AutoCloner

Multiple sequence alignment - TraesCS2D01G534700

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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	TraesCS2D01G534700	chr2D	100.000	2945	0	0	1	2945	618201754	618204698	0.000000e+00	5439.0
1	TraesCS2D01G534700	chr2D	82.160	1491	201	33	723	2171	605778351	605776884	0.000000e+00	1219.0
2	TraesCS2D01G534700	chr2D	79.325	1630	265	44	590	2171	22311853	22310248	0.000000e+00	1077.0
3	TraesCS2D01G534700	chr2D	79.215	1631	266	44	590	2171	22333953	22332347	0.000000e+00	1066.0
4	TraesCS2D01G534700	chr2D	79.230	1507	248	36	590	2066	22351609	22350138	0.000000e+00	989.0
5	TraesCS2D01G534700	chr2D	81.728	1215	175	28	894	2084	22248560	22247369	0.000000e+00	970.0
6	TraesCS2D01G534700	chr2D	80.471	1188	195	21	593	1751	22361135	22359956	0.000000e+00	874.0
7	TraesCS2D01G534700	chr2A	93.210	2489	104	24	494	2945	749058349	749060809	0.000000e+00	3600.0
8	TraesCS2D01G534700	chr2A	90.549	328	21	5	1	319	749057152	749057478	2.710000e-115	425.0
9	TraesCS2D01G534700	chr2A	97.475	198	5	0	315	512	749058135	749058332	3.640000e-89	339.0
10	TraesCS2D01G534700	chr2B	93.168	1771	91	17	440	2189	754782480	754784241	0.000000e+00	2573.0
11	TraesCS2D01G534700	chr2B	91.933	719	27	3	2227	2945	754784325	754785012	0.000000e+00	977.0
12	TraesCS2D01G534700	chr2B	88.533	375	22	3	1	358	754782017	754782387	4.510000e-118	435.0
13	TraesCS2D01G534700	chr2B	94.872	39	2	0	2203	2241	710979802	710979764	8.810000e-06	62.1
14	TraesCS2D01G534700	chr2B	100.000	28	0	0	2175	2202	2344372	2344399	5.000000e-03	52.8
15	TraesCS2D01G534700	chr6D	90.064	1882	149	20	320	2175	26003736	26001867	0.000000e+00	2405.0
16	TraesCS2D01G534700	chr6D	89.308	159	12	5	1	159	26004010	26003857	8.330000e-46	195.0
17	TraesCS2D01G534700	chr6D	92.857	56	4	0	2890	2945	25993218	25993163	6.760000e-12	82.4
18	TraesCS2D01G534700	chrUn	78.333	1320	221	34	889	2171	12741679	12740388	0.000000e+00	793.0
19	TraesCS2D01G534700	chrUn	78.387	1314	219	34	889	2165	227694410	227695695	0.000000e+00	793.0
20	TraesCS2D01G534700	chrUn	78.258	1320	222	34	889	2171	203473152	203471861	0.000000e+00	787.0
21	TraesCS2D01G534700	chrUn	82.028	868	137	7	889	1740	232604490	232605354	0.000000e+00	721.0
22	TraesCS2D01G534700	chrUn	82.028	868	137	7	889	1740	337161685	337162549	0.000000e+00	721.0
23	TraesCS2D01G534700	chr7D	97.222	36	1	0	2203	2238	554586113	554586148	8.810000e-06	62.1
24	TraesCS2D01G534700	chr7A	97.222	36	1	0	2203	2238	115859513	115859478	8.810000e-06	62.1
25	TraesCS2D01G534700	chr6A	97.222	36	1	0	2203	2238	24039624	24039659	8.810000e-06	62.1
26	TraesCS2D01G534700	chr3B	97.222	36	1	0	2203	2238	27056240	27056275	8.810000e-06	62.1
27	TraesCS2D01G534700	chr1B	97.222	36	1	0	2203	2238	652634881	652634846	8.810000e-06	62.1
28	TraesCS2D01G534700	chr5D	94.737	38	2	0	2199	2236	302377912	302377875	3.170000e-05	60.2
29	TraesCS2D01G534700	chr5B	92.857	42	2	1	2198	2238	16006781	16006740	3.170000e-05	60.2
30	TraesCS2D01G534700	chr5A	94.872	39	0	2	2208	2246	457905306	457905270	3.170000e-05	60.2

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	TraesCS2D01G534700	chr2D	618201754	618204698	2944	False	5439.000000	5439	100.000000	1	2945	1	chr2D.!!$F1	2944
1	TraesCS2D01G534700	chr2D	605776884	605778351	1467	True	1219.000000	1219	82.160000	723	2171	1	chr2D.!!$R6	1448
2	TraesCS2D01G534700	chr2D	22310248	22311853	1605	True	1077.000000	1077	79.325000	590	2171	1	chr2D.!!$R2	1581
3	TraesCS2D01G534700	chr2D	22332347	22333953	1606	True	1066.000000	1066	79.215000	590	2171	1	chr2D.!!$R3	1581
4	TraesCS2D01G534700	chr2D	22350138	22351609	1471	True	989.000000	989	79.230000	590	2066	1	chr2D.!!$R4	1476
5	TraesCS2D01G534700	chr2D	22247369	22248560	1191	True	970.000000	970	81.728000	894	2084	1	chr2D.!!$R1	1190
6	TraesCS2D01G534700	chr2D	22359956	22361135	1179	True	874.000000	874	80.471000	593	1751	1	chr2D.!!$R5	1158
7	TraesCS2D01G534700	chr2A	749057152	749060809	3657	False	1454.666667	3600	93.744667	1	2945	3	chr2A.!!$F1	2944
8	TraesCS2D01G534700	chr2B	754782017	754785012	2995	False	1328.333333	2573	91.211333	1	2945	3	chr2B.!!$F2	2944
9	TraesCS2D01G534700	chr6D	26001867	26004010	2143	True	1300.000000	2405	89.686000	1	2175	2	chr6D.!!$R2	2174
10	TraesCS2D01G534700	chrUn	12740388	12741679	1291	True	793.000000	793	78.333000	889	2171	1	chrUn.!!$R1	1282
11	TraesCS2D01G534700	chrUn	227694410	227695695	1285	False	793.000000	793	78.387000	889	2165	1	chrUn.!!$F1	1276
12	TraesCS2D01G534700	chrUn	203471861	203473152	1291	True	787.000000	787	78.258000	889	2171	1	chrUn.!!$R2	1282
13	TraesCS2D01G534700	chrUn	232604490	232605354	864	False	721.000000	721	82.028000	889	1740	1	chrUn.!!$F2	851
14	TraesCS2D01G534700	chrUn	337161685	337162549	864	False	721.000000	721	82.028000	889	1740	1	chrUn.!!$F3	851

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
141	143	0.905357	CGGGAGTGGAAGAAGTGGAT	59.095	55.0	0.00	0.00	0.0	3.41	F
1064	1910	0.527169	ATCATCGACGCTGTGCAGAG	60.527	55.0	6.48	6.48	0.0	3.35	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1353	2199	0.601558	GCTGTAAGGTGGAGACGACA	59.398	55.0	0.0	0.0	0.0	4.35	R
2874	3797	0.673644	CCTAGGTTCTTGGGCGTGTG	60.674	60.0	0.0	0.0	0.0	3.82	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
141	143	0.905357	CGGGAGTGGAAGAAGTGGAT	59.095	55.000	0.00	0.00	0.00	3.41
151	153	4.072131	GGAAGAAGTGGATGTAAAGCACA	58.928	43.478	0.00	0.00	42.69	4.57
169	171	3.763897	GCACATCAAAATACCACTCCCTT	59.236	43.478	0.00	0.00	0.00	3.95
171	173	5.009631	CACATCAAAATACCACTCCCTTCA	58.990	41.667	0.00	0.00	0.00	3.02
191	195	9.647797	CCCTTCATAAACTAATATACATGCGTA	57.352	33.333	0.00	0.00	0.00	4.42
422	1182	2.315925	ACATAGAATGTGGAGCACCG	57.684	50.000	0.00	0.00	43.01	4.94
425	1185	3.270027	CATAGAATGTGGAGCACCGAAA	58.730	45.455	0.00	0.00	39.42	3.46
687	1489	2.825836	GACATTCCTGCTGCCGGG	60.826	66.667	10.32	6.35	38.98	5.73
1013	1859	1.598701	GCTGTGATGTGCCCTTTCCC	61.599	60.000	0.00	0.00	0.00	3.97
1064	1910	0.527169	ATCATCGACGCTGTGCAGAG	60.527	55.000	6.48	6.48	0.00	3.35
1101	1947	2.458610	CCACGTCGTCGATCTCGGA	61.459	63.158	9.47	0.00	40.62	4.55
1300	2146	1.138266	ACCCGGTGAAACTCCATATCG	59.862	52.381	0.00	0.00	36.74	2.92
1549	2398	2.650196	CCAACCACAACGGCATGG	59.350	61.111	0.00	0.00	42.13	3.66
1554	2403	0.467290	ACCACAACGGCATGGAGTTT	60.467	50.000	7.96	0.00	39.46	2.66
1556	2405	1.883275	CCACAACGGCATGGAGTTTAA	59.117	47.619	0.00	0.00	38.34	1.52
1995	2844	3.872182	CCTGTGATCTTCTTGCAGATCTG	59.128	47.826	18.84	18.84	46.64	2.90
2009	2858	2.037144	AGATCTGCCCAATTCATTGCC	58.963	47.619	0.00	0.00	36.48	4.52
2068	2921	7.178274	TGGTTATTTGCCTGAACTTGTTATCAT	59.822	33.333	0.00	0.00	0.00	2.45
2098	2962	4.398549	TGTTGTTATCGTACTGCAAAGC	57.601	40.909	0.00	0.00	0.00	3.51
2126	2998	1.334869	CACACCAGCAGACTTTGGAAC	59.665	52.381	9.28	0.00	37.89	3.62
2189	3064	7.270779	ACATTTTAATTAGTACTCCCTCCGTC	58.729	38.462	0.00	0.00	0.00	4.79
2190	3065	5.505173	TTTAATTAGTACTCCCTCCGTCG	57.495	43.478	0.00	0.00	0.00	5.12
2191	3066	1.316651	ATTAGTACTCCCTCCGTCGC	58.683	55.000	0.00	0.00	0.00	5.19
2192	3067	0.035152	TTAGTACTCCCTCCGTCGCA	60.035	55.000	0.00	0.00	0.00	5.10
2198	3073	1.276989	ACTCCCTCCGTCGCAAAATAA	59.723	47.619	0.00	0.00	0.00	1.40
2199	3074	1.933853	CTCCCTCCGTCGCAAAATAAG	59.066	52.381	0.00	0.00	0.00	1.73
2203	3078	3.255725	CCTCCGTCGCAAAATAAGTGTA	58.744	45.455	0.00	0.00	0.00	2.90
2204	3079	3.680937	CCTCCGTCGCAAAATAAGTGTAA	59.319	43.478	0.00	0.00	0.00	2.41
2208	3083	5.640357	TCCGTCGCAAAATAAGTGTAAGATT	59.360	36.000	0.00	0.00	0.00	2.40
2209	3084	5.732647	CCGTCGCAAAATAAGTGTAAGATTG	59.267	40.000	0.00	0.00	0.00	2.67
2211	3086	6.678663	CGTCGCAAAATAAGTGTAAGATTGAG	59.321	38.462	0.00	0.00	0.00	3.02
2212	3087	7.411480	CGTCGCAAAATAAGTGTAAGATTGAGA	60.411	37.037	0.00	0.00	0.00	3.27
2213	3088	7.688578	GTCGCAAAATAAGTGTAAGATTGAGAC	59.311	37.037	0.00	0.00	38.34	3.36
2215	3090	7.478667	CGCAAAATAAGTGTAAGATTGAGACAC	59.521	37.037	0.00	0.00	43.08	3.67
2305	3226	1.514678	GCCGCCATGTGAAGACAACA	61.515	55.000	0.00	0.00	35.11	3.33
2325	3246	2.857186	TCCTTATCACACTGCTTGCA	57.143	45.000	0.00	0.00	0.00	4.08
2336	3257	2.102578	ACTGCTTGCAACCAGTCTTTT	58.897	42.857	19.50	0.00	37.77	2.27
2436	3358	1.002468	CTTCGTTTGTTGTGGGAGCAG	60.002	52.381	0.00	0.00	0.00	4.24
2437	3359	0.107410	TCGTTTGTTGTGGGAGCAGT	60.107	50.000	0.00	0.00	0.00	4.40
2438	3360	1.139256	TCGTTTGTTGTGGGAGCAGTA	59.861	47.619	0.00	0.00	0.00	2.74
2439	3361	1.531149	CGTTTGTTGTGGGAGCAGTAG	59.469	52.381	0.00	0.00	0.00	2.57
2519	3442	9.238368	TGTTCTTCCTTTTCAGTTTCTTCTTTA	57.762	29.630	0.00	0.00	0.00	1.85
2549	3472	3.779850	ATTCGCTCCATGCCGGCAT	62.780	57.895	36.10	36.10	38.78	4.40
2674	3597	5.293324	GTGCATACATCGGATTGTTCTAACA	59.707	40.000	0.00	0.00	37.08	2.41
2698	3621	1.929836	GCGAGTAAAGCATGACTGAGG	59.070	52.381	0.00	0.00	34.19	3.86
2705	3628	0.837691	AGCATGACTGAGGTGGTGGA	60.838	55.000	0.00	0.00	0.00	4.02
2847	3770	3.486383	TCAAAAATCGCTTGAGGGTTCT	58.514	40.909	0.00	0.00	0.00	3.01
2848	3771	3.888930	TCAAAAATCGCTTGAGGGTTCTT	59.111	39.130	0.00	0.00	0.00	2.52
2849	3772	5.067273	TCAAAAATCGCTTGAGGGTTCTTA	58.933	37.500	0.00	0.00	0.00	2.10
2850	3773	5.048991	TCAAAAATCGCTTGAGGGTTCTTAC	60.049	40.000	0.00	0.00	0.00	2.34
2851	3774	3.695830	AATCGCTTGAGGGTTCTTACA	57.304	42.857	0.00	0.00	0.00	2.41
2852	3775	3.695830	ATCGCTTGAGGGTTCTTACAA	57.304	42.857	0.00	0.00	0.00	2.41
2853	3776	3.478857	TCGCTTGAGGGTTCTTACAAA	57.521	42.857	0.00	0.00	0.00	2.83
2854	3777	3.399330	TCGCTTGAGGGTTCTTACAAAG	58.601	45.455	0.00	0.00	0.00	2.77
2855	3778	3.070446	TCGCTTGAGGGTTCTTACAAAGA	59.930	43.478	0.00	0.00	35.26	2.52
2856	3779	3.813166	CGCTTGAGGGTTCTTACAAAGAA	59.187	43.478	0.00	0.00	44.82	2.52
2874	3797	1.886542	GAAAGGGATGTGTGTGAACCC	59.113	52.381	0.00	0.00	40.71	4.11

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
141	143	6.072175	GGAGTGGTATTTTGATGTGCTTTACA	60.072	38.462	0.00	0.00	44.87	2.41
151	153	8.116026	AGTTTATGAAGGGAGTGGTATTTTGAT	58.884	33.333	0.00	0.00	0.00	2.57
284	305	2.445565	ACGTTCTAAAACTCCGACCC	57.554	50.000	0.00	0.00	32.95	4.46
422	1182	8.566008	ACGAGATGCTTAAATATGCAAATTTC	57.434	30.769	5.28	0.01	42.74	2.17
425	1185	7.042051	ACGTACGAGATGCTTAAATATGCAAAT	60.042	33.333	24.41	0.00	42.74	2.32
738	1546	2.876645	CGCGCTCCTCGTCTTGAC	60.877	66.667	5.56	0.00	41.07	3.18
802	1610	0.987294	CCAGCTCCTTCTTCCCTTCA	59.013	55.000	0.00	0.00	0.00	3.02
1064	1910	3.567797	GCACGGCATTCCTCTCGC	61.568	66.667	0.00	0.00	0.00	5.03
1353	2199	0.601558	GCTGTAAGGTGGAGACGACA	59.398	55.000	0.00	0.00	0.00	4.35
1549	2398	1.673923	CCCGAACCGGTCCTTAAACTC	60.674	57.143	8.04	0.00	46.80	3.01
1554	2403	1.876497	CGTTCCCGAACCGGTCCTTA	61.876	60.000	8.04	0.00	46.80	2.69
1556	2405	3.688159	CGTTCCCGAACCGGTCCT	61.688	66.667	8.04	0.00	46.80	3.85
1779	2628	4.473520	CCGGGGCTCATTGTCGCT	62.474	66.667	0.00	0.00	0.00	4.93
1995	2844	2.888834	ATTACGGCAATGAATTGGGC	57.111	45.000	5.25	0.00	38.21	5.36
1997	2846	7.202526	ACTATGAAATTACGGCAATGAATTGG	58.797	34.615	5.25	0.00	38.21	3.16
2009	2858	6.806739	TGCATCCGATCTACTATGAAATTACG	59.193	38.462	0.00	0.00	0.00	3.18
2068	2921	6.908284	GCAGTACGATAACAACAACTCAAAAA	59.092	34.615	0.00	0.00	0.00	1.94
2181	3056	1.396996	CACTTATTTTGCGACGGAGGG	59.603	52.381	0.00	0.00	0.00	4.30
2189	3064	7.478667	GTGTCTCAATCTTACACTTATTTTGCG	59.521	37.037	0.00	0.00	40.25	4.85
2190	3065	8.660968	GTGTCTCAATCTTACACTTATTTTGC	57.339	34.615	0.00	0.00	40.25	3.68
2203	3078	7.549488	CCGTCCTAAAATAAGTGTCTCAATCTT	59.451	37.037	0.00	0.00	0.00	2.40
2204	3079	7.042335	CCGTCCTAAAATAAGTGTCTCAATCT	58.958	38.462	0.00	0.00	0.00	2.40
2208	3083	5.105473	CCTCCGTCCTAAAATAAGTGTCTCA	60.105	44.000	0.00	0.00	0.00	3.27
2209	3084	5.126707	TCCTCCGTCCTAAAATAAGTGTCTC	59.873	44.000	0.00	0.00	0.00	3.36
2211	3086	5.334724	TCCTCCGTCCTAAAATAAGTGTC	57.665	43.478	0.00	0.00	0.00	3.67
2212	3087	5.247792	ACTTCCTCCGTCCTAAAATAAGTGT	59.752	40.000	0.00	0.00	0.00	3.55
2213	3088	5.731591	ACTTCCTCCGTCCTAAAATAAGTG	58.268	41.667	0.00	0.00	0.00	3.16
2215	3090	6.870769	TGTACTTCCTCCGTCCTAAAATAAG	58.129	40.000	0.00	0.00	0.00	1.73
2216	3091	6.855763	TGTACTTCCTCCGTCCTAAAATAA	57.144	37.500	0.00	0.00	0.00	1.40
2222	3097	2.042162	ACCTTGTACTTCCTCCGTCCTA	59.958	50.000	0.00	0.00	0.00	2.94
2224	3099	1.264295	ACCTTGTACTTCCTCCGTCC	58.736	55.000	0.00	0.00	0.00	4.79
2274	3195	2.292267	CATGGCGGCTGTTAGAAAGAT	58.708	47.619	11.43	0.00	0.00	2.40
2305	3226	3.354948	TGCAAGCAGTGTGATAAGGAT	57.645	42.857	0.00	0.00	0.00	3.24
2325	3246	6.292703	CGATGAAGTCGTTAAAAAGACTGGTT	60.293	38.462	11.24	0.00	44.94	3.67
2436	3358	5.179555	CCAGTCAAAGGAACAAAGTAGCTAC	59.820	44.000	16.43	16.43	0.00	3.58
2437	3359	5.305585	CCAGTCAAAGGAACAAAGTAGCTA	58.694	41.667	0.00	0.00	0.00	3.32
2438	3360	4.137543	CCAGTCAAAGGAACAAAGTAGCT	58.862	43.478	0.00	0.00	0.00	3.32
2439	3361	3.304726	GCCAGTCAAAGGAACAAAGTAGC	60.305	47.826	0.00	0.00	0.00	3.58
2481	3403	5.700402	AAGGAAGAACACTAGTGGCATAT	57.300	39.130	26.12	8.77	34.19	1.78
2549	3472	0.761323	TTCACCAAGTCCTCCGACCA	60.761	55.000	0.00	0.00	40.12	4.02
2674	3597	1.210478	AGTCATGCTTTACTCGCCCAT	59.790	47.619	0.00	0.00	0.00	4.00
2698	3621	2.616510	CCATCAACTCCTTCTCCACCAC	60.617	54.545	0.00	0.00	0.00	4.16
2757	3680	1.273327	GGATGGTTGTTTGGAAGCTGG	59.727	52.381	0.00	0.00	0.00	4.85
2847	3770	5.441500	TCACACACATCCCTTTCTTTGTAA	58.558	37.500	0.00	0.00	0.00	2.41
2848	3771	5.042463	TCACACACATCCCTTTCTTTGTA	57.958	39.130	0.00	0.00	0.00	2.41
2849	3772	3.897239	TCACACACATCCCTTTCTTTGT	58.103	40.909	0.00	0.00	0.00	2.83
2850	3773	4.499696	GGTTCACACACATCCCTTTCTTTG	60.500	45.833	0.00	0.00	0.00	2.77
2851	3774	3.636764	GGTTCACACACATCCCTTTCTTT	59.363	43.478	0.00	0.00	0.00	2.52
2852	3775	3.222603	GGTTCACACACATCCCTTTCTT	58.777	45.455	0.00	0.00	0.00	2.52
2853	3776	2.489073	GGGTTCACACACATCCCTTTCT	60.489	50.000	0.00	0.00	35.63	2.52
2854	3777	1.886542	GGGTTCACACACATCCCTTTC	59.113	52.381	0.00	0.00	35.63	2.62
2855	3778	1.216678	TGGGTTCACACACATCCCTTT	59.783	47.619	0.00	0.00	38.95	3.11
2856	3779	0.850100	TGGGTTCACACACATCCCTT	59.150	50.000	0.00	0.00	38.95	3.95
2857	3780	2.550787	TGGGTTCACACACATCCCT	58.449	52.632	0.00	0.00	38.95	4.20
2874	3797	0.673644	CCTAGGTTCTTGGGCGTGTG	60.674	60.000	0.00	0.00	0.00	3.82

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.