AutoCloner

Multiple sequence alignment - TraesCS4A01G153700

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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	TraesCS4A01G153700	chr4A	100.000	3065	0	0	1	3065	309513381	309516445	0.000000e+00	5661
1	TraesCS4A01G153700	chr3D	96.413	3067	95	10	1	3065	589281283	589278230	0.000000e+00	5040
2	TraesCS4A01G153700	chr5D	96.381	3067	99	9	1	3065	503279967	503276911	0.000000e+00	5038
3	TraesCS4A01G153700	chr5D	96.317	3068	100	9	1	3065	6187198	6190255	0.000000e+00	5027
4	TraesCS4A01G153700	chr5D	95.275	3069	128	13	1	3065	432405237	432402182	0.000000e+00	4848
5	TraesCS4A01G153700	chr5D	96.820	2767	84	3	300	3065	503216770	503219533	0.000000e+00	4619
6	TraesCS4A01G153700	chr1A	96.317	3068	93	9	1	3065	554510513	554513563	0.000000e+00	5022
7	TraesCS4A01G153700	chr1D	96.219	3068	103	9	1	3065	254399852	254396795	0.000000e+00	5011
8	TraesCS4A01G153700	chr5A	95.532	3066	126	8	2	3065	607272658	607275714	0.000000e+00	4892
9	TraesCS4A01G153700	chr2A	95.112	3069	116	13	1	3065	335836906	335839944	0.000000e+00	4806
10	TraesCS4A01G153700	chr6D	96.785	2768	84	4	300	3065	168253477	168256241	0.000000e+00	4614
11	TraesCS4A01G153700	chr6D	95.570	1219	40	9	1	1214	45517828	45519037	0.000000e+00	1940
12	TraesCS4A01G153700	chr3B	96.785	2768	83	5	300	3065	201525576	201528339	0.000000e+00	4614
13	TraesCS4A01G153700	chrUn	96.357	549	13	4	1	548	239346006	239345464	0.000000e+00	896
14	TraesCS4A01G153700	chr2B	94.981	259	12	1	56	313	755374313	755374055	3.680000e-109	405
15	TraesCS4A01G153700	chr6B	94.466	253	7	4	1	252	450081058	450080812	1.720000e-102	383
16	TraesCS4A01G153700	chr2D	97.674	129	2	1	231	358	235487354	235487226	1.430000e-53	220

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	TraesCS4A01G153700	chr4A	309513381	309516445	3064	False	5661	5661	100.000	1	3065	1	chr4A.!!$F1	3064
1	TraesCS4A01G153700	chr3D	589278230	589281283	3053	True	5040	5040	96.413	1	3065	1	chr3D.!!$R1	3064
2	TraesCS4A01G153700	chr5D	503276911	503279967	3056	True	5038	5038	96.381	1	3065	1	chr5D.!!$R2	3064
3	TraesCS4A01G153700	chr5D	6187198	6190255	3057	False	5027	5027	96.317	1	3065	1	chr5D.!!$F1	3064
4	TraesCS4A01G153700	chr5D	432402182	432405237	3055	True	4848	4848	95.275	1	3065	1	chr5D.!!$R1	3064
5	TraesCS4A01G153700	chr5D	503216770	503219533	2763	False	4619	4619	96.820	300	3065	1	chr5D.!!$F2	2765
6	TraesCS4A01G153700	chr1A	554510513	554513563	3050	False	5022	5022	96.317	1	3065	1	chr1A.!!$F1	3064
7	TraesCS4A01G153700	chr1D	254396795	254399852	3057	True	5011	5011	96.219	1	3065	1	chr1D.!!$R1	3064
8	TraesCS4A01G153700	chr5A	607272658	607275714	3056	False	4892	4892	95.532	2	3065	1	chr5A.!!$F1	3063
9	TraesCS4A01G153700	chr2A	335836906	335839944	3038	False	4806	4806	95.112	1	3065	1	chr2A.!!$F1	3064
10	TraesCS4A01G153700	chr6D	168253477	168256241	2764	False	4614	4614	96.785	300	3065	1	chr6D.!!$F2	2765
11	TraesCS4A01G153700	chr6D	45517828	45519037	1209	False	1940	1940	95.570	1	1214	1	chr6D.!!$F1	1213
12	TraesCS4A01G153700	chr3B	201525576	201528339	2763	False	4614	4614	96.785	300	3065	1	chr3B.!!$F1	2765
13	TraesCS4A01G153700	chrUn	239345464	239346006	542	True	896	896	96.357	1	548	1	chrUn.!!$R1	547

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
431	435	0.530288	AATTCCCCCAATTTGCGACG	59.470	50.0	0.0	0.0	29.6	5.12	F
1550	1561	0.165944	GGTTTCTGCGTTCCGTCATG	59.834	55.0	0.0	0.0	0.0	3.07	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1735	1746	1.250840	GGAAGCGCCCCTTGTTTCAT	61.251	55.000	2.29	0.0	32.78	2.57	R
2460	2472	3.369175	TGGGCCATACAATGCATTACAA	58.631	40.909	12.53	0.6	0.00	2.41	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
61	62	6.763610	GGTTTCAATTTCAACCACAACCAATA	59.236	34.615	9.76	0.00	41.97	1.90
62	63	7.254624	GGTTTCAATTTCAACCACAACCAATAC	60.255	37.037	9.76	0.00	41.97	1.89
82	83	7.255569	CAATACGTAGTTGATAGTCAAGGTCA	58.744	38.462	0.08	0.00	37.78	4.02
100	101	6.549433	AGGTCACGTTATTAATACTTGGGA	57.451	37.500	0.00	0.00	0.00	4.37
389	393	8.470002	AGTATCCTTTCTTGCATTTTCATAACC	58.530	33.333	0.00	0.00	0.00	2.85
431	435	0.530288	AATTCCCCCAATTTGCGACG	59.470	50.000	0.00	0.00	29.60	5.12
454	458	8.652810	ACGTACCATAGGATTTGTTATGTAAC	57.347	34.615	0.00	0.00	36.74	2.50
526	530	2.370189	GTGGGTAGAATGCTAGATGCCT	59.630	50.000	0.00	0.00	42.00	4.75
552	556	6.650390	GGGACCACGTTACTATTGTTTCTTTA	59.350	38.462	0.00	0.00	0.00	1.85
557	561	8.943002	CCACGTTACTATTGTTTCTTTATCCTT	58.057	33.333	0.00	0.00	0.00	3.36
642	646	5.411831	TTCATGTCACAGCTGATTACTCT	57.588	39.130	23.35	4.52	0.00	3.24
768	775	1.119574	TAGCTGGATAAGGGGCGGAC	61.120	60.000	0.00	0.00	0.00	4.79
888	896	8.815565	TGCAATTTTCCATATTCCTAGTTACA	57.184	30.769	0.00	0.00	0.00	2.41
1146	1156	2.489985	CCCAACATTACCCACTTGTCCA	60.490	50.000	0.00	0.00	0.00	4.02
1154	1164	1.005450	ACCCACTTGTCCAACTGTTGT	59.995	47.619	18.38	0.00	0.00	3.32
1192	1202	2.023695	ACTAAACGGACCTCCCCAGATA	60.024	50.000	0.00	0.00	0.00	1.98
1272	1282	1.141858	GCTCTAGCTAATTGCCCACCT	59.858	52.381	0.00	0.00	44.23	4.00
1499	1510	3.099141	GGAAAGGAATCCAAATCTGCCA	58.901	45.455	0.61	0.00	39.42	4.92
1514	1525	2.677836	TCTGCCAAATCGCTCATGTTAC	59.322	45.455	0.00	0.00	0.00	2.50
1534	1545	6.832384	TGTTACGATCTTCTACATCCTAGGTT	59.168	38.462	9.08	0.00	0.00	3.50
1550	1561	0.165944	GGTTTCTGCGTTCCGTCATG	59.834	55.000	0.00	0.00	0.00	3.07
1564	1575	3.449377	TCCGTCATGTGGCTTATGTTCTA	59.551	43.478	0.00	0.00	0.00	2.10
1654	1665	3.056832	GGAGACATCCCTATTTTCCCCT	58.943	50.000	0.00	0.00	40.03	4.79
1674	1685	4.042174	CCTGGGGGTCTTAATTACCACTA	58.958	47.826	8.78	3.08	40.51	2.74
1679	1690	6.910290	TGGGGGTCTTAATTACCACTACTTAT	59.090	38.462	8.78	0.00	40.51	1.73
1723	1734	8.820831	ACCATCAAATTAAATGTGAATAACCCA	58.179	29.630	0.00	0.00	0.00	4.51
1735	1746	5.148502	GTGAATAACCCATCCTCCTCTCTA	58.851	45.833	0.00	0.00	0.00	2.43
1778	1789	1.330521	TCTCTGCGTGCTTCAAACAAC	59.669	47.619	0.00	0.00	0.00	3.32
1791	1802	5.163612	GCTTCAAACAACTTTGTCTTCTCCT	60.164	40.000	0.00	0.00	41.31	3.69
1855	1866	3.813443	ACTGAACTCAATCACTTGCTGT	58.187	40.909	0.00	0.00	32.11	4.40
1866	1877	3.990092	TCACTTGCTGTCGTTACTCAAT	58.010	40.909	0.00	0.00	0.00	2.57
1892	1903	4.760530	TTCTGTTGAGGTCTATCCCATG	57.239	45.455	0.00	0.00	36.75	3.66
1911	1922	5.203528	CCATGGAGGTAGTCAAATTGGATT	58.796	41.667	5.56	0.00	0.00	3.01
1936	1947	6.464222	AGTGATCGATTTCTAGGTTTTGTCA	58.536	36.000	0.00	0.00	0.00	3.58
1987	1998	5.732647	CGTAAATCAATAGTTCAAACCGCAG	59.267	40.000	0.00	0.00	0.00	5.18
2081	2093	8.986991	AGCCCTCTAGGATGTAAAATATATCTG	58.013	37.037	0.00	0.00	38.24	2.90
2149	2161	9.096823	TCAATTAGGGTCGTATTCTATGGTTAT	57.903	33.333	0.00	0.00	0.00	1.89
2219	2231	0.603569	ATAGGCGCTTATGACCTCCG	59.396	55.000	11.70	0.00	34.92	4.63
2220	2232	0.466739	TAGGCGCTTATGACCTCCGA	60.467	55.000	7.64	0.00	34.92	4.55
2249	2261	3.494398	GCCTTGCGGTAATGATTCCTCTA	60.494	47.826	0.00	0.00	0.00	2.43
2257	2269	7.152645	GCGGTAATGATTCCTCTAGAATTACA	58.847	38.462	18.02	6.82	45.52	2.41
2365	2377	5.071250	TGCTCGGGATAGGTGTTTTGTATAT	59.929	40.000	0.00	0.00	0.00	0.86
2460	2472	5.820947	GGTTGAAGGGTAATGATCATACGTT	59.179	40.000	9.04	10.09	0.00	3.99
2637	2650	4.963276	TGATTCTTGCCCAATAAACGAG	57.037	40.909	0.00	0.00	0.00	4.18
2698	2712	6.329197	TCCATAAATCGACTTTCCCTCCTATT	59.671	38.462	0.00	0.00	0.00	1.73
2701	2715	5.959583	AATCGACTTTCCCTCCTATTCTT	57.040	39.130	0.00	0.00	0.00	2.52
2709	2723	6.273495	ACTTTCCCTCCTATTCTTTGAGTTCT	59.727	38.462	0.00	0.00	0.00	3.01
2952	2966	4.023107	ACAGGGATCATCGTACATCGTAAG	60.023	45.833	0.00	0.00	40.80	2.34
3057	3071	2.305927	TGAAAACACCTCTCTGGATCCC	59.694	50.000	9.90	0.00	39.71	3.85

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
47	48	4.778904	CAACTACGTATTGGTTGTGGTTG	58.221	43.478	14.72	9.89	44.62	3.77
48	49	4.706035	TCAACTACGTATTGGTTGTGGTT	58.294	39.130	19.59	5.87	40.52	3.67
49	50	4.339872	TCAACTACGTATTGGTTGTGGT	57.660	40.909	19.59	0.44	40.52	4.16
50	51	6.103997	ACTATCAACTACGTATTGGTTGTGG	58.896	40.000	19.59	13.64	40.52	4.17
51	52	6.809689	TGACTATCAACTACGTATTGGTTGTG	59.190	38.462	19.59	14.86	40.52	3.33
52	53	6.927416	TGACTATCAACTACGTATTGGTTGT	58.073	36.000	19.59	16.35	40.52	3.32
61	62	4.379186	CGTGACCTTGACTATCAACTACGT	60.379	45.833	0.00	0.00	32.21	3.57
62	63	4.096311	CGTGACCTTGACTATCAACTACG	58.904	47.826	0.00	0.00	32.21	3.51
100	101	4.997395	GGTTAGCACGGTTGATGATATCAT	59.003	41.667	18.21	18.21	39.39	2.45
238	240	8.533569	TGGGTATTTCTGTCTTTTCTTTCTTT	57.466	30.769	0.00	0.00	0.00	2.52
389	393	2.677971	CCTACTCGGCATTTCACGG	58.322	57.895	0.00	0.00	0.00	4.94
526	530	4.040706	AGAAACAATAGTAACGTGGTCCCA	59.959	41.667	0.00	0.00	0.00	4.37
768	775	1.656652	CCTTGATCCACTTGGCTACG	58.343	55.000	0.00	0.00	34.44	3.51
888	896	7.781548	ATTCTTCGTTGCCGTAAGTAAATAT	57.218	32.000	0.00	0.00	35.01	1.28
1086	1096	1.000052	GGTAGAGCCGGATCTAAGTGC	60.000	57.143	29.95	17.47	33.66	4.40
1154	1164	6.149807	CCGTTTAGTATCCCAAAACTGCTTAA	59.850	38.462	0.00	0.00	32.25	1.85
1192	1202	6.541278	GGTAAATCGGCCACTTTAAGATTACT	59.459	38.462	2.24	0.00	32.05	2.24
1272	1282	5.147330	ACATAGAAATCACACGTGGAAGA	57.853	39.130	21.57	14.78	0.00	2.87
1312	1322	2.622064	ACTTCAACCGATATGCCCTC	57.378	50.000	0.00	0.00	0.00	4.30
1477	1488	2.432146	GGCAGATTTGGATTCCTTTCCC	59.568	50.000	3.95	0.00	34.67	3.97
1499	1510	5.352284	AGAAGATCGTAACATGAGCGATTT	58.648	37.500	18.67	13.35	44.06	2.17
1514	1525	6.442952	CAGAAACCTAGGATGTAGAAGATCG	58.557	44.000	17.98	0.00	0.00	3.69
1550	1561	5.116180	TGCTACATGTAGAACATAAGCCAC	58.884	41.667	32.39	12.97	41.94	5.01
1654	1665	4.702196	AGTAGTGGTAATTAAGACCCCCA	58.298	43.478	6.83	0.00	35.99	4.96
1674	1685	6.151817	GGTCAGAGGCAAATTGAAAGATAAGT	59.848	38.462	0.00	0.00	0.00	2.24
1679	1690	3.831323	TGGTCAGAGGCAAATTGAAAGA	58.169	40.909	0.00	0.00	0.00	2.52
1723	1734	4.657969	CCCTTGTTTCATAGAGAGGAGGAT	59.342	45.833	0.00	0.00	0.00	3.24
1735	1746	1.250840	GGAAGCGCCCCTTGTTTCAT	61.251	55.000	2.29	0.00	32.78	2.57
1761	1772	2.193306	AAGTTGTTTGAAGCACGCAG	57.807	45.000	0.00	0.00	0.00	5.18
1855	1866	7.384115	CCTCAACAGAAAACTATTGAGTAACGA	59.616	37.037	14.28	0.00	44.28	3.85
1866	1877	5.783360	TGGGATAGACCTCAACAGAAAACTA	59.217	40.000	0.00	0.00	38.98	2.24
1892	1903	6.650120	TCACTAATCCAATTTGACTACCTCC	58.350	40.000	0.00	0.00	0.00	4.30
1911	1922	7.608153	TGACAAAACCTAGAAATCGATCACTA	58.392	34.615	0.00	4.95	0.00	2.74
2081	2093	2.505819	ACACTATGGGGATGGTGAGAAC	59.494	50.000	5.65	0.00	36.65	3.01
2125	2137	9.096823	TCATAACCATAGAATACGACCCTAATT	57.903	33.333	0.00	0.00	0.00	1.40
2249	2261	5.239963	CCGTTGTGGTAAAGGTTGTAATTCT	59.760	40.000	0.00	0.00	0.00	2.40
2278	2290	6.777091	TCCACGAAATAATTTGATCCATGGAT	59.223	34.615	27.66	27.66	37.59	3.41
2460	2472	3.369175	TGGGCCATACAATGCATTACAA	58.631	40.909	12.53	0.60	0.00	2.41
2624	2637	4.514781	AAAAAGTCCTCGTTTATTGGGC	57.485	40.909	0.00	0.00	0.00	5.36
2701	2715	9.880064	CGAATTCTTATCGATACTAGAACTCAA	57.120	33.333	20.09	4.45	42.76	3.02
2761	2775	6.708502	TCCATACATAACGAATTGGTATGGTG	59.291	38.462	21.76	7.96	45.91	4.17
2874	2888	7.102346	CCCAACTCATAATTGGTAAATTTGCA	58.898	34.615	8.59	0.00	44.46	4.08

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.