Multiple sequence alignment - TraesCS3D01G413900

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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 TraesCS3D01G413900 chr3D 100.000 2852 0 0 1 2852 526047783 526050634 0.000000e+00 5267.0
1 TraesCS3D01G413900 chr3B 93.796 2869 127 23 1 2844 694323627 694326469 0.000000e+00 4265.0
2 TraesCS3D01G413900 chr3B 80.749 374 48 15 2229 2590 140589901 140590262 1.300000e-68 270.0
3 TraesCS3D01G413900 chr3A 93.836 2839 142 14 27 2844 660235965 660238791 0.000000e+00 4242.0
4 TraesCS3D01G413900 chr7D 82.210 371 40 15 2229 2590 162017692 162017339 2.150000e-76 296.0
5 TraesCS3D01G413900 chr7D 80.480 333 43 13 2229 2551 440588632 440588312 4.750000e-58 235.0
6 TraesCS3D01G413900 chr5A 81.744 367 50 8 2229 2588 580593646 580593290 1.000000e-74 291.0
7 TraesCS3D01G413900 chrUn 75.733 375 53 20 2229 2590 37388224 37387875 1.370000e-33 154.0
8 TraesCS3D01G413900 chr5D 92.683 41 3 0 2552 2592 109455128 109455088 3.070000e-05 60.2


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 TraesCS3D01G413900 chr3D 526047783 526050634 2851 False 5267 5267 100.000 1 2852 1 chr3D.!!$F1 2851
1 TraesCS3D01G413900 chr3B 694323627 694326469 2842 False 4265 4265 93.796 1 2844 1 chr3B.!!$F2 2843
2 TraesCS3D01G413900 chr3A 660235965 660238791 2826 False 4242 4242 93.836 27 2844 1 chr3A.!!$F1 2817

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
113 119 0.036952 CACGTTGCAGGATCTCTGGT 60.037 55.0 11.63 1.09 43.54 4.00 F
921 937 0.038744 CAAGCCCACCCACTCATCTT 59.961 55.0 0.00 0.00 0.00 2.40 F
1501 1528 0.806868 CCGCAGCACAGTGATGAAAT 59.193 50.0 23.11 0.00 35.45 2.17 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1104 1131 0.179113 GGCTCCTCTTCTGAGAAGCG 60.179 60.0 17.14 11.18 42.73 4.68 R
1821 1848 0.317160 TCACTTCCTCAATCGCACGT 59.683 50.0 0.00 0.00 0.00 4.49 R
2708 2745 0.618458 TACCTGGAACTCACCATGGC 59.382 55.0 13.04 0.00 39.34 4.40 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
23 24 0.387202 CTGCCGGACCTATCAGTGAG 59.613 60.000 5.05 0.00 0.00 3.51
24 25 1.043116 TGCCGGACCTATCAGTGAGG 61.043 60.000 5.05 0.00 40.22 3.86
31 32 2.035632 ACCTATCAGTGAGGTAGCTGC 58.964 52.381 0.00 0.00 45.82 5.25
35 36 1.449246 CAGTGAGGTAGCTGCTGCC 60.449 63.158 26.79 26.79 40.80 4.85
36 37 1.915266 AGTGAGGTAGCTGCTGCCA 60.915 57.895 33.32 15.23 38.73 4.92
37 38 1.449246 GTGAGGTAGCTGCTGCCAG 60.449 63.158 33.32 0.00 38.73 4.85
70 75 1.005347 GCGATGGATACGTGGTTTTCG 60.005 52.381 0.00 2.91 42.51 3.46
90 96 1.870458 CCTTGCGTCGCGATCGTAA 60.870 57.895 23.75 23.75 36.96 3.18
99 105 3.758035 CGATCGTAACCGCACGTT 58.242 55.556 7.03 0.00 42.51 3.99
113 119 0.036952 CACGTTGCAGGATCTCTGGT 60.037 55.000 11.63 1.09 43.54 4.00
204 210 3.635373 ACATTGCCATCCAAGCTAGATTG 59.365 43.478 13.85 13.85 36.76 2.67
278 284 2.048970 ACGCGCACGGTACAATCA 60.049 55.556 5.73 0.00 46.04 2.57
291 297 6.916387 CACGGTACAATCACGATCTATACTTT 59.084 38.462 0.00 0.00 0.00 2.66
292 298 7.113124 CACGGTACAATCACGATCTATACTTTC 59.887 40.741 0.00 0.00 0.00 2.62
294 300 6.581542 GGTACAATCACGATCTATACTTTCGG 59.418 42.308 0.00 0.00 37.20 4.30
400 413 1.305219 TGCCCTGAATTACGCTGCAC 61.305 55.000 0.00 0.00 0.00 4.57
411 424 2.113860 ACGCTGCACCATGAAAGTAT 57.886 45.000 0.00 0.00 0.00 2.12
412 425 3.260475 ACGCTGCACCATGAAAGTATA 57.740 42.857 0.00 0.00 0.00 1.47
415 428 4.273480 ACGCTGCACCATGAAAGTATATTC 59.727 41.667 0.00 0.00 0.00 1.75
451 467 5.899299 AGCATCATGAAAGTAATTGAAGCC 58.101 37.500 0.00 0.00 34.34 4.35
481 497 0.179179 GATGAAGACAAAGCAGGCGC 60.179 55.000 0.00 0.00 38.99 6.53
482 498 0.890542 ATGAAGACAAAGCAGGCGCA 60.891 50.000 10.83 0.00 42.27 6.09
487 503 0.591170 GACAAAGCAGGCGCAGTAAA 59.409 50.000 10.83 0.00 42.27 2.01
560 576 7.496346 TTCCATGTACTCCTAATATCCATCC 57.504 40.000 0.00 0.00 0.00 3.51
571 587 7.487338 TCCTAATATCCATCCTGATACCTCAA 58.513 38.462 0.00 0.00 30.36 3.02
650 666 0.106149 CATAAGGTCCGTAGCCCACC 59.894 60.000 0.00 0.00 0.00 4.61
673 689 3.051392 GCCGGTGCAAGTGCCATAC 62.051 63.158 1.90 0.00 41.18 2.39
685 701 2.008752 TGCCATACACAGATGTCACG 57.991 50.000 0.00 0.00 40.48 4.35
688 704 2.345876 CCATACACAGATGTCACGCAA 58.654 47.619 0.00 0.00 40.48 4.85
708 724 1.639298 GCTGTCCGTGGAACAGATGC 61.639 60.000 17.24 4.87 41.80 3.91
717 733 0.244721 GGAACAGATGCAACAAGGGC 59.755 55.000 0.00 0.00 0.00 5.19
741 757 2.436646 CAGGCCACCACACGATCC 60.437 66.667 5.01 0.00 0.00 3.36
842 858 2.456119 GCAGCCACGTCCATTCTCG 61.456 63.158 0.00 0.00 0.00 4.04
861 877 1.373570 GGAAGAAACCATCTCTGCCG 58.626 55.000 0.00 0.00 37.42 5.69
921 937 0.038744 CAAGCCCACCCACTCATCTT 59.961 55.000 0.00 0.00 0.00 2.40
922 938 1.281867 CAAGCCCACCCACTCATCTTA 59.718 52.381 0.00 0.00 0.00 2.10
923 939 1.207791 AGCCCACCCACTCATCTTAG 58.792 55.000 0.00 0.00 0.00 2.18
955 982 2.631062 CCACTCTGTACACCACCAACTA 59.369 50.000 0.00 0.00 0.00 2.24
992 1019 2.223745 GCGTTACCTTCCAAAACTCCA 58.776 47.619 0.00 0.00 0.00 3.86
1137 1164 1.078143 GAGCCTGATGGTGGTGTCC 60.078 63.158 0.00 0.00 35.27 4.02
1361 1388 2.497273 GTGCAAGCCCCATACATTTCTT 59.503 45.455 0.00 0.00 0.00 2.52
1402 1429 5.809562 CACTGATGAACTACTGTCTCAATCC 59.190 44.000 0.00 0.00 0.00 3.01
1408 1435 4.744795 ACTACTGTCTCAATCCCACATC 57.255 45.455 0.00 0.00 0.00 3.06
1415 1442 2.092753 TCTCAATCCCACATCTTCCTGC 60.093 50.000 0.00 0.00 0.00 4.85
1428 1455 3.374764 TCTTCCTGCCATACAAGCTAGA 58.625 45.455 0.00 0.00 0.00 2.43
1451 1478 7.743749 AGACCAGATTATTTAGAGATGCATGT 58.256 34.615 2.46 0.00 0.00 3.21
1452 1479 8.874156 AGACCAGATTATTTAGAGATGCATGTA 58.126 33.333 2.46 0.00 0.00 2.29
1490 1517 1.153289 AGATGTCATCCCGCAGCAC 60.153 57.895 9.29 0.00 0.00 4.40
1501 1528 0.806868 CCGCAGCACAGTGATGAAAT 59.193 50.000 23.11 0.00 35.45 2.17
1644 1671 4.640771 AGAAACTGGAACCATCTTGCTA 57.359 40.909 0.00 0.00 0.00 3.49
1698 1725 2.436417 TCATGGTAAGCTTCTTGGTGC 58.564 47.619 0.00 0.00 0.00 5.01
1699 1726 2.040278 TCATGGTAAGCTTCTTGGTGCT 59.960 45.455 0.00 0.00 41.82 4.40
1821 1848 4.035558 GGTGCGAAGATTGATGAATTAGCA 59.964 41.667 0.00 0.00 0.00 3.49
1875 1902 4.248058 CAATTCCCTGGAAAGAAATGCAC 58.752 43.478 2.15 0.00 37.69 4.57
2098 2125 3.282021 TGATCTCACTAATTTGCAGGCC 58.718 45.455 0.00 0.00 0.00 5.19
2169 2196 5.469373 GATGTAAGCATCGTGACATTGAA 57.531 39.130 0.00 0.00 41.60 2.69
2186 2213 9.066892 TGACATTGAACTAAGATTGCTTTACTT 57.933 29.630 0.00 0.00 35.56 2.24
2383 2410 5.520748 AACTGAACCCCAACTCTATCATT 57.479 39.130 0.00 0.00 0.00 2.57
2434 2461 9.381033 CCCATGCTTATCTGATTCTCTAATAAG 57.619 37.037 0.00 0.00 34.51 1.73
2592 2627 7.059147 GCAAAGCACGTACAATTTACTAGTTTC 59.941 37.037 0.00 0.00 0.00 2.78
2724 2761 2.787473 TTAGCCATGGTGAGTTCCAG 57.213 50.000 14.67 0.00 41.05 3.86
2769 2806 3.107601 TGAAGGTACCTTGCTAGCATCT 58.892 45.455 31.81 3.14 36.26 2.90
2817 2854 5.260424 TCAATTAGCCATGTTTTCTGCCTA 58.740 37.500 0.00 0.00 0.00 3.93
2818 2855 5.893255 TCAATTAGCCATGTTTTCTGCCTAT 59.107 36.000 0.00 0.00 0.00 2.57
2819 2856 5.779529 ATTAGCCATGTTTTCTGCCTATG 57.220 39.130 0.00 0.00 0.00 2.23
2820 2857 3.091633 AGCCATGTTTTCTGCCTATGT 57.908 42.857 0.00 0.00 0.00 2.29
2844 2881 4.755123 AGCCTGCACCGATTTAACATATAC 59.245 41.667 0.00 0.00 0.00 1.47
2845 2882 4.755123 GCCTGCACCGATTTAACATATACT 59.245 41.667 0.00 0.00 0.00 2.12
2846 2883 5.107065 GCCTGCACCGATTTAACATATACTC 60.107 44.000 0.00 0.00 0.00 2.59
2847 2884 5.408604 CCTGCACCGATTTAACATATACTCC 59.591 44.000 0.00 0.00 0.00 3.85
2848 2885 5.302360 TGCACCGATTTAACATATACTCCC 58.698 41.667 0.00 0.00 0.00 4.30
2849 2886 5.071250 TGCACCGATTTAACATATACTCCCT 59.929 40.000 0.00 0.00 0.00 4.20
2850 2887 5.638234 GCACCGATTTAACATATACTCCCTC 59.362 44.000 0.00 0.00 0.00 4.30
2851 2888 6.164176 CACCGATTTAACATATACTCCCTCC 58.836 44.000 0.00 0.00 0.00 4.30
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
8 9 1.609555 GCTACCTCACTGATAGGTCCG 59.390 57.143 8.58 4.38 44.20 4.79
9 10 2.625790 CAGCTACCTCACTGATAGGTCC 59.374 54.545 8.58 3.48 44.20 4.46
18 19 1.897225 CTGGCAGCAGCTACCTCACT 61.897 60.000 13.23 0.00 41.70 3.41
70 75 2.908088 TACGATCGCGACGCAAGGTC 62.908 60.000 24.04 9.24 41.38 3.85
99 105 1.189752 GAGACACCAGAGATCCTGCA 58.810 55.000 5.86 0.00 41.57 4.41
113 119 3.319972 CGGAGATATTTTACCGGGAGACA 59.680 47.826 6.32 0.00 41.41 3.41
204 210 1.884235 AACCTCTACAGCTTGCACAC 58.116 50.000 0.00 0.00 0.00 3.82
267 273 6.630444 AAGTATAGATCGTGATTGTACCGT 57.370 37.500 0.00 0.00 0.00 4.83
278 284 6.757237 TCTCTCTACCGAAAGTATAGATCGT 58.243 40.000 0.00 0.00 34.63 3.73
291 297 1.282447 ACTGGCTTCTCTCTCTACCGA 59.718 52.381 0.00 0.00 0.00 4.69
292 298 1.403679 CACTGGCTTCTCTCTCTACCG 59.596 57.143 0.00 0.00 0.00 4.02
294 300 2.452505 ACCACTGGCTTCTCTCTCTAC 58.547 52.381 0.00 0.00 0.00 2.59
451 467 5.003590 GCTTTGTCTTCATCTAGTACGTTCG 59.996 44.000 0.00 0.00 0.00 3.95
481 497 8.294341 TCTGACTGAAACGAGTAAATTTACTG 57.706 34.615 30.66 23.52 43.64 2.74
482 498 8.882415 TTCTGACTGAAACGAGTAAATTTACT 57.118 30.769 27.01 27.01 46.11 2.24
487 503 6.934645 TCCATTTCTGACTGAAACGAGTAAAT 59.065 34.615 9.40 0.00 46.08 1.40
560 576 6.219417 AGTTGATGACTCTTGAGGTATCAG 57.781 41.667 14.15 0.00 32.58 2.90
571 587 3.422796 ACCGTGACTAGTTGATGACTCT 58.577 45.455 0.00 0.00 39.86 3.24
650 666 3.716006 CACTTGCACCGGCGACTG 61.716 66.667 9.30 4.04 45.35 3.51
668 684 2.008752 TGCGTGACATCTGTGTATGG 57.991 50.000 0.00 0.00 39.09 2.74
673 689 0.165295 CAGCTTGCGTGACATCTGTG 59.835 55.000 0.00 0.00 0.00 3.66
685 701 1.845809 CTGTTCCACGGACAGCTTGC 61.846 60.000 0.00 0.00 0.00 4.01
688 704 0.036952 CATCTGTTCCACGGACAGCT 60.037 55.000 9.50 0.00 36.13 4.24
722 738 4.722700 ATCGTGTGGTGGCCTGCC 62.723 66.667 3.32 7.19 0.00 4.85
728 744 0.175760 AAGATCGGATCGTGTGGTGG 59.824 55.000 12.08 0.00 0.00 4.61
842 858 1.373570 CGGCAGAGATGGTTTCTTCC 58.626 55.000 0.00 0.00 33.74 3.46
861 877 5.739358 GCTTGGTGGTATATATCGGCTATCC 60.739 48.000 0.00 0.00 0.00 2.59
907 923 1.134280 CCTGCTAAGATGAGTGGGTGG 60.134 57.143 0.00 0.00 0.00 4.61
921 937 2.438021 ACAGAGTGGTGTTTTCCTGCTA 59.562 45.455 0.00 0.00 0.00 3.49
922 938 1.212935 ACAGAGTGGTGTTTTCCTGCT 59.787 47.619 0.00 0.00 0.00 4.24
923 939 1.680338 ACAGAGTGGTGTTTTCCTGC 58.320 50.000 0.00 0.00 0.00 4.85
992 1019 2.393557 CGTAACGCCATTGGATGCT 58.606 52.632 6.95 0.00 0.00 3.79
1104 1131 0.179113 GGCTCCTCTTCTGAGAAGCG 60.179 60.000 17.14 11.18 42.73 4.68
1361 1388 3.068165 TCAGTGAAGAAGAGCTGAAACGA 59.932 43.478 0.00 0.00 35.36 3.85
1402 1429 2.715749 TGTATGGCAGGAAGATGTGG 57.284 50.000 0.00 0.00 0.00 4.17
1408 1435 3.462021 GTCTAGCTTGTATGGCAGGAAG 58.538 50.000 0.00 0.00 0.00 3.46
1415 1442 9.429359 CTAAATAATCTGGTCTAGCTTGTATGG 57.571 37.037 0.00 0.00 0.00 2.74
1466 1493 1.069668 TGCGGGATGACATCTGATCTG 59.930 52.381 14.95 4.87 0.00 2.90
1470 1497 1.144716 GCTGCGGGATGACATCTGA 59.855 57.895 14.95 0.00 0.00 3.27
1490 1517 5.159209 GCAGACAAGGAAATTTCATCACTG 58.841 41.667 19.49 19.55 0.00 3.66
1501 1528 1.165907 CGCACCTGCAGACAAGGAAA 61.166 55.000 17.39 0.00 42.21 3.13
1698 1725 4.999950 AGAGGCTACAATTGACAAGACAAG 59.000 41.667 13.59 0.00 33.22 3.16
1699 1726 4.973168 AGAGGCTACAATTGACAAGACAA 58.027 39.130 13.59 0.00 0.00 3.18
1700 1727 4.623932 AGAGGCTACAATTGACAAGACA 57.376 40.909 13.59 0.00 0.00 3.41
1701 1728 4.378874 GCAAGAGGCTACAATTGACAAGAC 60.379 45.833 13.59 8.59 40.25 3.01
1702 1729 3.753272 GCAAGAGGCTACAATTGACAAGA 59.247 43.478 13.59 0.00 40.25 3.02
1821 1848 0.317160 TCACTTCCTCAATCGCACGT 59.683 50.000 0.00 0.00 0.00 4.49
1875 1902 4.987285 CACTAGTGATAGCATGCTAACTGG 59.013 45.833 29.87 28.90 31.73 4.00
2153 2180 4.820897 TCTTAGTTCAATGTCACGATGCT 58.179 39.130 0.00 0.00 0.00 3.79
2241 2268 9.616156 TCCAACGGCTAATATTTGAAGTTATTA 57.384 29.630 0.77 0.00 0.00 0.98
2383 2410 7.174946 GGGAAAGATGTTTCTAGAACACATCAA 59.825 37.037 33.29 12.46 46.30 2.57
2434 2461 7.122650 CCCTCTAGAATCCAGATGTTCTATCTC 59.877 44.444 0.00 0.00 36.61 2.75
2436 2463 6.154363 CCCCTCTAGAATCCAGATGTTCTATC 59.846 46.154 0.00 0.00 36.61 2.08
2438 2465 5.103043 ACCCCTCTAGAATCCAGATGTTCTA 60.103 44.000 0.00 0.00 36.23 2.10
2439 2466 4.230455 CCCCTCTAGAATCCAGATGTTCT 58.770 47.826 0.00 0.00 38.22 3.01
2440 2467 3.970640 ACCCCTCTAGAATCCAGATGTTC 59.029 47.826 0.00 0.00 0.00 3.18
2441 2468 4.014273 ACCCCTCTAGAATCCAGATGTT 57.986 45.455 0.00 0.00 0.00 2.71
2506 2541 9.981460 ACACTCTGATATTTATTTCCTTTCCTT 57.019 29.630 0.00 0.00 0.00 3.36
2708 2745 0.618458 TACCTGGAACTCACCATGGC 59.382 55.000 13.04 0.00 39.34 4.40
2724 2761 8.677300 TCATTTCTTCACAGCTCATTTTATACC 58.323 33.333 0.00 0.00 0.00 2.73
2769 2806 8.621532 AACTATCAAGAATGCAACTAAGTTGA 57.378 30.769 0.00 0.00 45.28 3.18
2817 2854 2.943033 GTTAAATCGGTGCAGGCTACAT 59.057 45.455 0.00 0.00 0.00 2.29
2818 2855 2.289756 TGTTAAATCGGTGCAGGCTACA 60.290 45.455 0.00 0.00 0.00 2.74
2819 2856 2.352388 TGTTAAATCGGTGCAGGCTAC 58.648 47.619 0.00 0.00 0.00 3.58
2820 2857 2.772077 TGTTAAATCGGTGCAGGCTA 57.228 45.000 0.00 0.00 0.00 3.93


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

AutoCloner maintained by Alex Coulton.