Multiple sequence alignment - TraesCS2A01G284500

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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 TraesCS2A01G284500 chr2A 100.000 4683 0 0 1 4683 477104900 477109582 0.000000e+00 8648.0
1 TraesCS2A01G284500 chr2D 94.118 4743 149 51 1 4679 356722556 356727232 0.000000e+00 7094.0
2 TraesCS2A01G284500 chr2B 94.383 4451 142 45 1 4394 424477956 424482355 0.000000e+00 6735.0
3 TraesCS2A01G284500 chr2B 82.712 295 24 11 4393 4683 424482459 424482730 2.180000e-58 237.0
4 TraesCS2A01G284500 chr6B 100.000 38 0 0 3645 3682 583443664 583443627 2.340000e-08 71.3


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 TraesCS2A01G284500 chr2A 477104900 477109582 4682 False 8648 8648 100.0000 1 4683 1 chr2A.!!$F1 4682
1 TraesCS2A01G284500 chr2D 356722556 356727232 4676 False 7094 7094 94.1180 1 4679 1 chr2D.!!$F1 4678
2 TraesCS2A01G284500 chr2B 424477956 424482730 4774 False 3486 6735 88.5475 1 4683 2 chr2B.!!$F1 4682

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
666 684 0.319297 GACACGTCACCTGGTGTACC 60.319 60.0 25.15 13.74 46.64 3.34 F
1743 1811 0.038166 TGATGTGGTTGGCTTCCTCC 59.962 55.0 0.00 0.00 0.00 4.30 F
2105 2181 0.038744 CCTTGAGGCCACATGTCCTT 59.961 55.0 5.01 0.00 31.71 3.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2304 2380 0.179020 CCTTGTGTGCCTTGGAGTCA 60.179 55.000 0.0 0.0 0.0 3.41 R
3220 3303 1.070786 GCCCTTCACCGTCACTTCA 59.929 57.895 0.0 0.0 0.0 3.02 R
4104 4189 0.260523 ATTCATTTACCCCACCCCGG 59.739 55.000 0.0 0.0 0.0 5.73 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
24 25 1.906253 AGCCATGCTCTCCTGTCTG 59.094 57.895 0.00 0.00 30.62 3.51
34 35 0.531657 CTCCTGTCTGTGAGCTGGAG 59.468 60.000 0.00 0.00 41.87 3.86
39 40 3.470709 CTGTCTGTGAGCTGGAGAAAAA 58.529 45.455 0.00 0.00 0.00 1.94
74 75 7.011109 GCTCTAAATGCCGATTAGTAACTGAAA 59.989 37.037 0.00 0.00 33.17 2.69
78 79 8.687824 AAATGCCGATTAGTAACTGAAAAATG 57.312 30.769 0.00 0.00 0.00 2.32
87 88 6.670695 AGTAACTGAAAAATGGCTTGGAAT 57.329 33.333 0.00 0.00 0.00 3.01
88 89 7.066307 AGTAACTGAAAAATGGCTTGGAATT 57.934 32.000 0.00 0.00 0.00 2.17
114 115 3.562141 TGCGGATTTCGTTTTCTTGAGAA 59.438 39.130 0.00 0.00 41.72 2.87
229 232 8.498054 TGTCTCTGAGCTGGAAAAATAAATAG 57.502 34.615 0.00 0.00 0.00 1.73
282 288 8.962884 AAAACTTGGATGCTTTTGTAGATTTT 57.037 26.923 0.00 0.00 0.00 1.82
361 369 7.346175 TCATACTAGTTGGTTAGCCCTTAATCA 59.654 37.037 0.00 0.00 30.51 2.57
364 372 5.514500 AGTTGGTTAGCCCTTAATCAAGA 57.486 39.130 0.00 0.00 41.73 3.02
389 397 7.921786 ACCCCAAAGAAAAGAAAAGAAAAAG 57.078 32.000 0.00 0.00 0.00 2.27
666 684 0.319297 GACACGTCACCTGGTGTACC 60.319 60.000 25.15 13.74 46.64 3.34
682 700 5.045872 GGTGTACCAGAATGTTCGTATACC 58.954 45.833 0.00 9.30 35.64 2.73
711 729 1.405105 CCCAAATACAATGTGCTCCGG 59.595 52.381 0.00 0.00 0.00 5.14
712 730 1.405105 CCAAATACAATGTGCTCCGGG 59.595 52.381 0.00 0.00 0.00 5.73
973 998 1.672356 CCAACGCCACCAGAGAAGG 60.672 63.158 0.00 0.00 0.00 3.46
974 999 1.672356 CAACGCCACCAGAGAAGGG 60.672 63.158 0.00 0.00 0.00 3.95
976 1001 4.785453 CGCCACCAGAGAAGGGGC 62.785 72.222 0.00 0.00 39.91 5.80
977 1002 3.650950 GCCACCAGAGAAGGGGCA 61.651 66.667 0.00 0.00 41.71 5.36
978 1003 2.673523 CCACCAGAGAAGGGGCAG 59.326 66.667 0.00 0.00 0.00 4.85
979 1004 1.920325 CCACCAGAGAAGGGGCAGA 60.920 63.158 0.00 0.00 0.00 4.26
981 1006 1.614824 ACCAGAGAAGGGGCAGAGG 60.615 63.158 0.00 0.00 0.00 3.69
982 1007 1.306482 CCAGAGAAGGGGCAGAGGA 60.306 63.158 0.00 0.00 0.00 3.71
983 1008 1.621672 CCAGAGAAGGGGCAGAGGAC 61.622 65.000 0.00 0.00 0.00 3.85
1026 1065 1.549170 GAGGTAAGGAAGGACGCTTGA 59.451 52.381 0.00 0.00 0.00 3.02
1035 1074 0.607489 AGGACGCTTGATTGCTTGCT 60.607 50.000 0.00 0.00 0.00 3.91
1105 1150 3.748568 GGTTGAATCTTGACTGACTGACC 59.251 47.826 0.00 0.00 0.00 4.02
1110 1155 1.004277 CTTGACTGACTGACCGACGC 61.004 60.000 0.00 0.00 0.00 5.19
1111 1156 2.126424 GACTGACTGACCGACGCC 60.126 66.667 0.00 0.00 0.00 5.68
1210 1270 1.383803 CAAGGAGGGGGAGGAGGAG 60.384 68.421 0.00 0.00 0.00 3.69
1441 1501 5.645497 TCTCTAATTTCCTCTGCTTTGCTTC 59.355 40.000 0.00 0.00 0.00 3.86
1578 1639 4.134546 CGAGTTCGTTCGACATTTTCTTG 58.865 43.478 0.00 0.00 43.03 3.02
1603 1671 0.320421 TGTTCTTAGGGAGTGCGTGC 60.320 55.000 0.00 0.00 0.00 5.34
1743 1811 0.038166 TGATGTGGTTGGCTTCCTCC 59.962 55.000 0.00 0.00 0.00 4.30
1823 1894 4.883585 TGTTTTTCTCTGTGCTGTTCTGAT 59.116 37.500 0.00 0.00 0.00 2.90
1881 1952 4.469586 TGCAATTCATAGTGGACTAGGTCA 59.530 41.667 0.00 0.00 33.68 4.02
1882 1953 5.053145 GCAATTCATAGTGGACTAGGTCAG 58.947 45.833 0.00 0.00 33.68 3.51
1883 1954 5.395768 GCAATTCATAGTGGACTAGGTCAGT 60.396 44.000 0.00 0.00 41.47 3.41
1884 1955 6.183360 GCAATTCATAGTGGACTAGGTCAGTA 60.183 42.308 0.00 0.00 37.72 2.74
1993 2068 4.526770 TCATGAGCCGCACATGAG 57.473 55.556 24.30 5.74 45.71 2.90
2026 2101 6.713762 TGATTAATTGTGATGGGAATGACC 57.286 37.500 0.00 0.00 38.08 4.02
2105 2181 0.038744 CCTTGAGGCCACATGTCCTT 59.961 55.000 5.01 0.00 31.71 3.36
2123 2199 8.514594 CATGTCCTTAAAAGTTAAGCTGATTCA 58.485 33.333 0.00 0.00 0.00 2.57
2124 2200 7.871853 TGTCCTTAAAAGTTAAGCTGATTCAC 58.128 34.615 0.00 0.00 0.00 3.18
2304 2380 0.824759 GGGTAGAGGACGTCATTGCT 59.175 55.000 18.91 7.29 0.00 3.91
2346 2422 2.587522 GTTGTGAAGGGAAAGAAGGCT 58.412 47.619 0.00 0.00 0.00 4.58
2602 2678 5.750067 GCAAAACTGACTGAATGATGTTTGT 59.250 36.000 0.00 0.00 0.00 2.83
2712 2788 0.963355 TGAAAGGTGCGTAATGGGCC 60.963 55.000 0.00 0.00 0.00 5.80
2776 2852 6.376978 GTCATTTTCATCAGGACAGAAACAG 58.623 40.000 0.00 0.00 31.60 3.16
2794 2870 5.379706 AACAGCTATGGCCTTTCTCTTAT 57.620 39.130 3.32 0.00 39.73 1.73
3053 3129 6.153942 TCACCTACCTGTCTGGCTATATAT 57.846 41.667 0.00 0.00 40.22 0.86
3220 3303 2.286523 CCCAGACCTGAAGGCGTCT 61.287 63.158 1.41 0.00 39.96 4.18
3262 3345 1.130054 TTGAGGAGGTCAAGCTGGCT 61.130 55.000 0.00 0.00 40.45 4.75
3952 4037 7.923878 TGTAGATTTTTCTTTTTGCCTTGTACC 59.076 33.333 0.00 0.00 0.00 3.34
4096 4181 2.432874 TCGTGAAAGGGAGAAGTCACAA 59.567 45.455 3.81 0.00 40.32 3.33
4101 4186 0.842467 AGGGAGAAGTCACAAGGGGG 60.842 60.000 0.00 0.00 0.00 5.40
4102 4187 1.134438 GGGAGAAGTCACAAGGGGGT 61.134 60.000 0.00 0.00 0.00 4.95
4103 4188 0.036875 GGAGAAGTCACAAGGGGGTG 59.963 60.000 0.00 0.00 40.16 4.61
4104 4189 0.606673 GAGAAGTCACAAGGGGGTGC 60.607 60.000 0.00 0.00 38.66 5.01
4105 4190 1.603739 GAAGTCACAAGGGGGTGCC 60.604 63.158 0.00 0.00 38.66 5.01
4118 4203 3.969119 GTGCCGGGGTGGGGTAAA 61.969 66.667 2.18 0.00 38.63 2.01
4119 4204 2.942143 TGCCGGGGTGGGGTAAAT 60.942 61.111 2.18 0.00 38.63 1.40
4120 4205 2.441348 GCCGGGGTGGGGTAAATG 60.441 66.667 2.18 0.00 38.63 2.32
4444 4635 3.637229 CCTGCGATTCCTTTCTACTCCTA 59.363 47.826 0.00 0.00 0.00 2.94
4445 4636 4.500035 CCTGCGATTCCTTTCTACTCCTAC 60.500 50.000 0.00 0.00 0.00 3.18
4446 4637 3.383825 TGCGATTCCTTTCTACTCCTACC 59.616 47.826 0.00 0.00 0.00 3.18
4447 4638 3.550436 GCGATTCCTTTCTACTCCTACCG 60.550 52.174 0.00 0.00 0.00 4.02
4448 4639 3.631227 CGATTCCTTTCTACTCCTACCGT 59.369 47.826 0.00 0.00 0.00 4.83
4449 4640 4.818546 CGATTCCTTTCTACTCCTACCGTA 59.181 45.833 0.00 0.00 0.00 4.02
4463 4654 2.025418 CCGTACCGTGTGGCTTGTC 61.025 63.158 0.00 0.00 39.70 3.18
4468 4659 0.321298 ACCGTGTGGCTTGTCATACC 60.321 55.000 0.00 0.00 39.70 2.73
4517 4709 4.049869 TGCGAAAAATTTCCGTAAAACCC 58.950 39.130 12.47 0.00 33.68 4.11
4522 4714 6.867293 CGAAAAATTTCCGTAAAACCCCAATA 59.133 34.615 0.00 0.00 33.68 1.90
4580 4784 0.681175 ACATGGGGCTGTTTGAAAGC 59.319 50.000 0.00 0.00 40.06 3.51
4622 4830 9.661563 ATTGAATTTCATGCATCAGTTTTGTAT 57.338 25.926 0.00 0.00 0.00 2.29
4624 4832 9.571810 TGAATTTCATGCATCAGTTTTGTATAC 57.428 29.630 0.00 0.00 0.00 1.47
4675 4883 8.757982 AATGTAAAATGCTTCTACCATCATCT 57.242 30.769 0.00 0.00 0.00 2.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
88 89 5.103000 TCAAGAAAACGAAATCCGCAAAAA 58.897 33.333 0.00 0.00 43.32 1.94
178 181 2.404186 ATGGCTCGTGCATGCACAG 61.404 57.895 40.95 34.80 46.47 3.66
304 312 9.468532 GCAGAAGTTTATTCTCAAAGAACAAAT 57.531 29.630 0.00 0.00 33.76 2.32
327 335 6.201806 GCTAACCAACTAGTATGAATCAGCAG 59.798 42.308 0.00 0.00 0.00 4.24
361 369 6.867519 TCTTTTCTTTTCTTTGGGGTTCTT 57.132 33.333 0.00 0.00 0.00 2.52
364 372 8.160765 TCTTTTTCTTTTCTTTTCTTTGGGGTT 58.839 29.630 0.00 0.00 0.00 4.11
389 397 2.044135 CTCAAAGCGGCTTTCGTTTTC 58.956 47.619 24.19 0.00 46.53 2.29
394 402 1.130613 CGTCTCAAAGCGGCTTTCG 59.869 57.895 24.19 19.75 42.76 3.46
578 596 1.948145 CGGCCGAGATCTGTAGTTAGT 59.052 52.381 24.07 0.00 0.00 2.24
579 597 1.948145 ACGGCCGAGATCTGTAGTTAG 59.052 52.381 35.90 0.00 0.00 2.34
580 598 1.945394 GACGGCCGAGATCTGTAGTTA 59.055 52.381 35.90 0.00 0.00 2.24
581 599 0.739561 GACGGCCGAGATCTGTAGTT 59.260 55.000 35.90 3.54 0.00 2.24
646 664 0.662374 GTACACCAGGTGACGTGTCG 60.662 60.000 27.39 0.00 42.14 4.35
666 684 4.621991 CCAGGAGGTATACGAACATTCTG 58.378 47.826 0.00 0.00 0.00 3.02
682 700 2.214376 TTGTATTTGGGTGCCAGGAG 57.786 50.000 0.00 0.00 33.81 3.69
845 863 1.520787 CTTAAGTAGCGGGTGGGCG 60.521 63.158 0.00 0.00 38.18 6.13
973 998 3.086600 CCCTCCTGTCCTCTGCCC 61.087 72.222 0.00 0.00 0.00 5.36
974 999 2.039624 TCCCTCCTGTCCTCTGCC 59.960 66.667 0.00 0.00 0.00 4.85
976 1001 2.716017 GCGTCCCTCCTGTCCTCTG 61.716 68.421 0.00 0.00 0.00 3.35
977 1002 2.363147 GCGTCCCTCCTGTCCTCT 60.363 66.667 0.00 0.00 0.00 3.69
978 1003 3.827898 CGCGTCCCTCCTGTCCTC 61.828 72.222 0.00 0.00 0.00 3.71
1005 1044 1.275291 CAAGCGTCCTTCCTTACCTCA 59.725 52.381 0.00 0.00 0.00 3.86
1026 1065 0.529378 GTAGCAGGCAAGCAAGCAAT 59.471 50.000 9.92 0.00 36.85 3.56
1210 1270 1.578206 GCTTGTCGTCCTTGGGCTTC 61.578 60.000 0.00 0.00 0.00 3.86
1441 1501 0.454600 AATCCTGATGCAGCAAAGCG 59.545 50.000 5.96 0.00 37.31 4.68
1549 1610 3.044986 TGTCGAACGAACTCGGTAAAAG 58.955 45.455 3.88 0.00 40.66 2.27
1578 1639 0.896226 ACTCCCTAAGAACACTCGCC 59.104 55.000 0.00 0.00 0.00 5.54
1603 1671 5.784750 TTCGTGAATCAAGATGCACTAAG 57.215 39.130 16.89 4.44 43.67 2.18
1823 1894 9.747898 AACCTTACAATATCACTTAATTGGACA 57.252 29.630 0.00 0.00 37.40 4.02
1881 1952 4.921644 TTAAAAGCTTAGCCCACCTACT 57.078 40.909 0.00 0.00 0.00 2.57
1882 1953 7.634671 TTATTTAAAAGCTTAGCCCACCTAC 57.365 36.000 0.00 0.00 0.00 3.18
1883 1954 7.670559 TGTTTATTTAAAAGCTTAGCCCACCTA 59.329 33.333 0.00 0.00 0.00 3.08
1884 1955 6.495526 TGTTTATTTAAAAGCTTAGCCCACCT 59.504 34.615 0.00 0.00 0.00 4.00
1958 2033 7.256475 GGCTCATGAGAAAGGAGGATCTTATTA 60.256 40.741 27.04 0.00 37.18 0.98
1993 2068 5.957842 TCACAATTAATCAACCACCAGAC 57.042 39.130 0.00 0.00 0.00 3.51
2099 2175 7.040686 GGTGAATCAGCTTAACTTTTAAGGACA 60.041 37.037 5.04 0.00 0.00 4.02
2105 2181 8.402798 TGATTGGTGAATCAGCTTAACTTTTA 57.597 30.769 13.84 0.00 42.56 1.52
2123 2199 5.121380 AGCAGTATTTGGAGATGATTGGT 57.879 39.130 0.00 0.00 0.00 3.67
2124 2200 5.128205 TGAGCAGTATTTGGAGATGATTGG 58.872 41.667 0.00 0.00 0.00 3.16
2188 2264 8.422577 ACTTTAATTTTCCCTTGATAGCAACT 57.577 30.769 0.00 0.00 0.00 3.16
2304 2380 0.179020 CCTTGTGTGCCTTGGAGTCA 60.179 55.000 0.00 0.00 0.00 3.41
2443 2519 2.765699 CCTCCTTCTTCTCCTCTTCCTG 59.234 54.545 0.00 0.00 0.00 3.86
2602 2678 2.955660 AGATCACCGTTGGCTTCAAAAA 59.044 40.909 0.00 0.00 31.46 1.94
2776 2852 9.508642 AAATACTAATAAGAGAAAGGCCATAGC 57.491 33.333 5.01 0.00 38.76 2.97
3053 3129 6.406370 ACGATCCAGATTAATCTTGTCACAA 58.594 36.000 15.49 0.00 34.22 3.33
3098 3174 6.862209 AGGATGATCTATCTAGCGTGATTTC 58.138 40.000 0.00 0.00 36.03 2.17
3106 3182 4.199310 AGCTCGAGGATGATCTATCTAGC 58.801 47.826 15.58 13.03 36.03 3.42
3220 3303 1.070786 GCCCTTCACCGTCACTTCA 59.929 57.895 0.00 0.00 0.00 3.02
3262 3345 2.307309 GCGCTTGTGCACGTACTCA 61.307 57.895 13.13 0.00 39.64 3.41
3433 3516 2.230025 CTCCTCTTTCTTCTCGTCTGCA 59.770 50.000 0.00 0.00 0.00 4.41
4076 4161 2.526304 TGTGACTTCTCCCTTTCACG 57.474 50.000 0.00 0.00 41.11 4.35
4101 4186 3.291031 ATTTACCCCACCCCGGCAC 62.291 63.158 0.00 0.00 0.00 5.01
4102 4187 2.942143 ATTTACCCCACCCCGGCA 60.942 61.111 0.00 0.00 0.00 5.69
4103 4188 2.441348 CATTTACCCCACCCCGGC 60.441 66.667 0.00 0.00 0.00 6.13
4104 4189 0.260523 ATTCATTTACCCCACCCCGG 59.739 55.000 0.00 0.00 0.00 5.73
4105 4190 1.064314 TCATTCATTTACCCCACCCCG 60.064 52.381 0.00 0.00 0.00 5.73
4117 4202 5.825679 CCATTGCCATTCCATTTCATTCATT 59.174 36.000 0.00 0.00 0.00 2.57
4118 4203 5.104277 ACCATTGCCATTCCATTTCATTCAT 60.104 36.000 0.00 0.00 0.00 2.57
4119 4204 4.225492 ACCATTGCCATTCCATTTCATTCA 59.775 37.500 0.00 0.00 0.00 2.57
4120 4205 4.573201 CACCATTGCCATTCCATTTCATTC 59.427 41.667 0.00 0.00 0.00 2.67
4354 4440 5.565439 GCAAGCAACCTCAAGTCACATAATT 60.565 40.000 0.00 0.00 0.00 1.40
4358 4444 1.610522 GCAAGCAACCTCAAGTCACAT 59.389 47.619 0.00 0.00 0.00 3.21
4447 4638 1.997606 GTATGACAAGCCACACGGTAC 59.002 52.381 0.00 0.00 33.28 3.34
4448 4639 1.066716 GGTATGACAAGCCACACGGTA 60.067 52.381 0.00 0.00 33.28 4.02
4449 4640 0.321298 GGTATGACAAGCCACACGGT 60.321 55.000 0.00 0.00 33.28 4.83
4490 4681 8.274248 GGTTTTACGGAAATTTTTCGCATTAAA 58.726 29.630 9.73 5.17 38.06 1.52
4546 4738 9.600432 ACAGCCCCATGTATTATTATTATTGTT 57.400 29.630 0.00 0.00 0.00 2.83
4552 4744 8.546083 TTCAAACAGCCCCATGTATTATTATT 57.454 30.769 0.00 0.00 31.70 1.40
4555 4747 6.630188 GCTTTCAAACAGCCCCATGTATTATT 60.630 38.462 0.00 0.00 31.70 1.40
4558 4762 3.055891 GCTTTCAAACAGCCCCATGTATT 60.056 43.478 0.00 0.00 31.70 1.89
4564 4768 1.144913 AGTAGCTTTCAAACAGCCCCA 59.855 47.619 0.00 0.00 38.09 4.96
4568 4772 5.532025 AATACGAGTAGCTTTCAAACAGC 57.468 39.130 0.00 0.00 37.56 4.40
4604 4812 9.612066 TGAATAGTATACAAAACTGATGCATGA 57.388 29.630 2.46 0.00 0.00 3.07
4622 4830 9.290988 TGAAACAATTGCCTACTTTGAATAGTA 57.709 29.630 5.05 0.00 0.00 1.82
4624 4832 9.474920 TTTGAAACAATTGCCTACTTTGAATAG 57.525 29.630 5.05 0.00 0.00 1.73
4659 4867 6.798427 AGTCTAAAGATGATGGTAGAAGCA 57.202 37.500 0.00 0.00 0.00 3.91


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

AutoCloner maintained by Alex Coulton.