AutoCloner

Multiple sequence alignment - TraesCS4B01G132700

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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	TraesCS4B01G132700	chr4B	100.000	5404	0	0	1	5404	172506960	172512363	0.000000e+00	9980.0
1	TraesCS4B01G132700	chr4A	94.206	4712	123	41	87	4696	465408391	465403728	0.000000e+00	7051.0
2	TraesCS4B01G132700	chr4A	95.122	41	2	0	1710	1750	581757230	581757270	1.260000e-06	65.8
3	TraesCS4B01G132700	chr4D	97.165	1799	28	6	2065	3860	111941269	111943047	0.000000e+00	3018.0
4	TraesCS4B01G132700	chr4D	92.336	2153	63	22	1	2079	111939128	111941252	0.000000e+00	2968.0
5	TraesCS4B01G132700	chr4D	94.607	853	25	6	3859	4696	111943100	111943946	0.000000e+00	1301.0
6	TraesCS4B01G132700	chr6B	93.679	443	27	1	4963	5404	469200900	469201342	0.000000e+00	662.0
7	TraesCS4B01G132700	chr6B	94.074	270	15	1	4697	4966	469200599	469200867	5.040000e-110	409.0
8	TraesCS4B01G132700	chr7D	92.777	443	27	3	4963	5404	442777068	442777506	2.120000e-178	636.0
9	TraesCS4B01G132700	chr7D	95.185	270	12	1	4697	4966	442776767	442777035	5.000000e-115	425.0
10	TraesCS4B01G132700	chr3D	92.325	443	32	2	4963	5404	407223943	407223502	3.550000e-176	628.0
11	TraesCS4B01G132700	chr3D	93.233	266	18	0	4697	4962	407224244	407223979	5.070000e-105	392.0
12	TraesCS4B01G132700	chr3A	90.971	443	39	1	4963	5404	57783323	57782881	3.600000e-166	595.0
13	TraesCS4B01G132700	chr2B	93.979	382	12	2	5024	5404	92598859	92599230	7.860000e-158	568.0
14	TraesCS4B01G132700	chr2B	90.909	66	6	0	1703	1768	583411881	583411816	7.460000e-14	89.8
15	TraesCS4B01G132700	chr1D	96.341	82	2	1	1767	1847	479730164	479730245	3.400000e-27	134.0
16	TraesCS4B01G132700	chr1D	89.899	99	8	2	1770	1866	323952246	323952344	5.680000e-25	126.0
17	TraesCS4B01G132700	chr1D	97.297	37	1	0	1724	1760	293296385	293296421	4.520000e-06	63.9
18	TraesCS4B01G132700	chr1B	94.253	87	3	1	1770	1854	637983822	637983736	1.220000e-26	132.0
19	TraesCS4B01G132700	chr1B	93.103	87	4	2	1762	1847	392878900	392878985	5.680000e-25	126.0
20	TraesCS4B01G132700	chr1B	95.062	81	3	1	1769	1848	392878986	392878906	5.680000e-25	126.0
21	TraesCS4B01G132700	chr1B	97.436	39	1	0	1730	1768	198640303	198640341	3.490000e-07	67.6
22	TraesCS4B01G132700	chrUn	93.182	88	6	0	1769	1856	65136691	65136778	4.390000e-26	130.0
23	TraesCS4B01G132700	chr5D	93.182	88	4	1	1770	1855	389245419	389245506	1.580000e-25	128.0
24	TraesCS4B01G132700	chr5D	89.286	56	6	0	1703	1758	9467007	9467062	2.700000e-08	71.3
25	TraesCS4B01G132700	chr2D	89.394	66	7	0	1703	1768	495780465	495780400	3.470000e-12	84.2
26	TraesCS4B01G132700	chr7A	82.292	96	15	2	1985	2080	227997090	227996997	1.250000e-11	82.4
27	TraesCS4B01G132700	chr5A	93.478	46	3	0	1703	1748	7599615	7599660	9.710000e-08	69.4

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	TraesCS4B01G132700	chr4B	172506960	172512363	5403	False	9980.0	9980	100.000000	1	5404	1	chr4B.!!$F1	5403
1	TraesCS4B01G132700	chr4A	465403728	465408391	4663	True	7051.0	7051	94.206000	87	4696	1	chr4A.!!$R1	4609
2	TraesCS4B01G132700	chr4D	111939128	111943946	4818	False	2429.0	3018	94.702667	1	4696	3	chr4D.!!$F1	4695
3	TraesCS4B01G132700	chr6B	469200599	469201342	743	False	535.5	662	93.876500	4697	5404	2	chr6B.!!$F1	707
4	TraesCS4B01G132700	chr7D	442776767	442777506	739	False	530.5	636	93.981000	4697	5404	2	chr7D.!!$F1	707
5	TraesCS4B01G132700	chr3D	407223502	407224244	742	True	510.0	628	92.779000	4697	5404	2	chr3D.!!$R1	707

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
755	833	0.033504	TCTCTGTGCTTGTTCGGGAC	59.966	55.000	0.00	0.00	0.00	4.46	F
1130	1217	0.335361	GTAGAGGAGGAGGTGGTGGA	59.665	60.000	0.00	0.00	0.00	4.02	F
1921	2011	0.807667	CGCTAGCATGGATATCGGGC	60.808	60.000	16.45	0.35	0.00	6.13	F
3460	3584	2.247790	CAAAGGAGGTCCGTTGCTG	58.752	57.895	11.10	0.00	45.57	4.41	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Hairpin	End Stability	Orientation
1691	1781	3.431912	GCACACGATTACAGATGAACACA	59.568	43.478	0.00	0.0	3.72	R
2892	3015	7.043961	TGACAGTAGGAGCATTTGTATCTAG	57.956	40.000	0.00	0.0	2.43	R
3521	3645	1.639635	CCATAAGCAGGAGGGGCACT	61.640	60.000	0.00	0.0	4.40	R
4699	4903	0.390860	ATCTTGGATTCTCCGAGCCG	59.609	55.000	5.65	45.8	5.52	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
152	172	2.488087	AAGTCCGTCGCGCTAGCTTT	62.488	55.000	13.93	0.00	42.32	3.51
223	264	1.207329	GGTTAGGAGCACCTCGTGAAT	59.793	52.381	5.75	0.00	46.43	2.57
401	477	0.807667	GCATCCTAGCATATCCCGCG	60.808	60.000	0.00	0.00	0.00	6.46
540	617	8.450578	TCCATGCTATATTTACTTGAGTTTGG	57.549	34.615	0.00	0.00	0.00	3.28
679	757	0.179018	ATTAAGCCATCAGCCCGTCC	60.179	55.000	0.00	0.00	45.47	4.79
714	792	0.322816	AGTGCATCGCCTTGACCATT	60.323	50.000	0.00	0.00	0.00	3.16
755	833	0.033504	TCTCTGTGCTTGTTCGGGAC	59.966	55.000	0.00	0.00	0.00	4.46
786	864	3.051803	TGAGAACCTCCCTGTATCATCCT	60.052	47.826	0.00	0.00	0.00	3.24
942	1020	1.339055	TGTCCTCAATTTGCTCTCCCG	60.339	52.381	0.00	0.00	0.00	5.14
1035	1122	4.518211	ACAGAAGATGCTGAACCAAAAGAG	59.482	41.667	0.00	0.00	39.20	2.85
1127	1214	0.632294	GAGGTAGAGGAGGAGGTGGT	59.368	60.000	0.00	0.00	0.00	4.16
1130	1217	0.335361	GTAGAGGAGGAGGTGGTGGA	59.665	60.000	0.00	0.00	0.00	4.02
1143	1230	1.075600	GGTGGAGGAGGAGGAGGAG	60.076	68.421	0.00	0.00	0.00	3.69
1144	1231	1.075600	GTGGAGGAGGAGGAGGAGG	60.076	68.421	0.00	0.00	0.00	4.30
1145	1232	1.230650	TGGAGGAGGAGGAGGAGGA	60.231	63.158	0.00	0.00	0.00	3.71
1146	1233	1.292941	TGGAGGAGGAGGAGGAGGAG	61.293	65.000	0.00	0.00	0.00	3.69
1147	1234	1.541672	GAGGAGGAGGAGGAGGAGG	59.458	68.421	0.00	0.00	0.00	4.30
1148	1235	0.996762	GAGGAGGAGGAGGAGGAGGA	60.997	65.000	0.00	0.00	0.00	3.71
1149	1236	0.998945	AGGAGGAGGAGGAGGAGGAG	60.999	65.000	0.00	0.00	0.00	3.69
1251	1341	4.989168	AGTGACAGTAAATCGGAAGTTGTC	59.011	41.667	0.00	0.00	35.31	3.18
1395	1485	5.344066	TCTGACGATCTCAAGAAACTATGC	58.656	41.667	0.00	0.00	0.00	3.14
1432	1522	0.963962	TGTGGAAGTGAGTACCGTCC	59.036	55.000	0.00	0.00	33.91	4.79
1691	1781	5.888161	CCCCTATTTATGCACTCAAGTCTTT	59.112	40.000	0.00	0.00	0.00	2.52
1712	1802	5.590104	TTGTGTTCATCTGTAATCGTGTG	57.410	39.130	0.00	0.00	0.00	3.82
1796	1886	5.024118	CCCTCCGTCCCATAATATAAGAGT	58.976	45.833	0.00	0.00	0.00	3.24
1823	1913	1.326548	GACACGTGTCAAAAACGCTCT	59.673	47.619	37.16	4.94	44.80	4.09
1874	1964	7.684670	TGATAAGATCTTAATTGCACGTCAAC	58.315	34.615	18.79	0.00	37.53	3.18
1921	2011	0.807667	CGCTAGCATGGATATCGGGC	60.808	60.000	16.45	0.35	0.00	6.13
2625	2748	7.012421	GGAAATATACCTCACAGTTGGTCATTC	59.988	40.741	0.00	1.60	37.74	2.67
2892	3015	5.291971	AGATGACTGCACCAAATTTCAAAC	58.708	37.500	0.00	0.00	0.00	2.93
2987	3110	3.499918	CACAGGTTCCTGAAACATCTGAC	59.500	47.826	23.45	0.00	39.81	3.51
3299	3423	5.129634	TCTTCTTGTGTTGGAATGCTGTAA	58.870	37.500	0.00	0.00	0.00	2.41
3300	3424	5.769662	TCTTCTTGTGTTGGAATGCTGTAAT	59.230	36.000	0.00	0.00	0.00	1.89
3301	3425	6.939730	TCTTCTTGTGTTGGAATGCTGTAATA	59.060	34.615	0.00	0.00	0.00	0.98
3302	3426	7.446931	TCTTCTTGTGTTGGAATGCTGTAATAA	59.553	33.333	0.00	0.00	0.00	1.40
3303	3427	7.517614	TCTTGTGTTGGAATGCTGTAATAAA	57.482	32.000	0.00	0.00	0.00	1.40
3304	3428	8.121305	TCTTGTGTTGGAATGCTGTAATAAAT	57.879	30.769	0.00	0.00	0.00	1.40
3305	3429	9.237187	TCTTGTGTTGGAATGCTGTAATAAATA	57.763	29.630	0.00	0.00	0.00	1.40
3460	3584	2.247790	CAAAGGAGGTCCGTTGCTG	58.752	57.895	11.10	0.00	45.57	4.41
3521	3645	1.334384	TGGTGCGCCTCCTGCTTATA	61.334	55.000	18.96	0.00	38.05	0.98
3736	3863	4.019174	CAATGGTTCCAATGCTTCTACCT	58.981	43.478	0.00	0.00	0.00	3.08
3768	3895	7.221452	CCGTCTTGTATATGTTGTGTAAGTACC	59.779	40.741	0.00	0.00	0.00	3.34
3798	3925	7.626390	TCTATTTTCCTGAAAACCCGATAAGA	58.374	34.615	7.18	1.24	42.32	2.10
3994	4180	4.035675	GCATATACCTCTTTCTTGGCACAC	59.964	45.833	0.00	0.00	39.29	3.82
4050	4236	3.367395	GGCCTCTTTCCATTTTACAGCAC	60.367	47.826	0.00	0.00	0.00	4.40
4070	4256	3.315191	CACACGGAGACTTGGTCATTTTT	59.685	43.478	0.52	0.00	34.60	1.94
4116	4302	6.034577	TGTCGTTTTAAATCTGCTATCGTGAG	59.965	38.462	0.00	0.00	0.00	3.51
4126	4312	2.123342	GCTATCGTGAGTGATGTGAGC	58.877	52.381	0.00	0.00	0.00	4.26
4141	4327	4.403015	TGTGAGCGTTGTGTTTGATATG	57.597	40.909	0.00	0.00	0.00	1.78
4250	4436	1.621107	GGCAACATCAGCATTTCACG	58.379	50.000	0.00	0.00	0.00	4.35
4284	4470	2.642129	CACGGCAAATTGGACGCA	59.358	55.556	8.35	0.00	45.15	5.24
4285	4471	1.442520	CACGGCAAATTGGACGCAG	60.443	57.895	8.35	0.00	45.15	5.18
4322	4508	2.187946	GGAGGCAGTGGTGGATCG	59.812	66.667	0.00	0.00	0.00	3.69
4334	4520	4.575180	GGATCGAGTAGGTCCGGT	57.425	61.111	0.00	0.00	40.92	5.28
4589	4792	7.064134	TGTCTAGGCGTAATTTCTTGTAATGTG	59.936	37.037	0.00	0.00	0.00	3.21
4631	4835	1.662629	GAACAGCATCGGTGTCTGATG	59.337	52.381	21.66	12.53	43.73	3.07
4636	4840	2.360483	AGCATCGGTGTCTGATGTCTAG	59.640	50.000	16.53	0.00	44.02	2.43
4699	4903	4.093408	TGATCGCAGAATAACAGCAACTTC	59.907	41.667	0.00	0.00	43.58	3.01
4846	5050	1.966451	CGAAAAAGCGCCAGGACCT	60.966	57.895	2.29	0.00	0.00	3.85
4984	5223	1.964223	TGACTCGCTCAAAGACTTCCT	59.036	47.619	0.00	0.00	0.00	3.36
5136	5376	6.476378	AGAACTTCCTGTACATACAAAGCAT	58.524	36.000	0.00	0.00	35.50	3.79
5246	5486	3.362399	CTGGACATGCTCGAGGCGT	62.362	63.158	15.58	5.16	45.43	5.68
5315	5555	0.323629	ATCCACGTCACGGGTGATTT	59.676	50.000	0.35	0.00	42.18	2.17
5326	5566	1.269998	CGGGTGATTTTAAACGGGCAA	59.730	47.619	0.00	0.00	0.00	4.52
5336	5576	0.107410	AAACGGGCAACTCACTGACA	60.107	50.000	0.00	0.00	0.00	3.58

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
75	76	2.500229	TCTTGGCGAGTTTACCTTTGG	58.500	47.619	0.77	0.00	0.00	3.28
223	264	2.119484	AATCGACGCAACAGGGGGAA	62.119	55.000	0.00	0.00	0.00	3.97
288	357	0.749454	GCCCAGGTTCATGCCACTAG	60.749	60.000	0.00	0.00	0.00	2.57
387	463	1.135373	CACTACCGCGGGATATGCTAG	60.135	57.143	31.76	21.23	0.00	3.42
401	477	1.449601	CATGTCGGGGCACACTACC	60.450	63.158	0.00	0.00	0.00	3.18
414	490	5.063060	GCAAATGATTGGAGAAAAGCATGTC	59.937	40.000	0.00	0.00	36.35	3.06
714	792	9.832445	AGAGAAGAAAACAAGAGTATACAAACA	57.168	29.630	5.50	0.00	0.00	2.83
786	864	3.000041	ACGAAGAAATTGCGTATGCTCA	59.000	40.909	8.69	0.00	43.34	4.26
942	1020	4.459330	AGAGCAGAGGAGGCAAAAATATC	58.541	43.478	0.00	0.00	0.00	1.63
1035	1122	6.441093	TCATTATCATCAAACTCCAAGCAC	57.559	37.500	0.00	0.00	0.00	4.40
1127	1214	1.230650	TCCTCCTCCTCCTCCTCCA	60.231	63.158	0.00	0.00	0.00	3.86
1130	1217	0.998945	CTCCTCCTCCTCCTCCTCCT	60.999	65.000	0.00	0.00	0.00	3.69
1143	1230	0.689412	CCTCCACTTCCTCCTCCTCC	60.689	65.000	0.00	0.00	0.00	4.30
1144	1231	0.336737	TCCTCCACTTCCTCCTCCTC	59.663	60.000	0.00	0.00	0.00	3.71
1145	1232	0.338120	CTCCTCCACTTCCTCCTCCT	59.662	60.000	0.00	0.00	0.00	3.69
1146	1233	0.689412	CCTCCTCCACTTCCTCCTCC	60.689	65.000	0.00	0.00	0.00	4.30
1147	1234	0.041982	ACCTCCTCCACTTCCTCCTC	59.958	60.000	0.00	0.00	0.00	3.71
1148	1235	1.289530	CTACCTCCTCCACTTCCTCCT	59.710	57.143	0.00	0.00	0.00	3.69
1149	1236	1.288335	TCTACCTCCTCCACTTCCTCC	59.712	57.143	0.00	0.00	0.00	4.30
1251	1341	4.468829	TCCTGCTGAGGAAGAGGG	57.531	61.111	0.00	0.00	46.19	4.30
1432	1522	5.734720	TGAAATGCTAACCCTAAGAGAGTG	58.265	41.667	0.00	0.00	0.00	3.51
1662	1752	7.680730	ACTTGAGTGCATAAATAGGGGTATAG	58.319	38.462	0.00	0.00	0.00	1.31
1691	1781	3.431912	GCACACGATTACAGATGAACACA	59.568	43.478	0.00	0.00	0.00	3.72
1712	1802	5.865552	CCTAATATTAATGTGCATTGCAGGC	59.134	40.000	12.53	1.60	40.08	4.85
1823	1913	9.629649	AAATACTCCCTCTGTCCCATAATATAA	57.370	33.333	0.00	0.00	0.00	0.98
1917	2007	4.832248	TCTCCTAATTAATAGCATGCCCG	58.168	43.478	15.66	0.00	0.00	6.13
1921	2011	8.944029	CACAATCCTCTCCTAATTAATAGCATG	58.056	37.037	0.00	0.00	0.00	4.06
2031	2125	9.635404	ACTAAATCTAGCAGTCTGTATTACTCT	57.365	33.333	0.93	0.00	0.00	3.24
2403	2526	7.715265	ATAATCATGGTTAGTCATCGACAAC	57.285	36.000	4.46	0.00	34.60	3.32
2892	3015	7.043961	TGACAGTAGGAGCATTTGTATCTAG	57.956	40.000	0.00	0.00	0.00	2.43
3310	3434	9.398170	CCAAACATAACAAACAAGACATAGAAG	57.602	33.333	0.00	0.00	0.00	2.85
3311	3435	8.908903	ACCAAACATAACAAACAAGACATAGAA	58.091	29.630	0.00	0.00	0.00	2.10
3312	3436	8.349245	CACCAAACATAACAAACAAGACATAGA	58.651	33.333	0.00	0.00	0.00	1.98
3521	3645	1.639635	CCATAAGCAGGAGGGGCACT	61.640	60.000	0.00	0.00	0.00	4.40
3631	3755	6.075315	ACATTTAGCAAGTTTTACCCTTCCT	58.925	36.000	0.00	0.00	0.00	3.36
3736	3863	4.126437	CAACATATACAAGACGGCCATCA	58.874	43.478	0.00	0.00	0.00	3.07
3768	3895	4.440112	GGGTTTTCAGGAAAATAGATGGCG	60.440	45.833	10.10	0.00	41.64	5.69
3798	3925	5.366768	TCCCAACAGCAGCTAATAAGAGTAT	59.633	40.000	0.00	0.00	0.00	2.12
3922	4107	4.750098	CCCCTGCATATCTTTGTTACTACG	59.250	45.833	0.00	0.00	0.00	3.51
3994	4180	3.793559	ACGGAATTTTCTCTACCCATCG	58.206	45.455	0.00	0.00	0.00	3.84
4050	4236	3.304659	CCAAAAATGACCAAGTCTCCGTG	60.305	47.826	0.00	0.00	33.15	4.94
4070	4256	1.075212	TCCATCAGCACCATTCAACCA	59.925	47.619	0.00	0.00	0.00	3.67
4116	4302	2.031560	TCAAACACAACGCTCACATCAC	59.968	45.455	0.00	0.00	0.00	3.06
4126	4312	6.399880	GCATTGGAAACATATCAAACACAACG	60.400	38.462	0.00	0.00	42.32	4.10
4141	4327	5.807011	GGAATATGTGTTCAGCATTGGAAAC	59.193	40.000	0.00	0.00	0.00	2.78
4250	4436	4.459089	GCCTGTGGCGGAGGAGAC	62.459	72.222	5.82	0.00	39.62	3.36
4334	4520	2.358984	GGGCGCTTTGTACCGGAA	60.359	61.111	9.46	0.00	0.00	4.30
4445	4631	9.444600	AATCCGACAGTACTTATTACACAATTT	57.555	29.630	0.00	0.00	32.41	1.82
4589	4792	6.515272	TCTTGCCATTTCTAAACTTGATCC	57.485	37.500	0.00	0.00	0.00	3.36
4631	4835	5.010933	TGCAGCCTATGGATACTACTAGAC	58.989	45.833	0.00	0.00	37.61	2.59
4636	4840	3.862642	GCACTGCAGCCTATGGATACTAC	60.863	52.174	15.27	0.00	37.61	2.73
4699	4903	0.390860	ATCTTGGATTCTCCGAGCCG	59.609	55.000	5.65	0.00	45.80	5.52
4846	5050	1.698506	AACCGCCTGAAAAACCATCA	58.301	45.000	0.00	0.00	0.00	3.07
4855	5059	2.225491	CGATTTGAAGAAACCGCCTGAA	59.775	45.455	0.00	0.00	0.00	3.02
4984	5223	3.457234	CTGTGCAATAGCGAGATTGGTA	58.543	45.455	10.59	0.00	46.23	3.25
5136	5376	3.433274	CGCTTTGTGTAGCTTTCTGATCA	59.567	43.478	0.00	0.00	39.03	2.92
5315	5555	2.215196	GTCAGTGAGTTGCCCGTTTAA	58.785	47.619	0.00	0.00	0.00	1.52
5326	5566	3.494398	GGTGTTGTATGGTGTCAGTGAGT	60.494	47.826	0.00	0.00	0.00	3.41
5336	5576	1.271163	CCCTTGTCGGTGTTGTATGGT	60.271	52.381	0.00	0.00	0.00	3.55
5379	5619	0.613260	CAGGATGAACAGGAACGGGA	59.387	55.000	0.00	0.00	39.69	5.14

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.