AutoCloner

Multiple sequence alignment - TraesCS2A01G082900

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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	TraesCS2A01G082900	chr2A	100.000	3705	0	0	1	3705	37968435	37972139	0.000000e+00	6842.0
1	TraesCS2A01G082900	chr2A	93.416	2415	120	20	1296	3705	37862285	37864665	0.000000e+00	3542.0
2	TraesCS2A01G082900	chr2A	96.782	1740	31	11	1970	3705	37384230	37385948	0.000000e+00	2880.0
3	TraesCS2A01G082900	chr2A	88.042	1915	192	18	1134	3024	37952741	37954642	0.000000e+00	2233.0
4	TraesCS2A01G082900	chr2A	89.611	1261	62	24	43	1297	37860885	37862082	0.000000e+00	1539.0
5	TraesCS2A01G082900	chr2A	91.194	829	33	12	1	818	37948398	37949197	0.000000e+00	1090.0
6	TraesCS2A01G082900	chr2A	94.455	523	18	2	382	893	37383660	37384182	0.000000e+00	795.0
7	TraesCS2A01G082900	chr2A	90.636	566	36	6	870	1418	37949193	37949758	0.000000e+00	736.0
8	TraesCS2A01G082900	chr2A	92.605	311	23	0	2872	3182	38018849	38019159	7.300000e-122	448.0
9	TraesCS2A01G082900	chr2A	88.360	189	22	0	920	1108	37952555	37952743	1.040000e-55	228.0
10	TraesCS2A01G082900	chr2A	80.488	82	15	1	3088	3168	61414807	61414726	1.110000e-05	62.1
11	TraesCS2A01G082900	chr2B	91.579	3052	180	23	667	3705	57039932	57042919	0.000000e+00	4141.0
12	TraesCS2A01G082900	chr2B	91.983	2844	158	18	655	3487	57115657	57118441	0.000000e+00	3925.0
13	TraesCS2A01G082900	chr2B	80.976	1393	211	31	955	2335	57110620	57111970	0.000000e+00	1055.0
14	TraesCS2A01G082900	chr2B	80.302	1391	218	36	955	2335	57035066	57036410	0.000000e+00	1000.0
15	TraesCS2A01G082900	chr2B	90.459	545	30	11	2349	2875	57036508	57037048	0.000000e+00	699.0
16	TraesCS2A01G082900	chr2B	86.935	398	36	9	2461	2843	57112155	57112551	2.040000e-117	433.0
17	TraesCS2A01G082900	chr2B	89.384	292	16	4	373	664	57115363	57115639	1.640000e-93	353.0
18	TraesCS2A01G082900	chr2B	87.541	305	30	5	3402	3705	158041548	158041251	2.740000e-91	346.0
19	TraesCS2A01G082900	chr2D	90.656	2151	136	16	655	2795	34581404	34583499	0.000000e+00	2798.0
20	TraesCS2A01G082900	chr2D	92.081	985	63	5	1319	2300	34560144	34561116	0.000000e+00	1373.0
21	TraesCS2A01G082900	chr2D	80.613	1109	164	33	1240	2336	34538773	34539842	0.000000e+00	809.0
22	TraesCS2A01G082900	chr2D	88.035	677	36	20	655	1322	34547604	34548244	0.000000e+00	760.0
23	TraesCS2A01G082900	chr2D	90.354	508	44	3	2901	3407	34584994	34585497	0.000000e+00	662.0
24	TraesCS2A01G082900	chr2D	79.242	660	105	16	886	1542	34579608	34580238	7.350000e-117	431.0
25	TraesCS2A01G082900	chr2D	87.667	300	36	1	3407	3705	572043282	572042983	7.620000e-92	348.0
26	TraesCS2A01G082900	chr2D	87.671	292	20	5	373	664	34581103	34581378	3.570000e-85	326.0
27	TraesCS2A01G082900	chr2D	84.615	299	26	6	374	664	34547294	34547580	2.820000e-71	279.0
28	TraesCS2A01G082900	chr2D	83.813	278	29	10	35	312	56806679	56806418	2.210000e-62	250.0
29	TraesCS2A01G082900	chr3A	81.481	513	91	3	898	1409	698834871	698834362	5.720000e-113	418.0
30	TraesCS2A01G082900	chr1D	89.404	302	29	2	3404	3705	239550822	239551120	9.710000e-101	377.0
31	TraesCS2A01G082900	chr1A	89.073	302	30	2	3404	3705	303647487	303647785	4.520000e-99	372.0
32	TraesCS2A01G082900	chr3B	79.497	517	101	4	898	1413	751998066	751997554	2.720000e-96	363.0
33	TraesCS2A01G082900	chr6D	87.000	300	35	2	3407	3705	265994567	265994271	5.930000e-88	335.0
34	TraesCS2A01G082900	chr4D	86.799	303	37	3	3404	3705	126153954	126154254	5.930000e-88	335.0

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	TraesCS2A01G082900	chr2A	37968435	37972139	3704	False	6842.000000	6842	100.000000	1	3705	1	chr2A.!!$F1	3704
1	TraesCS2A01G082900	chr2A	37860885	37864665	3780	False	2540.500000	3542	91.513500	43	3705	2	chr2A.!!$F4	3662
2	TraesCS2A01G082900	chr2A	37383660	37385948	2288	False	1837.500000	2880	95.618500	382	3705	2	chr2A.!!$F3	3323
3	TraesCS2A01G082900	chr2A	37948398	37954642	6244	False	1071.750000	2233	89.558000	1	3024	4	chr2A.!!$F5	3023
4	TraesCS2A01G082900	chr2B	57035066	57042919	7853	False	1946.666667	4141	87.446667	667	3705	3	chr2B.!!$F1	3038
5	TraesCS2A01G082900	chr2B	57110620	57118441	7821	False	1441.500000	3925	87.319500	373	3487	4	chr2B.!!$F2	3114
6	TraesCS2A01G082900	chr2D	34560144	34561116	972	False	1373.000000	1373	92.081000	1319	2300	1	chr2D.!!$F2	981
7	TraesCS2A01G082900	chr2D	34579608	34585497	5889	False	1054.250000	2798	86.980750	373	3407	4	chr2D.!!$F4	3034
8	TraesCS2A01G082900	chr2D	34538773	34539842	1069	False	809.000000	809	80.613000	1240	2336	1	chr2D.!!$F1	1096
9	TraesCS2A01G082900	chr2D	34547294	34548244	950	False	519.500000	760	86.325000	374	1322	2	chr2D.!!$F3	948
10	TraesCS2A01G082900	chr3A	698834362	698834871	509	True	418.000000	418	81.481000	898	1409	1	chr3A.!!$R1	511
11	TraesCS2A01G082900	chr3B	751997554	751998066	512	True	363.000000	363	79.497000	898	1413	1	chr3B.!!$R1	515

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
366	370	0.168128	AAACACCAGAAATAGCGCGC	59.832	50.0	26.66	26.66	0.0	6.86	F
1758	9754	0.530650	TCGCCGCATCTCCAAATCTC	60.531	55.0	0.00	0.00	0.0	2.75	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1954	9950	1.20002	GATGTGAAGTTTCGGGGCAAG	59.800	52.381	0.0	0.0	0.0	4.01	R
3094	12522	0.24445	ACGTCCGGACATAAAAGCGA	59.756	50.000	32.8	0.0	0.0	4.93	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
105	106	4.320608	ACAACGGTTCGACCTAAAGTTA	57.679	40.909	0.00	0.00	35.66	2.24
131	134	8.423349	ACATCTTCATTCTTTATGAGAGAGAGG	58.577	37.037	0.00	0.00	43.87	3.69
191	195	5.184671	TGCATGCTGACAAAATGGTGTAATA	59.815	36.000	20.33	0.00	0.00	0.98
316	320	0.396435	ACGTCAACTCTTCCCATGCA	59.604	50.000	0.00	0.00	0.00	3.96
362	366	5.239525	ACAGAGAACAAACACCAGAAATAGC	59.760	40.000	0.00	0.00	0.00	2.97
364	368	2.989422	ACAAACACCAGAAATAGCGC	57.011	45.000	0.00	0.00	0.00	5.92
366	370	0.168128	AAACACCAGAAATAGCGCGC	59.832	50.000	26.66	26.66	0.00	6.86
368	372	3.564027	ACCAGAAATAGCGCGCGC	61.564	61.111	45.10	45.10	42.33	6.86
405	4837	0.532573	CACACCTGTCTATCTGCCGT	59.467	55.000	0.00	0.00	0.00	5.68
422	4862	2.042831	GTGCAGCCTCCATCCACAC	61.043	63.158	0.00	0.00	0.00	3.82
464	4914	2.609459	GCACTCACACATATACACCTGC	59.391	50.000	0.00	0.00	0.00	4.85
573	5026	6.347061	AGATATTTGGAAGGAGGGATTTGT	57.653	37.500	0.00	0.00	0.00	2.83
913	5412	3.281787	TCCTTCCCCCTCTCCCGT	61.282	66.667	0.00	0.00	0.00	5.28
918	5417	1.886730	TTCCCCCTCTCCCGTCTCAT	61.887	60.000	0.00	0.00	0.00	2.90
922	5421	1.282157	CCCCTCTCCCGTCTCATTTTT	59.718	52.381	0.00	0.00	0.00	1.94
942	5441	2.590092	CATTCCCTCGACCCCCAC	59.410	66.667	0.00	0.00	0.00	4.61
944	5443	3.572715	ATTCCCTCGACCCCCACCA	62.573	63.158	0.00	0.00	0.00	4.17
1010	5530	1.153229	GCTAACCCATGACCCCGAC	60.153	63.158	0.00	0.00	0.00	4.79
1292	5812	1.228245	GCTGGAAACACCTCTGGCA	60.228	57.895	0.00	0.00	39.86	4.92
1305	6029	0.538746	TCTGGCACGACTACACTCCA	60.539	55.000	0.00	0.00	0.00	3.86
1563	9551	1.371183	CGAACCACTTCAGGCTGGA	59.629	57.895	15.73	4.57	0.00	3.86
1729	9723	2.135933	CAAACTCCGAGAACACACTCC	58.864	52.381	1.33	0.00	33.83	3.85
1730	9724	1.410004	AACTCCGAGAACACACTCCA	58.590	50.000	1.33	0.00	33.83	3.86
1758	9754	0.530650	TCGCCGCATCTCCAAATCTC	60.531	55.000	0.00	0.00	0.00	2.75
1876	9872	3.118992	TGATGTGATGGAAGAACTCCTCG	60.119	47.826	0.00	0.00	45.64	4.63
1884	9880	3.118555	TGGAAGAACTCCTCGTTGTCAAA	60.119	43.478	0.00	0.00	45.64	2.69
1892	9888	3.611970	TCCTCGTTGTCAAAACTCCAAA	58.388	40.909	0.00	0.00	0.00	3.28
1937	9933	2.175931	ACCAAGGTTATTGTGGTCCACA	59.824	45.455	21.21	21.21	42.00	4.17
1954	9950	2.936498	CCACAAATCATACGTGTCCTCC	59.064	50.000	0.00	0.00	0.00	4.30
1962	9958	4.760047	CGTGTCCTCCTTGCCCCG	62.760	72.222	0.00	0.00	0.00	5.73
2081	10078	9.322773	CACTTAGGGCATCTGTATATATCATTG	57.677	37.037	0.00	0.00	0.00	2.82
2167	10183	4.173290	TGATGATTGATCCAGGCAATGA	57.827	40.909	0.00	0.00	36.19	2.57
2424	10452	3.266636	TCTTGCTTCGTTTTCAGACACA	58.733	40.909	0.00	0.00	0.00	3.72
2718	10751	2.614779	CGAGTGAGCACATGATCAACT	58.385	47.619	0.00	0.00	42.53	3.16
2905	12333	9.944376	ATATATGAACCATACCAACTACATGTC	57.056	33.333	0.00	0.00	0.00	3.06
2907	12335	6.121776	TGAACCATACCAACTACATGTCTT	57.878	37.500	0.00	0.00	0.00	3.01
2988	12416	6.756542	TGTGAGTATGATGAATTACCTTGACG	59.243	38.462	0.00	0.00	0.00	4.35
3181	12609	5.300752	CAAACATCCGCCTCTAGTAATGAT	58.699	41.667	0.00	0.00	0.00	2.45
3231	12660	9.466497	AACTAATCTTCAGCCAATAGAAAATCA	57.534	29.630	0.00	0.00	0.00	2.57
3239	12668	5.185635	CAGCCAATAGAAAATCAACCTTCCA	59.814	40.000	0.00	0.00	0.00	3.53
3286	12715	1.750193	TGAATCAACCTTCCGCCATC	58.250	50.000	0.00	0.00	0.00	3.51
3341	12770	4.142902	CGTAATTTGAGGTGTGGCAGTTAG	60.143	45.833	0.00	0.00	0.00	2.34

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
10	11	3.044305	GACACAGGTGAGTGCCGC	61.044	66.667	6.40	0.00	43.23	6.53
105	106	8.423349	CCTCTCTCTCATAAAGAATGAAGATGT	58.577	37.037	0.00	0.00	44.05	3.06
120	121	3.033184	CCTCTTTCTGCCTCTCTCTCAT	58.967	50.000	0.00	0.00	0.00	2.90
131	134	1.485895	AGATGCTCTCCCTCTTTCTGC	59.514	52.381	0.00	0.00	0.00	4.26
191	195	4.081586	GGATTCAACTCGGTTTCCTCTAGT	60.082	45.833	0.00	0.00	0.00	2.57
368	372	3.858989	TGTGTGTGTGTGTGCGCG	61.859	61.111	0.00	0.00	0.00	6.86
405	4837	2.352422	GTGTGGATGGAGGCTGCA	59.648	61.111	12.23	12.23	0.00	4.41
532	4984	4.680237	TCCTTCCTGCCGTGCACG	62.680	66.667	31.77	31.77	33.79	5.34
543	4995	5.380900	CCTCCTTCCAAATATCTTCCTTCC	58.619	45.833	0.00	0.00	0.00	3.46
573	5026	0.874175	CGACAAAGGTGAGTGCGTGA	60.874	55.000	0.00	0.00	0.00	4.35
885	5384	2.683933	GGAAGGAGCACCGGGAGA	60.684	66.667	6.32	0.00	41.83	3.71
886	5385	3.787001	GGGAAGGAGCACCGGGAG	61.787	72.222	6.32	0.00	41.83	4.30
890	5389	3.787001	GAGGGGGAAGGAGCACCG	61.787	72.222	0.00	0.00	41.83	4.94
891	5390	2.285743	AGAGGGGGAAGGAGCACC	60.286	66.667	0.00	0.00	0.00	5.01
892	5391	2.371259	GGAGAGGGGGAAGGAGCAC	61.371	68.421	0.00	0.00	0.00	4.40
893	5392	2.041265	GGAGAGGGGGAAGGAGCA	59.959	66.667	0.00	0.00	0.00	4.26
894	5393	2.770475	GGGAGAGGGGGAAGGAGC	60.770	72.222	0.00	0.00	0.00	4.70
895	5394	2.444895	CGGGAGAGGGGGAAGGAG	60.445	72.222	0.00	0.00	0.00	3.69
896	5395	3.281787	ACGGGAGAGGGGGAAGGA	61.282	66.667	0.00	0.00	0.00	3.36
904	5403	2.633488	GGAAAAATGAGACGGGAGAGG	58.367	52.381	0.00	0.00	0.00	3.69
905	5404	2.027192	TGGGAAAAATGAGACGGGAGAG	60.027	50.000	0.00	0.00	0.00	3.20
913	5412	3.265737	TCGAGGGAATGGGAAAAATGAGA	59.734	43.478	0.00	0.00	0.00	3.27
918	5417	1.272258	GGGTCGAGGGAATGGGAAAAA	60.272	52.381	0.00	0.00	0.00	1.94
922	5421	2.366435	GGGGTCGAGGGAATGGGA	60.366	66.667	0.00	0.00	0.00	4.37
1108	5628	4.329545	TTCTCGGCCCTGCACCAC	62.330	66.667	0.00	0.00	0.00	4.16
1292	5812	1.612463	GGTTGAGTGGAGTGTAGTCGT	59.388	52.381	0.00	0.00	0.00	4.34
1305	6029	1.895707	ACGGTCGTCGAGGTTGAGT	60.896	57.895	4.85	0.00	42.43	3.41
1563	9551	1.376424	CAGCGGTGGCATCAACTCT	60.376	57.895	6.74	0.00	43.41	3.24
1670	9664	4.039245	TGAGGTCGATGAGATATGGGAAAC	59.961	45.833	0.00	0.00	0.00	2.78
1729	9723	2.109538	GATGCGGCGATCATGGTGTG	62.110	60.000	12.98	0.00	0.00	3.82
1730	9724	1.889105	GATGCGGCGATCATGGTGT	60.889	57.895	12.98	0.00	0.00	4.16
1758	9754	3.995199	TCTGTGAAGGTACAAGCTGAAG	58.005	45.455	0.00	0.00	0.00	3.02
1892	9888	2.027377	CAGAGCATCAGTTCCTCCAAGT	60.027	50.000	0.00	0.00	37.82	3.16
1937	9933	3.270877	GCAAGGAGGACACGTATGATTT	58.729	45.455	0.00	0.00	0.00	2.17
1954	9950	1.200020	GATGTGAAGTTTCGGGGCAAG	59.800	52.381	0.00	0.00	0.00	4.01
1962	9958	3.552890	GGCAACCCAAGATGTGAAGTTTC	60.553	47.826	0.00	0.00	0.00	2.78
2167	10183	4.676459	CGATGACACTAGACTGCTGTCAAT	60.676	45.833	23.61	8.39	45.56	2.57
2424	10452	4.340381	GCTTGTTTGGAATATGGCTCATCT	59.660	41.667	0.00	0.00	0.00	2.90
2718	10751	0.599991	ATTGACACTTCGTCTGCGCA	60.600	50.000	10.98	10.98	45.60	6.09
2737	10770	3.926729	TGCCAAAGGGGTACACAAA	57.073	47.368	0.00	0.00	39.65	2.83
3094	12522	0.244450	ACGTCCGGACATAAAAGCGA	59.756	50.000	32.80	0.00	0.00	4.93
3097	12525	1.997606	GACCACGTCCGGACATAAAAG	59.002	52.381	32.80	18.20	0.00	2.27
3231	12660	6.014584	GGTTGATTTCTATTTGGTGGAAGGTT	60.015	38.462	0.00	0.00	0.00	3.50
3239	12668	6.953520	TGATGGAAGGTTGATTTCTATTTGGT	59.046	34.615	0.00	0.00	0.00	3.67
3341	12770	9.841880	GTATTAAAAGAGGAAAGAAATCCACAC	57.158	33.333	0.00	0.00	42.27	3.82
3570	13000	7.711772	TCAATCGGTTTGTCTCAACTTTAGTAA	59.288	33.333	0.00	0.00	36.65	2.24

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.