Multiple sequence alignment - TraesCS1D01G108600

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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 TraesCS1D01G108600 chr1D 100.000 2363 0 0 1 2363 101277627 101279989 0.000000e+00 4364.0
1 TraesCS1D01G108600 chr1A 93.175 1934 62 30 1 1894 104223732 104221829 0.000000e+00 2776.0
2 TraesCS1D01G108600 chr1A 89.852 473 43 4 1896 2363 104221755 104221283 9.340000e-169 603.0
3 TraesCS1D01G108600 chr1B 91.851 1767 56 36 1 1734 150524460 150522749 0.000000e+00 2385.0
4 TraesCS1D01G108600 chr1B 96.528 144 4 1 2221 2363 150374743 150374600 1.090000e-58 237.0
5 TraesCS1D01G108600 chr1B 82.490 257 36 7 1895 2145 150521879 150521626 1.420000e-52 217.0
6 TraesCS1D01G108600 chr1B 84.516 155 11 5 1744 1897 150522081 150521939 8.800000e-30 141.0
7 TraesCS1D01G108600 chr5D 94.286 35 2 0 2010 2044 529361790 529361824 1.000000e-03 54.7


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 TraesCS1D01G108600 chr1D 101277627 101279989 2362 False 4364.000000 4364 100.000000 1 2363 1 chr1D.!!$F1 2362
1 TraesCS1D01G108600 chr1A 104221283 104223732 2449 True 1689.500000 2776 91.513500 1 2363 2 chr1A.!!$R1 2362
2 TraesCS1D01G108600 chr1B 150521626 150524460 2834 True 914.333333 2385 86.285667 1 2145 3 chr1B.!!$R2 2144

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
946 984 0.109458 TACGTACGCACTTGCCTCTG 60.109 55.0 16.72 0.0 37.91 3.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2341 3136 0.597568 TTGGTTGAGATGCGGCTTTG 59.402 50.0 0.0 0.0 0.0 2.77 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
77 78 3.135414 TGTGCAGCGAATTTGATTAGC 57.865 42.857 0.00 0.00 40.57 3.09
125 126 1.701292 CATACCATGATCAGCTCCCCA 59.299 52.381 0.09 0.00 0.00 4.96
147 148 0.904394 GGGGAACATGGTGGCACATT 60.904 55.000 20.82 7.64 44.52 2.71
148 149 1.618345 GGGGAACATGGTGGCACATTA 60.618 52.381 20.82 5.41 44.52 1.90
149 150 2.387757 GGGAACATGGTGGCACATTAT 58.612 47.619 20.82 7.67 44.52 1.28
150 151 2.765699 GGGAACATGGTGGCACATTATT 59.234 45.455 20.82 8.02 44.52 1.40
151 152 3.957497 GGGAACATGGTGGCACATTATTA 59.043 43.478 20.82 0.00 44.52 0.98
152 153 4.588528 GGGAACATGGTGGCACATTATTAT 59.411 41.667 20.82 0.00 44.52 1.28
153 154 5.509501 GGGAACATGGTGGCACATTATTATG 60.510 44.000 20.82 14.34 44.52 1.90
154 155 5.301551 GGAACATGGTGGCACATTATTATGA 59.698 40.000 20.82 0.00 44.52 2.15
155 156 5.772825 ACATGGTGGCACATTATTATGAC 57.227 39.130 20.82 0.00 44.52 3.06
156 157 5.199723 ACATGGTGGCACATTATTATGACA 58.800 37.500 20.82 4.12 44.52 3.58
157 158 5.834742 ACATGGTGGCACATTATTATGACAT 59.165 36.000 20.82 6.42 44.52 3.06
177 178 6.595326 TGACATTATCTCAACCAGTGCTTAAG 59.405 38.462 0.00 0.00 0.00 1.85
352 364 1.200716 CCCTTGACACATCACACATGC 59.799 52.381 0.00 0.00 33.38 4.06
353 365 1.881324 CCTTGACACATCACACATGCA 59.119 47.619 0.00 0.00 33.38 3.96
354 366 2.490509 CCTTGACACATCACACATGCAT 59.509 45.455 0.00 0.00 33.38 3.96
355 367 3.690628 CCTTGACACATCACACATGCATA 59.309 43.478 0.00 0.00 33.38 3.14
414 426 2.693864 ATGCAGTGGAGGGAGGGG 60.694 66.667 0.00 0.00 0.00 4.79
439 451 3.199508 CAGGGTGTTCTGATGAGGAGATT 59.800 47.826 0.00 0.00 36.93 2.40
444 457 6.317391 GGGTGTTCTGATGAGGAGATTAAAAG 59.683 42.308 0.00 0.00 0.00 2.27
486 503 1.899814 GGTGGTGTATGAGAGGTGTCA 59.100 52.381 0.00 0.00 0.00 3.58
487 504 2.353803 GGTGGTGTATGAGAGGTGTCAC 60.354 54.545 0.00 0.00 0.00 3.67
664 687 9.764363 TCACTAGCATCACATAAATAAAGTAGG 57.236 33.333 0.00 0.00 0.00 3.18
946 984 0.109458 TACGTACGCACTTGCCTCTG 60.109 55.000 16.72 0.00 37.91 3.35
1236 1287 2.778679 GATCACCGCAGCAACGAC 59.221 61.111 0.00 0.00 34.06 4.34
1237 1288 3.071459 GATCACCGCAGCAACGACG 62.071 63.158 0.00 0.00 34.06 5.12
1238 1289 3.567478 ATCACCGCAGCAACGACGA 62.567 57.895 0.00 0.00 34.06 4.20
1605 1663 0.249322 AACTTGCGTGAGTGCGTACT 60.249 50.000 5.62 5.62 40.66 2.73
1606 1664 0.939577 ACTTGCGTGAGTGCGTACTG 60.940 55.000 12.07 0.00 37.25 2.74
1607 1665 1.617755 CTTGCGTGAGTGCGTACTGG 61.618 60.000 12.07 1.03 37.25 4.00
1608 1666 2.077821 TTGCGTGAGTGCGTACTGGA 62.078 55.000 12.07 0.00 37.25 3.86
1609 1667 1.801913 GCGTGAGTGCGTACTGGAG 60.802 63.158 12.07 2.65 37.25 3.86
1692 1750 5.738619 ACATCGGGTATATGATGCTACAA 57.261 39.130 10.68 0.00 44.57 2.41
1693 1751 6.299805 ACATCGGGTATATGATGCTACAAT 57.700 37.500 10.68 0.00 44.57 2.71
1746 1804 9.952030 TTTACAAATCACTATGACAGGACAATA 57.048 29.630 0.00 0.00 0.00 1.90
1790 2506 9.765795 TGTTTCGGAATAAATGTTTATTTTGGT 57.234 25.926 10.97 0.00 41.88 3.67
1830 2546 8.018537 TCAATTACCTGAGAATAGAAATCGGA 57.981 34.615 0.00 0.00 0.00 4.55
1843 2559 9.921637 GAATAGAAATCGGATTAGTCAGAGAAT 57.078 33.333 3.22 0.00 32.08 2.40
1870 2586 4.993705 AGTGGTTTGATGGTTAAGAGGA 57.006 40.909 0.00 0.00 0.00 3.71
1961 2750 2.525055 TGTGCTTTTCGTTTTGTCTGC 58.475 42.857 0.00 0.00 0.00 4.26
1972 2761 3.596214 GTTTTGTCTGCCTCTCGGATTA 58.404 45.455 0.00 0.00 31.70 1.75
1994 2783 2.080693 ACAACAACAAAGCTCGACACA 58.919 42.857 0.00 0.00 0.00 3.72
2008 2797 2.019249 CGACACAAGGATGCCATCAAT 58.981 47.619 7.06 0.00 0.00 2.57
2043 2832 4.323477 CCGGAGGCGGGAACAACA 62.323 66.667 0.00 0.00 46.14 3.33
2044 2833 3.047877 CGGAGGCGGGAACAACAC 61.048 66.667 0.00 0.00 0.00 3.32
2099 2891 2.563261 AGATATGGTGATGGCTGCTG 57.437 50.000 0.00 0.00 0.00 4.41
2107 2899 1.404391 GTGATGGCTGCTGGATTTCAG 59.596 52.381 0.00 0.00 46.03 3.02
2124 2917 7.454380 TGGATTTCAGTCCAATGTTAGGAAAAT 59.546 33.333 0.00 0.00 45.03 1.82
2126 2919 6.494893 TTCAGTCCAATGTTAGGAAAATCG 57.505 37.500 0.00 0.00 36.80 3.34
2131 2924 7.651704 CAGTCCAATGTTAGGAAAATCGTTTTT 59.348 33.333 3.91 3.91 36.80 1.94
2148 2941 4.498513 CGTTTTTCCAAGGTAGTTGTTCCC 60.499 45.833 0.00 0.00 33.87 3.97
2158 2951 3.516700 GGTAGTTGTTCCCTAGGTGCTTA 59.483 47.826 8.29 0.00 0.00 3.09
2159 2952 3.697619 AGTTGTTCCCTAGGTGCTTAC 57.302 47.619 8.29 0.36 0.00 2.34
2202 2996 0.393448 AGCATGCAAAATGTGTGCCA 59.607 45.000 21.98 0.00 41.49 4.92
2211 3005 4.327087 GCAAAATGTGTGCCATAGCTTTAC 59.673 41.667 0.00 0.00 40.80 2.01
2254 3048 5.531287 ACAAGAATTACAGACAAACTCCCAC 59.469 40.000 0.00 0.00 0.00 4.61
2262 3056 0.106719 ACAAACTCCCACCACACCTG 60.107 55.000 0.00 0.00 0.00 4.00
2279 3074 3.325135 CACCTGGTGAGAAGTAAACTCCT 59.675 47.826 22.33 0.00 35.23 3.69
2285 3080 4.283722 GGTGAGAAGTAAACTCCTCTCCAA 59.716 45.833 11.29 0.00 38.49 3.53
2288 3083 5.244178 TGAGAAGTAAACTCCTCTCCAACTC 59.756 44.000 8.60 0.00 31.84 3.01
2292 3087 4.773149 AGTAAACTCCTCTCCAACTCGAAT 59.227 41.667 0.00 0.00 0.00 3.34
2295 3090 1.205655 CTCCTCTCCAACTCGAATGCA 59.794 52.381 0.00 0.00 0.00 3.96
2312 3107 4.870123 ATGCACACATTACAACCACAAT 57.130 36.364 0.00 0.00 30.07 2.71
2313 3108 3.974912 TGCACACATTACAACCACAATG 58.025 40.909 0.00 0.00 37.99 2.82
2325 3120 3.861276 ACCACAATGCACAAGATCATG 57.139 42.857 0.00 0.00 0.00 3.07
2341 3136 3.281727 TCATGTCCTAAACTGGCCATC 57.718 47.619 5.51 0.00 0.00 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
63 64 5.831997 ACTAATTGGGCTAATCAAATTCGC 58.168 37.500 0.00 0.00 0.00 4.70
77 78 8.257306 ACCATTGTGCTTATTTAACTAATTGGG 58.743 33.333 0.00 0.00 0.00 4.12
125 126 1.852157 TGCCACCATGTTCCCCTCT 60.852 57.895 0.00 0.00 0.00 3.69
147 148 8.432013 AGCACTGGTTGAGATAATGTCATAATA 58.568 33.333 0.00 0.00 0.00 0.98
148 149 7.285566 AGCACTGGTTGAGATAATGTCATAAT 58.714 34.615 0.00 0.00 0.00 1.28
149 150 6.653020 AGCACTGGTTGAGATAATGTCATAA 58.347 36.000 0.00 0.00 0.00 1.90
150 151 6.239217 AGCACTGGTTGAGATAATGTCATA 57.761 37.500 0.00 0.00 0.00 2.15
151 152 5.108187 AGCACTGGTTGAGATAATGTCAT 57.892 39.130 0.00 0.00 0.00 3.06
152 153 4.558226 AGCACTGGTTGAGATAATGTCA 57.442 40.909 0.00 0.00 0.00 3.58
153 154 6.595716 ACTTAAGCACTGGTTGAGATAATGTC 59.404 38.462 17.08 0.00 32.36 3.06
154 155 6.476378 ACTTAAGCACTGGTTGAGATAATGT 58.524 36.000 17.08 0.00 32.36 2.71
155 156 6.992063 ACTTAAGCACTGGTTGAGATAATG 57.008 37.500 17.08 0.00 32.36 1.90
156 157 9.988815 CTATACTTAAGCACTGGTTGAGATAAT 57.011 33.333 17.08 10.55 32.36 1.28
157 158 8.978472 ACTATACTTAAGCACTGGTTGAGATAA 58.022 33.333 17.08 5.21 32.36 1.75
171 172 9.086758 TCCTCCCTATGTTAACTATACTTAAGC 57.913 37.037 7.22 0.00 0.00 3.09
177 178 7.894364 TCTCCATCCTCCCTATGTTAACTATAC 59.106 40.741 7.22 0.00 0.00 1.47
414 426 2.832129 TCCTCATCAGAACACCCTGTAC 59.168 50.000 0.00 0.00 35.71 2.90
439 451 2.101783 CCATGCATGCACTCCCTTTTA 58.898 47.619 25.37 0.00 0.00 1.52
444 457 1.514087 CAACCATGCATGCACTCCC 59.486 57.895 25.37 0.00 0.00 4.30
486 503 0.889186 GTCCATCCAAACACAGGCGT 60.889 55.000 0.00 0.00 0.00 5.68
487 504 1.875963 GTCCATCCAAACACAGGCG 59.124 57.895 0.00 0.00 0.00 5.52
623 646 1.383963 AGTGAGAGAGTAGGGGTGGA 58.616 55.000 0.00 0.00 0.00 4.02
823 846 3.964031 GGTGCCATATATAGGAGAGGAGG 59.036 52.174 0.00 0.00 0.00 4.30
946 984 3.717400 TGGAATGAGAGATAGACGCAC 57.283 47.619 0.00 0.00 0.00 5.34
949 987 6.627395 ACTACTTGGAATGAGAGATAGACG 57.373 41.667 0.00 0.00 0.00 4.18
950 988 7.308951 GGCTACTACTTGGAATGAGAGATAGAC 60.309 44.444 0.00 0.00 0.00 2.59
1231 1282 2.623915 CGTCCTCCACCTCGTCGTT 61.624 63.158 0.00 0.00 0.00 3.85
1236 1287 3.812019 CCGTCGTCCTCCACCTCG 61.812 72.222 0.00 0.00 0.00 4.63
1237 1288 4.131088 GCCGTCGTCCTCCACCTC 62.131 72.222 0.00 0.00 0.00 3.85
1371 1422 5.292834 CGACACGACCTAGTAGTAGAAATGA 59.707 44.000 6.14 0.00 0.00 2.57
1377 1428 2.539274 GCTCGACACGACCTAGTAGTAG 59.461 54.545 0.00 0.00 0.00 2.57
1378 1429 2.094026 TGCTCGACACGACCTAGTAGTA 60.094 50.000 0.00 0.00 0.00 1.82
1379 1430 1.338484 TGCTCGACACGACCTAGTAGT 60.338 52.381 0.00 0.00 0.00 2.73
1504 1561 7.972832 ACGTATTTCATACTTCTCCAAAACA 57.027 32.000 0.00 0.00 33.59 2.83
1527 1584 5.243060 ACCCGTATAATTAACCCCTACGTAC 59.757 44.000 12.24 0.00 34.81 3.67
1719 1777 8.862325 TTGTCCTGTCATAGTGATTTGTAAAT 57.138 30.769 0.00 0.00 0.00 1.40
1746 1804 8.788806 TCCGAAACAAACATCACATAAGTAAAT 58.211 29.630 0.00 0.00 0.00 1.40
1790 2506 6.152661 CAGGTAATTGAGAAATAGCAAACCCA 59.847 38.462 0.00 0.00 29.32 4.51
1830 2546 7.726033 ACCACTAGTTGATTCTCTGACTAAT 57.274 36.000 0.08 0.00 0.00 1.73
1843 2559 6.833041 TCTTAACCATCAAACCACTAGTTGA 58.167 36.000 0.08 0.00 39.19 3.18
1926 2715 3.717294 ACATCCACCCCCTCGTGC 61.717 66.667 0.00 0.00 32.10 5.34
1972 2761 3.057876 TGTGTCGAGCTTTGTTGTTGTTT 60.058 39.130 0.00 0.00 0.00 2.83
2055 2844 3.135279 TCCTCCAATCTACTCTCCTCCT 58.865 50.000 0.00 0.00 0.00 3.69
2063 2852 6.022315 CCATATCTTCCTCCTCCAATCTACT 58.978 44.000 0.00 0.00 0.00 2.57
2099 2891 6.834168 TTTCCTAACATTGGACTGAAATCC 57.166 37.500 0.00 0.00 39.45 3.01
2107 2899 7.940178 AAAAACGATTTTCCTAACATTGGAC 57.060 32.000 0.00 0.00 33.48 4.02
2124 2917 4.336153 GGAACAACTACCTTGGAAAAACGA 59.664 41.667 0.00 0.00 33.66 3.85
2126 2919 4.647853 AGGGAACAACTACCTTGGAAAAAC 59.352 41.667 0.00 0.00 33.66 2.43
2131 2924 3.178865 CCTAGGGAACAACTACCTTGGA 58.821 50.000 0.00 0.00 46.13 3.53
2138 2931 4.422984 AGTAAGCACCTAGGGAACAACTA 58.577 43.478 14.81 0.00 0.00 2.24
2174 2967 7.408123 CACACATTTTGCATGCTTTAGAAAAA 58.592 30.769 20.33 15.52 0.00 1.94
2179 2972 3.123959 GGCACACATTTTGCATGCTTTAG 59.876 43.478 20.33 7.65 42.12 1.85
2180 2973 3.065655 GGCACACATTTTGCATGCTTTA 58.934 40.909 20.33 3.88 42.12 1.85
2182 2975 1.202663 TGGCACACATTTTGCATGCTT 60.203 42.857 20.33 0.00 42.12 3.91
2240 3034 1.308998 GTGTGGTGGGAGTTTGTCTG 58.691 55.000 0.00 0.00 0.00 3.51
2279 3074 1.069978 TGTGTGCATTCGAGTTGGAGA 59.930 47.619 0.00 0.00 0.00 3.71
2285 3080 3.188460 GGTTGTAATGTGTGCATTCGAGT 59.812 43.478 0.00 0.00 43.61 4.18
2288 3083 3.233578 GTGGTTGTAATGTGTGCATTCG 58.766 45.455 0.00 0.00 43.61 3.34
2292 3087 3.798206 GCATTGTGGTTGTAATGTGTGCA 60.798 43.478 0.00 0.00 36.81 4.57
2295 3090 3.382865 TGTGCATTGTGGTTGTAATGTGT 59.617 39.130 0.00 0.00 36.81 3.72
2312 3107 4.696877 CAGTTTAGGACATGATCTTGTGCA 59.303 41.667 27.34 15.03 40.09 4.57
2313 3108 4.095483 CCAGTTTAGGACATGATCTTGTGC 59.905 45.833 21.10 21.10 38.14 4.57
2325 3120 2.164422 GCTTTGATGGCCAGTTTAGGAC 59.836 50.000 13.05 0.00 37.13 3.85
2341 3136 0.597568 TTGGTTGAGATGCGGCTTTG 59.402 50.000 0.00 0.00 0.00 2.77


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

AutoCloner maintained by Alex Coulton.