AutoCloner

Multiple sequence alignment - TraesCS1B01G136200

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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	TraesCS1B01G136200	chr1B	100.000	7345	0	0	1	7345	173978777	173971433	0.000000e+00	13564.0
1	TraesCS1B01G136200	chr1D	96.541	5349	112	23	1589	6918	113876039	113870745	0.000000e+00	8785.0
2	TraesCS1B01G136200	chr1D	92.450	1245	50	15	363	1592	113877321	113876106	0.000000e+00	1738.0
3	TraesCS1B01G136200	chr1D	91.160	181	14	2	200	378	121437330	121437150	2.050000e-60	244.0
4	TraesCS1B01G136200	chr1D	91.018	167	14	1	1	166	323071303	323071137	2.670000e-54	224.0
5	TraesCS1B01G136200	chr1D	98.113	53	1	0	6916	6968	113870777	113870725	7.850000e-15	93.5
6	TraesCS1B01G136200	chr1A	96.543	5004	129	20	1589	6577	121745217	121740243	0.000000e+00	8242.0
7	TraesCS1B01G136200	chr1A	90.885	746	39	15	366	1099	121746511	121745783	0.000000e+00	974.0
8	TraesCS1B01G136200	chr1A	95.732	328	11	3	1128	1453	121745788	121745462	6.530000e-145	525.0
9	TraesCS1B01G136200	chr1A	92.373	354	15	8	6576	6918	121740160	121739808	1.840000e-135	494.0
10	TraesCS1B01G136200	chr6B	94.180	3969	179	17	1589	5544	84125000	84128929	0.000000e+00	6002.0
11	TraesCS1B01G136200	chr6B	84.102	1258	106	46	5655	6857	84128962	84130180	0.000000e+00	1129.0
12	TraesCS1B01G136200	chr6B	80.930	645	64	32	779	1396	84124213	84124825	8.690000e-124	455.0
13	TraesCS1B01G136200	chr6B	86.058	208	12	3	552	742	84120029	84120236	2.690000e-49	207.0
14	TraesCS1B01G136200	chr6B	84.211	133	14	3	443	569	84119864	84119995	1.000000e-23	122.0
15	TraesCS1B01G136200	chr6A	93.720	3981	192	24	1589	5544	47898357	47902304	0.000000e+00	5914.0
16	TraesCS1B01G136200	chr6A	88.058	829	65	14	5651	6467	47902334	47903140	0.000000e+00	952.0
17	TraesCS1B01G136200	chr6A	81.067	581	55	32	845	1396	47897625	47898179	5.300000e-111	412.0
18	TraesCS1B01G136200	chr6A	87.273	165	20	1	1	164	109066204	109066040	3.500000e-43	187.0
19	TraesCS1B01G136200	chr6A	87.273	165	20	1	1	164	109092998	109092834	3.500000e-43	187.0
20	TraesCS1B01G136200	chr6A	82.791	215	13	10	552	742	47893471	47893685	3.520000e-38	171.0
21	TraesCS1B01G136200	chr6A	82.297	209	15	13	6479	6677	47903187	47903383	2.120000e-35	161.0
22	TraesCS1B01G136200	chr6A	79.365	252	30	15	6641	6872	47903386	47903635	2.740000e-34	158.0
23	TraesCS1B01G136200	chr6A	82.877	146	13	6	435	569	47893302	47893446	3.600000e-23	121.0
24	TraesCS1B01G136200	chrUn	94.338	3197	148	10	1589	4773	143899029	143902204	0.000000e+00	4870.0
25	TraesCS1B01G136200	chrUn	93.694	777	35	9	4778	5550	143902244	143903010	0.000000e+00	1151.0
26	TraesCS1B01G136200	chrUn	90.231	737	52	10	5745	6465	143903089	143903821	0.000000e+00	944.0
27	TraesCS1B01G136200	chrUn	80.995	663	69	30	779	1399	143898214	143898861	2.400000e-129	473.0
28	TraesCS1B01G136200	chrUn	79.230	727	96	32	1628	2305	75223049	75223769	8.690000e-124	455.0
29	TraesCS1B01G136200	chrUn	86.242	298	27	9	7041	7329	50799244	50798952	1.990000e-80	311.0
30	TraesCS1B01G136200	chrUn	91.556	225	18	1	1590	1813	104961974	104962198	7.160000e-80	309.0
31	TraesCS1B01G136200	chrUn	80.056	356	25	11	427	738	143894325	143894678	9.590000e-54	222.0
32	TraesCS1B01G136200	chrUn	87.273	165	20	1	1	164	477248543	477248379	3.500000e-43	187.0
33	TraesCS1B01G136200	chr3D	93.839	1331	65	9	1589	2912	7924894	7923574	0.000000e+00	1988.0
34	TraesCS1B01G136200	chr7D	92.544	228	16	1	1590	1816	27866305	27866078	7.110000e-85	326.0
35	TraesCS1B01G136200	chr7D	94.375	160	8	1	201	359	45837348	45837507	2.050000e-60	244.0
36	TraesCS1B01G136200	chr7B	85.526	304	35	3	7041	7341	36601672	36601375	7.160000e-80	309.0
37	TraesCS1B01G136200	chr7B	84.365	307	37	5	7042	7341	28066638	28066336	2.590000e-74	291.0
38	TraesCS1B01G136200	chr6D	84.967	306	37	5	7041	7341	459281413	459281112	1.200000e-77	302.0
39	TraesCS1B01G136200	chr6D	79.134	254	32	12	1628	1869	468945629	468945873	9.870000e-34	156.0
40	TraesCS1B01G136200	chr6D	83.226	155	13	7	2045	2189	468585696	468585545	5.980000e-26	130.0
41	TraesCS1B01G136200	chr6D	89.535	86	6	2	2135	2217	468916504	468916589	1.010000e-18	106.0
42	TraesCS1B01G136200	chr6D	80.000	135	20	4	931	1064	468914789	468914917	7.850000e-15	93.5
43	TraesCS1B01G136200	chr5B	84.918	305	37	5	7041	7341	188021039	188020740	4.310000e-77	300.0
44	TraesCS1B01G136200	chr5B	84.667	300	37	4	7041	7335	636932097	636932392	2.590000e-74	291.0
45	TraesCS1B01G136200	chr5B	84.142	309	37	8	7041	7343	678441921	678441619	9.320000e-74	289.0
46	TraesCS1B01G136200	chr5B	89.778	225	22	1	1590	1813	380783005	380783229	3.350000e-73	287.0
47	TraesCS1B01G136200	chr5B	92.982	171	11	1	200	369	521152509	521152679	1.580000e-61	248.0
48	TraesCS1B01G136200	chr5B	89.820	167	13	4	2	166	106247950	106248114	2.080000e-50	211.0
49	TraesCS1B01G136200	chr7A	84.488	303	38	6	7047	7345	669403132	669403429	2.590000e-74	291.0
50	TraesCS1B01G136200	chr7A	92.529	174	11	2	195	366	6316658	6316831	1.580000e-61	248.0
51	TraesCS1B01G136200	chr5D	84.314	306	39	5	7041	7341	16748996	16748695	2.590000e-74	291.0
52	TraesCS1B01G136200	chr5D	92.045	176	12	2	194	367	274578002	274578177	5.690000e-61	246.0
53	TraesCS1B01G136200	chr4B	92.655	177	12	1	199	374	80990645	80990821	3.400000e-63	254.0
54	TraesCS1B01G136200	chr4B	86.061	165	20	2	1	164	364199752	364199914	2.720000e-39	174.0
55	TraesCS1B01G136200	chr3B	92.135	178	12	2	197	373	571752694	571752518	4.400000e-62	250.0
56	TraesCS1B01G136200	chr3B	87.574	169	16	3	1	164	789543855	789544023	2.700000e-44	191.0
57	TraesCS1B01G136200	chr3B	77.742	310	67	2	3332	3640	525608744	525609052	9.730000e-44	189.0
58	TraesCS1B01G136200	chr2D	92.135	178	12	2	199	375	5663392	5663216	4.400000e-62	250.0
59	TraesCS1B01G136200	chr2D	91.713	181	13	2	200	378	309971416	309971596	4.400000e-62	250.0
60	TraesCS1B01G136200	chr2D	91.617	167	13	1	1	166	556043129	556043295	5.730000e-56	230.0
61	TraesCS1B01G136200	chr5A	87.879	165	19	1	1	164	642507594	642507430	7.520000e-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	TraesCS1B01G136200	chr1B	173971433	173978777	7344	True	13564.000000	13564	100.000000	1	7345	1	chr1B.!!$R1	7344
1	TraesCS1B01G136200	chr1D	113870725	113877321	6596	True	3538.833333	8785	95.701333	363	6968	3	chr1D.!!$R3	6605
2	TraesCS1B01G136200	chr1A	121739808	121746511	6703	True	2558.750000	8242	93.883250	366	6918	4	chr1A.!!$R1	6552
3	TraesCS1B01G136200	chr6B	84119864	84130180	10316	False	1583.000000	6002	85.896200	443	6857	5	chr6B.!!$F1	6414
4	TraesCS1B01G136200	chr6A	47893302	47903635	10333	False	1127.000000	5914	84.310714	435	6872	7	chr6A.!!$F1	6437
5	TraesCS1B01G136200	chrUn	143894325	143903821	9496	False	1532.000000	4870	87.862800	427	6465	5	chrUn.!!$F3	6038
6	TraesCS1B01G136200	chrUn	75223049	75223769	720	False	455.000000	455	79.230000	1628	2305	1	chrUn.!!$F1	677
7	TraesCS1B01G136200	chr3D	7923574	7924894	1320	True	1988.000000	1988	93.839000	1589	2912	1	chr3D.!!$R1	1323

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
26	27	0.032515	TCTAGAAGGATGCCACCCGA	60.033	55.000	0.00	0.00	0.00	5.14	F
103	104	0.036952	ATGTTCGAGCTCCCAGTGTG	60.037	55.000	8.47	0.00	0.00	3.82	F
807	5095	0.106217	GAGTGGAGGAGGAGGAGGAG	60.106	65.000	0.00	0.00	0.00	3.69	F
1157	5482	1.154225	GTCGGCGCCATTTCTGTTG	60.154	57.895	28.98	6.54	0.00	3.33	F
1513	5920	1.280457	ATCTGTTCCAGACCTCACCC	58.720	55.000	0.00	0.00	43.63	4.61	F
2580	7213	1.351017	GTGAGGATTGTGGACCCTTCA	59.649	52.381	0.00	0.00	0.00	3.02	F
2985	7623	1.999648	TTCCTGCAAACCAGCTCAAT	58.000	45.000	0.00	0.00	40.36	2.57	F
3195	7833	2.012673	GACAGGCTTGCATTGAGGTAG	58.987	52.381	0.00	0.00	0.00	3.18	F
4089	8745	2.093973	ACTGGTATGCGTTCTCTTCTGG	60.094	50.000	0.00	0.00	0.00	3.86	F
4404	9060	2.434336	TGTAAGTCTGGTGCTGTCTGTT	59.566	45.455	0.00	0.00	0.00	3.16	F
6266	10960	1.045350	TCGCCTCCATCTTCTCCCTG	61.045	60.000	0.00	0.00	0.00	4.45	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1214	5539	1.280142	CTAGATCCACCGACTCGCG	59.720	63.158	0.00	0.00	40.47	5.87	R
1264	5606	1.691976	AGATTCATGCGTAATCGGGGA	59.308	47.619	0.00	0.00	38.20	4.81	R
2583	7216	2.839228	AGCCCATAGGAGTTCAAGTCT	58.161	47.619	0.00	0.00	33.47	3.24	R
2905	7542	4.215109	ACCCTGCAAAGACAAAAGTACAT	58.785	39.130	0.00	0.00	0.00	2.29	R
3195	7833	3.929094	TGTAGACCCATTTGTCGTAACC	58.071	45.455	0.00	0.00	40.26	2.85	R
4404	9060	3.044235	AGTGCTGTCGTCATGATGAAA	57.956	42.857	19.12	13.25	0.00	2.69	R
4420	9076	4.453819	AGCATGTAAGAGACAAGAAAGTGC	59.546	41.667	0.00	0.00	42.78	4.40	R
4866	9558	6.371595	AACCTGATGAGATTCAGAAAGAGT	57.628	37.500	3.10	0.00	44.88	3.24	R
5864	10557	4.226761	CAATAACCCAAAACTGCTCGTTC	58.773	43.478	0.00	0.00	33.90	3.95	R
6329	11023	0.671472	CAGATCAGCAGTTGACGCCA	60.671	55.000	0.00	0.00	38.99	5.69	R
7322	12260	0.687354	AGAATGGAAGTCACGGTGCT	59.313	50.000	2.51	1.17	30.01	4.40	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	Hairpin	End Stability
21	22	4.412796	CTTGACATCTAGAAGGATGCCA	57.587	45.455	0.00	44.81	4.92
22	23	3.827008	TGACATCTAGAAGGATGCCAC	57.173	47.619	0.00	44.81	5.01
23	24	2.435805	TGACATCTAGAAGGATGCCACC	59.564	50.000	0.00	44.81	4.61
24	25	1.771255	ACATCTAGAAGGATGCCACCC	59.229	52.381	0.00	44.81	4.61
25	26	1.051812	ATCTAGAAGGATGCCACCCG	58.948	55.000	0.00	0.00	5.28
26	27	0.032515	TCTAGAAGGATGCCACCCGA	60.033	55.000	0.00	0.00	5.14
27	28	0.390860	CTAGAAGGATGCCACCCGAG	59.609	60.000	0.00	0.00	4.63
28	29	0.325296	TAGAAGGATGCCACCCGAGT	60.325	55.000	0.00	0.00	4.18
29	30	1.450312	GAAGGATGCCACCCGAGTG	60.450	63.158	0.00	44.12	3.51
46	47	4.537433	GGCCTGCGCTCCCACTAG	62.537	72.222	9.73	34.44	2.57
47	48	3.461773	GCCTGCGCTCCCACTAGA	61.462	66.667	9.73	0.00	2.43
48	49	3.019003	GCCTGCGCTCCCACTAGAA	62.019	63.158	9.73	0.00	2.10
49	50	1.142748	CCTGCGCTCCCACTAGAAG	59.857	63.158	9.73	0.00	2.85
50	51	1.142748	CTGCGCTCCCACTAGAAGG	59.857	63.158	9.73	0.00	3.46
58	59	2.998493	CCACTAGAAGGGAGCCAGT	58.002	57.895	0.00	0.00	4.00
59	60	0.539051	CCACTAGAAGGGAGCCAGTG	59.461	60.000	0.00	37.06	3.66
60	61	0.107945	CACTAGAAGGGAGCCAGTGC	60.108	60.000	0.00	31.14	4.40
61	62	1.268283	ACTAGAAGGGAGCCAGTGCC	61.268	60.000	0.00	38.69	5.01
62	63	1.229496	TAGAAGGGAGCCAGTGCCA	60.229	57.895	0.00	39.84	4.92
63	64	0.840288	TAGAAGGGAGCCAGTGCCAA	60.840	55.000	0.00	39.84	4.52
64	65	1.676967	GAAGGGAGCCAGTGCCAAG	60.677	63.158	0.00	39.84	3.61
65	66	3.875510	AAGGGAGCCAGTGCCAAGC	62.876	63.158	0.00	39.84	4.01
66	67	4.666253	GGGAGCCAGTGCCAAGCA	62.666	66.667	0.00	36.40	3.91
67	68	2.598394	GGAGCCAGTGCCAAGCAA	60.598	61.111	0.00	41.47	3.91
68	69	2.202395	GGAGCCAGTGCCAAGCAAA	61.202	57.895	0.00	41.47	3.68

Showing 1 to 25 of 485 entries

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Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
3	4	2.224402	GGGTGGCATCCTTCTAGATGTC	60.224	54.545	10.27	0.00	46.81	3.06
4	5	1.771255	GGGTGGCATCCTTCTAGATGT	59.229	52.381	10.27	0.00	44.58	3.06
6	7	1.051812	CGGGTGGCATCCTTCTAGAT	58.948	55.000	16.16	0.00	0.00	1.98
7	8	0.032515	TCGGGTGGCATCCTTCTAGA	60.033	55.000	16.16	0.65	0.00	2.43
8	9	0.390860	CTCGGGTGGCATCCTTCTAG	59.609	60.000	16.16	3.15	0.00	2.43
9	10	0.325296	ACTCGGGTGGCATCCTTCTA	60.325	55.000	16.16	0.00	0.00	2.10
10	11	1.613630	ACTCGGGTGGCATCCTTCT	60.614	57.895	16.16	0.00	0.00	2.85
11	12	1.450312	CACTCGGGTGGCATCCTTC	60.450	63.158	16.16	0.00	39.59	3.46
12	13	2.671070	CACTCGGGTGGCATCCTT	59.329	61.111	16.16	0.00	39.59	3.36
29	30	4.537433	CTAGTGGGAGCGCAGGCC	62.537	72.222	11.47	7.92	41.24	5.19
30	31	2.914777	CTTCTAGTGGGAGCGCAGGC	62.915	65.000	11.47	0.00	40.37	4.85
31	32	1.142748	CTTCTAGTGGGAGCGCAGG	59.857	63.158	11.47	0.00	0.00	4.85
32	33	1.142748	CCTTCTAGTGGGAGCGCAG	59.857	63.158	11.47	0.00	0.00	5.18
33	34	3.298958	CCTTCTAGTGGGAGCGCA	58.701	61.111	11.47	0.00	0.00	6.09
39	40	0.618968	ACTGGCTCCCTTCTAGTGGG	60.619	60.000	14.67	14.67	45.90	4.61
40	41	0.539051	CACTGGCTCCCTTCTAGTGG	59.461	60.000	0.00	0.00	36.12	4.00
41	42	0.107945	GCACTGGCTCCCTTCTAGTG	60.108	60.000	0.00	0.00	41.15	2.74
42	43	1.268283	GGCACTGGCTCCCTTCTAGT	61.268	60.000	0.00	0.00	40.87	2.57
43	44	1.267574	TGGCACTGGCTCCCTTCTAG	61.268	60.000	3.97	0.00	40.87	2.43
44	45	0.840288	TTGGCACTGGCTCCCTTCTA	60.840	55.000	3.97	0.00	40.87	2.10
45	46	2.134630	CTTGGCACTGGCTCCCTTCT	62.135	60.000	3.97	0.00	40.87	2.85
46	47	1.676967	CTTGGCACTGGCTCCCTTC	60.677	63.158	3.97	0.00	40.87	3.46
47	48	2.437897	CTTGGCACTGGCTCCCTT	59.562	61.111	3.97	0.00	40.87	3.95
48	49	4.357279	GCTTGGCACTGGCTCCCT	62.357	66.667	3.97	0.00	40.87	4.20
49	50	4.666253	TGCTTGGCACTGGCTCCC	62.666	66.667	3.97	0.00	40.87	4.30

Showing 1 to 25 of 489 entries

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Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.