Multiple sequence alignment - TraesCS2A01G208500

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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 TraesCS2A01G208500 chr2A 100.000 3281 0 0 1 3281 190320061 190316781 0.000000e+00 6059.0
1 TraesCS2A01G208500 chr2D 94.737 3230 100 31 1 3187 177462668 177459466 0.000000e+00 4959.0
2 TraesCS2A01G208500 chr2D 86.299 489 51 14 2554 3032 633320460 633320942 4.850000e-143 518.0
3 TraesCS2A01G208500 chr2D 88.593 263 26 4 2553 2814 633322571 633322830 1.900000e-82 316.0
4 TraesCS2A01G208500 chr2D 100.000 59 0 0 3223 3281 177459082 177459024 3.460000e-20 110.0
5 TraesCS2A01G208500 chr2B 97.813 1463 32 0 1022 2484 234369447 234367985 0.000000e+00 2525.0
6 TraesCS2A01G208500 chr2B 91.145 847 70 4 5 849 234371256 234370413 0.000000e+00 1144.0
7 TraesCS2A01G208500 chr2B 89.730 740 47 13 2544 3281 234367971 234367259 0.000000e+00 918.0
8 TraesCS2A01G208500 chr2B 78.302 212 34 8 669 874 234370508 234370303 3.440000e-25 126.0
9 TraesCS2A01G208500 chr2B 94.444 54 3 0 821 874 234369712 234369659 2.100000e-12 84.2
10 TraesCS2A01G208500 chr7A 84.901 404 45 8 2551 2944 341441777 341442174 8.530000e-106 394.0
11 TraesCS2A01G208500 chr7A 89.062 256 22 6 2553 2805 341443366 341443618 2.460000e-81 313.0
12 TraesCS2A01G208500 chr4D 89.961 259 23 3 2553 2810 119237699 119237443 6.790000e-87 331.0
13 TraesCS2A01G208500 chr7D 88.976 254 26 2 2553 2805 312572689 312572941 2.460000e-81 313.0
14 TraesCS2A01G208500 chr4A 88.372 258 28 2 2554 2810 467684647 467684903 3.180000e-80 309.0
15 TraesCS2A01G208500 chr6A 85.897 156 19 2 3120 3273 237740243 237740089 2.620000e-36 163.0


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 TraesCS2A01G208500 chr2A 190316781 190320061 3280 True 6059.00 6059 100.0000 1 3281 1 chr2A.!!$R1 3280
1 TraesCS2A01G208500 chr2D 177459024 177462668 3644 True 2534.50 4959 97.3685 1 3281 2 chr2D.!!$R1 3280
2 TraesCS2A01G208500 chr2D 633320460 633322830 2370 False 417.00 518 87.4460 2553 3032 2 chr2D.!!$F1 479
3 TraesCS2A01G208500 chr2B 234367259 234371256 3997 True 959.44 2525 90.2868 5 3281 5 chr2B.!!$R1 3276
4 TraesCS2A01G208500 chr7A 341441777 341443618 1841 False 353.50 394 86.9815 2551 2944 2 chr7A.!!$F1 393

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
328 331 0.460284 GGACAACGTCGCATGGAGAT 60.46 55.0 0.0 0.0 32.65 2.75 F
1663 2474 0.380378 GGTGCTGTGCGAAAACAAGA 59.62 50.0 0.0 0.0 0.00 3.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2070 2881 0.033011 AGTACTCCTCATCCGCACCT 60.033 55.0 0.0 0.0 0.00 4.00 R
3166 4631 1.644786 GGGTGCAGCCATAACGTCAC 61.645 60.0 29.7 0.0 39.65 3.67 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
27 28 7.596494 CAACCTATCTGTTTGTTGTGATTGAT 58.404 34.615 0.00 0.00 34.76 2.57
78 79 5.393027 GCTTCAACCTTGACTTGAAACTTCA 60.393 40.000 0.00 0.00 37.22 3.02
96 97 3.562567 TCAATGACGACGACACACATA 57.437 42.857 0.00 0.00 0.00 2.29
106 107 3.371965 ACGACACACATAATCTACCCCT 58.628 45.455 0.00 0.00 0.00 4.79
176 177 3.659092 CTCAGGGTGCGCGCAAAA 61.659 61.111 38.24 17.85 0.00 2.44
179 180 3.522731 AGGGTGCGCGCAAAACAA 61.523 55.556 38.24 9.43 0.00 2.83
186 187 2.845530 GCGCAAAACAATGCCACG 59.154 55.556 0.30 0.00 43.47 4.94
191 192 1.336702 GCAAAACAATGCCACGATGGA 60.337 47.619 8.04 0.00 40.96 3.41
231 232 3.369157 GGGTGATTAGGTTAGTTGAGCGT 60.369 47.826 0.00 0.00 0.00 5.07
233 234 3.617263 GTGATTAGGTTAGTTGAGCGTGG 59.383 47.826 0.00 0.00 0.00 4.94
264 265 1.671054 CGGTGAAACACGGCTCCAT 60.671 57.895 0.00 0.00 39.98 3.41
328 331 0.460284 GGACAACGTCGCATGGAGAT 60.460 55.000 0.00 0.00 32.65 2.75
360 363 1.143684 CGGAGGGATGGTTCATGGATT 59.856 52.381 0.00 0.00 0.00 3.01
385 388 2.081725 TGGTACGAATAAGCGCAACA 57.918 45.000 11.47 0.00 33.86 3.33
386 389 2.623535 TGGTACGAATAAGCGCAACAT 58.376 42.857 11.47 0.00 33.86 2.71
389 392 1.635844 ACGAATAAGCGCAACATCGA 58.364 45.000 25.11 0.00 34.62 3.59
398 401 2.004583 CGCAACATCGAAGAAGGGTA 57.995 50.000 0.00 0.00 43.58 3.69
401 404 2.935238 GCAACATCGAAGAAGGGTAGCA 60.935 50.000 0.00 0.00 43.58 3.49
491 494 1.518572 CCACCTACACCGTCGATGC 60.519 63.158 0.00 0.00 0.00 3.91
494 497 1.216977 CCTACACCGTCGATGCCAA 59.783 57.895 0.00 0.00 0.00 4.52
626 629 5.535030 GTCTGAGGGGTAAATGTGTCTTTTT 59.465 40.000 0.00 0.00 0.00 1.94
689 692 8.883731 CGAGAAAGAGATAAAATTTAGAGGCAA 58.116 33.333 0.00 0.00 0.00 4.52
791 794 4.159557 AGGTAGTGCCAAACATGGAAAAT 58.840 39.130 0.00 0.00 40.61 1.82
965 1776 1.618837 GGTTACAGACAGAGCTCCACA 59.381 52.381 10.93 0.00 0.00 4.17
1014 1825 3.289836 CCACATCATGGCCTCACAATTA 58.710 45.455 3.32 0.00 43.24 1.40
1020 1831 3.780294 TCATGGCCTCACAATTACCTACT 59.220 43.478 3.32 0.00 0.00 2.57
1098 1909 2.985456 CCTCCACAGCTCCAGGTC 59.015 66.667 0.00 0.00 0.00 3.85
1108 1919 1.081092 CTCCAGGTCTCCCTCCCAA 59.919 63.158 0.00 0.00 39.89 4.12
1663 2474 0.380378 GGTGCTGTGCGAAAACAAGA 59.620 50.000 0.00 0.00 0.00 3.02
1776 2587 0.892063 TGTATGCACGCTGTGGACTA 59.108 50.000 10.02 1.52 36.59 2.59
2070 2881 5.072055 CCCAATTATCACTGGTGCATCATA 58.928 41.667 0.00 0.00 0.00 2.15
2253 3064 1.364171 CCTGTATCGAGGCTTCCCG 59.636 63.158 0.00 0.00 35.76 5.14
2300 3111 3.194968 TGAGGTAGTAAGGTTGCTACTGC 59.805 47.826 15.00 9.45 43.25 4.40
2418 3229 7.359262 CAATCATGATTGTTTCTTGTGCAAT 57.641 32.000 31.74 0.35 42.32 3.56
2650 3469 5.024785 AGGAAAGAGTCGAGTCAGTTTTT 57.975 39.130 21.89 13.01 0.00 1.94
2666 3485 3.808174 AGTTTTTGAGACCGTGTTAGAGC 59.192 43.478 0.00 0.00 0.00 4.09
2911 3738 1.738099 CCTTCACGCTCCAACGAGG 60.738 63.158 0.00 0.00 36.55 4.63
2932 3759 2.680352 GGACCAGGTGCTCCTCGA 60.680 66.667 3.81 0.00 43.07 4.04
2998 3846 0.918983 CTGCCCCCACCTTCAGATAA 59.081 55.000 0.00 0.00 0.00 1.75
3034 3882 2.124983 CCATGACGCCACCTCTGG 60.125 66.667 0.00 0.00 41.13 3.86
3166 4631 1.501741 CACCTGCCAACCGATTTCG 59.498 57.895 0.00 0.00 39.44 3.46
3169 4636 0.953471 CCTGCCAACCGATTTCGTGA 60.953 55.000 0.00 0.00 37.74 4.35
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 7.231317 ACATCAATCACAACAAACAGATAGGTT 59.769 33.333 0.00 0.00 0.00 3.50
78 79 4.744570 AGATTATGTGTGTCGTCGTCATT 58.255 39.130 0.00 0.00 0.00 2.57
96 97 1.338136 CCGTCAGCCAGGGGTAGATT 61.338 60.000 0.00 0.00 0.00 2.40
176 177 0.034186 ACCATCCATCGTGGCATTGT 60.034 50.000 0.00 0.00 40.49 2.71
179 180 0.749091 CACACCATCCATCGTGGCAT 60.749 55.000 0.00 0.00 40.49 4.40
186 187 1.524621 CCGCCTCACACCATCCATC 60.525 63.158 0.00 0.00 0.00 3.51
191 192 3.785859 ATCGCCGCCTCACACCAT 61.786 61.111 0.00 0.00 0.00 3.55
231 232 2.751036 CCGTGTCATGCCATGCCA 60.751 61.111 0.00 0.00 0.00 4.92
233 234 1.585267 TTCACCGTGTCATGCCATGC 61.585 55.000 0.00 0.00 0.00 4.06
247 248 0.889186 ACATGGAGCCGTGTTTCACC 60.889 55.000 8.54 0.00 42.86 4.02
264 265 1.152798 TGGTGCACCATGCTCAACA 60.153 52.632 34.74 8.74 45.31 3.33
328 331 1.302431 CCCTCCGTGTGCAATGTCA 60.302 57.895 0.00 0.00 0.00 3.58
385 388 1.568504 TGGTGCTACCCTTCTTCGAT 58.431 50.000 3.33 0.00 37.50 3.59
386 389 1.001633 GTTGGTGCTACCCTTCTTCGA 59.998 52.381 3.33 0.00 37.50 3.71
389 392 3.008049 CACTAGTTGGTGCTACCCTTCTT 59.992 47.826 0.00 0.00 37.50 2.52
573 576 9.740239 CTTTTGAGACATGGTTGAATATATTGG 57.260 33.333 1.78 0.00 0.00 3.16
637 640 9.066892 GCAACTTCCATCCATTTAGTCATTATA 57.933 33.333 0.00 0.00 0.00 0.98
644 647 3.941483 CTCGCAACTTCCATCCATTTAGT 59.059 43.478 0.00 0.00 0.00 2.24
828 916 5.130705 AGAATTCCTCCCTATTTGGTTCC 57.869 43.478 0.65 0.00 0.00 3.62
908 1026 1.502640 GACTGTCTCTCGGGTGTCG 59.497 63.158 0.00 0.00 40.90 4.35
949 1711 0.394565 GGTTGTGGAGCTCTGTCTGT 59.605 55.000 14.64 0.00 0.00 3.41
960 1722 3.931247 CCGACGGTGGGTTGTGGA 61.931 66.667 5.48 0.00 0.00 4.02
1003 1814 2.822764 CGGAGTAGGTAATTGTGAGGC 58.177 52.381 0.00 0.00 0.00 4.70
1004 1815 2.483188 GGCGGAGTAGGTAATTGTGAGG 60.483 54.545 0.00 0.00 0.00 3.86
1098 1909 2.037772 CAGGATATCGTTTGGGAGGGAG 59.962 54.545 0.00 0.00 0.00 4.30
1108 1919 3.076785 AGGATCTCCTCCAGGATATCGTT 59.923 47.826 12.55 3.94 44.77 3.85
1663 2474 5.642919 GTGAAGAGAAGATGAAGACAGCAAT 59.357 40.000 0.00 0.00 34.60 3.56
1776 2587 1.525765 TGCATAATGGCGCCGATGT 60.526 52.632 26.97 14.31 36.28 3.06
2070 2881 0.033011 AGTACTCCTCATCCGCACCT 60.033 55.000 0.00 0.00 0.00 4.00
2253 3064 2.099756 GCTTGGTGGAGACAATAATGGC 59.900 50.000 0.00 0.00 46.06 4.40
2418 3229 6.650427 TCAGTCTTCAGAACAGCTAGTTTA 57.350 37.500 3.56 0.00 41.51 2.01
2650 3469 2.235891 TCAAGCTCTAACACGGTCTCA 58.764 47.619 0.00 0.00 0.00 3.27
2666 3485 6.090898 CCAACAAGTCGGTAACTCTATTCAAG 59.909 42.308 0.00 0.00 37.17 3.02
2945 3772 2.428569 TCGAGTGTCGTCAAGCGC 60.429 61.111 0.00 0.00 41.35 5.92
3166 4631 1.644786 GGGTGCAGCCATAACGTCAC 61.645 60.000 29.70 0.00 39.65 3.67
3169 4636 2.045340 GGGGTGCAGCCATAACGT 60.045 61.111 34.28 0.00 39.65 3.99
3214 4681 2.285368 AAGGGAGGTGATGGGCGA 60.285 61.111 0.00 0.00 0.00 5.54


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

AutoCloner maintained by Alex Coulton.