Multiple sequence alignment - TraesCS2A01G262400

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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 TraesCS2A01G262400 chr2A 100.000 1714 0 0 1 1714 413489993 413488280 0.000000e+00 3166
1 TraesCS2A01G262400 chr2A 100.000 692 0 0 2001 2692 413487993 413487302 0.000000e+00 1279
2 TraesCS2A01G262400 chr2D 94.435 1725 56 16 9 1714 318247344 318249047 0.000000e+00 2617
3 TraesCS2A01G262400 chr2D 85.109 732 36 21 2001 2692 318249134 318249832 0.000000e+00 680
4 TraesCS2A01G262400 chr2B 94.850 1534 41 13 206 1714 385888294 385889814 0.000000e+00 2361
5 TraesCS2A01G262400 chr2B 82.369 726 50 28 2001 2692 385889901 385890582 6.510000e-156 560


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 TraesCS2A01G262400 chr2A 413487302 413489993 2691 True 2222.5 3166 100.0000 1 2692 2 chr2A.!!$R1 2691
1 TraesCS2A01G262400 chr2D 318247344 318249832 2488 False 1648.5 2617 89.7720 9 2692 2 chr2D.!!$F1 2683
2 TraesCS2A01G262400 chr2B 385888294 385890582 2288 False 1460.5 2361 88.6095 206 2692 2 chr2B.!!$F1 2486

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
781 807 0.182061 GGCCAGGCAGATGAATCTCA 59.818 55.0 15.19 0.0 34.22 3.27 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2660 2790 0.100682 GTGTGCGCGGAGAGAATAGA 59.899 55.0 8.83 0.0 0.0 1.98 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
85 89 8.348507 CCCTGTAAATAACTTACTAGTCGGTAG 58.651 40.741 0.00 0.00 40.62 3.18
93 97 9.709495 ATAACTTACTAGTCGGTAGATGTAGAG 57.291 37.037 0.00 0.00 31.99 2.43
105 109 8.188799 TCGGTAGATGTAGAGAGTTTAATGTTG 58.811 37.037 0.00 0.00 0.00 3.33
154 158 5.709071 CTCTCCGTGAGTTGCAACTAGCA 62.709 52.174 31.20 22.45 43.65 3.49
441 450 4.128925 TGCATCATACAAGTCCTGAGAC 57.871 45.455 0.00 0.00 43.89 3.36
510 526 5.188359 ACCCTGCAAAGAAATGAAATGCTAT 59.812 36.000 0.00 0.00 37.86 2.97
598 622 7.086376 AGTGCATTCTTTAGCAAATAACACTG 58.914 34.615 0.00 0.00 43.20 3.66
732 758 3.981071 TGGCTCTGCTGTACTTTGTAT 57.019 42.857 0.00 0.00 0.00 2.29
733 759 5.359756 CATGGCTCTGCTGTACTTTGTATA 58.640 41.667 0.00 0.00 0.00 1.47
780 806 0.473326 AGGCCAGGCAGATGAATCTC 59.527 55.000 15.19 0.00 34.22 2.75
781 807 0.182061 GGCCAGGCAGATGAATCTCA 59.818 55.000 15.19 0.00 34.22 3.27
827 853 4.321304 CCTTCAGACAGTGGTACAGTACAG 60.321 50.000 12.89 2.21 41.96 2.74
908 934 0.320771 CCAACAACCTCACTCCCTCG 60.321 60.000 0.00 0.00 0.00 4.63
938 968 5.551583 TCCCCACCCGTAATATAGACTACTA 59.448 44.000 0.00 0.00 0.00 1.82
1208 1238 2.436115 GCACCGCCCCTTCTACAC 60.436 66.667 0.00 0.00 0.00 2.90
1324 1354 0.325203 AGCTTGGTTGGTTGGTTGGT 60.325 50.000 0.00 0.00 0.00 3.67
1325 1355 0.179086 GCTTGGTTGGTTGGTTGGTG 60.179 55.000 0.00 0.00 0.00 4.17
1346 1376 2.059541 GCAGTGTTCGAGTACCAGAAC 58.940 52.381 18.66 18.66 44.93 3.01
1614 1650 4.489771 CCTCCAAATCCGCCGCCT 62.490 66.667 0.00 0.00 0.00 5.52
1710 1761 2.402305 GATCAGTTGATCTGGCTAGCG 58.598 52.381 9.00 0.00 45.60 4.26
2041 2092 3.121778 GTGCGCTTGATTGTTCCATTTTC 59.878 43.478 9.73 0.00 0.00 2.29
2048 2099 6.073058 GCTTGATTGTTCCATTTTCCCTTTTC 60.073 38.462 0.00 0.00 0.00 2.29
2049 2100 6.745794 TGATTGTTCCATTTTCCCTTTTCT 57.254 33.333 0.00 0.00 0.00 2.52
2052 2103 7.498570 TGATTGTTCCATTTTCCCTTTTCTTTG 59.501 33.333 0.00 0.00 0.00 2.77
2072 2123 4.153958 TGTTTTGTCGATTTGATTCCGG 57.846 40.909 0.00 0.00 0.00 5.14
2097 2148 1.067142 TGTCTGGTCGATGGTTGTAGC 60.067 52.381 0.00 0.00 0.00 3.58
2106 2157 0.036388 ATGGTTGTAGCCGAGGTGTG 60.036 55.000 0.00 0.00 0.00 3.82
2115 2171 2.973945 AGCCGAGGTGTGAAAGATTAC 58.026 47.619 0.00 0.00 0.00 1.89
2168 2224 4.583907 TGCTCTGGTTGATGATTTGTTGAA 59.416 37.500 0.00 0.00 0.00 2.69
2177 2262 7.218773 GGTTGATGATTTGTTGAATGATGTACG 59.781 37.037 0.00 0.00 0.00 3.67
2194 2279 8.078959 TGATGTACGTATATTGTATTTGTGCC 57.921 34.615 6.26 0.00 0.00 5.01
2195 2280 6.513609 TGTACGTATATTGTATTTGTGCCG 57.486 37.500 0.00 0.00 0.00 5.69
2271 2392 2.861462 AGCAAGCTCTCGTACATCTC 57.139 50.000 0.00 0.00 0.00 2.75
2321 2447 1.000145 CCTGCCCGGGTATGGTTTT 60.000 57.895 24.63 0.00 0.00 2.43
2324 2450 1.755395 GCCCGGGTATGGTTTTCCC 60.755 63.158 24.63 0.00 39.73 3.97
2360 2490 6.616774 ACTCTTTCTCTCTTTTGCTTTGAG 57.383 37.500 0.00 0.00 0.00 3.02
2392 2522 7.330946 TGAAACTTCACATGCTACAGTACATAC 59.669 37.037 0.00 0.00 31.01 2.39
2400 2530 4.441792 TGCTACAGTACATACAGGCATTG 58.558 43.478 0.00 0.00 0.00 2.82
2401 2531 3.248602 GCTACAGTACATACAGGCATTGC 59.751 47.826 0.00 0.00 0.00 3.56
2413 2543 2.048444 GGCATTGCCTTCTCAGATGA 57.952 50.000 20.66 0.00 46.69 2.92
2414 2544 2.584236 GGCATTGCCTTCTCAGATGAT 58.416 47.619 20.66 0.00 46.69 2.45
2415 2545 2.957006 GGCATTGCCTTCTCAGATGATT 59.043 45.455 20.66 0.00 46.69 2.57
2416 2546 3.004524 GGCATTGCCTTCTCAGATGATTC 59.995 47.826 20.66 0.00 46.69 2.52
2417 2547 3.630769 GCATTGCCTTCTCAGATGATTCA 59.369 43.478 0.00 0.00 0.00 2.57
2418 2548 4.278669 GCATTGCCTTCTCAGATGATTCAT 59.721 41.667 0.00 0.00 0.00 2.57
2419 2549 5.221263 GCATTGCCTTCTCAGATGATTCATT 60.221 40.000 0.00 0.00 0.00 2.57
2420 2550 6.683110 GCATTGCCTTCTCAGATGATTCATTT 60.683 38.462 0.00 0.00 0.00 2.32
2421 2551 6.845758 TTGCCTTCTCAGATGATTCATTTT 57.154 33.333 0.00 0.00 0.00 1.82
2449 2579 6.825213 TCTCTGAATTTCAATGTAGACCATGG 59.175 38.462 11.19 11.19 32.82 3.66
2451 2581 6.825213 TCTGAATTTCAATGTAGACCATGGAG 59.175 38.462 21.47 0.00 34.90 3.86
2452 2582 6.484288 TGAATTTCAATGTAGACCATGGAGT 58.516 36.000 21.47 7.34 34.90 3.85
2453 2583 7.629157 TGAATTTCAATGTAGACCATGGAGTA 58.371 34.615 21.47 6.21 34.90 2.59
2553 2683 8.106462 TGAGATGTATCCAAATCCAAACAGTAA 58.894 33.333 0.00 0.00 0.00 2.24
2554 2684 8.281212 AGATGTATCCAAATCCAAACAGTAAC 57.719 34.615 0.00 0.00 0.00 2.50
2566 2696 5.992829 TCCAAACAGTAACGATTTTAGCTGA 59.007 36.000 0.00 0.00 0.00 4.26
2567 2697 6.147164 TCCAAACAGTAACGATTTTAGCTGAG 59.853 38.462 0.00 0.00 0.00 3.35
2650 2780 2.291190 GCTACTAGTTACTCGCAGGAGG 59.709 54.545 0.00 0.00 44.93 4.30
2658 2788 4.414956 TCGCAGGAGGGGGTGGAT 62.415 66.667 0.00 0.00 0.00 3.41
2659 2789 3.866582 CGCAGGAGGGGGTGGATC 61.867 72.222 0.00 0.00 0.00 3.36
2660 2790 2.367512 GCAGGAGGGGGTGGATCT 60.368 66.667 0.00 0.00 0.00 2.75
2661 2791 2.447714 GCAGGAGGGGGTGGATCTC 61.448 68.421 0.00 0.00 0.00 2.75
2662 2792 1.316266 CAGGAGGGGGTGGATCTCT 59.684 63.158 0.00 0.00 0.00 3.10
2663 2793 0.563173 CAGGAGGGGGTGGATCTCTA 59.437 60.000 0.00 0.00 0.00 2.43
2664 2794 1.150986 CAGGAGGGGGTGGATCTCTAT 59.849 57.143 0.00 0.00 0.00 1.98
2677 2807 0.663688 TCTCTATTCTCTCCGCGCAC 59.336 55.000 8.75 0.00 0.00 5.34
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 9.553064 AATACTTTGAGGTAATTCATCTAGCAG 57.447 33.333 0.00 0.00 0.00 4.24
1 2 9.547753 GAATACTTTGAGGTAATTCATCTAGCA 57.452 33.333 0.00 0.00 0.00 3.49
2 3 8.994170 GGAATACTTTGAGGTAATTCATCTAGC 58.006 37.037 0.00 0.00 0.00 3.42
3 4 9.495572 GGGAATACTTTGAGGTAATTCATCTAG 57.504 37.037 0.00 0.00 0.00 2.43
4 5 9.225682 AGGGAATACTTTGAGGTAATTCATCTA 57.774 33.333 0.00 0.00 0.00 1.98
5 6 7.995488 CAGGGAATACTTTGAGGTAATTCATCT 59.005 37.037 0.00 0.00 0.00 2.90
6 7 7.775561 ACAGGGAATACTTTGAGGTAATTCATC 59.224 37.037 0.00 0.00 0.00 2.92
7 8 7.643123 ACAGGGAATACTTTGAGGTAATTCAT 58.357 34.615 0.00 0.00 0.00 2.57
105 109 4.606961 ACACCAACGACACATGAAAATTC 58.393 39.130 0.00 0.00 0.00 2.17
115 119 0.942252 GAGGGAAACACCAACGACAC 59.058 55.000 0.00 0.00 41.20 3.67
116 120 0.834612 AGAGGGAAACACCAACGACA 59.165 50.000 0.00 0.00 41.20 4.35
117 121 1.509703 GAGAGGGAAACACCAACGAC 58.490 55.000 0.00 0.00 41.20 4.34
523 539 3.557185 TGTCGCTGCTAGATTGCTAAATG 59.443 43.478 0.00 0.00 0.00 2.32
598 622 0.107945 AATTCAGCTCCCGACTCTGC 60.108 55.000 0.00 0.00 0.00 4.26
732 758 4.328536 TCTGGCGGTAATTTTTCTTGCTA 58.671 39.130 0.00 0.00 0.00 3.49
733 759 3.153919 TCTGGCGGTAATTTTTCTTGCT 58.846 40.909 0.00 0.00 0.00 3.91
749 775 0.179034 CCTGGCCTGTAAGATCTGGC 60.179 60.000 12.35 12.35 46.76 4.85
827 853 1.548973 CGTCTTGTCTGTCACGGTGC 61.549 60.000 2.51 0.00 0.00 5.01
865 891 3.688673 GGCTCAAGGTGAAGATGAAGAAG 59.311 47.826 0.00 0.00 0.00 2.85
908 934 1.623542 ATTACGGGTGGGGAGTGAGC 61.624 60.000 0.00 0.00 0.00 4.26
938 968 2.210013 TGTGCTGGACTTCGCTCCT 61.210 57.895 0.00 0.00 0.00 3.69
1229 1259 3.077359 GGAGGAGAAATGTGAAGTGTGG 58.923 50.000 0.00 0.00 0.00 4.17
1324 1354 0.317160 CTGGTACTCGAACACTGCCA 59.683 55.000 0.00 0.00 0.00 4.92
1325 1355 0.601558 TCTGGTACTCGAACACTGCC 59.398 55.000 0.00 0.00 0.00 4.85
1382 1412 1.060713 CCTTGTCGCAGTTGTCGTAG 58.939 55.000 0.00 0.00 0.00 3.51
1442 1472 1.210204 TGGCCTCCTTGAGCTGGAAT 61.210 55.000 3.32 0.00 32.61 3.01
1565 1595 2.835895 GGCGAGGAGGAGGAGGAC 60.836 72.222 0.00 0.00 0.00 3.85
1663 1714 4.529219 TGAGTAGCATGGCGGCGG 62.529 66.667 9.78 0.00 39.27 6.13
1664 1715 2.963854 CTGAGTAGCATGGCGGCG 60.964 66.667 0.51 0.51 39.27 6.46
1665 1716 2.388890 ATCCTGAGTAGCATGGCGGC 62.389 60.000 0.00 0.00 0.00 6.53
1666 1717 0.602106 CATCCTGAGTAGCATGGCGG 60.602 60.000 0.00 0.00 0.00 6.13
1667 1718 1.226686 GCATCCTGAGTAGCATGGCG 61.227 60.000 0.00 0.00 0.00 5.69
1668 1719 0.108207 AGCATCCTGAGTAGCATGGC 59.892 55.000 0.00 0.00 0.00 4.40
1669 1720 1.693062 AGAGCATCCTGAGTAGCATGG 59.307 52.381 0.00 0.00 33.66 3.66
2041 2092 6.533367 TCAAATCGACAAAACAAAGAAAAGGG 59.467 34.615 0.00 0.00 0.00 3.95
2048 2099 5.116983 CCGGAATCAAATCGACAAAACAAAG 59.883 40.000 0.00 0.00 0.00 2.77
2049 2100 4.979197 CCGGAATCAAATCGACAAAACAAA 59.021 37.500 0.00 0.00 0.00 2.83
2052 2103 4.413495 TCCGGAATCAAATCGACAAAAC 57.587 40.909 0.00 0.00 0.00 2.43
2072 2123 0.537188 ACCATCGACCAGACACCATC 59.463 55.000 0.00 0.00 0.00 3.51
2097 2148 4.152402 CACTTGTAATCTTTCACACCTCGG 59.848 45.833 0.00 0.00 0.00 4.63
2106 2157 9.515020 TTGTTCAATTCACACTTGTAATCTTTC 57.485 29.630 0.00 0.00 0.00 2.62
2115 2171 5.973565 GGAGTTCTTGTTCAATTCACACTTG 59.026 40.000 0.00 0.00 0.00 3.16
2168 2224 8.717821 GGCACAAATACAATATACGTACATCAT 58.282 33.333 0.00 0.00 0.00 2.45
2177 2262 5.454232 GCACAACGGCACAAATACAATATAC 59.546 40.000 0.00 0.00 0.00 1.47
2195 2280 2.147749 CATCACATGCGCGCACAAC 61.148 57.895 39.05 4.43 0.00 3.32
2239 2352 4.319177 AGAGCTTGCTTAACTGTAACCAG 58.681 43.478 0.00 0.00 44.68 4.00
2286 2407 2.496817 GAGCGGCAGTGGAGTAGG 59.503 66.667 1.45 0.00 0.00 3.18
2321 2447 0.326238 GAGTAGGTGGACATGGGGGA 60.326 60.000 0.00 0.00 0.00 4.81
2324 2450 2.840651 AGAAAGAGTAGGTGGACATGGG 59.159 50.000 0.00 0.00 0.00 4.00
2360 2490 4.978083 AGCATGTGAAGTTTCATCATCC 57.022 40.909 0.00 0.00 39.73 3.51
2400 2530 5.593502 AGGAAAATGAATCATCTGAGAAGGC 59.406 40.000 0.00 0.00 0.00 4.35
2401 2531 7.055378 AGAGGAAAATGAATCATCTGAGAAGG 58.945 38.462 0.00 0.00 36.65 3.46
2402 2532 7.988599 AGAGAGGAAAATGAATCATCTGAGAAG 59.011 37.037 0.00 0.00 38.00 2.85
2403 2533 7.769507 CAGAGAGGAAAATGAATCATCTGAGAA 59.230 37.037 0.00 0.00 38.00 2.87
2404 2534 7.125356 TCAGAGAGGAAAATGAATCATCTGAGA 59.875 37.037 0.00 0.00 38.00 3.27
2405 2535 7.273712 TCAGAGAGGAAAATGAATCATCTGAG 58.726 38.462 0.00 0.00 38.00 3.35
2406 2536 7.191593 TCAGAGAGGAAAATGAATCATCTGA 57.808 36.000 0.00 0.52 38.00 3.27
2407 2537 7.860918 TTCAGAGAGGAAAATGAATCATCTG 57.139 36.000 0.00 0.00 38.00 2.90
2408 2538 9.476928 AAATTCAGAGAGGAAAATGAATCATCT 57.523 29.630 0.00 0.00 40.54 2.90
2409 2539 9.733219 GAAATTCAGAGAGGAAAATGAATCATC 57.267 33.333 0.00 0.10 40.54 2.92
2410 2540 9.251440 TGAAATTCAGAGAGGAAAATGAATCAT 57.749 29.630 0.00 0.00 40.54 2.45
2411 2541 8.640063 TGAAATTCAGAGAGGAAAATGAATCA 57.360 30.769 0.00 0.00 40.54 2.57
2413 2543 9.871238 CATTGAAATTCAGAGAGGAAAATGAAT 57.129 29.630 0.00 0.00 42.61 2.57
2414 2544 8.863086 ACATTGAAATTCAGAGAGGAAAATGAA 58.137 29.630 0.00 0.00 36.22 2.57
2415 2545 8.413309 ACATTGAAATTCAGAGAGGAAAATGA 57.587 30.769 0.00 0.00 30.99 2.57
2416 2546 9.784680 CTACATTGAAATTCAGAGAGGAAAATG 57.215 33.333 0.00 0.00 31.96 2.32
2417 2547 9.745018 TCTACATTGAAATTCAGAGAGGAAAAT 57.255 29.630 0.00 0.00 0.00 1.82
2418 2548 9.003658 GTCTACATTGAAATTCAGAGAGGAAAA 57.996 33.333 0.00 0.00 0.00 2.29
2419 2549 7.607991 GGTCTACATTGAAATTCAGAGAGGAAA 59.392 37.037 0.00 0.00 0.00 3.13
2420 2550 7.106239 GGTCTACATTGAAATTCAGAGAGGAA 58.894 38.462 0.00 0.00 0.00 3.36
2421 2551 6.213397 TGGTCTACATTGAAATTCAGAGAGGA 59.787 38.462 0.00 0.00 0.00 3.71
2469 2599 6.623767 GCAATCTGTATGTCTGTTTTCCCTTC 60.624 42.308 0.00 0.00 0.00 3.46
2553 2683 4.757149 AGCAAAAGTCTCAGCTAAAATCGT 59.243 37.500 0.00 0.00 35.19 3.73
2554 2684 5.288543 AGCAAAAGTCTCAGCTAAAATCG 57.711 39.130 0.00 0.00 35.19 3.34
2566 2696 1.202651 ACCGCACTGTAGCAAAAGTCT 60.203 47.619 0.00 0.00 0.00 3.24
2567 2697 1.069906 CACCGCACTGTAGCAAAAGTC 60.070 52.381 0.00 0.00 0.00 3.01
2650 2780 3.169908 GGAGAGAATAGAGATCCACCCC 58.830 54.545 0.00 0.00 0.00 4.95
2658 2788 0.663688 GTGCGCGGAGAGAATAGAGA 59.336 55.000 8.83 0.00 0.00 3.10
2659 2789 0.382158 TGTGCGCGGAGAGAATAGAG 59.618 55.000 8.83 0.00 0.00 2.43
2660 2790 0.100682 GTGTGCGCGGAGAGAATAGA 59.899 55.000 8.83 0.00 0.00 1.98
2661 2791 0.872021 GGTGTGCGCGGAGAGAATAG 60.872 60.000 8.83 0.00 0.00 1.73
2662 2792 1.141019 GGTGTGCGCGGAGAGAATA 59.859 57.895 8.83 0.00 0.00 1.75
2663 2793 2.125512 GGTGTGCGCGGAGAGAAT 60.126 61.111 8.83 0.00 0.00 2.40
2664 2794 3.282745 GAGGTGTGCGCGGAGAGAA 62.283 63.158 8.83 0.00 0.00 2.87


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

AutoCloner maintained by Alex Coulton.