AutoCloner

Multiple sequence alignment - TraesCS3A01G034700

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	TraesCS3A01G034700	chr3A	100.000	2735	0	0	1	2735	19475807	19473073	0.000000e+00	5051
1	TraesCS3A01G034700	chr3A	81.591	1999	187	78	859	2735	19371143	19373082	0.000000e+00	1485
2	TraesCS3A01G034700	chr3A	86.136	678	87	3	1062	1733	26396075	26396751	0.000000e+00	725
3	TraesCS3A01G034700	chr3A	85.347	662	77	14	1080	1730	26469246	26469898	0.000000e+00	667
4	TraesCS3A01G034700	chr3A	79.112	608	102	15	37	636	26415309	26415899	1.970000e-106	396
5	TraesCS3A01G034700	chr3A	80.322	559	75	20	61	618	19303441	19303965	9.180000e-105	390
6	TraesCS3A01G034700	chr3A	81.963	438	62	9	331	760	25937407	25936979	3.350000e-94	355
7	TraesCS3A01G034700	chr3A	77.815	595	94	25	37	622	26451514	26452079	1.570000e-87	333
8	TraesCS3A01G034700	chr3A	82.186	247	13	10	1845	2087	25935281	25935062	1.670000e-42	183
9	TraesCS3A01G034700	chr3A	80.645	248	18	14	1847	2087	19305136	19305360	6.060000e-37	165
10	TraesCS3A01G034700	chr3A	82.237	152	25	1	2562	2711	19306013	19306164	2.210000e-26	130
11	TraesCS3A01G034700	chr3D	87.868	2786	229	41	1	2735	17373365	17376092	0.000000e+00	3171
12	TraesCS3A01G034700	chr3D	78.697	2164	289	70	13	2070	17646382	17644285	0.000000e+00	1284
13	TraesCS3A01G034700	chr3D	83.582	1273	131	29	859	2085	17516952	17515712	0.000000e+00	1122
14	TraesCS3A01G034700	chr3D	78.434	728	124	15	35	757	18894729	18895428	6.950000e-121	444
15	TraesCS3A01G034700	chr3D	79.605	608	103	15	39	643	18881217	18881806	1.520000e-112	416
16	TraesCS3A01G034700	chr3D	74.629	607	134	15	10	609	18949814	18950407	1.630000e-62	250
17	TraesCS3A01G034700	chr3D	90.184	163	16	0	2180	2342	17515646	17515484	2.130000e-51	213
18	TraesCS3A01G034700	chr3D	75.355	422	47	25	2005	2400	11353322	11353712	1.700000e-32	150
19	TraesCS3A01G034700	chr3B	92.886	984	56	7	7	980	24940573	24941552	0.000000e+00	1417
20	TraesCS3A01G034700	chr3B	91.531	921	63	5	1040	1952	24941554	24942467	0.000000e+00	1254
21	TraesCS3A01G034700	chr3B	82.143	1568	151	49	859	2342	27516542	27518064	0.000000e+00	1225
22	TraesCS3A01G034700	chr3B	84.823	705	93	12	1034	1730	30231887	30232585	0.000000e+00	697
23	TraesCS3A01G034700	chr3B	92.151	344	23	1	2003	2342	24942485	24942828	1.470000e-132	483
24	TraesCS3A01G034700	chr3B	78.114	594	113	11	44	636	29618564	29619141	7.200000e-96	361
25	TraesCS3A01G034700	chr3B	87.500	120	12	2	639	757	27516359	27516476	4.750000e-28	135
26	TraesCS3A01G034700	chrUn	80.970	1072	140	25	852	1865	37955631	37956696	0.000000e+00	791
27	TraesCS3A01G034700	chrUn	75.947	607	63	35	1844	2401	37956753	37957325	4.550000e-58	235
28	TraesCS3A01G034700	chrUn	75.856	613	65	35	1844	2407	392408114	392407536	4.550000e-58	235

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	TraesCS3A01G034700	chr3A	19473073	19475807	2734	True	5051.000000	5051	100.000000	1	2735	1	chr3A.!!$R1	2734
1	TraesCS3A01G034700	chr3A	19371143	19373082	1939	False	1485.000000	1485	81.591000	859	2735	1	chr3A.!!$F1	1876
2	TraesCS3A01G034700	chr3A	26396075	26396751	676	False	725.000000	725	86.136000	1062	1733	1	chr3A.!!$F2	671
3	TraesCS3A01G034700	chr3A	26469246	26469898	652	False	667.000000	667	85.347000	1080	1730	1	chr3A.!!$F5	650
4	TraesCS3A01G034700	chr3A	26415309	26415899	590	False	396.000000	396	79.112000	37	636	1	chr3A.!!$F3	599
5	TraesCS3A01G034700	chr3A	26451514	26452079	565	False	333.000000	333	77.815000	37	622	1	chr3A.!!$F4	585
6	TraesCS3A01G034700	chr3A	25935062	25937407	2345	True	269.000000	355	82.074500	331	2087	2	chr3A.!!$R2	1756
7	TraesCS3A01G034700	chr3A	19303441	19306164	2723	False	228.333333	390	81.068000	61	2711	3	chr3A.!!$F6	2650
8	TraesCS3A01G034700	chr3D	17373365	17376092	2727	False	3171.000000	3171	87.868000	1	2735	1	chr3D.!!$F2	2734
9	TraesCS3A01G034700	chr3D	17644285	17646382	2097	True	1284.000000	1284	78.697000	13	2070	1	chr3D.!!$R1	2057
10	TraesCS3A01G034700	chr3D	17515484	17516952	1468	True	667.500000	1122	86.883000	859	2342	2	chr3D.!!$R2	1483
11	TraesCS3A01G034700	chr3D	18894729	18895428	699	False	444.000000	444	78.434000	35	757	1	chr3D.!!$F4	722
12	TraesCS3A01G034700	chr3D	18881217	18881806	589	False	416.000000	416	79.605000	39	643	1	chr3D.!!$F3	604
13	TraesCS3A01G034700	chr3D	18949814	18950407	593	False	250.000000	250	74.629000	10	609	1	chr3D.!!$F5	599
14	TraesCS3A01G034700	chr3B	24940573	24942828	2255	False	1051.333333	1417	92.189333	7	2342	3	chr3B.!!$F3	2335
15	TraesCS3A01G034700	chr3B	30231887	30232585	698	False	697.000000	697	84.823000	1034	1730	1	chr3B.!!$F2	696
16	TraesCS3A01G034700	chr3B	27516359	27518064	1705	False	680.000000	1225	84.821500	639	2342	2	chr3B.!!$F4	1703
17	TraesCS3A01G034700	chr3B	29618564	29619141	577	False	361.000000	361	78.114000	44	636	1	chr3B.!!$F1	592
18	TraesCS3A01G034700	chrUn	37955631	37957325	1694	False	513.000000	791	78.458500	852	2401	2	chrUn.!!$F1	1549
19	TraesCS3A01G034700	chrUn	392407536	392408114	578	True	235.000000	235	75.856000	1844	2407	1	chrUn.!!$R1	563

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
118	125	0.032515	TCGGGCTATGAGGAGAACCA	60.033	55.0	0.00	0.0	38.94	3.67	F
273	292	0.458543	GCTCGGCGACTTCAATCTCA	60.459	55.0	4.99	0.0	0.00	3.27	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1706	2394	0.460459	TTTCGTCAACTCACCGCACA	60.460	50.0	0.0	0.0	0.0	4.57	R
1737	2425	0.684153	AGGGAAATTCATGGTGGCGG	60.684	55.0	0.0	0.0	0.0	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)

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
118	125	0.032515	TCGGGCTATGAGGAGAACCA	60.033	55.000	0.00	0.00	38.94	3.67
131	144	3.181169	GAACCAGTGCGCGCAGTTT	62.181	57.895	37.21	29.17	0.00	2.66
273	292	0.458543	GCTCGGCGACTTCAATCTCA	60.459	55.000	4.99	0.00	0.00	3.27
381	403	0.647410	CATCTTCTACAACTGCGCCG	59.353	55.000	4.18	0.00	0.00	6.46
501	541	4.221422	TGATCGCCGGCAGCTACC	62.221	66.667	28.98	9.21	40.39	3.18
506	546	1.522806	CGCCGGCAGCTACCATTTA	60.523	57.895	28.98	0.00	40.39	1.40
711	762	1.223211	GCCTCAGCTTCCCTTCTCC	59.777	63.158	0.00	0.00	35.50	3.71
780	843	4.319133	CCATGGTTGGCGCTACTT	57.681	55.556	7.64	0.00	35.85	2.24
993	1621	2.204136	AGTCAGCCATCCCCACCA	60.204	61.111	0.00	0.00	0.00	4.17
1048	1679	1.080501	CTCCTGCTCGTCGCTTCAA	60.081	57.895	0.00	0.00	40.11	2.69
1055	1686	1.896345	CTCGTCGCTTCAATTCTCGA	58.104	50.000	0.00	0.00	0.00	4.04
1277	1911	2.125912	CTTCCTCGCCGTGGACAG	60.126	66.667	7.51	5.38	32.65	3.51
1339	1985	3.663815	ATCTCGCTGGGTCTCGGGT	62.664	63.158	0.00	0.00	0.00	5.28
1419	2086	4.680237	CAGAAGGTGACGCCGCCA	62.680	66.667	3.54	0.00	45.32	5.69
1656	2344	0.673644	GTCAGTGCAGGTACGCCAAT	60.674	55.000	0.00	0.00	37.19	3.16
1706	2394	1.664321	GGCGACGTGTACCCTGAGAT	61.664	60.000	0.00	0.00	0.00	2.75
1737	2425	6.627671	GTGAGTTGACGAAAATTAACTGACAC	59.372	38.462	0.00	0.00	37.27	3.67
1763	2457	5.203528	CCACCATGAATTTCCCTAGTCAAT	58.796	41.667	0.00	0.00	0.00	2.57
1766	2460	7.201821	CCACCATGAATTTCCCTAGTCAATAAC	60.202	40.741	0.00	0.00	0.00	1.89
1834	2553	0.179134	CGACCGATTCAGTGACTCCC	60.179	60.000	5.01	0.00	0.00	4.30
1876	2674	2.991190	CAATTTTGACACTGCCATCTGC	59.009	45.455	0.00	0.00	41.77	4.26
1952	2770	4.518211	GGAGGAACATAGAATGCTGATTGG	59.482	45.833	0.00	0.00	0.00	3.16
1953	2771	5.371526	GAGGAACATAGAATGCTGATTGGA	58.628	41.667	0.00	0.00	0.00	3.53
1954	2772	5.128919	AGGAACATAGAATGCTGATTGGAC	58.871	41.667	0.00	0.00	0.00	4.02
1955	2773	4.883585	GGAACATAGAATGCTGATTGGACA	59.116	41.667	0.00	0.00	0.00	4.02
1956	2774	5.220931	GGAACATAGAATGCTGATTGGACAC	60.221	44.000	0.00	0.00	0.00	3.67
1957	2775	5.108187	ACATAGAATGCTGATTGGACACT	57.892	39.130	0.00	0.00	0.00	3.55
1958	2776	4.880120	ACATAGAATGCTGATTGGACACTG	59.120	41.667	0.00	0.00	0.00	3.66
1959	2777	3.708403	AGAATGCTGATTGGACACTGA	57.292	42.857	0.00	0.00	0.00	3.41
1960	2778	4.232188	AGAATGCTGATTGGACACTGAT	57.768	40.909	0.00	0.00	0.00	2.90
1961	2779	5.363562	AGAATGCTGATTGGACACTGATA	57.636	39.130	0.00	0.00	0.00	2.15
1962	2780	5.938279	AGAATGCTGATTGGACACTGATAT	58.062	37.500	0.00	0.00	0.00	1.63
1963	2781	6.363065	AGAATGCTGATTGGACACTGATATT	58.637	36.000	0.00	0.00	0.00	1.28
1983	2817	9.950680	TGATATTTTGTTGTTCTTTCAACTCTC	57.049	29.630	10.18	1.39	45.26	3.20
1987	2821	9.710900	ATTTTGTTGTTCTTTCAACTCTCTTTT	57.289	25.926	10.18	0.00	45.26	2.27
1988	2822	9.541143	TTTTGTTGTTCTTTCAACTCTCTTTTT	57.459	25.926	10.18	0.00	45.26	1.94
2110	2944	1.706866	TGGATGATTGGAGCCTATGGG	59.293	52.381	0.00	0.00	0.00	4.00
2128	3140	4.853468	TGGGTTCCTAGTCAAATGCATA	57.147	40.909	0.00	0.00	0.00	3.14
2236	3280	1.541588	CTTACTTTTCTGTGCCCTGGC	59.458	52.381	0.00	0.00	42.35	4.85
2262	3313	5.229887	CGTTTTTCAAACATGTGGAAGTCAG	59.770	40.000	0.00	0.00	0.00	3.51
2263	3314	6.329496	GTTTTTCAAACATGTGGAAGTCAGA	58.671	36.000	0.00	0.00	0.00	3.27
2267	3318	4.576053	TCAAACATGTGGAAGTCAGAGTTG	59.424	41.667	0.00	0.00	0.00	3.16
2309	3460	6.661805	TGGAATTAGGGGTGTAAAGTTGAATC	59.338	38.462	0.00	0.00	0.00	2.52
2332	3483	2.949644	GGCACTGTGGTTAGTTTCAGTT	59.050	45.455	10.21	0.00	38.79	3.16
2342	3493	7.386848	TGTGGTTAGTTTCAGTTGATACTTAGC	59.613	37.037	9.87	10.71	37.48	3.09
2366	3528	2.427812	TGCTGATGCACATGGTAATTGG	59.572	45.455	0.00	0.00	45.31	3.16
2372	3534	3.767711	TGCACATGGTAATTGGGTGTTA	58.232	40.909	0.00	0.00	0.00	2.41
2373	3535	4.152647	TGCACATGGTAATTGGGTGTTAA	58.847	39.130	0.00	0.00	0.00	2.01
2384	3550	6.664428	AATTGGGTGTTAACACTGCTTAAT	57.336	33.333	31.82	21.77	45.73	1.40
2385	3551	5.446143	TTGGGTGTTAACACTGCTTAATG	57.554	39.130	31.82	0.00	45.73	1.90
2401	3567	4.274459	GCTTAATGAGTGCAGAATAGTGGG	59.726	45.833	0.00	0.00	0.00	4.61
2443	3621	5.410067	GCAGCTTACAGCATTCCATTTAAA	58.590	37.500	0.00	0.00	45.56	1.52
2490	3680	7.552050	AGCTAGCTTCAATGGAACTATCTAT	57.448	36.000	12.68	0.00	0.00	1.98
2502	3692	9.965902	AATGGAACTATCTATTCAACTCTGTTT	57.034	29.630	0.00	0.00	31.78	2.83
2608	3810	7.672660	TCTGGTGTCACTTTTAGGATCTAAGTA	59.327	37.037	2.35	0.00	31.30	2.24
2660	3871	6.967135	TCTTAGTATACATTGCTACCGTCAG	58.033	40.000	5.50	0.00	0.00	3.51
2664	3875	2.543777	ACATTGCTACCGTCAGTTGT	57.456	45.000	0.00	0.00	0.00	3.32
2667	3878	2.148916	TTGCTACCGTCAGTTGTGAG	57.851	50.000	0.00	0.00	31.53	3.51
2704	3915	6.662865	TGTTGCTGGATTTTCCTCATTAAA	57.337	33.333	0.00	0.00	37.46	1.52
2724	3935	2.561569	ACAGTCACAAAAGGGAGTTCG	58.438	47.619	0.00	0.00	0.00	3.95
2731	3942	5.469084	GTCACAAAAGGGAGTTCGACTTTAT	59.531	40.000	0.00	0.00	33.64	1.40

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
106	113	1.078848	GCGCACTGGTTCTCCTCAT	60.079	57.895	0.30	0.00	34.23	2.90
131	144	2.829384	GCAGTGGACCTGGAACCCA	61.829	63.158	0.00	1.66	41.81	4.51
194	210	5.363562	AGAATATGTTGAGGATCTGCACA	57.636	39.130	0.00	0.00	34.92	4.57
195	211	6.283694	TGTAGAATATGTTGAGGATCTGCAC	58.716	40.000	0.00	0.00	34.92	4.57
501	541	1.136565	CGTTGCAGCCCGGTAAATG	59.863	57.895	0.00	0.00	0.00	2.32
546	586	1.304381	TGGCATTCACCTTCCCAGC	60.304	57.895	0.00	0.00	0.00	4.85
711	762	0.175302	TAATTTTGCATGGCCCGCTG	59.825	50.000	14.73	4.42	0.00	5.18
861	943	3.860536	GGTCAGAGTCAACGCTCTATTTC	59.139	47.826	0.00	0.00	43.37	2.17
993	1621	4.802051	AGCGGCGGCATGGATTGT	62.802	61.111	19.21	0.00	43.41	2.71
1048	1679	4.880537	CGCCGGCAGCTCGAGAAT	62.881	66.667	28.98	0.00	40.39	2.40
1339	1985	1.668919	GCTGATGACGAACGGACTCAA	60.669	52.381	0.00	0.00	0.00	3.02
1419	2086	4.636435	CCCGTGCGGTTGAACCCT	62.636	66.667	9.08	0.00	33.75	4.34
1638	2326	0.673333	CATTGGCGTACCTGCACTGA	60.673	55.000	0.00	0.00	36.63	3.41
1656	2344	2.592287	GAAAACCCGGTGCCGTCA	60.592	61.111	9.90	0.00	37.81	4.35
1706	2394	0.460459	TTTCGTCAACTCACCGCACA	60.460	50.000	0.00	0.00	0.00	4.57
1737	2425	0.684153	AGGGAAATTCATGGTGGCGG	60.684	55.000	0.00	0.00	0.00	6.13
1770	2464	6.261158	GGGGATTAGCTTGATCAAAGAACTAC	59.739	42.308	9.88	0.00	38.24	2.73
1876	2674	3.189080	TGTTCTTGACAGCGATTCAATGG	59.811	43.478	0.00	0.00	32.57	3.16
1952	2770	9.515020	TTGAAAGAACAACAAAATATCAGTGTC	57.485	29.630	0.00	0.00	0.00	3.67
1953	2771	9.301153	GTTGAAAGAACAACAAAATATCAGTGT	57.699	29.630	0.00	0.00	46.19	3.55
1997	2831	3.893326	AACCAAGCAAGCACTCTTTTT	57.107	38.095	0.00	0.00	0.00	1.94
1998	2832	3.448660	AGAAACCAAGCAAGCACTCTTTT	59.551	39.130	0.00	0.00	0.00	2.27
1999	2833	3.026694	AGAAACCAAGCAAGCACTCTTT	58.973	40.909	0.00	0.00	0.00	2.52
2000	2834	2.659428	AGAAACCAAGCAAGCACTCTT	58.341	42.857	0.00	0.00	0.00	2.85
2001	2835	2.355010	AGAAACCAAGCAAGCACTCT	57.645	45.000	0.00	0.00	0.00	3.24
2110	2944	7.320443	TCAACATATGCATTTGACTAGGAAC	57.680	36.000	21.91	0.00	0.00	3.62
2236	3280	3.444703	TCCACATGTTTGAAAAACGGG	57.555	42.857	0.00	0.00	0.00	5.28
2309	3460	0.872388	GAAACTAACCACAGTGCCCG	59.128	55.000	0.00	0.00	0.00	6.13
2332	3483	2.803133	GCATCAGCACCGCTAAGTATCA	60.803	50.000	0.00	0.00	36.40	2.15
2384	3550	0.253044	GCCCCACTATTCTGCACTCA	59.747	55.000	0.00	0.00	0.00	3.41
2385	3551	0.811616	CGCCCCACTATTCTGCACTC	60.812	60.000	0.00	0.00	0.00	3.51
2443	3621	3.084786	GGTGCCTTGCTACAGAGAAATT	58.915	45.455	0.00	0.00	0.00	1.82
2455	3633	1.246737	AAGCTAGCTTGGTGCCTTGC	61.247	55.000	28.83	0.00	44.23	4.01
2490	3680	8.879342	TTTTCAAGAAAACAAACAGAGTTGAA	57.121	26.923	3.98	0.00	35.57	2.69
2552	3742	5.133221	GGATTCATACATTTGGCAGTAGGT	58.867	41.667	0.00	0.00	0.00	3.08
2556	3746	3.620488	ACGGATTCATACATTTGGCAGT	58.380	40.909	0.00	0.00	0.00	4.40
2559	3749	7.379529	CAGAAATAACGGATTCATACATTTGGC	59.620	37.037	0.00	0.00	0.00	4.52
2560	3750	7.862372	CCAGAAATAACGGATTCATACATTTGG	59.138	37.037	0.00	0.00	0.00	3.28
2608	3810	7.834881	AATTCATAGAAGCCACAATCATGAT	57.165	32.000	1.18	1.18	0.00	2.45
2652	3863	2.578786	TCAGACTCACAACTGACGGTA	58.421	47.619	0.00	0.00	38.08	4.02
2656	3867	5.991328	TGAATTTCAGACTCACAACTGAC	57.009	39.130	0.00	0.00	41.82	3.51
2704	3915	2.169769	TCGAACTCCCTTTTGTGACTGT	59.830	45.455	0.00	0.00	0.00	3.55

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.