AutoCloner

Multiple sequence alignment - TraesCS3B01G055400

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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	TraesCS3B01G055400	chr3B	100.000	3510	0	0	1	3510	28608901	28605392	0.000000e+00	6482
1	TraesCS3B01G055400	chr3B	86.842	532	67	3	1685	2214	825849966	825850496	3.020000e-165	592
2	TraesCS3B01G055400	chr3B	83.520	625	83	15	870	1488	825849241	825849851	1.830000e-157	566
3	TraesCS3B01G055400	chr3B	86.874	419	43	8	2239	2655	825850484	825850892	3.190000e-125	459
4	TraesCS3B01G055400	chr3B	85.933	327	35	7	2656	2974	804547967	804547644	4.340000e-89	339
5	TraesCS3B01G055400	chr3B	81.570	293	27	16	3184	3474	804547231	804546964	2.120000e-52	217
6	TraesCS3B01G055400	chr3B	86.111	144	9	6	560	692	825848186	825848329	1.020000e-30	145
7	TraesCS3B01G055400	chr3B	97.015	67	2	0	1	67	189756770	189756836	2.860000e-21	113
8	TraesCS3B01G055400	chr3B	94.366	71	4	0	1	71	397546814	397546744	3.700000e-20	110
9	TraesCS3B01G055400	chr3A	95.790	3183	99	13	336	3510	748338827	748341982	0.000000e+00	5103
10	TraesCS3B01G055400	chr3A	87.269	974	107	12	1685	2655	749876818	749875859	0.000000e+00	1096
11	TraesCS3B01G055400	chr3A	82.791	645	85	17	858	1488	749877561	749876929	1.420000e-153	553
12	TraesCS3B01G055400	chr3A	96.333	300	11	0	7	306	748338531	748338830	8.750000e-136	494
13	TraesCS3B01G055400	chr3D	88.695	2008	159	23	1513	3510	615456590	615458539	0.000000e+00	2388
14	TraesCS3B01G055400	chr3D	86.735	490	58	7	975	1462	615455467	615455951	3.990000e-149	538
15	TraesCS3B01G055400	chr3D	82.353	153	27	0	709	861	426160492	426160644	2.200000e-27	134
16	TraesCS3B01G055400	chrUn	87.826	1150	126	11	1513	2655	37114789	37113647	0.000000e+00	1336
17	TraesCS3B01G055400	chrUn	87.826	1150	126	11	1513	2655	247032487	247033629	0.000000e+00	1336
18	TraesCS3B01G055400	chrUn	87.826	1150	126	11	1513	2655	300943518	300942376	0.000000e+00	1336
19	TraesCS3B01G055400	chrUn	83.826	643	75	17	858	1477	247031250	247031886	5.050000e-163	584
20	TraesCS3B01G055400	chrUn	86.654	517	59	8	965	1477	37115900	37115390	6.580000e-157	564
21	TraesCS3B01G055400	chrUn	86.654	517	59	8	965	1477	300944629	300944119	6.580000e-157	564
22	TraesCS3B01G055400	chrUn	83.489	321	41	9	2658	2977	44702525	44702834	4.430000e-74	289
23	TraesCS3B01G055400	chrUn	88.971	136	11	4	2664	2799	451870149	451870280	7.790000e-37	165
24	TraesCS3B01G055400	chr2B	86.196	326	35	6	2656	2974	671087766	671087444	9.330000e-91	344
25	TraesCS3B01G055400	chr2B	81.852	270	22	14	3184	3451	671087029	671086785	5.940000e-48	202
26	TraesCS3B01G055400	chr4A	81.232	341	60	4	98	435	664243248	664243587	4.460000e-69	272
27	TraesCS3B01G055400	chr4A	78.477	302	58	7	98	396	664244267	664244564	1.290000e-44	191
28	TraesCS3B01G055400	chr4A	76.763	241	50	2	1012	1252	639196012	639196246	2.840000e-26	130
29	TraesCS3B01G055400	chr4A	97.015	67	2	0	1	67	699936939	699936873	2.860000e-21	113
30	TraesCS3B01G055400	chr7A	78.605	430	73	14	84	508	279187621	279188036	2.080000e-67	267
31	TraesCS3B01G055400	chr7A	97.015	67	2	0	1	67	26811292	26811358	2.860000e-21	113
32	TraesCS3B01G055400	chr6B	95.062	162	8	0	698	859	364904387	364904226	4.500000e-64	255
33	TraesCS3B01G055400	chr6B	90.604	149	14	0	700	848	610827622	610827474	7.690000e-47	198
34	TraesCS3B01G055400	chr4B	93.210	162	11	0	698	859	437930471	437930632	4.530000e-59	239
35	TraesCS3B01G055400	chr5B	84.519	239	28	5	2656	2887	410726491	410726255	9.800000e-56	228
36	TraesCS3B01G055400	chr5B	84.848	165	25	0	698	862	375943558	375943394	2.170000e-37	167
37	TraesCS3B01G055400	chr1D	79.139	302	63	0	1000	1301	28165396	28165697	3.550000e-50	209
38	TraesCS3B01G055400	chr1D	93.243	74	3	1	1	72	71046795	71046722	1.330000e-19	108
39	TraesCS3B01G055400	chr5A	83.237	173	20	7	698	862	422040599	422040428	2.180000e-32	150
40	TraesCS3B01G055400	chr2D	83.133	166	27	1	696	861	636546117	636546281	2.180000e-32	150
41	TraesCS3B01G055400	chr6D	80.240	167	28	4	696	861	459267926	459268088	1.710000e-23	121
42	TraesCS3B01G055400	chr7B	74.497	298	65	6	98	393	423564817	423565105	6.150000e-23	119
43	TraesCS3B01G055400	chr4D	97.101	69	2	0	1	69	397076088	397076020	2.210000e-22	117
44	TraesCS3B01G055400	chr2A	97.015	67	2	0	1	67	379119832	379119766	2.860000e-21	113
45	TraesCS3B01G055400	chr2A	95.652	69	3	0	1	69	399995780	399995712	1.030000e-20	111

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	TraesCS3B01G055400	chr3B	28605392	28608901	3509	True	6482.0	6482	100.00000	1	3510	1	chr3B.!!$R1	3509
1	TraesCS3B01G055400	chr3B	825848186	825850892	2706	False	440.5	592	85.83675	560	2655	4	chr3B.!!$F2	2095
2	TraesCS3B01G055400	chr3B	804546964	804547967	1003	True	278.0	339	83.75150	2656	3474	2	chr3B.!!$R3	818
3	TraesCS3B01G055400	chr3A	748338531	748341982	3451	False	2798.5	5103	96.06150	7	3510	2	chr3A.!!$F1	3503
4	TraesCS3B01G055400	chr3A	749875859	749877561	1702	True	824.5	1096	85.03000	858	2655	2	chr3A.!!$R1	1797
5	TraesCS3B01G055400	chr3D	615455467	615458539	3072	False	1463.0	2388	87.71500	975	3510	2	chr3D.!!$F2	2535
6	TraesCS3B01G055400	chrUn	247031250	247033629	2379	False	960.0	1336	85.82600	858	2655	2	chrUn.!!$F3	1797
7	TraesCS3B01G055400	chrUn	37113647	37115900	2253	True	950.0	1336	87.24000	965	2655	2	chrUn.!!$R1	1690
8	TraesCS3B01G055400	chrUn	300942376	300944629	2253	True	950.0	1336	87.24000	965	2655	2	chrUn.!!$R2	1690
9	TraesCS3B01G055400	chr2B	671086785	671087766	981	True	273.0	344	84.02400	2656	3451	2	chr2B.!!$R1	795
10	TraesCS3B01G055400	chr4A	664243248	664244564	1316	False	231.5	272	79.85450	98	435	2	chr4A.!!$F2	337

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
324	326	0.028902	GTTCAGGTGTTGTCAACGGC	59.971	55.000	11.03	6.41	36.22	5.68	F
367	369	0.033601	TGCAGTGGGTTGTTCACCTT	60.034	50.000	0.00	0.00	46.38	3.50	F
805	823	0.036199	TGGTGTGGCCGGTGTTATAC	60.036	55.000	1.90	0.00	41.21	1.47	F
1243	2188	0.462047	CGATGTGGCCTCTTACACCC	60.462	60.000	3.32	0.00	36.80	4.61	F
1796	3355	1.198408	CGGCACTCGTGAACACTAGTA	59.802	52.381	10.82	0.00	35.50	1.82	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1351	2296	0.035725	TGCTCATGTGCTTCTCTGGG	60.036	55.000	19.60	0.00	0.00	4.45	R
2300	4082	2.449031	TACTTGGTCGGCACCTGCAG	62.449	60.000	6.78	6.78	44.17	4.41	R
2379	4161	1.065418	CATCCTCCTTAAAGCCACCGT	60.065	52.381	0.00	0.00	0.00	4.83	R
2434	4216	1.077787	CTGGATAAAGTGGCCGGCA	60.078	57.895	30.85	12.04	0.00	5.69	R
3486	5527	0.617413	AGTGTTAGCATCTGCAGGCT	59.383	50.000	19.42	19.42	45.16	4.58	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
20	21	2.363683	ACCGTACAAACCGAAAAACCA	58.636	42.857	0.00	0.00	0.00	3.67
21	22	2.950975	ACCGTACAAACCGAAAAACCAT	59.049	40.909	0.00	0.00	0.00	3.55
27	28	7.482428	CCGTACAAACCGAAAAACCATATAAAG	59.518	37.037	0.00	0.00	0.00	1.85
43	44	2.981400	AAAGCGAACCATGTAAACCG	57.019	45.000	0.00	0.00	0.00	4.44
81	82	2.076100	GAGTGAATGACGGTGAATGCA	58.924	47.619	0.00	0.00	0.00	3.96
199	201	4.081642	TGGAAATACTCGGTCCTTCTCTTG	60.082	45.833	0.00	0.00	32.28	3.02
226	228	3.050619	CGAAACCCATGATCTAGCGTAC	58.949	50.000	0.00	0.00	0.00	3.67
271	273	3.615496	GTGTTCATGCATCATTTCCTTGC	59.385	43.478	0.00	0.00	36.91	4.01
313	315	2.240493	ACCTTCTCGTTGTTCAGGTG	57.760	50.000	0.00	0.00	36.46	4.00
321	323	2.417239	TCGTTGTTCAGGTGTTGTCAAC	59.583	45.455	8.86	8.86	38.26	3.18
323	325	1.374560	TGTTCAGGTGTTGTCAACGG	58.625	50.000	11.03	1.40	36.22	4.44
324	326	0.028902	GTTCAGGTGTTGTCAACGGC	59.971	55.000	11.03	6.41	36.22	5.68
339	341	0.606604	ACGGCAGTGGTAGTAGTTGG	59.393	55.000	0.00	0.00	0.00	3.77
367	369	0.033601	TGCAGTGGGTTGTTCACCTT	60.034	50.000	0.00	0.00	46.38	3.50
368	370	1.111277	GCAGTGGGTTGTTCACCTTT	58.889	50.000	0.00	0.00	46.38	3.11
460	467	7.883217	ACCAGGTATATACTCTTATGTTCGTG	58.117	38.462	12.54	0.00	0.00	4.35
735	753	1.127951	CTTTTCACGGCGTCATACACC	59.872	52.381	10.85	0.00	0.00	4.16
754	772	8.746530	CATACACCTGTAATATATACGGACCTT	58.253	37.037	0.00	0.00	33.76	3.50
786	804	5.466393	CGTTTTCATTTCCAGGCAAAAATCT	59.534	36.000	0.00	0.00	0.00	2.40
805	823	0.036199	TGGTGTGGCCGGTGTTATAC	60.036	55.000	1.90	0.00	41.21	1.47
962	1899	6.166279	CACAGTAAAGACACATACACCAGAT	58.834	40.000	0.00	0.00	0.00	2.90
1139	2084	1.878656	GAGCTGTGGTACTCGTGGCT	61.879	60.000	0.00	0.00	0.00	4.75
1173	2118	2.006888	CACTTGGCGATTCGTGGTTAT	58.993	47.619	8.03	0.00	0.00	1.89
1243	2188	0.462047	CGATGTGGCCTCTTACACCC	60.462	60.000	3.32	0.00	36.80	4.61
1301	2246	2.092375	ACACCTTAGGGATAGCAAAGGC	60.092	50.000	2.32	0.00	41.87	4.35
1455	2401	7.816640	TGCTTACACTGATTAAGATCCAAAAC	58.183	34.615	0.00	0.00	0.00	2.43
1648	3205	2.807967	GCCGTCTGCTGCATATATGAAA	59.192	45.455	17.10	2.83	36.87	2.69
1796	3355	1.198408	CGGCACTCGTGAACACTAGTA	59.802	52.381	10.82	0.00	35.50	1.82
1889	3448	2.857489	GCATACGGCTCCAACTACTACG	60.857	54.545	0.00	0.00	40.25	3.51
1946	3509	2.740447	GTCCGGAACATTCAACTGGTAC	59.260	50.000	5.23	0.00	0.00	3.34
1948	3511	2.081462	CGGAACATTCAACTGGTACCC	58.919	52.381	10.07	0.00	0.00	3.69
2278	4060	1.962822	CAAGAACTGCGAGCTGGCA	60.963	57.895	22.69	22.69	41.45	4.92
2434	4216	3.387947	GTGGTCGTCATCCCCGGT	61.388	66.667	0.00	0.00	0.00	5.28
2468	4250	4.016790	AGCAGGAGAGGGCCCAGA	62.017	66.667	27.56	0.00	0.00	3.86
2471	4253	1.920325	CAGGAGAGGGCCCAGAACA	60.920	63.158	27.56	0.00	0.00	3.18
2551	4338	2.401583	AACTATCCATGTGCTTGCGA	57.598	45.000	0.00	0.00	0.00	5.10
2876	4674	2.565841	AGCTTTAATGGCGCCTAGAAG	58.434	47.619	29.70	23.95	34.52	2.85
2877	4675	2.170607	AGCTTTAATGGCGCCTAGAAGA	59.829	45.455	29.70	6.08	34.52	2.87
2878	4676	2.943033	GCTTTAATGGCGCCTAGAAGAA	59.057	45.455	29.70	13.38	0.00	2.52
2879	4677	3.242772	GCTTTAATGGCGCCTAGAAGAAC	60.243	47.826	29.70	7.34	0.00	3.01
2880	4678	2.614829	TAATGGCGCCTAGAAGAACC	57.385	50.000	29.70	0.00	0.00	3.62
2881	4679	0.618458	AATGGCGCCTAGAAGAACCA	59.382	50.000	29.70	2.45	0.00	3.67
2882	4680	0.179000	ATGGCGCCTAGAAGAACCAG	59.821	55.000	29.70	0.00	0.00	4.00
2883	4681	1.153349	GGCGCCTAGAAGAACCAGG	60.153	63.158	22.15	0.00	0.00	4.45
2997	4974	1.263217	GAAGCCACGTGTCGAATTTGT	59.737	47.619	15.65	0.00	0.00	2.83
3030	5009	7.461918	GTTTCCACGGAATTCACTTAATCTAC	58.538	38.462	7.93	0.00	33.79	2.59
3121	5160	9.643693	AACAGCCTAAAAATATCTTGTCAAATG	57.356	29.630	0.00	0.00	0.00	2.32
3158	5197	1.354368	GTCCTGATTCCCCAAGTCCAA	59.646	52.381	0.00	0.00	0.00	3.53
3194	5233	1.206132	TCCGACCGCATTGTAGATTGT	59.794	47.619	0.00	0.00	0.00	2.71
3295	5334	1.160329	CCATCTTCGTCCGAATGCCC	61.160	60.000	2.20	0.00	33.28	5.36
3486	5527	2.432456	CTGCTTGTCGCGCCTACA	60.432	61.111	0.00	3.54	43.27	2.74

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
0	1	2.363683	TGGTTTTTCGGTTTGTACGGT	58.636	42.857	0.00	0.00	0.00	4.83
1	2	3.629438	ATGGTTTTTCGGTTTGTACGG	57.371	42.857	0.00	0.00	0.00	4.02
2	3	7.007636	GCTTTATATGGTTTTTCGGTTTGTACG	59.992	37.037	0.00	0.00	0.00	3.67
3	4	7.007636	CGCTTTATATGGTTTTTCGGTTTGTAC	59.992	37.037	0.00	0.00	0.00	2.90
4	5	7.022384	CGCTTTATATGGTTTTTCGGTTTGTA	58.978	34.615	0.00	0.00	0.00	2.41
5	6	5.859648	CGCTTTATATGGTTTTTCGGTTTGT	59.140	36.000	0.00	0.00	0.00	2.83
20	21	6.050432	TCGGTTTACATGGTTCGCTTTATAT	58.950	36.000	0.00	0.00	0.00	0.86
21	22	5.417811	TCGGTTTACATGGTTCGCTTTATA	58.582	37.500	0.00	0.00	0.00	0.98
27	28	4.603231	TTATTCGGTTTACATGGTTCGC	57.397	40.909	0.00	0.00	0.00	4.70
43	44	2.735134	ACTCTGTGCGTTCGGTTTATTC	59.265	45.455	0.00	0.00	0.00	1.75
81	82	2.757077	CCCCGAACTTGAGGCCTT	59.243	61.111	6.77	0.00	0.00	4.35
123	124	3.702048	TGGCCAGGTACGACCAGC	61.702	66.667	0.00	8.13	41.95	4.85
199	201	0.931005	GATCATGGGTTTCGACTCGC	59.069	55.000	0.00	0.00	0.00	5.03
226	228	2.416547	GTCATCACTGGATTGAACCACG	59.583	50.000	0.00	0.00	35.91	4.94
271	273	1.230635	CCCAACAGCGACACCTTCAG	61.231	60.000	0.00	0.00	0.00	3.02
302	304	2.477189	CCGTTGACAACACCTGAACAAC	60.477	50.000	18.09	0.00	39.71	3.32
304	306	1.374560	CCGTTGACAACACCTGAACA	58.625	50.000	18.09	0.00	0.00	3.18
307	309	0.813610	CTGCCGTTGACAACACCTGA	60.814	55.000	18.09	0.00	0.00	3.86
310	312	1.355210	CACTGCCGTTGACAACACC	59.645	57.895	18.09	8.42	0.00	4.16
313	315	0.865769	CTACCACTGCCGTTGACAAC	59.134	55.000	8.34	8.34	0.00	3.32
321	323	0.606604	ACCAACTACTACCACTGCCG	59.393	55.000	0.00	0.00	0.00	5.69
323	325	2.833631	ACACCAACTACTACCACTGC	57.166	50.000	0.00	0.00	0.00	4.40
324	326	4.261031	GCAAAACACCAACTACTACCACTG	60.261	45.833	0.00	0.00	0.00	3.66
339	341	0.175531	AACCCACTGCAGCAAAACAC	59.824	50.000	15.27	0.00	0.00	3.32
427	434	5.898120	AGAGTATATACCTGGTCTCTGCAT	58.102	41.667	12.66	0.00	32.19	3.96
438	445	8.784994	CAGACACGAACATAAGAGTATATACCT	58.215	37.037	9.32	3.95	0.00	3.08
460	467	3.557185	TCATAATGTCGCATCAAGCAGAC	59.443	43.478	0.00	0.00	46.13	3.51
754	772	3.403968	TGGAAATGAAAACGACGGATGA	58.596	40.909	0.00	0.00	0.00	2.92
786	804	0.036199	GTATAACACCGGCCACACCA	60.036	55.000	0.00	0.00	39.03	4.17
789	807	0.391927	GCTGTATAACACCGGCCACA	60.392	55.000	0.00	0.00	0.00	4.17
962	1899	1.298693	TCCCTCCCCTCTCTCTCTCTA	59.701	57.143	0.00	0.00	0.00	2.43
1063	2008	0.838987	TCCACCTTAGGACCGGCTTT	60.839	55.000	4.77	0.00	31.23	3.51
1075	2020	3.966543	CCCCTTGGCGTCCACCTT	61.967	66.667	0.00	0.00	30.78	3.50
1223	2168	0.535335	GGTGTAAGAGGCCACATCGA	59.465	55.000	5.01	0.00	33.19	3.59
1243	2188	2.035832	GGTCACCAACAATGTGAAAGGG	59.964	50.000	0.00	0.00	43.82	3.95
1301	2246	8.958175	TTGGTTACGAAATAAGCTTAATTGTG	57.042	30.769	11.50	6.55	41.13	3.33
1351	2296	0.035725	TGCTCATGTGCTTCTCTGGG	60.036	55.000	19.60	0.00	0.00	4.45
1606	3163	6.434028	ACGGCTTATGGATTATATTGCACAAT	59.566	34.615	0.94	0.94	34.93	2.71
1648	3205	9.220767	GAGGTCAAAATTACATCAGTTAGAACT	57.779	33.333	0.00	0.00	40.60	3.01
1753	3312	3.744719	CGCTCCGGACGGAACAGA	61.745	66.667	14.98	0.00	44.66	3.41
1786	3345	3.491267	GCATGAAGGCGATACTAGTGTTC	59.509	47.826	5.39	1.56	0.00	3.18
2300	4082	2.449031	TACTTGGTCGGCACCTGCAG	62.449	60.000	6.78	6.78	44.17	4.41
2379	4161	1.065418	CATCCTCCTTAAAGCCACCGT	60.065	52.381	0.00	0.00	0.00	4.83
2386	4168	4.518249	GGAGTGGAACATCCTCCTTAAAG	58.482	47.826	0.00	0.00	45.03	1.85
2434	4216	1.077787	CTGGATAAAGTGGCCGGCA	60.078	57.895	30.85	12.04	0.00	5.69
2468	4250	5.244851	AGTCATAGATATGGTCGCTGATGTT	59.755	40.000	0.19	0.00	34.50	2.71
2471	4253	5.478332	TGAAGTCATAGATATGGTCGCTGAT	59.522	40.000	0.19	0.00	34.50	2.90
2551	4338	3.610114	GCGCAAGATCAAACAGTGACAAT	60.610	43.478	0.30	0.00	37.04	2.71
2682	4471	1.302511	GCTTCAGAGTTCGCCCCAA	60.303	57.895	0.00	0.00	0.00	4.12
2716	4507	5.184096	TGTGTGTTATCTGTGTTGGTTTTGT	59.816	36.000	0.00	0.00	0.00	2.83
3121	5160	2.438434	CCTCGGGATGGGTTGCAC	60.438	66.667	0.00	0.00	0.00	4.57
3258	5297	5.292815	AGATGGATAGGAGGAGAAAAAGGT	58.707	41.667	0.00	0.00	0.00	3.50
3486	5527	0.617413	AGTGTTAGCATCTGCAGGCT	59.383	50.000	19.42	19.42	45.16	4.58

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.