AutoCloner

Multiple sequence alignment - TraesCS6B01G318800

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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	TraesCS6B01G318800	chr6B	100.000	3572	0	0	1	3572	566538905	566535334	0.000000e+00	6597
1	TraesCS6B01G318800	chr6B	86.236	1780	164	40	608	2349	147961114	147962850	0.000000e+00	1855
2	TraesCS6B01G318800	chr6B	84.824	850	105	8	983	1808	140451435	140450586	0.000000e+00	833
3	TraesCS6B01G318800	chr6B	80.688	378	47	10	1456	1808	140413214	140412838	1.630000e-68	270
4	TraesCS6B01G318800	chr6D	94.840	2403	105	12	343	2732	379720811	379723207	0.000000e+00	3733
5	TraesCS6B01G318800	chr6D	86.584	1774	177	30	613	2360	73587624	73589362	0.000000e+00	1901
6	TraesCS6B01G318800	chr6D	90.654	642	29	9	2943	3572	379723552	379724174	0.000000e+00	824
7	TraesCS6B01G318800	chr6D	84.314	867	103	6	983	1816	65390056	65389190	0.000000e+00	817
8	TraesCS6B01G318800	chr6A	92.055	2530	136	28	1	2490	520873464	520870960	0.000000e+00	3498
9	TraesCS6B01G318800	chr6A	86.244	1781	177	35	613	2360	90032316	90034061	0.000000e+00	1869
10	TraesCS6B01G318800	chr6A	92.471	611	25	11	2976	3565	520870345	520869735	0.000000e+00	854
11	TraesCS6B01G318800	chr6A	84.660	867	97	7	983	1816	83362151	83363014	0.000000e+00	832
12	TraesCS6B01G318800	chr7B	96.282	511	12	3	1	510	651358909	651359413	0.000000e+00	832
13	TraesCS6B01G318800	chr7B	96.767	433	7	3	79	510	442800712	442801138	0.000000e+00	715
14	TraesCS6B01G318800	chr3B	96.282	511	12	3	1	510	278404243	278404747	0.000000e+00	832
15	TraesCS6B01G318800	chr5B	95.499	511	16	3	1	510	141600803	141600299	0.000000e+00	809
16	TraesCS6B01G318800	chr5B	95.989	349	8	2	162	510	524924650	524924992	2.410000e-156	562
17	TraesCS6B01G318800	chr5B	95.181	166	8	0	1	166	524914490	524914655	2.730000e-66	263
18	TraesCS6B01G318800	chr7A	87.500	184	18	3	686	869	310667506	310667684	1.300000e-49	207
19	TraesCS6B01G318800	chr2A	85.606	132	14	4	976	1104	22184903	22184774	2.240000e-27	134

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	TraesCS6B01G318800	chr6B	566535334	566538905	3571	True	6597.0	6597	100.000	1	3572	1	chr6B.!!$R3	3571
1	TraesCS6B01G318800	chr6B	147961114	147962850	1736	False	1855.0	1855	86.236	608	2349	1	chr6B.!!$F1	1741
2	TraesCS6B01G318800	chr6B	140450586	140451435	849	True	833.0	833	84.824	983	1808	1	chr6B.!!$R2	825
3	TraesCS6B01G318800	chr6D	379720811	379724174	3363	False	2278.5	3733	92.747	343	3572	2	chr6D.!!$F2	3229
4	TraesCS6B01G318800	chr6D	73587624	73589362	1738	False	1901.0	1901	86.584	613	2360	1	chr6D.!!$F1	1747
5	TraesCS6B01G318800	chr6D	65389190	65390056	866	True	817.0	817	84.314	983	1816	1	chr6D.!!$R1	833
6	TraesCS6B01G318800	chr6A	520869735	520873464	3729	True	2176.0	3498	92.263	1	3565	2	chr6A.!!$R1	3564
7	TraesCS6B01G318800	chr6A	90032316	90034061	1745	False	1869.0	1869	86.244	613	2360	1	chr6A.!!$F2	1747
8	TraesCS6B01G318800	chr6A	83362151	83363014	863	False	832.0	832	84.660	983	1816	1	chr6A.!!$F1	833
9	TraesCS6B01G318800	chr7B	651358909	651359413	504	False	832.0	832	96.282	1	510	1	chr7B.!!$F2	509
10	TraesCS6B01G318800	chr3B	278404243	278404747	504	False	832.0	832	96.282	1	510	1	chr3B.!!$F1	509
11	TraesCS6B01G318800	chr5B	141600299	141600803	504	True	809.0	809	95.499	1	510	1	chr5B.!!$R1	509

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
592	623	0.464452	ACTCTAATCCCCTTTCCGCG	59.536	55.0	0.0	0.0	0.00	6.46	F
1650	1707	0.947244	CAACTCACAGTCAAGGTGCC	59.053	55.0	0.0	0.0	36.22	5.01	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1992	2067	0.392863	CATGCATCACGTCCTTGGGA	60.393	55.0	0.0	0.00	0.0	4.37	R
2719	2850	0.038892	AAAATGAAGGCAGCGCTGTG	60.039	50.0	35.8	15.92	0.0	3.66	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
62	64	8.482852	TCCTTGAGATATGATATTCAGTGTCA	57.517	34.615	0.00	0.00	32.16	3.58
106	108	5.711506	ATGAGTTTGTCATTATGCCTTGACA	59.288	36.000	1.84	1.84	44.05	3.58
248	252	4.264460	TGTGAACTTGCTGGTTGTTTTT	57.736	36.364	0.02	0.00	0.00	1.94
249	253	3.993081	TGTGAACTTGCTGGTTGTTTTTG	59.007	39.130	0.02	0.00	0.00	2.44
262	280	7.383102	TGGTTGTTTTTGTGTAATTTGCATT	57.617	28.000	0.00	0.00	0.00	3.56
549	579	1.985473	ACAATTCTGCCAGCAACTGA	58.015	45.000	0.00	0.00	32.44	3.41
550	580	1.610522	ACAATTCTGCCAGCAACTGAC	59.389	47.619	0.00	0.00	32.44	3.51
552	582	0.610232	ATTCTGCCAGCAACTGACCC	60.610	55.000	0.00	0.00	32.44	4.46
591	622	3.323979	TGATACTCTAATCCCCTTTCCGC	59.676	47.826	0.00	0.00	0.00	5.54
592	623	0.464452	ACTCTAATCCCCTTTCCGCG	59.536	55.000	0.00	0.00	0.00	6.46
930	963	3.480470	CCAGCTCAGTTTTCTTCAAGGA	58.520	45.455	0.00	0.00	0.00	3.36
953	986	1.824230	AGCAGCTACTCTCACTTCTGG	59.176	52.381	0.00	0.00	0.00	3.86
1410	1446	4.074259	CTGATGTTGACATGAGGGACAAA	58.926	43.478	0.00	0.00	34.57	2.83
1650	1707	0.947244	CAACTCACAGTCAAGGTGCC	59.053	55.000	0.00	0.00	36.22	5.01
1975	2050	1.079543	CAGCTCAAGGGTGTCCTCG	60.080	63.158	0.00	0.00	44.07	4.63
1992	2067	2.041405	GCCTCCTCAGCCCTACCT	60.041	66.667	0.00	0.00	0.00	3.08
2038	2113	3.499406	AGGCACTCTTCCATGGCA	58.501	55.556	6.96	0.00	43.55	4.92
2091	2166	2.180432	ACAAGAAGTACCTTTCCGCC	57.820	50.000	0.00	0.00	0.00	6.13
2355	2430	1.154131	CGACGAGTGAGAGGCAGTG	60.154	63.158	0.00	0.00	0.00	3.66
2450	2527	3.634568	TCCGTATTTGCCTGTTGTTTG	57.365	42.857	0.00	0.00	0.00	2.93
2501	2626	4.297299	TGAGTCAGTTAAACGAACGACT	57.703	40.909	11.79	11.79	45.81	4.18
2514	2639	3.314635	ACGAACGACTATATGTCTGGTCC	59.685	47.826	0.14	0.00	43.25	4.46
2544	2669	2.094286	TGGTGTGCCTGTTTGTTTTCTG	60.094	45.455	0.00	0.00	35.27	3.02
2546	2671	2.094234	GTGTGCCTGTTTGTTTTCTGGT	60.094	45.455	0.00	0.00	0.00	4.00
2555	2680	6.405731	CCTGTTTGTTTTCTGGTCATCTTTCA	60.406	38.462	0.00	0.00	0.00	2.69
2556	2681	7.111247	TGTTTGTTTTCTGGTCATCTTTCAT	57.889	32.000	0.00	0.00	0.00	2.57
2607	2735	8.565896	TGTGAGATGCTGTTATATCAAGTTTT	57.434	30.769	0.00	0.00	30.88	2.43
2608	2736	8.453320	TGTGAGATGCTGTTATATCAAGTTTTG	58.547	33.333	0.00	0.00	30.88	2.44
2610	2738	7.611467	TGAGATGCTGTTATATCAAGTTTTGGT	59.389	33.333	0.00	0.00	0.00	3.67
2657	2786	2.228582	TGCGTTATTGAGTTGCATGCTT	59.771	40.909	20.33	4.32	0.00	3.91
2661	2790	5.097529	CGTTATTGAGTTGCATGCTTGAAT	58.902	37.500	20.33	12.27	0.00	2.57
2719	2850	6.431234	AGACAGGTAATGTTGATTTTCCAGTC	59.569	38.462	0.00	0.00	44.17	3.51
2723	2854	6.207417	AGGTAATGTTGATTTTCCAGTCACAG	59.793	38.462	0.00	0.00	0.00	3.66
2724	2855	3.988379	TGTTGATTTTCCAGTCACAGC	57.012	42.857	0.00	0.00	0.00	4.40
2732	2863	2.667536	CAGTCACAGCGCTGCCTT	60.668	61.111	36.28	15.72	0.00	4.35
2733	2864	2.358003	AGTCACAGCGCTGCCTTC	60.358	61.111	36.28	22.72	0.00	3.46
2734	2865	2.666190	GTCACAGCGCTGCCTTCA	60.666	61.111	36.28	13.47	0.00	3.02
2735	2866	2.037136	GTCACAGCGCTGCCTTCAT	61.037	57.895	36.28	14.06	0.00	2.57
2737	2868	0.890542	TCACAGCGCTGCCTTCATTT	60.891	50.000	36.28	12.43	0.00	2.32
2772	2940	4.277257	TGATTGTGCAATTACATCGCTC	57.723	40.909	0.00	0.00	0.00	5.03
2777	2945	3.557185	TGTGCAATTACATCGCTCTCATC	59.443	43.478	0.00	0.00	0.00	2.92
2778	2946	3.557185	GTGCAATTACATCGCTCTCATCA	59.443	43.478	0.00	0.00	0.00	3.07
2788	2956	4.736126	TCGCTCTCATCAAAATCACCTA	57.264	40.909	0.00	0.00	0.00	3.08
2799	2967	9.993454	TCATCAAAATCACCTAGATAGATTCTG	57.007	33.333	0.00	0.00	35.39	3.02
2800	2968	8.719648	CATCAAAATCACCTAGATAGATTCTGC	58.280	37.037	0.00	0.00	35.39	4.26
2814	2982	8.481314	AGATAGATTCTGCTTGTATTTCTGTGA	58.519	33.333	0.00	0.00	31.79	3.58
2815	2983	6.734104	AGATTCTGCTTGTATTTCTGTGAC	57.266	37.500	0.00	0.00	0.00	3.67
2816	2984	4.990543	TTCTGCTTGTATTTCTGTGACG	57.009	40.909	0.00	0.00	0.00	4.35
2817	2985	4.251543	TCTGCTTGTATTTCTGTGACGA	57.748	40.909	0.00	0.00	0.00	4.20
2935	3230	3.561143	AGTACATGGCAAAACTGGACAA	58.439	40.909	4.14	0.00	0.00	3.18
2936	3231	2.888834	ACATGGCAAAACTGGACAAC	57.111	45.000	0.00	0.00	0.00	3.32
2940	3235	2.023673	TGGCAAAACTGGACAACTCAG	58.976	47.619	0.00	0.00	38.16	3.35
2972	3267	6.825610	TGCCAACATTTTCTTATTTGGAACT	58.174	32.000	2.83	0.00	39.33	3.01
3073	3386	8.364894	AGGTACAAAAATGGTAATTCAAGTTCC	58.635	33.333	0.00	0.00	0.00	3.62
3122	3441	0.536687	CATATCACCCTGGGCAGCAG	60.537	60.000	14.08	0.00	0.00	4.24
3142	3461	1.451936	AAGCTCAACTTGTCCCGCT	59.548	52.632	0.00	0.00	37.17	5.52
3148	3467	1.004918	AACTTGTCCCGCTTCCTCG	60.005	57.895	0.00	0.00	0.00	4.63
3151	3470	3.277211	TTGTCCCGCTTCCTCGACG	62.277	63.158	0.00	0.00	0.00	5.12

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
106	108	5.755375	CCATTTACTCTTGATCACGTGCTAT	59.245	40.000	11.67	0.00	0.00	2.97
248	252	8.429493	TTTGAATGTTCAATGCAAATTACACA	57.571	26.923	8.82	0.00	45.65	3.72
262	280	9.753674	AAAGAGGGTAAGATATTTGAATGTTCA	57.246	29.630	0.00	0.00	34.92	3.18
549	579	5.178096	TCACACAGTATCAATTCATGGGT	57.822	39.130	0.00	0.00	0.00	4.51
550	580	6.994496	AGTATCACACAGTATCAATTCATGGG	59.006	38.462	0.00	0.00	0.00	4.00
552	582	8.883954	AGAGTATCACACAGTATCAATTCATG	57.116	34.615	0.00	0.00	37.82	3.07
579	610	0.250467	CATCATCGCGGAAAGGGGAT	60.250	55.000	6.13	0.00	39.85	3.85
591	622	9.787532	ACTGAATTAAAAATTACACCATCATCG	57.212	29.630	0.00	0.00	0.00	3.84
682	715	3.118112	AGCAATACAGAGGCTGCTACATT	60.118	43.478	0.00	0.00	43.17	2.71
684	717	1.833630	AGCAATACAGAGGCTGCTACA	59.166	47.619	0.00	0.00	43.17	2.74
930	963	1.548269	GAAGTGAGAGTAGCTGCTGGT	59.452	52.381	9.82	0.00	0.00	4.00
953	986	8.983724	GCAGGTACTATCAGATGTAGAAAATTC	58.016	37.037	0.00	0.00	36.02	2.17
975	1008	0.522180	CTCAAGCTTTCTGCAGCAGG	59.478	55.000	22.62	7.67	45.94	4.85
1950	2025	2.350134	CCCTTGAGCTGAGCTGCA	59.650	61.111	13.71	7.12	39.88	4.41
1975	2050	2.041405	AGGTAGGGCTGAGGAGGC	60.041	66.667	0.00	0.00	44.21	4.70
1992	2067	0.392863	CATGCATCACGTCCTTGGGA	60.393	55.000	0.00	0.00	0.00	4.37
2091	2166	3.197790	CCTTCATCAGGCACCGCG	61.198	66.667	0.00	0.00	35.13	6.46
2355	2430	1.523938	GGTGGTAGGGAATCGCAGC	60.524	63.158	0.00	0.00	0.00	5.25
2431	2508	2.058057	GCAAACAACAGGCAAATACGG	58.942	47.619	0.00	0.00	0.00	4.02
2450	2527	6.705825	AGAAATAACCAAAAACTCAATGGTGC	59.294	34.615	0.00	0.00	46.46	5.01
2480	2602	4.297299	AGTCGTTCGTTTAACTGACTCA	57.703	40.909	0.00	0.00	42.73	3.41
2501	2626	3.641436	AGATGCAACGGACCAGACATATA	59.359	43.478	0.00	0.00	0.00	0.86
2514	2639	1.968017	AGGCACACCAGATGCAACG	60.968	57.895	0.00	0.00	45.27	4.10
2544	2669	6.481954	ACGTAGTTTCAATGAAAGATGACC	57.518	37.500	8.88	0.00	37.78	4.02
2580	2705	9.836864	AAACTTGATATAACAGCATCTCACATA	57.163	29.630	0.00	0.00	0.00	2.29
2628	2757	7.078011	TGCAACTCAATAACGCATATAACAA	57.922	32.000	0.00	0.00	0.00	2.83
2636	2765	1.811965	AGCATGCAACTCAATAACGCA	59.188	42.857	21.98	0.00	36.95	5.24
2657	2786	8.585471	AGATTTCTGGATAAGCAAAAGATTCA	57.415	30.769	0.00	0.00	0.00	2.57
2661	2790	7.067859	CCATGAGATTTCTGGATAAGCAAAAGA	59.932	37.037	0.00	0.00	31.38	2.52
2693	2824	7.458397	ACTGGAAAATCAACATTACCTGTCTA	58.542	34.615	0.00	0.00	36.98	2.59
2719	2850	0.038892	AAAATGAAGGCAGCGCTGTG	60.039	50.000	35.80	15.92	0.00	3.66
2723	2854	2.724349	CTGATAAAATGAAGGCAGCGC	58.276	47.619	0.00	0.00	0.00	5.92
2724	2855	2.724349	GCTGATAAAATGAAGGCAGCG	58.276	47.619	0.00	0.00	39.23	5.18
2732	2863	9.791820	CACAATCAACATTAGCTGATAAAATGA	57.208	29.630	12.09	5.47	35.18	2.57
2733	2864	8.537223	GCACAATCAACATTAGCTGATAAAATG	58.463	33.333	0.00	0.00	36.80	2.32
2734	2865	8.252417	TGCACAATCAACATTAGCTGATAAAAT	58.748	29.630	0.00	0.00	30.66	1.82
2735	2866	7.600960	TGCACAATCAACATTAGCTGATAAAA	58.399	30.769	0.00	0.00	30.66	1.52
2737	2868	6.756299	TGCACAATCAACATTAGCTGATAA	57.244	33.333	0.00	0.00	30.66	1.75
2777	2945	8.557864	CAAGCAGAATCTATCTAGGTGATTTTG	58.442	37.037	13.81	13.81	36.32	2.44
2778	2946	8.270744	ACAAGCAGAATCTATCTAGGTGATTTT	58.729	33.333	0.00	0.00	36.32	1.82
2788	2956	8.481314	TCACAGAAATACAAGCAGAATCTATCT	58.519	33.333	0.00	0.00	39.68	1.98
2797	2965	3.990469	ACTCGTCACAGAAATACAAGCAG	59.010	43.478	0.00	0.00	0.00	4.24
2799	2967	4.992381	AACTCGTCACAGAAATACAAGC	57.008	40.909	0.00	0.00	0.00	4.01
2800	2968	9.710979	TTTAAAAACTCGTCACAGAAATACAAG	57.289	29.630	0.00	0.00	0.00	3.16
2898	3109	8.261522	TGCCATGTACTCATGTACTATAACAAA	58.738	33.333	7.67	0.00	46.99	2.83
2900	3111	7.354751	TGCCATGTACTCATGTACTATAACA	57.645	36.000	7.67	0.00	46.99	2.41
2901	3112	8.657074	TTTGCCATGTACTCATGTACTATAAC	57.343	34.615	7.67	0.00	46.99	1.89
2903	3114	8.482943	AGTTTTGCCATGTACTCATGTACTATA	58.517	33.333	7.67	0.00	46.99	1.31
2904	3115	7.280876	CAGTTTTGCCATGTACTCATGTACTAT	59.719	37.037	7.67	0.00	46.99	2.12
2905	3116	6.593770	CAGTTTTGCCATGTACTCATGTACTA	59.406	38.462	7.67	0.00	46.99	1.82
2906	3117	5.412594	CAGTTTTGCCATGTACTCATGTACT	59.587	40.000	7.67	0.00	46.99	2.73
2909	3120	3.507233	CCAGTTTTGCCATGTACTCATGT	59.493	43.478	7.30	0.00	46.99	3.21
2911	3122	3.758554	GTCCAGTTTTGCCATGTACTCAT	59.241	43.478	0.00	0.00	34.21	2.90
2912	3123	3.146066	GTCCAGTTTTGCCATGTACTCA	58.854	45.455	0.00	0.00	0.00	3.41
2914	3125	3.222173	TGTCCAGTTTTGCCATGTACT	57.778	42.857	0.00	0.00	0.00	2.73
2915	3126	3.317993	AGTTGTCCAGTTTTGCCATGTAC	59.682	43.478	0.00	0.00	0.00	2.90
2916	3127	3.561143	AGTTGTCCAGTTTTGCCATGTA	58.439	40.909	0.00	0.00	0.00	2.29
2918	3129	2.361757	TGAGTTGTCCAGTTTTGCCATG	59.638	45.455	0.00	0.00	0.00	3.66
2921	3132	1.269257	GCTGAGTTGTCCAGTTTTGCC	60.269	52.381	0.00	0.00	34.29	4.52
2922	3133	1.405105	TGCTGAGTTGTCCAGTTTTGC	59.595	47.619	0.00	0.00	34.29	3.68
2923	3134	2.684881	AGTGCTGAGTTGTCCAGTTTTG	59.315	45.455	0.00	0.00	34.29	2.44
3135	3454	4.493747	CCGTCGAGGAAGCGGGAC	62.494	72.222	6.70	0.00	45.00	4.46

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.