AutoCloner

Multiple sequence alignment - TraesCS2D01G216000

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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	TraesCS2D01G216000	chr2D	100.000	2666	0	0	1	2666	178852203	178854868	0.000000e+00	4924.0
1	TraesCS2D01G216000	chr2D	98.429	1973	23	6	697	2666	178505381	178507348	0.000000e+00	3465.0
2	TraesCS2D01G216000	chr2D	92.337	1592	76	26	697	2270	178667104	178668667	0.000000e+00	2222.0
3	TraesCS2D01G216000	chr2D	97.153	281	8	0	2386	2666	178668853	178669133	2.400000e-130	475.0
4	TraesCS2D01G216000	chr2D	86.945	383	36	10	1	380	178504811	178505182	4.100000e-113	418.0
5	TraesCS2D01G216000	chr2D	86.305	387	38	11	1	380	178666568	178666946	8.890000e-110	407.0
6	TraesCS2D01G216000	chr2D	91.304	161	14	0	535	695	395623815	395623975	1.240000e-53	220.0
7	TraesCS2D01G216000	chr2D	90.798	163	15	0	534	696	24312359	24312197	4.470000e-53	219.0
8	TraesCS2D01G216000	chr2D	89.172	157	3	2	2260	2402	178668685	178668841	1.630000e-42	183.0
9	TraesCS2D01G216000	chr2D	98.592	71	1	0	2016	2086	178506766	178506696	2.790000e-25	126.0
10	TraesCS2D01G216000	chr2D	84.507	71	6	3	2007	2074	649506139	649506207	6.160000e-07	65.8
11	TraesCS2D01G216000	chr2B	94.948	1841	60	15	836	2666	235050957	235052774	0.000000e+00	2854.0
12	TraesCS2D01G216000	chr2B	93.035	1163	43	12	836	1990	235585077	235586209	0.000000e+00	1664.0
13	TraesCS2D01G216000	chr2B	93.988	682	27	4	1987	2666	235586321	235586990	0.000000e+00	1020.0
14	TraesCS2D01G216000	chr2A	92.444	1747	75	22	947	2666	193547242	193548958	0.000000e+00	2442.0
15	TraesCS2D01G216000	chr2A	89.617	183	17	1	776	956	193546769	193546951	5.740000e-57	231.0
16	TraesCS2D01G216000	chr2A	90.062	161	16	0	536	696	587332684	587332844	2.690000e-50	209.0
17	TraesCS2D01G216000	chr2A	97.500	40	1	0	2016	2055	14947802	14947763	4.760000e-08	69.4
18	TraesCS2D01G216000	chrUn	91.411	163	14	0	533	695	100214676	100214838	9.600000e-55	224.0
19	TraesCS2D01G216000	chr5D	90.303	165	15	1	533	696	67023145	67023309	5.780000e-52	215.0
20	TraesCS2D01G216000	chr1A	90.683	161	15	0	536	696	233421342	233421502	5.780000e-52	215.0
21	TraesCS2D01G216000	chr1A	90.062	161	16	0	536	696	452455087	452455247	2.690000e-50	209.0
22	TraesCS2D01G216000	chr1A	82.558	86	14	1	137	222	58067423	58067339	1.020000e-09	75.0
23	TraesCS2D01G216000	chr5A	88.136	177	18	2	534	710	357053961	357053788	9.670000e-50	207.0
24	TraesCS2D01G216000	chr4B	90.062	161	15	1	536	696	671703069	671702910	9.670000e-50	207.0
25	TraesCS2D01G216000	chr4A	74.747	198	36	13	175	364	627919118	627919309	2.850000e-10	76.8
26	TraesCS2D01G216000	chr3B	83.951	81	12	1	2006	2086	205684167	205684246	2.850000e-10	76.8
27	TraesCS2D01G216000	chr7D	75.497	151	30	5	73	222	611318533	611318677	1.710000e-07	67.6
28	TraesCS2D01G216000	chr7A	76.378	127	24	4	67	191	701382292	701382414	2.220000e-06	63.9
29	TraesCS2D01G216000	chr3D	92.683	41	1	2	188	226	496119203	496119163	1.030000e-04	58.4
30	TraesCS2D01G216000	chr1D	100.000	30	0	0	188	217	74419179	74419208	3.710000e-04	56.5

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	TraesCS2D01G216000	chr2D	178852203	178854868	2665	False	4924.00	4924	100.00000	1	2666	1	chr2D.!!$F1	2665
1	TraesCS2D01G216000	chr2D	178504811	178507348	2537	False	1941.50	3465	92.68700	1	2666	2	chr2D.!!$F4	2665
2	TraesCS2D01G216000	chr2D	178666568	178669133	2565	False	821.75	2222	91.24175	1	2666	4	chr2D.!!$F5	2665
3	TraesCS2D01G216000	chr2B	235050957	235052774	1817	False	2854.00	2854	94.94800	836	2666	1	chr2B.!!$F1	1830
4	TraesCS2D01G216000	chr2B	235585077	235586990	1913	False	1342.00	1664	93.51150	836	2666	2	chr2B.!!$F2	1830
5	TraesCS2D01G216000	chr2A	193546769	193548958	2189	False	1336.50	2442	91.03050	776	2666	2	chr2A.!!$F2	1890

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
274	284	0.950836	TCACACACGCCCTGATTTTG	59.049	50.0	0.0	0.0	0.0	2.44	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2078	2652	1.835494	TACACAAGGACTCTCCCTCG	58.165	55.0	0.0	0.0	37.19	4.63	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
71	76	5.982516	GCGAATATTCATTTATGCACCCAAA	59.017	36.000	15.57	0.00	0.00	3.28
77	82	5.999205	TCATTTATGCACCCAAACTCATT	57.001	34.783	0.00	0.00	0.00	2.57
100	105	9.480053	CATTTGATCTTGGTGAACAGTAAAATT	57.520	29.630	0.00	0.00	0.00	1.82
104	109	9.219603	TGATCTTGGTGAACAGTAAAATTAGAG	57.780	33.333	0.00	0.00	0.00	2.43
186	193	2.365293	GGTCCTTGCCAATTTTCAGTGT	59.635	45.455	0.00	0.00	0.00	3.55
190	197	6.223120	GTCCTTGCCAATTTTCAGTGTATTT	58.777	36.000	0.00	0.00	0.00	1.40
225	232	6.929606	AGTAGCTCTCAGTAAAACAAAATCGT	59.070	34.615	0.00	0.00	0.00	3.73
232	239	8.410141	TCTCAGTAAAACAAAATCGTTCCAAAT	58.590	29.630	0.00	0.00	0.00	2.32
239	246	9.541143	AAAACAAAATCGTTCCAAATAGTTCAT	57.459	25.926	0.00	0.00	0.00	2.57
274	284	0.950836	TCACACACGCCCTGATTTTG	59.049	50.000	0.00	0.00	0.00	2.44
277	287	1.336755	ACACACGCCCTGATTTTGTTC	59.663	47.619	0.00	0.00	0.00	3.18
279	289	2.034558	CACACGCCCTGATTTTGTTCTT	59.965	45.455	0.00	0.00	0.00	2.52
428	438	3.409026	CTGTTTACAGACAGGAGCCTT	57.591	47.619	3.80	0.00	46.59	4.35
483	611	5.705609	ATTTCACCGCTCTTTGTTATTGT	57.294	34.783	0.00	0.00	0.00	2.71
516	644	4.946157	AGATCTGCTCCTTGTTATTGTTGG	59.054	41.667	0.00	0.00	0.00	3.77
520	648	3.826157	TGCTCCTTGTTATTGTTGGGAAG	59.174	43.478	0.00	0.00	0.00	3.46
522	650	4.280929	GCTCCTTGTTATTGTTGGGAAGTT	59.719	41.667	0.00	0.00	0.00	2.66
523	651	5.475564	GCTCCTTGTTATTGTTGGGAAGTTA	59.524	40.000	0.00	0.00	0.00	2.24
524	652	6.152831	GCTCCTTGTTATTGTTGGGAAGTTAT	59.847	38.462	0.00	0.00	0.00	1.89
525	653	7.309805	GCTCCTTGTTATTGTTGGGAAGTTATT	60.310	37.037	0.00	0.00	0.00	1.40
526	654	7.891561	TCCTTGTTATTGTTGGGAAGTTATTG	58.108	34.615	0.00	0.00	0.00	1.90
527	655	7.507616	TCCTTGTTATTGTTGGGAAGTTATTGT	59.492	33.333	0.00	0.00	0.00	2.71
528	656	8.147704	CCTTGTTATTGTTGGGAAGTTATTGTT	58.852	33.333	0.00	0.00	0.00	2.83
529	657	8.879342	TTGTTATTGTTGGGAAGTTATTGTTG	57.121	30.769	0.00	0.00	0.00	3.33
530	658	7.437748	TGTTATTGTTGGGAAGTTATTGTTGG	58.562	34.615	0.00	0.00	0.00	3.77
531	659	4.946478	TTGTTGGGAAGTTATTGTTGGG	57.054	40.909	0.00	0.00	0.00	4.12
532	660	3.235200	TGTTGGGAAGTTATTGTTGGGG	58.765	45.455	0.00	0.00	0.00	4.96
533	661	3.117093	TGTTGGGAAGTTATTGTTGGGGA	60.117	43.478	0.00	0.00	0.00	4.81
534	662	3.449746	TGGGAAGTTATTGTTGGGGAG	57.550	47.619	0.00	0.00	0.00	4.30
535	663	2.719705	TGGGAAGTTATTGTTGGGGAGT	59.280	45.455	0.00	0.00	0.00	3.85
536	664	3.917629	TGGGAAGTTATTGTTGGGGAGTA	59.082	43.478	0.00	0.00	0.00	2.59
537	665	4.263594	TGGGAAGTTATTGTTGGGGAGTAC	60.264	45.833	0.00	0.00	0.00	2.73
538	666	4.018688	GGGAAGTTATTGTTGGGGAGTACT	60.019	45.833	0.00	0.00	0.00	2.73
539	667	5.183969	GGAAGTTATTGTTGGGGAGTACTC	58.816	45.833	14.87	14.87	0.00	2.59
553	681	5.859205	GGAGTACTCCCTCCGTTTATAAA	57.141	43.478	28.87	0.00	43.94	1.40
554	682	6.416631	GGAGTACTCCCTCCGTTTATAAAT	57.583	41.667	28.87	0.00	43.94	1.40
555	683	7.530426	GGAGTACTCCCTCCGTTTATAAATA	57.470	40.000	28.87	0.00	43.94	1.40
556	684	8.131847	GGAGTACTCCCTCCGTTTATAAATAT	57.868	38.462	28.87	0.00	43.94	1.28
557	685	8.591940	GGAGTACTCCCTCCGTTTATAAATATT	58.408	37.037	28.87	0.00	43.94	1.28
558	686	9.993454	GAGTACTCCCTCCGTTTATAAATATTT	57.007	33.333	12.13	5.89	0.00	1.40
608	736	8.565896	AACTACATATGAAGCAAAATGAGTGA	57.434	30.769	10.38	0.00	0.00	3.41
609	737	7.978982	ACTACATATGAAGCAAAATGAGTGAC	58.021	34.615	10.38	0.00	0.00	3.67
610	738	7.826252	ACTACATATGAAGCAAAATGAGTGACT	59.174	33.333	10.38	0.00	0.00	3.41
611	739	7.081526	ACATATGAAGCAAAATGAGTGACTC	57.918	36.000	10.38	5.47	0.00	3.36
612	740	6.883217	ACATATGAAGCAAAATGAGTGACTCT	59.117	34.615	14.42	0.00	0.00	3.24
613	741	8.043113	ACATATGAAGCAAAATGAGTGACTCTA	58.957	33.333	14.42	0.68	0.00	2.43
614	742	6.734104	ATGAAGCAAAATGAGTGACTCTAC	57.266	37.500	14.42	0.00	0.00	2.59
615	743	5.610398	TGAAGCAAAATGAGTGACTCTACA	58.390	37.500	14.42	0.00	0.00	2.74
616	744	5.466728	TGAAGCAAAATGAGTGACTCTACAC	59.533	40.000	14.42	0.00	40.60	2.90
661	789	9.996554	ACATCCGTATATGATACTTCATTTGAA	57.003	29.630	0.00	0.00	42.61	2.69
676	804	9.354673	ACTTCATTTGAAATCTCTAAAAGGACA	57.645	29.630	0.00	0.00	33.07	4.02
694	822	7.625828	AAGGACAAATATTTAGAAACGGAGG	57.374	36.000	0.00	0.00	0.00	4.30
695	823	6.120220	AGGACAAATATTTAGAAACGGAGGG	58.880	40.000	0.00	0.00	0.00	4.30
719	848	2.224967	GGCAAATAGATGGATCAGGCCT	60.225	50.000	0.00	0.00	36.04	5.19
1685	2125	7.906327	AGCTAAGTTTTCAATTCTCTCTCTCT	58.094	34.615	0.00	0.00	0.00	3.10
1686	2126	8.034804	AGCTAAGTTTTCAATTCTCTCTCTCTC	58.965	37.037	0.00	0.00	0.00	3.20
2008	2570	5.443185	AGTAGCGTGTTACAGTCAGTTAA	57.557	39.130	0.00	0.00	0.00	2.01
2078	2652	7.454260	AAATCCAGACACTTATTTTGAGACC	57.546	36.000	0.00	0.00	0.00	3.85

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
71	76	5.380043	ACTGTTCACCAAGATCAAATGAGT	58.620	37.500	0.00	0.00	0.00	3.41
77	82	9.567776	TCTAATTTTACTGTTCACCAAGATCAA	57.432	29.630	0.00	0.00	0.00	2.57
158	165	1.821216	ATTGGCAAGGACCTTACACG	58.179	50.000	6.38	0.00	0.00	4.49
186	193	6.398234	GAGAGCTACTCAGATGTCCAAATA	57.602	41.667	7.93	0.00	44.36	1.40
286	296	2.917933	TGGACATTTGAATAGCCCTCG	58.082	47.619	0.00	0.00	0.00	4.63
290	300	4.165779	CGTGTTTGGACATTTGAATAGCC	58.834	43.478	0.00	0.00	38.23	3.93
299	309	5.401550	CAATATTCAGCGTGTTTGGACATT	58.598	37.500	0.00	0.00	38.23	2.71
401	411	5.106908	GCTCCTGTCTGTAAACAGTGAAATC	60.107	44.000	9.81	0.00	44.22	2.17
406	416	2.037772	AGGCTCCTGTCTGTAAACAGTG	59.962	50.000	9.81	0.00	44.22	3.66
489	617	8.514594	CAACAATAACAAGGAGCAGATCTTAAA	58.485	33.333	0.00	0.00	0.00	1.52
503	631	8.977505	CAACAATAACTTCCCAACAATAACAAG	58.022	33.333	0.00	0.00	0.00	3.16
516	644	5.175388	AGTACTCCCCAACAATAACTTCC	57.825	43.478	0.00	0.00	0.00	3.46
532	660	9.993454	AAATATTTATAAACGGAGGGAGTACTC	57.007	33.333	14.87	14.87	36.76	2.59
582	710	9.665719	TCACTCATTTTGCTTCATATGTAGTTA	57.334	29.630	10.61	0.00	0.00	2.24
583	711	8.454106	GTCACTCATTTTGCTTCATATGTAGTT	58.546	33.333	10.61	0.00	0.00	2.24
584	712	7.826252	AGTCACTCATTTTGCTTCATATGTAGT	59.174	33.333	10.61	0.00	0.00	2.73
585	713	8.206325	AGTCACTCATTTTGCTTCATATGTAG	57.794	34.615	5.04	5.04	0.00	2.74
586	714	8.043113	AGAGTCACTCATTTTGCTTCATATGTA	58.957	33.333	7.77	0.00	32.06	2.29
587	715	6.883217	AGAGTCACTCATTTTGCTTCATATGT	59.117	34.615	7.77	0.00	32.06	2.29
588	716	7.317842	AGAGTCACTCATTTTGCTTCATATG	57.682	36.000	7.77	0.00	32.06	1.78
589	717	8.043113	TGTAGAGTCACTCATTTTGCTTCATAT	58.957	33.333	7.77	0.00	32.06	1.78
590	718	7.331934	GTGTAGAGTCACTCATTTTGCTTCATA	59.668	37.037	7.77	0.00	35.68	2.15
591	719	6.148480	GTGTAGAGTCACTCATTTTGCTTCAT	59.852	38.462	7.77	0.00	35.68	2.57
592	720	5.466728	GTGTAGAGTCACTCATTTTGCTTCA	59.533	40.000	7.77	0.00	35.68	3.02
593	721	5.698545	AGTGTAGAGTCACTCATTTTGCTTC	59.301	40.000	7.77	0.00	44.07	3.86
594	722	5.615289	AGTGTAGAGTCACTCATTTTGCTT	58.385	37.500	7.77	0.00	44.07	3.91
595	723	5.220710	AGTGTAGAGTCACTCATTTTGCT	57.779	39.130	7.77	0.00	44.07	3.91
635	763	9.996554	TTCAAATGAAGTATCATATACGGATGT	57.003	29.630	0.00	0.00	45.60	3.06
650	778	9.354673	TGTCCTTTTAGAGATTTCAAATGAAGT	57.645	29.630	0.00	0.00	35.21	3.01
668	796	8.520351	CCTCCGTTTCTAAATATTTGTCCTTTT	58.480	33.333	11.05	0.00	0.00	2.27
669	797	7.122204	CCCTCCGTTTCTAAATATTTGTCCTTT	59.878	37.037	11.05	0.00	0.00	3.11
670	798	6.602009	CCCTCCGTTTCTAAATATTTGTCCTT	59.398	38.462	11.05	0.00	0.00	3.36
671	799	6.120220	CCCTCCGTTTCTAAATATTTGTCCT	58.880	40.000	11.05	0.00	0.00	3.85
672	800	5.220989	GCCCTCCGTTTCTAAATATTTGTCC	60.221	44.000	11.05	0.00	0.00	4.02
673	801	5.355910	TGCCCTCCGTTTCTAAATATTTGTC	59.644	40.000	11.05	0.00	0.00	3.18
674	802	5.258051	TGCCCTCCGTTTCTAAATATTTGT	58.742	37.500	11.05	0.00	0.00	2.83
675	803	5.221048	CCTGCCCTCCGTTTCTAAATATTTG	60.221	44.000	11.05	1.65	0.00	2.32
676	804	4.887655	CCTGCCCTCCGTTTCTAAATATTT	59.112	41.667	5.89	5.89	0.00	1.40
677	805	4.461198	CCTGCCCTCCGTTTCTAAATATT	58.539	43.478	0.00	0.00	0.00	1.28
678	806	3.747708	GCCTGCCCTCCGTTTCTAAATAT	60.748	47.826	0.00	0.00	0.00	1.28
679	807	2.420967	GCCTGCCCTCCGTTTCTAAATA	60.421	50.000	0.00	0.00	0.00	1.40
680	808	1.682087	GCCTGCCCTCCGTTTCTAAAT	60.682	52.381	0.00	0.00	0.00	1.40
681	809	0.322187	GCCTGCCCTCCGTTTCTAAA	60.322	55.000	0.00	0.00	0.00	1.85
682	810	1.298667	GCCTGCCCTCCGTTTCTAA	59.701	57.895	0.00	0.00	0.00	2.10
683	811	1.485294	TTGCCTGCCCTCCGTTTCTA	61.485	55.000	0.00	0.00	0.00	2.10
684	812	2.351924	TTTGCCTGCCCTCCGTTTCT	62.352	55.000	0.00	0.00	0.00	2.52
685	813	1.250840	ATTTGCCTGCCCTCCGTTTC	61.251	55.000	0.00	0.00	0.00	2.78
686	814	0.039035	TATTTGCCTGCCCTCCGTTT	59.961	50.000	0.00	0.00	0.00	3.60
687	815	0.394352	CTATTTGCCTGCCCTCCGTT	60.394	55.000	0.00	0.00	0.00	4.44
688	816	1.224592	CTATTTGCCTGCCCTCCGT	59.775	57.895	0.00	0.00	0.00	4.69
689	817	0.109342	ATCTATTTGCCTGCCCTCCG	59.891	55.000	0.00	0.00	0.00	4.63
690	818	1.613836	CATCTATTTGCCTGCCCTCC	58.386	55.000	0.00	0.00	0.00	4.30
691	819	1.143684	TCCATCTATTTGCCTGCCCTC	59.856	52.381	0.00	0.00	0.00	4.30
692	820	1.225373	TCCATCTATTTGCCTGCCCT	58.775	50.000	0.00	0.00	0.00	5.19
693	821	2.165998	GATCCATCTATTTGCCTGCCC	58.834	52.381	0.00	0.00	0.00	5.36
694	822	2.818432	CTGATCCATCTATTTGCCTGCC	59.182	50.000	0.00	0.00	0.00	4.85
695	823	2.818432	CCTGATCCATCTATTTGCCTGC	59.182	50.000	0.00	0.00	0.00	4.85
719	848	1.550072	GGGCTGCTGGAATTTTAAGCA	59.450	47.619	0.00	9.45	44.36	3.91
1685	2125	4.769688	ACAATTCGAGGATGCAATAGTGA	58.230	39.130	0.00	0.00	0.00	3.41
1686	2126	5.490139	AACAATTCGAGGATGCAATAGTG	57.510	39.130	0.00	0.00	0.00	2.74
2008	2570	2.747177	TGTGACGGAGGGAGTAATGAT	58.253	47.619	0.00	0.00	0.00	2.45
2078	2652	1.835494	TACACAAGGACTCTCCCTCG	58.165	55.000	0.00	0.00	37.19	4.63

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.