AutoCloner

Multiple sequence alignment - TraesCS3A01G215700

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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	TraesCS3A01G215700	chr3A	100.000	2393	0	0	1	2393	393234585	393236977	0.000000e+00	4420.0
1	TraesCS3A01G215700	chr3A	90.909	44	3	1	1	44	702674567	702674525	9.240000e-05	58.4
2	TraesCS3A01G215700	chr3B	97.935	1017	21	0	28	1044	201512431	201513447	0.000000e+00	1762.0
3	TraesCS3A01G215700	chr3B	92.628	312	22	1	1973	2284	386604455	386604765	4.690000e-122	448.0
4	TraesCS3A01G215700	chr3B	97.436	78	2	0	1512	1589	201501340	201501263	1.490000e-27	134.0
5	TraesCS3A01G215700	chr5D	97.741	1018	22	1	28	1044	6201976	6200959	0.000000e+00	1751.0
6	TraesCS3A01G215700	chr5D	98.853	436	5	0	1042	1477	560872848	560873283	0.000000e+00	778.0
7	TraesCS3A01G215700	chr5D	97.936	436	7	2	1042	1477	6200901	6200468	0.000000e+00	754.0
8	TraesCS3A01G215700	chr5D	97.018	436	13	0	1042	1477	329162557	329162992	0.000000e+00	734.0
9	TraesCS3A01G215700	chr5D	97.954	391	7	1	1580	1969	6217027	6217417	0.000000e+00	676.0
10	TraesCS3A01G215700	chr5D	94.048	84	5	0	1506	1589	6212876	6212959	6.940000e-26	128.0
11	TraesCS3A01G215700	chr5D	96.154	78	3	0	1512	1589	6213740	6213663	6.940000e-26	128.0
12	TraesCS3A01G215700	chr5D	94.048	84	5	0	1506	1589	483800772	483800855	6.940000e-26	128.0
13	TraesCS3A01G215700	chr1D	97.649	1021	20	3	28	1044	254497300	254498320	0.000000e+00	1749.0
14	TraesCS3A01G215700	chr1D	95.088	1018	46	4	28	1044	244484741	244483727	0.000000e+00	1600.0
15	TraesCS3A01G215700	chr1D	95.918	588	22	2	1587	2173	244396911	244396325	0.000000e+00	952.0
16	TraesCS3A01G215700	chr1D	95.741	587	23	2	1587	2173	244403349	244402765	0.000000e+00	944.0
17	TraesCS3A01G215700	chr1D	97.936	436	9	0	1042	1477	254498378	254498813	0.000000e+00	756.0
18	TraesCS3A01G215700	chr1D	98.450	387	6	0	1583	1969	254484139	254483753	0.000000e+00	682.0
19	TraesCS3A01G215700	chr1D	95.614	228	10	0	2166	2393	244394982	244394755	1.350000e-97	366.0
20	TraesCS3A01G215700	chr1D	94.872	78	4	0	1512	1589	244419252	244419175	3.230000e-24	122.0
21	TraesCS3A01G215700	chr1A	97.645	1019	21	3	28	1044	112776730	112775713	0.000000e+00	1746.0
22	TraesCS3A01G215700	chr1A	96.789	436	14	0	1042	1477	168450187	168449752	0.000000e+00	728.0
23	TraesCS3A01G215700	chr1A	94.048	84	5	0	1506	1589	554470262	554470345	6.940000e-26	128.0
24	TraesCS3A01G215700	chr1A	97.297	37	1	0	1	37	419784406	419784442	1.990000e-06	63.9
25	TraesCS3A01G215700	chr1A	92.857	42	1	2	1	41	221240125	221240085	2.570000e-05	60.2
26	TraesCS3A01G215700	chr3D	97.065	1022	24	3	28	1044	21903929	21904949	0.000000e+00	1716.0
27	TraesCS3A01G215700	chr3D	96.260	508	17	1	1876	2383	213385627	213385122	0.000000e+00	832.0
28	TraesCS3A01G215700	chr3D	98.624	436	6	0	1042	1477	21905007	21905442	0.000000e+00	773.0
29	TraesCS3A01G215700	chr3D	96.339	437	15	1	1042	1477	555743484	555743920	0.000000e+00	717.0
30	TraesCS3A01G215700	chr6B	97.059	1020	27	2	28	1044	22425247	22426266	0.000000e+00	1714.0
31	TraesCS3A01G215700	chr6B	97.691	433	10	0	1042	1474	22426324	22426756	0.000000e+00	745.0
32	TraesCS3A01G215700	chr4D	96.369	1019	34	3	28	1044	19915800	19916817	0.000000e+00	1674.0
33	TraesCS3A01G215700	chr7A	93.799	1016	62	1	30	1044	352194717	352193702	0.000000e+00	1526.0
34	TraesCS3A01G215700	chr7A	93.023	43	1	2	1	41	669326968	669327010	7.140000e-06	62.1
35	TraesCS3A01G215700	chr6A	97.744	798	18	0	1583	2380	192823393	192822596	0.000000e+00	1375.0
36	TraesCS3A01G215700	chr6A	94.419	215	12	0	2054	2268	119074185	119074399	4.930000e-87	331.0
37	TraesCS3A01G215700	chr7B	97.712	437	9	1	1042	1477	125509614	125510050	0.000000e+00	750.0
38	TraesCS3A01G215700	chr2D	98.708	387	4	1	1583	1969	643860512	643860127	0.000000e+00	686.0
39	TraesCS3A01G215700	chr2D	95.074	203	10	0	2169	2371	406835152	406835354	1.070000e-83	320.0
40	TraesCS3A01G215700	chr2D	96.154	78	3	0	1512	1589	643860878	643860801	6.940000e-26	128.0
41	TraesCS3A01G215700	chr2D	94.872	39	2	0	3	41	357146868	357146906	7.140000e-06	62.1
42	TraesCS3A01G215700	chrUn	98.210	391	6	1	1580	1969	443803942	443804332	0.000000e+00	682.0
43	TraesCS3A01G215700	chrUn	96.154	78	3	0	1512	1589	444442290	444442213	6.940000e-26	128.0
44	TraesCS3A01G215700	chrUn	100.000	34	0	0	1	34	368939929	368939896	1.990000e-06	63.9
45	TraesCS3A01G215700	chr6D	98.205	390	6	1	1580	1969	431396734	431397122	0.000000e+00	680.0
46	TraesCS3A01G215700	chr6D	92.857	84	6	0	1506	1589	431396365	431396448	3.230000e-24	122.0
47	TraesCS3A01G215700	chr2A	97.625	379	8	1	1683	2060	588082866	588082488	0.000000e+00	649.0
48	TraesCS3A01G215700	chr2A	100.000	33	0	0	1	33	126053798	126053830	7.140000e-06	62.1
49	TraesCS3A01G215700	chr2A	90.909	44	3	1	1	44	76971179	76971137	9.240000e-05	58.4
50	TraesCS3A01G215700	chr7D	97.904	334	6	1	1805	2138	566026191	566026523	5.740000e-161	577.0
51	TraesCS3A01G215700	chr7D	97.076	171	5	0	1580	1750	99832804	99832974	3.010000e-74	289.0
52	TraesCS3A01G215700	chr7D	98.639	147	2	0	2247	2393	509197437	509197291	6.560000e-66	261.0
53	TraesCS3A01G215700	chr4B	93.478	230	10	3	2075	2303	71701748	71701973	1.060000e-88	337.0
54	TraesCS3A01G215700	chr4B	92.609	230	12	3	2075	2303	117070448	117070223	2.290000e-85	326.0
55	TraesCS3A01G215700	chr4B	92.174	230	13	3	2075	2303	117091540	117091315	1.070000e-83	320.0
56	TraesCS3A01G215700	chr5B	91.111	45	4	0	3	47	428714876	428714832	7.140000e-06	62.1

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	TraesCS3A01G215700	chr3A	393234585	393236977	2392	False	4420.0	4420	100.0000	1	2393	1	chr3A.!!$F1	2392
1	TraesCS3A01G215700	chr3B	201512431	201513447	1016	False	1762.0	1762	97.9350	28	1044	1	chr3B.!!$F1	1016
2	TraesCS3A01G215700	chr5D	6200468	6201976	1508	True	1252.5	1751	97.8385	28	1477	2	chr5D.!!$R2	1449
3	TraesCS3A01G215700	chr1D	244483727	244484741	1014	True	1600.0	1600	95.0880	28	1044	1	chr1D.!!$R3	1016
4	TraesCS3A01G215700	chr1D	254497300	254498813	1513	False	1252.5	1749	97.7925	28	1477	2	chr1D.!!$F1	1449
5	TraesCS3A01G215700	chr1D	244402765	244403349	584	True	944.0	944	95.7410	1587	2173	1	chr1D.!!$R1	586
6	TraesCS3A01G215700	chr1D	244394755	244396911	2156	True	659.0	952	95.7660	1587	2393	2	chr1D.!!$R5	806
7	TraesCS3A01G215700	chr1A	112775713	112776730	1017	True	1746.0	1746	97.6450	28	1044	1	chr1A.!!$R1	1016
8	TraesCS3A01G215700	chr3D	21903929	21905442	1513	False	1244.5	1716	97.8445	28	1477	2	chr3D.!!$F2	1449
9	TraesCS3A01G215700	chr3D	213385122	213385627	505	True	832.0	832	96.2600	1876	2383	1	chr3D.!!$R1	507
10	TraesCS3A01G215700	chr6B	22425247	22426756	1509	False	1229.5	1714	97.3750	28	1474	2	chr6B.!!$F1	1446
11	TraesCS3A01G215700	chr4D	19915800	19916817	1017	False	1674.0	1674	96.3690	28	1044	1	chr4D.!!$F1	1016
12	TraesCS3A01G215700	chr7A	352193702	352194717	1015	True	1526.0	1526	93.7990	30	1044	1	chr7A.!!$R1	1014
13	TraesCS3A01G215700	chr6A	192822596	192823393	797	True	1375.0	1375	97.7440	1583	2380	1	chr6A.!!$R1	797
14	TraesCS3A01G215700	chr2D	643860127	643860878	751	True	407.0	686	97.4310	1512	1969	2	chr2D.!!$R1	457
15	TraesCS3A01G215700	chr6D	431396365	431397122	757	False	401.0	680	95.5310	1506	1969	2	chr6D.!!$F1	463

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
517	519	0.330267	GATCCTTTTGTTCCGGGGGA	59.67	55.0	0.0	0.0	0.0	4.81	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1504	1572	0.942962	CCGCTGCTGGATTCAGAATC	59.057	55.0	14.09	14.09	43.49	2.52	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
52	53	4.275689	TGGCTCAATGGCTTTATACGAATG	59.724	41.667	0.00	0.00	42.34	2.67
310	312	6.357579	AGAAATATTCTCTGATGAGCGGAT	57.642	37.500	0.00	0.00	40.03	4.18
517	519	0.330267	GATCCTTTTGTTCCGGGGGA	59.670	55.000	0.00	0.00	0.00	4.81
537	539	6.950619	GGGGGAAATAGCTTCTCATCATATTT	59.049	38.462	0.00	0.00	36.07	1.40
636	638	8.911918	ATTACGTATGGGCAATATTGAAACTA	57.088	30.769	19.73	6.68	0.00	2.24
748	754	2.973694	TTGGGCCTACTCGTTATCAC	57.026	50.000	4.53	0.00	0.00	3.06
827	833	8.561738	AGCCGAAAATCTTAGTTTATCAGAAA	57.438	30.769	0.00	0.00	0.00	2.52
964	971	2.640826	TGGTTAGGACATCCCGTCTTTT	59.359	45.455	0.00	0.00	44.70	2.27
1074	1142	2.093869	TGTAACGGTGGAGTTCTATGGC	60.094	50.000	0.00	0.00	35.70	4.40
1477	1545	7.864882	CCATCCTTTCTTTGACTCTTTTTCTTC	59.135	37.037	0.00	0.00	0.00	2.87
1478	1546	7.334844	TCCTTTCTTTGACTCTTTTTCTTCC	57.665	36.000	0.00	0.00	0.00	3.46
1479	1547	6.321435	TCCTTTCTTTGACTCTTTTTCTTCCC	59.679	38.462	0.00	0.00	0.00	3.97
1480	1548	6.096846	CCTTTCTTTGACTCTTTTTCTTCCCA	59.903	38.462	0.00	0.00	0.00	4.37
1481	1549	7.363793	CCTTTCTTTGACTCTTTTTCTTCCCAA	60.364	37.037	0.00	0.00	0.00	4.12
1482	1550	7.475137	TTCTTTGACTCTTTTTCTTCCCAAA	57.525	32.000	0.00	0.00	0.00	3.28
1483	1551	7.660030	TCTTTGACTCTTTTTCTTCCCAAAT	57.340	32.000	0.00	0.00	0.00	2.32
1484	1552	7.491682	TCTTTGACTCTTTTTCTTCCCAAATG	58.508	34.615	0.00	0.00	0.00	2.32
1485	1553	7.341769	TCTTTGACTCTTTTTCTTCCCAAATGA	59.658	33.333	0.00	0.00	0.00	2.57
1486	1554	6.639632	TGACTCTTTTTCTTCCCAAATGAG	57.360	37.500	6.71	6.71	39.55	2.90
1487	1555	6.364701	TGACTCTTTTTCTTCCCAAATGAGA	58.635	36.000	12.65	0.00	37.50	3.27
1488	1556	7.006509	TGACTCTTTTTCTTCCCAAATGAGAT	58.993	34.615	12.65	1.60	37.50	2.75
1489	1557	7.040201	TGACTCTTTTTCTTCCCAAATGAGATG	60.040	37.037	12.65	0.00	37.50	2.90
1490	1558	6.210185	ACTCTTTTTCTTCCCAAATGAGATGG	59.790	38.462	12.65	0.00	37.50	3.51
1524	1592	1.099879	ATTCTGAATCCAGCAGCGGC	61.100	55.000	0.00	0.00	40.20	6.53
1938	2302	7.618137	AGAAAGCGGTTAGAATTTACTTCCTA	58.382	34.615	0.00	0.00	34.11	2.94
2026	2390	9.517868	TCAATCAAAATCAAAGGGCAAATTATT	57.482	25.926	0.00	0.00	0.00	1.40
2035	2399	8.423906	TCAAAGGGCAAATTATTTTACCTACA	57.576	30.769	9.44	0.00	32.93	2.74
2037	2401	8.931775	CAAAGGGCAAATTATTTTACCTACAAC	58.068	33.333	9.44	0.00	32.93	3.32
2234	3948	3.925379	TGGACGCATATAGTAGCATTGG	58.075	45.455	0.00	0.00	0.00	3.16
2236	3950	3.262420	GACGCATATAGTAGCATTGGGG	58.738	50.000	0.00	0.00	0.00	4.96
2245	3959	2.775384	AGTAGCATTGGGGTTCCGAATA	59.225	45.455	0.00	0.00	35.24	1.75
2371	4085	7.584123	GCATTGAAGTCTATAGCGTTGTATTTG	59.416	37.037	0.00	0.00	0.00	2.32

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
7	8	2.324541	CTGAGGGAGTCCTGGATTAGG	58.675	57.143	9.58	0.00	45.05	2.69
8	9	1.691434	GCTGAGGGAGTCCTGGATTAG	59.309	57.143	9.58	0.93	45.05	1.73
9	10	1.292242	AGCTGAGGGAGTCCTGGATTA	59.708	52.381	9.58	0.00	45.05	1.75
10	11	0.043940	AGCTGAGGGAGTCCTGGATT	59.956	55.000	9.58	0.00	45.05	3.01
11	12	0.690411	CAGCTGAGGGAGTCCTGGAT	60.690	60.000	8.42	0.00	45.05	3.41
12	13	1.305633	CAGCTGAGGGAGTCCTGGA	60.306	63.158	8.42	0.00	45.05	3.86
13	14	2.365586	CCAGCTGAGGGAGTCCTGG	61.366	68.421	17.39	3.65	45.05	4.45
14	15	3.028921	GCCAGCTGAGGGAGTCCTG	62.029	68.421	17.39	0.00	45.05	3.86
16	17	2.686835	AGCCAGCTGAGGGAGTCC	60.687	66.667	17.39	0.00	0.00	3.85
17	18	1.548357	TTGAGCCAGCTGAGGGAGTC	61.548	60.000	17.39	2.80	0.00	3.36
18	19	0.913451	ATTGAGCCAGCTGAGGGAGT	60.913	55.000	17.39	0.00	0.00	3.85
19	20	0.464013	CATTGAGCCAGCTGAGGGAG	60.464	60.000	17.39	0.00	0.00	4.30
20	21	1.605992	CATTGAGCCAGCTGAGGGA	59.394	57.895	17.39	0.00	0.00	4.20
21	22	1.453379	CCATTGAGCCAGCTGAGGG	60.453	63.158	17.39	1.24	0.00	4.30
22	23	2.119655	GCCATTGAGCCAGCTGAGG	61.120	63.158	17.39	0.00	0.00	3.86
23	24	0.680280	AAGCCATTGAGCCAGCTGAG	60.680	55.000	17.39	6.56	35.30	3.35
24	25	0.251474	AAAGCCATTGAGCCAGCTGA	60.251	50.000	17.39	0.00	35.30	4.26
25	26	1.466856	TAAAGCCATTGAGCCAGCTG	58.533	50.000	6.78	6.78	35.30	4.24
26	27	2.449137	ATAAAGCCATTGAGCCAGCT	57.551	45.000	0.00	0.00	37.10	4.24
52	53	3.679389	TCAGAGGGATCAAAAACTGCTC	58.321	45.455	0.00	0.00	0.00	4.26
92	93	5.670792	TTACGAACATACCTTGTCTCCAT	57.329	39.130	0.00	0.00	37.68	3.41
517	519	7.094890	CCGCAGAAATATGATGAGAAGCTATTT	60.095	37.037	0.00	0.00	0.00	1.40
537	539	1.502690	ATACCCAATGTACCCGCAGA	58.497	50.000	0.00	0.00	30.62	4.26
636	638	4.585162	AGCAGCGATACTACTGGAAAGTAT	59.415	41.667	0.00	0.00	41.70	2.12
748	754	3.495806	GCTGAAAGTATCCCTGATCCCAG	60.496	52.174	0.00	0.00	36.80	4.45
827	833	6.911250	ATTTTCGGGAATTTTAGACCAAGT	57.089	33.333	0.00	0.00	0.00	3.16
964	971	5.946942	AGCTCATGTCCTTCTTTATCTCA	57.053	39.130	0.00	0.00	0.00	3.27
1029	1037	5.699458	ACCTACTTGTTCATCTACCAAAACG	59.301	40.000	0.00	0.00	0.00	3.60
1074	1142	3.518590	ACTTACTCCATTAAGTTCGCCG	58.481	45.455	0.00	0.00	38.87	6.46
1164	1232	3.973206	TCAGATTTCAAAGTAGCCCGA	57.027	42.857	0.00	0.00	0.00	5.14
1257	1325	1.875420	CGCCATGCCAAATGTGTCCA	61.875	55.000	0.00	0.00	0.00	4.02
1499	1567	4.616604	CGCTGCTGGATTCAGAATCAAAAA	60.617	41.667	22.23	6.58	43.49	1.94
1500	1568	3.119743	CGCTGCTGGATTCAGAATCAAAA	60.120	43.478	22.23	8.42	43.49	2.44
1501	1569	2.421073	CGCTGCTGGATTCAGAATCAAA	59.579	45.455	22.23	10.61	43.49	2.69
1502	1570	2.011947	CGCTGCTGGATTCAGAATCAA	58.988	47.619	22.23	12.21	43.49	2.57
1503	1571	1.660167	CGCTGCTGGATTCAGAATCA	58.340	50.000	22.23	9.51	43.49	2.57
1504	1572	0.942962	CCGCTGCTGGATTCAGAATC	59.057	55.000	14.09	14.09	43.49	2.52
1505	1573	1.099879	GCCGCTGCTGGATTCAGAAT	61.100	55.000	4.75	0.00	43.49	2.40
1506	1574	1.746615	GCCGCTGCTGGATTCAGAA	60.747	57.895	4.75	0.00	43.49	3.02
1507	1575	2.124983	GCCGCTGCTGGATTCAGA	60.125	61.111	4.75	0.00	43.49	3.27
1585	1948	2.035576	AGTAGGCTTAGTATTTCCGGCG	59.964	50.000	0.00	0.00	0.00	6.46
2026	2390	5.596763	AGTAGGGGATCTGTTGTAGGTAAA	58.403	41.667	0.00	0.00	0.00	2.01
2035	2399	2.866454	AGAGGGTAGTAGGGGATCTGTT	59.134	50.000	0.00	0.00	0.00	3.16
2037	2401	3.621682	AAGAGGGTAGTAGGGGATCTG	57.378	52.381	0.00	0.00	0.00	2.90

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.