AutoCloner

Multiple sequence alignment - TraesCS6D01G215200

Loading Multiple Alignment...

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	TraesCS6D01G215200	chr6D	100.000	2972	0	0	1	2972	305366251	305363280	0.000000e+00	5489.0
1	TraesCS6D01G215200	chr6D	92.919	918	59	5	2	916	258034335	258035249	0.000000e+00	1330.0
2	TraesCS6D01G215200	chr6B	95.168	1904	75	12	914	2805	471180615	471182513	0.000000e+00	2990.0
3	TraesCS6D01G215200	chr6B	82.995	394	42	11	532	909	470912761	470913145	1.710000e-87	333.0
4	TraesCS6D01G215200	chr6B	90.798	163	15	0	2810	2972	471182608	471182770	4.990000e-53	219.0
5	TraesCS6D01G215200	chr6A	97.546	1630	34	4	914	2540	409083114	409084740	0.000000e+00	2784.0
6	TraesCS6D01G215200	chr6A	85.156	256	23	8	2562	2802	409085017	409085272	6.360000e-62	248.0
7	TraesCS6D01G215200	chr6A	89.506	162	15	2	2811	2972	409085375	409085534	1.400000e-48	204.0
8	TraesCS6D01G215200	chr2D	93.913	920	50	3	2	917	630069066	630068149	0.000000e+00	1384.0
9	TraesCS6D01G215200	chr2D	92.308	910	65	3	2	909	87968849	87969755	0.000000e+00	1288.0
10	TraesCS6D01G215200	chr1D	92.179	716	50	4	2	715	383329170	383328459	0.000000e+00	1007.0
11	TraesCS6D01G215200	chr1D	90.265	226	21	1	693	917	383328450	383328225	8.060000e-76	294.0
12	TraesCS6D01G215200	chr5D	83.477	926	74	24	31	909	36575864	36576757	0.000000e+00	789.0
13	TraesCS6D01G215200	chr5D	98.000	50	1	0	2	51	36575813	36575862	1.470000e-13	87.9
14	TraesCS6D01G215200	chr3B	91.540	461	36	3	2	459	43487620	43488080	1.500000e-177	632.0
15	TraesCS6D01G215200	chr5B	89.441	322	32	2	2	321	447451692	447451371	3.570000e-109	405.0
16	TraesCS6D01G215200	chr5B	86.667	180	17	3	273	451	531711732	531711559	3.020000e-45	193.0
17	TraesCS6D01G215200	chr4A	84.518	394	34	15	78	451	713747349	713746963	6.050000e-97	364.0
18	TraesCS6D01G215200	chr4A	82.776	389	40	13	538	908	617790376	617789997	3.700000e-84	322.0
19	TraesCS6D01G215200	chr4A	100.000	32	0	0	49	80	713747390	713747359	3.200000e-05	60.2
20	TraesCS6D01G215200	chr2B	84.224	393	37	14	78	451	790116185	790115799	2.820000e-95	359.0
21	TraesCS6D01G215200	chr2B	81.481	432	44	16	49	451	658211842	658211418	3.700000e-84	322.0
22	TraesCS6D01G215200	chr2B	82.094	363	36	12	109	448	670339869	670340225	1.740000e-72	283.0
23	TraesCS6D01G215200	chr5A	83.668	398	37	12	72	448	693855615	693856005	1.700000e-92	350.0
24	TraesCS6D01G215200	chr7D	83.505	388	34	16	538	909	560756769	560756396	4.750000e-88	335.0
25	TraesCS6D01G215200	chr7A	82.915	398	37	17	538	917	635104702	635104318	2.210000e-86	329.0
26	TraesCS6D01G215200	chr7A	81.519	395	51	13	72	451	15509079	15508692	3.720000e-79	305.0
27	TraesCS6D01G215200	chr2A	81.481	432	52	16	501	909	30593380	30593806	2.210000e-86	329.0
28	TraesCS6D01G215200	chr3A	82.487	394	48	11	72	451	17901198	17900812	2.860000e-85	326.0
29	TraesCS6D01G215200	chrUn	82.519	389	41	13	538	908	235771997	235771618	1.720000e-82	316.0
30	TraesCS6D01G215200	chr3D	80.890	382	37	17	546	909	305600391	305600028	4.880000e-68	268.0

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	TraesCS6D01G215200	chr6D	305363280	305366251	2971	True	5489.000000	5489	100.0000	1	2972	1	chr6D.!!$R1	2971
1	TraesCS6D01G215200	chr6D	258034335	258035249	914	False	1330.000000	1330	92.9190	2	916	1	chr6D.!!$F1	914
2	TraesCS6D01G215200	chr6B	471180615	471182770	2155	False	1604.500000	2990	92.9830	914	2972	2	chr6B.!!$F2	2058
3	TraesCS6D01G215200	chr6A	409083114	409085534	2420	False	1078.666667	2784	90.7360	914	2972	3	chr6A.!!$F1	2058
4	TraesCS6D01G215200	chr2D	630068149	630069066	917	True	1384.000000	1384	93.9130	2	917	1	chr2D.!!$R1	915
5	TraesCS6D01G215200	chr2D	87968849	87969755	906	False	1288.000000	1288	92.3080	2	909	1	chr2D.!!$F1	907
6	TraesCS6D01G215200	chr1D	383328225	383329170	945	True	650.500000	1007	91.2220	2	917	2	chr1D.!!$R1	915
7	TraesCS6D01G215200	chr5D	36575813	36576757	944	False	438.450000	789	90.7385	2	909	2	chr5D.!!$F1	907

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
472	512	1.503542	CACACAGCAAGGCGATTCC	59.496	57.895	0.00	0.0	0.0	3.01	F
703	755	2.038033	AGTTTCGAAATGGGAGGAACGA	59.962	45.455	14.69	0.0	0.0	3.85	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1830	1920	0.389391	CCACCACTGTCTCGTTGAGT	59.611	55.0	0.00	0.0	0.00	3.41	R
2268	2359	0.955919	ACTTTAGCCTTCCAGCGCAC	60.956	55.0	11.47	0.0	38.01	5.34	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
158	189	7.415095	CCAAAATTAACGAGTGCTTCATCCATA	60.415	37.037	0.00	0.00	0.00	2.74
168	199	6.077993	AGTGCTTCATCCATACTACCATCTA	58.922	40.000	0.00	0.00	0.00	1.98
306	346	3.495753	GTCGATTTGGACAACCTAAACGT	59.504	43.478	0.00	0.00	43.17	3.99
410	450	2.947532	CGCTGTTCCTCCTCTGCCA	61.948	63.158	0.00	0.00	0.00	4.92
438	478	3.356639	TACTGCTGCTCCTTCCGCG	62.357	63.158	0.00	0.00	0.00	6.46
472	512	1.503542	CACACAGCAAGGCGATTCC	59.496	57.895	0.00	0.00	0.00	3.01
490	530	3.995669	GCAGCGCGAACAACACGA	61.996	61.111	12.10	0.00	0.00	4.35
522	562	4.025858	TCGTCCCTCCTCGGTCGT	62.026	66.667	0.00	0.00	32.58	4.34
661	713	2.367947	AGTGGAAGGAAAGGGGATCT	57.632	50.000	0.00	0.00	0.00	2.75
672	724	4.166888	GGGATCTGCTCCGCTGCA	62.167	66.667	0.00	0.93	46.01	4.41
703	755	2.038033	AGTTTCGAAATGGGAGGAACGA	59.962	45.455	14.69	0.00	0.00	3.85
704	756	2.809696	GTTTCGAAATGGGAGGAACGAA	59.190	45.455	14.69	0.00	37.83	3.85
798	886	2.802667	GCGCACGCATCGATGAAGT	61.803	57.895	29.20	22.59	41.49	3.01
1479	1569	3.499737	GTCGCCATTGCCCTCGTG	61.500	66.667	0.00	0.00	0.00	4.35
1480	1570	3.700970	TCGCCATTGCCCTCGTGA	61.701	61.111	0.00	0.00	0.00	4.35
1881	1971	0.804989	GCATGTACGAGCTTGCCTTT	59.195	50.000	0.00	0.00	34.65	3.11
2234	2325	6.788243	TGAAATGCAGTGATCATATGTGTTC	58.212	36.000	0.00	7.33	0.00	3.18
2257	2348	9.615295	GTTCGGAATACTTTTTGCATACTTTAA	57.385	29.630	0.00	0.00	0.00	1.52
2324	2415	8.359875	TGATCATATGTATTTGGTGTTTGGTT	57.640	30.769	1.90	0.00	0.00	3.67
2477	2568	5.039920	TGTAAGATGGCAGCTATGTGATT	57.960	39.130	5.34	0.00	0.00	2.57
2478	2569	5.439721	TGTAAGATGGCAGCTATGTGATTT	58.560	37.500	5.34	0.00	0.00	2.17
2499	2590	6.656632	TTTACAAATGTTGTGGCCAAGATA	57.343	33.333	7.24	0.00	45.03	1.98
2713	3066	6.310956	GCAATAATTATGTCAGTTGCTTTGCA	59.689	34.615	10.54	0.00	38.97	4.08
2729	3082	7.110043	TGCTTTGCATATTGGAACATTATCA	57.890	32.000	0.00	0.00	33.28	2.15
2802	3164	7.953005	TTTCATTCCATGCCTCAGTTAATAA	57.047	32.000	0.00	0.00	0.00	1.40
2805	3167	8.853077	TCATTCCATGCCTCAGTTAATAATAG	57.147	34.615	0.00	0.00	0.00	1.73
2806	3168	7.391554	TCATTCCATGCCTCAGTTAATAATAGC	59.608	37.037	0.00	0.00	0.00	2.97
2833	3290	7.343691	TGCTTGCGAAATACAAATTTTCTTTG	58.656	30.769	0.00	0.00	35.41	2.77
2854	3311	2.028203	GCTCTGGGGCAAGCAAATTTAA	60.028	45.455	0.00	0.00	38.42	1.52
2861	3318	3.337358	GGCAAGCAAATTTAACTGCCAT	58.663	40.909	22.41	2.14	39.47	4.40
2866	3323	4.088634	AGCAAATTTAACTGCCATCCTCA	58.911	39.130	0.00	0.00	39.47	3.86
2877	3334	5.263599	ACTGCCATCCTCACAATAAAATGA	58.736	37.500	0.00	0.00	0.00	2.57
2880	3337	5.657745	TGCCATCCTCACAATAAAATGACAT	59.342	36.000	0.00	0.00	0.00	3.06
2948	3405	8.210946	TGATTAGTATTAAGAGGTTCATGGGTG	58.789	37.037	0.00	0.00	0.00	4.61
2955	3412	1.834263	GAGGTTCATGGGTGCTAGAGT	59.166	52.381	0.00	0.00	0.00	3.24

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
12	13	2.439507	GGGTTAGGATGCTCATGAAGGA	59.560	50.000	0.00	0.00	0.00	3.36
128	159	3.482436	AGCACTCGTTAATTTTGGGACA	58.518	40.909	0.00	0.00	0.00	4.02
158	189	6.054295	ACGAAATCGACTAGTAGATGGTAGT	58.946	40.000	17.86	12.51	43.02	2.73
168	199	4.625742	CCATGTTTGACGAAATCGACTAGT	59.374	41.667	10.16	0.00	43.02	2.57
209	240	3.449227	AGAGGTGCCGAATCGCGA	61.449	61.111	13.09	13.09	44.57	5.87
251	282	2.672307	AGAGGAGGAACGACGCGT	60.672	61.111	13.85	13.85	43.97	6.01
306	346	0.741326	CGATCTCTTCCGCTCTTCCA	59.259	55.000	0.00	0.00	0.00	3.53
395	435	1.816863	GACGTGGCAGAGGAGGAACA	61.817	60.000	0.00	0.00	0.00	3.18
672	724	0.531974	TTTCGAAACTGCTGCCGAGT	60.532	50.000	6.47	0.00	32.41	4.18
703	755	0.909610	TCATCTCGCCTCCCCACTTT	60.910	55.000	0.00	0.00	0.00	2.66
704	756	1.306141	TCATCTCGCCTCCCCACTT	60.306	57.895	0.00	0.00	0.00	3.16
830	918	2.737180	CCGACCGATCCCCATCTG	59.263	66.667	0.00	0.00	0.00	2.90
941	1031	5.354234	GGAAGACGCCAATGATTTTCTTCTA	59.646	40.000	8.58	0.00	39.20	2.10
947	1037	2.755103	GGAGGAAGACGCCAATGATTTT	59.245	45.455	0.00	0.00	39.13	1.82
1236	1326	2.190578	CCGGGATCTGGGTGAAGC	59.809	66.667	0.00	0.00	0.00	3.86
1803	1893	4.521062	GGCATCGTCTCCAGCGCT	62.521	66.667	2.64	2.64	0.00	5.92
1830	1920	0.389391	CCACCACTGTCTCGTTGAGT	59.611	55.000	0.00	0.00	0.00	3.41
1881	1971	1.135960	TGACCTCACCATGGTTGACA	58.864	50.000	16.84	10.51	38.03	3.58
2180	2271	6.405731	GCACAACATAATGCTAGAAATTCCCA	60.406	38.462	0.00	0.00	38.84	4.37
2257	2348	2.710377	TCCAGCGCACATTAGTCATTT	58.290	42.857	11.47	0.00	0.00	2.32
2268	2359	0.955919	ACTTTAGCCTTCCAGCGCAC	60.956	55.000	11.47	0.00	38.01	5.34
2331	2422	9.802039	TTTTAGTAAGGATAACAACAGGAACAT	57.198	29.630	0.00	0.00	0.00	2.71
2379	2470	2.058057	GGTGCAGCGGTAAAACATTTG	58.942	47.619	0.00	0.00	0.00	2.32
2440	2531	7.778470	CCATCTTACAGGCTTTAGTTAAGAG	57.222	40.000	0.00	0.00	35.80	2.85
2477	2568	6.849085	ATATCTTGGCCACAACATTTGTAA	57.151	33.333	3.88	0.00	43.23	2.41
2478	2569	7.342581	TCTATATCTTGGCCACAACATTTGTA	58.657	34.615	3.88	0.00	43.23	2.41
2523	2615	1.506028	GGGGGTGGAGGGTGAAATCA	61.506	60.000	0.00	0.00	0.00	2.57
2638	2986	9.675464	ATGAAACTGCAAATGGAAATCATAATT	57.325	25.926	0.00	0.00	34.44	1.40
2649	3002	5.064198	CCATGCTTAATGAAACTGCAAATGG	59.936	40.000	0.00	0.00	38.72	3.16
2706	3059	7.205297	AGTGATAATGTTCCAATATGCAAAGC	58.795	34.615	0.00	0.00	0.00	3.51
2710	3063	8.978874	ACTAAGTGATAATGTTCCAATATGCA	57.021	30.769	0.00	0.00	0.00	3.96
2729	3082	5.837438	ACCTACACAACTCAAGGTACTAAGT	59.163	40.000	0.00	0.00	40.57	2.24
2802	3164	7.278424	AAAATTTGTATTTCGCAAGCATGCTAT	59.722	29.630	23.00	12.16	40.48	2.97
2805	3167	5.620467	AAAATTTGTATTTCGCAAGCATGC	58.380	33.333	10.51	10.51	39.85	4.06
2806	3168	7.052565	AGAAAATTTGTATTTCGCAAGCATG	57.947	32.000	0.00	0.00	40.78	4.06
2814	3271	7.148755	CCCAGAGCAAAGAAAATTTGTATTTCG	60.149	37.037	0.00	0.00	40.78	3.46
2821	3278	3.069289	GCCCCAGAGCAAAGAAAATTTG	58.931	45.455	0.00	0.00	0.00	2.32
2823	3280	2.328319	TGCCCCAGAGCAAAGAAAATT	58.672	42.857	0.00	0.00	40.56	1.82
2833	3290	0.322648	AAATTTGCTTGCCCCAGAGC	59.677	50.000	0.00	0.00	39.33	4.09
2854	3311	5.126061	GTCATTTTATTGTGAGGATGGCAGT	59.874	40.000	0.00	0.00	0.00	4.40
2861	3318	7.959658	ATTCCATGTCATTTTATTGTGAGGA	57.040	32.000	0.00	0.00	0.00	3.71
2928	3385	4.781934	AGCACCCATGAACCTCTTAATAC	58.218	43.478	0.00	0.00	0.00	1.89
2933	3390	2.503356	CTCTAGCACCCATGAACCTCTT	59.497	50.000	0.00	0.00	0.00	2.85

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.