AutoCloner

Multiple sequence alignment - TraesCS2D01G278400

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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	TraesCS2D01G278400	chr2D	100.000	3831	0	0	1	3831	349584428	349588258	0.000000e+00	7075.0
1	TraesCS2D01G278400	chr2D	92.241	232	16	2	3601	3831	566453126	566452896	1.030000e-85	327.0
2	TraesCS2D01G278400	chr2D	92.070	227	17	1	3603	3829	383863207	383863432	6.180000e-83	318.0
3	TraesCS2D01G278400	chr2D	92.342	222	17	0	3605	3826	222599455	222599676	2.220000e-82	316.0
4	TraesCS2D01G278400	chr2D	95.000	60	3	0	2991	3050	145733496	145733437	1.130000e-15	95.3
5	TraesCS2D01G278400	chr6B	93.137	2914	107	26	1	2855	552512705	552515584	0.000000e+00	4187.0
6	TraesCS2D01G278400	chr6B	91.928	223	18	0	3605	3827	72830220	72830442	2.870000e-81	313.0
7	TraesCS2D01G278400	chr6B	92.273	220	15	2	3608	3827	681080455	681080238	1.030000e-80	311.0
8	TraesCS2D01G278400	chr6B	91.189	227	20	0	3605	3831	72901096	72901322	3.720000e-80	309.0
9	TraesCS2D01G278400	chr2B	98.318	1784	27	2	1017	2797	416187832	416186049	0.000000e+00	3125.0
10	TraesCS2D01G278400	chr2B	86.391	992	68	13	30	976	416189059	416188090	0.000000e+00	1022.0
11	TraesCS2D01G278400	chr2B	94.198	586	17	2	3263	3831	416185030	416184445	0.000000e+00	878.0
12	TraesCS2D01G278400	chr2B	95.724	421	18	0	2783	3203	416185972	416185552	0.000000e+00	678.0
13	TraesCS2D01G278400	chr2B	87.361	269	34	0	76	344	801215313	801215581	3.720000e-80	309.0
14	TraesCS2D01G278400	chr2B	95.946	74	3	0	3204	3277	416185366	416185293	1.870000e-23	121.0
15	TraesCS2D01G278400	chr2A	95.761	1911	40	11	853	2757	464935160	464937035	0.000000e+00	3042.0
16	TraesCS2D01G278400	chr2A	97.152	1299	32	3	853	2147	465343023	465344320	0.000000e+00	2189.0
17	TraesCS2D01G278400	chr2A	95.591	1066	41	2	2143	3203	465344662	465345726	0.000000e+00	1703.0
18	TraesCS2D01G278400	chr2A	92.506	774	32	5	1	752	464934251	464935020	0.000000e+00	1085.0
19	TraesCS2D01G278400	chr2A	93.592	671	38	4	1	670	465337782	465338448	0.000000e+00	996.0
20	TraesCS2D01G278400	chr2A	89.806	775	53	6	1	752	465330393	465331164	0.000000e+00	970.0
21	TraesCS2D01G278400	chr2A	94.366	568	26	2	2625	3187	464953716	464954282	0.000000e+00	867.0
22	TraesCS2D01G278400	chr2A	94.785	441	20	2	2749	3187	464937469	464937908	0.000000e+00	684.0
23	TraesCS2D01G278400	chr2A	94.792	288	12	2	3406	3691	465345755	465346041	2.720000e-121	446.0
24	TraesCS2D01G278400	chr2A	89.956	229	14	2	762	981	465331229	465331457	1.740000e-73	287.0
25	TraesCS2D01G278400	chr2A	86.222	225	14	2	3296	3503	464954293	464954517	1.070000e-55	228.0
26	TraesCS2D01G278400	chr2A	94.253	87	2	2	747	832	464935083	464935167	3.110000e-26	130.0
27	TraesCS2D01G278400	chr2A	84.828	145	5	2	3296	3423	464937919	464938063	3.110000e-26	130.0
28	TraesCS2D01G278400	chr2A	93.590	78	5	0	675	752	465342791	465342868	2.420000e-22	117.0
29	TraesCS2D01G278400	chr4D	78.261	1541	264	35	1067	2560	444908435	444906919	0.000000e+00	924.0
30	TraesCS2D01G278400	chr4D	78.182	1540	267	33	1067	2560	445000000	444998484	0.000000e+00	918.0
31	TraesCS2D01G278400	chr4A	77.704	1507	268	37	1087	2546	22095401	22093916	0.000000e+00	859.0
32	TraesCS2D01G278400	chr4A	77.443	1525	273	36	1087	2560	22142352	22140848	0.000000e+00	845.0
33	TraesCS2D01G278400	chr4B	76.408	1420	236	49	1067	2429	554986123	554987500	0.000000e+00	675.0
34	TraesCS2D01G278400	chr4B	88.235	272	31	1	75	346	42938152	42938422	1.330000e-84	324.0
35	TraesCS2D01G278400	chr3D	95.595	227	10	0	3605	3831	613620741	613620967	7.820000e-97	364.0
36	TraesCS2D01G278400	chr1B	92.105	228	16	1	3606	3831	286952192	286952419	1.720000e-83	320.0
37	TraesCS2D01G278400	chr5B	87.361	269	32	2	74	342	665738349	665738615	1.340000e-79	307.0
38	TraesCS2D01G278400	chr7B	87.085	271	33	2	78	348	595747214	595746946	4.810000e-79	305.0
39	TraesCS2D01G278400	chr5D	86.813	273	35	1	75	347	260866120	260866391	1.730000e-78	303.0
40	TraesCS2D01G278400	chr1D	86.111	108	12	1	3230	3334	470889156	470889263	3.130000e-21	113.0

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	TraesCS2D01G278400	chr2D	349584428	349588258	3830	False	7075.00	7075	100.00000	1	3831	1	chr2D.!!$F2	3830
1	TraesCS2D01G278400	chr6B	552512705	552515584	2879	False	4187.00	4187	93.13700	1	2855	1	chr6B.!!$F3	2854
2	TraesCS2D01G278400	chr2B	416184445	416189059	4614	True	1164.80	3125	94.11540	30	3831	5	chr2B.!!$R1	3801
3	TraesCS2D01G278400	chr2A	465342791	465346041	3250	False	1113.75	2189	95.28125	675	3691	4	chr2A.!!$F5	3016
4	TraesCS2D01G278400	chr2A	464934251	464938063	3812	False	1014.20	3042	92.42660	1	3423	5	chr2A.!!$F2	3422
5	TraesCS2D01G278400	chr2A	465337782	465338448	666	False	996.00	996	93.59200	1	670	1	chr2A.!!$F1	669
6	TraesCS2D01G278400	chr2A	465330393	465331457	1064	False	628.50	970	89.88100	1	981	2	chr2A.!!$F4	980
7	TraesCS2D01G278400	chr2A	464953716	464954517	801	False	547.50	867	90.29400	2625	3503	2	chr2A.!!$F3	878
8	TraesCS2D01G278400	chr4D	444906919	444908435	1516	True	924.00	924	78.26100	1067	2560	1	chr4D.!!$R1	1493
9	TraesCS2D01G278400	chr4D	444998484	445000000	1516	True	918.00	918	78.18200	1067	2560	1	chr4D.!!$R2	1493
10	TraesCS2D01G278400	chr4A	22093916	22095401	1485	True	859.00	859	77.70400	1087	2546	1	chr4A.!!$R1	1459
11	TraesCS2D01G278400	chr4A	22140848	22142352	1504	True	845.00	845	77.44300	1087	2560	1	chr4A.!!$R2	1473
12	TraesCS2D01G278400	chr4B	554986123	554987500	1377	False	675.00	675	76.40800	1067	2429	1	chr4B.!!$F2	1362

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
481	484	1.071699	TGAACACACCCCTACTTGAGC	59.928	52.381	0.0	0.0	0.0	4.26	F
2276	3092	0.387750	GTCCAAGTACCGTCACCGTC	60.388	60.000	0.0	0.0	0.0	4.79	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2279	3095	1.079543	CGACCACCAGCTCCTTGAG	60.08	63.158	0.00	0.00	0.0	3.02	R
3326	5170	3.519973	CTGACAGGGAGTGCACGCA	62.52	63.158	22.36	7.15	0.0	5.24	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
157	158	7.694093	ACAGGAGAGAGAAACCATAAGAAAAT	58.306	34.615	0.00	0.00	0.00	1.82
371	373	2.393764	CGTTCTTTGGTCATTTGCACC	58.606	47.619	0.00	0.00	0.00	5.01
393	395	8.437742	GCACCAAAACAAATTATCAAAGATCAG	58.562	33.333	0.00	0.00	0.00	2.90
474	477	6.617784	TCCATTAAGATATGAACACACCCCTA	59.382	38.462	0.00	0.00	0.00	3.53
475	478	6.710744	CCATTAAGATATGAACACACCCCTAC	59.289	42.308	0.00	0.00	0.00	3.18
476	479	7.420214	CCATTAAGATATGAACACACCCCTACT	60.420	40.741	0.00	0.00	0.00	2.57
478	481	5.359194	AGATATGAACACACCCCTACTTG	57.641	43.478	0.00	0.00	0.00	3.16
479	482	5.030147	AGATATGAACACACCCCTACTTGA	58.970	41.667	0.00	0.00	0.00	3.02
480	483	3.703001	ATGAACACACCCCTACTTGAG	57.297	47.619	0.00	0.00	0.00	3.02
481	484	1.071699	TGAACACACCCCTACTTGAGC	59.928	52.381	0.00	0.00	0.00	4.26
482	485	1.348036	GAACACACCCCTACTTGAGCT	59.652	52.381	0.00	0.00	0.00	4.09
530	534	7.093771	CCATTCCTTTAGTATGGAAGCTTGTTT	60.094	37.037	2.10	0.00	44.37	2.83
532	536	8.927675	TTCCTTTAGTATGGAAGCTTGTTTAA	57.072	30.769	2.10	0.00	37.42	1.52
745	794	7.231607	TCTAGTTTGATTTCGCAAAATACGAC	58.768	34.615	0.00	0.00	39.26	4.34
786	963	9.774742	GTTCACCTAATTGTGATTCTTAACATC	57.225	33.333	0.00	0.00	44.27	3.06
853	1031	5.469760	CCACATTATACCTGATTGCGATTCA	59.530	40.000	0.00	0.00	0.00	2.57
871	1057	3.591196	TCATGCCATTTTTACCAGCAC	57.409	42.857	0.00	0.00	36.06	4.40
945	1132	5.006746	GTGTGTGACACTCTTCTACTTTTGG	59.993	44.000	17.47	0.00	45.27	3.28
2018	2470	3.943691	TTAACCCTGCGGCCGTGT	61.944	61.111	28.70	16.01	0.00	4.49
2274	3090	1.443194	CGTCCAAGTACCGTCACCG	60.443	63.158	0.00	0.00	0.00	4.94
2275	3091	1.662044	GTCCAAGTACCGTCACCGT	59.338	57.895	0.00	0.00	0.00	4.83
2276	3092	0.387750	GTCCAAGTACCGTCACCGTC	60.388	60.000	0.00	0.00	0.00	4.79
2277	3093	0.822944	TCCAAGTACCGTCACCGTCA	60.823	55.000	0.00	0.00	0.00	4.35
2278	3094	0.665369	CCAAGTACCGTCACCGTCAC	60.665	60.000	0.00	0.00	0.00	3.67
2279	3095	0.665369	CAAGTACCGTCACCGTCACC	60.665	60.000	0.00	0.00	0.00	4.02
2280	3096	0.825010	AAGTACCGTCACCGTCACCT	60.825	55.000	0.00	0.00	0.00	4.00
2281	3097	1.211190	GTACCGTCACCGTCACCTC	59.789	63.158	0.00	0.00	0.00	3.85
2282	3098	1.228215	TACCGTCACCGTCACCTCA	60.228	57.895	0.00	0.00	0.00	3.86
2283	3099	0.822944	TACCGTCACCGTCACCTCAA	60.823	55.000	0.00	0.00	0.00	3.02
2284	3100	1.372997	CCGTCACCGTCACCTCAAG	60.373	63.158	0.00	0.00	0.00	3.02
2285	3101	1.372997	CGTCACCGTCACCTCAAGG	60.373	63.158	0.00	0.00	42.17	3.61
2286	3102	1.802337	CGTCACCGTCACCTCAAGGA	61.802	60.000	2.30	0.00	38.94	3.36
2287	3103	0.038159	GTCACCGTCACCTCAAGGAG	60.038	60.000	2.30	0.00	38.94	3.69
2288	3104	1.374758	CACCGTCACCTCAAGGAGC	60.375	63.158	2.30	0.00	38.94	4.70
2289	3105	1.534235	ACCGTCACCTCAAGGAGCT	60.534	57.895	2.30	0.00	38.94	4.09
2290	3106	1.079543	CCGTCACCTCAAGGAGCTG	60.080	63.158	2.30	0.00	38.94	4.24
2291	3107	1.079543	CGTCACCTCAAGGAGCTGG	60.080	63.158	2.30	0.00	38.94	4.85
2292	3108	1.821061	CGTCACCTCAAGGAGCTGGT	61.821	60.000	2.30	0.00	38.94	4.00
2293	3109	4.709840	CACCTCAAGGAGCTGGTG	57.290	61.111	2.30	4.43	42.98	4.17
2462	3300	3.991536	GAGAACGGCTGGAGCGACC	62.992	68.421	0.00	0.00	43.26	4.79
2898	4280	5.272167	CAGGCAATTGCATGTTTAACTTG	57.728	39.130	31.36	7.78	46.46	3.16
2997	4379	6.310956	TCATGACAACTTCAAAACAAGCAAAG	59.689	34.615	0.00	0.00	37.92	2.77
3032	4414	2.302733	TCTGTGAAGCCTATGTGCAGAA	59.697	45.455	0.00	0.00	0.00	3.02
3187	4569	6.873076	CAGAGAGAAAGAAACTGCAGTCTTAT	59.127	38.462	21.95	11.97	32.90	1.73
3188	4570	6.873076	AGAGAGAAAGAAACTGCAGTCTTATG	59.127	38.462	21.95	0.00	32.90	1.90
3218	4785	7.648510	CCGTAGAGAACCATTACAGTTTAGATC	59.351	40.741	0.00	0.00	0.00	2.75
3480	5342	7.569639	TTGGCTGTGTAAAGTGTACAATAAA	57.430	32.000	0.00	0.00	0.00	1.40
3482	5344	7.419204	TGGCTGTGTAAAGTGTACAATAAAAC	58.581	34.615	0.00	0.00	0.00	2.43
3484	5346	7.377662	GGCTGTGTAAAGTGTACAATAAAACAC	59.622	37.037	20.10	20.10	45.06	3.32
3683	5547	7.504403	ACAAGAGTATCAACAATCTCTATGGG	58.496	38.462	0.00	0.00	37.82	4.00
3721	5585	2.930040	CCCGCACACACATTACTTCTAG	59.070	50.000	0.00	0.00	0.00	2.43
3803	5667	1.434555	TACGGGAAATCACACGCAAG	58.565	50.000	0.00	0.00	40.59	4.01

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
133	134	7.414984	GCATTTTCTTATGGTTTCTCTCTCCTG	60.415	40.741	0.00	0.00	0.00	3.86
296	298	5.983540	AGACAGTCTTATCTTAAGCCTTGG	58.016	41.667	0.00	0.00	0.00	3.61
326	328	6.376018	GGTTTTATTAAGGGCATGTACAGTGA	59.624	38.462	0.33	0.00	0.00	3.41
423	425	2.235891	TCTCAAGTTACCTCGCAGACA	58.764	47.619	0.00	0.00	0.00	3.41
438	440	9.973661	TTCATATCTTAATGGAAGGTTTCTCAA	57.026	29.630	0.00	0.00	35.67	3.02
442	444	8.956426	TGTGTTCATATCTTAATGGAAGGTTTC	58.044	33.333	0.00	0.00	35.67	2.78
474	477	2.307098	AGATGTTGCCCTAAGCTCAAGT	59.693	45.455	0.00	0.00	44.23	3.16
475	478	2.941720	GAGATGTTGCCCTAAGCTCAAG	59.058	50.000	0.00	0.00	44.23	3.02
476	479	2.305635	TGAGATGTTGCCCTAAGCTCAA	59.694	45.455	0.00	0.00	44.23	3.02
478	481	2.698855	TGAGATGTTGCCCTAAGCTC	57.301	50.000	0.00	0.00	44.23	4.09
479	482	3.659183	ATTGAGATGTTGCCCTAAGCT	57.341	42.857	0.00	0.00	44.23	3.74
480	483	3.696051	TGAATTGAGATGTTGCCCTAAGC	59.304	43.478	0.00	0.00	44.14	3.09
481	484	5.009410	GGATGAATTGAGATGTTGCCCTAAG	59.991	44.000	0.00	0.00	0.00	2.18
482	485	4.889409	GGATGAATTGAGATGTTGCCCTAA	59.111	41.667	0.00	0.00	0.00	2.69
691	740	8.812513	ATTCACACTTGGATTCATTTCATCTA	57.187	30.769	0.00	0.00	0.00	1.98
786	963	4.394795	GCAGTTGTTACATGCGAGTAAAG	58.605	43.478	0.00	0.00	35.88	1.85
820	998	4.904853	TCAGGTATAATGTGGCCATGTAGA	59.095	41.667	9.72	0.00	0.00	2.59
853	1031	1.892474	ACGTGCTGGTAAAAATGGCAT	59.108	42.857	0.00	0.00	35.37	4.40
871	1057	3.628053	ACATACGCGACAATTGTTACG	57.372	42.857	24.18	24.18	34.33	3.18
945	1132	7.332182	TGGTAGGAAACACAATTTGAAACAAAC	59.668	33.333	2.79	0.00	0.00	2.93
2277	3093	1.462238	ACCACCAGCTCCTTGAGGT	60.462	57.895	0.00	0.00	41.33	3.85
2278	3094	1.298014	GACCACCAGCTCCTTGAGG	59.702	63.158	0.00	0.00	0.00	3.86
2279	3095	1.079543	CGACCACCAGCTCCTTGAG	60.080	63.158	0.00	0.00	0.00	3.02
2280	3096	1.816863	GACGACCACCAGCTCCTTGA	61.817	60.000	0.00	0.00	0.00	3.02
2281	3097	1.374758	GACGACCACCAGCTCCTTG	60.375	63.158	0.00	0.00	0.00	3.61
2282	3098	2.932234	CGACGACCACCAGCTCCTT	61.932	63.158	0.00	0.00	0.00	3.36
2283	3099	3.374402	CGACGACCACCAGCTCCT	61.374	66.667	0.00	0.00	0.00	3.69
2284	3100	4.436998	CCGACGACCACCAGCTCC	62.437	72.222	0.00	0.00	0.00	4.70
2285	3101	4.436998	CCCGACGACCACCAGCTC	62.437	72.222	0.00	0.00	0.00	4.09
2287	3103	4.309950	AACCCGACGACCACCAGC	62.310	66.667	0.00	0.00	0.00	4.85
2288	3104	2.048503	GAACCCGACGACCACCAG	60.049	66.667	0.00	0.00	0.00	4.00
2289	3105	3.980989	CGAACCCGACGACCACCA	61.981	66.667	0.00	0.00	38.22	4.17
2290	3106	3.621892	CTCGAACCCGACGACCACC	62.622	68.421	0.00	0.00	40.30	4.61
2291	3107	2.126580	CTCGAACCCGACGACCAC	60.127	66.667	0.00	0.00	40.30	4.16
2292	3108	4.047059	GCTCGAACCCGACGACCA	62.047	66.667	0.00	0.00	40.30	4.02
2293	3109	3.745803	AGCTCGAACCCGACGACC	61.746	66.667	0.00	0.00	40.30	4.79
2856	4237	8.348285	TGCCTGCTTTATGATTTTAAAGTAGT	57.652	30.769	15.86	0.00	44.08	2.73
2857	4238	9.807649	ATTGCCTGCTTTATGATTTTAAAGTAG	57.192	29.630	12.34	12.34	44.65	2.57
2859	4240	8.938906	CAATTGCCTGCTTTATGATTTTAAAGT	58.061	29.630	0.00	0.00	40.02	2.66
2860	4241	7.906527	GCAATTGCCTGCTTTATGATTTTAAAG	59.093	33.333	20.06	0.00	39.34	1.85
2866	4248	4.475051	TGCAATTGCCTGCTTTATGATT	57.525	36.364	26.94	0.00	43.07	2.57
2898	4280	2.626088	AAAGTACTACTGTCGCCGAC	57.374	50.000	10.96	10.96	0.00	4.79
2997	4379	6.206243	AGGCTTCACAGAATATATGCAATGTC	59.794	38.462	0.00	0.00	0.00	3.06
3032	4414	1.633432	TGTGTATTGGCCTAACCTGCT	59.367	47.619	3.32	0.00	40.22	4.24
3187	4569	5.011329	ACTGTAATGGTTCTCTACGGAAACA	59.989	40.000	0.00	0.00	45.30	2.83
3188	4570	5.476614	ACTGTAATGGTTCTCTACGGAAAC	58.523	41.667	0.00	0.00	33.87	2.78
3218	4785	9.947669	GAATCTGAACTTGAATTCTATTGGATG	57.052	33.333	7.05	0.00	0.00	3.51
3270	4837	6.672657	CCTAATGTATACCAGGGGCTTATAGT	59.327	42.308	0.00	0.00	0.00	2.12
3326	5170	3.519973	CTGACAGGGAGTGCACGCA	62.520	63.158	22.36	7.15	0.00	5.24
3393	5250	8.198109	TCTGTTCTTTGCTATCAGAAGGTATAC	58.802	37.037	0.00	0.00	33.18	1.47
3480	5342	6.062095	AGCATGGTTCAGTTTAGTAAGTGTT	58.938	36.000	0.00	0.00	36.33	3.32
3482	5344	7.602644	TCTTAGCATGGTTCAGTTTAGTAAGTG	59.397	37.037	1.12	0.00	36.26	3.16
3484	5346	7.819900	AGTCTTAGCATGGTTCAGTTTAGTAAG	59.180	37.037	1.12	0.00	0.00	2.34
3485	5347	7.676947	AGTCTTAGCATGGTTCAGTTTAGTAA	58.323	34.615	1.12	0.00	0.00	2.24
3611	5473	9.643693	CCTTGCAATAAAGAGTATTTTGATGTT	57.356	29.630	0.00	0.00	0.00	2.71
3620	5484	7.559590	GTGATCACCTTGCAATAAAGAGTAT	57.440	36.000	15.31	0.00	0.00	2.12
3721	5585	4.142182	TGCCCATGATTTAGCAAAACTAGC	60.142	41.667	0.00	0.00	30.97	3.42
3803	5667	9.988350	CGGCAGTTTTTGATTATATATATCACC	57.012	33.333	0.00	0.00	0.00	4.02

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.