AutoCloner

Multiple sequence alignment - TraesCS2D01G445200

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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	TraesCS2D01G445200	chr2D	100.000	3808	0	0	1	3808	556016369	556012562	0.000000e+00	7033.0
1	TraesCS2D01G445200	chr2D	87.730	1304	99	24	1743	3039	555948778	555947529	0.000000e+00	1465.0
2	TraesCS2D01G445200	chr2D	91.026	312	26	2	1270	1580	555949357	555949047	1.640000e-113	420.0
3	TraesCS2D01G445200	chr2D	90.050	201	20	0	46	246	128025767	128025967	1.050000e-65	261.0
4	TraesCS2D01G445200	chr2D	87.215	219	16	6	1067	1273	555949602	555949384	4.920000e-59	239.0
5	TraesCS2D01G445200	chr2D	88.947	190	15	3	3619	3808	641121434	641121251	2.960000e-56	230.0
6	TraesCS2D01G445200	chr2A	88.128	1314	107	16	1739	3039	695421689	695420412	0.000000e+00	1517.0
7	TraesCS2D01G445200	chr2A	89.547	287	28	2	1295	1580	695422242	695421957	2.800000e-96	363.0
8	TraesCS2D01G445200	chr2A	85.714	189	15	4	1097	1273	695422482	695422294	5.020000e-44	189.0
9	TraesCS2D01G445200	chr2A	94.845	97	5	0	3488	3584	695420397	695420301	6.590000e-33	152.0
10	TraesCS2D01G445200	chr2B	93.333	630	41	1	2197	2826	662882875	662882247	0.000000e+00	929.0
11	TraesCS2D01G445200	chr2B	94.937	474	15	5	2824	3295	662882144	662881678	0.000000e+00	734.0
12	TraesCS2D01G445200	chr2B	90.546	476	31	7	1726	2197	662886393	662885928	5.400000e-173	617.0
13	TraesCS2D01G445200	chr2B	90.113	354	15	5	444	779	662897307	662896956	3.490000e-120	442.0
14	TraesCS2D01G445200	chr2B	93.243	296	15	4	3291	3584	662828638	662828346	7.560000e-117	431.0
15	TraesCS2D01G445200	chr2B	88.056	360	23	7	799	1158	662896823	662896484	3.540000e-110	409.0
16	TraesCS2D01G445200	chr2B	90.323	310	27	1	1154	1463	662891429	662891123	1.650000e-108	403.0
17	TraesCS2D01G445200	chr2B	95.652	46	2	0	1	46	662897382	662897337	1.470000e-09	75.0
18	TraesCS2D01G445200	chr2B	93.182	44	3	0	1664	1707	796974869	796974912	8.830000e-07	65.8
19	TraesCS2D01G445200	chr7B	76.923	689	113	32	1793	2455	99660705	99660037	2.180000e-92	350.0
20	TraesCS2D01G445200	chr7B	89.372	207	22	0	44	250	606481928	606481722	1.050000e-65	261.0
21	TraesCS2D01G445200	chr7D	76.856	687	111	32	1793	2452	136313176	136313841	1.010000e-90	344.0
22	TraesCS2D01G445200	chr7D	87.565	193	13	7	3616	3808	458208293	458208474	2.980000e-51	213.0
23	TraesCS2D01G445200	chr5A	94.059	202	11	1	45	245	218605829	218606030	4.780000e-79	305.0
24	TraesCS2D01G445200	chr5A	88.421	190	15	4	3619	3808	220089570	220089388	4.950000e-54	222.0
25	TraesCS2D01G445200	chr5A	92.857	42	3	0	1664	1705	524672236	524672277	1.140000e-05	62.1
26	TraesCS2D01G445200	chr6B	90.338	207	18	2	44	249	612537303	612537098	1.740000e-68	270.0
27	TraesCS2D01G445200	chr6B	90.400	125	10	2	577	700	703681454	703681577	3.040000e-36	163.0
28	TraesCS2D01G445200	chr6B	80.631	222	31	7	490	700	350017049	350016829	1.090000e-35	161.0
29	TraesCS2D01G445200	chr6B	79.825	228	31	7	485	700	469706655	469706431	6.590000e-33	152.0
30	TraesCS2D01G445200	chr7A	81.873	331	48	9	2128	2452	135925027	135925351	6.270000e-68	268.0
31	TraesCS2D01G445200	chr7A	89.372	207	22	0	43	249	353071899	353071693	1.050000e-65	261.0
32	TraesCS2D01G445200	chr7A	87.245	196	19	5	3614	3808	200689365	200689555	6.400000e-53	219.0
33	TraesCS2D01G445200	chr7A	95.000	40	2	0	1664	1703	164785618	164785579	3.180000e-06	63.9
34	TraesCS2D01G445200	chr7A	91.304	46	4	0	1661	1706	460448402	460448447	3.180000e-06	63.9
35	TraesCS2D01G445200	chr7A	93.023	43	3	0	1664	1706	460754604	460754646	3.180000e-06	63.9
36	TraesCS2D01G445200	chr6A	89.855	207	21	0	44	250	549989982	549989776	2.260000e-67	267.0
37	TraesCS2D01G445200	chr6A	88.889	207	23	0	42	248	607089162	607089368	4.880000e-64	255.0
38	TraesCS2D01G445200	chr6A	88.889	207	23	0	42	248	607224348	607224554	4.880000e-64	255.0
39	TraesCS2D01G445200	chr3A	88.406	207	23	1	46	252	585158775	585158570	8.170000e-62	248.0
40	TraesCS2D01G445200	chr3A	87.565	193	18	3	3616	3808	588548286	588548472	6.400000e-53	219.0
41	TraesCS2D01G445200	chr5B	88.205	195	16	6	3616	3808	208591607	208591796	3.830000e-55	226.0
42	TraesCS2D01G445200	chr5B	87.368	190	21	2	3619	3808	322925772	322925586	8.290000e-52	215.0
43	TraesCS2D01G445200	chr5B	89.362	47	5	0	1659	1705	13377359	13377313	4.110000e-05	60.2
44	TraesCS2D01G445200	chr3D	87.895	190	17	3	3619	3808	268953396	268953213	6.400000e-53	219.0
45	TraesCS2D01G445200	chr1D	86.802	197	19	5	3608	3804	93044417	93044228	2.980000e-51	213.0
46	TraesCS2D01G445200	chr1B	82.960	223	25	7	485	696	553450055	553450275	5.020000e-44	189.0
47	TraesCS2D01G445200	chr1B	82.143	224	27	4	485	696	589055885	589055663	3.020000e-41	180.0
48	TraesCS2D01G445200	chr1B	95.349	43	2	0	1664	1706	432758710	432758668	6.830000e-08	69.4
49	TraesCS2D01G445200	chr4D	82.883	222	24	10	488	696	500823475	500823255	1.810000e-43	187.0
50	TraesCS2D01G445200	chr4D	82.727	220	26	9	485	693	331709828	331710046	6.500000e-43	185.0
51	TraesCS2D01G445200	chr3B	81.818	220	28	6	485	694	519399103	519399320	1.410000e-39	174.0
52	TraesCS2D01G445200	chr3B	92.857	42	3	0	1664	1705	701409670	701409711	1.140000e-05	62.1
53	TraesCS2D01G445200	chrUn	89.474	57	6	0	1650	1706	83668051	83668107	5.280000e-09	73.1

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	TraesCS2D01G445200	chr2D	556012562	556016369	3807	True	7033.000000	7033	100.000000	1	3808	1	chr2D.!!$R1	3807
1	TraesCS2D01G445200	chr2D	555947529	555949602	2073	True	708.000000	1465	88.657000	1067	3039	3	chr2D.!!$R3	1972
2	TraesCS2D01G445200	chr2A	695420301	695422482	2181	True	555.250000	1517	89.558500	1097	3584	4	chr2A.!!$R1	2487
3	TraesCS2D01G445200	chr2B	662881678	662886393	4715	True	760.000000	929	92.938667	1726	3295	3	chr2B.!!$R3	1569
4	TraesCS2D01G445200	chr2B	662896484	662897382	898	True	308.666667	442	91.273667	1	1158	3	chr2B.!!$R4	1157
5	TraesCS2D01G445200	chr7B	99660037	99660705	668	True	350.000000	350	76.923000	1793	2455	1	chr7B.!!$R1	662
6	TraesCS2D01G445200	chr7D	136313176	136313841	665	False	344.000000	344	76.856000	1793	2452	1	chr7D.!!$F1	659

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
97	98	0.115152	CCCCCTCTTTCCCAGCTTTT	59.885	55.0	0.0	0.0	0.00	2.27	F
616	634	0.179129	GCCATGTTTGCCAATCCTCG	60.179	55.0	0.0	0.0	0.00	4.63	F
1181	1313	0.032952	GGCTATGGTAATGCCGACGA	59.967	55.0	0.0	0.0	41.21	4.20	F
1186	1318	0.104120	TGGTAATGCCGACGAGATGG	59.896	55.0	0.0	0.0	41.21	3.51	F
1187	1319	0.387929	GGTAATGCCGACGAGATGGA	59.612	55.0	0.0	0.0	0.00	3.41	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1015	1147	0.183971	TCTCCGTCCATCTCCTCCTC	59.816	60.000	0.00	0.0	0.0	3.71	R
2088	2483	0.250295	TCAACGTGAGAGGGCCAAAG	60.250	55.000	6.18	0.0	0.0	2.77	R
2708	6183	0.099613	CAGTCATCTCCACCTCGACG	59.900	60.000	0.00	0.0	0.0	5.12	R
2711	6186	2.001812	CAACAGTCATCTCCACCTCG	57.998	55.000	0.00	0.0	0.0	4.63	R
3181	6761	3.788333	AAATTGCTGGATGAATGACGG	57.212	42.857	0.00	0.0	0.0	4.79	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
46	47	7.148069	GGATAAGAATGTGGTGACCCTTTTTAG	60.148	40.741	0.00	0.00	0.00	1.85
47	48	4.407365	AGAATGTGGTGACCCTTTTTAGG	58.593	43.478	0.00	0.00	0.00	2.69
56	57	2.604912	CCCTTTTTAGGGCCAGTTCT	57.395	50.000	6.18	0.00	42.99	3.01
57	58	2.889512	CCCTTTTTAGGGCCAGTTCTT	58.110	47.619	6.18	0.00	42.99	2.52
58	59	3.239449	CCCTTTTTAGGGCCAGTTCTTT	58.761	45.455	6.18	0.00	42.99	2.52
59	60	3.646162	CCCTTTTTAGGGCCAGTTCTTTT	59.354	43.478	6.18	0.00	42.99	2.27
60	61	4.503123	CCCTTTTTAGGGCCAGTTCTTTTG	60.503	45.833	6.18	0.00	42.99	2.44
61	62	4.503123	CCTTTTTAGGGCCAGTTCTTTTGG	60.503	45.833	6.18	0.00	38.78	3.28
66	67	3.763671	CCAGTTCTTTTGGCGGCT	58.236	55.556	11.43	0.00	0.00	5.52
67	68	2.041153	CCAGTTCTTTTGGCGGCTT	58.959	52.632	11.43	0.00	0.00	4.35
68	69	1.243902	CCAGTTCTTTTGGCGGCTTA	58.756	50.000	11.43	0.00	0.00	3.09
69	70	1.611491	CCAGTTCTTTTGGCGGCTTAA	59.389	47.619	11.43	1.34	0.00	1.85
70	71	2.035321	CCAGTTCTTTTGGCGGCTTAAA	59.965	45.455	11.43	9.87	0.00	1.52
71	72	3.491792	CCAGTTCTTTTGGCGGCTTAAAA	60.492	43.478	11.43	8.74	0.00	1.52
72	73	4.116238	CAGTTCTTTTGGCGGCTTAAAAA	58.884	39.130	11.43	8.00	0.00	1.94
90	91	2.848678	AAATAAGCCCCCTCTTTCCC	57.151	50.000	0.00	0.00	0.00	3.97
91	92	1.693799	AATAAGCCCCCTCTTTCCCA	58.306	50.000	0.00	0.00	0.00	4.37
92	93	1.226311	ATAAGCCCCCTCTTTCCCAG	58.774	55.000	0.00	0.00	0.00	4.45
93	94	1.571773	TAAGCCCCCTCTTTCCCAGC	61.572	60.000	0.00	0.00	0.00	4.85
94	95	3.342477	GCCCCCTCTTTCCCAGCT	61.342	66.667	0.00	0.00	0.00	4.24
95	96	2.923910	GCCCCCTCTTTCCCAGCTT	61.924	63.158	0.00	0.00	0.00	3.74
96	97	1.776969	CCCCCTCTTTCCCAGCTTT	59.223	57.895	0.00	0.00	0.00	3.51
97	98	0.115152	CCCCCTCTTTCCCAGCTTTT	59.885	55.000	0.00	0.00	0.00	2.27
98	99	1.550327	CCCCTCTTTCCCAGCTTTTC	58.450	55.000	0.00	0.00	0.00	2.29
99	100	1.076187	CCCCTCTTTCCCAGCTTTTCT	59.924	52.381	0.00	0.00	0.00	2.52

Showing 1 to 25 of 567 entries

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Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
10	11	4.396166	CCACATTCTTATCCACAACTCACC	59.604	45.833	0.00	0.00	0.00	4.02
11	12	5.003804	ACCACATTCTTATCCACAACTCAC	58.996	41.667	0.00	0.00	0.00	3.51
49	50	1.243902	TAAGCCGCCAAAAGAACTGG	58.756	50.000	0.00	0.00	36.99	4.00
50	51	3.363341	TTTAAGCCGCCAAAAGAACTG	57.637	42.857	0.00	0.00	0.00	3.16
51	52	4.394439	TTTTTAAGCCGCCAAAAGAACT	57.606	36.364	0.00	0.00	0.00	3.01
69	70	3.181400	TGGGAAAGAGGGGGCTTATTTTT	60.181	43.478	0.00	0.00	0.00	1.94
70	71	2.385417	TGGGAAAGAGGGGGCTTATTTT	59.615	45.455	0.00	0.00	0.00	1.82
71	72	2.007636	TGGGAAAGAGGGGGCTTATTT	58.992	47.619	0.00	0.00	0.00	1.40
72	73	1.570979	CTGGGAAAGAGGGGGCTTATT	59.429	52.381	0.00	0.00	0.00	1.40
73	74	1.226311	CTGGGAAAGAGGGGGCTTAT	58.774	55.000	0.00	0.00	0.00	1.73
74	75	1.571773	GCTGGGAAAGAGGGGGCTTA	61.572	60.000	0.00	0.00	0.00	3.09
75	76	2.923910	GCTGGGAAAGAGGGGGCTT	61.924	63.158	0.00	0.00	0.00	4.35
76	77	3.342477	GCTGGGAAAGAGGGGGCT	61.342	66.667	0.00	0.00	0.00	5.19
77	78	2.446982	AAAGCTGGGAAAGAGGGGGC	62.447	60.000	0.00	0.00	0.00	5.80
78	79	0.115152	AAAAGCTGGGAAAGAGGGGG	59.885	55.000	0.00	0.00	0.00	5.40
79	80	1.076187	AGAAAAGCTGGGAAAGAGGGG	59.924	52.381	0.00	0.00	0.00	4.79
80	81	2.224867	TGAGAAAAGCTGGGAAAGAGGG	60.225	50.000	0.00	0.00	0.00	4.30
81	82	3.146104	TGAGAAAAGCTGGGAAAGAGG	57.854	47.619	0.00	0.00	0.00	3.69
82	83	5.163673	GCTTATGAGAAAAGCTGGGAAAGAG	60.164	44.000	0.00	0.00	44.75	2.85
83	84	4.702131	GCTTATGAGAAAAGCTGGGAAAGA	59.298	41.667	0.00	0.00	44.75	2.52
84	85	4.142293	GGCTTATGAGAAAAGCTGGGAAAG	60.142	45.833	7.65	0.00	46.81	2.62
85	86	3.763897	GGCTTATGAGAAAAGCTGGGAAA	59.236	43.478	7.65	0.00	46.81	3.13
86	87	3.356290	GGCTTATGAGAAAAGCTGGGAA	58.644	45.455	7.65	0.00	46.81	3.97
87	88	3.004752	GGCTTATGAGAAAAGCTGGGA	57.995	47.619	7.65	0.00	46.81	4.37
91	92	3.526534	GAGACGGCTTATGAGAAAAGCT	58.473	45.455	0.00	0.00	46.81	3.74

Showing 1 to 25 of 578 entries

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Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.