AutoCloner

Multiple sequence alignment - TraesCS1B01G181800

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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	TraesCS1B01G181800	chr1B	100.000	7626	0	0	1	7626	328827442	328819817	0.000000e+00	14083.0
1	TraesCS1B01G181800	chr1B	92.982	114	6	2	1930	2042	328825401	328825513	1.700000e-36	165.0
2	TraesCS1B01G181800	chr1D	89.189	2664	136	59	2041	4617	229488492	229485894	0.000000e+00	3184.0
3	TraesCS1B01G181800	chr1D	94.164	1919	90	13	5075	6983	229485308	229483402	0.000000e+00	2904.0
4	TraesCS1B01G181800	chr1D	91.206	1012	39	16	724	1725	229489657	229488686	0.000000e+00	1330.0
5	TraesCS1B01G181800	chr1D	92.547	483	33	3	4595	5076	229485817	229485337	0.000000e+00	689.0
6	TraesCS1B01G181800	chr1D	83.821	581	44	25	7068	7626	229483336	229482784	2.460000e-139	507.0
7	TraesCS1B01G181800	chr1D	89.474	114	6	3	1818	1931	229488598	229488491	1.030000e-28	139.0
8	TraesCS1B01G181800	chr1A	93.743	1918	95	16	5075	6983	297746714	297744813	0.000000e+00	2854.0
9	TraesCS1B01G181800	chr1A	88.570	2336	226	24	4635	6959	99657894	99660199	0.000000e+00	2796.0
10	TraesCS1B01G181800	chr1A	89.139	2044	183	22	4642	6663	99700118	99698092	0.000000e+00	2508.0
11	TraesCS1B01G181800	chr1A	88.951	1077	72	21	3560	4617	297748351	297747303	0.000000e+00	1286.0
12	TraesCS1B01G181800	chr1A	82.025	1057	80	44	2111	3070	297749979	297748936	0.000000e+00	798.0
13	TraesCS1B01G181800	chr1A	93.154	482	33	0	4595	5076	297747224	297746743	0.000000e+00	708.0
14	TraesCS1B01G181800	chr1A	86.385	639	29	26	724	1321	297751211	297750590	0.000000e+00	645.0
15	TraesCS1B01G181800	chr1A	89.002	491	31	16	3066	3538	297748834	297748349	3.070000e-163	586.0
16	TraesCS1B01G181800	chr1A	88.325	394	25	9	1427	1813	297750550	297750171	3.240000e-123	453.0
17	TraesCS1B01G181800	chr1A	85.304	313	38	5	7320	7625	297740833	297740522	4.440000e-82	316.0
18	TraesCS1B01G181800	chr1A	88.462	260	27	2	4361	4617	99700473	99700214	2.070000e-80	311.0
19	TraesCS1B01G181800	chr1A	80.412	291	42	10	833	1121	99621631	99621908	2.790000e-49	207.0
20	TraesCS1B01G181800	chr1A	80.534	262	22	14	2585	2836	99701085	99700843	2.830000e-39	174.0
21	TraesCS1B01G181800	chr1A	87.500	160	5	6	7179	7323	297741047	297740888	3.660000e-38	171.0
22	TraesCS1B01G181800	chr1A	93.103	116	5	3	1930	2042	53467522	53467637	4.730000e-37	167.0
23	TraesCS1B01G181800	chr1A	92.308	117	6	2	1929	2042	53467638	53467522	6.120000e-36	163.0
24	TraesCS1B01G181800	chr1A	90.984	122	7	2	1929	2046	72678886	72678765	2.200000e-35	161.0
25	TraesCS1B01G181800	chr1A	91.453	117	6	2	1930	2042	72678769	72678885	2.850000e-34	158.0
26	TraesCS1B01G181800	chr1A	100.000	30	0	0	2842	2871	99700602	99700573	1.000000e-03	56.5
27	TraesCS1B01G181800	chr5D	88.544	2322	219	33	4657	6959	11433350	11435643	0.000000e+00	2771.0
28	TraesCS1B01G181800	chr5D	87.590	2079	187	33	4637	6663	11531493	11529434	0.000000e+00	2344.0
29	TraesCS1B01G181800	chr5D	88.846	260	26	2	4361	4617	11531844	11531585	4.440000e-82	316.0
30	TraesCS1B01G181800	chr5D	85.315	286	37	2	4311	4592	388408339	388408055	2.690000e-74	291.0
31	TraesCS1B01G181800	chr5D	85.121	289	34	4	4308	4592	462800470	462800753	3.480000e-73	287.0
32	TraesCS1B01G181800	chr5D	81.379	290	40	9	833	1121	11431665	11431941	2.770000e-54	224.0
33	TraesCS1B01G181800	chr5D	77.384	367	55	17	2584	2933	11432355	11432710	7.810000e-45	193.0
34	TraesCS1B01G181800	chr5D	79.693	261	26	16	2585	2836	11532462	11532220	6.120000e-36	163.0
35	TraesCS1B01G181800	chr5D	90.833	120	5	3	1924	2042	478223404	478223290	1.020000e-33	156.0
36	TraesCS1B01G181800	chr5D	89.655	116	7	3	1927	2042	478223287	478223397	7.980000e-30	143.0
37	TraesCS1B01G181800	chr5B	88.443	2042	187	32	4642	6657	11515163	11517181	0.000000e+00	2418.0
38	TraesCS1B01G181800	chr5B	86.523	1996	184	42	4895	6867	11552402	11550469	0.000000e+00	2117.0
39	TraesCS1B01G181800	chr5B	96.566	728	22	3	1	728	212410240	212410964	0.000000e+00	1203.0
40	TraesCS1B01G181800	chr5B	96.547	724	24	1	1	724	341066071	341066793	0.000000e+00	1197.0
41	TraesCS1B01G181800	chr5B	83.791	401	51	8	4197	4591	11555393	11555001	1.210000e-97	368.0
42	TraesCS1B01G181800	chr5B	88.519	270	27	2	4635	4902	11554897	11554630	2.650000e-84	324.0
43	TraesCS1B01G181800	chr5B	88.258	264	24	3	4361	4617	11514802	11515065	7.430000e-80	309.0
44	TraesCS1B01G181800	chr5B	80.756	291	46	9	833	1121	11513307	11513589	1.290000e-52	219.0
45	TraesCS1B01G181800	chr5B	83.556	225	25	6	2584	2805	11555711	11555496	4.670000e-47	200.0
46	TraesCS1B01G181800	chr5B	87.050	139	18	0	2689	2827	11514285	11514423	2.850000e-34	158.0
47	TraesCS1B01G181800	chr6B	96.828	725	21	2	1	724	407168695	407167972	0.000000e+00	1210.0
48	TraesCS1B01G181800	chr6B	95.576	746	28	5	1	742	77620348	77619604	0.000000e+00	1190.0
49	TraesCS1B01G181800	chr6B	93.043	115	7	1	1929	2042	39203609	39203495	4.730000e-37	167.0
50	TraesCS1B01G181800	chr4B	96.690	725	22	2	1	725	244918597	244919319	0.000000e+00	1205.0
51	TraesCS1B01G181800	chr4B	91.379	116	8	2	1929	2042	646978752	646978867	2.850000e-34	158.0
52	TraesCS1B01G181800	chr2B	96.690	725	21	3	1	724	23675888	23676610	0.000000e+00	1203.0
53	TraesCS1B01G181800	chr2B	96.685	724	22	2	1	724	232743172	232742451	0.000000e+00	1203.0
54	TraesCS1B01G181800	chr4A	96.301	730	25	2	1	730	37012640	37011913	0.000000e+00	1197.0
55	TraesCS1B01G181800	chr4A	89.344	122	8	1	1930	2046	558550976	558551097	1.710000e-31	148.0
56	TraesCS1B01G181800	chr3B	96.547	724	23	2	1	724	166167435	166166714	0.000000e+00	1197.0
57	TraesCS1B01G181800	chr3B	91.597	119	5	2	1929	2042	346682716	346682598	7.920000e-35	159.0
58	TraesCS1B01G181800	chr4D	86.301	292	36	2	4311	4599	505952201	505951911	1.600000e-81	315.0
59	TraesCS1B01G181800	chr4D	82.031	128	9	5	1930	2043	120692672	120692545	6.300000e-16	97.1
60	TraesCS1B01G181800	chr4D	82.051	117	7	7	1924	2026	337135965	337136081	3.790000e-13	87.9
61	TraesCS1B01G181800	chr4D	80.645	124	10	4	1933	2042	108906247	108906370	4.900000e-12	84.2
62	TraesCS1B01G181800	chr4D	96.000	50	2	0	1984	2033	366320078	366320127	1.760000e-11	82.4
63	TraesCS1B01G181800	chr4D	96.000	50	2	0	1935	1984	366320131	366320082	1.760000e-11	82.4
64	TraesCS1B01G181800	chr4D	79.688	128	12	7	1929	2042	16924180	16924053	6.340000e-11	80.5
65	TraesCS1B01G181800	chr4D	79.528	127	12	8	1930	2042	120692546	120692672	2.280000e-10	78.7
66	TraesCS1B01G181800	chr4D	94.444	36	2	0	1929	1964	69190388	69190423	1.000000e-03	56.5
67	TraesCS1B01G181800	chr4D	100.000	28	0	0	1930	1957	30008037	30008064	1.400000e-02	52.8
68	TraesCS1B01G181800	chr4D	100.000	28	0	0	1930	1957	45701903	45701930	1.400000e-02	52.8
69	TraesCS1B01G181800	chr4D	100.000	28	0	0	1930	1957	392514708	392514735	1.400000e-02	52.8
70	TraesCS1B01G181800	chr6A	93.443	122	5	1	1925	2043	543531423	543531544	2.190000e-40	178.0
71	TraesCS1B01G181800	chr6A	91.667	132	6	1	1926	2052	572335429	572335560	2.190000e-40	178.0
72	TraesCS1B01G181800	chr6A	91.935	124	6	3	1930	2050	543531543	543531421	3.660000e-38	171.0
73	TraesCS1B01G181800	chr6A	89.831	118	7	2	1930	2042	572335550	572335433	6.170000e-31	147.0
74	TraesCS1B01G181800	chrUn	84.444	135	7	2	1926	2046	258882	259016	3.740000e-23	121.0
75	TraesCS1B01G181800	chrUn	85.124	121	4	3	1926	2032	48357372	48357252	2.250000e-20	111.0
76	TraesCS1B01G181800	chrUn	85.124	121	4	3	1926	2032	282070297	282070177	2.250000e-20	111.0
77	TraesCS1B01G181800	chrUn	85.124	121	4	3	1926	2032	293225989	293225869	2.250000e-20	111.0
78	TraesCS1B01G181800	chrUn	84.746	118	4	7	1929	2032	82049353	82049470	1.050000e-18	106.0
79	TraesCS1B01G181800	chrUn	84.615	117	4	1	1929	2031	30405422	30405306	3.760000e-18	104.0
80	TraesCS1B01G181800	chrUn	84.762	105	12	3	1929	2033	43095516	43095616	1.350000e-17	102.0
81	TraesCS1B01G181800	chrUn	84.762	105	12	3	1929	2033	43259042	43258942	1.350000e-17	102.0
82	TraesCS1B01G181800	chrUn	84.762	105	12	3	1929	2033	262842372	262842472	1.350000e-17	102.0
83	TraesCS1B01G181800	chrUn	84.762	105	12	3	1929	2033	293234339	293234439	1.350000e-17	102.0
84	TraesCS1B01G181800	chrUn	86.905	84	7	3	1943	2026	43095612	43095533	2.930000e-14	91.6
85	TraesCS1B01G181800	chrUn	86.207	87	8	3	1940	2026	43258943	43259025	2.930000e-14	91.6
86	TraesCS1B01G181800	chrUn	86.905	84	7	3	1943	2026	262842468	262842389	2.930000e-14	91.6
87	TraesCS1B01G181800	chrUn	86.905	84	7	3	1943	2026	293234435	293234356	2.930000e-14	91.6
88	TraesCS1B01G181800	chr7B	84.146	82	12	1	4942	5023	547966533	547966613	2.280000e-10	78.7

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	TraesCS1B01G181800	chr1B	328819817	328827442	7625	True	14083.000000	14083	100.000000	1	7626	1	chr1B.!!$R1	7625
1	TraesCS1B01G181800	chr1D	229482784	229489657	6873	True	1458.833333	3184	90.066833	724	7626	6	chr1D.!!$R1	6902
2	TraesCS1B01G181800	chr1A	99657894	99660199	2305	False	2796.000000	2796	88.570000	4635	6959	1	chr1A.!!$F4	2324
3	TraesCS1B01G181800	chr1A	297740522	297751211	10689	True	868.555556	2854	88.265444	724	7625	9	chr1A.!!$R4	6901
4	TraesCS1B01G181800	chr1A	99698092	99701085	2993	True	762.375000	2508	89.533750	2585	6663	4	chr1A.!!$R3	4078
5	TraesCS1B01G181800	chr5D	11431665	11435643	3978	False	1062.666667	2771	82.435667	833	6959	3	chr5D.!!$F3	6126
6	TraesCS1B01G181800	chr5D	11529434	11532462	3028	True	941.000000	2344	85.376333	2585	6663	3	chr5D.!!$R3	4078
7	TraesCS1B01G181800	chr5B	212410240	212410964	724	False	1203.000000	1203	96.566000	1	728	1	chr5B.!!$F1	727
8	TraesCS1B01G181800	chr5B	341066071	341066793	722	False	1197.000000	1197	96.547000	1	724	1	chr5B.!!$F2	723
9	TraesCS1B01G181800	chr5B	11513307	11517181	3874	False	776.000000	2418	86.126750	833	6657	4	chr5B.!!$F3	5824
10	TraesCS1B01G181800	chr5B	11550469	11555711	5242	True	752.250000	2117	85.597250	2584	6867	4	chr5B.!!$R1	4283
11	TraesCS1B01G181800	chr6B	407167972	407168695	723	True	1210.000000	1210	96.828000	1	724	1	chr6B.!!$R3	723
12	TraesCS1B01G181800	chr6B	77619604	77620348	744	True	1190.000000	1190	95.576000	1	742	1	chr6B.!!$R2	741
13	TraesCS1B01G181800	chr4B	244918597	244919319	722	False	1205.000000	1205	96.690000	1	725	1	chr4B.!!$F1	724
14	TraesCS1B01G181800	chr2B	23675888	23676610	722	False	1203.000000	1203	96.690000	1	724	1	chr2B.!!$F1	723
15	TraesCS1B01G181800	chr2B	232742451	232743172	721	True	1203.000000	1203	96.685000	1	724	1	chr2B.!!$R1	723
16	TraesCS1B01G181800	chr4A	37011913	37012640	727	True	1197.000000	1197	96.301000	1	730	1	chr4A.!!$R1	729
17	TraesCS1B01G181800	chr3B	166166714	166167435	721	True	1197.000000	1197	96.547000	1	724	1	chr3B.!!$R1	723

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
643	645	1.211709	GCGGGCGCTACACAAAAAT	59.788	52.632	7.64	38.26	1.82	F
1399	1449	0.110869	CCCTCGGGAGTAGGAGTAGG	59.889	65.000	0.00	36.08	3.18	F
1936	2040	0.253160	TTGGCCACCATCTACTCCCT	60.253	55.000	3.88	31.53	4.20	F
3458	4414	0.034337	TACAAGGAACACGACAGCCC	59.966	55.000	0.00	0.00	5.19	F
4242	5230	0.668535	GAGTTGGGTTGTTGGTGCTC	59.331	55.000	0.00	0.00	4.26	F
5035	8402	0.811616	AAATGCCAGGATCGCTCGAC	60.812	55.000	0.00	0.00	4.20	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2457	2909	0.242286	CCGACACACACAGAGAGGAG	59.758	60.000	0.00	0.0	0.00	3.69	R
2763	3293	0.891449	GATCTCCTCGCTGATCCCGA	60.891	60.000	5.60	5.6	34.60	5.14	R
3560	4525	0.108019	AAAGGAGAAAAGGCGTCCGT	59.892	50.000	0.00	0.0	35.33	4.69	R
5454	8863	1.272212	CCCTAAACGGCAAAAGCACAT	59.728	47.619	0.00	0.0	0.00	3.21	R
5503	8912	0.478507	AGCTATTACCACCCATGCCC	59.521	55.000	0.00	0.0	0.00	5.36	R
6838	10332	0.098200	GGCGCTACGAAAACCCATTC	59.902	55.000	7.64	0.0	0.00	2.67	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)

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Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
571	573	3.702048	GGCTGCCACGGTGGACTA	61.702	66.667	30.65	14.20	40.96	2.59
573	575	2.646175	GCTGCCACGGTGGACTAGA	61.646	63.158	30.65	7.16	40.96	2.43
643	645	1.211709	GCGGGCGCTACACAAAAAT	59.788	52.632	7.64	0.00	38.26	1.82
976	999	2.784356	CCTCCTCTGCTCCTGCTCG	61.784	68.421	0.00	0.00	40.48	5.03
977	1000	3.429080	CTCCTCTGCTCCTGCTCGC	62.429	68.421	0.00	0.00	40.48	5.03
979	1002	2.104729	CTCTGCTCCTGCTCGCTC	59.895	66.667	0.00	0.00	40.48	5.03
980	1003	3.754740	CTCTGCTCCTGCTCGCTCG	62.755	68.421	0.00	0.00	40.48	5.03
1213	1246	4.083862	GCCACCGTCCACCTCCTC	62.084	72.222	0.00	0.00	0.00	3.71
1238	1271	4.127171	TCTTGTCTTTTCCTCCTCGTTTG	58.873	43.478	0.00	0.00	0.00	2.93
1306	1349	2.969238	CTGCCGCCCGATTAGCAG	60.969	66.667	0.00	0.00	45.92	4.24
1321	1364	4.701956	TTAGCAGGAACAAAGCAATAGC	57.298	40.909	0.00	0.00	42.56	2.97
1322	1365	2.517959	AGCAGGAACAAAGCAATAGCA	58.482	42.857	0.00	0.00	45.49	3.49
1324	1367	4.272489	AGCAGGAACAAAGCAATAGCATA	58.728	39.130	0.00	0.00	45.49	3.14
1370	1420	6.759497	ACCAGAACAAATTAGTAAGATGGC	57.241	37.500	0.00	0.00	0.00	4.40
1372	1422	6.948309	ACCAGAACAAATTAGTAAGATGGCTT	59.052	34.615	0.00	0.00	38.15	4.35
1375	1425	7.965107	CAGAACAAATTAGTAAGATGGCTTCAC	59.035	37.037	3.03	0.00	35.56	3.18
1385	1435	3.787001	GGCTTCACCCCTCCCTCG	61.787	72.222	0.00	0.00	0.00	4.63
1396	1446	4.183398	TCCCTCGGGAGTAGGAGT	57.817	61.111	0.00	0.00	39.76	3.85
1399	1449	0.110869	CCCTCGGGAGTAGGAGTAGG	59.889	65.000	0.00	0.00	36.08	3.18
1400	1450	1.138568	CCTCGGGAGTAGGAGTAGGA	58.861	60.000	0.00	0.00	36.08	2.94
1401	1451	1.072648	CCTCGGGAGTAGGAGTAGGAG	59.927	61.905	0.00	0.00	36.08	3.69
1402	1452	1.770061	CTCGGGAGTAGGAGTAGGAGT	59.230	57.143	0.00	0.00	0.00	3.85
1403	1453	2.971330	CTCGGGAGTAGGAGTAGGAGTA	59.029	54.545	0.00	0.00	0.00	2.59
1404	1454	2.971330	TCGGGAGTAGGAGTAGGAGTAG	59.029	54.545	0.00	0.00	0.00	2.57
1405	1455	2.038820	CGGGAGTAGGAGTAGGAGTAGG	59.961	59.091	0.00	0.00	0.00	3.18

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Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Hairpin	End Stability
667	669	0.400213	TTCACGGAATGAACTGGCCT	59.600	50.000	3.32	42.62	5.19
784	786	9.331282	GCACCATTATTTTCTTCTAGTGATACT	57.669	33.333	0.00	0.00	2.12
785	787	8.560374	GGCACCATTATTTTCTTCTAGTGATAC	58.440	37.037	0.00	0.00	2.24
789	808	6.150976	TGTGGCACCATTATTTTCTTCTAGTG	59.849	38.462	16.26	0.00	2.74
977	1000	4.277593	CCTAGCCGCTCTGCCGAG	62.278	72.222	0.00	40.35	4.63
980	1003	4.906792	CTGCCTAGCCGCTCTGCC	62.907	72.222	0.00	0.00	4.85
1206	1239	2.424684	AAAGACAAGAGGGAGGAGGT	57.575	50.000	0.00	0.00	3.85
1207	1240	2.026729	GGAAAAGACAAGAGGGAGGAGG	60.027	54.545	0.00	0.00	4.30
1208	1241	2.909662	AGGAAAAGACAAGAGGGAGGAG	59.090	50.000	0.00	0.00	3.69
1209	1242	2.907042	GAGGAAAAGACAAGAGGGAGGA	59.093	50.000	0.00	0.00	3.71
1210	1243	2.026729	GGAGGAAAAGACAAGAGGGAGG	60.027	54.545	0.00	0.00	4.30
1212	1245	2.907042	GAGGAGGAAAAGACAAGAGGGA	59.093	50.000	0.00	0.00	4.20
1213	1246	2.354203	CGAGGAGGAAAAGACAAGAGGG	60.354	54.545	0.00	0.00	4.30
1238	1271	1.566018	GCATGCTATACCGGGCGAAC	61.566	60.000	11.37	0.00	3.95
1385	1435	3.325605	TCCTACTCCTACTCCTACTCCC	58.674	54.545	0.00	0.00	4.30
1394	1444	5.608015	CCTACTTCCTACTCCTACTCCTACT	59.392	48.000	0.00	0.00	2.57
1396	1446	5.797305	TCCTACTTCCTACTCCTACTCCTA	58.203	45.833	0.00	0.00	2.94
1399	1449	5.635278	ACTCCTACTTCCTACTCCTACTC	57.365	47.826	0.00	0.00	2.59
1400	1450	5.608015	CCTACTCCTACTTCCTACTCCTACT	59.392	48.000	0.00	0.00	2.57
1401	1451	5.606329	TCCTACTCCTACTTCCTACTCCTAC	59.394	48.000	0.00	0.00	3.18
1402	1452	5.797305	TCCTACTCCTACTTCCTACTCCTA	58.203	45.833	0.00	0.00	2.94
1403	1453	4.644010	TCCTACTCCTACTTCCTACTCCT	58.356	47.826	0.00	0.00	3.69
1404	1454	5.103982	ACTTCCTACTCCTACTTCCTACTCC	60.104	48.000	0.00	0.00	3.85
1405	1455	6.005066	ACTTCCTACTCCTACTTCCTACTC	57.995	45.833	0.00	0.00	2.59
1406	1456	6.101588	CCTACTTCCTACTCCTACTTCCTACT	59.898	46.154	0.00	0.00	2.57

Showing 1 to 25 of 285 entries

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Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.