AutoCloner

Multiple sequence alignment - TraesCS2B01G162700

Loading Multiple Alignment...

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	TraesCS2B01G162700	chr2B	100.000	2927	0	0	1	2927	135197225	135200151	0.000000e+00	5406.0
1	TraesCS2B01G162700	chr2B	93.872	2350	101	19	593	2927	182153548	182151227	0.000000e+00	3502.0
2	TraesCS2B01G162700	chr2B	90.815	2515	154	44	443	2927	135357595	135360062	0.000000e+00	3293.0
3	TraesCS2B01G162700	chr2B	92.188	2240	82	50	590	2781	135463419	135465613	0.000000e+00	3081.0
4	TraesCS2B01G162700	chr2B	92.620	1992	79	26	811	2783	135126679	135128621	0.000000e+00	2802.0
5	TraesCS2B01G162700	chr2B	89.163	1744	125	33	830	2547	137814510	137812805	0.000000e+00	2115.0
6	TraesCS2B01G162700	chr2B	89.043	1734	127	32	837	2547	137349337	137347644	0.000000e+00	2091.0
7	TraesCS2B01G162700	chr2B	95.439	285	13	0	306	590	182153943	182153659	3.440000e-124	455.0
8	TraesCS2B01G162700	chr2B	86.856	388	32	7	18	389	182161932	182161548	1.620000e-112	416.0
9	TraesCS2B01G162700	chr2B	93.532	201	13	0	1	201	182156641	182156441	1.710000e-77	300.0
10	TraesCS2B01G162700	chr2B	92.623	122	9	0	186	307	182154161	182154040	3.000000e-40	176.0
11	TraesCS2B01G162700	chr2B	83.505	97	9	1	2838	2927	135515489	135515585	1.870000e-12	84.2
12	TraesCS2B01G162700	chr2D	95.332	2271	59	17	675	2927	83225071	83227312	0.000000e+00	3563.0
13	TraesCS2B01G162700	chr2D	91.354	2556	127	45	433	2927	83187978	83190500	0.000000e+00	3410.0
14	TraesCS2B01G162700	chr2D	92.286	1050	58	14	1656	2689	83530715	83531757	0.000000e+00	1469.0
15	TraesCS2B01G162700	chr2D	92.637	910	50	5	729	1632	83529823	83530721	0.000000e+00	1293.0
16	TraesCS2B01G162700	chr2D	82.781	151	18	7	389	533	4779577	4779725	8.510000e-26	128.0
17	TraesCS2B01G162700	chr2D	82.781	151	18	7	389	533	4822122	4822270	8.510000e-26	128.0
18	TraesCS2B01G162700	chr2D	82.119	151	20	6	389	533	4737076	4737225	3.960000e-24	122.0
19	TraesCS2B01G162700	chr2A	91.663	2087	101	30	808	2870	83984965	83987002	0.000000e+00	2822.0
20	TraesCS2B01G162700	chr2A	87.342	1746	135	45	813	2547	86062003	86060333	0.000000e+00	1921.0
21	TraesCS2B01G162700	chr2A	93.116	828	51	1	811	1632	134867511	134866684	0.000000e+00	1208.0
22	TraesCS2B01G162700	chr2A	91.736	121	5	2	2525	2641	84231272	84231391	2.330000e-36	163.0
23	TraesCS2B01G162700	chr2A	74.931	363	62	19	433	769	83984601	83984960	3.930000e-29	139.0
24	TraesCS2B01G162700	chr2A	84.956	113	10	1	2822	2927	83992267	83992379	1.110000e-19	108.0
25	TraesCS2B01G162700	chr5A	91.088	1066	66	21	1656	2704	326437152	326436099	0.000000e+00	1415.0
26	TraesCS2B01G162700	chr5A	93.599	828	46	3	811	1632	326437972	326437146	0.000000e+00	1229.0
27	TraesCS2B01G162700	chr5A	84.884	86	13	0	30	115	362724043	362724128	1.450000e-13	87.9
28	TraesCS2B01G162700	chrUn	89.825	629	39	13	2316	2927	25418011	25417391	0.000000e+00	784.0
29	TraesCS2B01G162700	chrUn	91.711	567	27	10	675	1240	362506287	362506834	0.000000e+00	769.0
30	TraesCS2B01G162700	chr7B	79.259	270	41	12	390	650	339033112	339033375	1.080000e-39	174.0
31	TraesCS2B01G162700	chr7B	84.211	114	14	4	22	134	270524043	270524153	1.110000e-19	108.0
32	TraesCS2B01G162700	chr1A	79.835	243	35	9	390	623	234226996	234227233	6.490000e-37	165.0

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	TraesCS2B01G162700	chr2B	135197225	135200151	2926	False	5406.00	5406	100.0000	1	2927	1	chr2B.!!$F2	2926
1	TraesCS2B01G162700	chr2B	135357595	135360062	2467	False	3293.00	3293	90.8150	443	2927	1	chr2B.!!$F3	2484
2	TraesCS2B01G162700	chr2B	135463419	135465613	2194	False	3081.00	3081	92.1880	590	2781	1	chr2B.!!$F4	2191
3	TraesCS2B01G162700	chr2B	135126679	135128621	1942	False	2802.00	2802	92.6200	811	2783	1	chr2B.!!$F1	1972
4	TraesCS2B01G162700	chr2B	137812805	137814510	1705	True	2115.00	2115	89.1630	830	2547	1	chr2B.!!$R2	1717
5	TraesCS2B01G162700	chr2B	137347644	137349337	1693	True	2091.00	2091	89.0430	837	2547	1	chr2B.!!$R1	1710
6	TraesCS2B01G162700	chr2B	182151227	182156641	5414	True	1108.25	3502	93.8665	1	2927	4	chr2B.!!$R4	2926
7	TraesCS2B01G162700	chr2D	83225071	83227312	2241	False	3563.00	3563	95.3320	675	2927	1	chr2D.!!$F5	2252
8	TraesCS2B01G162700	chr2D	83187978	83190500	2522	False	3410.00	3410	91.3540	433	2927	1	chr2D.!!$F4	2494
9	TraesCS2B01G162700	chr2D	83529823	83531757	1934	False	1381.00	1469	92.4615	729	2689	2	chr2D.!!$F6	1960
10	TraesCS2B01G162700	chr2A	86060333	86062003	1670	True	1921.00	1921	87.3420	813	2547	1	chr2A.!!$R1	1734
11	TraesCS2B01G162700	chr2A	83984601	83987002	2401	False	1480.50	2822	83.2970	433	2870	2	chr2A.!!$F3	2437
12	TraesCS2B01G162700	chr2A	134866684	134867511	827	True	1208.00	1208	93.1160	811	1632	1	chr2A.!!$R2	821
13	TraesCS2B01G162700	chr5A	326436099	326437972	1873	True	1322.00	1415	92.3435	811	2704	2	chr5A.!!$R1	1893
14	TraesCS2B01G162700	chrUn	25417391	25418011	620	True	784.00	784	89.8250	2316	2927	1	chrUn.!!$R1	611
15	TraesCS2B01G162700	chrUn	362506287	362506834	547	False	769.00	769	91.7110	675	1240	1	chrUn.!!$F1	565

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
39	40	0.259938	AAGAATGGGGCATGGGAGAC	59.740	55.0	0.00	0.0	0.00	3.36	F
284	2580	0.321653	GTGCTGACCGGTCATTCCTT	60.322	55.0	36.21	0.0	39.13	3.36	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1899	4485	0.174162	GGCGTAATACCACTGGACGT	59.826	55.000	0.71	0.0	35.97	4.34	R
2056	4644	1.824230	GATGGAGACTCTGCTGACACT	59.176	52.381	1.74	0.0	0.00	3.55	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
39	40	0.259938	AAGAATGGGGCATGGGAGAC	59.740	55.000	0.00	0.00	0.00	3.36
77	78	2.340078	GAGCCAGTGCGTGTCTCA	59.660	61.111	0.00	0.00	44.33	3.27
123	124	2.203294	ACCAACACTTCGTGGGGC	60.203	61.111	6.81	0.00	37.94	5.80
164	165	1.963855	CATGGCCGGAACAACACGA	60.964	57.895	5.05	0.00	0.00	4.35
230	2526	8.570488	TGTAATCTTATGGATGTGATGATTTGC	58.430	33.333	0.00	0.00	34.45	3.68
284	2580	0.321653	GTGCTGACCGGTCATTCCTT	60.322	55.000	36.21	0.00	39.13	3.36
569	2990	1.547372	ACATCATTTTGGGCTGTGCTC	59.453	47.619	0.00	0.00	0.00	4.26
587	3008	4.676924	GTGCTCAAGAACAATGCTACAAAC	59.323	41.667	0.00	0.00	0.00	2.93
862	3415	3.712016	TCGATCCCAGTTCCAATTCAA	57.288	42.857	0.00	0.00	0.00	2.69
1113	3675	4.100084	CTGGAGATGCGGGTGCCA	62.100	66.667	0.00	0.00	41.78	4.92
1830	4416	1.601759	GCTCAGCTGCAAGGTTCCA	60.602	57.895	9.47	0.00	46.63	3.53
2833	5499	9.251792	CAATCTGATTGTCAAGAATGTGAAAAA	57.748	29.630	19.74	0.00	35.57	1.94
2834	5500	9.472361	AATCTGATTGTCAAGAATGTGAAAAAG	57.528	29.630	1.31	0.00	28.59	2.27
2835	5501	7.428020	TCTGATTGTCAAGAATGTGAAAAAGG	58.572	34.615	0.00	0.00	28.59	3.11
2836	5502	7.068593	TCTGATTGTCAAGAATGTGAAAAAGGT	59.931	33.333	0.00	0.00	28.59	3.50
2837	5503	7.555087	TGATTGTCAAGAATGTGAAAAAGGTT	58.445	30.769	0.00	0.00	28.59	3.50
2838	5504	7.492020	TGATTGTCAAGAATGTGAAAAAGGTTG	59.508	33.333	0.00	0.00	28.59	3.77
2839	5505	5.108517	TGTCAAGAATGTGAAAAAGGTTGC	58.891	37.500	0.00	0.00	0.00	4.17
2840	5506	5.108517	GTCAAGAATGTGAAAAAGGTTGCA	58.891	37.500	0.00	0.00	0.00	4.08
2841	5507	5.232838	GTCAAGAATGTGAAAAAGGTTGCAG	59.767	40.000	0.00	0.00	0.00	4.41
2842	5508	3.721035	AGAATGTGAAAAAGGTTGCAGC	58.279	40.909	0.00	0.00	0.00	5.25
2843	5509	3.385755	AGAATGTGAAAAAGGTTGCAGCT	59.614	39.130	0.00	0.00	0.00	4.24
2844	5510	2.582728	TGTGAAAAAGGTTGCAGCTG	57.417	45.000	10.11	10.11	0.00	4.24
2845	5511	1.824230	TGTGAAAAAGGTTGCAGCTGT	59.176	42.857	16.64	0.00	0.00	4.40
2846	5512	2.233431	TGTGAAAAAGGTTGCAGCTGTT	59.767	40.909	16.64	0.00	0.00	3.16
2847	5513	3.261580	GTGAAAAAGGTTGCAGCTGTTT	58.738	40.909	16.64	5.73	35.98	2.83
2848	5514	3.062504	GTGAAAAAGGTTGCAGCTGTTTG	59.937	43.478	16.64	0.00	33.64	2.93
2849	5515	2.314323	AAAAGGTTGCAGCTGTTTGG	57.686	45.000	16.64	0.00	0.00	3.28
2850	5516	0.179076	AAAGGTTGCAGCTGTTTGGC	60.179	50.000	16.64	0.00	0.00	4.52
2851	5517	1.329171	AAGGTTGCAGCTGTTTGGCA	61.329	50.000	16.64	3.15	35.41	4.92
2852	5518	1.143620	GGTTGCAGCTGTTTGGCAA	59.856	52.632	16.64	10.04	44.50	4.52

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
12	13	3.436906	CCATGCCCCATTCTTCCTCATTA	60.437	47.826	0.00	0.00	0.00	1.90
13	14	2.674420	CATGCCCCATTCTTCCTCATT	58.326	47.619	0.00	0.00	0.00	2.57
45	46	1.803519	GCTCACAGGACTCGAAGCG	60.804	63.158	0.00	0.00	0.00	4.68
57	58	2.280119	GACACGCACTGGCTCACA	60.280	61.111	0.00	0.00	38.10	3.58
77	78	1.887198	CGGCGAGGTAGAATAGGACAT	59.113	52.381	0.00	0.00	0.00	3.06
128	129	0.110295	TGTCCATATCCAATGGCCGG	59.890	55.000	0.00	0.00	39.01	6.13
136	137	0.766288	TCCGGCCATGTCCATATCCA	60.766	55.000	2.24	0.00	0.00	3.41
140	141	0.621082	TTGTTCCGGCCATGTCCATA	59.379	50.000	2.24	0.00	0.00	2.74
164	165	1.869342	GCATTTTTGCCTGCGACTGTT	60.869	47.619	0.00	0.00	0.00	3.16
230	2526	1.340889	CATAACCGGATGGCCCATTTG	59.659	52.381	9.46	0.00	39.70	2.32
256	2552	1.754226	ACCGGTCAGCACACAATTTTT	59.246	42.857	0.00	0.00	0.00	1.94
257	2553	1.336755	GACCGGTCAGCACACAATTTT	59.663	47.619	29.75	0.00	0.00	1.82
258	2554	0.951558	GACCGGTCAGCACACAATTT	59.048	50.000	29.75	0.00	0.00	1.82
259	2555	0.179032	TGACCGGTCAGCACACAATT	60.179	50.000	33.23	0.00	34.14	2.32
260	2556	0.036732	ATGACCGGTCAGCACACAAT	59.963	50.000	37.98	19.28	43.61	2.71
273	2569	0.734889	GCATGTCCAAGGAATGACCG	59.265	55.000	12.43	0.00	44.74	4.79
310	2704	8.723942	ACAGGCTTCATACTTATTACTTTCTG	57.276	34.615	0.00	0.00	0.00	3.02
320	2714	9.817809	CAGAATTAGTTACAGGCTTCATACTTA	57.182	33.333	0.00	0.00	0.00	2.24
486	2884	7.973388	GGCATGTACTGAATTTTGCTGTTTATA	59.027	33.333	0.00	0.00	0.00	0.98
619	3148	8.000171	TGGCTAATATGGATTTAGGGAGATTT	58.000	34.615	0.00	0.00	0.00	2.17
862	3415	3.665675	GATTGGAGCTGTCGCCGGT	62.666	63.158	1.90	0.00	34.60	5.28
974	3530	0.387202	CGTGCCTAGGTCTGGAGATG	59.613	60.000	11.31	0.00	0.00	2.90
1030	3592	4.681978	GAGCACCTTGCCGTCGGT	62.682	66.667	13.94	0.00	46.52	4.69
1571	4139	0.812549	GGACTCCTCGTCTTCAGTCC	59.187	60.000	1.31	1.31	46.26	3.85
1573	4141	1.587933	GCGGACTCCTCGTCTTCAGT	61.588	60.000	0.00	0.00	42.44	3.41
1612	4180	2.034221	GGAAGCCTTGGAAGCCGT	59.966	61.111	0.00	0.00	0.00	5.68
1830	4416	2.807392	CAATGGCGATTGGTTTTGCTTT	59.193	40.909	13.19	0.00	36.12	3.51
1899	4485	0.174162	GGCGTAATACCACTGGACGT	59.826	55.000	0.71	0.00	35.97	4.34
2056	4644	1.824230	GATGGAGACTCTGCTGACACT	59.176	52.381	1.74	0.00	0.00	3.55
2833	5499	1.329171	TTGCCAAACAGCTGCAACCT	61.329	50.000	15.27	0.00	39.86	3.50
2834	5500	0.461693	TTTGCCAAACAGCTGCAACC	60.462	50.000	15.27	0.00	44.02	3.77
2835	5501	1.585297	ATTTGCCAAACAGCTGCAAC	58.415	45.000	15.27	0.00	44.02	4.17
2836	5502	2.288948	CCTATTTGCCAAACAGCTGCAA	60.289	45.455	15.27	9.15	42.77	4.08
2837	5503	1.273048	CCTATTTGCCAAACAGCTGCA	59.727	47.619	15.27	1.80	0.00	4.41
2838	5504	1.273327	ACCTATTTGCCAAACAGCTGC	59.727	47.619	15.27	0.00	0.00	5.25
2839	5505	3.319755	CAACCTATTTGCCAAACAGCTG	58.680	45.455	13.48	13.48	0.00	4.24
2840	5506	2.299867	CCAACCTATTTGCCAAACAGCT	59.700	45.455	0.00	0.00	33.34	4.24
2841	5507	2.612721	CCCAACCTATTTGCCAAACAGC	60.613	50.000	0.00	0.00	33.34	4.40
2842	5508	2.632512	ACCCAACCTATTTGCCAAACAG	59.367	45.455	0.00	0.00	33.34	3.16
2843	5509	2.683768	ACCCAACCTATTTGCCAAACA	58.316	42.857	0.00	0.00	33.34	2.83
2844	5510	3.762407	AACCCAACCTATTTGCCAAAC	57.238	42.857	0.00	0.00	33.34	2.93
2845	5511	4.779993	AAAACCCAACCTATTTGCCAAA	57.220	36.364	0.00	0.00	33.34	3.28
2846	5512	4.410555	AGAAAAACCCAACCTATTTGCCAA	59.589	37.500	0.00	0.00	33.34	4.52
2847	5513	3.970640	AGAAAAACCCAACCTATTTGCCA	59.029	39.130	0.00	0.00	33.34	4.92
2848	5514	4.039852	TGAGAAAAACCCAACCTATTTGCC	59.960	41.667	0.00	0.00	33.34	4.52
2849	5515	5.010617	TCTGAGAAAAACCCAACCTATTTGC	59.989	40.000	0.00	0.00	33.34	3.68
2850	5516	6.648879	TCTGAGAAAAACCCAACCTATTTG	57.351	37.500	0.00	0.00	34.63	2.32
2851	5517	7.010160	TGATCTGAGAAAAACCCAACCTATTT	58.990	34.615	0.00	0.00	0.00	1.40
2852	5518	6.552008	TGATCTGAGAAAAACCCAACCTATT	58.448	36.000	0.00	0.00	0.00	1.73

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.