AutoCloner

Multiple sequence alignment - TraesCS2A01G253300

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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	TraesCS2A01G253300	chr2A	100.000	3347	0	0	1	3347	385331323	385334669	0.000000e+00	6181.0
1	TraesCS2A01G253300	chr6A	96.495	2254	71	6	1097	3347	536549445	536551693	0.000000e+00	3718.0
2	TraesCS2A01G253300	chr6A	96.186	2255	79	6	1097	3347	239129240	239126989	0.000000e+00	3681.0
3	TraesCS2A01G253300	chr6A	90.469	640	51	10	1	632	578543746	578543109	0.000000e+00	835.0
4	TraesCS2A01G253300	chr6A	91.017	590	47	4	678	1265	536548984	536549569	0.000000e+00	791.0
5	TraesCS2A01G253300	chr6A	89.316	599	59	3	674	1271	239129704	239129110	0.000000e+00	747.0
6	TraesCS2A01G253300	chr3B	94.787	2302	77	15	1074	3347	59952170	59954456	0.000000e+00	3546.0
7	TraesCS2A01G253300	chr3B	90.837	633	50	7	7	635	598911497	598910869	0.000000e+00	841.0
8	TraesCS2A01G253300	chr3B	89.623	636	62	4	1	632	770106364	770106999	0.000000e+00	806.0
9	TraesCS2A01G253300	chr3B	88.215	594	54	6	679	1271	59951705	59952283	0.000000e+00	695.0
10	TraesCS2A01G253300	chr3B	91.964	112	9	0	679	790	395708962	395708851	1.240000e-34	158.0
11	TraesCS2A01G253300	chr2B	95.112	2271	71	10	1097	3347	178681385	178679135	0.000000e+00	3542.0
12	TraesCS2A01G253300	chr2B	94.109	696	20	11	1599	2275	753017274	753016581	0.000000e+00	1038.0
13	TraesCS2A01G253300	chr2B	87.395	595	52	9	678	1271	178681917	178681345	0.000000e+00	662.0
14	TraesCS2A01G253300	chr2B	85.405	370	42	5	864	1232	753031319	753030961	1.130000e-99	374.0
15	TraesCS2A01G253300	chr2B	94.928	138	5	1	1473	1610	753025361	753025226	7.270000e-52	215.0
16	TraesCS2A01G253300	chr2B	96.809	94	3	0	1382	1475	753030953	753030860	1.240000e-34	158.0
17	TraesCS2A01G253300	chr2B	85.106	141	15	3	678	818	36506336	36506202	4.500000e-29	139.0
18	TraesCS2A01G253300	chr5B	94.806	2272	78	10	1097	3347	486023736	486021484	0.000000e+00	3506.0
19	TraesCS2A01G253300	chr5B	89.796	637	56	9	1	632	427963926	427963294	0.000000e+00	808.0
20	TraesCS2A01G253300	chr5B	88.033	610	51	8	662	1270	486024285	486023697	0.000000e+00	702.0
21	TraesCS2A01G253300	chr1B	93.027	2108	74	22	1047	3103	114483849	114481764	0.000000e+00	3011.0
22	TraesCS2A01G253300	chr1B	93.640	456	28	1	679	1134	114484284	114483830	0.000000e+00	680.0
23	TraesCS2A01G253300	chr1B	96.761	247	8	0	3101	3347	114472755	114472509	2.400000e-111	412.0
24	TraesCS2A01G253300	chr3D	95.432	1795	57	7	1097	2871	453236921	453235132	0.000000e+00	2837.0
25	TraesCS2A01G253300	chr3D	86.408	412	38	8	862	1271	453237234	453236839	5.130000e-118	435.0
26	TraesCS2A01G253300	chr1D	95.844	1540	55	5	1811	3347	20898947	20897414	0.000000e+00	2481.0
27	TraesCS2A01G253300	chr4D	91.969	635	46	4	1	632	450005159	450004527	0.000000e+00	885.0
28	TraesCS2A01G253300	chr4D	81.185	287	38	11	3016	3298	100198700	100198426	2.020000e-52	217.0
29	TraesCS2A01G253300	chr4D	91.156	147	10	3	1533	1676	41913662	41913808	2.630000e-46	196.0
30	TraesCS2A01G253300	chr4A	91.167	634	49	7	5	632	621783117	621783749	0.000000e+00	854.0
31	TraesCS2A01G253300	chr4A	90.678	118	10	1	680	797	702432721	702432605	4.470000e-34	156.0
32	TraesCS2A01G253300	chr7A	90.808	631	50	8	7	632	85071123	85071750	0.000000e+00	837.0
33	TraesCS2A01G253300	chr7A	90.596	638	49	11	1	632	533500774	533500142	0.000000e+00	835.0
34	TraesCS2A01G253300	chr5D	89.905	634	57	6	5	632	448718566	448717934	0.000000e+00	809.0
35	TraesCS2A01G253300	chr6D	92.898	352	23	2	1097	1446	47075631	47075982	8.280000e-141	510.0
36	TraesCS2A01G253300	chr6D	86.650	412	38	11	862	1271	47075319	47075715	1.100000e-119	440.0
37	TraesCS2A01G253300	chr6D	87.437	199	21	2	1074	1271	47075566	47075761	3.360000e-55	226.0
38	TraesCS2A01G253300	chrUn	84.459	296	40	4	2713	3004	40880543	40880250	1.520000e-73	287.0
39	TraesCS2A01G253300	chr2D	81.185	287	37	9	3016	3298	118522199	118522472	7.270000e-52	215.0
40	TraesCS2A01G253300	chr4B	91.156	147	10	3	1533	1676	60372590	60372736	2.630000e-46	196.0
41	TraesCS2A01G253300	chr4B	91.489	47	4	0	634	680	507690572	507690618	7.750000e-07	65.8
42	TraesCS2A01G253300	chr3A	86.567	67	7	1	2357	2423	23890225	23890289	4.630000e-09	73.1

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	TraesCS2A01G253300	chr2A	385331323	385334669	3346	False	6181.0	6181	100.0000	1	3347	1	chr2A.!!$F1	3346
1	TraesCS2A01G253300	chr6A	536548984	536551693	2709	False	2254.5	3718	93.7560	678	3347	2	chr6A.!!$F1	2669
2	TraesCS2A01G253300	chr6A	239126989	239129704	2715	True	2214.0	3681	92.7510	674	3347	2	chr6A.!!$R2	2673
3	TraesCS2A01G253300	chr6A	578543109	578543746	637	True	835.0	835	90.4690	1	632	1	chr6A.!!$R1	631
4	TraesCS2A01G253300	chr3B	59951705	59954456	2751	False	2120.5	3546	91.5010	679	3347	2	chr3B.!!$F2	2668
5	TraesCS2A01G253300	chr3B	598910869	598911497	628	True	841.0	841	90.8370	7	635	1	chr3B.!!$R2	628
6	TraesCS2A01G253300	chr3B	770106364	770106999	635	False	806.0	806	89.6230	1	632	1	chr3B.!!$F1	631
7	TraesCS2A01G253300	chr2B	178679135	178681917	2782	True	2102.0	3542	91.2535	678	3347	2	chr2B.!!$R4	2669
8	TraesCS2A01G253300	chr2B	753016581	753017274	693	True	1038.0	1038	94.1090	1599	2275	1	chr2B.!!$R2	676
9	TraesCS2A01G253300	chr5B	486021484	486024285	2801	True	2104.0	3506	91.4195	662	3347	2	chr5B.!!$R2	2685
10	TraesCS2A01G253300	chr5B	427963294	427963926	632	True	808.0	808	89.7960	1	632	1	chr5B.!!$R1	631
11	TraesCS2A01G253300	chr1B	114481764	114484284	2520	True	1845.5	3011	93.3335	679	3103	2	chr1B.!!$R2	2424
12	TraesCS2A01G253300	chr3D	453235132	453237234	2102	True	1636.0	2837	90.9200	862	2871	2	chr3D.!!$R1	2009
13	TraesCS2A01G253300	chr1D	20897414	20898947	1533	True	2481.0	2481	95.8440	1811	3347	1	chr1D.!!$R1	1536
14	TraesCS2A01G253300	chr4D	450004527	450005159	632	True	885.0	885	91.9690	1	632	1	chr4D.!!$R2	631
15	TraesCS2A01G253300	chr4A	621783117	621783749	632	False	854.0	854	91.1670	5	632	1	chr4A.!!$F1	627
16	TraesCS2A01G253300	chr7A	85071123	85071750	627	False	837.0	837	90.8080	7	632	1	chr7A.!!$F1	625
17	TraesCS2A01G253300	chr7A	533500142	533500774	632	True	835.0	835	90.5960	1	632	1	chr7A.!!$R1	631
18	TraesCS2A01G253300	chr5D	448717934	448718566	632	True	809.0	809	89.9050	5	632	1	chr5D.!!$R1	627
19	TraesCS2A01G253300	chr6D	47075319	47075982	663	False	392.0	510	88.9950	862	1446	3	chr6D.!!$F1	584

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
795	809	1.337447	GCTACCAACCACGCACTTAGA	60.337	52.381	0.0	0.0	0.0	2.10	F
840	854	3.374402	CACGTCCTCTGTCGCCCT	61.374	66.667	0.0	0.0	0.0	5.19	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2225	2501	1.160137	GTACTTCTTGTGCCTGCAGG	58.84	55.0	29.34	29.34	38.53	4.85	R
2378	2655	2.290122	CTGGCCTCGATCGCTCTGTT	62.29	60.0	11.09	0.00	0.00	3.16	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
400	410	9.402320	TGCAACATGGTAATATACATACAAAGT	57.598	29.630	0.00	0.00	0.00	2.66
418	428	7.042797	ACAAAGTTGATAACTCACTGCAAAT	57.957	32.000	0.00	0.00	41.91	2.32
433	443	9.661187	CTCACTGCAAATATCATAATCACTTTC	57.339	33.333	0.00	0.00	0.00	2.62
511	522	9.880157	AAATGACACGGTAACTTATGTATAACT	57.120	29.630	0.00	0.00	0.00	2.24
532	543	6.635030	ACTGATATGATAACTCACGTAGCA	57.365	37.500	0.00	0.00	33.22	3.49
589	602	7.933577	GTCTTCAGAACATATCAACATGGGATA	59.066	37.037	10.58	10.58	0.00	2.59
609	622	6.869388	GGGATATAGTTTCGAAGATCTTGTCC	59.131	42.308	14.00	2.64	35.04	4.02
642	656	3.364889	TTGTGAAGACTGGAGTGTACG	57.635	47.619	0.00	0.00	0.00	3.67
643	657	2.304092	TGTGAAGACTGGAGTGTACGT	58.696	47.619	0.00	0.00	0.00	3.57
644	658	2.034179	TGTGAAGACTGGAGTGTACGTG	59.966	50.000	0.00	0.00	0.00	4.49
645	659	2.292569	GTGAAGACTGGAGTGTACGTGA	59.707	50.000	0.00	0.00	0.00	4.35
646	660	2.953648	TGAAGACTGGAGTGTACGTGAA	59.046	45.455	0.00	0.00	0.00	3.18
647	661	3.382227	TGAAGACTGGAGTGTACGTGAAA	59.618	43.478	0.00	0.00	0.00	2.69
648	662	3.644884	AGACTGGAGTGTACGTGAAAG	57.355	47.619	0.00	0.00	0.00	2.62
649	663	3.220110	AGACTGGAGTGTACGTGAAAGA	58.780	45.455	0.00	0.00	0.00	2.52
650	664	3.635373	AGACTGGAGTGTACGTGAAAGAA	59.365	43.478	0.00	0.00	0.00	2.52
651	665	4.098960	AGACTGGAGTGTACGTGAAAGAAA	59.901	41.667	0.00	0.00	0.00	2.52
652	666	4.761975	ACTGGAGTGTACGTGAAAGAAAA	58.238	39.130	0.00	0.00	0.00	2.29
653	667	5.180271	ACTGGAGTGTACGTGAAAGAAAAA	58.820	37.500	0.00	0.00	0.00	1.94
654	668	5.064325	ACTGGAGTGTACGTGAAAGAAAAAC	59.936	40.000	0.00	0.00	0.00	2.43
655	669	5.180271	TGGAGTGTACGTGAAAGAAAAACT	58.820	37.500	0.00	0.00	0.00	2.66
656	670	6.339730	TGGAGTGTACGTGAAAGAAAAACTA	58.660	36.000	0.00	0.00	0.00	2.24
657	671	6.477688	TGGAGTGTACGTGAAAGAAAAACTAG	59.522	38.462	0.00	0.00	0.00	2.57
658	672	6.478016	GGAGTGTACGTGAAAGAAAAACTAGT	59.522	38.462	0.00	0.00	0.00	2.57
659	673	7.306457	GGAGTGTACGTGAAAGAAAAACTAGTC	60.306	40.741	0.00	0.00	0.00	2.59
660	674	7.037438	AGTGTACGTGAAAGAAAAACTAGTCA	58.963	34.615	0.00	0.00	0.00	3.41
661	675	7.709613	AGTGTACGTGAAAGAAAAACTAGTCAT	59.290	33.333	0.00	0.00	0.00	3.06
662	676	8.333186	GTGTACGTGAAAGAAAAACTAGTCATT	58.667	33.333	0.00	0.00	0.00	2.57
663	677	8.545420	TGTACGTGAAAGAAAAACTAGTCATTC	58.455	33.333	0.00	10.97	0.00	2.67
664	678	7.787725	ACGTGAAAGAAAAACTAGTCATTCT	57.212	32.000	14.29	14.29	33.73	2.40
665	679	8.882415	ACGTGAAAGAAAAACTAGTCATTCTA	57.118	30.769	18.33	5.82	32.13	2.10
666	680	9.321562	ACGTGAAAGAAAAACTAGTCATTCTAA	57.678	29.630	18.33	8.83	32.13	2.10
714	728	9.692325	ACTATAAAAGAAAGAGAATGGCAGATT	57.308	29.630	0.00	0.00	0.00	2.40
795	809	1.337447	GCTACCAACCACGCACTTAGA	60.337	52.381	0.00	0.00	0.00	2.10
840	854	3.374402	CACGTCCTCTGTCGCCCT	61.374	66.667	0.00	0.00	0.00	5.19
2027	2290	5.351465	CGTTATCAGTACCTTTGACATTGCT	59.649	40.000	0.00	0.00	0.00	3.91
2064	2327	6.184068	ACATGTGTATATGCAGGTTAACCAA	58.816	36.000	26.26	11.87	38.89	3.67
2225	2501	5.353678	ACTCATGCTTGCTATCTGAAAACTC	59.646	40.000	0.00	0.00	0.00	3.01
2311	2587	6.091305	TGTCATCATCATCACTCGAAGAAAAC	59.909	38.462	0.00	0.00	34.09	2.43
2363	2639	3.578282	TGTTAGAGCTCACTGTTGATGGA	59.422	43.478	17.77	0.00	0.00	3.41
2378	2655	2.170166	GATGGATTGGTTGGAACTGCA	58.830	47.619	0.00	0.00	0.00	4.41
2443	2720	4.106197	GGAGCTCTGTAGATTGTAACACG	58.894	47.826	14.64	0.00	0.00	4.49
2471	2751	0.898326	TCCTGCGTGAAGGTGAGCTA	60.898	55.000	0.00	0.00	38.58	3.32
2804	3086	4.822350	AGCCTTTGGTTGAGAGTTAAGAAC	59.178	41.667	0.00	0.00	0.00	3.01
2978	3262	5.396884	GGATGTTCTGTAGGAGCCTATGTTT	60.397	44.000	0.00	0.00	0.00	2.83
2996	3280	8.980481	CTATGTTTAGGATGAGGGTACAATTT	57.020	34.615	0.00	0.00	0.00	1.82
3031	3322	2.185350	CGAGGCAAGCAGACCGAT	59.815	61.111	0.00	0.00	0.00	4.18
3084	3381	4.256180	GGGCCTACTCCATGCGGG	62.256	72.222	0.84	0.00	38.37	6.13

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
94	95	5.361285	GGACCGAGAGCCTATATTATCATGT	59.639	44.000	0.00	0.00	0.00	3.21
112	113	7.977853	GTGTTTTATCTAAGTTATCAGGACCGA	59.022	37.037	0.00	0.00	0.00	4.69
211	214	9.535878	TTTTAACAACATTTTCCCATGTTACTC	57.464	29.630	0.00	0.00	44.08	2.59
212	215	9.892130	TTTTTAACAACATTTTCCCATGTTACT	57.108	25.926	0.00	0.00	44.08	2.24
360	367	4.320861	CCATGTTGCACAAAAGTTATCGGA	60.321	41.667	0.00	0.00	0.00	4.55
418	428	6.183361	CCAGGGGTCAGAAAGTGATTATGATA	60.183	42.308	0.00	0.00	41.03	2.15
433	443	3.739401	AACTTTTATCCCAGGGGTCAG	57.261	47.619	5.33	0.00	36.47	3.51
508	519	6.918569	GTGCTACGTGAGTTATCATATCAGTT	59.081	38.462	0.00	0.00	46.40	3.16
511	522	5.449304	CGTGCTACGTGAGTTATCATATCA	58.551	41.667	0.00	0.00	46.40	2.15
515	526	2.686405	TCCGTGCTACGTGAGTTATCAT	59.314	45.455	0.00	0.00	46.40	2.45
532	543	3.143728	GACCAAAAGTTACCACATCCGT	58.856	45.455	0.00	0.00	0.00	4.69
566	579	9.948964	CTATATCCCATGTTGATATGTTCTGAA	57.051	33.333	18.42	0.00	36.39	3.02
589	602	6.334202	GTCTGGACAAGATCTTCGAAACTAT	58.666	40.000	4.57	0.00	37.23	2.12
632	646	5.180271	AGTTTTTCTTTCACGTACACTCCA	58.820	37.500	0.00	0.00	0.00	3.86
634	648	7.221452	TGACTAGTTTTTCTTTCACGTACACTC	59.779	37.037	0.00	0.00	0.00	3.51
635	649	7.037438	TGACTAGTTTTTCTTTCACGTACACT	58.963	34.615	0.00	0.00	0.00	3.55
636	650	7.225523	TGACTAGTTTTTCTTTCACGTACAC	57.774	36.000	0.00	0.00	0.00	2.90
637	651	8.428186	AATGACTAGTTTTTCTTTCACGTACA	57.572	30.769	0.00	0.00	0.00	2.90
638	652	8.762426	AGAATGACTAGTTTTTCTTTCACGTAC	58.238	33.333	12.90	0.00	31.46	3.67
639	653	8.882415	AGAATGACTAGTTTTTCTTTCACGTA	57.118	30.769	12.90	0.00	31.46	3.57
640	654	7.787725	AGAATGACTAGTTTTTCTTTCACGT	57.212	32.000	12.90	0.00	31.46	4.49
651	665	9.618890	ACATGCATGTATTAGAATGACTAGTTT	57.381	29.630	30.50	0.00	39.68	2.66
667	681	8.879427	ATAGTGGTAGTAGATACATGCATGTA	57.121	34.615	35.03	35.03	46.21	2.29
668	682	7.782897	ATAGTGGTAGTAGATACATGCATGT	57.217	36.000	33.20	33.20	44.48	3.21
705	719	6.608405	TGGATCTAATTGTTTGAATCTGCCAT	59.392	34.615	0.00	0.00	0.00	4.40
706	720	5.951148	TGGATCTAATTGTTTGAATCTGCCA	59.049	36.000	0.00	0.00	0.00	4.92
714	728	9.473007	TGTTAATGGATGGATCTAATTGTTTGA	57.527	29.630	0.00	0.00	0.00	2.69
795	809	3.456277	AGAGATGGAGGGATTAGCGTTTT	59.544	43.478	0.00	0.00	0.00	2.43
840	854	3.488553	CGATATGTGTGAGCGGTTAGTGA	60.489	47.826	0.00	0.00	0.00	3.41
1171	1409	3.775654	CTGGCCTCCCCGTCTGAC	61.776	72.222	3.32	0.00	35.87	3.51
1521	1760	5.590259	GCATAAGAGGGCAGAAATTTCTACA	59.410	40.000	20.07	0.00	35.34	2.74
2064	2327	7.496346	TTCTTTCATACCAGGTAGATGAAGT	57.504	36.000	14.81	0.00	39.90	3.01
2225	2501	1.160137	GTACTTCTTGTGCCTGCAGG	58.840	55.000	29.34	29.34	38.53	4.85
2311	2587	4.235079	TGGAAATAATCAGACTGGGTGG	57.765	45.455	1.81	0.00	0.00	4.61
2363	2639	2.624838	CTCTGTTGCAGTTCCAACCAAT	59.375	45.455	2.97	0.00	43.36	3.16
2378	2655	2.290122	CTGGCCTCGATCGCTCTGTT	62.290	60.000	11.09	0.00	0.00	3.16
2471	2751	6.266103	TGATCTTGCTTTTGGAGAGTTGAATT	59.734	34.615	0.00	0.00	0.00	2.17
2525	2805	3.971971	GGTAGGACCTGGGCTTAATCTAA	59.028	47.826	3.53	0.00	34.73	2.10
2804	3086	5.235186	CGTTTCCAGAGCAACATAGGAATAG	59.765	44.000	0.00	0.00	38.10	1.73
2960	3244	5.138758	TCCTAAACATAGGCTCCTACAGA	57.861	43.478	0.00	0.00	37.16	3.41
2978	3262	6.894735	TGGTAAAATTGTACCCTCATCCTA	57.105	37.500	20.21	0.00	42.63	2.94
2996	3280	9.661563	CTTGCCTCGGTATATATAATTTGGTAA	57.338	33.333	0.00	1.46	0.00	2.85

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.