AutoCloner

Multiple sequence alignment - TraesCS7D01G376600

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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	TraesCS7D01G376600	chr7D	100.000	4534	0	0	1	4534	487737011	487741544	0.000000e+00	8373.0
1	TraesCS7D01G376600	chr7D	92.399	842	52	6	1967	2808	419767315	419768144	0.000000e+00	1190.0
2	TraesCS7D01G376600	chr7D	83.245	758	62	28	2809	3545	419768180	419768893	1.780000e-178	636.0
3	TraesCS7D01G376600	chr7D	95.951	247	10	0	3973	4219	487751790	487752036	7.070000e-108	401.0
4	TraesCS7D01G376600	chr7D	81.439	264	28	17	1422	1675	419766173	419766425	3.580000e-46	196.0
5	TraesCS7D01G376600	chr7D	81.675	191	21	3	981	1158	419765500	419765689	3.660000e-31	147.0
6	TraesCS7D01G376600	chr7D	82.114	123	18	4	4414	4533	575064996	575064875	8.020000e-18	102.0
7	TraesCS7D01G376600	chr7A	91.145	2078	76	41	1636	3684	555649802	555651800	0.000000e+00	2719.0
8	TraesCS7D01G376600	chr7A	88.612	1405	93	29	1967	3343	513415461	513414096	0.000000e+00	1646.0
9	TraesCS7D01G376600	chr7A	93.304	672	31	6	806	1475	555648847	555649506	0.000000e+00	979.0
10	TraesCS7D01G376600	chr7A	90.610	607	44	9	113	709	555646145	555646748	0.000000e+00	793.0
11	TraesCS7D01G376600	chr7A	88.014	292	24	5	3681	3969	555652069	555652352	7.270000e-88	335.0
12	TraesCS7D01G376600	chr7A	77.843	510	66	30	1204	1704	513417239	513416768	5.780000e-69	272.0
13	TraesCS7D01G376600	chr7A	88.750	160	11	2	1006	1158	513417550	513417391	5.990000e-44	189.0
14	TraesCS7D01G376600	chr7A	91.176	136	10	2	1509	1643	555649505	555649639	2.790000e-42	183.0
15	TraesCS7D01G376600	chr7A	79.444	180	28	6	39	216	396985135	396985307	7.970000e-23	119.0
16	TraesCS7D01G376600	chr7A	89.247	93	10	0	39	131	413096493	413096401	2.870000e-22	117.0
17	TraesCS7D01G376600	chr7B	93.294	1849	73	19	986	2808	516463123	516464946	0.000000e+00	2680.0
18	TraesCS7D01G376600	chr7B	87.410	1525	120	33	1967	3474	435789423	435790892	0.000000e+00	1687.0
19	TraesCS7D01G376600	chr7B	89.474	1178	51	29	2809	3969	516464982	516466103	0.000000e+00	1421.0
20	TraesCS7D01G376600	chr7B	85.167	809	80	16	1	782	516460857	516461652	0.000000e+00	793.0
21	TraesCS7D01G376600	chr7B	93.976	249	13	2	3985	4232	693791465	693791218	4.280000e-100	375.0
22	TraesCS7D01G376600	chr7B	91.593	226	15	4	4215	4436	71616876	71616651	4.410000e-80	309.0
23	TraesCS7D01G376600	chr7B	88.776	196	16	6	780	974	516462647	516462837	7.580000e-58	235.0
24	TraesCS7D01G376600	chr7B	96.694	121	4	0	4414	4534	693791231	693791111	7.690000e-48	202.0
25	TraesCS7D01G376600	chr7B	79.468	263	34	15	1422	1675	435787951	435788202	7.800000e-38	169.0
26	TraesCS7D01G376600	chr6A	89.550	689	69	1	2070	2758	595025232	595024547	0.000000e+00	870.0
27	TraesCS7D01G376600	chr6A	89.213	686	70	2	2070	2755	595048852	595048171	0.000000e+00	854.0
28	TraesCS7D01G376600	chr6A	94.248	226	12	1	3116	3341	595047680	595047456	1.210000e-90	344.0
29	TraesCS7D01G376600	chr6A	88.095	294	22	9	4145	4430	18654297	18654585	2.020000e-88	337.0
30	TraesCS7D01G376600	chr6A	90.270	185	18	0	2829	3013	595024360	595024176	4.530000e-60	243.0
31	TraesCS7D01G376600	chr6A	86.449	214	26	2	2809	3019	595047941	595047728	9.810000e-57	231.0
32	TraesCS7D01G376600	chr6A	91.270	126	10	1	1034	1158	595052108	595051983	2.170000e-38	171.0
33	TraesCS7D01G376600	chr6A	88.189	127	5	2	1033	1158	595070461	595070578	4.730000e-30	143.0
34	TraesCS7D01G376600	chr6B	91.209	637	54	2	2121	2756	680860995	680861630	0.000000e+00	865.0
35	TraesCS7D01G376600	chr6B	85.484	558	56	10	2809	3341	680862172	680862729	3.960000e-155	558.0
36	TraesCS7D01G376600	chr6B	85.633	529	53	9	2829	3334	680778068	680777540	6.680000e-148	534.0
37	TraesCS7D01G376600	chr6B	94.366	213	11	1	4215	4426	305729064	305729276	4.370000e-85	326.0
38	TraesCS7D01G376600	chr6B	83.212	137	10	4	1017	1149	680809150	680809277	3.710000e-21	113.0
39	TraesCS7D01G376600	chr6D	89.080	696	68	4	2070	2764	449187463	449186775	0.000000e+00	857.0
40	TraesCS7D01G376600	chr6D	84.201	557	53	13	2819	3341	449186249	449185694	4.050000e-140	508.0
41	TraesCS7D01G376600	chr6D	95.000	220	10	1	3116	3335	449216576	449216358	1.210000e-90	344.0
42	TraesCS7D01G376600	chr6D	88.983	118	4	1	1033	1150	449221357	449221249	2.200000e-28	137.0
43	TraesCS7D01G376600	chr6D	88.235	119	5	1	1033	1151	449247482	449247591	2.850000e-27	134.0
44	TraesCS7D01G376600	chr6D	88.136	118	5	1	1033	1150	449189470	449189362	1.020000e-26	132.0
45	TraesCS7D01G376600	chr1D	94.636	261	12	2	3973	4232	438145211	438144952	1.960000e-108	403.0
46	TraesCS7D01G376600	chr1D	92.829	251	16	2	3973	4223	438069321	438069073	3.330000e-96	363.0
47	TraesCS7D01G376600	chr1D	90.038	261	17	6	3973	4232	78983092	78983344	3.380000e-86	329.0
48	TraesCS7D01G376600	chr1D	92.800	125	5	3	4414	4534	78983330	78983454	1.300000e-40	178.0
49	TraesCS7D01G376600	chr1D	90.083	121	11	1	4414	4533	19110887	19110767	6.070000e-34	156.0
50	TraesCS7D01G376600	chr1D	95.161	62	2	1	4414	4474	438144966	438144905	3.730000e-16	97.1
51	TraesCS7D01G376600	chr1B	94.800	250	12	1	3972	4221	593701774	593701526	5.500000e-104	388.0
52	TraesCS7D01G376600	chr1B	93.600	250	14	2	3973	4221	593711976	593711728	5.540000e-99	372.0
53	TraesCS7D01G376600	chr5A	91.188	261	21	2	3973	4232	707073507	707073766	2.010000e-93	353.0
54	TraesCS7D01G376600	chr5A	89.868	227	22	1	3993	4219	707078314	707078539	1.600000e-74	291.0
55	TraesCS7D01G376600	chr3A	94.762	210	10	1	4219	4427	171790470	171790261	4.370000e-85	326.0
56	TraesCS7D01G376600	chr3A	80.000	215	33	7	29	239	191369772	191369564	2.830000e-32	150.0
57	TraesCS7D01G376600	chr3A	82.222	180	22	9	29	205	190250796	190250624	3.660000e-31	147.0
58	TraesCS7D01G376600	chr3A	84.967	153	14	6	29	178	190603388	190603242	3.660000e-31	147.0
59	TraesCS7D01G376600	chr2B	95.146	206	8	2	4219	4422	603410378	603410173	1.570000e-84	324.0
60	TraesCS7D01G376600	chr2B	85.890	163	18	5	31	192	693886659	693886501	7.800000e-38	169.0
61	TraesCS7D01G376600	chr5B	94.258	209	11	1	4219	4426	625133383	625133175	7.320000e-83	318.0
62	TraesCS7D01G376600	chr3B	93.839	211	12	1	4218	4427	571820656	571820446	2.630000e-82	316.0
63	TraesCS7D01G376600	chr3B	82.979	188	25	4	54	239	238296171	238295989	3.630000e-36	163.0
64	TraesCS7D01G376600	chr3B	88.095	126	11	4	4413	4534	359222060	359221935	3.660000e-31	147.0
65	TraesCS7D01G376600	chr2A	93.839	211	11	2	4218	4426	770103310	770103100	2.630000e-82	316.0
66	TraesCS7D01G376600	chr1A	80.217	460	57	26	3973	4414	582229631	582229188	9.470000e-82	315.0
67	TraesCS7D01G376600	chr1A	100.000	28	0	0	1	28	535157324	535157351	8.000000e-03	52.8
68	TraesCS7D01G376600	chr2D	90.164	122	11	1	4414	4534	226626891	226627012	1.690000e-34	158.0
69	TraesCS7D01G376600	chr3D	89.320	103	9	2	29	130	161690608	161690507	1.320000e-25	128.0

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	TraesCS7D01G376600	chr7D	487737011	487741544	4533	False	8373.000000	8373	100.000000	1	4534	1	chr7D.!!$F1	4533
1	TraesCS7D01G376600	chr7D	419765500	419768893	3393	False	542.250000	1190	84.689500	981	3545	4	chr7D.!!$F3	2564
2	TraesCS7D01G376600	chr7A	555646145	555652352	6207	False	1001.800000	2719	90.849800	113	3969	5	chr7A.!!$F2	3856
3	TraesCS7D01G376600	chr7A	513414096	513417550	3454	True	702.333333	1646	85.068333	1006	3343	3	chr7A.!!$R2	2337
4	TraesCS7D01G376600	chr7B	516460857	516466103	5246	False	1282.250000	2680	89.177750	1	3969	4	chr7B.!!$F2	3968
5	TraesCS7D01G376600	chr7B	435787951	435790892	2941	False	928.000000	1687	83.439000	1422	3474	2	chr7B.!!$F1	2052
6	TraesCS7D01G376600	chr6A	595024176	595025232	1056	True	556.500000	870	89.910000	2070	3013	2	chr6A.!!$R1	943
7	TraesCS7D01G376600	chr6A	595047456	595052108	4652	True	400.000000	854	90.295000	1034	3341	4	chr6A.!!$R2	2307
8	TraesCS7D01G376600	chr6B	680860995	680862729	1734	False	711.500000	865	88.346500	2121	3341	2	chr6B.!!$F3	1220
9	TraesCS7D01G376600	chr6B	680777540	680778068	528	True	534.000000	534	85.633000	2829	3334	1	chr6B.!!$R1	505
10	TraesCS7D01G376600	chr6D	449185694	449189470	3776	True	499.000000	857	87.139000	1033	3341	3	chr6D.!!$R3	2308

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
778	806	0.248843	CAAGCACCCTGACTCCTCTC	59.751	60.000	0.00	0.00	0.00	3.20	F
798	2834	0.744771	GAGTGGGCCCTGACGATTTC	60.745	60.000	25.70	3.34	0.00	2.17	F
1002	3627	1.021968	CTTAGAAATTTCCGGCGGGG	58.978	55.000	27.98	0.32	37.02	5.73	F
1716	7046	1.451927	ATGGCAGTGGCATACCGTG	60.452	57.895	29.11	0.00	46.84	4.94	F
2199	8374	1.202794	TCTGACCTGCACAGCATCAAA	60.203	47.619	0.00	0.00	38.13	2.69	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1724	7054	1.202915	ACTGTTCCATCATGTGCACCA	60.203	47.619	15.69	2.61	0.00	4.17	R
1940	7746	1.226101	GTCATGCGTGCAATCGGTG	60.226	57.895	0.00	0.00	0.00	4.94	R
2199	8374	1.301479	GGCGTCCTTCCAGTCGTTT	60.301	57.895	0.00	0.00	0.00	3.60	R
3344	10136	0.462225	CAGGCTGATCTGGCAGTCAG	60.462	60.000	27.93	27.93	42.82	3.51	R
4031	11141	0.036952	CTCACGCAACACCAGATCCT	60.037	55.000	0.00	0.00	0.00	3.24	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
31	32	5.129634	TGGCAACGATACCAATACATGAAT	58.870	37.500	0.00	0.00	42.51	2.57
35	36	7.362662	GCAACGATACCAATACATGAATCATT	58.637	34.615	0.00	0.00	0.00	2.57
62	63	8.984764	TGTATTGTTCTAATTAATCGGATTCGG	58.015	33.333	6.49	0.00	36.95	4.30
65	66	6.575267	TGTTCTAATTAATCGGATTCGGACA	58.425	36.000	6.49	1.13	36.95	4.02
69	70	8.083462	TCTAATTAATCGGATTCGGACATTTG	57.917	34.615	6.49	1.91	36.95	2.32
71	72	6.693315	ATTAATCGGATTCGGACATTTGTT	57.307	33.333	6.49	0.00	36.95	2.83
72	73	7.795482	ATTAATCGGATTCGGACATTTGTTA	57.205	32.000	6.49	0.00	36.95	2.41
73	74	7.795482	TTAATCGGATTCGGACATTTGTTAT	57.205	32.000	6.49	0.00	36.95	1.89
247	249	3.829601	ACGGATGCCCTAAATTTGTTTCA	59.170	39.130	0.00	0.00	0.00	2.69
325	328	3.621715	GTGGGACGTGCTTTTTAGGATAG	59.378	47.826	7.11	0.00	0.00	2.08
344	347	7.647827	AGGATAGGCTAGAGATGCTCTTATAA	58.352	38.462	1.88	0.00	41.50	0.98
351	356	9.331282	GGCTAGAGATGCTCTTATAAAAAGAAA	57.669	33.333	1.88	0.00	41.50	2.52
408	413	9.702726	CACTAAGAAAATGTTGACGGTATATTG	57.297	33.333	0.00	0.00	0.00	1.90
419	424	5.945155	TGACGGTATATTGCAAAAAGTTCC	58.055	37.500	1.71	1.07	0.00	3.62
430	435	3.313690	CAAAAAGTTCCCCGTGCATTAC	58.686	45.455	0.00	0.00	0.00	1.89
447	452	7.900864	CGTGCATTACTAAAATGTTCATCGTAA	59.099	33.333	0.00	0.00	0.00	3.18
571	582	6.140895	TCAACGTAATTTACACAAATGTTGCG	59.859	34.615	13.44	0.00	40.48	4.85
585	596	6.419413	ACAAATGTTGCGTATTCGAAAATTGT	59.581	30.769	0.00	1.87	36.28	2.71
591	602	5.511571	TGCGTATTCGAAAATTGTTCAACA	58.488	33.333	0.00	0.00	39.71	3.33
593	604	6.087423	TGCGTATTCGAAAATTGTTCAACATG	59.913	34.615	0.00	0.00	39.71	3.21
681	692	8.568732	TGTTCTAAATAAAAACCGAGCAAAAG	57.431	30.769	0.00	0.00	0.00	2.27
773	801	2.360475	GCCCAAGCACCCTGACTC	60.360	66.667	0.00	0.00	39.53	3.36
777	805	1.197430	CCAAGCACCCTGACTCCTCT	61.197	60.000	0.00	0.00	0.00	3.69
778	806	0.248843	CAAGCACCCTGACTCCTCTC	59.751	60.000	0.00	0.00	0.00	3.20
798	2834	0.744771	GAGTGGGCCCTGACGATTTC	60.745	60.000	25.70	3.34	0.00	2.17

Showing 1 to 25 of 451 entries

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Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
50	51	8.890124	TTATAACAAATGTCCGAATCCGATTA	57.110	30.769	0.00	0.00	38.22	1.75
218	220	1.906105	TTAGGGCATCCGTTTCGCCT	61.906	55.000	0.00	0.00	45.50	5.52
352	357	9.773328	CGATCAATTTTTGTAATACACACTGAT	57.227	29.630	0.00	0.00	36.69	2.90
384	389	8.394877	TGCAATATACCGTCAACATTTTCTTAG	58.605	33.333	0.00	0.00	0.00	2.18
408	413	0.033366	ATGCACGGGGAACTTTTTGC	59.967	50.000	0.00	0.00	0.00	3.68
419	424	5.303747	TGAACATTTTAGTAATGCACGGG	57.696	39.130	0.00	0.00	0.00	5.28
457	462	9.308000	TGGACCTTTTAAGTATTCATTGAACAT	57.692	29.630	0.15	0.00	0.00	2.71
481	486	7.116376	ACGCTGAATAACTCAAATATATCGTGG	59.884	37.037	0.00	0.00	32.17	4.94
499	504	7.298507	ACGTTTGTGTAAATATACGCTGAAT	57.701	32.000	0.00	0.00	41.96	2.57
571	582	7.332003	TGCATGTTGAACAATTTTCGAATAC	57.668	32.000	0.62	0.00	0.00	1.89
585	596	8.429493	TTGAACATTTTGTAATGCATGTTGAA	57.571	26.923	0.00	0.00	44.05	2.69
762	790	1.662438	CTCGAGAGGAGTCAGGGTGC	61.662	65.000	6.58	0.00	38.02	5.01
773	801	3.465403	CAGGGCCCACTCGAGAGG	61.465	72.222	27.56	21.20	0.00	3.69
777	805	3.957435	ATCGTCAGGGCCCACTCGA	62.957	63.158	27.56	27.73	0.00	4.04
778	806	2.521958	AAATCGTCAGGGCCCACTCG	62.522	60.000	27.56	23.56	0.00	4.18
787	2823	4.829064	TTTTGTTGAGGAAATCGTCAGG	57.171	40.909	6.00	0.00	41.09	3.86
897	3248	1.079750	GACGACAAGAGAGGTGGGC	60.080	63.158	0.00	0.00	0.00	5.36
961	3312	9.350951	CTAAGAGGGAGGAGTTTTTCTTTTTAA	57.649	33.333	0.00	0.00	0.00	1.52
962	3313	8.720537	TCTAAGAGGGAGGAGTTTTTCTTTTTA	58.279	33.333	0.00	0.00	0.00	1.52
968	3319	8.410673	AAATTTCTAAGAGGGAGGAGTTTTTC	57.589	34.615	0.00	0.00	0.00	2.29
974	3325	4.443598	CCGGAAATTTCTAAGAGGGAGGAG	60.444	50.000	17.42	0.00	0.00	3.69
977	3328	3.206964	GCCGGAAATTTCTAAGAGGGAG	58.793	50.000	17.42	0.00	0.00	4.30
984	3609	0.328926	ACCCCGCCGGAAATTTCTAA	59.671	50.000	17.42	0.00	34.64	2.10
998	3623	0.249657	GCAATCTCTAGAGCACCCCG	60.250	60.000	15.35	1.54	0.00	5.73
1000	3625	0.249657	CGGCAATCTCTAGAGCACCC	60.250	60.000	15.35	10.85	0.00	4.61

Showing 1 to 25 of 469 entries

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Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.