AutoCloner

Multiple sequence alignment - TraesCS5A01G004800

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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	TraesCS5A01G004800	chr5A	100.000	5491	0	0	1	5491	3219768	3214278	0.000000e+00	10141.0
1	TraesCS5A01G004800	chr5D	97.776	3012	48	8	1	3008	6443985	6446981	0.000000e+00	5173.0
2	TraesCS5A01G004800	chr5D	97.045	2504	44	9	2994	5491	6448537	6451016	0.000000e+00	4187.0
3	TraesCS5A01G004800	chr5D	77.016	831	151	28	3940	4751	5358026	5358835	1.820000e-119	440.0
4	TraesCS5A01G004800	chr5D	86.350	337	42	3	3443	3779	5357291	5357623	1.120000e-96	364.0
5	TraesCS5A01G004800	chr5D	82.337	368	51	12	2497	2861	328921769	328921413	1.920000e-79	307.0
6	TraesCS5A01G004800	chr5D	87.121	264	22	8	2005	2258	5356347	5356608	6.960000e-74	289.0
7	TraesCS5A01G004800	chr5D	86.154	260	31	3	1020	1279	5355326	5355580	5.420000e-70	276.0
8	TraesCS5A01G004800	chr5D	85.388	219	20	4	1734	1951	5356022	5356229	3.330000e-52	217.0
9	TraesCS5A01G004800	chr7B	76.512	860	153	36	3953	4794	717199717	717198889	1.830000e-114	424.0
10	TraesCS5A01G004800	chr7B	86.810	326	41	2	3464	3788	717200315	717199991	4.040000e-96	363.0
11	TraesCS5A01G004800	chr7B	86.462	325	42	1	3464	3788	716724571	716724893	6.770000e-94	355.0
12	TraesCS5A01G004800	chr7B	76.589	645	110	32	3953	4585	716725177	716725792	3.190000e-82	316.0
13	TraesCS5A01G004800	chr7B	81.330	391	52	11	1556	1943	717201869	717201497	1.160000e-76	298.0
14	TraesCS5A01G004800	chr7B	80.500	400	57	10	1547	1943	716723050	716723431	2.500000e-73	287.0
15	TraesCS5A01G004800	chr7A	85.440	364	49	3	3426	3788	715766426	715766066	5.190000e-100	375.0
16	TraesCS5A01G004800	chr7A	82.250	400	50	10	1547	1943	715768418	715768037	5.300000e-85	326.0
17	TraesCS5A01G004800	chr7A	87.701	187	23	0	649	835	127006211	127006025	9.260000e-53	219.0
18	TraesCS5A01G004800	chrUn	86.503	326	42	2	3464	3788	383782941	383782617	1.880000e-94	357.0
19	TraesCS5A01G004800	chrUn	84.774	243	35	2	3547	3788	456773174	456773415	5.500000e-60	243.0
20	TraesCS5A01G004800	chr3B	82.940	381	52	12	2481	2857	404620001	404620372	1.140000e-86	331.0
21	TraesCS5A01G004800	chr3B	88.571	175	19	1	660	834	795999022	795999195	1.550000e-50	211.0
22	TraesCS5A01G004800	chr1B	83.562	365	43	14	2502	2857	67055289	67054933	5.300000e-85	326.0
23	TraesCS5A01G004800	chr1B	84.071	339	46	7	2502	2837	511445463	511445796	2.470000e-83	320.0
24	TraesCS5A01G004800	chr1B	89.840	187	17	2	649	834	198145049	198145234	7.110000e-59	239.0
25	TraesCS5A01G004800	chr1B	89.130	184	19	1	649	832	12996034	12996216	1.540000e-55	228.0
26	TraesCS5A01G004800	chr1A	83.287	359	45	13	2502	2853	47213010	47212660	3.190000e-82	316.0
27	TraesCS5A01G004800	chr1D	82.873	362	50	11	2502	2857	47331087	47330732	1.150000e-81	315.0
28	TraesCS5A01G004800	chr1D	90.099	101	8	2	649	747	140543805	140543705	4.460000e-26	130.0
29	TraesCS5A01G004800	chr3A	82.730	359	54	7	2502	2858	40522	40170	4.130000e-81	313.0
30	TraesCS5A01G004800	chr3A	82.730	359	54	7	2502	2858	63439	63087	4.130000e-81	313.0
31	TraesCS5A01G004800	chr3A	89.024	82	7	1	752	831	71217081	71217000	3.500000e-17	100.0
32	TraesCS5A01G004800	chr2B	89.247	186	20	0	649	834	157678721	157678536	3.310000e-57	233.0
33	TraesCS5A01G004800	chr7D	88.710	186	20	1	649	834	638206232	638206416	5.530000e-55	226.0
34	TraesCS5A01G004800	chr2A	88.827	179	17	3	649	825	16978988	16978811	3.330000e-52	217.0
35	TraesCS5A01G004800	chr6D	80.992	121	9	6	2981	3088	10636501	10636620	3.520000e-12	84.2
36	TraesCS5A01G004800	chr4A	79.365	126	13	4	2973	3085	552719446	552719571	5.900000e-10	76.8

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	TraesCS5A01G004800	chr5A	3214278	3219768	5490	True	10141.000000	10141	100.000000	1	5491	1	chr5A.!!$R1	5490
1	TraesCS5A01G004800	chr5D	6443985	6451016	7031	False	4680.000000	5173	97.410500	1	5491	2	chr5D.!!$F2	5490
2	TraesCS5A01G004800	chr5D	5355326	5358835	3509	False	317.200000	440	84.405800	1020	4751	5	chr5D.!!$F1	3731
3	TraesCS5A01G004800	chr7B	717198889	717201869	2980	True	361.666667	424	81.550667	1556	4794	3	chr7B.!!$R1	3238
4	TraesCS5A01G004800	chr7B	716723050	716725792	2742	False	319.333333	355	81.183667	1547	4585	3	chr7B.!!$F1	3038
5	TraesCS5A01G004800	chr7A	715766066	715768418	2352	True	350.500000	375	83.845000	1547	3788	2	chr7A.!!$R2	2241

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
976	979	0.458669	TAACGGTAGCTAGCAGTGCC	59.541	55.0	21.99	9.28	0.00	5.01	F
2728	2908	0.389296	CATGGTTGCATGTGCTGGTG	60.389	55.0	6.55	0.00	42.66	4.17	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2971	3153	1.496429	ACTCCATCCAAATAGCCCCTG	59.504	52.381	0.0	0.0	0.0	4.45	R
4597	6907	2.100631	GTCCAAGATCGCCACCACG	61.101	63.158	0.0	0.0	0.0	4.94	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
99	100	7.007116	TGCAATTGCCACCAATAATACCTATA	58.993	34.615	26.94	0.00	40.69	1.31
100	101	7.673504	TGCAATTGCCACCAATAATACCTATAT	59.326	33.333	26.94	0.00	40.69	0.86
101	102	9.184523	GCAATTGCCACCAATAATACCTATATA	57.815	33.333	20.06	0.00	40.69	0.86
121	122	9.201989	CTATATATGATGCCCTTACTACAGGAA	57.798	37.037	0.00	0.00	35.71	3.36
145	146	9.356433	GAAGTCTTAGTAGTGGATTAGTTGAAC	57.644	37.037	0.00	0.00	0.00	3.18
250	251	3.621715	GGTTGTGGGATTCTCAATCGTAC	59.378	47.826	0.00	0.00	38.82	3.67
275	276	7.069569	CGGTCTTGTTAAAACACATCTACAAG	58.930	38.462	0.00	0.00	42.18	3.16
394	396	7.373493	GCTTAGATGTGCAATAATTAAGGCAT	58.627	34.615	14.95	3.49	38.68	4.40
675	678	4.162096	AGATCGTGTCTATTATGCGGAC	57.838	45.455	0.00	0.00	34.69	4.79
696	699	3.084039	CAAGGCACATCTGTATTGGTGT	58.916	45.455	0.00	0.00	33.88	4.16
705	708	5.105064	ACATCTGTATTGGTGTAGGTGTACC	60.105	44.000	0.00	0.00	33.05	3.34
720	723	1.066136	GTACCGACTTTGTTCGCCTC	58.934	55.000	0.00	0.00	37.70	4.70
733	736	3.717294	GCCTCGAAGGGGGCTTCA	61.717	66.667	6.18	0.00	41.74	3.02
735	738	2.294078	CCTCGAAGGGGGCTTCAGT	61.294	63.158	0.00	0.00	33.22	3.41
827	830	1.048724	CAGAGGCCCGAGGTAATCCA	61.049	60.000	0.00	0.00	35.89	3.41
863	866	2.600792	GCGAGCAGCTGTTATATTGCAC	60.601	50.000	16.64	0.00	44.04	4.57
958	961	4.417437	AGACAGAGGGAAGCAAGTACTTA	58.583	43.478	8.04	0.00	0.00	2.24
975	978	2.194271	CTTAACGGTAGCTAGCAGTGC	58.806	52.381	21.99	7.13	0.00	4.40
976	979	0.458669	TAACGGTAGCTAGCAGTGCC	59.541	55.000	21.99	9.28	0.00	5.01
977	980	1.541310	AACGGTAGCTAGCAGTGCCA	61.541	55.000	21.99	0.00	0.00	4.92
978	981	1.519455	CGGTAGCTAGCAGTGCCAC	60.519	63.158	21.99	0.97	0.00	5.01
979	982	1.901085	GGTAGCTAGCAGTGCCACT	59.099	57.895	18.83	9.41	0.00	4.00
1124	1127	2.107141	CGGCTCGGGAGATTGGTC	59.893	66.667	0.00	0.00	38.80	4.02
1660	1669	2.579207	AATGTCGAGGGTACGTCATG	57.421	50.000	0.00	0.00	44.35	3.07
1744	1798	6.903883	ACATCTTATTTTAGCACAGGTACG	57.096	37.500	0.00	0.00	0.00	3.67
1938	1992	2.157668	AGTCGATTTGCTTGTTACTGCG	59.842	45.455	0.00	0.00	0.00	5.18
2103	2232	2.813754	TCCAACGGAAGAAATGAGCTTG	59.186	45.455	0.00	0.00	0.00	4.01
2419	2595	3.930229	GTCGAATAAGCACACACACCATA	59.070	43.478	0.00	0.00	0.00	2.74
2498	2678	7.798071	TGAAGAAAAGTGGGTAGAAAGTCTTA	58.202	34.615	0.00	0.00	0.00	2.10
2728	2908	0.389296	CATGGTTGCATGTGCTGGTG	60.389	55.000	6.55	0.00	42.66	4.17
2920	3102	4.618920	ATCTACCAAGGTAAATAGGCCG	57.381	45.455	0.00	0.00	0.00	6.13
2971	3153	4.150451	GCCATCAAAATTACAAGCACACAC	59.850	41.667	0.00	0.00	0.00	3.82
3034	4866	1.004044	AGGCAACATTCCTGACCTCAG	59.996	52.381	0.00	0.00	41.06	3.35
3088	4920	3.922171	TTTTGTGGAAGCCAACCAAAT	57.078	38.095	0.00	0.00	39.22	2.32
3133	4991	1.271325	CCATCAAGTAGCACACCACCA	60.271	52.381	0.00	0.00	0.00	4.17
3341	5228	3.259625	GCCTCTAGAGATGGGTCCAATAC	59.740	52.174	21.76	0.00	0.00	1.89
3354	5241	1.224592	CAATACTGGAGGGCGCCTT	59.775	57.895	28.56	21.53	31.76	4.35
3355	5242	0.394352	CAATACTGGAGGGCGCCTTT	60.394	55.000	28.56	15.62	31.76	3.11
3575	5626	2.684374	GCATGGTCATGTATGTGCTGAA	59.316	45.455	11.92	0.00	40.80	3.02
3684	5736	8.883731	CACCTTATTATTCTCGTGACATCTTTT	58.116	33.333	0.00	0.00	0.00	2.27
4103	6403	7.956420	ATTTCTAACACGACAATAACAGACA	57.044	32.000	0.00	0.00	0.00	3.41
4164	6464	6.128795	GCCGATTCAGATTAAGAATACCTTCG	60.129	42.308	0.00	0.00	35.93	3.79
4290	6590	3.551890	AGTATGCAACGCTGAATAGAACG	59.448	43.478	0.00	0.00	0.00	3.95
4540	6841	4.469657	AGAGGGTGCACAATTAAGAAACA	58.530	39.130	20.43	0.00	0.00	2.83
4578	6888	8.309656	CACCAAGCAATGTCTAGATATCTATCA	58.690	37.037	12.86	14.40	35.17	2.15
4609	6919	0.110373	GTTGAAACGTGGTGGCGATC	60.110	55.000	0.00	0.00	35.59	3.69
4763	7076	7.833285	ATTTTGTGGCTAACTTCTAAAGGAA	57.167	32.000	0.00	0.00	0.00	3.36
4764	7077	7.833285	TTTTGTGGCTAACTTCTAAAGGAAT	57.167	32.000	0.00	0.00	33.01	3.01
4775	7088	4.150897	TCTAAAGGAATGCTTGGCGTAT	57.849	40.909	0.00	0.00	0.00	3.06
4981	7295	3.963665	TCAACCATTTTGAAGTCTTGCG	58.036	40.909	0.00	0.00	0.00	4.85
5089	7403	1.202222	GCATCTTGTCATTCCGCCAAG	60.202	52.381	0.00	0.00	37.51	3.61
5123	7437	8.696410	TTAGTTTTGGTGAAGTTGTTGAATTC	57.304	30.769	0.00	0.00	0.00	2.17
5132	7446	6.643770	GTGAAGTTGTTGAATTCTTCATGCAT	59.356	34.615	7.05	0.00	44.73	3.96
5196	7511	8.958119	TTCAATGTCCTAGGTACATGTATTTC	57.042	34.615	20.67	2.55	37.62	2.17
5271	7586	4.260170	CCCTCCAGATCTGAAACTCAAAG	58.740	47.826	24.62	3.94	0.00	2.77

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
99	100	5.846714	ACTTCCTGTAGTAAGGGCATCATAT	59.153	40.000	0.00	0.00	37.96	1.78
100	101	5.216622	ACTTCCTGTAGTAAGGGCATCATA	58.783	41.667	0.00	0.00	37.96	2.15
101	102	4.040755	ACTTCCTGTAGTAAGGGCATCAT	58.959	43.478	0.00	0.00	37.96	2.45
102	103	3.450904	ACTTCCTGTAGTAAGGGCATCA	58.549	45.455	0.00	0.00	37.96	3.07
121	122	8.653036	AGTTCAACTAATCCACTACTAAGACT	57.347	34.615	0.00	0.00	0.00	3.24
145	146	7.655328	CCTGAAATTCCATAGTGCTTCTACTAG	59.345	40.741	0.00	0.00	36.66	2.57
250	251	6.533819	TGTAGATGTGTTTTAACAAGACCG	57.466	37.500	0.00	0.00	41.21	4.79
456	458	0.323087	TAGCTGGAGCCACGTGTAGA	60.323	55.000	15.65	0.00	43.38	2.59
492	494	6.569179	GGATTTTCCTGCTGTTTTACAGTA	57.431	37.500	8.46	3.37	39.90	2.74
675	678	3.084039	ACACCAATACAGATGTGCCTTG	58.916	45.455	0.00	0.00	31.98	3.61
696	699	2.607771	GCGAACAAAGTCGGTACACCTA	60.608	50.000	0.00	0.00	41.40	3.08
705	708	0.435008	CTTCGAGGCGAACAAAGTCG	59.565	55.000	0.00	0.00	41.05	4.18
852	855	5.185056	AGGGAAAACACCAGTGCAATATAAC	59.815	40.000	0.00	0.00	0.00	1.89
863	866	3.819245	TCCACAGGGAAAACACCAG	57.181	52.632	0.00	0.00	41.32	4.00
958	961	1.218316	GGCACTGCTAGCTACCGTT	59.782	57.895	17.23	0.00	0.00	4.44
975	978	1.144936	GCTAGCTAGTGGGCAGTGG	59.855	63.158	21.62	0.00	34.17	4.00
976	979	0.103937	GAGCTAGCTAGTGGGCAGTG	59.896	60.000	19.38	0.00	34.17	3.66
977	980	0.324738	TGAGCTAGCTAGTGGGCAGT	60.325	55.000	19.38	0.00	34.17	4.40
978	981	1.000731	GATGAGCTAGCTAGTGGGCAG	59.999	57.143	19.38	0.00	34.17	4.85
979	982	1.043816	GATGAGCTAGCTAGTGGGCA	58.956	55.000	19.38	10.76	34.17	5.36
980	983	0.320050	GGATGAGCTAGCTAGTGGGC	59.680	60.000	19.38	8.55	0.00	5.36
981	984	1.709578	TGGATGAGCTAGCTAGTGGG	58.290	55.000	19.38	0.00	0.00	4.61
1660	1669	9.255304	CTGCTCAAAATAGGATTACTTCTACTC	57.745	37.037	0.00	0.00	0.00	2.59
1744	1798	2.208431	CAAGCCTCGATGACATTCCTC	58.792	52.381	0.00	0.00	0.00	3.71
2103	2232	3.179830	CAGGACGTATACAGCAAGTGAC	58.820	50.000	3.32	0.00	0.00	3.67
2419	2595	6.179906	TCTCCATTGTTCTTGAAGAGAAGT	57.820	37.500	0.00	0.00	44.78	3.01
2498	2678	3.740141	CGCGGGGTATCATCTAGTTTTGT	60.740	47.826	0.00	0.00	0.00	2.83
2785	2965	2.025898	CAAGCATGCCACATCACCATA	58.974	47.619	15.66	0.00	0.00	2.74
2863	3044	2.584835	TTGACTGGGTCCTTCCAATG	57.415	50.000	0.00	0.00	36.21	2.82
2920	3102	7.119846	AGGTAGTTTTCATTTGACTATGCTCAC	59.880	37.037	0.00	0.00	0.00	3.51
2971	3153	1.496429	ACTCCATCCAAATAGCCCCTG	59.504	52.381	0.00	0.00	0.00	4.45
3014	4846	1.004044	CTGAGGTCAGGAATGTTGCCT	59.996	52.381	0.00	0.00	40.20	4.75
3034	4866	1.556451	AGGCATTGGATTTTGAAGGCC	59.444	47.619	0.00	0.00	46.95	5.19
3063	4895	2.204237	GTTGGCTTCCACAAAAAGCTG	58.796	47.619	7.68	0.00	46.59	4.24
3088	4920	4.034410	TGTATCTAAGTGTGTATGGGGCA	58.966	43.478	0.00	0.00	0.00	5.36
3133	4991	1.174712	AGCTGGTCGTTGCTGCAATT	61.175	50.000	19.11	0.00	38.21	2.32
3341	5228	0.394352	ATTACAAAGGCGCCCTCCAG	60.394	55.000	26.15	11.74	30.89	3.86
3575	5626	6.649557	CACCGTCTATGGTAGAAAGAGTTTTT	59.350	38.462	0.00	0.00	41.38	1.94
3783	5835	8.913487	TGTAAACTAGGAAAGTAAAAGGGAAG	57.087	34.615	0.00	0.00	37.50	3.46
4103	6403	8.798859	ATGTCATGAACTTAGCTTTCTATGTT	57.201	30.769	0.00	4.07	42.39	2.71
4540	6841	3.769739	TGCTTGGTGTAGACAGTTGAT	57.230	42.857	0.00	0.00	0.00	2.57
4578	6888	6.148811	CACCACGTTTCAACCACTAATAGAAT	59.851	38.462	0.00	0.00	0.00	2.40
4597	6907	2.100631	GTCCAAGATCGCCACCACG	61.101	63.158	0.00	0.00	0.00	4.94
4609	6919	9.347240	AGATTGTGAATCTTATTATGGTCCAAG	57.653	33.333	0.00	0.00	45.75	3.61
4722	7032	7.359514	GCCACAAAATTCTTCAATAGTGAAAGC	60.360	37.037	7.08	0.00	43.18	3.51
4763	7076	1.340017	ACTTGACCATACGCCAAGCAT	60.340	47.619	0.00	0.00	40.51	3.79
4764	7077	0.036164	ACTTGACCATACGCCAAGCA	59.964	50.000	0.00	0.00	40.51	3.91
4981	7295	5.463061	TGCAAAATAAAGCTTGACTTCTTGC	59.537	36.000	17.52	17.52	37.75	4.01
5089	7403	3.460103	TCACCAAAACTAAGTGTCGGAC	58.540	45.455	0.00	0.00	33.21	4.79
5123	7437	5.470437	AGAGCTGTGAATGATATGCATGAAG	59.530	40.000	10.16	0.00	37.28	3.02
5132	7446	5.104776	ACAAGCCTAAGAGCTGTGAATGATA	60.105	40.000	0.00	0.00	44.11	2.15
5196	7511	3.433615	GGGTTCAACACTCTTTCTCATCG	59.566	47.826	0.00	0.00	0.00	3.84

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.