2880 2.145397 AAGGTGTGGCTAGATCTCGA 57.855 50.000 0.00 0.00 0.00 4.04
2804 2882 2.672098 AGGTGTGGCTAGATCTCGATT 58.328 47.619 0.00 0.00 0.00 3.34
2806 2884 2.362397 GGTGTGGCTAGATCTCGATTGA 59.638 50.000 0.00 0.00 0.00 2.57
2814 2895 4.496673 GCTAGATCTCGATTGACGTCAAGT 60.497 45.833 32.19 21.28 43.13 3.16
2974 3055 5.880341 TCTCAAGTGTGTATGTACATCTCG 58.120 41.667 12.68 0.00 38.63 4.04
3078 3163 3.166490 TTGCCACGTCCCGCAACTA 62.166 57.895 9.51 0.00 39.96 2.24
3095 3180 0.104725 CTATGCTCCCTCTCCCCCTT 60.105 60.000 0.00 0.00 0.00 3.95
3099 3184 1.074850 CTCCCTCTCCCCCTTCCTC 60.075 68.421 0.00 0.00 0.00 3.71
3160 3245 2.266055 GCACCTCCCTCCTTCACG 59.734 66.667 0.00 0.00 0.00 4.35
3165 3250 1.293498 CTCCCTCCTTCACGTGTGG 59.707 63.158 16.51 18.16 0.00 4.17
3167 3252 0.544357 TCCCTCCTTCACGTGTGGAT 60.544 55.000 24.84 0.00 0.00 3.41
3175 3260 2.554806 TCACGTGTGGATAACTAGCG 57.445 50.000 16.51 0.00 0.00 4.26
3177 3262 0.528924 ACGTGTGGATAACTAGCGCA 59.471 50.000 11.47 0.00 0.00 6.09
3178 3263 0.921347 CGTGTGGATAACTAGCGCAC 59.079 55.000 11.47 0.00 0.00 5.34
3197 3282 1.480954 ACGGTGGCACATCTAGTTAGG 59.519 52.381 20.82 0.00 44.52 2.69
3221 3306 3.766432 GAGCTAGGGTAGGGCTCG 58.234 66.667 0.00 0.00 42.03 5.03
3259 3344 1.071542 TCGTCCCAATGATGTGTGTGT 59.928 47.619 0.00 0.00 0.00 3.72
3265 3352 2.361757 CCAATGATGTGTGTGTGTTGGT 59.638 45.455 0.00 0.00 32.15 3.67
3267 3354 2.409948 TGATGTGTGTGTGTTGGTGA 57.590 45.000 0.00 0.00 0.00 4.02
3320 3407 1.742768 GTCCTACCTGGCCGATCTG 59.257 63.158 0.00 0.00 35.26 2.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
18 19 0.470766 AACGGTTGTAGCCCACTGAA 59.529 50.000 0.00 0.00 0.00 3.02
46 49 1.531149 CAGGAAAAACTCGCACGACAT 59.469 47.619 0.00 0.00 0.00 3.06
48 51 0.384353 GCAGGAAAAACTCGCACGAC 60.384 55.000 0.00 0.00 0.00 4.34
50 53 1.082104 GGCAGGAAAAACTCGCACG 60.082 57.895 0.00 0.00 0.00 5.34
62 65 2.639970 CAAACGATGGTTGGCAGGA 58.360 52.632 0.00 0.00 36.25 3.86
94 98 4.471025 TGATCTCCTCTAGGATTTGTTGCA 59.529 41.667 0.00 0.00 44.46 4.08
103 107 3.708631 CCAAGCTTTGATCTCCTCTAGGA 59.291 47.826 0.00 0.00 43.08 2.94
142 146 1.304630 TACGCAGCCCTACCACTCA 60.305 57.895 0.00 0.00 0.00 3.41
180 186 4.402829 ACACCTGCACCAACATAATTACA 58.597 39.130 0.00 0.00 0.00 2.41
181 187 5.163693 GGTACACCTGCACCAACATAATTAC 60.164 44.000 0.00 0.00 34.77 1.89
266 274 9.200817 AGTACATCAAAGGCAATACCATATTTT 57.799 29.630 0.00 0.00 43.14 1.82
343 369 3.491356 CACATGTACTGAAAATGCCGTG 58.509 45.455 0.00 0.00 0.00 4.94
354 380 6.385649 AAAAACTGTTACCCACATGTACTG 57.614 37.500 0.00 0.00 33.76 2.74
391 419 5.863935 GTGGGTGATACTTTTCAGAAAATGC 59.136 40.000 8.81 0.64 0.00 3.56
392 420 6.086222 CGTGGGTGATACTTTTCAGAAAATG 58.914 40.000 8.81 6.24 0.00 2.32
402 430 3.256631 AGTCGTAACGTGGGTGATACTTT 59.743 43.478 0.00 0.00 0.00 2.66
406 434 5.384063 TTTTAGTCGTAACGTGGGTGATA 57.616 39.130 0.00 0.00 0.00 2.15
407 435 3.940209 TTTAGTCGTAACGTGGGTGAT 57.060 42.857 0.00 0.00 0.00 3.06
416 444 9.872757 TCTTTTCATGACATTTTTAGTCGTAAC 57.127 29.630 0.00 0.00 38.83 2.50
431 459 3.561725 CGAAGGGCCTATCTTTTCATGAC 59.438 47.826 6.41 0.00 0.00 3.06
443 471 0.892755 CAGTACACACGAAGGGCCTA 59.107 55.000 6.41 0.00 0.00 3.93
456 484 1.068125 CCATCGTTCCGTGTCAGTACA 60.068 52.381 0.00 0.00 0.00 2.90
467 495 0.037605 ACGTTGACTCCCATCGTTCC 60.038 55.000 0.00 0.00 45.70 3.62
475 503 0.971386 TGGGTAGAACGTTGACTCCC 59.029 55.000 5.00 12.53 0.00 4.30
477 505 1.342174 TGGTGGGTAGAACGTTGACTC 59.658 52.381 5.00 3.95 0.00 3.36
558 586 2.356673 ACGTTTCCTTCCGGCGTC 60.357 61.111 6.01 0.00 0.00 5.19
627 684 4.422073 TCTGCCAAAGTTTTCTGAGAGA 57.578 40.909 0.00 0.00 0.00 3.10
628 685 4.758674 TGATCTGCCAAAGTTTTCTGAGAG 59.241 41.667 0.00 0.00 0.00 3.20
633 690 3.550842 GCGTTGATCTGCCAAAGTTTTCT 60.551 43.478 0.00 0.00 0.00 2.52
717 774 0.391661 AATTGCGAGATCGGCAGTGT 60.392 50.000 13.04 3.57 40.23 3.55
876 943 4.933330 TGCTCCGAGATGTATAGTGTTTC 58.067 43.478 0.00 0.00 0.00 2.78
1265 1333 3.678717 AAGGACGCATCGACGACGG 62.679 63.158 7.55 3.72 40.21 4.79
2352 2426 5.647225 CCTCTGAAAAATCTTTCTCAGGGAG 59.353 44.000 7.33 0.00 41.41 4.30
2596 2672 3.671008 AGTGCACCACAAATACTCGTA 57.329 42.857 14.63 0.00 36.74 3.43
2677 2754 3.270027 CCATGACGCCTGATCTAAAACA 58.730 45.455 0.00 0.00 0.00 2.83
2689 2766 0.958382 TAACCAAGCACCATGACGCC 60.958 55.000 0.00 0.00 0.00 5.68
2696 2773 4.894784 TGTTTGTTTTTAACCAAGCACCA 58.105 34.783 0.00 0.00 0.00 4.17
2708 2785 6.619660 GCATTGAGGTTTCGTTGTTTGTTTTT 60.620 34.615 0.00 0.00 0.00 1.94
2724 2801 3.726557 TCTCATTTCAGGCATTGAGGT 57.273 42.857 0.00 0.00 37.07 3.85
2773 2850 6.817765 TCTAGCCACACCTTTAAAAATCAG 57.182 37.500 0.00 0.00 0.00 2.90
2775 2852 7.466050 CGAGATCTAGCCACACCTTTAAAAATC 60.466 40.741 0.00 0.00 0.00 2.17
2782 2860 2.457598 TCGAGATCTAGCCACACCTTT 58.542 47.619 0.00 0.00 0.00 3.11
2784 2862 2.363680 CAATCGAGATCTAGCCACACCT 59.636 50.000 0.00 0.00 0.00 4.00
2792 2870 4.966970 CACTTGACGTCAATCGAGATCTAG 59.033 45.833 29.79 16.77 42.86 2.43
2801 2879 6.893958 ATGTTCTATCACTTGACGTCAATC 57.106 37.500 29.79 7.48 35.02 2.67
2804 2882 9.863845 TTTTATATGTTCTATCACTTGACGTCA 57.136 29.630 15.76 15.76 0.00 4.35
2965 3046 4.978083 TGGGTACTCTTTCGAGATGTAC 57.022 45.455 0.00 9.44 39.74 2.90
2974 3055 5.828328 CCCCTCAAATAATGGGTACTCTTTC 59.172 44.000 0.00 0.00 39.31 2.62
3078 3163 1.385206 GAAGGGGGAGAGGGAGCAT 60.385 63.158 0.00 0.00 0.00 3.79
3082 3167 2.647949 GGAGGAAGGGGGAGAGGGA 61.648 68.421 0.00 0.00 0.00 4.20
3112 3197 2.512515 ATCGCGAGGAGCTTTGCC 60.513 61.111 16.66 0.00 45.59 4.52
3147 3232 1.185618 TCCACACGTGAAGGAGGGAG 61.186 60.000 25.01 0.72 0.00 4.30
3160 3245 0.921347 CGTGCGCTAGTTATCCACAC 59.079 55.000 9.73 0.00 0.00 3.82
3165 3250 1.488261 GCCACCGTGCGCTAGTTATC 61.488 60.000 9.73 0.00 0.00 1.75
3167 3252 2.125832 GCCACCGTGCGCTAGTTA 60.126 61.111 9.73 0.00 0.00 2.24
3175 3260 0.673644 AACTAGATGTGCCACCGTGC 60.674 55.000 0.00 0.00 0.00 5.34
3177 3262 1.480954 CCTAACTAGATGTGCCACCGT 59.519 52.381 0.00 0.00 0.00 4.83
3178 3263 1.202533 CCCTAACTAGATGTGCCACCG 60.203 57.143 0.00 0.00 0.00 4.94
3221 3306 3.470567 CAACTCGCGTCGCTCACC 61.471 66.667 16.36 0.00 0.00 4.02
3259 3344 2.964925 GCTGTCGCGTCACCAACA 60.965 61.111 5.77 0.06 0.00 3.33
3292 3379 3.782443 GGTAGGACCAGGCCACCG 61.782 72.222 5.01 0.00 38.42 4.94
3301 3388 1.457831 AGATCGGCCAGGTAGGACC 60.458 63.158 2.24 0.00 45.73 4.46


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

AutoCloner maintained by Alex Coulton.