AutoCloner

Multiple sequence alignment - TraesCS3B01G457500

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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	TraesCS3B01G457500	chr3B	100.000	4675	0	0	1	4675	699697649	699692975	0.000000e+00	8634.0
1	TraesCS3B01G457500	chr3B	89.744	858	85	3	1	858	181468262	181469116	0.000000e+00	1094.0
2	TraesCS3B01G457500	chr3B	92.076	631	43	4	3556	4185	699285542	699284918	0.000000e+00	881.0
3	TraesCS3B01G457500	chr3B	97.694	477	11	0	2701	3177	699287226	699286750	0.000000e+00	821.0
4	TraesCS3B01G457500	chr3B	96.452	310	3	3	4367	4675	699284921	699284619	5.400000e-139	505.0
5	TraesCS3B01G457500	chr3B	95.708	233	9	1	3326	3557	699285933	699285701	1.590000e-99	374.0
6	TraesCS3B01G457500	chr3B	95.395	152	7	0	2565	2716	699297060	699296909	4.670000e-60	243.0
7	TraesCS3B01G457500	chr3D	91.743	3064	186	22	906	3920	529141345	529138300	0.000000e+00	4194.0
8	TraesCS3B01G457500	chr3D	95.487	421	19	0	2627	3047	528799763	528800183	0.000000e+00	673.0
9	TraesCS3B01G457500	chr3D	84.804	408	46	14	3535	3927	528806132	528806538	3.390000e-106	396.0
10	TraesCS3B01G457500	chr3D	91.154	260	11	4	3914	4173	529136935	529136688	4.480000e-90	342.0
11	TraesCS3B01G457500	chr3D	90.800	250	11	6	3043	3292	528804735	528804972	1.620000e-84	324.0
12	TraesCS3B01G457500	chr3D	84.685	333	19	15	4367	4674	529136682	529136357	2.110000e-78	303.0
13	TraesCS3B01G457500	chr3D	90.583	223	21	0	3290	3512	528805925	528806147	3.540000e-76	296.0
14	TraesCS3B01G457500	chr3D	87.755	245	25	4	4432	4675	528807197	528807437	9.900000e-72	281.0
15	TraesCS3B01G457500	chr3D	92.265	181	4	2	4001	4181	528806937	528807107	1.000000e-61	248.0
16	TraesCS3B01G457500	chr3D	96.154	52	2	0	2564	2615	528794878	528794929	8.330000e-13	86.1
17	TraesCS3B01G457500	chr3A	87.392	2197	190	46	2022	4184	662813723	662815866	0.000000e+00	2442.0
18	TraesCS3B01G457500	chr3A	88.498	1478	115	36	2728	4184	663293691	663292248	0.000000e+00	1736.0
19	TraesCS3B01G457500	chr3A	91.322	968	50	6	1783	2734	663296593	663295644	0.000000e+00	1291.0
20	TraesCS3B01G457500	chr3A	90.677	901	61	16	906	1789	663297724	663296830	0.000000e+00	1177.0
21	TraesCS3B01G457500	chr3A	83.652	471	48	9	3251	3718	662820445	662820889	2.600000e-112	416.0
22	TraesCS3B01G457500	chr3A	94.068	118	1	2	4563	4674	663291766	663291649	1.730000e-39	174.0
23	TraesCS3B01G457500	chr3A	87.719	114	14	0	3138	3251	662820249	662820362	2.930000e-27	134.0
24	TraesCS3B01G457500	chr3A	94.048	84	3	1	4563	4644	662816002	662816085	4.910000e-25	126.0
25	TraesCS3B01G457500	chr2B	97.436	858	22	0	1	858	30102908	30102051	0.000000e+00	1463.0
26	TraesCS3B01G457500	chr2B	92.123	584	46	0	275	858	72595304	72594721	0.000000e+00	824.0
27	TraesCS3B01G457500	chr2B	82.168	858	149	4	2	858	38425218	38426072	0.000000e+00	734.0
28	TraesCS3B01G457500	chr2B	90.175	285	27	1	1	285	72598510	72598227	2.050000e-98	370.0
29	TraesCS3B01G457500	chr5A	90.793	858	79	0	1	858	504919457	504920314	0.000000e+00	1147.0
30	TraesCS3B01G457500	chr5A	90.793	858	79	0	1	858	510441640	510440783	0.000000e+00	1147.0
31	TraesCS3B01G457500	chr5A	93.782	193	12	0	4184	4376	471707271	471707079	1.650000e-74	291.0
32	TraesCS3B01G457500	chr6B	92.371	603	45	1	256	858	643533905	643533304	0.000000e+00	857.0
33	TraesCS3B01G457500	chr6B	94.709	189	10	0	4180	4368	33072777	33072965	1.270000e-75	294.0
34	TraesCS3B01G457500	chr7A	84.687	862	123	8	1	858	610215554	610216410	0.000000e+00	852.0
35	TraesCS3B01G457500	chr2A	81.787	862	150	6	1	858	684126936	684126078	0.000000e+00	715.0
36	TraesCS3B01G457500	chr1A	95.722	187	8	0	4181	4367	582559479	582559665	7.600000e-78	302.0
37	TraesCS3B01G457500	chr4D	94.792	192	10	0	4184	4375	503922207	503922016	2.730000e-77	300.0
38	TraesCS3B01G457500	chr2D	95.263	190	7	2	4184	4372	591983011	591983199	2.730000e-77	300.0
39	TraesCS3B01G457500	chr4B	95.187	187	9	0	4181	4367	625223526	625223712	3.540000e-76	296.0
40	TraesCS3B01G457500	chrUn	94.709	189	10	0	4184	4372	255618818	255618630	1.270000e-75	294.0
41	TraesCS3B01G457500	chr5B	93.878	196	11	1	4180	4375	588535270	588535464	1.270000e-75	294.0
42	TraesCS3B01G457500	chr4A	94.271	192	11	0	4176	4367	574198076	574197885	1.270000e-75	294.0

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	TraesCS3B01G457500	chr3B	699692975	699697649	4674	True	8634.00	8634	100.00000	1	4675	1	chr3B.!!$R2	4674
1	TraesCS3B01G457500	chr3B	181468262	181469116	854	False	1094.00	1094	89.74400	1	858	1	chr3B.!!$F1	857
2	TraesCS3B01G457500	chr3B	699284619	699287226	2607	True	645.25	881	95.48250	2701	4675	4	chr3B.!!$R3	1974
3	TraesCS3B01G457500	chr3D	529136357	529141345	4988	True	1613.00	4194	89.19400	906	4674	3	chr3D.!!$R1	3768
4	TraesCS3B01G457500	chr3D	528804735	528807437	2702	False	309.00	396	89.24140	3043	4675	5	chr3D.!!$F3	1632
5	TraesCS3B01G457500	chr3A	662813723	662816085	2362	False	1284.00	2442	90.72000	2022	4644	2	chr3A.!!$F1	2622
6	TraesCS3B01G457500	chr3A	663291649	663297724	6075	True	1094.50	1736	91.14125	906	4674	4	chr3A.!!$R1	3768
7	TraesCS3B01G457500	chr3A	662820249	662820889	640	False	275.00	416	85.68550	3138	3718	2	chr3A.!!$F2	580
8	TraesCS3B01G457500	chr2B	30102051	30102908	857	True	1463.00	1463	97.43600	1	858	1	chr2B.!!$R1	857
9	TraesCS3B01G457500	chr2B	38425218	38426072	854	False	734.00	734	82.16800	2	858	1	chr2B.!!$F1	856
10	TraesCS3B01G457500	chr2B	72594721	72598510	3789	True	597.00	824	91.14900	1	858	2	chr2B.!!$R2	857
11	TraesCS3B01G457500	chr5A	504919457	504920314	857	False	1147.00	1147	90.79300	1	858	1	chr5A.!!$F1	857
12	TraesCS3B01G457500	chr5A	510440783	510441640	857	True	1147.00	1147	90.79300	1	858	1	chr5A.!!$R2	857
13	TraesCS3B01G457500	chr6B	643533304	643533905	601	True	857.00	857	92.37100	256	858	1	chr6B.!!$R1	602
14	TraesCS3B01G457500	chr7A	610215554	610216410	856	False	852.00	852	84.68700	1	858	1	chr7A.!!$F1	857
15	TraesCS3B01G457500	chr2A	684126078	684126936	858	True	715.00	715	81.78700	1	858	1	chr2A.!!$R1	857

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	Hairpin	End Stability	Orientation
123	124	0.107214	CTGTACCAATGGACCGGCAT	60.107	55.000	6.16	0.00	4.40	F
187	188	0.538057	CAGGCTGCCAAACTCCTTGA	60.538	55.000	22.65	37.17	3.02	F
868	3803	2.285756	CGAGACCAAAACTAAACGTGCA	59.714	45.455	0.00	0.00	4.57	F
2138	5367	1.333791	GCGTTTGCAACACAGGAGTAC	60.334	52.381	0.00	42.15	2.73	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Hairpin	End Stability	Orientation
1637	4604	1.281867	TCTTGGCCAGTATTGGGACAG	59.718	52.381	5.11	46.14	3.51	R
1641	4608	1.479389	GGGATCTTGGCCAGTATTGGG	60.479	57.143	5.11	45.16	4.12	R
2217	5453	1.078143	CTGCCCTCCACAGTAAGGC	60.078	63.158	0.00	44.13	4.35	R
3903	11006	0.095245	CATTAACAGCCGCACAGTCG	59.905	55.000	0.00	0.00	4.18	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)

Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
69	70	1.635487	TGATGCAAGGCCTCCTTTAGT	59.365	47.619	5.23	0.00	41.69	2.24
83	84	5.278022	CCTCCTTTAGTTTCTTGACAACAGC	60.278	44.000	0.00	0.00	0.00	4.40
123	124	0.107214	CTGTACCAATGGACCGGCAT	60.107	55.000	6.16	0.00	0.00	4.40
187	188	0.538057	CAGGCTGCCAAACTCCTTGA	60.538	55.000	22.65	0.00	37.17	3.02
354	3289	3.445805	ACTGTTTCCGTTTTGGTGTTGAT	59.554	39.130	0.00	0.00	39.52	2.57
631	3566	4.371786	CGCTGATCTACTAAAATGCTCCA	58.628	43.478	0.00	0.00	0.00	3.86
699	3634	4.435518	GCATGTGGTAACGTATGAAGTGTG	60.436	45.833	0.00	0.00	42.51	3.82
858	3793	5.411781	ACAGATACATCTCGAGACCAAAAC	58.588	41.667	19.30	8.13	34.22	2.43
859	3794	5.186021	ACAGATACATCTCGAGACCAAAACT	59.814	40.000	19.30	10.28	34.22	2.66
860	3795	6.377429	ACAGATACATCTCGAGACCAAAACTA	59.623	38.462	19.30	0.00	34.22	2.24
861	3796	7.093902	ACAGATACATCTCGAGACCAAAACTAA	60.094	37.037	19.30	0.00	34.22	2.24
862	3797	7.759886	CAGATACATCTCGAGACCAAAACTAAA	59.240	37.037	19.30	0.00	34.22	1.85
863	3798	7.760340	AGATACATCTCGAGACCAAAACTAAAC	59.240	37.037	19.30	1.03	29.30	2.01
864	3799	4.684703	ACATCTCGAGACCAAAACTAAACG	59.315	41.667	19.30	0.00	0.00	3.60
865	3800	4.311816	TCTCGAGACCAAAACTAAACGT	57.688	40.909	12.08	0.00	0.00	3.99
866	3801	4.046462	TCTCGAGACCAAAACTAAACGTG	58.954	43.478	12.08	0.00	0.00	4.49
867	3802	2.540931	TCGAGACCAAAACTAAACGTGC	59.459	45.455	0.00	0.00	0.00	5.34
868	3803	2.285756	CGAGACCAAAACTAAACGTGCA	59.714	45.455	0.00	0.00	0.00	4.57
869	3804	3.242478	CGAGACCAAAACTAAACGTGCAA	60.242	43.478	0.00	0.00	0.00	4.08
870	3805	4.279659	GAGACCAAAACTAAACGTGCAAG	58.720	43.478	0.00	0.00	0.00	4.01
871	3806	3.692593	AGACCAAAACTAAACGTGCAAGT	59.307	39.130	0.00	0.00	0.00	3.16
872	3807	4.157105	AGACCAAAACTAAACGTGCAAGTT	59.843	37.500	12.50	12.50	35.01	2.66
873	3808	4.170256	ACCAAAACTAAACGTGCAAGTTG	58.830	39.130	18.80	9.76	33.85	3.16
874	3809	4.170256	CCAAAACTAAACGTGCAAGTTGT	58.830	39.130	18.80	10.41	33.85	3.32
875	3810	5.106237	ACCAAAACTAAACGTGCAAGTTGTA	60.106	36.000	18.80	11.64	33.85	2.41

Showing 1 to 25 of 205 entries

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Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
69	70	3.117888	AGGAGGAAGCTGTTGTCAAGAAA	60.118	43.478	0.00	0.00	0.00	2.52
83	84	2.711922	CCGACGGTGGAGGAGGAAG	61.712	68.421	5.48	0.00	0.00	3.46
288	3222	5.278512	GCAGACTCATACAGATTATGACCGA	60.279	44.000	0.00	0.00	31.39	4.69
354	3289	1.583556	TTAAGGAGAGCCTGCCATCA	58.416	50.000	0.00	0.00	46.28	3.07
631	3566	8.993424	AGATTACAATGAGACACTATACCCTTT	58.007	33.333	0.00	0.00	0.00	3.11
745	3680	2.031930	GGCGTTTCACTGGTTTTTACGA	59.968	45.455	0.00	0.00	0.00	3.43
858	3793	5.652744	AGTCTTACAACTTGCACGTTTAG	57.347	39.130	5.74	4.81	0.00	1.85
859	3794	6.534436	TGTAAGTCTTACAACTTGCACGTTTA	59.466	34.615	20.73	0.57	43.83	2.01
860	3795	4.957759	AAGTCTTACAACTTGCACGTTT	57.042	36.364	5.74	1.48	38.06	3.60
861	3796	4.871557	TGTAAGTCTTACAACTTGCACGTT	59.128	37.500	20.73	2.17	43.83	3.99
862	3797	4.435425	TGTAAGTCTTACAACTTGCACGT	58.565	39.130	20.73	0.00	43.83	4.49
863	3798	5.006649	CTGTAAGTCTTACAACTTGCACG	57.993	43.478	22.59	8.05	43.83	5.34
885	3820	9.971922	ACCGTTAATACAGAGGTAATAATACAC	57.028	33.333	0.00	0.00	29.99	2.90
889	3824	8.588472	GGGTACCGTTAATACAGAGGTAATAAT	58.412	37.037	5.65	0.00	40.86	1.28
890	3825	7.951591	GGGTACCGTTAATACAGAGGTAATAA	58.048	38.462	5.65	0.00	40.86	1.40
891	3826	7.524717	GGGTACCGTTAATACAGAGGTAATA	57.475	40.000	5.65	0.00	40.86	0.98
892	3827	6.410942	GGGTACCGTTAATACAGAGGTAAT	57.589	41.667	5.65	0.00	40.86	1.89
893	3828	5.852282	GGGTACCGTTAATACAGAGGTAA	57.148	43.478	5.65	0.00	40.86	2.85
1262	4203	3.252458	AGAGATTGCGGTTTGGTTACAAC	59.748	43.478	0.00	0.00	36.06	3.32
1381	4344	6.511017	TGGATCTTCATCTGGAAATCTCAT	57.489	37.500	0.00	0.00	34.44	2.90
1382	4345	5.963214	TGGATCTTCATCTGGAAATCTCA	57.037	39.130	0.00	0.00	34.44	3.27
1386	4349	4.643784	GCACTTGGATCTTCATCTGGAAAT	59.356	41.667	0.00	0.00	34.44	2.17
1390	4353	2.995283	TGCACTTGGATCTTCATCTGG	58.005	47.619	0.00	0.00	0.00	3.86
1396	4359	5.958955	AGCTTATTTTGCACTTGGATCTTC	58.041	37.500	0.00	0.00	0.00	2.87
1397	4360	5.990120	AGCTTATTTTGCACTTGGATCTT	57.010	34.783	0.00	0.00	0.00	2.40

Showing 1 to 25 of 188 entries

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Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.