AutoCloner

Multiple sequence alignment - TraesCS6A01G181200

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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	TraesCS6A01G181200	chr6A	100.000	2548	0	0	991	3538	206133791	206136338	0.000000e+00	4706.0
1	TraesCS6A01G181200	chr6A	100.000	787	0	0	1	787	206132801	206133587	0.000000e+00	1454.0
2	TraesCS6A01G181200	chr6A	93.478	46	0	3	743	785	613912926	613912881	8.200000e-07	65.8
3	TraesCS6A01G181200	chr5A	94.442	2555	115	10	991	3537	210234464	210231929	0.000000e+00	3906.0
4	TraesCS6A01G181200	chr5A	94.016	2557	121	15	991	3537	147590503	147593037	0.000000e+00	3845.0
5	TraesCS6A01G181200	chr5A	93.699	2555	130	15	991	3537	213233968	213231437	0.000000e+00	3797.0
6	TraesCS6A01G181200	chr5A	86.935	597	72	6	3	595	219442504	219441910	0.000000e+00	665.0
7	TraesCS6A01G181200	chr5A	90.045	442	41	3	1180	1620	35913222	35913661	1.430000e-158	569.0
8	TraesCS6A01G181200	chr1A	94.251	2557	116	15	991	3537	147728859	147726324	0.000000e+00	3879.0
9	TraesCS6A01G181200	chr1A	85.902	610	82	3	4	611	248682052	248682659	0.000000e+00	647.0
10	TraesCS6A01G181200	chr1A	86.432	597	73	7	3	595	452530370	452530962	0.000000e+00	647.0
11	TraesCS6A01G181200	chr1A	88.557	201	21	1	587	787	147729213	147729015	3.530000e-60	243.0
12	TraesCS6A01G181200	chr4D	94.980	1972	89	6	991	2957	215033571	215035537	0.000000e+00	3085.0
13	TraesCS6A01G181200	chr4D	94.767	1032	43	8	2516	3537	313783419	313782389	0.000000e+00	1596.0
14	TraesCS6A01G181200	chr4D	87.141	941	77	25	1615	2518	15874836	15873903	0.000000e+00	1027.0
15	TraesCS6A01G181200	chr4D	93.771	594	27	6	2947	3537	215046728	215047314	0.000000e+00	883.0
16	TraesCS6A01G181200	chr4D	90.650	631	34	9	991	1620	313784507	313783901	0.000000e+00	815.0
17	TraesCS6A01G181200	chr4D	86.855	601	69	10	3	596	144599118	144598521	0.000000e+00	664.0
18	TraesCS6A01G181200	chr4D	89.091	165	8	6	632	787	215033247	215033410	2.790000e-46	196.0
19	TraesCS6A01G181200	chr4D	87.121	132	7	4	657	787	313784790	313784668	1.320000e-29	141.0
20	TraesCS6A01G181200	chr7A	92.823	1031	59	13	2516	3537	195277216	195276192	0.000000e+00	1480.0
21	TraesCS6A01G181200	chr7A	84.545	660	86	12	4	655	25146010	25145359	1.070000e-179	640.0
22	TraesCS6A01G181200	chr2A	92.502	1027	68	9	2516	3537	404058329	404059351	0.000000e+00	1461.0
23	TraesCS6A01G181200	chr2A	92.405	1027	69	9	2516	3537	402113211	402114233	0.000000e+00	1456.0
24	TraesCS6A01G181200	chr2A	86.111	432	43	6	1206	1620	404057436	404057867	1.940000e-122	449.0
25	TraesCS6A01G181200	chr4B	86.229	944	78	25	1615	2518	27398917	27397986	0.000000e+00	976.0
26	TraesCS6A01G181200	chr4B	86.913	596	68	10	3	593	295540284	295540874	0.000000e+00	660.0
27	TraesCS6A01G181200	chr4B	95.385	130	6	0	991	1120	206819769	206819898	1.290000e-49	207.0
28	TraesCS6A01G181200	chr3A	91.442	631	51	3	991	1620	281209406	281208778	0.000000e+00	863.0
29	TraesCS6A01G181200	chr7D	87.710	594	68	5	3	593	311375627	311375036	0.000000e+00	688.0
30	TraesCS6A01G181200	chr7D	86.891	595	71	6	3	593	325609647	325610238	0.000000e+00	660.0
31	TraesCS6A01G181200	chr7D	95.349	43	1	1	743	785	430413449	430413408	2.280000e-07	67.6
32	TraesCS6A01G181200	chr3D	87.374	594	69	6	3	593	280519451	280520041	0.000000e+00	676.0
33	TraesCS6A01G181200	chr3D	87.124	466	34	5	991	1454	604116969	604116528	4.080000e-139	505.0
34	TraesCS6A01G181200	chr3D	95.556	45	1	1	743	787	604117167	604117124	1.760000e-08	71.3
35	TraesCS6A01G181200	chr4A	91.152	486	37	4	2037	2518	584697312	584696829	0.000000e+00	654.0
36	TraesCS6A01G181200	chr6B	100.000	42	0	0	743	784	124325068	124325027	1.050000e-10	78.7
37	TraesCS6A01G181200	chr3B	97.561	41	1	0	744	784	283755108	283755068	1.760000e-08	71.3
38	TraesCS6A01G181200	chr3B	95.238	42	1	1	744	785	271735831	271735791	8.200000e-07	65.8

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	TraesCS6A01G181200	chr6A	206132801	206136338	3537	False	3080.000000	4706	100.0000	1	3538	2	chr6A.!!$F1	3537
1	TraesCS6A01G181200	chr5A	210231929	210234464	2535	True	3906.000000	3906	94.4420	991	3537	1	chr5A.!!$R1	2546
2	TraesCS6A01G181200	chr5A	147590503	147593037	2534	False	3845.000000	3845	94.0160	991	3537	1	chr5A.!!$F2	2546
3	TraesCS6A01G181200	chr5A	213231437	213233968	2531	True	3797.000000	3797	93.6990	991	3537	1	chr5A.!!$R2	2546
4	TraesCS6A01G181200	chr5A	219441910	219442504	594	True	665.000000	665	86.9350	3	595	1	chr5A.!!$R3	592
5	TraesCS6A01G181200	chr1A	147726324	147729213	2889	True	2061.000000	3879	91.4040	587	3537	2	chr1A.!!$R1	2950
6	TraesCS6A01G181200	chr1A	248682052	248682659	607	False	647.000000	647	85.9020	4	611	1	chr1A.!!$F1	607
7	TraesCS6A01G181200	chr1A	452530370	452530962	592	False	647.000000	647	86.4320	3	595	1	chr1A.!!$F2	592
8	TraesCS6A01G181200	chr4D	215033247	215035537	2290	False	1640.500000	3085	92.0355	632	2957	2	chr4D.!!$F2	2325
9	TraesCS6A01G181200	chr4D	15873903	15874836	933	True	1027.000000	1027	87.1410	1615	2518	1	chr4D.!!$R1	903
10	TraesCS6A01G181200	chr4D	215046728	215047314	586	False	883.000000	883	93.7710	2947	3537	1	chr4D.!!$F1	590
11	TraesCS6A01G181200	chr4D	313782389	313784790	2401	True	850.666667	1596	90.8460	657	3537	3	chr4D.!!$R3	2880
12	TraesCS6A01G181200	chr4D	144598521	144599118	597	True	664.000000	664	86.8550	3	596	1	chr4D.!!$R2	593
13	TraesCS6A01G181200	chr7A	195276192	195277216	1024	True	1480.000000	1480	92.8230	2516	3537	1	chr7A.!!$R2	1021
14	TraesCS6A01G181200	chr7A	25145359	25146010	651	True	640.000000	640	84.5450	4	655	1	chr7A.!!$R1	651
15	TraesCS6A01G181200	chr2A	402113211	402114233	1022	False	1456.000000	1456	92.4050	2516	3537	1	chr2A.!!$F1	1021
16	TraesCS6A01G181200	chr2A	404057436	404059351	1915	False	955.000000	1461	89.3065	1206	3537	2	chr2A.!!$F2	2331
17	TraesCS6A01G181200	chr4B	27397986	27398917	931	True	976.000000	976	86.2290	1615	2518	1	chr4B.!!$R1	903
18	TraesCS6A01G181200	chr4B	295540284	295540874	590	False	660.000000	660	86.9130	3	593	1	chr4B.!!$F2	590
19	TraesCS6A01G181200	chr3A	281208778	281209406	628	True	863.000000	863	91.4420	991	1620	1	chr3A.!!$R1	629
20	TraesCS6A01G181200	chr7D	311375036	311375627	591	True	688.000000	688	87.7100	3	593	1	chr7D.!!$R1	590
21	TraesCS6A01G181200	chr7D	325609647	325610238	591	False	660.000000	660	86.8910	3	593	1	chr7D.!!$F1	590
22	TraesCS6A01G181200	chr3D	280519451	280520041	590	False	676.000000	676	87.3740	3	593	1	chr3D.!!$F1	590
23	TraesCS6A01G181200	chr3D	604116528	604117167	639	True	288.150000	505	91.3400	743	1454	2	chr3D.!!$R1	711

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
661	675	0.033601	CCCCGATGGATTTGTTCCCA	60.034	55.0	0.0	0.0	44.77	4.37	F
1308	1333	0.035458	CCAACTCGTCTGCTTTCCCT	59.965	55.0	0.0	0.0	0.00	4.20	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2440	2890	1.063942	TCTTCGATCTAGGGTCTGGCA	60.064	52.381	0.0	0.0	0.00	4.92	R
2820	3276	1.600916	GGACTTGCTGGTTTCGCCT	60.601	57.895	0.0	0.0	38.35	5.52	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
112	115	4.333372	TGGAGTGAAAACAGTACCGAAAAC	59.667	41.667	0.00	0.00	0.00	2.43
175	179	7.924103	AATTTAAAACTGCTCTTAAACCGTG	57.076	32.000	0.00	0.00	31.63	4.94
248	252	4.368874	TTCCAATGGTGTATCATTTGCG	57.631	40.909	0.00	0.00	35.40	4.85
254	258	5.581126	ATGGTGTATCATTTGCGTCATTT	57.419	34.783	0.00	0.00	0.00	2.32
264	268	1.155889	TGCGTCATTTTGATGAGCGT	58.844	45.000	0.98	0.00	35.46	5.07
367	375	5.588240	AGGAATTTCGAAAAGTGTTCAACC	58.412	37.500	15.66	7.81	0.00	3.77
370	378	5.828299	ATTTCGAAAAGTGTTCAACCTGA	57.172	34.783	15.66	0.00	0.00	3.86
392	400	2.869801	CGAAGTTGCGCCTAATCCATAA	59.130	45.455	4.18	0.00	0.00	1.90
401	409	5.163663	TGCGCCTAATCCATAACTTTTCAAG	60.164	40.000	4.18	0.00	0.00	3.02
402	410	5.273944	CGCCTAATCCATAACTTTTCAAGC	58.726	41.667	0.00	0.00	0.00	4.01
403	411	5.163663	CGCCTAATCCATAACTTTTCAAGCA	60.164	40.000	0.00	0.00	0.00	3.91
527	539	2.698797	TCTGTAATGCAGTACCCTAGCC	59.301	50.000	20.63	0.00	45.23	3.93
536	548	2.832129	CAGTACCCTAGCCACAGAAAGA	59.168	50.000	0.00	0.00	0.00	2.52
552	564	0.882042	AAGAGCAGTGCCTTCGTGTG	60.882	55.000	12.58	0.00	0.00	3.82
578	590	1.459209	TGCAGTGCGAAAGTGTTATCG	59.541	47.619	11.20	0.00	41.81	2.92
599	613	5.386958	CGGAATAGTTATTCTGATCCCGA	57.613	43.478	13.16	0.00	46.90	5.14
600	614	5.779922	CGGAATAGTTATTCTGATCCCGAA	58.220	41.667	13.16	0.00	46.90	4.30
652	666	2.427889	CCCTATATAGGCCCCGATGGAT	60.428	54.545	21.75	0.00	42.26	3.41
661	675	0.033601	CCCCGATGGATTTGTTCCCA	60.034	55.000	0.00	0.00	44.77	4.37
669	683	1.899814	GGATTTGTTCCCAAACTCCCC	59.100	52.381	0.00	0.00	43.03	4.81
713	728	4.541648	ACCCTCCCTCGATCCCCG	62.542	72.222	0.00	0.00	40.25	5.73
723	738	2.829592	GATCCCCGACCATCCACC	59.170	66.667	0.00	0.00	0.00	4.61
726	741	0.993509	ATCCCCGACCATCCACCATT	60.994	55.000	0.00	0.00	0.00	3.16
1082	1105	3.610619	CTGGCACGCAGTCCATGGA	62.611	63.158	11.44	11.44	41.61	3.41
1158	1181	3.335183	TCCTCTTCTCCTTCTCTTCCTCA	59.665	47.826	0.00	0.00	0.00	3.86
1201	1224	2.040544	CCGTCAACACCAGGCATCC	61.041	63.158	0.00	0.00	0.00	3.51
1308	1333	0.035458	CCAACTCGTCTGCTTTCCCT	59.965	55.000	0.00	0.00	0.00	4.20
1430	1472	0.397564	TGCTGCTGTGTGAAGATCCA	59.602	50.000	0.00	0.00	0.00	3.41
1437	1479	2.124695	GTGAAGATCCACCGGCCC	60.125	66.667	0.00	0.00	0.00	5.80
1551	1594	4.225942	TGATGGATAAGCAAGAACAGAGGT	59.774	41.667	0.00	0.00	0.00	3.85
1561	1604	5.896678	AGCAAGAACAGAGGTAGATACAGAT	59.103	40.000	0.00	0.00	0.00	2.90
1562	1605	6.382570	AGCAAGAACAGAGGTAGATACAGATT	59.617	38.462	0.00	0.00	0.00	2.40
1728	2136	2.653726	ACAAGTTGCAGGTGTCATCAA	58.346	42.857	1.81	0.00	0.00	2.57
1758	2175	6.590234	AGTTTAATAGGCTTTTGTTCTGGG	57.410	37.500	0.00	0.00	0.00	4.45
2039	2481	3.589542	TGCCTGGGTTTGGGGGAG	61.590	66.667	0.00	0.00	0.00	4.30
2055	2497	2.623502	GGGGAGTGAGTAGTCCTGCTTA	60.624	54.545	0.00	0.00	44.49	3.09
2061	2503	4.959210	AGTGAGTAGTCCTGCTTATCACAT	59.041	41.667	5.36	0.00	40.74	3.21
2083	2526	8.327429	CACATGTTTTGTTTTGTTTATCTGTCC	58.673	33.333	0.00	0.00	36.00	4.02
2229	2674	1.024271	GGACCGTGTGTACCGCTATA	58.976	55.000	0.00	0.00	0.00	1.31
2235	2680	3.065233	CCGTGTGTACCGCTATAACTACA	59.935	47.826	0.00	0.00	0.00	2.74
2325	2770	1.180456	TCCCCGTCGTTGCAGAACTA	61.180	55.000	0.00	0.00	0.00	2.24
2417	2866	2.064434	TGTCACCTTGCAATTGGACA	57.936	45.000	17.87	17.87	33.31	4.02
2440	2890	6.607198	ACACATATCGGGGATTTGATCTTTTT	59.393	34.615	0.00	0.00	0.00	1.94
2457	2907	1.860641	TTTGCCAGACCCTAGATCGA	58.139	50.000	0.00	0.00	0.00	3.59
2462	2912	2.235016	CCAGACCCTAGATCGAAGAGG	58.765	57.143	0.00	0.00	43.63	3.69
2496	2946	0.390860	CAAGATACAGGAGGCCCTCG	59.609	60.000	4.29	0.00	42.02	4.63
2544	2994	9.273016	GTATTTATGCATCTTCCTAGTTGCTAA	57.727	33.333	0.19	0.00	44.07	3.09
2605	3059	6.035843	GCAAAAAGACAATCAAAGTGTGAGA	58.964	36.000	0.00	0.00	40.43	3.27
2606	3060	6.197842	GCAAAAAGACAATCAAAGTGTGAGAG	59.802	38.462	0.00	0.00	40.43	3.20
2704	3160	1.037579	GCCCATTTAGCCAGTGTCCC	61.038	60.000	0.00	0.00	0.00	4.46
2774	3230	7.878127	AGTATGTACTTACAATTGCAACTCTGT	59.122	33.333	18.18	8.57	39.99	3.41
2967	3431	5.124138	TGAACCTTCGCTGTTAAAAGTTGAA	59.876	36.000	0.00	0.00	0.00	2.69
3153	3625	9.331282	CCTAGAGGTTCAAATTTATCTAACTGG	57.669	37.037	0.00	0.00	0.00	4.00
3395	3872	9.899226	AATGGATTTCTCTCTTTTCTAAAAACG	57.101	29.630	0.00	0.00	0.00	3.60

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
248	252	7.851822	TTTCTAAAACGCTCATCAAAATGAC	57.148	32.000	0.00	0.00	36.98	3.06
290	298	4.603216	ACGACGAGTGACAACGAC	57.397	55.556	0.00	2.65	0.00	4.34
367	375	1.324736	GATTAGGCGCAACTTCGTCAG	59.675	52.381	10.83	0.00	36.38	3.51
370	378	0.036765	TGGATTAGGCGCAACTTCGT	60.037	50.000	10.83	0.00	0.00	3.85
401	409	4.377022	CGGAACAAGGCGTGTAATATATGC	60.377	45.833	6.48	0.00	40.60	3.14
402	410	4.986034	TCGGAACAAGGCGTGTAATATATG	59.014	41.667	6.48	0.00	40.60	1.78
403	411	4.986659	GTCGGAACAAGGCGTGTAATATAT	59.013	41.667	6.48	0.00	40.60	0.86
527	539	1.534595	GAAGGCACTGCTCTTTCTGTG	59.465	52.381	0.00	0.00	40.86	3.66
536	548	2.281070	CCACACGAAGGCACTGCT	60.281	61.111	0.00	0.00	40.86	4.24
578	590	7.878127	TGATTTCGGGATCAGAATAACTATTCC	59.122	37.037	5.95	0.00	42.29	3.01
617	631	0.185901	ATAGGGCCGGTGCATGATTT	59.814	50.000	1.90	0.00	40.13	2.17
618	632	1.064003	TATAGGGCCGGTGCATGATT	58.936	50.000	1.90	0.00	40.13	2.57
623	637	1.550130	GCCTATATAGGGCCGGTGCA	61.550	60.000	26.76	0.00	43.82	4.57
661	675	1.073923	CACTGCTAGGTTGGGGAGTTT	59.926	52.381	0.00	0.00	32.01	2.66
713	728	0.395724	GTGGGGAATGGTGGATGGTC	60.396	60.000	0.00	0.00	0.00	4.02
723	738	2.590092	GACGGGAGGTGGGGAATG	59.410	66.667	0.00	0.00	0.00	2.67
726	741	3.795977	TTTGGACGGGAGGTGGGGA	62.796	63.158	0.00	0.00	0.00	4.81
1158	1181	3.618351	CAGGATCCAGCAAAGATCACTT	58.382	45.455	15.82	0.00	41.64	3.16
1437	1479	1.469308	AGACTACCTCTTGCGTCTTCG	59.531	52.381	0.00	0.00	33.21	3.79
1561	1604	5.450550	CGAGCAGTCCATGTTCTACTCATAA	60.451	44.000	12.17	0.00	37.02	1.90
1562	1605	4.036852	CGAGCAGTCCATGTTCTACTCATA	59.963	45.833	12.17	0.00	37.02	2.15
1758	2175	1.103398	CGGGGATGGGTGATTCTTGC	61.103	60.000	0.00	0.00	0.00	4.01
2039	2481	4.720649	TGTGATAAGCAGGACTACTCAC	57.279	45.455	0.00	0.00	39.05	3.51
2055	2497	9.598517	ACAGATAAACAAAACAAAACATGTGAT	57.401	25.926	0.00	0.00	42.99	3.06
2061	2503	7.176589	AGGGACAGATAAACAAAACAAAACA	57.823	32.000	0.00	0.00	0.00	2.83
2229	2674	1.410153	ACCGAGGTCGTTGTTGTAGTT	59.590	47.619	0.00	0.00	37.74	2.24
2235	2680	1.300697	GCTCACCGAGGTCGTTGTT	60.301	57.895	0.00	0.00	37.74	2.83
2325	2770	1.075896	TTTTTGTTGGGGGTCGGCT	60.076	52.632	0.00	0.00	0.00	5.52
2417	2866	6.461509	GCAAAAAGATCAAATCCCCGATATGT	60.462	38.462	0.00	0.00	0.00	2.29
2440	2890	1.063942	TCTTCGATCTAGGGTCTGGCA	60.064	52.381	0.00	0.00	0.00	4.92
2462	2912	7.068839	TCCTGTATCTTGTAGTGAGGAATTCTC	59.931	40.741	5.23	1.99	42.74	2.87
2474	2924	2.630580	GAGGGCCTCCTGTATCTTGTAG	59.369	54.545	23.49	0.00	45.05	2.74
2496	2946	2.094659	CACGCGGGACAGTGATGTC	61.095	63.158	12.47	0.00	38.58	3.06
2544	2994	4.282703	GGATGATTAAATCCAGCATTGCCT	59.717	41.667	4.70	0.00	44.85	4.75
2605	3059	5.393569	CCTCTCATCATTGTACGTGTTCTCT	60.394	44.000	0.00	0.00	0.00	3.10
2606	3060	4.800993	CCTCTCATCATTGTACGTGTTCTC	59.199	45.833	0.00	0.00	0.00	2.87
2774	3230	5.294799	AGTTTACAAACATTACACAGACGCA	59.705	36.000	7.53	0.00	41.30	5.24
2820	3276	1.600916	GGACTTGCTGGTTTCGCCT	60.601	57.895	0.00	0.00	38.35	5.52
3096	3568	4.019950	AGAGATGGGGAAAAGCCATTTTTG	60.020	41.667	0.00	0.00	39.06	2.44
3153	3625	9.535878	TGGTTTTGTAATAAACATTGAACTTCC	57.464	29.630	0.00	0.00	39.27	3.46
3378	3855	7.201565	CCTCTATGGCGTTTTTAGAAAAGAGAG	60.202	40.741	5.05	4.00	29.69	3.20
3379	3856	6.594159	CCTCTATGGCGTTTTTAGAAAAGAGA	59.406	38.462	5.05	0.00	29.69	3.10
3394	3871	9.233232	GTTATTTAAATTTGAACCTCTATGGCG	57.767	33.333	5.91	0.00	40.22	5.69
3395	3872	9.233232	CGTTATTTAAATTTGAACCTCTATGGC	57.767	33.333	5.91	0.00	40.22	4.40

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.