Multiple sequence alignment - TraesCS3D01G281000

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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 TraesCS3D01G281000 chr3D 100.000 2960 0 0 1 2960 389075235 389072276 0.000000e+00 5467
1 TraesCS3D01G281000 chr3A 89.417 2589 104 47 440 2960 509997264 509994778 0.000000e+00 3107
2 TraesCS3D01G281000 chr3B 91.411 1991 72 30 403 2320 506621402 506619438 0.000000e+00 2638
3 TraesCS3D01G281000 chr3B 87.855 634 27 19 2343 2960 506619444 506618845 0.000000e+00 699
4 TraesCS3D01G281000 chr3B 93.333 390 17 5 1 382 506623494 506623106 4.280000e-158 568


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 TraesCS3D01G281000 chr3D 389072276 389075235 2959 True 5467.000000 5467 100.000000 1 2960 1 chr3D.!!$R1 2959
1 TraesCS3D01G281000 chr3A 509994778 509997264 2486 True 3107.000000 3107 89.417000 440 2960 1 chr3A.!!$R1 2520
2 TraesCS3D01G281000 chr3B 506618845 506623494 4649 True 1301.666667 2638 90.866333 1 2960 3 chr3B.!!$R1 2959

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
148 150 0.037605 AACAGCGTGTACTACAGCCC 60.038 55.0 0.00 0.0 31.95 5.19 F
390 399 0.248949 GATCGCCAACCGGTCTCTAC 60.249 60.0 8.04 0.0 43.67 2.59 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1065 2855 2.705821 CGAGCGCCTGGAGAAGACT 61.706 63.158 2.29 0.0 0.0 3.24 R
2320 4136 2.614057 CGGCCGAATGAATAAGAAAGCT 59.386 45.455 24.07 0.0 0.0 3.74 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
40 41 2.203983 TCAGCTGGGCTCCTTCCA 60.204 61.111 15.13 0.00 36.40 3.53
41 42 1.617536 TCAGCTGGGCTCCTTCCAT 60.618 57.895 15.13 0.00 36.40 3.41
77 79 2.530497 GGCGCGTTTGTCTGTCACA 61.530 57.895 8.43 0.00 0.00 3.58
100 102 8.030106 CACAAAACTCTAAACAACCCACTTAAA 58.970 33.333 0.00 0.00 0.00 1.52
115 117 2.725203 TTAAAGCCACGGAGCAGCGT 62.725 55.000 1.62 0.00 33.80 5.07
148 150 0.037605 AACAGCGTGTACTACAGCCC 60.038 55.000 0.00 0.00 31.95 5.19
161 163 2.435938 AGCCCATACGCGGTTGTG 60.436 61.111 12.47 3.01 0.00 3.33
181 183 6.533819 TGTGTTACGTAGGTTGATTGAAAG 57.466 37.500 0.00 0.00 0.00 2.62
197 200 8.319057 TGATTGAAAGGTATACTGATGGTACT 57.681 34.615 2.25 0.00 32.72 2.73
241 244 1.135083 GTAGCAGCGGTGTACAGACAT 60.135 52.381 17.07 0.00 38.04 3.06
242 245 1.182667 AGCAGCGGTGTACAGACATA 58.817 50.000 17.07 0.00 38.04 2.29
246 249 1.476891 AGCGGTGTACAGACATACAGG 59.523 52.381 0.00 0.00 38.04 4.00
283 292 2.637025 CCGTGGTCAAAACTGGCG 59.363 61.111 0.00 0.00 0.00 5.69
382 391 3.800685 TATGCCCGATCGCCAACCG 62.801 63.158 10.32 0.00 38.61 4.44
386 395 4.143333 CCGATCGCCAACCGGTCT 62.143 66.667 8.04 0.00 44.83 3.85
387 396 2.582498 CGATCGCCAACCGGTCTC 60.582 66.667 8.04 0.00 44.83 3.36
388 397 2.893398 GATCGCCAACCGGTCTCT 59.107 61.111 8.04 0.00 43.67 3.10
389 398 1.721664 CGATCGCCAACCGGTCTCTA 61.722 60.000 8.04 0.00 44.83 2.43
390 399 0.248949 GATCGCCAACCGGTCTCTAC 60.249 60.000 8.04 0.00 43.67 2.59
391 400 0.683504 ATCGCCAACCGGTCTCTACT 60.684 55.000 8.04 0.00 37.59 2.57
392 401 0.896940 TCGCCAACCGGTCTCTACTT 60.897 55.000 8.04 0.00 37.59 2.24
393 402 0.458025 CGCCAACCGGTCTCTACTTC 60.458 60.000 8.04 0.00 33.28 3.01
415 424 0.380733 CCCCGCTTCCTTTTAATCGC 59.619 55.000 0.00 0.00 0.00 4.58
429 2130 7.434013 TCCTTTTAATCGCAAAACTTTTCTGTC 59.566 33.333 0.00 0.00 0.00 3.51
432 2133 3.963383 TCGCAAAACTTTTCTGTCCTC 57.037 42.857 0.00 0.00 0.00 3.71
435 2136 4.037690 CGCAAAACTTTTCTGTCCTCAAG 58.962 43.478 0.00 0.00 0.00 3.02
438 2139 5.266242 CAAAACTTTTCTGTCCTCAAGTCG 58.734 41.667 0.00 0.00 0.00 4.18
449 2150 2.632996 TCCTCAAGTCGTGATGAAACCT 59.367 45.455 0.00 0.00 35.07 3.50
472 2173 1.805428 AAATTGCACCGTGTCCAGCC 61.805 55.000 0.00 0.00 0.00 4.85
499 2208 7.065894 CAGTTCTTACGAAGTTCACAAAGATG 58.934 38.462 3.32 2.02 37.78 2.90
506 2215 1.420138 AGTTCACAAAGATGGGTCGGT 59.580 47.619 0.00 0.00 0.00 4.69
556 2265 1.379916 CCACCACCTTCTCCATGCA 59.620 57.895 0.00 0.00 0.00 3.96
739 2480 1.070758 CCATTCCATCTCCCCACTACG 59.929 57.143 0.00 0.00 0.00 3.51
917 2693 4.880426 TCCCTCCATCTCCCGCCC 62.880 72.222 0.00 0.00 0.00 6.13
977 2767 2.331451 GCACGCACACAAAGGACC 59.669 61.111 0.00 0.00 0.00 4.46
981 2771 2.983592 GCACACAAAGGACCGGGG 60.984 66.667 6.32 0.00 0.00 5.73
1065 2855 4.100084 CTGGCGGCCATCCTGTCA 62.100 66.667 24.10 0.00 30.82 3.58
1176 2969 4.684134 GGGGGCAAGAAGGCTGCA 62.684 66.667 0.50 0.00 43.56 4.41
1177 2970 3.376918 GGGGCAAGAAGGCTGCAC 61.377 66.667 0.50 0.00 43.56 4.57
1965 3770 2.948720 GCTCTGCCCCTGAACTCGT 61.949 63.158 0.00 0.00 0.00 4.18
1966 3771 1.216710 CTCTGCCCCTGAACTCGTC 59.783 63.158 0.00 0.00 0.00 4.20
1967 3772 2.125912 CTGCCCCTGAACTCGTCG 60.126 66.667 0.00 0.00 0.00 5.12
1972 3777 3.744719 CCTGAACTCGTCGGGCGA 61.745 66.667 4.05 4.05 46.09 5.54
2007 3813 3.610242 GTGCGATCGATGTTGATAGGATC 59.390 47.826 21.57 0.00 0.00 3.36
2232 4044 4.330250 ACTTGTAGTAGTCCAGCGTTCTA 58.670 43.478 0.00 0.00 0.00 2.10
2274 4086 3.029320 TGTGCGTCCTGTAAATACGTT 57.971 42.857 0.00 0.00 38.81 3.99
2320 4136 4.345859 TTTTCGAGTTAGCTTTCCTCCA 57.654 40.909 0.00 0.00 0.00 3.86
2333 4149 4.702131 GCTTTCCTCCAGCTTTCTTATTCA 59.298 41.667 0.00 0.00 34.15 2.57
2334 4150 5.359292 GCTTTCCTCCAGCTTTCTTATTCAT 59.641 40.000 0.00 0.00 34.15 2.57
2335 4151 6.127507 GCTTTCCTCCAGCTTTCTTATTCATT 60.128 38.462 0.00 0.00 34.15 2.57
2362 4178 0.035439 TCCTCCTCCCGCAAAATCAC 60.035 55.000 0.00 0.00 0.00 3.06
2379 4195 7.574217 GCAAAATCACCTCATTCAAATTGCAAT 60.574 33.333 5.99 5.99 39.25 3.56
2402 4218 3.296854 TCAGTCGACCTACATATGGCTT 58.703 45.455 13.01 0.00 0.00 4.35
2436 4252 4.618965 TCATCTCTGCTTGATTCATCTCG 58.381 43.478 0.00 0.00 0.00 4.04
2438 4254 2.762887 TCTCTGCTTGATTCATCTCGGT 59.237 45.455 0.00 0.00 0.00 4.69
2439 4255 3.196469 TCTCTGCTTGATTCATCTCGGTT 59.804 43.478 0.00 0.00 0.00 4.44
2440 4256 4.402474 TCTCTGCTTGATTCATCTCGGTTA 59.598 41.667 0.00 0.00 0.00 2.85
2441 4257 5.084818 TCTGCTTGATTCATCTCGGTTAA 57.915 39.130 0.00 0.00 0.00 2.01
2442 4258 5.111989 TCTGCTTGATTCATCTCGGTTAAG 58.888 41.667 0.00 0.00 0.00 1.85
2443 4259 5.084818 TGCTTGATTCATCTCGGTTAAGA 57.915 39.130 0.00 0.00 0.00 2.10
2444 4260 5.487433 TGCTTGATTCATCTCGGTTAAGAA 58.513 37.500 0.00 0.00 0.00 2.52
2445 4261 5.937540 TGCTTGATTCATCTCGGTTAAGAAA 59.062 36.000 0.00 0.00 0.00 2.52
2446 4262 6.429692 TGCTTGATTCATCTCGGTTAAGAAAA 59.570 34.615 0.00 0.00 0.00 2.29
2447 4263 7.040755 TGCTTGATTCATCTCGGTTAAGAAAAA 60.041 33.333 0.00 0.00 0.00 1.94
2448 4264 7.271438 GCTTGATTCATCTCGGTTAAGAAAAAC 59.729 37.037 0.00 0.00 0.00 2.43
2449 4265 7.737972 TGATTCATCTCGGTTAAGAAAAACA 57.262 32.000 0.00 0.00 0.00 2.83
2450 4266 8.335532 TGATTCATCTCGGTTAAGAAAAACAT 57.664 30.769 0.00 0.00 0.00 2.71
2451 4267 8.792633 TGATTCATCTCGGTTAAGAAAAACATT 58.207 29.630 0.00 0.00 0.00 2.71
2452 4268 9.626045 GATTCATCTCGGTTAAGAAAAACATTT 57.374 29.630 0.00 0.00 0.00 2.32
2453 4269 9.981114 ATTCATCTCGGTTAAGAAAAACATTTT 57.019 25.926 0.00 0.00 0.00 1.82
2454 4270 9.458374 TTCATCTCGGTTAAGAAAAACATTTTC 57.542 29.630 7.34 7.34 0.00 2.29
2455 4271 8.079809 TCATCTCGGTTAAGAAAAACATTTTCC 58.920 33.333 10.96 0.00 0.00 3.13
2456 4272 7.336161 TCTCGGTTAAGAAAAACATTTTCCA 57.664 32.000 10.96 0.00 0.00 3.53
2457 4273 7.197703 TCTCGGTTAAGAAAAACATTTTCCAC 58.802 34.615 10.96 6.73 0.00 4.02
2458 4274 7.067737 TCTCGGTTAAGAAAAACATTTTCCACT 59.932 33.333 10.96 1.43 0.00 4.00
2459 4275 7.197703 TCGGTTAAGAAAAACATTTTCCACTC 58.802 34.615 10.96 2.50 0.00 3.51
2460 4276 6.141685 CGGTTAAGAAAAACATTTTCCACTCG 59.858 38.462 10.96 6.70 0.00 4.18
2461 4277 6.074516 GGTTAAGAAAAACATTTTCCACTCGC 60.075 38.462 10.96 0.29 0.00 5.03
2462 4278 4.647424 AGAAAAACATTTTCCACTCGCA 57.353 36.364 10.96 0.00 0.00 5.10
2463 4279 5.004922 AGAAAAACATTTTCCACTCGCAA 57.995 34.783 10.96 0.00 0.00 4.85
2464 4280 5.415221 AGAAAAACATTTTCCACTCGCAAA 58.585 33.333 10.96 0.00 0.00 3.68
2465 4281 5.519927 AGAAAAACATTTTCCACTCGCAAAG 59.480 36.000 10.96 0.00 0.00 2.77
2585 4408 2.201885 GCAAGAAACGACGACGCG 60.202 61.111 3.53 3.53 43.96 6.01
2602 4425 4.462394 GCATTCCTAGGCGCATGA 57.538 55.556 10.83 0.00 0.00 3.07
2811 4660 7.418597 GGGACATTACCGGATCTATAATATGCA 60.419 40.741 9.46 0.00 0.00 3.96
2904 4753 2.933401 GCCGGCTAGCTAGGTAGGC 61.933 68.421 34.01 34.01 41.18 3.93
2906 4755 2.651945 GGCTAGCTAGGTAGGCGC 59.348 66.667 31.79 18.42 36.03 6.53
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
69 71 5.355910 GGGTTGTTTAGAGTTTTGTGACAGA 59.644 40.000 0.00 0.00 0.00 3.41
77 79 7.262772 GCTTTAAGTGGGTTGTTTAGAGTTTT 58.737 34.615 0.00 0.00 0.00 2.43
115 117 8.995220 AGTACACGCTGTTAATTCTTAAATGAA 58.005 29.630 0.00 0.00 0.00 2.57
148 150 1.062258 ACGTAACACAACCGCGTATG 58.938 50.000 4.92 6.05 33.85 2.39
161 163 7.838771 ATACCTTTCAATCAACCTACGTAAC 57.161 36.000 0.00 0.00 0.00 2.50
181 183 6.912951 ACATACCAGTACCATCAGTATACC 57.087 41.667 0.00 0.00 32.28 2.73
197 200 1.628340 ACCAGCAGCAAGTACATACCA 59.372 47.619 0.00 0.00 0.00 3.25
266 275 2.637025 CGCCAGTTTTGACCACGG 59.363 61.111 0.00 0.00 0.00 4.94
268 277 1.299089 GTGCGCCAGTTTTGACCAC 60.299 57.895 4.18 0.00 0.00 4.16
382 391 0.389757 GCGGGGATGAAGTAGAGACC 59.610 60.000 0.00 0.00 0.00 3.85
383 392 1.404843 AGCGGGGATGAAGTAGAGAC 58.595 55.000 0.00 0.00 0.00 3.36
384 393 2.032620 GAAGCGGGGATGAAGTAGAGA 58.967 52.381 0.00 0.00 0.00 3.10
385 394 1.069358 GGAAGCGGGGATGAAGTAGAG 59.931 57.143 0.00 0.00 0.00 2.43
386 395 1.120530 GGAAGCGGGGATGAAGTAGA 58.879 55.000 0.00 0.00 0.00 2.59
387 396 1.123928 AGGAAGCGGGGATGAAGTAG 58.876 55.000 0.00 0.00 0.00 2.57
388 397 1.580059 AAGGAAGCGGGGATGAAGTA 58.420 50.000 0.00 0.00 0.00 2.24
389 398 0.698818 AAAGGAAGCGGGGATGAAGT 59.301 50.000 0.00 0.00 0.00 3.01
390 399 1.839424 AAAAGGAAGCGGGGATGAAG 58.161 50.000 0.00 0.00 0.00 3.02
391 400 3.443145 TTAAAAGGAAGCGGGGATGAA 57.557 42.857 0.00 0.00 0.00 2.57
392 401 3.551846 GATTAAAAGGAAGCGGGGATGA 58.448 45.455 0.00 0.00 0.00 2.92
393 402 2.290641 CGATTAAAAGGAAGCGGGGATG 59.709 50.000 0.00 0.00 34.68 3.51
415 424 5.163754 ACGACTTGAGGACAGAAAAGTTTTG 60.164 40.000 5.36 0.00 33.14 2.44
429 2130 2.738846 CAGGTTTCATCACGACTTGAGG 59.261 50.000 0.00 0.00 37.77 3.86
432 2133 3.130633 TGACAGGTTTCATCACGACTTG 58.869 45.455 0.00 0.00 0.00 3.16
435 2136 4.749245 ATTTGACAGGTTTCATCACGAC 57.251 40.909 0.00 0.00 0.00 4.34
438 2139 4.445385 GTGCAATTTGACAGGTTTCATCAC 59.555 41.667 0.00 0.00 0.00 3.06
449 2150 0.665835 GGACACGGTGCAATTTGACA 59.334 50.000 8.30 0.00 0.00 3.58
499 2208 3.708734 CGCAAACGTGACCGACCC 61.709 66.667 0.00 0.00 37.88 4.46
506 2215 2.340809 ACGGGATCGCAAACGTGA 59.659 55.556 10.70 0.00 41.18 4.35
543 2252 2.117156 GCGCATGCATGGAGAAGGT 61.117 57.895 27.34 0.00 42.15 3.50
723 2463 0.750546 CGTCGTAGTGGGGAGATGGA 60.751 60.000 0.00 0.00 0.00 3.41
729 2470 1.269448 GTAACAACGTCGTAGTGGGGA 59.731 52.381 0.00 0.00 0.00 4.81
739 2480 2.169327 GCGCCACGTAACAACGTC 59.831 61.111 0.00 0.00 45.26 4.34
803 2545 2.915137 GCAAAACCGCCAAGGGGA 60.915 61.111 4.54 0.00 46.96 4.81
994 2784 4.148825 GGAGCCGTCCATCGTGCT 62.149 66.667 0.00 0.00 43.31 4.40
1065 2855 2.705821 CGAGCGCCTGGAGAAGACT 61.706 63.158 2.29 0.00 0.00 3.24
1318 3111 4.821589 CGCCCTCTCCGCCTTGAC 62.822 72.222 0.00 0.00 0.00 3.18
1510 3306 2.820479 CTCGTCGTCGGAGGAGCT 60.820 66.667 1.55 0.00 45.11 4.09
2007 3813 2.734079 GCTCTCACTCTCGAAAAGGTTG 59.266 50.000 0.00 0.00 0.00 3.77
2161 3970 3.511540 CCATCACTGACAGAACTACAGGA 59.488 47.826 10.08 0.00 36.17 3.86
2232 4044 6.146184 CACAAACTGACGAGAACATTCATAGT 59.854 38.462 0.00 0.00 0.00 2.12
2320 4136 2.614057 CGGCCGAATGAATAAGAAAGCT 59.386 45.455 24.07 0.00 0.00 3.74
2333 4149 2.732619 GGAGGAGGAACGGCCGAAT 61.733 63.158 35.90 20.90 43.43 3.34
2334 4150 3.387947 GGAGGAGGAACGGCCGAA 61.388 66.667 35.90 0.00 43.43 4.30
2362 4178 6.183360 CGACTGAAATTGCAATTTGAATGAGG 60.183 38.462 35.57 20.07 38.64 3.86
2379 4195 3.704566 AGCCATATGTAGGTCGACTGAAA 59.295 43.478 16.46 0.00 0.00 2.69
2402 4218 3.118629 AGCAGAGATGATTCTACCGCAAA 60.119 43.478 0.00 0.00 30.30 3.68
2432 4248 7.067737 AGTGGAAAATGTTTTTCTTAACCGAGA 59.932 33.333 11.31 0.00 0.00 4.04
2436 4252 6.074516 GCGAGTGGAAAATGTTTTTCTTAACC 60.075 38.462 11.31 0.00 0.00 2.85
2438 4254 6.565234 TGCGAGTGGAAAATGTTTTTCTTAA 58.435 32.000 11.31 0.00 0.00 1.85
2439 4255 6.137794 TGCGAGTGGAAAATGTTTTTCTTA 57.862 33.333 11.31 1.17 0.00 2.10
2440 4256 5.004922 TGCGAGTGGAAAATGTTTTTCTT 57.995 34.783 11.31 0.65 0.00 2.52
2441 4257 4.647424 TGCGAGTGGAAAATGTTTTTCT 57.353 36.364 11.31 2.33 0.00 2.52
2442 4258 5.518487 TCTTTGCGAGTGGAAAATGTTTTTC 59.482 36.000 4.51 4.51 34.84 2.29
2443 4259 5.415221 TCTTTGCGAGTGGAAAATGTTTTT 58.585 33.333 0.00 0.00 34.84 1.94
2444 4260 5.004922 TCTTTGCGAGTGGAAAATGTTTT 57.995 34.783 0.00 0.00 34.84 2.43
2445 4261 4.647424 TCTTTGCGAGTGGAAAATGTTT 57.353 36.364 0.00 0.00 34.84 2.83
2446 4262 4.647424 TTCTTTGCGAGTGGAAAATGTT 57.353 36.364 0.00 0.00 34.84 2.71
2447 4263 4.647424 TTTCTTTGCGAGTGGAAAATGT 57.353 36.364 0.00 0.00 34.84 2.71
2448 4264 5.964887 TTTTTCTTTGCGAGTGGAAAATG 57.035 34.783 10.32 0.00 37.46 2.32
2585 4408 1.233285 CCTCATGCGCCTAGGAATGC 61.233 60.000 14.75 13.45 31.64 3.56
2811 4660 0.531311 ACGCCGAAGACTTCCGTTTT 60.531 50.000 12.08 0.00 0.00 2.43


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

AutoCloner maintained by Alex Coulton.