AutoCloner

Multiple sequence alignment - TraesCS2D01G387700

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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	TraesCS2D01G387700	chr2D	100.000	6619	0	0	1	6619	493083231	493076613	0.000000e+00	12224.0
1	TraesCS2D01G387700	chr2D	78.510	1638	304	37	3991	5619	493006019	493004421	0.000000e+00	1031.0
2	TraesCS2D01G387700	chr2D	82.753	603	78	20	1138	1726	493007899	493007309	1.270000e-141	514.0
3	TraesCS2D01G387700	chr2D	85.135	296	40	4	1161	1453	493177143	493176849	3.880000e-77	300.0
4	TraesCS2D01G387700	chr2D	91.053	190	16	1	3025	3213	298287618	298287807	8.520000e-64	255.0
5	TraesCS2D01G387700	chr2D	79.297	256	44	8	1192	1441	629074250	629074502	3.170000e-38	171.0
6	TraesCS2D01G387700	chr2D	77.323	269	51	7	1175	1438	477270174	477270437	4.130000e-32	150.0
7	TraesCS2D01G387700	chr2D	75.000	272	52	14	1178	1441	585501826	585502089	1.950000e-20	111.0
8	TraesCS2D01G387700	chr2D	74.444	270	57	10	1178	1441	34992135	34991872	9.080000e-19	106.0
9	TraesCS2D01G387700	chr2D	82.906	117	16	4	4013	4127	493175812	493175698	1.170000e-17	102.0
10	TraesCS2D01G387700	chr2B	95.126	2852	122	14	3025	5870	579688523	579685683	0.000000e+00	4481.0
11	TraesCS2D01G387700	chr2B	87.186	1194	78	39	1237	2414	579690425	579689291	0.000000e+00	1288.0
12	TraesCS2D01G387700	chr2B	78.150	1643	302	44	3991	5619	579573148	579571549	0.000000e+00	992.0
13	TraesCS2D01G387700	chr2B	89.352	648	31	16	603	1237	579690548	579691170	0.000000e+00	780.0
14	TraesCS2D01G387700	chr2B	83.276	580	74	17	1158	1726	579574981	579574414	4.580000e-141	512.0
15	TraesCS2D01G387700	chr2B	90.598	234	14	5	327	552	579691402	579691169	3.000000e-78	303.0
16	TraesCS2D01G387700	chr2B	84.797	296	41	4	1161	1453	581471086	581470792	1.810000e-75	294.0
17	TraesCS2D01G387700	chr2B	91.534	189	15	1	3025	3212	367687984	367687796	6.580000e-65	259.0
18	TraesCS2D01G387700	chr2B	83.761	117	15	4	4013	4127	581469815	581469701	2.520000e-19	108.0
19	TraesCS2D01G387700	chr2B	80.165	121	18	6	4010	4127	42565559	42565676	1.180000e-12	86.1
20	TraesCS2D01G387700	chr2A	95.316	2370	78	16	3517	5870	640708478	640710830	0.000000e+00	3731.0
21	TraesCS2D01G387700	chr2A	91.752	1661	83	27	160	1800	640705582	640707208	0.000000e+00	2259.0
22	TraesCS2D01G387700	chr2A	78.528	1644	293	46	3991	5619	640818508	640820106	0.000000e+00	1026.0
23	TraesCS2D01G387700	chr2A	89.455	825	51	17	1832	2641	640707204	640708007	0.000000e+00	1009.0
24	TraesCS2D01G387700	chr2A	91.765	425	34	1	3066	3489	640708055	640708479	2.060000e-164	590.0
25	TraesCS2D01G387700	chr2A	82.143	616	86	18	1126	1726	640816800	640817406	2.130000e-139	507.0
26	TraesCS2D01G387700	chr2A	91.606	274	18	3	2769	3037	141240043	141239770	2.250000e-99	374.0
27	TraesCS2D01G387700	chr2A	85.324	293	39	4	1161	1450	640269911	640270202	3.880000e-77	300.0
28	TraesCS2D01G387700	chr2A	91.579	190	13	3	3025	3213	522518833	522519020	6.580000e-65	259.0
29	TraesCS2D01G387700	chr2A	81.667	120	18	4	4010	4127	640271209	640271326	5.460000e-16	97.1
30	TraesCS2D01G387700	chr1D	97.344	753	13	3	5869	6619	463249902	463250649	0.000000e+00	1273.0
31	TraesCS2D01G387700	chr1D	92.553	188	14	0	3025	3212	150941581	150941768	3.040000e-68	270.0
32	TraesCS2D01G387700	chr4D	97.074	752	16	4	5869	6619	35124712	35123966	0.000000e+00	1262.0
33	TraesCS2D01G387700	chr4D	97.196	749	16	1	5871	6619	364026895	364026152	0.000000e+00	1262.0
34	TraesCS2D01G387700	chr6D	96.809	752	18	2	5869	6619	449814435	449815181	0.000000e+00	1251.0
35	TraesCS2D01G387700	chr6D	95.916	759	20	6	5864	6619	5060868	5061618	0.000000e+00	1219.0
36	TraesCS2D01G387700	chr7D	96.800	750	19	1	5870	6619	43790357	43789613	0.000000e+00	1247.0
37	TraesCS2D01G387700	chr7D	96.262	749	19	6	5873	6619	481609927	481609186	0.000000e+00	1219.0
38	TraesCS2D01G387700	chr7D	82.443	131	18	3	1538	1667	531439819	531439945	7.020000e-20	110.0
39	TraesCS2D01G387700	chrUn	96.164	756	23	2	5865	6619	45207428	45208178	0.000000e+00	1230.0
40	TraesCS2D01G387700	chr5D	95.664	761	26	3	5860	6619	510945245	510945999	0.000000e+00	1216.0
41	TraesCS2D01G387700	chr4B	92.857	266	14	3	2769	3029	137740681	137740416	1.350000e-101	381.0
42	TraesCS2D01G387700	chr5A	92.537	268	14	4	2765	3027	595903245	595903511	4.840000e-101	379.0
43	TraesCS2D01G387700	chr5A	92.453	265	15	3	2770	3029	523613862	523613598	2.250000e-99	374.0
44	TraesCS2D01G387700	chr3B	91.822	269	16	4	2769	3032	28514454	28514721	2.920000e-98	370.0
45	TraesCS2D01G387700	chr3B	92.337	261	15	3	2769	3024	706775290	706775550	3.770000e-97	366.0
46	TraesCS2D01G387700	chr3B	92.015	263	16	3	2770	3027	137748310	137748572	1.360000e-96	364.0
47	TraesCS2D01G387700	chr3B	91.667	192	15	1	3025	3215	342869826	342869635	1.420000e-66	265.0
48	TraesCS2D01G387700	chr1A	92.015	263	16	3	2770	3027	18354258	18354520	1.360000e-96	364.0
49	TraesCS2D01G387700	chr1A	93.684	190	12	0	3025	3214	208883942	208884131	1.090000e-72	285.0
50	TraesCS2D01G387700	chr1A	92.553	188	14	0	3025	3212	208894073	208893886	3.040000e-68	270.0
51	TraesCS2D01G387700	chr3A	91.667	264	17	3	2769	3027	510081853	510081590	1.750000e-95	361.0
52	TraesCS2D01G387700	chr6A	81.439	264	47	2	1175	1437	452099935	452099673	1.450000e-51	215.0
53	TraesCS2D01G387700	chr6A	81.690	142	23	3	1180	1320	409746381	409746242	1.510000e-21	115.0
54	TraesCS2D01G387700	chr6B	81.467	259	46	2	1175	1432	512234493	512234750	1.870000e-50	211.0
55	TraesCS2D01G387700	chr7A	80.519	154	24	6	1170	1320	705117444	705117294	5.420000e-21	113.0
56	TraesCS2D01G387700	chr7A	82.443	131	18	3	1538	1667	611728489	611728615	7.020000e-20	110.0

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	TraesCS2D01G387700	chr2D	493076613	493083231	6618	True	12224.00	12224	100.0000	1	6619	1	chr2D.!!$R2	6618
1	TraesCS2D01G387700	chr2D	493004421	493007899	3478	True	772.50	1031	80.6315	1138	5619	2	chr2D.!!$R3	4481
2	TraesCS2D01G387700	chr2D	493175698	493177143	1445	True	201.00	300	84.0205	1161	4127	2	chr2D.!!$R4	2966
3	TraesCS2D01G387700	chr2B	579685683	579691402	5719	True	2024.00	4481	90.9700	327	5870	3	chr2B.!!$R3	5543
4	TraesCS2D01G387700	chr2B	579690548	579691170	622	False	780.00	780	89.3520	603	1237	1	chr2B.!!$F2	634
5	TraesCS2D01G387700	chr2B	579571549	579574981	3432	True	752.00	992	80.7130	1158	5619	2	chr2B.!!$R2	4461
6	TraesCS2D01G387700	chr2B	581469701	581471086	1385	True	201.00	294	84.2790	1161	4127	2	chr2B.!!$R4	2966
7	TraesCS2D01G387700	chr2A	640705582	640710830	5248	False	1897.25	3731	92.0720	160	5870	4	chr2A.!!$F3	5710
8	TraesCS2D01G387700	chr2A	640816800	640820106	3306	False	766.50	1026	80.3355	1126	5619	2	chr2A.!!$F4	4493
9	TraesCS2D01G387700	chr1D	463249902	463250649	747	False	1273.00	1273	97.3440	5869	6619	1	chr1D.!!$F2	750
10	TraesCS2D01G387700	chr4D	35123966	35124712	746	True	1262.00	1262	97.0740	5869	6619	1	chr4D.!!$R1	750
11	TraesCS2D01G387700	chr4D	364026152	364026895	743	True	1262.00	1262	97.1960	5871	6619	1	chr4D.!!$R2	748
12	TraesCS2D01G387700	chr6D	449814435	449815181	746	False	1251.00	1251	96.8090	5869	6619	1	chr6D.!!$F2	750
13	TraesCS2D01G387700	chr6D	5060868	5061618	750	False	1219.00	1219	95.9160	5864	6619	1	chr6D.!!$F1	755
14	TraesCS2D01G387700	chr7D	43789613	43790357	744	True	1247.00	1247	96.8000	5870	6619	1	chr7D.!!$R1	749
15	TraesCS2D01G387700	chr7D	481609186	481609927	741	True	1219.00	1219	96.2620	5873	6619	1	chr7D.!!$R2	746
16	TraesCS2D01G387700	chrUn	45207428	45208178	750	False	1230.00	1230	96.1640	5865	6619	1	chrUn.!!$F1	754
17	TraesCS2D01G387700	chr5D	510945245	510945999	754	False	1216.00	1216	95.6640	5860	6619	1	chr5D.!!$F1	759

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
77	78	0.034198	TGCGGGAGAAATCGTGTTCA	59.966	50.0	4.17	0.00	0.00	3.18	F
154	155	0.035739	TTGCGGGAGGTTTACTGTCC	59.964	55.0	0.00	0.00	0.00	4.02	F
161	162	0.036306	AGGTTTACTGTCCGCCCTTG	59.964	55.0	0.00	0.00	0.00	3.61	F
685	699	0.251916	TTCCGTCGCCTTTCCATCAT	59.748	50.0	0.00	0.00	0.00	2.45	F
2416	3249	0.107268	GGGAACACCTTGTGGTACGT	59.893	55.0	0.00	0.00	46.60	3.57	F
3023	4392	0.101759	CTTATTCGCGAACGGAGGGA	59.898	55.0	26.00	0.00	40.63	4.20	F
3368	4737	0.179116	CGGACAGAGAGTGAGCCATG	60.179	60.0	0.00	0.00	0.00	3.66	F
3480	4851	0.249489	GATCTGACGGCGCCATAGTT	60.249	55.0	28.98	15.30	0.00	2.24	F
3499	4898	0.750249	TGTGAGTCATGACGTGTGGT	59.250	50.0	19.85	1.13	36.20	4.16	F
4793	6766	1.442769	ACTCTGGCTACGTTGCATTG	58.557	50.0	22.89	12.01	34.04	2.82	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1915	2660	1.101331	CAGGAGGAGCCAGCATTTTC	58.899	55.000	0.00	0.00	40.02	2.29	R
2062	2834	1.327460	CGCCAAACTACATCATCACCG	59.673	52.381	0.00	0.00	0.00	4.94	R
2080	2852	1.804151	TGAAAATGGTAGCACTGACGC	59.196	47.619	0.00	0.00	0.00	5.19	R
2650	3552	1.079888	GCATGACGCCCCCTTTTTG	60.080	57.895	0.00	0.00	32.94	2.44	R
3500	4899	0.106015	GCTGGCCACCTCCCATAATT	60.106	55.000	0.00	0.00	0.00	1.40	R
4982	6955	1.338200	CCAGCAACTACACCAGAGTCC	60.338	57.143	0.00	0.00	0.00	3.85	R
5352	7325	0.742505	CACCTACCATACTTCGGCGA	59.257	55.000	4.99	4.99	0.00	5.54	R
5482	7455	2.048444	CACCATCAGTGCAGCCTTAT	57.952	50.000	0.00	0.00	40.28	1.73	R
5534	7507	0.034089	AAGGGAAGATCCAAAGCCCG	60.034	55.000	0.00	0.00	43.64	6.13	R
6124	8101	0.725117	GGTGAAGTGATAAACGCCCG	59.275	55.000	0.00	0.00	0.00	6.13	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
24	25	4.268687	CTTGTGAGCAGTCCGGAC	57.731	61.111	27.67	27.67	0.00	4.79
25	26	1.668294	CTTGTGAGCAGTCCGGACT	59.332	57.895	31.69	31.69	43.61	3.85
26	27	0.389166	CTTGTGAGCAGTCCGGACTC	60.389	60.000	34.28	25.93	40.20	3.36
27	28	1.816863	TTGTGAGCAGTCCGGACTCC	61.817	60.000	34.28	26.65	40.20	3.85
28	29	1.979693	GTGAGCAGTCCGGACTCCT	60.980	63.158	34.28	31.35	40.20	3.69
29	30	0.680280	GTGAGCAGTCCGGACTCCTA	60.680	60.000	34.28	17.51	40.20	2.94
30	31	0.680280	TGAGCAGTCCGGACTCCTAC	60.680	60.000	34.28	22.63	40.20	3.18
31	32	0.680280	GAGCAGTCCGGACTCCTACA	60.680	60.000	34.28	0.00	40.20	2.74
32	33	0.251653	AGCAGTCCGGACTCCTACAA	60.252	55.000	34.28	0.00	40.20	2.41
33	34	0.606604	GCAGTCCGGACTCCTACAAA	59.393	55.000	34.28	0.00	40.20	2.83
34	35	1.207329	GCAGTCCGGACTCCTACAAAT	59.793	52.381	34.28	7.85	40.20	2.32
35	36	2.738964	GCAGTCCGGACTCCTACAAATC	60.739	54.545	34.28	10.62	40.20	2.17
36	37	2.761208	CAGTCCGGACTCCTACAAATCT	59.239	50.000	34.28	6.43	40.20	2.40
37	38	3.195825	CAGTCCGGACTCCTACAAATCTT	59.804	47.826	34.28	6.20	40.20	2.40
38	39	3.838903	AGTCCGGACTCCTACAAATCTTT	59.161	43.478	31.69	4.17	36.92	2.52
39	40	4.286291	AGTCCGGACTCCTACAAATCTTTT	59.714	41.667	31.69	3.44	36.92	2.27
40	41	5.001874	GTCCGGACTCCTACAAATCTTTTT	58.998	41.667	27.64	0.00	0.00	1.94
62	63	7.743520	TTTTAGTTTTGTCTTTAGTTTGCGG	57.256	32.000	0.00	0.00	0.00	5.69
63	64	4.301637	AGTTTTGTCTTTAGTTTGCGGG	57.698	40.909	0.00	0.00	0.00	6.13
64	65	3.949113	AGTTTTGTCTTTAGTTTGCGGGA	59.051	39.130	0.00	0.00	0.00	5.14
65	66	4.036380	AGTTTTGTCTTTAGTTTGCGGGAG	59.964	41.667	0.00	0.00	0.00	4.30
66	67	3.478857	TTGTCTTTAGTTTGCGGGAGA	57.521	42.857	0.00	0.00	0.00	3.71
67	68	3.478857	TGTCTTTAGTTTGCGGGAGAA	57.521	42.857	0.00	0.00	0.00	2.87
68	69	3.811083	TGTCTTTAGTTTGCGGGAGAAA	58.189	40.909	0.00	0.00	0.00	2.52
69	70	4.394729	TGTCTTTAGTTTGCGGGAGAAAT	58.605	39.130	0.00	0.00	0.00	2.17

Showing 1 to 25 of 435 entries

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Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
7	8	0.389166	GAGTCCGGACTGCTCACAAG	60.389	60.000	40.88	0.00	42.66	3.16
10	11	2.574399	GGAGTCCGGACTGCTCAC	59.426	66.667	39.66	25.93	44.92	3.51
15	16	2.761208	AGATTTGTAGGAGTCCGGACTG	59.239	50.000	40.88	0.00	42.66	3.51
16	17	3.103080	AGATTTGTAGGAGTCCGGACT	57.897	47.619	36.89	36.89	45.84	3.85
17	18	3.889520	AAGATTTGTAGGAGTCCGGAC	57.110	47.619	27.67	27.67	0.00	4.79
18	19	4.903045	AAAAGATTTGTAGGAGTCCGGA	57.097	40.909	0.00	0.00	0.00	5.14
37	38	7.275999	CCCGCAAACTAAAGACAAAACTAAAAA	59.724	33.333	0.00	0.00	0.00	1.94
38	39	6.752815	CCCGCAAACTAAAGACAAAACTAAAA	59.247	34.615	0.00	0.00	0.00	1.52
39	40	6.095160	TCCCGCAAACTAAAGACAAAACTAAA	59.905	34.615	0.00	0.00	0.00	1.85
40	41	5.589452	TCCCGCAAACTAAAGACAAAACTAA	59.411	36.000	0.00	0.00	0.00	2.24
41	42	5.124645	TCCCGCAAACTAAAGACAAAACTA	58.875	37.500	0.00	0.00	0.00	2.24
42	43	3.949113	TCCCGCAAACTAAAGACAAAACT	59.051	39.130	0.00	0.00	0.00	2.66
43	44	4.035909	TCTCCCGCAAACTAAAGACAAAAC	59.964	41.667	0.00	0.00	0.00	2.43
44	45	4.200874	TCTCCCGCAAACTAAAGACAAAA	58.799	39.130	0.00	0.00	0.00	2.44
45	46	3.811083	TCTCCCGCAAACTAAAGACAAA	58.189	40.909	0.00	0.00	0.00	2.83
46	47	3.478857	TCTCCCGCAAACTAAAGACAA	57.521	42.857	0.00	0.00	0.00	3.18
47	48	3.478857	TTCTCCCGCAAACTAAAGACA	57.521	42.857	0.00	0.00	0.00	3.41
48	49	4.435651	CGATTTCTCCCGCAAACTAAAGAC	60.436	45.833	0.00	0.00	0.00	3.01
49	50	3.682858	CGATTTCTCCCGCAAACTAAAGA	59.317	43.478	0.00	0.00	0.00	2.52
50	51	3.435671	ACGATTTCTCCCGCAAACTAAAG	59.564	43.478	0.00	0.00	0.00	1.85
51	52	3.187637	CACGATTTCTCCCGCAAACTAAA	59.812	43.478	0.00	0.00	0.00	1.85
52	53	2.739913	CACGATTTCTCCCGCAAACTAA	59.260	45.455	0.00	0.00	0.00	2.24
53	54	2.289195	ACACGATTTCTCCCGCAAACTA	60.289	45.455	0.00	0.00	0.00	2.24
54	55	1.156736	CACGATTTCTCCCGCAAACT	58.843	50.000	0.00	0.00	0.00	2.66
55	56	0.872388	ACACGATTTCTCCCGCAAAC	59.128	50.000	0.00	0.00	0.00	2.93

Showing 1 to 25 of 428 entries

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Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.