AutoCloner

Multiple sequence alignment - TraesCS3B01G069900

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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	TraesCS3B01G069900	chr3B	100.000	3635	0	0	1	3635	41799392	41803026	0.000000e+00	6713.0
1	TraesCS3B01G069900	chr3B	97.383	2828	40	4	1	2820	42049127	42046326	0.000000e+00	4782.0
2	TraesCS3B01G069900	chr3B	87.936	1376	147	17	1256	2617	42125661	42127031	0.000000e+00	1604.0
3	TraesCS3B01G069900	chr3B	85.704	1350	165	20	1283	2617	41015513	41014177	0.000000e+00	1399.0
4	TraesCS3B01G069900	chr3B	94.643	224	12	0	961	1184	42125438	42125661	7.470000e-92	348.0
5	TraesCS3B01G069900	chr3B	91.561	237	20	0	948	1184	41015776	41015540	9.730000e-86	327.0
6	TraesCS3B01G069900	chr3D	95.969	1910	68	6	916	2820	23857804	23859709	0.000000e+00	3092.0
7	TraesCS3B01G069900	chr3D	87.709	1375	143	20	1262	2617	23730796	23729429	0.000000e+00	1580.0
8	TraesCS3B01G069900	chr3D	85.957	1353	163	21	1283	2617	23230537	23229194	0.000000e+00	1421.0
9	TraesCS3B01G069900	chr3D	92.903	310	19	3	1	308	23856829	23857137	7.160000e-122	448.0
10	TraesCS3B01G069900	chr3D	92.339	248	16	3	938	1184	23731047	23730802	2.080000e-92	350.0
11	TraesCS3B01G069900	chr3D	87.072	263	31	1	925	1184	23230826	23230564	9.870000e-76	294.0
12	TraesCS3B01G069900	chr3D	88.742	151	5	4	758	902	23857408	23857552	1.340000e-39	174.0
13	TraesCS3B01G069900	chr3D	90.083	121	6	1	340	454	23857136	23857256	6.290000e-33	152.0
14	TraesCS3B01G069900	chr3D	96.512	86	2	1	687	771	23857295	23857380	1.360000e-29	141.0
15	TraesCS3B01G069900	chrUn	100.000	1383	0	0	1	1383	373566444	373565062	0.000000e+00	2555.0
16	TraesCS3B01G069900	chr2A	88.792	1374	133	20	1259	2617	672946345	672944978	0.000000e+00	1664.0
17	TraesCS3B01G069900	chr2D	88.501	1374	137	19	1259	2617	528099793	528098426	0.000000e+00	1642.0
18	TraesCS3B01G069900	chr2D	85.507	276	31	7	4	275	420735616	420735346	2.760000e-71	279.0
19	TraesCS3B01G069900	chr3A	88.099	1378	138	21	1259	2617	32876252	32874882	0.000000e+00	1613.0
20	TraesCS3B01G069900	chr3A	85.797	1380	169	21	1256	2617	32426647	32428017	0.000000e+00	1437.0
21	TraesCS3B01G069900	chr3A	93.304	224	15	0	961	1184	32876478	32876255	7.520000e-87	331.0
22	TraesCS3B01G069900	chr3A	89.434	265	23	2	925	1184	32426383	32426647	2.710000e-86	329.0
23	TraesCS3B01G069900	chr2B	87.991	1374	144	20	1259	2617	626091771	626090404	0.000000e+00	1604.0
24	TraesCS3B01G069900	chr6B	94.370	817	46	0	2818	3634	337861067	337861883	0.000000e+00	1254.0
25	TraesCS3B01G069900	chr6B	93.873	816	49	1	2819	3634	315288891	315288077	0.000000e+00	1229.0
26	TraesCS3B01G069900	chr6B	93.382	816	50	3	2820	3634	171434907	171435719	0.000000e+00	1205.0
27	TraesCS3B01G069900	chr6B	93.162	819	54	2	2817	3634	696192662	696191845	0.000000e+00	1201.0
28	TraesCS3B01G069900	chr5A	93.888	818	48	2	2817	3634	706704403	706703588	0.000000e+00	1232.0
29	TraesCS3B01G069900	chr5A	84.141	227	31	5	4	228	665075459	665075236	7.910000e-52	215.0
30	TraesCS3B01G069900	chr5A	82.008	239	40	3	12	250	444037525	444037290	2.210000e-47	200.0
31	TraesCS3B01G069900	chr5A	90.698	43	4	0	2737	2779	559838146	559838188	1.410000e-04	58.4
32	TraesCS3B01G069900	chr4B	93.620	815	51	1	2820	3634	404768903	404768090	0.000000e+00	1216.0
33	TraesCS3B01G069900	chr7B	93.497	815	49	4	2823	3634	695091658	695090845	0.000000e+00	1208.0
34	TraesCS3B01G069900	chr7A	93.284	819	51	4	2819	3634	709956928	709957745	0.000000e+00	1205.0
35	TraesCS3B01G069900	chr7A	91.057	123	11	0	324	446	46217628	46217506	2.250000e-37	167.0
36	TraesCS3B01G069900	chr1A	93.074	823	52	4	2815	3634	50685146	50684326	0.000000e+00	1199.0
37	TraesCS3B01G069900	chr7D	82.101	257	39	7	1	254	28543233	28543485	2.840000e-51	213.0
38	TraesCS3B01G069900	chr1D	81.890	254	37	7	23	271	483383617	483383368	4.760000e-49	206.0
39	TraesCS3B01G069900	chr5B	80.843	261	37	12	1	254	674489290	674489544	3.700000e-45	193.0

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	TraesCS3B01G069900	chr3B	41799392	41803026	3634	False	6713.0	6713	100.0000	1	3635	1	chr3B.!!$F1	3634
1	TraesCS3B01G069900	chr3B	42046326	42049127	2801	True	4782.0	4782	97.3830	1	2820	1	chr3B.!!$R1	2819
2	TraesCS3B01G069900	chr3B	42125438	42127031	1593	False	976.0	1604	91.2895	961	2617	2	chr3B.!!$F2	1656
3	TraesCS3B01G069900	chr3B	41014177	41015776	1599	True	863.0	1399	88.6325	948	2617	2	chr3B.!!$R2	1669
4	TraesCS3B01G069900	chr3D	23729429	23731047	1618	True	965.0	1580	90.0240	938	2617	2	chr3D.!!$R2	1679
5	TraesCS3B01G069900	chr3D	23229194	23230826	1632	True	857.5	1421	86.5145	925	2617	2	chr3D.!!$R1	1692
6	TraesCS3B01G069900	chr3D	23856829	23859709	2880	False	801.4	3092	92.8418	1	2820	5	chr3D.!!$F1	2819
7	TraesCS3B01G069900	chrUn	373565062	373566444	1382	True	2555.0	2555	100.0000	1	1383	1	chrUn.!!$R1	1382
8	TraesCS3B01G069900	chr2A	672944978	672946345	1367	True	1664.0	1664	88.7920	1259	2617	1	chr2A.!!$R1	1358
9	TraesCS3B01G069900	chr2D	528098426	528099793	1367	True	1642.0	1642	88.5010	1259	2617	1	chr2D.!!$R2	1358
10	TraesCS3B01G069900	chr3A	32874882	32876478	1596	True	972.0	1613	90.7015	961	2617	2	chr3A.!!$R1	1656
11	TraesCS3B01G069900	chr3A	32426383	32428017	1634	False	883.0	1437	87.6155	925	2617	2	chr3A.!!$F1	1692
12	TraesCS3B01G069900	chr2B	626090404	626091771	1367	True	1604.0	1604	87.9910	1259	2617	1	chr2B.!!$R1	1358
13	TraesCS3B01G069900	chr6B	337861067	337861883	816	False	1254.0	1254	94.3700	2818	3634	1	chr6B.!!$F2	816
14	TraesCS3B01G069900	chr6B	315288077	315288891	814	True	1229.0	1229	93.8730	2819	3634	1	chr6B.!!$R1	815
15	TraesCS3B01G069900	chr6B	171434907	171435719	812	False	1205.0	1205	93.3820	2820	3634	1	chr6B.!!$F1	814
16	TraesCS3B01G069900	chr6B	696191845	696192662	817	True	1201.0	1201	93.1620	2817	3634	1	chr6B.!!$R2	817
17	TraesCS3B01G069900	chr5A	706703588	706704403	815	True	1232.0	1232	93.8880	2817	3634	1	chr5A.!!$R3	817
18	TraesCS3B01G069900	chr4B	404768090	404768903	813	True	1216.0	1216	93.6200	2820	3634	1	chr4B.!!$R1	814
19	TraesCS3B01G069900	chr7B	695090845	695091658	813	True	1208.0	1208	93.4970	2823	3634	1	chr7B.!!$R1	811
20	TraesCS3B01G069900	chr7A	709956928	709957745	817	False	1205.0	1205	93.2840	2819	3634	1	chr7A.!!$F1	815
21	TraesCS3B01G069900	chr1A	50684326	50685146	820	True	1199.0	1199	93.0740	2815	3634	1	chr1A.!!$R1	819

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
1383	1693	2.261671	CTGTACCTGGTCGCGCTT	59.738	61.111	0.63	0.0	0.0	4.68	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2894	3252	0.028902	CGTGAGACTCGTGTGTGTGA	59.971	55.0	0.0	0.0	0.0	3.58	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
1383	1693	2.261671	CTGTACCTGGTCGCGCTT	59.738	61.111	0.63	0.00	0.00	4.68
1548	1858	1.301401	GCTGGTGTACGTGCAGGAA	60.301	57.895	14.38	0.00	0.00	3.36
1812	2137	3.621805	TTCCTCGACAAGGCGGCA	61.622	61.111	13.08	0.00	45.78	5.69
1902	2230	0.759346	AGGAACTCAAGAGCGTGGTT	59.241	50.000	0.00	0.00	0.00	3.67
2432	2760	1.432251	CGCTCGGGAACTACGTGAT	59.568	57.895	0.00	0.00	0.00	3.06
2478	2806	3.300765	GTGACGACGAGGGGTGGT	61.301	66.667	0.00	0.00	40.59	4.16
2519	2847	3.110178	GAACCTCAACGTCGGCCG	61.110	66.667	22.12	22.12	44.03	6.13
2601	2929	0.036388	CCATCGCCAACTGGTACACT	60.036	55.000	0.00	0.00	37.57	3.55
2726	3057	4.726825	AGAGCATTAGGGGAGAAAATGGTA	59.273	41.667	0.00	0.00	40.38	3.25
2727	3058	4.793201	AGCATTAGGGGAGAAAATGGTAC	58.207	43.478	0.00	0.00	39.00	3.34
2728	3059	4.478686	AGCATTAGGGGAGAAAATGGTACT	59.521	41.667	0.00	0.00	39.00	2.73
2729	3060	4.822350	GCATTAGGGGAGAAAATGGTACTC	59.178	45.833	0.00	0.00	32.44	2.59
2730	3061	5.377478	CATTAGGGGAGAAAATGGTACTCC	58.623	45.833	0.00	0.00	46.44	3.85
2734	3065	3.562343	GGAGAAAATGGTACTCCCTCC	57.438	52.381	0.00	0.00	42.84	4.30
2735	3066	2.172930	GGAGAAAATGGTACTCCCTCCC	59.827	54.545	0.00	0.00	42.84	4.30
2736	3067	2.844348	GAGAAAATGGTACTCCCTCCCA	59.156	50.000	0.00	0.00	0.00	4.37
2737	3068	3.459969	GAGAAAATGGTACTCCCTCCCAT	59.540	47.826	0.00	0.00	40.68	4.00
2738	3069	3.459969	AGAAAATGGTACTCCCTCCCATC	59.540	47.826	0.00	0.00	38.00	3.51
2739	3070	2.587060	AATGGTACTCCCTCCCATCA	57.413	50.000	0.00	0.00	38.00	3.07
2740	3071	2.587060	ATGGTACTCCCTCCCATCAA	57.413	50.000	0.00	0.00	33.73	2.57
2741	3072	1.879575	TGGTACTCCCTCCCATCAAG	58.120	55.000	0.00	0.00	0.00	3.02
2742	3073	1.080498	TGGTACTCCCTCCCATCAAGT	59.920	52.381	0.00	0.00	0.00	3.16
2743	3074	2.197465	GGTACTCCCTCCCATCAAGTT	58.803	52.381	0.00	0.00	0.00	2.66
2744	3075	2.092914	GGTACTCCCTCCCATCAAGTTG	60.093	54.545	0.00	0.00	0.00	3.16
2745	3076	1.747444	ACTCCCTCCCATCAAGTTGT	58.253	50.000	2.11	0.00	0.00	3.32
2746	3077	2.915869	ACTCCCTCCCATCAAGTTGTA	58.084	47.619	2.11	0.00	0.00	2.41
2747	3078	2.572104	ACTCCCTCCCATCAAGTTGTAC	59.428	50.000	2.11	0.00	0.00	2.90
2748	3079	2.571653	CTCCCTCCCATCAAGTTGTACA	59.428	50.000	2.11	0.00	0.00	2.90
2749	3080	2.983192	TCCCTCCCATCAAGTTGTACAA	59.017	45.455	3.59	3.59	0.00	2.41
2750	3081	3.396276	TCCCTCCCATCAAGTTGTACAAA	59.604	43.478	10.51	0.00	0.00	2.83
2830	3188	8.340443	GTTTGTTGACTCTATTACCGAAAAAGT	58.660	33.333	0.00	0.00	0.00	2.66
2882	3240	2.473816	CCACAGAGCATACATACCACG	58.526	52.381	0.00	0.00	0.00	4.94
2996	3357	1.525077	AACACAACGCACCCGACAT	60.525	52.632	0.00	0.00	38.29	3.06
2998	3359	0.669318	ACACAACGCACCCGACATAG	60.669	55.000	0.00	0.00	38.29	2.23
3094	3455	4.514577	AAGGCGGAGATGGCGTCG	62.515	66.667	0.13	0.00	39.82	5.12
3168	3529	0.255033	TAGAGAGCGTCAGTAGGGCA	59.745	55.000	0.00	0.00	0.00	5.36
3301	3662	1.133915	AGTTCAGCAAAAAGGTCCGGA	60.134	47.619	0.00	0.00	0.00	5.14
3319	3680	1.880027	GGAAAGTTAGTGTGGCACCAG	59.120	52.381	16.26	0.00	34.49	4.00
3325	3686	4.269523	GTGTGGCACCAGCTCCCA	62.270	66.667	16.26	0.00	41.70	4.37
3338	3699	4.608774	TCCCACCGACCACCTCGT	62.609	66.667	0.00	0.00	41.18	4.18
3344	3705	1.111116	ACCGACCACCTCGTGAAAGA	61.111	55.000	0.00	0.00	41.18	2.52
3355	3716	3.393800	CTCGTGAAAGAAGCTCCAAAGA	58.606	45.455	0.00	0.00	0.00	2.52
3431	3792	1.001760	AGAGGGCAGATACCGGTGT	59.998	57.895	19.93	11.68	0.00	4.16
3499	3860	1.750206	CGGATCCATTGCCACATGAAA	59.250	47.619	13.41	0.00	0.00	2.69
3503	3864	4.383335	GGATCCATTGCCACATGAAAATGT	60.383	41.667	6.95	0.00	34.64	2.71

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
1521	1831	1.214589	GTACACCAGCACCGACGAT	59.785	57.895	0.00	0.00	0.00	3.73
1762	2072	1.672030	TGTGCTCCATCTTGCCGTG	60.672	57.895	0.00	0.00	0.00	4.94
1763	2073	1.672356	GTGTGCTCCATCTTGCCGT	60.672	57.895	0.00	0.00	0.00	5.68
2432	2760	4.662961	CCGTCACCAGCAGCGTGA	62.663	66.667	0.00	0.00	37.91	4.35
2519	2847	2.159028	AGCCAGAAGAAATAGTCGAGGC	60.159	50.000	0.00	0.00	39.82	4.70
2529	2857	1.347707	ACGGTCATCAGCCAGAAGAAA	59.652	47.619	0.00	0.00	0.00	2.52
2601	2929	3.052455	TCATTGGCGCTCTTCTTGTAA	57.948	42.857	7.64	0.00	0.00	2.41
2726	3057	1.747444	ACAACTTGATGGGAGGGAGT	58.253	50.000	0.00	0.00	0.00	3.85
2727	3058	2.571653	TGTACAACTTGATGGGAGGGAG	59.428	50.000	0.00	0.00	0.00	4.30
2728	3059	2.626785	TGTACAACTTGATGGGAGGGA	58.373	47.619	0.00	0.00	0.00	4.20
2729	3060	3.433306	TTGTACAACTTGATGGGAGGG	57.567	47.619	3.59	0.00	0.00	4.30
2730	3061	4.022329	GGTTTTGTACAACTTGATGGGAGG	60.022	45.833	8.07	0.00	0.00	4.30
2731	3062	4.582656	TGGTTTTGTACAACTTGATGGGAG	59.417	41.667	8.07	0.00	0.00	4.30
2732	3063	4.537751	TGGTTTTGTACAACTTGATGGGA	58.462	39.130	8.07	0.00	0.00	4.37
2733	3064	4.340950	ACTGGTTTTGTACAACTTGATGGG	59.659	41.667	8.07	0.00	0.00	4.00
2734	3065	5.067153	TCACTGGTTTTGTACAACTTGATGG	59.933	40.000	8.07	0.00	0.00	3.51
2735	3066	5.971202	GTCACTGGTTTTGTACAACTTGATG	59.029	40.000	8.07	3.45	0.00	3.07
2736	3067	5.650266	TGTCACTGGTTTTGTACAACTTGAT	59.350	36.000	8.07	0.00	0.00	2.57
2737	3068	5.004448	TGTCACTGGTTTTGTACAACTTGA	58.996	37.500	8.07	2.28	0.00	3.02
2738	3069	5.303747	TGTCACTGGTTTTGTACAACTTG	57.696	39.130	8.07	0.17	0.00	3.16
2739	3070	5.968528	TTGTCACTGGTTTTGTACAACTT	57.031	34.783	8.07	0.00	0.00	2.66
2740	3071	6.524101	AATTGTCACTGGTTTTGTACAACT	57.476	33.333	8.07	0.00	30.40	3.16
2741	3072	8.865590	ATTAATTGTCACTGGTTTTGTACAAC	57.134	30.769	8.07	0.00	30.40	3.32
2748	3079	9.787532	CGATTCATATTAATTGTCACTGGTTTT	57.212	29.630	0.00	0.00	0.00	2.43
2749	3080	8.405531	CCGATTCATATTAATTGTCACTGGTTT	58.594	33.333	0.00	0.00	0.00	3.27
2750	3081	7.773224	TCCGATTCATATTAATTGTCACTGGTT	59.227	33.333	0.00	0.00	0.00	3.67
2830	3188	2.695127	TTATAAAGCGGGGCGAAAGA	57.305	45.000	0.00	0.00	0.00	2.52
2882	3240	1.411246	TGTGTGTGAGTGTGGACCTAC	59.589	52.381	0.00	0.00	0.00	3.18
2894	3252	0.028902	CGTGAGACTCGTGTGTGTGA	59.971	55.000	0.00	0.00	0.00	3.58
2957	3317	9.314321	TGTGTTGTTGTTGTTTTCTTCTTTTTA	57.686	25.926	0.00	0.00	0.00	1.52
2996	3357	1.074775	AGCCCGATTAGCCACCCTA	60.075	57.895	0.00	0.00	0.00	3.53
2998	3359	2.111251	GAGCCCGATTAGCCACCC	59.889	66.667	0.00	0.00	0.00	4.61
3301	3662	1.133792	AGCTGGTGCCACACTAACTTT	60.134	47.619	0.00	0.00	40.80	2.66
3319	3680	4.083862	GAGGTGGTCGGTGGGAGC	62.084	72.222	0.00	0.00	43.52	4.70
3338	3699	6.713762	TCAATTTCTTTGGAGCTTCTTTCA	57.286	33.333	0.00	0.00	35.92	2.69
3344	3705	2.229784	CCGCTCAATTTCTTTGGAGCTT	59.770	45.455	10.33	0.00	36.84	3.74
3355	3716	1.065199	TCCTGCATCTCCGCTCAATTT	60.065	47.619	0.00	0.00	0.00	1.82
3499	3860	3.350833	GGTGCCTCTGAAGATTCACATT	58.649	45.455	11.64	0.00	32.90	2.71
3503	3864	0.250234	CGGGTGCCTCTGAAGATTCA	59.750	55.000	0.00	0.00	35.57	2.57

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.