AutoCloner

Multiple sequence alignment - TraesCS4D01G067000

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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	TraesCS4D01G067000	chr4D	100.000	3670	0	0	1	3670	42097725	42101394	0.000000e+00	6778
1	TraesCS4D01G067000	chr4B	94.419	3082	126	22	1	3047	60425730	60428800	0.000000e+00	4697
2	TraesCS4D01G067000	chr4B	86.289	547	49	5	3150	3670	147373900	147373354	4.110000e-159	571
3	TraesCS4D01G067000	chr4B	95.455	110	5	0	3042	3151	60428891	60429000	3.770000e-40	176
4	TraesCS4D01G067000	chr4A	93.333	3210	122	34	1	3151	557871232	557868056	0.000000e+00	4658
5	TraesCS4D01G067000	chr4A	81.651	545	63	21	3159	3670	415721982	415721442	5.670000e-113	418
6	TraesCS4D01G067000	chr1B	89.945	1442	106	27	1321	2739	50399766	50398341	0.000000e+00	1823
7	TraesCS4D01G067000	chr1B	86.777	484	26	10	862	1318	50400325	50399853	4.230000e-139	505
8	TraesCS4D01G067000	chr1B	83.208	530	65	8	3164	3670	117174675	117174147	7.180000e-127	464
9	TraesCS4D01G067000	chr2D	86.380	558	38	14	3150	3669	423861711	423862268	3.180000e-160	575
10	TraesCS4D01G067000	chr2D	79.667	541	75	20	3159	3669	550629912	550629377	1.250000e-94	357
11	TraesCS4D01G067000	chr3A	84.066	546	49	17	3161	3670	540651552	540652095	3.290000e-135	492
12	TraesCS4D01G067000	chr3A	82.784	546	57	18	3159	3670	219729222	219728680	1.550000e-123	453
13	TraesCS4D01G067000	chr7A	83.005	559	56	12	3150	3670	63087111	63087668	1.540000e-128	470
14	TraesCS4D01G067000	chr7A	82.226	557	57	20	3151	3670	20757428	20756877	3.360000e-120	442
15	TraesCS4D01G067000	chr7D	82.418	546	70	12	3151	3670	36064174	36064719	1.550000e-123	453
16	TraesCS4D01G067000	chr7D	86.990	392	35	8	3295	3670	439466652	439467043	9.420000e-116	427
17	TraesCS4D01G067000	chr5D	80.254	552	63	20	3161	3670	438448984	438449531	1.240000e-99	374
18	TraesCS4D01G067000	chr3B	79.853	546	78	21	3150	3667	363322466	363321925	1.610000e-98	370
19	TraesCS4D01G067000	chr1D	79.592	490	75	18	3164	3629	370534962	370535450	9.830000e-86	327
20	TraesCS4D01G067000	chr1D	82.301	226	24	12	3150	3365	339302877	339302658	8.100000e-42	182
21	TraesCS4D01G067000	chr1A	77.022	544	72	23	3152	3670	126373201	126372686	2.810000e-66	263

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	TraesCS4D01G067000	chr4D	42097725	42101394	3669	False	6778.0	6778	100.000	1	3670	1	chr4D.!!$F1	3669
1	TraesCS4D01G067000	chr4B	60425730	60429000	3270	False	2436.5	4697	94.937	1	3151	2	chr4B.!!$F1	3150
2	TraesCS4D01G067000	chr4B	147373354	147373900	546	True	571.0	571	86.289	3150	3670	1	chr4B.!!$R1	520
3	TraesCS4D01G067000	chr4A	557868056	557871232	3176	True	4658.0	4658	93.333	1	3151	1	chr4A.!!$R2	3150
4	TraesCS4D01G067000	chr4A	415721442	415721982	540	True	418.0	418	81.651	3159	3670	1	chr4A.!!$R1	511
5	TraesCS4D01G067000	chr1B	50398341	50400325	1984	True	1164.0	1823	88.361	862	2739	2	chr1B.!!$R2	1877
6	TraesCS4D01G067000	chr1B	117174147	117174675	528	True	464.0	464	83.208	3164	3670	1	chr1B.!!$R1	506
7	TraesCS4D01G067000	chr2D	423861711	423862268	557	False	575.0	575	86.380	3150	3669	1	chr2D.!!$F1	519
8	TraesCS4D01G067000	chr2D	550629377	550629912	535	True	357.0	357	79.667	3159	3669	1	chr2D.!!$R1	510
9	TraesCS4D01G067000	chr3A	540651552	540652095	543	False	492.0	492	84.066	3161	3670	1	chr3A.!!$F1	509
10	TraesCS4D01G067000	chr3A	219728680	219729222	542	True	453.0	453	82.784	3159	3670	1	chr3A.!!$R1	511
11	TraesCS4D01G067000	chr7A	63087111	63087668	557	False	470.0	470	83.005	3150	3670	1	chr7A.!!$F1	520
12	TraesCS4D01G067000	chr7A	20756877	20757428	551	True	442.0	442	82.226	3151	3670	1	chr7A.!!$R1	519
13	TraesCS4D01G067000	chr7D	36064174	36064719	545	False	453.0	453	82.418	3151	3670	1	chr7D.!!$F1	519
14	TraesCS4D01G067000	chr5D	438448984	438449531	547	False	374.0	374	80.254	3161	3670	1	chr5D.!!$F1	509
15	TraesCS4D01G067000	chr3B	363321925	363322466	541	True	370.0	370	79.853	3150	3667	1	chr3B.!!$R1	517
16	TraesCS4D01G067000	chr1A	126372686	126373201	515	True	263.0	263	77.022	3152	3670	1	chr1A.!!$R1	518

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	Hairpin	End Stability	Orientation
125	126	0.675522	CATTTCGTGTAGCCCCGGTT	60.676	55.000	0.00	4.44	F
233	234	1.133181	TGGCACACTCCCTTCATGGA	61.133	55.000	38.35	3.41	F
491	493	1.468506	TAGACAGTTCGTGCAGCCCA	61.469	55.000	0.00	5.36	F
783	788	1.682087	GGTCATTAGCTTGTCCCACCC	60.682	57.143	0.00	4.61	F

Position	MSA Position	Penalty	Sequence	TM	GC	Hairpin	End Stability	Orientation
1638	1761	3.515502	AGGTCTAGCTCACACTTATGCAA	59.484	43.478	0.00	4.08	R
1846	1972	8.667076	CACAAATAGTGGTCAGATATGATGAA	57.333	34.615	44.69	2.57	R
2369	2509	6.582295	GCTTATTATTGCCCATTACGTTGATG	59.418	38.462	0.00	3.07	R
2682	2852	0.685097	AGGCTTAGCGACCACAGAAA	59.315	50.000	0.00	2.52	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
24	25	2.568509	CAAAATCATGGGGTTTGGCTCT	59.431	45.455	0.00	0.00	0.00	4.09
124	125	1.078708	CATTTCGTGTAGCCCCGGT	60.079	57.895	0.00	0.00	0.00	5.28
125	126	0.675522	CATTTCGTGTAGCCCCGGTT	60.676	55.000	0.00	0.00	0.00	4.44
144	145	3.058501	GGTTGATTGTTCACCACCGTAAG	60.059	47.826	0.00	0.00	0.00	2.34
174	175	1.815003	CAGATTCAGCCTTTCACACCC	59.185	52.381	0.00	0.00	0.00	4.61
186	187	4.579384	ACACCCCACGGCCTTGTG	62.579	66.667	8.63	6.13	39.60	3.33
233	234	1.133181	TGGCACACTCCCTTCATGGA	61.133	55.000	0.00	0.00	38.35	3.41
241	242	1.671054	CCCTTCATGGACGCGTTGT	60.671	57.895	15.53	0.00	38.35	3.32
277	278	2.906389	TGCCCATCAGTGAACTAACTCT	59.094	45.455	0.00	0.00	0.00	3.24
424	425	2.490217	CAGTGCCGAGGGAGTACG	59.510	66.667	0.00	0.00	0.00	3.67
491	493	1.468506	TAGACAGTTCGTGCAGCCCA	61.469	55.000	0.00	0.00	0.00	5.36
520	522	7.924412	TGCTGGTTGTTACAATAGTAGTATAGC	59.076	37.037	0.00	2.69	0.00	2.97
593	595	2.416701	GCCCCCATTTTACAATGTCACG	60.417	50.000	0.00	0.00	38.58	4.35
700	705	6.157904	TGGTATGCACATTCTGTCAAAATTG	58.842	36.000	0.00	0.00	0.00	2.32
743	748	7.988737	TGATTGACTACAAAAGCCATAGATTG	58.011	34.615	0.00	0.00	39.54	2.67
783	788	1.682087	GGTCATTAGCTTGTCCCACCC	60.682	57.143	0.00	0.00	0.00	4.61
799	804	3.494506	CCCCCATGTGTCAGGTGA	58.505	61.111	0.00	0.00	0.00	4.02
895	900	5.041951	TGTGCATCTTTGTTCGATTTACC	57.958	39.130	0.00	0.00	0.00	2.85
963	975	2.606725	CTGGCTTCGAATTGCTGTCTAG	59.393	50.000	9.01	0.00	0.00	2.43
1094	1122	7.112287	TGACTTATTTTGTATGCACGTTTTTCG	59.888	33.333	0.00	0.00	46.00	3.46
1278	1313	5.870433	ACATTGCAACATGACATGGTAAATG	59.130	36.000	25.40	25.40	38.33	2.32
1279	1314	3.847542	TGCAACATGACATGGTAAATGC	58.152	40.909	19.39	18.42	33.60	3.56
1291	1326	5.767665	ACATGGTAAATGCAAGTGTGTAGAA	59.232	36.000	0.00	0.00	0.00	2.10
1318	1353	9.014297	AGTCTTGAACTTAATCCAGGTTTTATG	57.986	33.333	0.00	0.00	33.03	1.90
1390	1510	8.553459	AATATGTCAAAGGGCTTATATTCGAG	57.447	34.615	0.00	0.00	0.00	4.04
1435	1555	9.520204	CTTTTGCATTTTATGGTACTATGAAGG	57.480	33.333	1.31	0.44	0.00	3.46
1638	1761	5.594317	AGCTAATGAAAACAACTGAACTGGT	59.406	36.000	0.00	0.00	0.00	4.00
1831	1957	7.660617	CCTATGATGGATGAAGATGGTATATGC	59.339	40.741	0.00	0.00	0.00	3.14
1846	1972	9.284968	GATGGTATATGCCTTGTTACTTGTATT	57.715	33.333	11.44	0.00	0.00	1.89
2300	2440	8.563123	AGCTAAGATAAACCTTTTGTAACTCC	57.437	34.615	0.00	0.00	0.00	3.85
2308	2448	6.879276	AACCTTTTGTAACTCCTTCTAAGC	57.121	37.500	0.00	0.00	0.00	3.09
2369	2509	8.196802	TGTCATGCACAAGTGTATACTTAATC	57.803	34.615	4.38	0.00	45.12	1.75
2682	2852	2.679837	CAAGTATGAGCCGCAAAGTGAT	59.320	45.455	0.00	0.00	0.00	3.06
2746	2917	4.284123	CAGTTTGCGCCTGCTCTA	57.716	55.556	4.18	0.00	43.34	2.43
2819	2990	3.066760	CGCAAAGAACCTGTTCCTCTTTT	59.933	43.478	6.41	0.00	37.31	2.27
2820	2991	4.611943	GCAAAGAACCTGTTCCTCTTTTC	58.388	43.478	6.41	0.00	37.31	2.29
2821	2992	4.097892	GCAAAGAACCTGTTCCTCTTTTCA	59.902	41.667	6.41	0.00	37.31	2.69
2837	3008	9.745018	TCCTCTTTTCATATTTTGAGATCTTGT	57.255	29.630	0.00	0.00	35.27	3.16
2848	3019	3.942829	TGAGATCTTGTGGTGCCTAAAG	58.057	45.455	0.00	0.00	0.00	1.85
2865	3045	5.338463	GCCTAAAGTGGTGGAGAATTCTAGT	60.338	44.000	8.25	0.00	0.00	2.57
2885	3065	3.057734	GTTACTTCACGTTCAGTCAGGG	58.942	50.000	0.00	0.00	0.00	4.45
2905	3085	0.396278	GGCTAGAATTTGCCTGGGCT	60.396	55.000	13.05	0.00	45.26	5.19
2918	3098	3.774216	TGCCTGGGCTGCTTTTTATAATT	59.226	39.130	13.05	0.00	42.51	1.40
2975	3164	4.987285	CGTGAGATCATGCTTTACTGCTAT	59.013	41.667	0.00	0.00	0.00	2.97
2979	3168	9.645059	GTGAGATCATGCTTTACTGCTATTATA	57.355	33.333	0.00	0.00	0.00	0.98
2980	3169	9.866798	TGAGATCATGCTTTACTGCTATTATAG	57.133	33.333	0.00	0.00	0.00	1.31
3006	3198	4.457466	TGATGATTGTGGATCTGTGATGG	58.543	43.478	0.00	0.00	35.69	3.51
3025	3219	7.068470	TGTGATGGACATACAATTATTGCACAT	59.932	33.333	4.68	1.44	0.00	3.21
3082	3372	1.814772	TTCATTGGTTTGCCTGGCCG	61.815	55.000	17.53	0.00	35.27	6.13
3211	3503	0.322975	ACACCTAGCCTCTGCACTTG	59.677	55.000	0.00	0.00	41.13	3.16
3308	3658	1.556911	CTCCTCTAGCACACCAACCAT	59.443	52.381	0.00	0.00	0.00	3.55
3312	3662	1.977854	TCTAGCACACCAACCATCACT	59.022	47.619	0.00	0.00	0.00	3.41
3324	3674	6.206634	CACCAACCATCACTAAATACAACACT	59.793	38.462	0.00	0.00	0.00	3.55
3352	3704	5.385198	ACATAAGAGGTCTCCAAAAGCAAA	58.615	37.500	0.00	0.00	0.00	3.68
3358	3710	2.103094	GGTCTCCAAAAGCAAAGCCTTT	59.897	45.455	0.00	0.00	36.65	3.11
3404	3769	6.109359	CGATCCAAGATCTAAGGTTTTCACT	58.891	40.000	12.46	0.00	0.00	3.41
3407	3772	6.702329	TCCAAGATCTAAGGTTTTCACTCTC	58.298	40.000	12.46	0.00	0.00	3.20
3469	3834	1.039068	TTGTCAGGCACAACCAATGG	58.961	50.000	0.00	0.00	40.29	3.16
3470	3835	0.827089	TGTCAGGCACAACCAATGGG	60.827	55.000	3.55	0.00	43.14	4.00

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
24	25	1.382240	ATGGCCGGTCACCATTTCA	59.618	52.632	13.07	0.00	45.86	2.69
124	125	3.810941	GACTTACGGTGGTGAACAATCAA	59.189	43.478	0.00	0.00	37.30	2.57
125	126	3.395639	GACTTACGGTGGTGAACAATCA	58.604	45.455	0.00	0.00	0.00	2.57
233	234	3.582120	CAACCTGGCACAACGCGT	61.582	61.111	5.58	5.58	43.84	6.01
241	242	2.277591	GGCATGCTTCAACCTGGCA	61.278	57.895	18.92	0.00	40.32	4.92
277	278	5.750067	GTGTTCAACAAAGACGGTCTTAGTA	59.250	40.000	22.67	5.69	35.27	1.82
363	364	1.188219	TTCTCTTCGCTGGACTGGCT	61.188	55.000	0.00	0.00	0.00	4.75
408	409	2.035312	ACGTACTCCCTCGGCACT	59.965	61.111	0.00	0.00	0.00	4.40
424	425	4.470462	CATTACTGCTCAAGAACAAGCAC	58.530	43.478	0.00	0.00	43.30	4.40
491	493	6.531021	ACTACTATTGTAACAACCAGCAAGT	58.469	36.000	0.00	0.00	0.00	3.16
520	522	7.409697	CCCTTTGATACATAACAGTCGAATTG	58.590	38.462	0.00	0.00	0.00	2.32
526	528	4.335594	GTGGCCCTTTGATACATAACAGTC	59.664	45.833	0.00	0.00	0.00	3.51
700	705	5.049198	TCAATCAAATGTGCAGTTCTCTGAC	60.049	40.000	0.00	0.00	43.76	3.51
706	711	6.000891	TGTAGTCAATCAAATGTGCAGTTC	57.999	37.500	0.00	0.00	0.00	3.01
743	748	2.223340	CCAGACGGCAATTATCAGCAAC	60.223	50.000	0.00	0.00	0.00	4.17
783	788	0.401738	AGTTCACCTGACACATGGGG	59.598	55.000	0.00	0.00	0.00	4.96
796	801	5.419542	TGCACAGACCATCTAATAGTTCAC	58.580	41.667	0.00	0.00	0.00	3.18
799	804	5.994250	ACATGCACAGACCATCTAATAGTT	58.006	37.500	0.00	0.00	0.00	2.24
860	865	4.660789	AGATGCACATATTTTGGGAAGC	57.339	40.909	0.00	0.00	0.00	3.86
861	866	6.400568	ACAAAGATGCACATATTTTGGGAAG	58.599	36.000	17.41	4.51	30.64	3.46
862	867	6.357579	ACAAAGATGCACATATTTTGGGAA	57.642	33.333	17.41	0.00	30.64	3.97
963	975	7.548427	TCTGATGAGTGAAGATCAAGAAATGTC	59.452	37.037	0.00	0.00	0.00	3.06
1278	1313	5.294552	AGTTCAAGACTTTCTACACACTTGC	59.705	40.000	0.00	0.00	33.92	4.01
1279	1314	6.910536	AGTTCAAGACTTTCTACACACTTG	57.089	37.500	0.00	0.00	33.92	3.16
1435	1555	6.145048	GGCAACATCAATGCTATTTTCTATGC	59.855	38.462	0.00	0.00	43.34	3.14
1638	1761	3.515502	AGGTCTAGCTCACACTTATGCAA	59.484	43.478	0.00	0.00	0.00	4.08
1846	1972	8.667076	CACAAATAGTGGTCAGATATGATGAA	57.333	34.615	0.00	0.00	44.69	2.57
2369	2509	6.582295	GCTTATTATTGCCCATTACGTTGATG	59.418	38.462	0.00	0.00	0.00	3.07
2579	2749	3.105782	TCGTTTGCAGCTCGCTCG	61.106	61.111	9.12	10.32	43.06	5.03
2595	2765	1.883725	GCGGGTTTGTCTTCGACGTC	61.884	60.000	5.18	5.18	34.95	4.34
2610	2780	2.959484	TTGCCTTCTCTCCTGCGGG	61.959	63.158	4.71	4.71	0.00	6.13
2682	2852	0.685097	AGGCTTAGCGACCACAGAAA	59.315	50.000	0.00	0.00	0.00	2.52
2746	2917	4.240881	ACAAGGATCCAGCAATACACAT	57.759	40.909	15.82	0.00	0.00	3.21
2819	2990	5.357878	GGCACCACAAGATCTCAAAATATGA	59.642	40.000	0.00	0.00	36.38	2.15
2820	2991	5.359009	AGGCACCACAAGATCTCAAAATATG	59.641	40.000	0.00	0.00	0.00	1.78
2821	2992	5.513233	AGGCACCACAAGATCTCAAAATAT	58.487	37.500	0.00	0.00	0.00	1.28
2833	3004	1.608590	CACCACTTTAGGCACCACAAG	59.391	52.381	0.00	0.00	0.00	3.16
2837	3008	0.400213	CTCCACCACTTTAGGCACCA	59.600	55.000	0.00	0.00	0.00	4.17
2848	3019	6.590677	GTGAAGTAACTAGAATTCTCCACCAC	59.409	42.308	12.24	5.26	0.00	4.16
2865	3045	2.036733	CCCCTGACTGAACGTGAAGTAA	59.963	50.000	3.54	0.00	0.00	2.24
2905	3085	8.635765	ACTCAGTTCCAGAATTATAAAAAGCA	57.364	30.769	0.00	0.00	0.00	3.91
2918	3098	6.351881	GGTTGTCCATATAACTCAGTTCCAGA	60.352	42.308	0.00	0.00	0.00	3.86
2975	3164	6.932960	CAGATCCACAATCATCAGCACTATAA	59.067	38.462	0.00	0.00	36.79	0.98
2979	3168	3.054582	ACAGATCCACAATCATCAGCACT	60.055	43.478	0.00	0.00	36.79	4.40
2980	3169	3.064958	CACAGATCCACAATCATCAGCAC	59.935	47.826	0.00	0.00	36.79	4.40
3006	3198	9.801873	ACCTTAAATGTGCAATAATTGTATGTC	57.198	29.630	0.00	0.00	0.00	3.06
3034	3228	7.552687	ACTGAACTGAACAATGAAAGTAGTGAA	59.447	33.333	0.00	0.00	0.00	3.18
3037	3231	8.204836	ACTACTGAACTGAACAATGAAAGTAGT	58.795	33.333	5.97	5.97	41.64	2.73
3040	3234	7.552687	TGAACTACTGAACTGAACAATGAAAGT	59.447	33.333	0.00	0.00	0.00	2.66
3082	3372	2.024176	TCTCATAAGCCGTTTCCAGC	57.976	50.000	0.00	0.00	0.00	4.85
3324	3674	6.016276	GCTTTTGGAGACCTCTTATGTTTTGA	60.016	38.462	0.00	0.00	0.00	2.69
3358	3710	2.223745	GCAACAACGGTTCCCTTCTTA	58.776	47.619	0.00	0.00	34.21	2.10
3404	3769	2.820787	GAGAGTTCGGACTTCCTTGAGA	59.179	50.000	0.00	0.00	35.88	3.27
3407	3772	3.386768	TTGAGAGTTCGGACTTCCTTG	57.613	47.619	0.00	0.00	35.88	3.61
3469	3834	2.374170	TGAAAACCTAAGGTCTGACCCC	59.626	50.000	22.81	0.00	39.75	4.95
3470	3835	3.782656	TGAAAACCTAAGGTCTGACCC	57.217	47.619	22.81	5.74	39.75	4.46

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.