AutoCloner

Multiple sequence alignment - TraesCS4A01G133400

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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	TraesCS4A01G133400	chr4A	100.000	4228	0	0	1	4228	180394994	180399221	0.000000e+00	7808.0
1	TraesCS4A01G133400	chr4A	77.778	243	50	3	2878	3118	60926375	60926135	3.410000e-31	147.0
2	TraesCS4A01G133400	chr4D	96.400	3556	111	11	1	3548	301302455	301298909	0.000000e+00	5842.0
3	TraesCS4A01G133400	chr4D	77.778	243	50	3	2878	3118	403396615	403396375	3.410000e-31	147.0
4	TraesCS4A01G133400	chr4B	95.776	2320	91	6	1	2317	375140465	375138150	0.000000e+00	3735.0
5	TraesCS4A01G133400	chr4B	93.680	981	43	9	2568	3548	375137748	375136787	0.000000e+00	1450.0
6	TraesCS4A01G133400	chr4B	79.231	130	27	0	2989	3118	500253403	500253274	1.620000e-14	91.6
7	TraesCS4A01G133400	chr7A	98.176	658	12	0	3571	4228	727382253	727382910	0.000000e+00	1149.0
8	TraesCS4A01G133400	chr6A	98.021	657	13	0	3572	4228	247530953	247531609	0.000000e+00	1142.0
9	TraesCS4A01G133400	chr6A	98.018	656	13	0	3573	4228	247529255	247529910	0.000000e+00	1140.0
10	TraesCS4A01G133400	chrUn	98.018	656	13	0	3573	4228	147887822	147887167	0.000000e+00	1140.0
11	TraesCS4A01G133400	chrUn	97.557	655	16	0	3572	4226	147886125	147885471	0.000000e+00	1122.0
12	TraesCS4A01G133400	chr3A	98.018	656	13	0	3573	4228	647697201	647697856	0.000000e+00	1140.0
13	TraesCS4A01G133400	chr3A	86.777	121	16	0	2970	3090	131406668	131406788	7.370000e-28	135.0
14	TraesCS4A01G133400	chr3A	80.451	133	21	5	2962	3090	398881171	398881040	3.480000e-16	97.1
15	TraesCS4A01G133400	chr2B	97.451	667	15	2	3564	4228	347644417	347645083	0.000000e+00	1136.0
16	TraesCS4A01G133400	chr2B	97.451	667	15	2	3564	4228	347646116	347646782	0.000000e+00	1136.0
17	TraesCS4A01G133400	chr2B	97.451	667	15	2	3564	4228	347647815	347648481	0.000000e+00	1136.0
18	TraesCS4A01G133400	chr2B	75.513	1266	271	25	1038	2282	88839293	88840540	6.090000e-163	584.0
19	TraesCS4A01G133400	chr2A	75.257	1265	276	23	1038	2282	57547287	57548534	6.130000e-158	568.0
20	TraesCS4A01G133400	chr3D	80.303	132	23	2	2962	3090	323698839	323698970	3.480000e-16	97.1
21	TraesCS4A01G133400	chr3B	79.137	139	24	4	2962	3097	395380212	395380076	1.620000e-14	91.6
22	TraesCS4A01G133400	chr5B	88.889	45	4	1	3508	3552	636609486	636609443	2.000000e-03	54.7

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	TraesCS4A01G133400	chr4A	180394994	180399221	4227	False	7808.0	7808	100.0000	1	4228	1	chr4A.!!$F1	4227
1	TraesCS4A01G133400	chr4D	301298909	301302455	3546	True	5842.0	5842	96.4000	1	3548	1	chr4D.!!$R1	3547
2	TraesCS4A01G133400	chr4B	375136787	375140465	3678	True	2592.5	3735	94.7280	1	3548	2	chr4B.!!$R2	3547
3	TraesCS4A01G133400	chr7A	727382253	727382910	657	False	1149.0	1149	98.1760	3571	4228	1	chr7A.!!$F1	657
4	TraesCS4A01G133400	chr6A	247529255	247531609	2354	False	1141.0	1142	98.0195	3572	4228	2	chr6A.!!$F1	656
5	TraesCS4A01G133400	chrUn	147885471	147887822	2351	True	1131.0	1140	97.7875	3572	4228	2	chrUn.!!$R1	656
6	TraesCS4A01G133400	chr3A	647697201	647697856	655	False	1140.0	1140	98.0180	3573	4228	1	chr3A.!!$F2	655
7	TraesCS4A01G133400	chr2B	347644417	347648481	4064	False	1136.0	1136	97.4510	3564	4228	3	chr2B.!!$F2	664
8	TraesCS4A01G133400	chr2B	88839293	88840540	1247	False	584.0	584	75.5130	1038	2282	1	chr2B.!!$F1	1244
9	TraesCS4A01G133400	chr2A	57547287	57548534	1247	False	568.0	568	75.2570	1038	2282	1	chr2A.!!$F1	1244

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
687	689	0.099436	GTCTTTCATGGCATGACCGC	59.901	55.0	28.83	15.41	43.94	5.68	F
1806	1831	0.313043	CTGTTGGAGGCTTTGCTGTG	59.687	55.0	0.00	0.00	0.00	3.66	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1875	1900	1.271379	GCTCCCTTGCTCTTGTAACCA	60.271	52.381	0.0	0.0	0.0	3.67	R
3472	3694	0.321564	TTGGGTGCGATCTTGTGAGG	60.322	55.000	0.0	0.0	0.0	3.86	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
80	81	1.131126	CGTGATGTGGTTTCCTGATGC	59.869	52.381	0.00	0.00	0.00	3.91
127	128	8.433421	AGACTATATTTGGTTTGTGGTAATCG	57.567	34.615	0.00	0.00	0.00	3.34
211	212	7.337942	CCAGTATTGATGAGCTTTAGTTTCCTT	59.662	37.037	0.00	0.00	0.00	3.36
217	218	3.498397	TGAGCTTTAGTTTCCTTCTTGCG	59.502	43.478	0.00	0.00	0.00	4.85
378	380	4.610945	CCGTTCTTTGGATGCATAATTCC	58.389	43.478	0.00	0.00	0.00	3.01
405	407	4.336433	CCCTGGTGTTGATTAGCTGTTATG	59.664	45.833	0.00	0.00	0.00	1.90
419	421	8.972458	TTAGCTGTTATGCATTTGTTATCCTA	57.028	30.769	3.54	0.00	34.99	2.94
523	525	0.179034	CCTAGAGGCTTCCCATGCAC	60.179	60.000	0.00	0.00	0.00	4.57
650	652	5.760743	GTCAGGCTCCAGTAGGAATATTTTC	59.239	44.000	0.00	0.00	45.19	2.29
687	689	0.099436	GTCTTTCATGGCATGACCGC	59.901	55.000	28.83	15.41	43.94	5.68
719	722	3.513515	TGCCTTTGTGTTTGTTCTTCCTT	59.486	39.130	0.00	0.00	0.00	3.36
731	734	8.383175	TGTTTGTTCTTCCTTAGTCCTCATTAT	58.617	33.333	0.00	0.00	0.00	1.28
738	741	6.732896	TCCTTAGTCCTCATTATGTCTTCC	57.267	41.667	0.00	0.00	0.00	3.46
814	817	1.290203	CGTGCACACCCACATATCTC	58.710	55.000	18.64	0.00	35.47	2.75
819	822	3.282021	GCACACCCACATATCTCATGTT	58.718	45.455	0.00	0.00	0.00	2.71
930	934	5.693104	TCTTCATTTTCATTGCAGCTGTTTC	59.307	36.000	16.64	0.00	0.00	2.78
963	967	3.880490	TGGCGTAAACAGATGAAGTTGTT	59.120	39.130	0.00	0.00	39.08	2.83
964	968	4.219033	GGCGTAAACAGATGAAGTTGTTG	58.781	43.478	0.00	0.00	37.57	3.33
975	979	7.020010	CAGATGAAGTTGTTGCTCATTTAGTC	58.980	38.462	0.00	0.00	0.00	2.59
977	981	6.691754	TGAAGTTGTTGCTCATTTAGTCAA	57.308	33.333	0.00	0.00	0.00	3.18
978	982	6.728200	TGAAGTTGTTGCTCATTTAGTCAAG	58.272	36.000	0.00	0.00	0.00	3.02
996	1000	5.897050	GTCAAGTTGACTCCGAGATATTCT	58.103	41.667	25.56	0.00	43.73	2.40
1005	1009	5.646215	ACTCCGAGATATTCTCTAATGGGT	58.354	41.667	1.33	0.00	41.26	4.51
1173	1177	4.002982	TCAACTGGGATCAAAACATCTCG	58.997	43.478	0.00	0.00	0.00	4.04
1420	1424	3.192212	GTCAGGAGATTTGCCTTCCTTTG	59.808	47.826	0.00	0.00	32.12	2.77
1592	1596	8.976986	AGCTTAAGACAATTAAATTTGAGCAG	57.023	30.769	6.67	0.00	28.91	4.24
1806	1831	0.313043	CTGTTGGAGGCTTTGCTGTG	59.687	55.000	0.00	0.00	0.00	3.66
2163	2188	1.342496	CAGCAGATGGAGCTTATCGGA	59.658	52.381	13.48	0.00	41.14	4.55
2310	2340	2.501316	GCCTTTCACCCCTGCATAATTT	59.499	45.455	0.00	0.00	0.00	1.82
2312	2342	4.506758	CCTTTCACCCCTGCATAATTTTG	58.493	43.478	0.00	0.00	0.00	2.44
2380	2438	2.991250	TCATCCCTGAGCTAGCAAAAC	58.009	47.619	18.83	5.92	0.00	2.43
2395	2453	6.146021	GCTAGCAAAACTTACATGCACAAAAT	59.854	34.615	10.63	0.00	42.45	1.82
2456	2677	7.338800	ACACATTCATGAACTTCACTTTCTT	57.661	32.000	11.07	0.00	0.00	2.52
2489	2710	4.042809	AGAGGACATTGTTGATTACCCACA	59.957	41.667	0.00	0.00	0.00	4.17
2518	2739	7.315142	TGAAAATGGCTCTAATTGTTTAGCAG	58.685	34.615	0.00	0.00	35.72	4.24
2594	2816	5.630121	TGATTAAAGTGGTGATGAACAGGT	58.370	37.500	0.00	0.00	0.00	4.00
2604	2826	3.883489	GTGATGAACAGGTATTAAGGGCC	59.117	47.826	0.00	0.00	0.00	5.80
2741	2963	1.961277	GTCCACCAACGTGCTCCTG	60.961	63.158	0.00	0.00	38.79	3.86
2852	3074	1.686325	GCGCCCCAGAGACCTATGAA	61.686	60.000	0.00	0.00	0.00	2.57
2868	3090	5.194537	ACCTATGAATCCAGGAAATTCACCT	59.805	40.000	7.53	0.00	43.76	4.00
3177	3399	2.276116	TTCACCGCTTCCGAGAGCT	61.276	57.895	8.09	0.00	40.52	4.09
3229	3451	0.544697	AACCCTCCATCGGCGTAAAT	59.455	50.000	6.85	0.00	0.00	1.40
3263	3485	0.944386	GCTTGTTCGTCCAGAAGCAA	59.056	50.000	0.00	0.00	40.47	3.91
3305	3527	2.689983	CCATGAACAAGCCTTGTATCCC	59.310	50.000	11.10	1.80	44.59	3.85
3315	3537	5.552870	AGCCTTGTATCCCTATAACTGTG	57.447	43.478	0.00	0.00	0.00	3.66
3322	3544	7.004555	TGTATCCCTATAACTGTGCCAATAG	57.995	40.000	0.00	0.00	0.00	1.73
3327	3549	5.221925	CCCTATAACTGTGCCAATAGTCCAT	60.222	44.000	0.00	0.00	0.00	3.41
3335	3557	1.093972	CCAATAGTCCATGCGTGCAA	58.906	50.000	0.00	0.00	0.00	4.08
3552	3774	9.660180	ACATAAGATGTTCTAACCTTTTCTCTC	57.340	33.333	0.00	0.00	41.63	3.20
3553	3775	9.883142	CATAAGATGTTCTAACCTTTTCTCTCT	57.117	33.333	0.00	0.00	0.00	3.10
3555	3777	7.790782	AGATGTTCTAACCTTTTCTCTCTCT	57.209	36.000	0.00	0.00	0.00	3.10
3556	3778	8.201242	AGATGTTCTAACCTTTTCTCTCTCTT	57.799	34.615	0.00	0.00	0.00	2.85
3557	3779	8.655901	AGATGTTCTAACCTTTTCTCTCTCTTT	58.344	33.333	0.00	0.00	0.00	2.52
3558	3780	9.278978	GATGTTCTAACCTTTTCTCTCTCTTTT	57.721	33.333	0.00	0.00	0.00	2.27
3559	3781	9.634021	ATGTTCTAACCTTTTCTCTCTCTTTTT	57.366	29.630	0.00	0.00	0.00	1.94
4039	5960	2.018727	AACGTGCCGTGGAGTGTGTA	62.019	55.000	0.94	0.00	39.99	2.90
4064	5985	5.625150	AGTCTGCTATGTTTGAAGGAAGTT	58.375	37.500	0.00	0.00	0.00	2.66

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
61	62	2.163010	CAGCATCAGGAAACCACATCAC	59.837	50.000	0.00	0.00	0.00	3.06
211	212	0.321671	CAGAGAAAGGGGACGCAAGA	59.678	55.000	0.00	0.00	43.62	3.02
217	218	4.589908	TCAATAAAGCAGAGAAAGGGGAC	58.410	43.478	0.00	0.00	0.00	4.46
378	380	2.026822	AGCTAATCAACACCAGGGACAG	60.027	50.000	0.00	0.00	0.00	3.51
405	407	9.754382	ATTGTCAAATCATAGGATAACAAATGC	57.246	29.630	13.43	0.00	32.09	3.56
419	421	5.578005	CTCCTGAAGCATTGTCAAATCAT	57.422	39.130	0.00	0.00	0.00	2.45
523	525	6.959871	CGAAGAGTGTGAATGATCAGAAATTG	59.040	38.462	0.09	0.00	35.88	2.32
626	628	4.965200	AATATTCCTACTGGAGCCTGAC	57.035	45.455	0.08	0.00	44.24	3.51
650	652	3.690460	AGACCAAAGCACTATCAAAGGG	58.310	45.455	0.00	0.00	0.00	3.95
652	654	6.317789	TGAAAGACCAAAGCACTATCAAAG	57.682	37.500	0.00	0.00	0.00	2.77
719	722	5.363868	CCTGTGGAAGACATAATGAGGACTA	59.636	44.000	0.00	0.00	32.74	2.59
731	734	2.280797	GCGCACCTGTGGAAGACA	60.281	61.111	0.30	0.00	0.00	3.41
738	741	2.509111	TAGATGCGCGCACCTGTG	60.509	61.111	37.70	0.00	0.00	3.66
804	807	6.147581	GCAAGCAATAACATGAGATATGTGG	58.852	40.000	0.00	0.00	31.80	4.17
814	817	8.313227	CGTTATAAAACTGCAAGCAATAACATG	58.687	33.333	18.80	0.00	37.60	3.21
819	822	7.372451	ACTCGTTATAAAACTGCAAGCAATA	57.628	32.000	0.00	0.00	37.60	1.90
858	862	9.921637	AACTGAAAGAACAACTTCAAACATAAA	57.078	25.926	0.00	0.00	37.93	1.40
930	934	8.341903	TCATCTGTTTACGCCAATGTAATAATG	58.658	33.333	0.00	0.00	34.50	1.90
1005	1009	8.894768	GCAAAGAGCCTCTAAGATTTAGATAA	57.105	34.615	0.00	0.00	37.23	1.75
1420	1424	1.680249	GGTGATGAGGCCTGGAGAAAC	60.680	57.143	12.00	0.00	0.00	2.78
1659	1663	3.249189	GGCCCACACAGTCCAGGA	61.249	66.667	0.00	0.00	0.00	3.86
1875	1900	1.271379	GCTCCCTTGCTCTTGTAACCA	60.271	52.381	0.00	0.00	0.00	3.67
1877	1902	1.454201	GGCTCCCTTGCTCTTGTAAC	58.546	55.000	0.00	0.00	0.00	2.50
2310	2340	6.418057	AACAATGGATCTTTAGGCAAACAA	57.582	33.333	0.00	0.00	0.00	2.83
2312	2342	6.705825	ACAAAACAATGGATCTTTAGGCAAAC	59.294	34.615	0.00	0.00	0.00	2.93
2380	2438	4.327898	GCATGGTCATTTTGTGCATGTAAG	59.672	41.667	0.00	0.00	33.44	2.34
2456	2677	9.739276	AATCAACAATGTCCTCTTAACAGAATA	57.261	29.630	0.00	0.00	0.00	1.75
2489	2710	6.655078	AACAATTAGAGCCATTTTCAGTGT	57.345	33.333	0.00	0.00	0.00	3.55
2542	2764	2.715046	ACATTGCCACACCATCTACAG	58.285	47.619	0.00	0.00	0.00	2.74
2594	2816	4.080526	GTCTTCTCCACAAGGCCCTTAATA	60.081	45.833	0.00	0.00	33.74	0.98
2604	2826	2.440409	CAATGGGGTCTTCTCCACAAG	58.560	52.381	0.00	0.00	44.56	3.16
2741	2963	1.351017	TGAGGGTTGTGGTCTTGATCC	59.649	52.381	0.00	0.00	0.00	3.36
2840	3062	6.388100	TGAATTTCCTGGATTCATAGGTCTCT	59.612	38.462	8.33	0.00	38.29	3.10
2843	3065	5.532779	GGTGAATTTCCTGGATTCATAGGTC	59.467	44.000	14.09	3.50	43.22	3.85
2852	3074	5.501156	GACTTGTAGGTGAATTTCCTGGAT	58.499	41.667	11.73	0.00	36.60	3.41
2868	3090	1.466167	GCTGTAGACGTCCGACTTGTA	59.534	52.381	13.01	0.00	0.00	2.41
3024	3246	2.224185	TGTTGTGGTACTTCATCAGCGT	60.224	45.455	0.00	0.00	0.00	5.07
3119	3341	1.126488	TCCTGATCACCTCTGCCATC	58.874	55.000	0.00	0.00	0.00	3.51
3177	3399	1.269448	GTTTTCATTGGAAGAGGCGCA	59.731	47.619	10.83	0.00	33.82	6.09
3284	3506	2.689983	GGGATACAAGGCTTGTTCATGG	59.310	50.000	35.13	7.57	42.22	3.66
3295	3517	4.102524	TGGCACAGTTATAGGGATACAAGG	59.897	45.833	0.00	0.00	39.74	3.61
3296	3518	5.290493	TGGCACAGTTATAGGGATACAAG	57.710	43.478	0.00	0.00	39.74	3.16
3305	3527	5.180117	GCATGGACTATTGGCACAGTTATAG	59.820	44.000	2.70	2.53	42.39	1.31
3315	3537	1.356624	GCACGCATGGACTATTGGC	59.643	57.895	0.00	0.00	0.00	4.52
3322	3544	2.916716	CAATTAACTTGCACGCATGGAC	59.083	45.455	9.41	0.00	0.00	4.02
3327	3549	3.142951	ACTACCAATTAACTTGCACGCA	58.857	40.909	0.00	0.00	33.20	5.24
3366	3588	3.871006	CACGAGCAGAGGCAATGTATTAA	59.129	43.478	0.00	0.00	44.61	1.40
3411	3633	8.635877	AGTAGAAGATAATCAATGTCGTCAAC	57.364	34.615	0.00	0.00	0.00	3.18
3463	3685	2.200067	GATCTTGTGAGGAGCGATGTG	58.800	52.381	0.00	0.00	0.00	3.21
3468	3690	1.153765	TGCGATCTTGTGAGGAGCG	60.154	57.895	0.00	0.00	43.99	5.03
3470	3692	0.460987	GGGTGCGATCTTGTGAGGAG	60.461	60.000	0.00	0.00	0.00	3.69
3471	3693	1.191489	TGGGTGCGATCTTGTGAGGA	61.191	55.000	0.00	0.00	0.00	3.71
3472	3694	0.321564	TTGGGTGCGATCTTGTGAGG	60.322	55.000	0.00	0.00	0.00	3.86
3473	3695	1.081892	CTTGGGTGCGATCTTGTGAG	58.918	55.000	0.00	0.00	0.00	3.51
3474	3696	0.955428	GCTTGGGTGCGATCTTGTGA	60.955	55.000	0.00	0.00	0.00	3.58
3556	3778	3.367498	CGTATCATTTTCCCCCGCAAAAA	60.367	43.478	0.00	0.00	0.00	1.94
3557	3779	2.164624	CGTATCATTTTCCCCCGCAAAA	59.835	45.455	0.00	0.00	0.00	2.44
3558	3780	1.746220	CGTATCATTTTCCCCCGCAAA	59.254	47.619	0.00	0.00	0.00	3.68
3559	3781	1.065345	TCGTATCATTTTCCCCCGCAA	60.065	47.619	0.00	0.00	0.00	4.85
3560	3782	0.542333	TCGTATCATTTTCCCCCGCA	59.458	50.000	0.00	0.00	0.00	5.69
3561	3783	0.942252	GTCGTATCATTTTCCCCCGC	59.058	55.000	0.00	0.00	0.00	6.13
3562	3784	1.589803	GGTCGTATCATTTTCCCCCG	58.410	55.000	0.00	0.00	0.00	5.73
3563	3785	1.493446	AGGGTCGTATCATTTTCCCCC	59.507	52.381	0.00	0.00	35.90	5.40
3564	3786	3.211865	GAAGGGTCGTATCATTTTCCCC	58.788	50.000	0.00	0.00	35.90	4.81
3565	3787	3.881220	TGAAGGGTCGTATCATTTTCCC	58.119	45.455	0.00	0.00	35.56	3.97
3566	3788	7.745620	ATTATGAAGGGTCGTATCATTTTCC	57.254	36.000	0.00	0.00	35.53	3.13
4039	5960	5.012561	ACTTCCTTCAAACATAGCAGACTCT	59.987	40.000	0.00	0.00	0.00	3.24

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.