Multiple sequence alignment - TraesCS1A01G072100

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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 TraesCS1A01G072100 chr1A 100.000 4079 0 0 1 4079 54457948 54462026 0.000000e+00 7533.0
1 TraesCS1A01G072100 chr1A 93.530 1561 60 11 2023 3571 56370413 56371944 0.000000e+00 2285.0
2 TraesCS1A01G072100 chr1A 93.060 1513 85 9 289 1788 56336697 56338202 0.000000e+00 2194.0
3 TraesCS1A01G072100 chr1A 93.191 1263 66 12 1896 3147 56338344 56339597 0.000000e+00 1838.0
4 TraesCS1A01G072100 chr1A 91.995 787 63 0 3146 3932 56340308 56341094 0.000000e+00 1105.0
5 TraesCS1A01G072100 chr1A 85.468 1101 68 29 1007 2016 56369273 56370372 0.000000e+00 1062.0
6 TraesCS1A01G072100 chr1A 92.453 583 41 2 430 1011 56368136 56368716 0.000000e+00 830.0
7 TraesCS1A01G072100 chr1A 89.532 449 40 3 1 444 56367676 56368122 2.750000e-156 562.0
8 TraesCS1A01G072100 chr1A 97.778 45 1 0 19 63 56367783 56367827 1.220000e-10 78.7
9 TraesCS1A01G072100 chr1D 95.961 2055 70 5 2023 4069 56428939 56426890 0.000000e+00 3323.0
10 TraesCS1A01G072100 chr1D 93.308 1554 78 9 187 1738 56531619 56530090 0.000000e+00 2270.0
11 TraesCS1A01G072100 chr1D 87.698 1707 133 39 103 1788 56430895 56429245 0.000000e+00 1917.0
12 TraesCS1A01G072100 chr1D 94.081 1267 62 9 2023 3286 56874171 56872915 0.000000e+00 1912.0
13 TraesCS1A01G072100 chr1D 91.964 1319 68 12 2329 3610 56529579 56528262 0.000000e+00 1814.0
14 TraesCS1A01G072100 chr1D 92.532 1232 58 7 2023 3252 56609360 56608161 0.000000e+00 1735.0
15 TraesCS1A01G072100 chr1D 88.633 1390 110 26 367 1738 56610980 56609621 0.000000e+00 1648.0
16 TraesCS1A01G072100 chr1D 91.954 783 49 11 966 1738 56875272 56874494 0.000000e+00 1085.0
17 TraesCS1A01G072100 chr1D 89.564 642 50 7 289 922 56875904 56875272 0.000000e+00 798.0
18 TraesCS1A01G072100 chr1D 87.946 589 54 10 1 582 56612920 56612342 0.000000e+00 678.0
19 TraesCS1A01G072100 chr1D 92.944 411 27 2 3533 3942 56869027 56868618 7.550000e-167 597.0
20 TraesCS1A01G072100 chr1D 89.071 366 28 9 1896 2254 56529934 56529574 1.040000e-120 444.0
21 TraesCS1A01G072100 chr1D 93.609 266 17 0 3311 3576 56608151 56607886 8.220000e-107 398.0
22 TraesCS1A01G072100 chr1D 83.973 443 42 16 335 774 56618434 56618018 8.220000e-107 398.0
23 TraesCS1A01G072100 chr1D 88.433 268 27 3 984 1251 57219350 57219087 1.830000e-83 320.0
24 TraesCS1A01G072100 chr1D 88.048 251 24 4 103 348 56618699 56618450 3.990000e-75 292.0
25 TraesCS1A01G072100 chr1D 94.444 180 10 0 1 180 56531843 56531664 1.120000e-70 278.0
26 TraesCS1A01G072100 chr1D 96.203 158 6 0 3287 3444 56869542 56869385 4.040000e-65 259.0
27 TraesCS1A01G072100 chr1D 88.832 197 22 0 1248 1444 57212907 57212711 4.070000e-60 243.0
28 TraesCS1A01G072100 chr1D 78.248 331 22 20 2023 2326 57073563 57073256 2.520000e-37 167.0
29 TraesCS1A01G072100 chr1D 92.857 70 3 2 1 70 56618710 56618643 2.590000e-17 100.0
30 TraesCS1A01G072100 chr1D 92.754 69 4 1 1 68 56430907 56430839 9.330000e-17 99.0
31 TraesCS1A01G072100 chr1D 90.769 65 6 0 4 68 56611236 56611172 2.020000e-13 87.9
32 TraesCS1A01G072100 chr1D 97.778 45 1 0 19 63 56612814 56612770 1.220000e-10 78.7
33 TraesCS1A01G072100 chr1B 92.553 2068 110 17 1898 3932 91881256 91879200 0.000000e+00 2926.0
34 TraesCS1A01G072100 chr1B 92.198 769 51 6 966 1727 91882373 91881607 0.000000e+00 1079.0
35 TraesCS1A01G072100 chr1B 90.057 523 32 8 294 816 91882937 91882435 0.000000e+00 660.0
36 TraesCS1A01G072100 chr1B 86.408 103 12 2 1298 1399 608950044 608950145 1.200000e-20 111.0
37 TraesCS1A01G072100 chr7B 76.676 373 68 18 1298 1662 409712036 409711675 5.380000e-44 189.0
38 TraesCS1A01G072100 chr7D 76.203 374 70 16 1298 1663 400171045 400170683 3.240000e-41 180.0
39 TraesCS1A01G072100 chr5D 82.192 73 13 0 1109 1181 315485471 315485399 3.400000e-06 63.9


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 TraesCS1A01G072100 chr1A 54457948 54462026 4078 False 7533.000000 7533 100.000000 1 4079 1 chr1A.!!$F1 4078
1 TraesCS1A01G072100 chr1A 56336697 56341094 4397 False 1712.333333 2194 92.748667 289 3932 3 chr1A.!!$F2 3643
2 TraesCS1A01G072100 chr1A 56367676 56371944 4268 False 963.540000 2285 91.752200 1 3571 5 chr1A.!!$F3 3570
3 TraesCS1A01G072100 chr1D 56426890 56430907 4017 True 1779.666667 3323 92.137667 1 4069 3 chr1D.!!$R4 4068
4 TraesCS1A01G072100 chr1D 56528262 56531843 3581 True 1201.500000 2270 92.196750 1 3610 4 chr1D.!!$R5 3609
5 TraesCS1A01G072100 chr1D 56868618 56875904 7286 True 930.200000 1912 92.949200 289 3942 5 chr1D.!!$R8 3653
6 TraesCS1A01G072100 chr1D 56607886 56612920 5034 True 770.933333 1735 91.877833 1 3576 6 chr1D.!!$R6 3575
7 TraesCS1A01G072100 chr1D 56618018 56618710 692 True 263.333333 398 88.292667 1 774 3 chr1D.!!$R7 773
8 TraesCS1A01G072100 chr1B 91879200 91882937 3737 True 1555.000000 2926 91.602667 294 3932 3 chr1B.!!$R1 3638

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
141 232 2.744202 GACGTCCTTCACATTGCTCATT 59.256 45.455 3.51 0.0 0.00 2.57 F
744 2511 3.481839 CATGTATGGCGCGTAATCATTG 58.518 45.455 8.43 0.0 0.00 2.82 F
1310 3708 0.176680 GACGTGCAGGTGGATCTCAT 59.823 55.000 18.18 0.0 0.00 2.90 F
2494 5270 0.106819 CATCCTCCAAGGGAAGCTGG 60.107 60.000 0.00 0.0 39.02 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1275 3673 0.160392 CGTCGATCGATCAAGCATGC 59.840 55.0 22.50 10.51 42.86 4.06 R
2459 5235 0.179037 GATGAGCTGCAGTATGGCCA 60.179 55.0 16.64 8.56 35.86 5.36 R
2898 5681 0.251653 TGTGGAAGTACTCGGCTCCT 60.252 55.0 11.68 0.00 0.00 3.69 R
3490 10368 0.744414 CCGGTCTCATCGTTGGCATT 60.744 55.0 0.00 0.00 0.00 3.56 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
93 184 7.715265 TTTATGCGAAAAGGATCAGATCTAC 57.285 36.000 10.36 0.00 31.61 2.59
141 232 2.744202 GACGTCCTTCACATTGCTCATT 59.256 45.455 3.51 0.00 0.00 2.57
149 240 7.327032 GTCCTTCACATTGCTCATTTTCTAAAC 59.673 37.037 0.00 0.00 0.00 2.01
150 241 6.306356 CCTTCACATTGCTCATTTTCTAAACG 59.694 38.462 0.00 0.00 0.00 3.60
166 257 8.800231 TTTCTAAACGGGCTTTTTAATTGTAC 57.200 30.769 0.00 0.00 0.00 2.90
333 2012 4.637483 AAAACCCATCTCATATTGTGCG 57.363 40.909 0.00 0.00 0.00 5.34
376 2112 5.326900 CATTGATTCCCACATATCCATCCA 58.673 41.667 0.00 0.00 0.00 3.41
462 2226 9.739276 TCCATCTTGTATGTTAACTCTTCAATT 57.261 29.630 7.22 0.00 0.00 2.32
558 2323 6.852853 CACCATAAATACATGATCTCAAACGC 59.147 38.462 0.00 0.00 0.00 4.84
619 2385 6.455646 CGACCTTCTCCAATGAAGTTAATTCG 60.456 42.308 0.00 0.00 41.17 3.34
644 2410 4.814771 CCAAATAAGTTCAGATACGGGGAC 59.185 45.833 0.00 0.00 0.00 4.46
744 2511 3.481839 CATGTATGGCGCGTAATCATTG 58.518 45.455 8.43 0.00 0.00 2.82
809 2585 7.893302 ACCAATTCATAGTGGATTGAAACCTTA 59.107 33.333 11.58 0.00 42.09 2.69
852 2628 6.482308 CCTTACTTGCGCCTATAAATACACTT 59.518 38.462 4.18 0.00 0.00 3.16
905 2691 5.418840 TGATCACTCTACTGCACACATAAGA 59.581 40.000 0.00 0.00 0.00 2.10
1275 3673 1.307355 TGGTTCGTGCATGATGCTGG 61.307 55.000 19.19 10.20 45.31 4.85
1310 3708 0.176680 GACGTGCAGGTGGATCTCAT 59.823 55.000 18.18 0.00 0.00 2.90
1362 3760 2.938798 TTCGGGTTCCCCATGGCT 60.939 61.111 6.09 0.00 45.83 4.75
1815 4291 8.036575 CAGATTACACAATGGATGGTCAAAAAT 58.963 33.333 0.00 0.00 0.00 1.82
1859 4359 1.269166 AGAAAATAGAGCGACGCACG 58.731 50.000 23.70 0.00 45.66 5.34
1863 4363 2.033793 AATAGAGCGACGCACGTATC 57.966 50.000 23.70 10.33 44.60 2.24
1890 4390 4.916183 TGCCCTTTAAATTGGGGAAATTG 58.084 39.130 13.82 0.00 40.95 2.32
1894 4549 5.641636 CCCTTTAAATTGGGGAAATTGAACG 59.358 40.000 5.26 0.00 42.58 3.95
1903 4558 1.471287 GGAAATTGAACGGTGGCTACC 59.529 52.381 9.66 9.66 43.89 3.18
1917 4572 5.546526 GGTGGCTACCATCAATTTGAAAAA 58.453 37.500 15.42 0.00 46.71 1.94
1918 4573 6.172630 GGTGGCTACCATCAATTTGAAAAAT 58.827 36.000 15.42 0.00 46.71 1.82
1920 4575 7.821846 GGTGGCTACCATCAATTTGAAAAATAA 59.178 33.333 15.42 0.00 46.71 1.40
1921 4576 9.382275 GTGGCTACCATCAATTTGAAAAATAAT 57.618 29.630 2.68 0.00 35.28 1.28
1947 4664 8.756927 TGTGATGGGATTTATTTAGCAAATCAA 58.243 29.630 9.33 1.45 41.92 2.57
2019 4740 2.543777 TGCTAGAAAACTGAAGCCGT 57.456 45.000 0.00 0.00 33.99 5.68
2020 4741 2.143122 TGCTAGAAAACTGAAGCCGTG 58.857 47.619 0.00 0.00 33.99 4.94
2021 4742 1.464997 GCTAGAAAACTGAAGCCGTGG 59.535 52.381 0.00 0.00 0.00 4.94
2040 4795 4.143030 CGTGGTCAGCTAATTTCTTGAGTG 60.143 45.833 0.00 0.00 0.00 3.51
2195 4968 9.630098 ACAATAATGAACAGAAAAATAGCAGTG 57.370 29.630 0.00 0.00 0.00 3.66
2316 5090 3.894947 GCCGGCACCAACAACGTT 61.895 61.111 24.80 0.00 0.00 3.99
2434 5210 5.353123 GTCTGGTGAAGTGACAACAACTTTA 59.647 40.000 0.00 0.00 37.03 1.85
2459 5235 5.128499 AGCTTCAGTAACTGATGACTATGCT 59.872 40.000 0.00 0.00 40.39 3.79
2494 5270 0.106819 CATCCTCCAAGGGAAGCTGG 60.107 60.000 0.00 0.00 39.02 4.85
2625 5401 0.916358 ACCTGCAGCCCTGGTCTAAT 60.916 55.000 8.66 0.00 41.44 1.73
2663 5439 0.525668 GCGATGTTCGTCCTCGTCAT 60.526 55.000 0.00 0.00 42.81 3.06
2898 5681 0.392998 GGAAGATCTCCTGCGGCAAA 60.393 55.000 3.44 0.00 41.61 3.68
3071 5854 0.723981 GTTCTTGCTAGGCTTCTGCG 59.276 55.000 0.00 0.00 40.82 5.18
3432 10310 4.697756 TTTCCCGGCCGTCAGCAG 62.698 66.667 26.12 7.18 46.50 4.24
3676 10839 2.897207 CCTCCGCCGAATGTGGTA 59.103 61.111 0.00 0.00 45.41 3.25
3693 10856 1.134907 GGTACCATGGTCACCGTAGTG 60.135 57.143 23.76 0.00 46.00 2.74
3703 10866 0.810031 CACCGTAGTGTATGGCTGCC 60.810 60.000 12.87 12.87 39.30 4.85
3715 10878 2.429069 GCTGCCGCAACCTTTTCG 60.429 61.111 0.00 0.00 35.78 3.46
3730 10893 2.272230 TTTCGGTGACCAAGGCCACA 62.272 55.000 5.01 0.00 35.13 4.17
3745 10908 2.035626 ACACCAATGGGAAGGCCG 59.964 61.111 3.55 0.00 38.05 6.13
3783 10947 4.523083 GCCAAGGTCATTATGTCAGGTAA 58.477 43.478 0.00 0.00 0.00 2.85
3848 11012 0.746063 ACCACATTGCACCTGTGTTG 59.254 50.000 21.16 12.73 41.93 3.33
3874 11038 7.323420 CAAACAGTAGATTAGATGTCTCCACA 58.677 38.462 0.00 0.00 36.78 4.17
4022 11186 3.753272 ACAATGATCAGAAAGTTGTCCCG 59.247 43.478 0.09 0.00 0.00 5.14
4069 11233 0.179056 AATACATTCCCTGCCGGACG 60.179 55.000 5.05 0.00 41.83 4.79
4070 11234 2.660258 ATACATTCCCTGCCGGACGC 62.660 60.000 5.05 0.00 41.83 5.19
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
17 19 3.001414 GAGGGCCGTCTAAGAAGAAAAC 58.999 50.000 18.26 0.00 32.16 2.43
127 218 6.148948 CCGTTTAGAAAATGAGCAATGTGAA 58.851 36.000 0.00 0.00 0.00 3.18
141 232 8.631797 AGTACAATTAAAAAGCCCGTTTAGAAA 58.368 29.630 0.00 0.00 0.00 2.52
149 240 4.776795 ACCAGTACAATTAAAAAGCCCG 57.223 40.909 0.00 0.00 0.00 6.13
150 241 4.688879 GCAACCAGTACAATTAAAAAGCCC 59.311 41.667 0.00 0.00 0.00 5.19
166 257 3.645884 CTTCCATCAAACAAGCAACCAG 58.354 45.455 0.00 0.00 0.00 4.00
397 2133 1.888018 GGCTGTGCCTACGTGAGTA 59.112 57.895 0.00 0.00 46.69 2.59
415 2151 6.904498 TGGATAATGAAAAACGTTACACTGG 58.096 36.000 0.00 0.00 33.54 4.00
422 2158 9.787532 CATACAAGATGGATAATGAAAAACGTT 57.212 29.630 0.00 0.00 0.00 3.99
462 2226 9.426534 TCTGAGATCTGAATACTATCTTTGGAA 57.573 33.333 0.00 0.00 30.19 3.53
480 2244 8.177119 AGGACTGTATTGATTACTCTGAGATC 57.823 38.462 12.44 5.58 0.00 2.75
619 2385 3.564225 CCCGTATCTGAACTTATTTGGCC 59.436 47.826 0.00 0.00 0.00 5.36
644 2410 4.523813 GGTGCCAAATGTAAATCGTATCG 58.476 43.478 0.00 0.00 0.00 2.92
651 2418 1.931635 ACCGGGTGCCAAATGTAAAT 58.068 45.000 6.32 0.00 0.00 1.40
809 2585 1.296523 AGGAGATGGGGTGAGAGGAAT 59.703 52.381 0.00 0.00 0.00 3.01
873 2654 3.547214 GCAGTAGAGTGATCAGCGAGTAC 60.547 52.174 0.00 0.00 0.00 2.73
905 2691 5.419788 TCCTATCGTTGTATTGTACCACTGT 59.580 40.000 0.00 0.00 0.00 3.55
1215 3570 1.895231 ACATGCATGCATCGCCGAT 60.895 52.632 30.07 5.99 33.90 4.18
1275 3673 0.160392 CGTCGATCGATCAAGCATGC 59.840 55.000 22.50 10.51 42.86 4.06
1310 3708 2.124983 AGTCGTAGTAGCCGCCGA 60.125 61.111 0.00 0.00 0.00 5.54
1362 3760 0.317160 AGAGCATCGTCACCGTGAAA 59.683 50.000 1.88 0.00 42.67 2.69
1467 3873 3.960136 TGCGCCTTGGCCAGGTAA 61.960 61.111 14.60 0.00 46.07 2.85
1788 4244 3.947196 TGACCATCCATTGTGTAATCTGC 59.053 43.478 0.00 0.00 0.00 4.26
1853 4353 0.450184 GGGCAAATTGATACGTGCGT 59.550 50.000 0.00 2.05 37.89 5.24
1863 4363 4.916183 TCCCCAATTTAAAGGGCAAATTG 58.084 39.130 11.68 11.68 46.10 2.32
1884 4384 2.913777 GGTAGCCACCGTTCAATTTC 57.086 50.000 0.00 0.00 34.36 2.17
1894 4549 4.799564 TTTCAAATTGATGGTAGCCACC 57.200 40.909 0.00 0.00 46.00 4.61
1920 4575 8.926374 TGATTTGCTAAATAAATCCCATCACAT 58.074 29.630 0.00 0.00 41.55 3.21
1921 4576 8.303780 TGATTTGCTAAATAAATCCCATCACA 57.696 30.769 0.00 0.00 41.55 3.58
1944 4661 3.680490 TGACCACGGCTTTATGAATTGA 58.320 40.909 0.00 0.00 0.00 2.57
1947 4664 6.650807 CACTATATGACCACGGCTTTATGAAT 59.349 38.462 0.00 0.00 0.00 2.57
2017 4738 3.997021 ACTCAAGAAATTAGCTGACCACG 59.003 43.478 0.00 0.00 0.00 4.94
2019 4740 4.997395 GTCACTCAAGAAATTAGCTGACCA 59.003 41.667 0.00 0.00 0.00 4.02
2020 4741 5.241662 AGTCACTCAAGAAATTAGCTGACC 58.758 41.667 0.00 0.00 0.00 4.02
2021 4742 6.597614 CAAGTCACTCAAGAAATTAGCTGAC 58.402 40.000 0.00 0.00 0.00 3.51
2195 4968 8.628882 ACAAGTTTCAGTATTTGCTTTACAAC 57.371 30.769 0.00 0.00 38.23 3.32
2305 5079 3.213402 CCCGCCAACGTTGTTGGT 61.213 61.111 25.63 0.00 41.53 3.67
2434 5210 5.814705 GCATAGTCATCAGTTACTGAAGCTT 59.185 40.000 19.42 0.00 44.04 3.74
2459 5235 0.179037 GATGAGCTGCAGTATGGCCA 60.179 55.000 16.64 8.56 35.86 5.36
2550 5326 0.943835 CGTCACCATGCTGAACGACA 60.944 55.000 7.00 0.00 0.00 4.35
2625 5401 2.643272 GTCGTGACGTCCTGCAGA 59.357 61.111 17.39 0.00 0.00 4.26
2848 5631 2.106938 GATGGATGGCAGCGACGA 59.893 61.111 0.00 0.00 0.00 4.20
2898 5681 0.251653 TGTGGAAGTACTCGGCTCCT 60.252 55.000 11.68 0.00 0.00 3.69
3071 5854 6.619801 ACTGAAAACAGGAACATCAGTTAC 57.380 37.500 1.13 0.00 46.22 2.50
3432 10310 1.200948 GCTTGGATGCTGGTGTCTTTC 59.799 52.381 0.00 0.00 0.00 2.62
3490 10368 0.744414 CCGGTCTCATCGTTGGCATT 60.744 55.000 0.00 0.00 0.00 3.56
3676 10839 1.927487 TACACTACGGTGACCATGGT 58.073 50.000 19.89 19.89 45.61 3.55
3693 10856 1.595093 AAAGGTTGCGGCAGCCATAC 61.595 55.000 32.83 15.04 44.33 2.39
3715 10878 2.597510 GGTGTGGCCTTGGTCACC 60.598 66.667 20.04 15.44 42.40 4.02
3730 10893 1.606313 CAACGGCCTTCCCATTGGT 60.606 57.895 0.00 0.00 0.00 3.67
3783 10947 3.436470 GGCCCATGAGGTTTATGGTGTAT 60.436 47.826 0.00 0.00 42.85 2.29
3802 10966 1.299976 CACAGGTTACCTCTGGGCC 59.700 63.158 0.00 0.00 36.62 5.80
3848 11012 6.256757 GTGGAGACATCTAATCTACTGTTTGC 59.743 42.308 0.00 0.00 46.14 3.68
3851 11015 7.667575 ATGTGGAGACATCTAATCTACTGTT 57.332 36.000 0.00 0.00 46.14 3.16
3874 11038 7.814264 AGTTCAACTTCTGTCAATTTGAGAT 57.186 32.000 0.00 0.00 0.00 2.75


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

AutoCloner maintained by Alex Coulton.