Multiple sequence alignment - TraesCS7D01G417500

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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 TraesCS7D01G417500 chr7D 100.000 2561 0 0 1 2561 536462843 536460283 0.000000e+00 4730
1 TraesCS7D01G417500 chr1A 83.133 2579 369 36 11 2555 555932437 555934983 0.000000e+00 2292
2 TraesCS7D01G417500 chr2A 86.731 2080 234 19 11 2069 190314120 190312062 0.000000e+00 2274
3 TraesCS7D01G417500 chr4D 86.888 1960 214 23 105 2049 333768410 333766479 0.000000e+00 2156
4 TraesCS7D01G417500 chr4D 88.310 1805 182 17 257 2049 333678064 333676277 0.000000e+00 2137
5 TraesCS7D01G417500 chr2D 85.113 2042 266 20 41 2050 338339216 338341251 0.000000e+00 2052
6 TraesCS7D01G417500 chr4B 84.375 2080 281 23 3 2050 609588877 609586810 0.000000e+00 2001
7 TraesCS7D01G417500 chr5A 87.136 1749 201 16 311 2050 584544690 584546423 0.000000e+00 1962
8 TraesCS7D01G417500 chr1D 87.298 1669 184 10 393 2050 447450580 447448929 0.000000e+00 1882
9 TraesCS7D01G417500 chr2B 89.803 1422 135 7 636 2050 234361418 234360000 0.000000e+00 1814
10 TraesCS7D01G417500 chr5D 85.668 1535 176 23 116 1639 487745626 487744125 0.000000e+00 1576
11 TraesCS7D01G417500 chr5D 87.699 691 76 8 1873 2559 458530845 458530160 0.000000e+00 797
12 TraesCS7D01G417500 chrUn 74.817 409 74 18 3 397 217850501 217850894 9.490000e-35 158
13 TraesCS7D01G417500 chr6D 79.058 191 29 5 2 182 86381165 86380976 1.240000e-23 121


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 TraesCS7D01G417500 chr7D 536460283 536462843 2560 True 4730 4730 100.000 1 2561 1 chr7D.!!$R1 2560
1 TraesCS7D01G417500 chr1A 555932437 555934983 2546 False 2292 2292 83.133 11 2555 1 chr1A.!!$F1 2544
2 TraesCS7D01G417500 chr2A 190312062 190314120 2058 True 2274 2274 86.731 11 2069 1 chr2A.!!$R1 2058
3 TraesCS7D01G417500 chr4D 333766479 333768410 1931 True 2156 2156 86.888 105 2049 1 chr4D.!!$R2 1944
4 TraesCS7D01G417500 chr4D 333676277 333678064 1787 True 2137 2137 88.310 257 2049 1 chr4D.!!$R1 1792
5 TraesCS7D01G417500 chr2D 338339216 338341251 2035 False 2052 2052 85.113 41 2050 1 chr2D.!!$F1 2009
6 TraesCS7D01G417500 chr4B 609586810 609588877 2067 True 2001 2001 84.375 3 2050 1 chr4B.!!$R1 2047
7 TraesCS7D01G417500 chr5A 584544690 584546423 1733 False 1962 1962 87.136 311 2050 1 chr5A.!!$F1 1739
8 TraesCS7D01G417500 chr1D 447448929 447450580 1651 True 1882 1882 87.298 393 2050 1 chr1D.!!$R1 1657
9 TraesCS7D01G417500 chr2B 234360000 234361418 1418 True 1814 1814 89.803 636 2050 1 chr2B.!!$R1 1414
10 TraesCS7D01G417500 chr5D 487744125 487745626 1501 True 1576 1576 85.668 116 1639 1 chr5D.!!$R2 1523
11 TraesCS7D01G417500 chr5D 458530160 458530845 685 True 797 797 87.699 1873 2559 1 chr5D.!!$R1 686

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
911 966 0.322098 CCGATGCCCACAACCTGTTA 60.322 55.0 0.0 0.0 0.0 2.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2084 2166 0.037882 CCCGTCATCATGCTAGCGAT 60.038 55.0 10.77 4.7 0.0 4.58 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
36 37 0.952010 ACGCGCCGACCTATTTTGTT 60.952 50.000 5.73 0.00 0.00 2.83
63 64 4.025401 CTGTTTGGGTCGCCGTGC 62.025 66.667 0.00 0.00 0.00 5.34
73 74 2.427410 CGCCGTGCACAGAAAAGC 60.427 61.111 18.64 8.14 0.00 3.51
83 84 2.197324 AGAAAAGCCGGCCCAACA 59.803 55.556 26.15 0.00 0.00 3.33
86 87 4.887190 AAAGCCGGCCCAACACGT 62.887 61.111 26.15 0.00 0.00 4.49
109 121 3.990806 CAAACGGACGCGCGTTCA 61.991 61.111 37.62 0.00 0.00 3.18
195 207 2.126618 TCGCCGCACGTCAACTAG 60.127 61.111 0.00 0.00 44.19 2.57
198 211 1.080705 GCCGCACGTCAACTAGTCT 60.081 57.895 0.00 0.00 0.00 3.24
200 213 0.793478 CCGCACGTCAACTAGTCTCG 60.793 60.000 0.00 4.35 0.00 4.04
223 236 1.079819 CCTGTCAGTCGGTCGCAAT 60.080 57.895 0.00 0.00 0.00 3.56
309 326 2.029666 GGATGACGCCCTCGATGG 59.970 66.667 1.78 1.78 39.41 3.51
342 359 3.441290 CTCCCTCGCCTCGTTCGT 61.441 66.667 0.00 0.00 0.00 3.85
373 406 1.533753 CCCCTCTGGCAAAGGCAAA 60.534 57.895 0.00 0.00 43.71 3.68
507 543 4.373116 GGGACGAAGCAGCGGTGA 62.373 66.667 20.69 0.00 35.12 4.02
554 591 4.572571 AGGAAACCAACGCCCGCA 62.573 61.111 0.00 0.00 0.00 5.69
575 615 2.707849 GCGGTAGCAACGAGGGAGA 61.708 63.158 0.00 0.00 44.35 3.71
750 792 2.415608 CGCAAGCCTCCCGACTCTA 61.416 63.158 0.00 0.00 0.00 2.43
819 872 2.819595 CGTGCCCATTGACCTCCG 60.820 66.667 0.00 0.00 0.00 4.63
853 907 1.381872 CCTCGTCATCTGGAGGGGT 60.382 63.158 0.00 0.00 44.94 4.95
911 966 0.322098 CCGATGCCCACAACCTGTTA 60.322 55.000 0.00 0.00 0.00 2.41
928 983 1.895020 TTAGACAGAATGCCGGCGGT 61.895 55.000 28.82 12.42 42.53 5.68
931 986 4.812476 CAGAATGCCGGCGGTCGA 62.812 66.667 28.82 12.45 42.43 4.20
1048 1103 2.103339 GACCCCGACGAGACCCAAAA 62.103 60.000 0.00 0.00 0.00 2.44
1451 1519 4.889856 ATGCATAGCACGCGCGGA 62.890 61.111 35.22 16.54 43.04 5.54
1486 1554 0.389391 AAGCGATGGAGGGTGATACG 59.611 55.000 0.00 0.00 0.00 3.06
1488 1556 0.603569 GCGATGGAGGGTGATACGAT 59.396 55.000 0.00 0.00 0.00 3.73
1599 1673 3.117512 GCCCTCTTCATTTCCATTCCCTA 60.118 47.826 0.00 0.00 0.00 3.53
1608 1682 6.613699 TCATTTCCATTCCCTATATGCTTGT 58.386 36.000 0.00 0.00 0.00 3.16
1627 1701 5.565439 GCTTGTATGTCCATTTGCATATCCC 60.565 44.000 0.00 0.00 31.33 3.85
1636 1710 2.244486 TTGCATATCCCTTTGCCCAA 57.756 45.000 0.00 0.00 38.08 4.12
1658 1732 6.480651 CCAAATGCTTGCATGCTATTCATTTA 59.519 34.615 25.80 2.36 33.15 1.40
1676 1750 7.422465 TCATTTATAGGCATTCCAAGCTTTT 57.578 32.000 0.00 0.00 33.74 2.27
1774 1848 1.472480 GTTCAAGGTGCAATATGCCGT 59.528 47.619 0.00 0.00 44.23 5.68
1852 1933 4.796495 GCCGCGGGGAAGACCAAT 62.796 66.667 29.38 0.00 42.91 3.16
1888 1969 2.406616 GCGGGATGCGGTGTTGATT 61.407 57.895 0.00 0.00 0.00 2.57
1891 1972 1.315257 GGGATGCGGTGTTGATTGCT 61.315 55.000 0.00 0.00 0.00 3.91
1932 2014 3.350833 GCATGATGACCAAGAAGGACTT 58.649 45.455 0.00 0.00 41.22 3.01
1947 2029 2.188817 GGACTTAAGGGAGGAGAAGCA 58.811 52.381 7.53 0.00 0.00 3.91
1970 2052 3.470709 TGACAAGACAAGGAAGAGCAAG 58.529 45.455 0.00 0.00 0.00 4.01
2081 2163 1.141053 AGACCAAGGCGAAAGAAGTGT 59.859 47.619 0.00 0.00 0.00 3.55
2084 2166 2.367567 ACCAAGGCGAAAGAAGTGTCTA 59.632 45.455 0.00 0.00 32.16 2.59
2105 2187 1.302033 GCTAGCATGATGACGGGGG 60.302 63.158 10.63 0.00 0.00 5.40
2121 2203 0.179006 GGGGTGGAGATCATGAAGGC 60.179 60.000 0.00 0.00 0.00 4.35
2139 2221 1.661480 CGGACCTCAACACCGTGTA 59.339 57.895 4.17 0.00 41.47 2.90
2152 2234 1.226717 CGTGTAGCCGAGGAAGAGC 60.227 63.158 0.00 0.00 0.00 4.09
2158 2240 4.821589 CCGAGGAAGAGCCCGTGC 62.822 72.222 0.00 0.00 37.37 5.34
2211 2293 1.598132 CGACGACGAGTGATCTATGGT 59.402 52.381 0.00 0.00 42.66 3.55
2213 2295 2.612672 GACGACGAGTGATCTATGGTGA 59.387 50.000 0.00 0.00 0.00 4.02
2217 2299 2.355132 ACGAGTGATCTATGGTGACGAC 59.645 50.000 0.00 0.00 0.00 4.34
2263 2345 1.174712 AAGTGTGCTGGCATGACCAC 61.175 55.000 0.00 0.00 46.36 4.16
2264 2346 1.898094 GTGTGCTGGCATGACCACA 60.898 57.895 6.55 6.55 46.36 4.17
2285 2367 0.744414 CCGAGATGGCGTGGTTGAAT 60.744 55.000 0.00 0.00 0.00 2.57
2286 2368 1.086696 CGAGATGGCGTGGTTGAATT 58.913 50.000 0.00 0.00 0.00 2.17
2345 2430 0.665369 GCAAGTGTGCCAGCATGAAC 60.665 55.000 0.00 0.00 45.68 3.18
2413 2498 1.152860 TGCCGGCAAGAACTTTGGA 60.153 52.632 30.74 0.00 0.00 3.53
2421 2506 0.883370 AAGAACTTTGGACGACGGCC 60.883 55.000 14.55 14.55 0.00 6.13
2463 2549 1.137404 CGCGGGCCTTCTCAAATTG 59.863 57.895 0.84 0.00 0.00 2.32
2473 2559 2.198827 TCTCAAATTGGTGTGCGGAT 57.801 45.000 0.00 0.00 0.00 4.18
2482 2568 1.675483 TGGTGTGCGGATATGAAATGC 59.325 47.619 0.00 0.00 0.00 3.56
2490 2576 1.136690 GATATGAAATGCGTCGCGGA 58.863 50.000 13.38 0.00 0.00 5.54
2491 2577 1.525197 GATATGAAATGCGTCGCGGAA 59.475 47.619 13.38 0.00 0.00 4.30
2497 2583 3.583276 ATGCGTCGCGGAAGTTGGA 62.583 57.895 13.38 0.00 0.00 3.53
2517 2603 1.971167 GCACTGCCGACCCAAATCA 60.971 57.895 0.00 0.00 0.00 2.57
2523 2609 3.016736 CTGCCGACCCAAATCATAAACT 58.983 45.455 0.00 0.00 0.00 2.66
2524 2610 4.196193 CTGCCGACCCAAATCATAAACTA 58.804 43.478 0.00 0.00 0.00 2.24
2527 2613 4.777463 CCGACCCAAATCATAAACTAGGT 58.223 43.478 0.00 0.00 0.00 3.08
2539 2625 3.449227 CTAGGTGGACGCCGAGCA 61.449 66.667 0.00 0.00 0.00 4.26
2556 2642 4.531426 AGGCGGCCAACCCAAACA 62.531 61.111 23.09 0.00 0.00 2.83
2559 2645 3.039134 CGGCCAACCCAAACAGAC 58.961 61.111 2.24 0.00 0.00 3.51
2560 2646 1.826054 CGGCCAACCCAAACAGACA 60.826 57.895 2.24 0.00 0.00 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.123959 GCGCGTTGGAGTTTCACTAATTA 59.876 43.478 8.43 0.00 0.00 1.40
1 2 2.095919 GCGCGTTGGAGTTTCACTAATT 60.096 45.455 8.43 0.00 0.00 1.40
7 8 3.342627 CGGCGCGTTGGAGTTTCA 61.343 61.111 8.43 0.00 0.00 2.69
36 37 1.885388 CCCAAACAGACGTGCACGA 60.885 57.895 42.94 0.00 43.02 4.35
63 64 2.199652 TTGGGCCGGCTTTTCTGTG 61.200 57.895 28.56 0.00 0.00 3.66
73 74 2.433664 GTAGACGTGTTGGGCCGG 60.434 66.667 0.00 0.00 0.00 6.13
83 84 1.286880 CGTCCGTTTGGGTAGACGT 59.713 57.895 3.39 0.00 45.25 4.34
86 87 2.259204 CGCGTCCGTTTGGGTAGA 59.741 61.111 0.00 0.00 37.00 2.59
109 121 1.153168 CGGAAATGGGTCGGCAGAT 60.153 57.895 0.00 0.00 0.00 2.90
178 190 2.126618 CTAGTTGACGTGCGGCGA 60.127 61.111 12.98 0.00 44.77 5.54
195 207 2.125753 CTGACAGGCCAGCGAGAC 60.126 66.667 5.01 0.00 0.00 3.36
198 211 4.056125 CGACTGACAGGCCAGCGA 62.056 66.667 5.01 0.00 37.68 4.93
200 213 3.941657 GACCGACTGACAGGCCAGC 62.942 68.421 5.01 0.00 37.68 4.85
223 236 2.284625 AGGGAGATGGTGGACGCA 60.285 61.111 0.00 0.00 0.00 5.24
235 248 4.079970 GGTTTTTAGGAAAGTGGAGGGAG 58.920 47.826 0.00 0.00 0.00 4.30
342 359 4.414956 AGGGGGCGGAGGTGATGA 62.415 66.667 0.00 0.00 0.00 2.92
405 438 2.369860 TCAGCTGCTTCTTCTTCTTGGA 59.630 45.455 9.47 0.00 0.00 3.53
554 591 2.104331 CCTCGTTGCTACCGCGAT 59.896 61.111 8.23 0.00 39.65 4.58
707 749 2.582436 GTGGAAGCCGGGAATCGA 59.418 61.111 2.18 0.00 42.43 3.59
845 898 2.890766 GCGTTTCCTCACCCCTCCA 61.891 63.158 0.00 0.00 0.00 3.86
911 966 3.665675 GACCGCCGGCATTCTGTCT 62.666 63.158 28.98 0.00 0.00 3.41
928 983 2.429069 TCGTCTCGTCGTCGTCGA 60.429 61.111 13.59 13.59 44.12 4.20
931 986 2.246739 TTGGTCGTCTCGTCGTCGT 61.247 57.895 1.33 0.00 38.33 4.34
1031 1086 1.670083 GTTTTGGGTCTCGTCGGGG 60.670 63.158 0.00 0.00 0.00 5.73
1081 1136 2.158726 TGCATGGCAGCTTGATCATAGA 60.159 45.455 0.00 0.00 33.32 1.98
1190 1257 1.636340 GCCGTCGATGTCCATTTCG 59.364 57.895 3.52 0.00 36.72 3.46
1451 1519 1.620822 GCTTTGAAGTGGACACCCAT 58.379 50.000 0.00 0.00 45.68 4.00
1462 1530 1.089920 CACCCTCCATCGCTTTGAAG 58.910 55.000 0.00 0.00 0.00 3.02
1486 1554 5.173854 GCACAAAACTTGTTGCACTCTTATC 59.826 40.000 0.00 0.00 43.23 1.75
1488 1556 4.420168 GCACAAAACTTGTTGCACTCTTA 58.580 39.130 0.00 0.00 43.23 2.10
1599 1673 6.659745 ATGCAAATGGACATACAAGCATAT 57.340 33.333 0.00 0.00 36.41 1.78
1608 1682 5.010922 GCAAAGGGATATGCAAATGGACATA 59.989 40.000 0.00 0.00 42.12 2.29
1627 1701 1.466950 CATGCAAGCATTTGGGCAAAG 59.533 47.619 4.52 0.00 40.02 2.77
1636 1710 8.033038 CCTATAAATGAATAGCATGCAAGCATT 58.967 33.333 21.98 18.83 37.28 3.56
1658 1732 3.703052 CCTCAAAAGCTTGGAATGCCTAT 59.297 43.478 0.00 0.00 37.80 2.57
1676 1750 1.144708 TGTTGGACCTTGAATGCCTCA 59.855 47.619 0.00 0.00 0.00 3.86
1774 1848 3.716195 CCCCACGCACCATGAGGA 61.716 66.667 0.00 0.00 38.69 3.71
1798 1878 1.677637 CCCAACCTCCTCTACGGCTC 61.678 65.000 0.00 0.00 0.00 4.70
1805 1885 2.456840 CCCTCCCCAACCTCCTCT 59.543 66.667 0.00 0.00 0.00 3.69
1852 1933 1.270839 CGCTTGTCCTCCTTCTTGGAA 60.271 52.381 0.00 0.00 45.63 3.53
1884 1965 2.884012 ACGGTTGTGATCAAAGCAATCA 59.116 40.909 0.00 0.00 35.20 2.57
1932 2014 2.180276 GTCAGTGCTTCTCCTCCCTTA 58.820 52.381 0.00 0.00 0.00 2.69
1947 2029 2.435805 TGCTCTTCCTTGTCTTGTCAGT 59.564 45.455 0.00 0.00 0.00 3.41
2081 2163 2.162408 CCGTCATCATGCTAGCGATAGA 59.838 50.000 12.82 5.48 39.76 1.98
2084 2166 0.037882 CCCGTCATCATGCTAGCGAT 60.038 55.000 10.77 4.70 0.00 4.58
2105 2187 0.465705 TCCGCCTTCATGATCTCCAC 59.534 55.000 0.00 0.00 0.00 4.02
2152 2234 1.424493 GCATCTTCTCGAAGCACGGG 61.424 60.000 1.81 0.38 44.81 5.28
2158 2240 1.150567 CGGCCTGCATCTTCTCGAAG 61.151 60.000 0.00 0.22 39.71 3.79
2211 2293 0.250553 AAAAAGGATGGCGGTCGTCA 60.251 50.000 3.97 0.00 33.11 4.35
2213 2295 4.813346 AAAAAGGATGGCGGTCGT 57.187 50.000 0.00 0.00 0.00 4.34
2232 2314 1.673993 CACACTTGCCCGGCATACA 60.674 57.895 14.30 0.00 38.76 2.29
2269 2351 1.818674 GGAAATTCAACCACGCCATCT 59.181 47.619 0.00 0.00 0.00 2.90
2281 2363 1.346068 CAAAAAGGGGCGGGAAATTCA 59.654 47.619 0.00 0.00 0.00 2.57
2285 2367 2.034048 GCACAAAAAGGGGCGGGAAA 62.034 55.000 0.00 0.00 0.00 3.13
2286 2368 2.503382 GCACAAAAAGGGGCGGGAA 61.503 57.895 0.00 0.00 0.00 3.97
2403 2488 1.301479 GGCCGTCGTCCAAAGTTCT 60.301 57.895 0.00 0.00 0.00 3.01
2421 2506 0.390492 TAGATCATGCCAGCGGTCAG 59.610 55.000 0.00 0.00 0.00 3.51
2455 2540 3.627123 TCATATCCGCACACCAATTTGAG 59.373 43.478 0.00 0.00 0.00 3.02
2463 2549 1.334059 CGCATTTCATATCCGCACACC 60.334 52.381 0.00 0.00 0.00 4.16
2473 2559 0.927537 CTTCCGCGACGCATTTCATA 59.072 50.000 21.35 0.00 0.00 2.15
2482 2568 3.467119 CGTCCAACTTCCGCGACG 61.467 66.667 8.23 2.27 41.70 5.12
2490 2576 2.972505 CGGCAGTGCGTCCAACTT 60.973 61.111 9.45 0.00 0.00 2.66
2491 2577 3.923864 TCGGCAGTGCGTCCAACT 61.924 61.111 9.45 0.00 0.00 3.16
2497 2583 3.842925 ATTTGGGTCGGCAGTGCGT 62.843 57.895 9.45 0.00 0.00 5.24
2517 2603 1.407979 CTCGGCGTCCACCTAGTTTAT 59.592 52.381 6.85 0.00 0.00 1.40
2523 2609 3.449227 CTGCTCGGCGTCCACCTA 61.449 66.667 6.85 0.00 0.00 3.08
2539 2625 4.531426 TGTTTGGGTTGGCCGCCT 62.531 61.111 11.61 0.00 34.97 5.52


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

AutoCloner maintained by Alex Coulton.