AutoCloner

Multiple sequence alignment - TraesCS6B01G398600

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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	TraesCS6B01G398600	chr6B	100.000	2984	0	0	1	2984	674203813	674200830	0.000000e+00	5511
1	TraesCS6B01G398600	chr4D	94.993	2996	117	14	1	2983	410307050	410310025	0.000000e+00	4671
2	TraesCS6B01G398600	chr4D	93.041	2601	110	27	1	2561	132437788	132435219	0.000000e+00	3735
3	TraesCS6B01G398600	chr7D	97.000	2567	55	8	1	2561	72314849	72312299	0.000000e+00	4294
4	TraesCS6B01G398600	chr7D	96.014	1104	28	7	1475	2573	235509466	235508374	0.000000e+00	1781
5	TraesCS6B01G398600	chr7D	98.187	386	7	0	2599	2984	72312305	72311920	0.000000e+00	675
6	TraesCS6B01G398600	chr5B	96.262	2568	69	11	1	2561	236068639	236066092	0.000000e+00	4185
7	TraesCS6B01G398600	chr5B	96.791	374	10	1	2611	2984	236066074	236065703	9.080000e-175	623
8	TraesCS6B01G398600	chr4A	96.220	2090	54	8	478	2561	740667875	740669945	0.000000e+00	3398
9	TraesCS6B01G398600	chr4A	95.887	389	15	1	2597	2984	740669939	740670327	1.950000e-176	628
10	TraesCS6B01G398600	chr5A	96.833	1579	32	6	1	1578	257555258	257556819	0.000000e+00	2623
11	TraesCS6B01G398600	chr5A	96.770	1579	33	6	1	1578	302992119	302993680	0.000000e+00	2617
12	TraesCS6B01G398600	chr5A	92.741	1419	59	20	1576	2984	302993783	302995167	0.000000e+00	2010
13	TraesCS6B01G398600	chr5A	95.875	994	33	4	1576	2561	257556922	257557915	0.000000e+00	1602
14	TraesCS6B01G398600	chr5A	97.043	372	10	1	2613	2984	257557935	257558305	2.530000e-175	625
15	TraesCS6B01G398600	chr2A	96.772	1580	33	5	1	1578	755095340	755093777	0.000000e+00	2619
16	TraesCS6B01G398600	chr2A	96.789	1557	32	6	1	1555	618957688	618959228	0.000000e+00	2582
17	TraesCS6B01G398600	chr2A	96.327	1579	40	6	1	1578	755103111	755101550	0.000000e+00	2579
18	TraesCS6B01G398600	chr2A	95.674	994	31	5	1576	2561	618964302	618965291	0.000000e+00	1587
19	TraesCS6B01G398600	chr2A	95.578	995	35	5	1576	2561	755093674	755092680	0.000000e+00	1585
20	TraesCS6B01G398600	chr2A	97.312	372	10	0	2613	2984	755092660	755092289	1.510000e-177	632
21	TraesCS6B01G398600	chr2A	97.312	372	9	1	2613	2984	618965311	618965681	5.430000e-177	630
22	TraesCS6B01G398600	chr1D	94.286	385	21	1	2600	2984	432821041	432821424	3.310000e-164	588

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	TraesCS6B01G398600	chr6B	674200830	674203813	2983	True	5511.000000	5511	100.000000	1	2984	1	chr6B.!!$R1	2983
1	TraesCS6B01G398600	chr4D	410307050	410310025	2975	False	4671.000000	4671	94.993000	1	2983	1	chr4D.!!$F1	2982
2	TraesCS6B01G398600	chr4D	132435219	132437788	2569	True	3735.000000	3735	93.041000	1	2561	1	chr4D.!!$R1	2560
3	TraesCS6B01G398600	chr7D	72311920	72314849	2929	True	2484.500000	4294	97.593500	1	2984	2	chr7D.!!$R2	2983
4	TraesCS6B01G398600	chr7D	235508374	235509466	1092	True	1781.000000	1781	96.014000	1475	2573	1	chr7D.!!$R1	1098
5	TraesCS6B01G398600	chr5B	236065703	236068639	2936	True	2404.000000	4185	96.526500	1	2984	2	chr5B.!!$R1	2983
6	TraesCS6B01G398600	chr4A	740667875	740670327	2452	False	2013.000000	3398	96.053500	478	2984	2	chr4A.!!$F1	2506
7	TraesCS6B01G398600	chr5A	302992119	302995167	3048	False	2313.500000	2617	94.755500	1	2984	2	chr5A.!!$F2	2983
8	TraesCS6B01G398600	chr5A	257555258	257558305	3047	False	1616.666667	2623	96.583667	1	2984	3	chr5A.!!$F1	2983
9	TraesCS6B01G398600	chr2A	618957688	618959228	1540	False	2582.000000	2582	96.789000	1	1555	1	chr2A.!!$F1	1554
10	TraesCS6B01G398600	chr2A	755101550	755103111	1561	True	2579.000000	2579	96.327000	1	1578	1	chr2A.!!$R1	1577
11	TraesCS6B01G398600	chr2A	755092289	755095340	3051	True	1612.000000	2619	96.554000	1	2984	3	chr2A.!!$R2	2983
12	TraesCS6B01G398600	chr2A	618964302	618965681	1379	False	1108.500000	1587	96.493000	1576	2984	2	chr2A.!!$F2	1408

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
862	866	1.202348	GGAAGTGGCACAATAGGTTGC	59.798	52.381	21.41	5.59	44.16	4.17	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2566	2727	0.871057	CACACACACACACACACACA	59.129	50.0	0.0	0.0	0.0	3.72	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
403	406	1.272480	GGGGTTCCTTAGTGGTTGCAT	60.272	52.381	0.00	0.00	37.07	3.96
436	439	6.301486	TGGCAATAGATAGCACATTCTTGAT	58.699	36.000	0.00	0.00	0.00	2.57
440	443	4.785346	AGATAGCACATTCTTGATGGGT	57.215	40.909	0.00	0.00	41.45	4.51
473	476	3.082579	GCTGGCTAGTGCTACCGCT	62.083	63.158	0.00	0.00	39.59	5.52
724	728	1.618343	GTTCCATGGGAAGGTGTTTGG	59.382	52.381	13.02	0.00	42.88	3.28
731	735	1.480498	GGGAAGGTGTTTGGTGACCAT	60.480	52.381	4.56	0.00	34.36	3.55
773	777	7.060421	ACTCATGGAACCCGTATTTATTTGAT	58.940	34.615	0.00	0.00	0.00	2.57
789	793	8.770438	TTTATTTGATAAACATTGGGTTGCTC	57.230	30.769	0.00	0.00	40.35	4.26
796	800	1.637553	ACATTGGGTTGCTCTGGAGAT	59.362	47.619	1.35	0.00	0.00	2.75
799	803	4.079558	ACATTGGGTTGCTCTGGAGATAAT	60.080	41.667	1.35	0.00	0.00	1.28
806	810	5.825151	GGTTGCTCTGGAGATAATAAAGCTT	59.175	40.000	0.00	0.00	0.00	3.74
807	811	6.319911	GGTTGCTCTGGAGATAATAAAGCTTT	59.680	38.462	17.30	17.30	0.00	3.51
808	812	6.932356	TGCTCTGGAGATAATAAAGCTTTG	57.068	37.500	22.02	0.75	0.00	2.77
809	813	5.824624	TGCTCTGGAGATAATAAAGCTTTGG	59.175	40.000	22.02	0.00	0.00	3.28
810	814	5.240403	GCTCTGGAGATAATAAAGCTTTGGG	59.760	44.000	22.02	1.70	0.00	4.12
811	815	6.327386	TCTGGAGATAATAAAGCTTTGGGT	57.673	37.500	22.02	8.90	0.00	4.51
812	816	6.731467	TCTGGAGATAATAAAGCTTTGGGTT	58.269	36.000	22.02	14.90	34.34	4.11
813	817	6.603201	TCTGGAGATAATAAAGCTTTGGGTTG	59.397	38.462	22.02	2.24	33.11	3.77
814	818	6.252995	TGGAGATAATAAAGCTTTGGGTTGT	58.747	36.000	22.02	11.44	33.11	3.32
815	819	6.723977	TGGAGATAATAAAGCTTTGGGTTGTT	59.276	34.615	22.02	8.91	33.11	2.83
816	820	7.035612	GGAGATAATAAAGCTTTGGGTTGTTG	58.964	38.462	22.02	0.00	33.11	3.33
817	821	6.398095	AGATAATAAAGCTTTGGGTTGTTGC	58.602	36.000	22.02	2.62	33.11	4.17
818	822	4.687901	AATAAAGCTTTGGGTTGTTGCT	57.312	36.364	22.02	0.00	33.11	3.91
819	823	4.687901	ATAAAGCTTTGGGTTGTTGCTT	57.312	36.364	22.02	0.00	44.51	3.91
820	824	5.799827	ATAAAGCTTTGGGTTGTTGCTTA	57.200	34.783	22.02	0.00	42.23	3.09
821	825	3.452755	AAGCTTTGGGTTGTTGCTTAC	57.547	42.857	0.00	0.00	41.42	2.34
822	826	2.666317	AGCTTTGGGTTGTTGCTTACT	58.334	42.857	0.00	0.00	0.00	2.24
823	827	2.623416	AGCTTTGGGTTGTTGCTTACTC	59.377	45.455	0.00	0.00	0.00	2.59
824	828	2.360801	GCTTTGGGTTGTTGCTTACTCA	59.639	45.455	0.00	0.00	0.00	3.41
862	866	1.202348	GGAAGTGGCACAATAGGTTGC	59.798	52.381	21.41	5.59	44.16	4.17
1223	1227	2.290641	GTCGACAATGGCAAGTTTCTGT	59.709	45.455	11.55	0.00	0.00	3.41
1668	1777	6.039382	GTGTGTAGAGAACCACCAAAGAAAAT	59.961	38.462	0.00	0.00	0.00	1.82
1688	1797	7.659390	AGAAAATGACAAAGACAACCAAAACAA	59.341	29.630	0.00	0.00	0.00	2.83
1691	1800	5.601662	TGACAAAGACAACCAAAACAACAA	58.398	33.333	0.00	0.00	0.00	2.83
1873	2001	7.520451	AAAAGGGGAAACATGTTAACTCTAC	57.480	36.000	12.39	0.00	0.00	2.59
1911	2039	9.450807	CAAAAAGGTGATTACAACTAGTTCAAG	57.549	33.333	4.77	0.00	43.96	3.02
1984	2116	4.005650	TCTCACCATAGCAAAAGCTTGAG	58.994	43.478	0.00	9.48	34.14	3.02
1985	2117	4.005650	CTCACCATAGCAAAAGCTTGAGA	58.994	43.478	0.00	0.00	34.14	3.27
2179	2316	5.590259	CCAATTTCCATCGAGTTTCCTATGT	59.410	40.000	0.00	0.00	0.00	2.29
2234	2374	1.065126	GGGCAAGAGTAAGGAGTGCAT	60.065	52.381	0.00	0.00	36.93	3.96
2243	2383	5.703130	AGAGTAAGGAGTGCATTGAAAAGAC	59.297	40.000	0.00	0.00	0.00	3.01
2352	2492	1.812571	AGGCGGCTTAGTTTGTGATTG	59.187	47.619	5.25	0.00	0.00	2.67
2423	2564	4.002982	GCTCATGTGATGTACTTGTGGAA	58.997	43.478	0.00	0.00	36.23	3.53
2509	2667	9.679661	AATGTGAACCTAAATGTGATGTATGTA	57.320	29.630	0.00	0.00	0.00	2.29
2566	2727	3.120234	CGATGCATATTGTGTGTGTGTGT	60.120	43.478	0.00	0.00	0.00	3.72
2569	2730	3.243002	TGCATATTGTGTGTGTGTGTGTG	60.243	43.478	0.00	0.00	0.00	3.82
2571	2732	2.917701	ATTGTGTGTGTGTGTGTGTG	57.082	45.000	0.00	0.00	0.00	3.82
2575	2736	0.871057	TGTGTGTGTGTGTGTGTGTG	59.129	50.000	0.00	0.00	0.00	3.82
2577	2738	0.871057	TGTGTGTGTGTGTGTGTGTG	59.129	50.000	0.00	0.00	0.00	3.82
2579	2740	0.871057	TGTGTGTGTGTGTGTGTGTG	59.129	50.000	0.00	0.00	0.00	3.82
2581	2742	0.871057	TGTGTGTGTGTGTGTGTGTG	59.129	50.000	0.00	0.00	0.00	3.82
2583	2744	0.871057	TGTGTGTGTGTGTGTGTGTG	59.129	50.000	0.00	0.00	0.00	3.82
2585	2746	0.871057	TGTGTGTGTGTGTGTGTGTG	59.129	50.000	0.00	0.00	0.00	3.82
2587	2748	0.871057	TGTGTGTGTGTGTGTGTGTG	59.129	50.000	0.00	0.00	0.00	3.82
2589	2750	0.871057	TGTGTGTGTGTGTGTGTGTG	59.129	50.000	0.00	0.00	0.00	3.82
2591	2752	0.871057	TGTGTGTGTGTGTGTGTGTG	59.129	50.000	0.00	0.00	0.00	3.82
2593	2754	0.871057	TGTGTGTGTGTGTGTGTGTG	59.129	50.000	0.00	0.00	0.00	3.82
2595	2756	0.871057	TGTGTGTGTGTGTGTGTGTG	59.129	50.000	0.00	0.00	0.00	3.82
2597	2758	0.871057	TGTGTGTGTGTGTGTGTGTG	59.129	50.000	0.00	0.00	0.00	3.82
2599	2760	0.871057	TGTGTGTGTGTGTGTGTGTG	59.129	50.000	0.00	0.00	0.00	3.82
2601	2762	0.871057	TGTGTGTGTGTGTGTGTGTG	59.129	50.000	0.00	0.00	0.00	3.82
2603	2764	0.871057	TGTGTGTGTGTGTGTGTGTG	59.129	50.000	0.00	0.00	0.00	3.82
2605	2766	0.871057	TGTGTGTGTGTGTGTGTGTG	59.129	50.000	0.00	0.00	0.00	3.82
2607	2768	0.871057	TGTGTGTGTGTGTGTGTGTG	59.129	50.000	0.00	0.00	0.00	3.82
2608	2769	0.871722	GTGTGTGTGTGTGTGTGTGT	59.128	50.000	0.00	0.00	0.00	3.72
2609	2770	0.871057	TGTGTGTGTGTGTGTGTGTG	59.129	50.000	0.00	0.00	0.00	3.82
2837	3013	5.778241	ACCAGGGGTAAAAAGGTATTTTCAG	59.222	40.000	0.00	0.00	37.65	3.02
2922	3098	3.638160	AGTGCATGTGTCAAACAAGGAAT	59.362	39.130	0.00	0.00	43.61	3.01

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
24	26	3.900966	TGCACTAGAGCAATCATGACT	57.099	42.857	12.75	0.00	42.46	3.41
436	439	1.464395	TGCCCCTTGAACCTACCCA	60.464	57.895	0.00	0.00	0.00	4.51
440	443	1.685224	CAGCTGCCCCTTGAACCTA	59.315	57.895	0.00	0.00	0.00	3.08
724	728	1.270550	CAGCAACCCAAAGATGGTCAC	59.729	52.381	0.00	0.00	46.01	3.67
731	735	2.158682	TGAGTAAGCAGCAACCCAAAGA	60.159	45.455	0.00	0.00	0.00	2.52
773	777	3.073798	TCTCCAGAGCAACCCAATGTTTA	59.926	43.478	0.00	0.00	34.00	2.01
789	793	6.378280	ACAACCCAAAGCTTTATTATCTCCAG	59.622	38.462	12.25	0.00	0.00	3.86
796	800	5.799827	AGCAACAACCCAAAGCTTTATTA	57.200	34.783	12.25	0.00	29.98	0.98
799	803	4.647399	AGTAAGCAACAACCCAAAGCTTTA	59.353	37.500	12.25	0.00	42.36	1.85
806	810	2.295909	GCATGAGTAAGCAACAACCCAA	59.704	45.455	0.00	0.00	0.00	4.12
807	811	1.885887	GCATGAGTAAGCAACAACCCA	59.114	47.619	0.00	0.00	0.00	4.51
808	812	1.885887	TGCATGAGTAAGCAACAACCC	59.114	47.619	0.00	0.00	37.90	4.11
809	813	3.641437	TTGCATGAGTAAGCAACAACC	57.359	42.857	0.00	0.00	44.98	3.77
862	866	4.158764	AGTTGAGAATTGACTCCTAGACCG	59.841	45.833	0.00	0.00	36.22	4.79
1668	1777	5.201713	TGTTGTTTTGGTTGTCTTTGTCA	57.798	34.783	0.00	0.00	0.00	3.58
1688	1797	4.561326	GCAAGGCACAATGGATAACTTTGT	60.561	41.667	0.00	0.00	45.22	2.83
1691	1800	2.164219	CGCAAGGCACAATGGATAACTT	59.836	45.455	0.00	0.00	0.00	2.66
1984	2116	6.485313	CCCCTTTTCCCTTTTTGTTTGTATTC	59.515	38.462	0.00	0.00	0.00	1.75
1985	2117	6.361433	CCCCTTTTCCCTTTTTGTTTGTATT	58.639	36.000	0.00	0.00	0.00	1.89
2082	2219	5.407387	CAGCAGCAGTTTTTAGCAATTGAAT	59.593	36.000	10.34	0.00	0.00	2.57
2179	2316	3.057596	GGAACATTTGTTTCATCGCTGGA	60.058	43.478	0.00	0.00	38.56	3.86
2234	2374	3.073798	TGGCACCATAGGAGTCTTTTCAA	59.926	43.478	0.00	0.00	0.00	2.69
2243	2383	1.278985	TGTCTTGTGGCACCATAGGAG	59.721	52.381	16.26	3.80	0.00	3.69
2352	2492	6.924111	ACCATGACATTAAGGAAAACATGAC	58.076	36.000	0.00	0.00	36.70	3.06
2423	2564	3.118261	ACTGTTTCACACATGAGGTCAGT	60.118	43.478	0.00	4.37	37.20	3.41
2509	2667	1.272313	ACCAGAAGCAGCCATGTTCAT	60.272	47.619	0.00	0.00	0.00	2.57
2566	2727	0.871057	CACACACACACACACACACA	59.129	50.000	0.00	0.00	0.00	3.72
2569	2730	0.871722	ACACACACACACACACACAC	59.128	50.000	0.00	0.00	0.00	3.82
2571	2732	0.871722	ACACACACACACACACACAC	59.128	50.000	0.00	0.00	0.00	3.82
2575	2736	0.871722	ACACACACACACACACACAC	59.128	50.000	0.00	0.00	0.00	3.82
2577	2738	0.871722	ACACACACACACACACACAC	59.128	50.000	0.00	0.00	0.00	3.82
2579	2740	0.871722	ACACACACACACACACACAC	59.128	50.000	0.00	0.00	0.00	3.82
2581	2742	0.871722	ACACACACACACACACACAC	59.128	50.000	0.00	0.00	0.00	3.82
2583	2744	0.871722	ACACACACACACACACACAC	59.128	50.000	0.00	0.00	0.00	3.82
2585	2746	0.871722	ACACACACACACACACACAC	59.128	50.000	0.00	0.00	0.00	3.82
2587	2748	0.871722	ACACACACACACACACACAC	59.128	50.000	0.00	0.00	0.00	3.82
2589	2750	0.871722	ACACACACACACACACACAC	59.128	50.000	0.00	0.00	0.00	3.82
2591	2752	0.871722	ACACACACACACACACACAC	59.128	50.000	0.00	0.00	0.00	3.82
2593	2754	2.933260	TCATACACACACACACACACAC	59.067	45.455	0.00	0.00	0.00	3.82
2595	2756	4.811555	ATTCATACACACACACACACAC	57.188	40.909	0.00	0.00	0.00	3.82
2597	2758	4.969395	CACAATTCATACACACACACACAC	59.031	41.667	0.00	0.00	0.00	3.82
2599	2760	4.969395	CACACAATTCATACACACACACAC	59.031	41.667	0.00	0.00	0.00	3.82
2601	2762	5.236263	TCTCACACAATTCATACACACACAC	59.764	40.000	0.00	0.00	0.00	3.82
2603	2764	5.922739	TCTCACACAATTCATACACACAC	57.077	39.130	0.00	0.00	0.00	3.82
2605	2766	7.254898	CCCATATCTCACACAATTCATACACAC	60.255	40.741	0.00	0.00	0.00	3.82
2607	2768	6.992123	TCCCATATCTCACACAATTCATACAC	59.008	38.462	0.00	0.00	0.00	2.90
2608	2769	7.135591	TCCCATATCTCACACAATTCATACA	57.864	36.000	0.00	0.00	0.00	2.29
2609	2770	7.879677	TGATCCCATATCTCACACAATTCATAC	59.120	37.037	0.00	0.00	0.00	2.39
2837	3013	6.154445	TCACTAACGGTGTTAAAGACAGATC	58.846	40.000	0.00	0.00	45.50	2.75
2922	3098	7.310983	CCCTATTTGGCCCTGAAGAAATTTTTA	60.311	37.037	0.00	0.00	0.00	1.52

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.