AutoCloner

Multiple sequence alignment - TraesCS5D01G525800

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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	TraesCS5D01G525800	chr5D	100.000	4426	0	0	1	4426	543834206	543838631	0.000000e+00	8174.0
1	TraesCS5D01G525800	chr5D	77.895	1615	254	59	1359	2913	543707121	543705550	0.000000e+00	909.0
2	TraesCS5D01G525800	chr5D	80.801	724	116	18	1	718	232423903	232424609	3.010000e-151	545.0
3	TraesCS5D01G525800	chr5D	76.584	931	202	13	1525	2447	480031144	480032066	8.550000e-137	497.0
4	TraesCS5D01G525800	chr5D	83.117	77	11	2	3189	3264	543667994	543668069	7.940000e-08	69.4
5	TraesCS5D01G525800	chr4A	93.155	2133	116	18	1359	3462	625252790	625250659	0.000000e+00	3103.0
6	TraesCS5D01G525800	chr4A	79.620	1580	263	46	1360	2906	625394764	625396317	0.000000e+00	1079.0
7	TraesCS5D01G525800	chr4A	94.272	646	23	7	31	669	625255312	625254674	0.000000e+00	976.0
8	TraesCS5D01G525800	chr4A	94.253	348	15	1	723	1070	625253572	625253230	1.090000e-145	527.0
9	TraesCS5D01G525800	chr4A	84.942	518	33	19	3716	4195	625250339	625249829	2.390000e-132	483.0
10	TraesCS5D01G525800	chr4A	76.221	921	184	29	1535	2439	623337827	623338728	5.220000e-124	455.0
11	TraesCS5D01G525800	chr4A	90.997	311	21	3	1066	1370	625253126	625252817	3.190000e-111	412.0
12	TraesCS5D01G525800	chr4A	93.694	222	14	0	3464	3685	625250552	625250331	2.550000e-87	333.0
13	TraesCS5D01G525800	chr4A	93.464	153	8	1	4199	4349	625249776	625249624	4.450000e-55	226.0
14	TraesCS5D01G525800	chr4A	84.524	168	24	1	2639	2804	625538839	625539006	9.850000e-37	165.0
15	TraesCS5D01G525800	chr5B	90.932	2018	117	26	921	2913	685653795	685651819	0.000000e+00	2652.0
16	TraesCS5D01G525800	chr5B	92.337	783	44	10	2914	3680	685651791	685651009	0.000000e+00	1099.0
17	TraesCS5D01G525800	chr5B	79.082	1568	274	43	1384	2913	685604917	685603366	0.000000e+00	1029.0
18	TraesCS5D01G525800	chr5B	86.826	668	32	23	3812	4426	685990771	685991435	0.000000e+00	695.0
19	TraesCS5D01G525800	chr5B	93.820	356	21	1	3223	3577	685989965	685990320	6.520000e-148	534.0
20	TraesCS5D01G525800	chr5B	76.262	931	205	15	1525	2447	587786811	587787733	8.610000e-132	481.0
21	TraesCS5D01G525800	chr5B	76.564	943	180	31	1535	2457	689210177	689209256	3.100000e-131	479.0
22	TraesCS5D01G525800	chr5B	76.961	803	177	8	1525	2323	587762615	587763413	6.750000e-123	451.0
23	TraesCS5D01G525800	chr5B	94.961	258	12	1	3559	3815	685990412	685990669	1.920000e-108	403.0
24	TraesCS5D01G525800	chr5B	94.760	229	9	2	4199	4425	685650421	685650194	1.960000e-93	353.0
25	TraesCS5D01G525800	chr5B	80.682	352	21	10	3888	4193	685650826	685650476	3.440000e-56	230.0
26	TraesCS5D01G525800	chr5B	74.899	494	99	19	1980	2457	689148704	689148220	7.510000e-48	202.0
27	TraesCS5D01G525800	chr5B	77.493	351	63	16	2105	2447	687168792	687168450	3.490000e-46	196.0
28	TraesCS5D01G525800	chr5B	84.524	168	26	0	2635	2802	685438992	685439159	2.740000e-37	167.0
29	TraesCS5D01G525800	chr5B	83.626	171	28	0	2635	2805	685197830	685197660	1.270000e-35	161.0
30	TraesCS5D01G525800	chr1D	83.967	736	92	13	2994	3722	15061766	15061050	0.000000e+00	682.0
31	TraesCS5D01G525800	chr1D	80.689	668	110	17	62	721	290353368	290354024	6.610000e-138	501.0
32	TraesCS5D01G525800	chr1D	90.878	296	25	2	2204	2497	15604973	15605268	3.210000e-106	396.0
33	TraesCS5D01G525800	chr5A	76.948	924	199	13	1531	2447	598520692	598521608	8.490000e-142	514.0
34	TraesCS5D01G525800	chr5A	80.531	678	110	13	15	679	291533432	291534100	6.610000e-138	501.0
35	TraesCS5D01G525800	chr6A	78.926	726	125	23	4	720	102044978	102044272	6.700000e-128	468.0
36	TraesCS5D01G525800	chr2B	82.661	496	74	12	63	552	69076935	69076446	3.160000e-116	429.0
37	TraesCS5D01G525800	chr2B	81.382	521	85	10	62	575	453333672	453334187	8.860000e-112	414.0
38	TraesCS5D01G525800	chr2D	81.004	558	85	15	62	608	630345649	630345102	1.470000e-114	424.0
39	TraesCS5D01G525800	chr2A	79.928	558	91	19	60	608	632536716	632537261	1.490000e-104	390.0
40	TraesCS5D01G525800	chr2A	76.016	763	111	40	7	718	160015650	160014909	3.300000e-86	329.0
41	TraesCS5D01G525800	chr1A	83.140	172	27	2	2635	2805	569457991	569457821	5.930000e-34	156.0

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	TraesCS5D01G525800	chr5D	543834206	543838631	4425	False	8174.000000	8174	100.00000	1	4426	1	chr5D.!!$F4	4425
1	TraesCS5D01G525800	chr5D	543705550	543707121	1571	True	909.000000	909	77.89500	1359	2913	1	chr5D.!!$R1	1554
2	TraesCS5D01G525800	chr5D	232423903	232424609	706	False	545.000000	545	80.80100	1	718	1	chr5D.!!$F1	717
3	TraesCS5D01G525800	chr5D	480031144	480032066	922	False	497.000000	497	76.58400	1525	2447	1	chr5D.!!$F2	922
4	TraesCS5D01G525800	chr4A	625394764	625396317	1553	False	1079.000000	1079	79.62000	1360	2906	1	chr4A.!!$F2	1546
5	TraesCS5D01G525800	chr4A	625249624	625255312	5688	True	865.714286	3103	92.11100	31	4349	7	chr4A.!!$R1	4318
6	TraesCS5D01G525800	chr4A	623337827	623338728	901	False	455.000000	455	76.22100	1535	2439	1	chr4A.!!$F1	904
7	TraesCS5D01G525800	chr5B	685650194	685653795	3601	True	1083.500000	2652	89.67775	921	4425	4	chr5B.!!$R6	3504
8	TraesCS5D01G525800	chr5B	685603366	685604917	1551	True	1029.000000	1029	79.08200	1384	2913	1	chr5B.!!$R2	1529
9	TraesCS5D01G525800	chr5B	685989965	685991435	1470	False	544.000000	695	91.86900	3223	4426	3	chr5B.!!$F4	1203
10	TraesCS5D01G525800	chr5B	587786811	587787733	922	False	481.000000	481	76.26200	1525	2447	1	chr5B.!!$F2	922
11	TraesCS5D01G525800	chr5B	689209256	689210177	921	True	479.000000	479	76.56400	1535	2457	1	chr5B.!!$R5	922
12	TraesCS5D01G525800	chr5B	587762615	587763413	798	False	451.000000	451	76.96100	1525	2323	1	chr5B.!!$F1	798
13	TraesCS5D01G525800	chr1D	15061050	15061766	716	True	682.000000	682	83.96700	2994	3722	1	chr1D.!!$R1	728
14	TraesCS5D01G525800	chr1D	290353368	290354024	656	False	501.000000	501	80.68900	62	721	1	chr1D.!!$F2	659
15	TraesCS5D01G525800	chr5A	598520692	598521608	916	False	514.000000	514	76.94800	1531	2447	1	chr5A.!!$F2	916
16	TraesCS5D01G525800	chr5A	291533432	291534100	668	False	501.000000	501	80.53100	15	679	1	chr5A.!!$F1	664
17	TraesCS5D01G525800	chr6A	102044272	102044978	706	True	468.000000	468	78.92600	4	720	1	chr6A.!!$R1	716
18	TraesCS5D01G525800	chr2B	453333672	453334187	515	False	414.000000	414	81.38200	62	575	1	chr2B.!!$F1	513
19	TraesCS5D01G525800	chr2D	630345102	630345649	547	True	424.000000	424	81.00400	62	608	1	chr2D.!!$R1	546
20	TraesCS5D01G525800	chr2A	632536716	632537261	545	False	390.000000	390	79.92800	60	608	1	chr2A.!!$F1	548
21	TraesCS5D01G525800	chr2A	160014909	160015650	741	True	329.000000	329	76.01600	7	718	1	chr2A.!!$R1	711

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	Hairpin	End Stability	Orientation
801	2160	1.497309	AAATCTGGGACTTGGCCGGA	61.497	55.000	5.05	0.00	5.14	F
1401	2911	0.320374	TGTGCTAGTTTGGGTCTCGG	59.680	55.000	0.00	0.00	4.63	F
1542	3073	1.019673	ATTTCTGTATGCAGCAGCCG	58.980	50.000	14.18	42.29	5.52	F
2034	3565	1.885388	TGTGTTCGGTTGCCTCACG	60.885	57.895	0.00	32.55	4.35	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2230	3764	1.558756	CTCCAGTTCTGGAAGGCAGAT	59.441	52.381	20.06	0.00	37.55	2.90	R
2945	4567	1.384525	TTTTGGTGTGTGTTCGAGGG	58.615	50.000	0.00	0.00	0.00	4.30	R
3200	4832	2.240493	ACGCAAACTGCTGTTCTAGT	57.760	45.000	9.60	7.06	42.25	2.57	R
3671	5529	2.723322	CAATCTTGGAGGCCATCTCA	57.277	50.000	5.01	0.00	44.19	3.27	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
111	219	6.668323	TCAAATCCGATGAACTTTCTTGAAC	58.332	36.000	0.00	0.00	0.00	3.18
166	320	8.560355	ACTTTTTCCAAATTTAGTGCACTTTT	57.440	26.923	27.06	16.69	0.00	2.27
167	321	9.008965	ACTTTTTCCAAATTTAGTGCACTTTTT	57.991	25.926	27.06	18.55	0.00	1.94
190	344	8.709386	TTTTCAAATTCGATGAACTTTTTCCA	57.291	26.923	0.00	0.00	36.57	3.53
191	345	8.885494	TTTCAAATTCGATGAACTTTTTCCAT	57.115	26.923	0.00	0.00	36.57	3.41
192	346	9.973450	TTTCAAATTCGATGAACTTTTTCCATA	57.027	25.926	0.00	0.00	36.57	2.74
200	354	8.673711	TCGATGAACTTTTTCCATATTTAGTGG	58.326	33.333	0.00	0.00	38.11	4.00
201	355	8.673711	CGATGAACTTTTTCCATATTTAGTGGA	58.326	33.333	0.00	0.00	43.77	4.02
202	356	9.788960	GATGAACTTTTTCCATATTTAGTGGAC	57.211	33.333	0.00	0.00	45.05	4.02
203	357	8.934023	TGAACTTTTTCCATATTTAGTGGACT	57.066	30.769	0.00	0.00	45.05	3.85
204	358	9.010029	TGAACTTTTTCCATATTTAGTGGACTC	57.990	33.333	0.00	0.00	45.05	3.36
205	359	7.611213	ACTTTTTCCATATTTAGTGGACTCG	57.389	36.000	0.00	0.00	45.05	4.18
223	377	6.695278	TGGACTCGTTTTCAAATTCAATGAAC	59.305	34.615	0.00	0.00	36.57	3.18
298	540	3.037549	TGCACCTTTTTCCCTTTCATGT	58.962	40.909	0.00	0.00	0.00	3.21
721	2080	3.597728	CCGAGTAGGCGCTCCCTC	61.598	72.222	7.64	8.94	44.96	4.30
728	2087	2.589610	TAGGCGCTCCCTCCATCTGT	62.590	60.000	7.64	0.00	44.96	3.41
801	2160	1.497309	AAATCTGGGACTTGGCCGGA	61.497	55.000	5.05	0.00	0.00	5.14
1025	2384	2.746277	CCCCGTGGCGAAGAAAGG	60.746	66.667	0.00	0.00	0.00	3.11
1142	2609	7.533900	CCGATTTGTAATCAAAACAGTGTAGTG	59.466	37.037	0.00	0.00	44.97	2.74
1164	2631	3.317430	GGTTCTTCATTGATGATCAGGGC	59.683	47.826	0.09	0.00	36.56	5.19
1173	2640	4.508551	TGATGATCAGGGCAATTACAGT	57.491	40.909	0.09	0.00	0.00	3.55
1216	2688	1.346068	ACAGAACAGACTCCTGAAGGC	59.654	52.381	0.00	0.00	43.02	4.35
1225	2697	1.242076	CTCCTGAAGGCTTTGGTGTG	58.758	55.000	16.29	7.65	34.44	3.82
1278	2750	1.826024	CATTCTCCTCGACCCCCAG	59.174	63.158	0.00	0.00	0.00	4.45
1284	2756	2.279073	CTCGACCCCCAGCTAGGA	59.721	66.667	0.00	0.00	41.22	2.94

Showing 1 to 25 of 78 entries

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Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Hairpin	End Stability
2	3	3.915437	TTGGAAAAAGCCTCATCGAAC	57.085	42.857	0.00	0.00	3.95
12	13	6.908870	AAGTTCACTGAATTTGGAAAAAGC	57.091	33.333	0.00	0.00	3.51
75	183	6.902341	TCATCGGATTTGAAAAAGACTTCAG	58.098	36.000	0.00	36.69	3.02
80	188	7.862873	AGAAAGTTCATCGGATTTGAAAAAGAC	59.137	33.333	0.00	35.03	3.01
166	320	8.885494	ATGGAAAAAGTTCATCGAATTTGAAA	57.115	26.923	0.00	35.03	2.69
174	328	8.673711	CCACTAAATATGGAAAAAGTTCATCGA	58.326	33.333	0.00	39.87	3.59
175	329	8.673711	TCCACTAAATATGGAAAAAGTTCATCG	58.326	33.333	0.00	43.43	3.84
187	341	6.703319	TGAAAACGAGTCCACTAAATATGGA	58.297	36.000	0.00	44.20	3.41
188	342	6.978343	TGAAAACGAGTCCACTAAATATGG	57.022	37.500	0.00	38.71	2.74
189	343	9.840427	AATTTGAAAACGAGTCCACTAAATATG	57.160	29.630	0.00	0.00	1.78
191	345	9.058174	TGAATTTGAAAACGAGTCCACTAAATA	57.942	29.630	0.00	0.00	1.40
192	346	7.936584	TGAATTTGAAAACGAGTCCACTAAAT	58.063	30.769	0.00	0.00	1.40
193	347	7.323049	TGAATTTGAAAACGAGTCCACTAAA	57.677	32.000	0.00	0.00	1.85
194	348	6.928979	TGAATTTGAAAACGAGTCCACTAA	57.071	33.333	0.00	0.00	2.24
195	349	6.928979	TTGAATTTGAAAACGAGTCCACTA	57.071	33.333	0.00	0.00	2.74
196	350	5.828299	TTGAATTTGAAAACGAGTCCACT	57.172	34.783	0.00	0.00	4.00
197	351	6.205784	TCATTGAATTTGAAAACGAGTCCAC	58.794	36.000	0.00	0.00	4.02
198	352	6.384258	TCATTGAATTTGAAAACGAGTCCA	57.616	33.333	0.00	0.00	4.02
199	353	6.918022	AGTTCATTGAATTTGAAAACGAGTCC	59.082	34.615	1.78	35.03	3.85
200	354	7.914537	AGTTCATTGAATTTGAAAACGAGTC	57.085	32.000	1.78	35.03	3.36
201	355	8.702163	AAAGTTCATTGAATTTGAAAACGAGT	57.298	26.923	7.78	35.03	4.18
202	356	9.971744	AAAAAGTTCATTGAATTTGAAAACGAG	57.028	25.926	7.78	35.03	4.18
231	385	4.973663	ACAATGAAAAACGACCACGAATTC	59.026	37.500	0.00	42.66	2.17
235	389	3.127203	ACAACAATGAAAAACGACCACGA	59.873	39.130	0.00	42.66	4.35
282	524	8.716646	AACAAAAGTACATGAAAGGGAAAAAG	57.283	30.769	0.00	0.00	2.27

Showing 1 to 25 of 85 entries

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Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.