AutoCloner

Multiple sequence alignment - TraesCS3B01G249800

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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	TraesCS3B01G249800	chr3B	100.000	2954	0	0	1	2954	398590851	398587898	0.000000e+00	5456.0
1	TraesCS3B01G249800	chr3A	96.086	2657	66	20	1	2638	403005595	403008232	0.000000e+00	4296.0
2	TraesCS3B01G249800	chr3A	93.728	287	17	1	2667	2953	403008233	403008518	2.100000e-116	429.0
3	TraesCS3B01G249800	chr3D	96.840	2563	57	9	1	2559	321717998	321720540	0.000000e+00	4263.0
4	TraesCS3B01G249800	chr3D	92.027	301	12	6	2654	2954	321720577	321720865	2.120000e-111	412.0
5	TraesCS3B01G249800	chr7D	84.656	189	25	3	2640	2827	333705363	333705178	5.030000e-43	185.0
6	TraesCS3B01G249800	chr7D	85.246	61	8	1	2507	2566	174149005	174148945	8.840000e-06	62.1
7	TraesCS3B01G249800	chr7B	84.127	189	28	2	2640	2827	640082279	640082092	6.500000e-42	182.0
8	TraesCS3B01G249800	chr7B	84.127	189	28	2	2640	2827	640141174	640140987	6.500000e-42	182.0
9	TraesCS3B01G249800	chr7B	80.172	116	18	5	2452	2566	746049045	746048934	6.790000e-12	82.4
10	TraesCS3B01G249800	chr1B	83.251	203	28	5	2628	2827	53263429	53263628	6.500000e-42	182.0
11	TraesCS3B01G249800	chr4B	82.673	202	31	4	2628	2827	556067317	556067516	3.030000e-40	176.0
12	TraesCS3B01G249800	chr6B	83.422	187	29	2	2642	2827	76272167	76272352	3.910000e-39	172.0
13	TraesCS3B01G249800	chr6A	79.902	204	34	6	2641	2840	112583335	112583535	3.070000e-30	143.0
14	TraesCS3B01G249800	chr5D	82.203	118	15	6	2452	2566	215302114	215302000	2.420000e-16	97.1
15	TraesCS3B01G249800	chr2A	83.962	106	12	5	2452	2555	445716879	445716777	2.420000e-16	97.1
16	TraesCS3B01G249800	chr5B	81.481	108	15	5	2454	2559	503219503	503219607	1.890000e-12	84.2
17	TraesCS3B01G249800	chr6D	92.593	54	3	1	2507	2559	112433563	112433616	3.160000e-10	76.8
18	TraesCS3B01G249800	chr6D	82.558	86	9	6	2452	2535	383494823	383494904	1.470000e-08	71.3
19	TraesCS3B01G249800	chr2D	79.464	112	18	5	2457	2566	633849077	633849185	1.140000e-09	75.0

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	TraesCS3B01G249800	chr3B	398587898	398590851	2953	True	5456.0	5456	100.0000	1	2954	1	chr3B.!!$R1	2953
1	TraesCS3B01G249800	chr3A	403005595	403008518	2923	False	2362.5	4296	94.9070	1	2953	2	chr3A.!!$F1	2952
2	TraesCS3B01G249800	chr3D	321717998	321720865	2867	False	2337.5	4263	94.4335	1	2954	2	chr3D.!!$F1	2953

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
482	487	1.179174	CGGATCGATGGAGGGCAGTA	61.179	60.000	0.54	0.00	0.00	2.74	F
1059	1067	1.297967	CTGCCGATCTCGTGTCTCG	60.298	63.158	0.00	5.61	41.41	4.04	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1380	1388	0.038744	CCTTGGTCCAATGGCTGACT	59.961	55.0	4.34	0.0	0.0	3.41	R
2643	2695	0.259065	ACTCCCTCTCGATGGCTACA	59.741	55.0	0.00	0.0	0.0	2.74	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
198	203	4.124943	TCCTCGCCGCTACCCTCT	62.125	66.667	0.00	0.00	0.00	3.69
417	422	3.380637	GGAACTTGCGGACTATGTCTCTA	59.619	47.826	0.00	0.00	32.47	2.43
482	487	1.179174	CGGATCGATGGAGGGCAGTA	61.179	60.000	0.54	0.00	0.00	2.74
507	512	2.885266	TGCCGCTGTATTTTGGTTTGTA	59.115	40.909	0.00	0.00	0.00	2.41
537	542	2.807622	GCCGGATTGTTGATGGCC	59.192	61.111	5.05	0.00	39.83	5.36
632	637	5.560966	TGTCCTGATTTTTAGGCGATTTC	57.439	39.130	0.00	0.00	35.23	2.17
657	662	6.114221	CTTGTAAAGTTTGTCTGGTTTCGA	57.886	37.500	0.00	0.00	39.70	3.71
745	752	3.635331	CCAGACTTGTGAATTGCTTGTG	58.365	45.455	0.00	0.00	0.00	3.33
758	765	7.596248	GTGAATTGCTTGTGTGTGAAGATTAAT	59.404	33.333	0.00	0.00	0.00	1.40
767	774	4.394920	TGTGTGAAGATTAATTCGCCTTCC	59.605	41.667	10.50	5.02	38.62	3.46
1035	1043	1.513158	CTCCCGTTCAGTCTCGCAT	59.487	57.895	0.00	0.00	0.00	4.73
1059	1067	1.297967	CTGCCGATCTCGTGTCTCG	60.298	63.158	0.00	5.61	41.41	4.04
1272	1280	2.191128	ACAGACACTCCAATTGCCTC	57.809	50.000	0.00	0.00	0.00	4.70
2077	2085	1.072159	GTGCCAGCTTGTCTCAGGT	59.928	57.895	0.00	0.00	0.00	4.00
2123	2131	2.669391	GCAAGCAAGAAGAAATCACGGG	60.669	50.000	0.00	0.00	0.00	5.28
2317	2328	3.119388	GCTGCCTTGTAATTGCATCTGAA	60.119	43.478	0.00	0.00	33.97	3.02
2358	2369	9.691362	ATTTGAAGAATTTGTTGTATAGCGTTT	57.309	25.926	0.00	0.00	0.00	3.60
2466	2477	5.812642	AGACACGTGAGATGTTTTGGATATC	59.187	40.000	25.01	2.89	0.00	1.63
2541	2552	6.863275	ACGTGTCTACATACATCTGATTCAA	58.137	36.000	0.00	0.00	0.00	2.69
2568	2579	9.624373	AAAAAGCTAGAACATCTGATGATACAT	57.376	29.630	23.59	7.54	0.00	2.29
2569	2580	8.830201	AAAGCTAGAACATCTGATGATACATC	57.170	34.615	23.59	12.47	0.00	3.06
2570	2581	7.779754	AGCTAGAACATCTGATGATACATCT	57.220	36.000	23.59	17.60	0.00	2.90
2571	2582	7.604549	AGCTAGAACATCTGATGATACATCTG	58.395	38.462	23.59	11.34	0.00	2.90
2572	2583	7.450944	AGCTAGAACATCTGATGATACATCTGA	59.549	37.037	23.59	18.26	0.00	3.27
2573	2584	8.252417	GCTAGAACATCTGATGATACATCTGAT	58.748	37.037	23.59	20.26	37.24	2.90
2576	2587	8.648693	AGAACATCTGATGATACATCTGATTCA	58.351	33.333	23.59	6.05	35.46	2.57
2577	2588	8.834749	AACATCTGATGATACATCTGATTCAG	57.165	34.615	23.59	7.38	35.46	3.02
2578	2589	8.191534	ACATCTGATGATACATCTGATTCAGA	57.808	34.615	23.59	18.29	44.99	3.27
2579	2590	8.648693	ACATCTGATGATACATCTGATTCAGAA	58.351	33.333	23.59	4.80	44.04	3.02
2580	2591	9.490379	CATCTGATGATACATCTGATTCAGAAA	57.510	33.333	19.73	9.36	44.04	2.52
2582	2593	9.895138	TCTGATGATACATCTGATTCAGAAAAA	57.105	29.630	19.73	8.70	44.04	1.94
2584	2595	8.618677	TGATGATACATCTGATTCAGAAAAAGC	58.381	33.333	19.73	11.04	44.04	3.51
2633	2685	0.606401	CAGCGTGATGGAAACCCACT	60.606	55.000	0.00	0.00	36.36	4.00
2638	2690	3.670625	CGTGATGGAAACCCACTTAAGA	58.329	45.455	10.09	0.00	36.36	2.10
2639	2691	4.261801	CGTGATGGAAACCCACTTAAGAT	58.738	43.478	10.09	0.00	36.36	2.40
2640	2692	5.424757	CGTGATGGAAACCCACTTAAGATA	58.575	41.667	10.09	0.00	36.36	1.98
2641	2693	5.523916	CGTGATGGAAACCCACTTAAGATAG	59.476	44.000	10.09	0.00	36.36	2.08
2642	2694	6.415573	GTGATGGAAACCCACTTAAGATAGT	58.584	40.000	10.09	0.00	36.36	2.12
2643	2695	6.884836	GTGATGGAAACCCACTTAAGATAGTT	59.115	38.462	10.09	6.25	36.36	2.24
2644	2696	6.884295	TGATGGAAACCCACTTAAGATAGTTG	59.116	38.462	10.09	0.00	36.36	3.16
2645	2697	6.195600	TGGAAACCCACTTAAGATAGTTGT	57.804	37.500	10.09	1.35	0.00	3.32
2646	2698	7.319052	TGGAAACCCACTTAAGATAGTTGTA	57.681	36.000	10.09	0.00	0.00	2.41
2647	2699	7.391620	TGGAAACCCACTTAAGATAGTTGTAG	58.608	38.462	10.09	0.00	0.00	2.74
2648	2700	6.315642	GGAAACCCACTTAAGATAGTTGTAGC	59.684	42.308	10.09	1.39	0.00	3.58
2649	2701	5.354842	ACCCACTTAAGATAGTTGTAGCC	57.645	43.478	10.09	0.00	0.00	3.93
2650	2702	4.781087	ACCCACTTAAGATAGTTGTAGCCA	59.219	41.667	10.09	0.00	0.00	4.75
2651	2703	5.428783	ACCCACTTAAGATAGTTGTAGCCAT	59.571	40.000	10.09	0.00	0.00	4.40
2652	2704	5.992217	CCCACTTAAGATAGTTGTAGCCATC	59.008	44.000	10.09	0.00	0.00	3.51
2653	2705	5.692204	CCACTTAAGATAGTTGTAGCCATCG	59.308	44.000	10.09	0.00	0.00	3.84
2654	2706	6.461092	CCACTTAAGATAGTTGTAGCCATCGA	60.461	42.308	10.09	0.00	0.00	3.59
2745	2797	7.176690	ACAGTCGGAAAATTAAAGACCATCATT	59.823	33.333	0.00	0.00	32.70	2.57
2890	2942	7.015682	CACTAGGGAGTATAACATCCACTCATT	59.984	40.741	0.00	0.00	40.38	2.57

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
372	377	2.808315	GAGAGGCAGCCGAATCGA	59.192	61.111	5.55	0.00	0.00	3.59
408	413	1.012086	AGAACGCGCGTAGAGACATA	58.988	50.000	37.93	0.00	0.00	2.29
482	487	1.271379	ACCAAAATACAGCGGCAGACT	60.271	47.619	1.45	0.00	0.00	3.24
507	512	3.679738	CCGGCCCAAACAACGCAT	61.680	61.111	0.00	0.00	0.00	4.73
537	542	5.205056	AGTTGGAGGACTACATCTAGGAAG	58.795	45.833	0.00	0.00	0.00	3.46
632	637	5.737290	CGAAACCAGACAAACTTTACAAGTG	59.263	40.000	0.00	0.00	41.91	3.16
657	662	2.716424	TCTGGAAATGAACACCTCCCTT	59.284	45.455	0.00	0.00	0.00	3.95
745	752	4.636206	AGGAAGGCGAATTAATCTTCACAC	59.364	41.667	13.60	1.44	37.82	3.82
1035	1043	3.531207	CGAGATCGGCAGCCCTCA	61.531	66.667	5.63	0.00	35.37	3.86
1059	1067	0.447801	CACTCCGCAACTTGTATGGC	59.552	55.000	0.00	0.00	0.00	4.40
1140	1148	0.108138	AGCGAACTTCCTCCCATTCG	60.108	55.000	1.06	1.06	45.15	3.34
1152	1160	1.595382	GCACACAGGACAGCGAACT	60.595	57.895	0.00	0.00	0.00	3.01
1272	1280	0.460284	AGGCTTTGCGGTACTGATCG	60.460	55.000	5.68	0.00	0.00	3.69
1380	1388	0.038744	CCTTGGTCCAATGGCTGACT	59.961	55.000	4.34	0.00	0.00	3.41
1515	1523	1.080298	CACCTCCGTTGGTCGTACC	60.080	63.158	0.00	0.00	38.45	3.34
1817	1825	0.179034	ATTGCCGCTTGATCCTCCTC	60.179	55.000	0.00	0.00	0.00	3.71
2042	2050	1.818674	GCACGGATGTTTCTTCCCAAT	59.181	47.619	0.00	0.00	0.00	3.16
2123	2131	3.637273	AGCTCCACCACGTTCCCC	61.637	66.667	0.00	0.00	0.00	4.81
2552	2563	8.648693	TCTGAATCAGATGTATCATCAGATGTT	58.351	33.333	9.18	4.80	37.49	2.71
2553	2564	8.191534	TCTGAATCAGATGTATCATCAGATGT	57.808	34.615	9.18	1.04	37.49	3.06
2554	2565	9.490379	TTTCTGAATCAGATGTATCATCAGATG	57.510	33.333	14.31	3.71	40.39	2.90
2556	2567	9.895138	TTTTTCTGAATCAGATGTATCATCAGA	57.105	29.630	14.31	6.24	40.39	3.27
2558	2569	8.618677	GCTTTTTCTGAATCAGATGTATCATCA	58.381	33.333	14.31	0.00	40.39	3.07
2559	2570	8.838365	AGCTTTTTCTGAATCAGATGTATCATC	58.162	33.333	14.31	1.98	40.39	2.92
2560	2571	8.749026	AGCTTTTTCTGAATCAGATGTATCAT	57.251	30.769	14.31	0.00	40.39	2.45
2561	2572	9.322773	CTAGCTTTTTCTGAATCAGATGTATCA	57.677	33.333	14.31	0.00	40.39	2.15
2562	2573	9.539825	TCTAGCTTTTTCTGAATCAGATGTATC	57.460	33.333	14.31	4.31	40.39	2.24
2563	2574	9.896645	TTCTAGCTTTTTCTGAATCAGATGTAT	57.103	29.630	14.31	1.70	40.39	2.29
2564	2575	9.155975	GTTCTAGCTTTTTCTGAATCAGATGTA	57.844	33.333	14.31	0.00	40.39	2.29
2565	2576	7.663081	TGTTCTAGCTTTTTCTGAATCAGATGT	59.337	33.333	14.31	0.00	40.39	3.06
2566	2577	8.037382	TGTTCTAGCTTTTTCTGAATCAGATG	57.963	34.615	14.31	6.30	40.39	2.90
2567	2578	8.804912	ATGTTCTAGCTTTTTCTGAATCAGAT	57.195	30.769	14.31	0.29	40.39	2.90
2568	2579	8.099537	AGATGTTCTAGCTTTTTCTGAATCAGA	58.900	33.333	9.18	9.18	38.87	3.27
2569	2580	8.266392	AGATGTTCTAGCTTTTTCTGAATCAG	57.734	34.615	3.38	3.38	0.00	2.90
2570	2581	9.725019	TTAGATGTTCTAGCTTTTTCTGAATCA	57.275	29.630	0.00	0.00	29.56	2.57
2581	2592	9.035607	CGTTCACAATATTAGATGTTCTAGCTT	57.964	33.333	0.00	0.00	29.56	3.74
2582	2593	7.653713	CCGTTCACAATATTAGATGTTCTAGCT	59.346	37.037	0.00	0.00	29.56	3.32
2583	2594	7.095607	CCCGTTCACAATATTAGATGTTCTAGC	60.096	40.741	0.00	0.00	29.56	3.42
2584	2595	7.385205	CCCCGTTCACAATATTAGATGTTCTAG	59.615	40.741	0.00	0.00	29.56	2.43
2633	2685	6.016192	CCTCTCGATGGCTACAACTATCTTAA	60.016	42.308	0.00	0.00	0.00	1.85
2638	2690	2.894126	CCCTCTCGATGGCTACAACTAT	59.106	50.000	0.00	0.00	0.00	2.12
2639	2691	2.092049	TCCCTCTCGATGGCTACAACTA	60.092	50.000	0.00	0.00	0.00	2.24
2640	2692	1.115467	CCCTCTCGATGGCTACAACT	58.885	55.000	0.00	0.00	0.00	3.16
2641	2693	1.067821	CTCCCTCTCGATGGCTACAAC	59.932	57.143	0.00	0.00	0.00	3.32
2642	2694	1.342076	ACTCCCTCTCGATGGCTACAA	60.342	52.381	0.00	0.00	0.00	2.41
2643	2695	0.259065	ACTCCCTCTCGATGGCTACA	59.741	55.000	0.00	0.00	0.00	2.74
2644	2696	0.671251	CACTCCCTCTCGATGGCTAC	59.329	60.000	0.00	0.00	0.00	3.58
2645	2697	1.109920	GCACTCCCTCTCGATGGCTA	61.110	60.000	0.00	0.00	0.00	3.93
2646	2698	2.430610	GCACTCCCTCTCGATGGCT	61.431	63.158	0.00	0.00	0.00	4.75
2647	2699	2.107953	GCACTCCCTCTCGATGGC	59.892	66.667	0.00	0.00	0.00	4.40
2648	2700	1.760086	AGGCACTCCCTCTCGATGG	60.760	63.158	0.00	0.00	41.21	3.51
2649	2701	3.947173	AGGCACTCCCTCTCGATG	58.053	61.111	0.00	0.00	41.21	3.84
2832	2884	8.182881	GGATATACTCTCCACAATATGTCGTAC	58.817	40.741	0.00	0.00	32.72	3.67
2835	2887	6.565234	GGGATATACTCTCCACAATATGTCG	58.435	44.000	0.00	0.00	34.24	4.35
2890	2942	3.761752	TCATGACACACGACATTAGGAGA	59.238	43.478	0.00	0.00	0.00	3.71

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.