AutoCloner

Multiple sequence alignment - TraesCS2D01G040200

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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	TraesCS2D01G040200	chr2D	100.000	2771	0	0	1	2771	14646515	14649285	0.000000e+00	5118
1	TraesCS2D01G040200	chr2D	90.890	966	85	3	952	1916	14565514	14566477	0.000000e+00	1293
2	TraesCS2D01G040200	chr2D	87.566	949	82	17	1853	2771	14443945	14444887	0.000000e+00	1066
3	TraesCS2D01G040200	chr2D	89.480	808	65	5	994	1796	14596239	14597031	0.000000e+00	1003
4	TraesCS2D01G040200	chr2D	92.025	652	52	0	1145	1796	14443195	14443846	0.000000e+00	917
5	TraesCS2D01G040200	chr2D	84.874	952	83	32	1852	2771	14597120	14598042	0.000000e+00	904
6	TraesCS2D01G040200	chr2D	84.224	786	93	24	2	768	14564543	14565316	0.000000e+00	736
7	TraesCS2D01G040200	chr2D	88.776	490	43	7	1962	2443	14567875	14568360	8.550000e-165	590
8	TraesCS2D01G040200	chr2D	84.032	620	69	13	1146	1765	14704170	14704759	1.110000e-158	569
9	TraesCS2D01G040200	chr2D	88.889	423	37	7	21	437	14595030	14595448	1.900000e-141	512
10	TraesCS2D01G040200	chr2D	88.862	413	34	5	14	420	14441603	14442009	5.330000e-137	497
11	TraesCS2D01G040200	chr2D	81.574	559	90	9	19	572	14702284	14702834	1.510000e-122	449
12	TraesCS2D01G040200	chr2D	90.265	339	32	1	2434	2771	14568553	14568891	2.530000e-120	442
13	TraesCS2D01G040200	chr2D	89.167	360	31	5	114	467	14595446	14595803	2.530000e-120	442
14	TraesCS2D01G040200	chr2D	94.853	136	3	2	636	768	14442720	14442854	2.800000e-50	209
15	TraesCS2D01G040200	chr2D	86.364	198	15	5	774	961	14442969	14443164	3.620000e-49	206
16	TraesCS2D01G040200	chr2D	86.047	129	15	1	989	1114	14704040	14704168	4.810000e-28	135
17	TraesCS2D01G040200	chr2D	95.294	85	3	1	635	719	14596012	14596095	1.730000e-27	134
18	TraesCS2D01G040200	chr2A	93.463	2004	71	24	774	2771	16750851	16752800	0.000000e+00	2920
19	TraesCS2D01G040200	chr2A	85.125	1237	132	32	1221	2428	16771383	16772596	0.000000e+00	1218
20	TraesCS2D01G040200	chr2A	85.787	788	77	27	2	771	16749965	16750735	0.000000e+00	802
21	TraesCS2D01G040200	chr2A	83.734	541	69	13	1232	1764	16745994	16746523	6.890000e-136	494
22	TraesCS2D01G040200	chr2A	75.988	329	40	24	794	1114	16771030	16771327	1.730000e-27	134
23	TraesCS2D01G040200	chr2B	85.445	1697	164	38	774	2428	26354080	26355735	0.000000e+00	1688
24	TraesCS2D01G040200	chr2B	84.034	833	97	23	1624	2428	26359029	26359853	0.000000e+00	769
25	TraesCS2D01G040200	chr2B	87.520	625	62	10	6	615	26353128	26353751	0.000000e+00	708
26	TraesCS2D01G040200	chr2B	88.182	550	61	4	1205	1752	26348931	26349478	0.000000e+00	652
27	TraesCS2D01G040200	chr2B	92.647	136	6	2	636	768	26353831	26353965	2.820000e-45	193
28	TraesCS2D01G040200	chr4B	77.154	499	102	7	73	564	663901024	663900531	2.100000e-71	279
29	TraesCS2D01G040200	chr6B	74.524	420	84	17	44	455	199932873	199933277	7.940000e-36	161
30	TraesCS2D01G040200	chr3D	77.444	266	53	6	198	457	457061471	457061735	4.780000e-33	152

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	TraesCS2D01G040200	chr2D	14646515	14649285	2770	False	5118.000000	5118	100.000000	1	2771	1	chr2D.!!$F1	2770
1	TraesCS2D01G040200	chr2D	14564543	14568891	4348	False	765.250000	1293	88.538750	2	2771	4	chr2D.!!$F3	2769
2	TraesCS2D01G040200	chr2D	14595030	14598042	3012	False	599.000000	1003	89.540800	21	2771	5	chr2D.!!$F4	2750
3	TraesCS2D01G040200	chr2D	14441603	14444887	3284	False	579.000000	1066	89.934000	14	2771	5	chr2D.!!$F2	2757
4	TraesCS2D01G040200	chr2D	14702284	14704759	2475	False	384.333333	569	83.884333	19	1765	3	chr2D.!!$F5	1746
5	TraesCS2D01G040200	chr2A	16745994	16752800	6806	False	1405.333333	2920	87.661333	2	2771	3	chr2A.!!$F1	2769
6	TraesCS2D01G040200	chr2A	16771030	16772596	1566	False	676.000000	1218	80.556500	794	2428	2	chr2A.!!$F2	1634
7	TraesCS2D01G040200	chr2B	26348931	26359853	10922	False	802.000000	1688	87.565600	6	2428	5	chr2B.!!$F1	2422

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
310	4621	0.107017	CGAACAGGATGGGAAGCCAT	60.107	55.0	0.0	0.0	43.62	4.40	F
958	6749	0.814010	GGGCTGACAACACACGACTT	60.814	55.0	0.0	0.0	0.00	3.01	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1142	6963	0.393537	ATTCCAAGAAGCTGGAGCGG	60.394	55.000	0.0	0.0	46.2	5.52	R
2618	10194	1.911766	GGTCAAGACGGGACAGGGA	60.912	63.158	0.0	0.0	37.0	4.20	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
69	4377	6.017400	AGAAAATCACAGGTACATTGCTTG	57.983	37.500	0.00	0.00	0.00	4.01
177	4486	9.023967	GTATCAATCTTTGCAACATGAAATACC	57.976	33.333	0.00	0.00	0.00	2.73
196	4505	2.039348	ACCGCCAAGGCTTTAGTAAAGA	59.961	45.455	23.89	0.00	46.52	2.52
300	4611	3.628989	TCGCCCATCGAACAGGAT	58.371	55.556	3.11	0.00	45.36	3.24
308	4619	0.181350	ATCGAACAGGATGGGAAGCC	59.819	55.000	0.00	0.00	43.62	4.35
309	4620	1.198094	TCGAACAGGATGGGAAGCCA	61.198	55.000	0.00	0.00	43.62	4.75
310	4621	0.107017	CGAACAGGATGGGAAGCCAT	60.107	55.000	0.00	0.00	43.62	4.40
311	4622	1.396653	GAACAGGATGGGAAGCCATG	58.603	55.000	0.00	0.00	43.62	3.66
312	4623	1.002069	AACAGGATGGGAAGCCATGA	58.998	50.000	0.00	0.00	43.62	3.07
314	4625	0.822532	CAGGATGGGAAGCCATGAGC	60.823	60.000	0.00	0.00	44.25	4.26
330	4641	7.452880	GCCATGAGCATTTAATATACTTGGA	57.547	36.000	0.00	0.00	42.97	3.53
331	4642	7.533426	GCCATGAGCATTTAATATACTTGGAG	58.467	38.462	0.00	0.00	42.97	3.86
342	4653	2.391926	TACTTGGAGCGGGGATATCA	57.608	50.000	4.83	0.00	0.00	2.15
359	4677	7.419750	GGGGATATCACCTAAAAGTACATGTCA	60.420	40.741	17.38	0.00	36.20	3.58
382	4700	8.734386	GTCAAACCACAAGATCTTCAATAGAAT	58.266	33.333	4.57	0.00	36.22	2.40
409	5170	2.939103	AGCACAACTCTGAAGTCACAAC	59.061	45.455	0.00	0.00	33.48	3.32
517	5282	1.674817	CCACAAGGTCGGATACACCAC	60.675	57.143	0.22	0.00	39.39	4.16
519	5284	1.275291	ACAAGGTCGGATACACCACAG	59.725	52.381	0.22	0.00	39.39	3.66
520	5285	1.275291	CAAGGTCGGATACACCACAGT	59.725	52.381	0.22	0.00	39.39	3.55
573	6147	2.425668	ACCGCCCAATAATAGTTTGCAC	59.574	45.455	0.00	0.00	0.00	4.57
633	6208	8.574251	TTAGAATTTAGAATAGTTTGCAGGCA	57.426	30.769	0.00	0.00	0.00	4.75
672	6320	2.342179	CACCAGCAAACAAAACGGTTT	58.658	42.857	0.00	0.00	41.44	3.27
685	6333	5.237779	ACAAAACGGTTTAGCGGGATATATG	59.762	40.000	6.53	0.00	0.00	1.78
771	6422	2.341101	CCGCCCTACGTCAGTCAGT	61.341	63.158	0.00	0.00	41.42	3.41
774	6425	1.248785	GCCCTACGTCAGTCAGTGGA	61.249	60.000	0.00	0.00	0.00	4.02
775	6426	1.475403	CCCTACGTCAGTCAGTGGAT	58.525	55.000	0.00	0.00	0.00	3.41
777	6428	1.064208	CCTACGTCAGTCAGTGGATCG	59.936	57.143	0.00	0.00	0.00	3.69
778	6429	2.007608	CTACGTCAGTCAGTGGATCGA	58.992	52.381	0.00	0.00	0.00	3.59
862	6633	2.125350	CCCAAGGCTCGTCAGCTC	60.125	66.667	0.00	0.00	46.03	4.09
875	6663	6.128661	GGCTCGTCAGCTCGATCTATATATAG	60.129	46.154	12.84	12.84	46.03	1.31
954	6745	3.345808	CCGGGCTGACAACACACG	61.346	66.667	0.00	0.00	0.00	4.49
955	6746	2.279851	CGGGCTGACAACACACGA	60.280	61.111	0.00	0.00	0.00	4.35
956	6747	2.594962	CGGGCTGACAACACACGAC	61.595	63.158	0.00	0.00	0.00	4.34
958	6749	0.814010	GGGCTGACAACACACGACTT	60.814	55.000	0.00	0.00	0.00	3.01
961	6752	1.004927	GCTGACAACACACGACTTGAC	60.005	52.381	0.00	0.00	0.00	3.18
962	6753	2.540515	CTGACAACACACGACTTGACT	58.459	47.619	0.00	0.00	0.00	3.41
963	6754	2.535984	CTGACAACACACGACTTGACTC	59.464	50.000	0.00	0.00	0.00	3.36
977	6768	2.988010	TGACTCTCATTTCCATCCCG	57.012	50.000	0.00	0.00	0.00	5.14
1012	6806	1.069432	ACGGCGATATGTACTACTGCG	60.069	52.381	16.62	0.00	0.00	5.18
1230	7060	0.263172	CCAGCTCCTCCTCCTCCTTA	59.737	60.000	0.00	0.00	0.00	2.69
1507	7337	0.320374	CACCGCACTCAACTTCCCTA	59.680	55.000	0.00	0.00	0.00	3.53
1539	7369	2.202987	GAGTCGCTCCATGCCCTG	60.203	66.667	0.00	0.00	38.78	4.45
1687	7517	2.593725	CGATGGCCATGCAGGAGG	60.594	66.667	26.56	0.00	41.22	4.30
1752	7582	3.181489	ACGAGCTTCTTAGGATTACGTGG	60.181	47.826	0.00	0.00	0.00	4.94
1785	7617	9.158233	GCTTACCAATAACACTATCAACAGTAA	57.842	33.333	0.00	0.00	0.00	2.24
1936	8095	6.042552	CCTTAATCAGCTCCTTCTCCTTCATA	59.957	42.308	0.00	0.00	0.00	2.15
2117	9383	4.043750	CGTCAAAGTGAATTGCAACATGT	58.956	39.130	0.00	0.00	0.00	3.21
2122	9391	7.009999	GTCAAAGTGAATTGCAACATGTAACAA	59.990	33.333	13.91	13.91	0.00	2.83
2123	9392	6.826893	AAGTGAATTGCAACATGTAACAAC	57.173	33.333	13.85	4.61	0.00	3.32
2124	9393	5.288804	AGTGAATTGCAACATGTAACAACC	58.711	37.500	13.85	10.23	0.00	3.77
2521	10026	1.695242	ACTCAACCGGACATACCACAA	59.305	47.619	9.46	0.00	38.90	3.33
2618	10194	1.097232	CACATGGTGCCATTCGACAT	58.903	50.000	0.13	0.00	33.90	3.06

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
63	4371	5.195185	TCTTGAATCTATGATGCCAAGCAA	58.805	37.500	13.31	0.00	43.62	3.91
177	4486	3.596214	TCTCTTTACTAAAGCCTTGGCG	58.404	45.455	5.95	0.00	38.39	5.69
196	4505	2.038164	TGCTTCAATCTGACTGCACTCT	59.962	45.455	0.00	0.00	33.32	3.24
268	4577	0.955919	GGCGACTCAAGGGTTTCTGG	60.956	60.000	0.00	0.00	0.00	3.86
302	4613	7.693969	AGTATATTAAATGCTCATGGCTTCC	57.306	36.000	7.54	0.00	42.39	3.46
303	4614	8.025445	CCAAGTATATTAAATGCTCATGGCTTC	58.975	37.037	7.54	0.00	42.39	3.86
305	4616	7.233632	TCCAAGTATATTAAATGCTCATGGCT	58.766	34.615	7.54	0.00	42.39	4.75
308	4619	7.239271	CGCTCCAAGTATATTAAATGCTCATG	58.761	38.462	0.00	0.00	0.00	3.07
309	4620	6.372659	CCGCTCCAAGTATATTAAATGCTCAT	59.627	38.462	0.00	0.00	0.00	2.90
310	4621	5.700832	CCGCTCCAAGTATATTAAATGCTCA	59.299	40.000	0.00	0.00	0.00	4.26
311	4622	5.122396	CCCGCTCCAAGTATATTAAATGCTC	59.878	44.000	0.00	0.00	0.00	4.26
312	4623	5.003804	CCCGCTCCAAGTATATTAAATGCT	58.996	41.667	0.00	0.00	0.00	3.79
314	4625	5.556915	TCCCCGCTCCAAGTATATTAAATG	58.443	41.667	0.00	0.00	0.00	2.32
330	4641	3.046374	ACTTTTAGGTGATATCCCCGCT	58.954	45.455	0.00	0.00	0.00	5.52
331	4642	3.487120	ACTTTTAGGTGATATCCCCGC	57.513	47.619	0.00	0.00	0.00	6.13
342	4653	6.123651	TGTGGTTTGACATGTACTTTTAGGT	58.876	36.000	0.00	0.00	0.00	3.08
359	4677	7.363268	GGCATTCTATTGAAGATCTTGTGGTTT	60.363	37.037	14.00	0.00	35.44	3.27
382	4700	2.945440	ACTTCAGAGTTGTGCTTTGGCA	60.945	45.455	0.00	0.00	38.46	4.92
409	5170	0.109597	GCTTTTGCTGGTGTGATCCG	60.110	55.000	0.00	0.00	43.35	4.18
517	5282	2.607635	AGCGTTTGTGTGTCTACAACTG	59.392	45.455	0.00	0.00	40.04	3.16
519	5284	2.864343	AGAGCGTTTGTGTGTCTACAAC	59.136	45.455	0.00	0.00	40.04	3.32
520	5285	2.863740	CAGAGCGTTTGTGTGTCTACAA	59.136	45.455	0.00	0.00	38.82	2.41
566	5339	3.003689	CCCCTAATCATGATCGTGCAAAC	59.996	47.826	9.06	0.00	0.00	2.93
573	6147	5.242393	AGAATTTTGCCCCTAATCATGATCG	59.758	40.000	9.06	3.37	0.00	3.69
615	6190	4.009675	CCAGTGCCTGCAAACTATTCTAA	58.990	43.478	0.00	0.00	0.00	2.10
616	6191	3.263170	TCCAGTGCCTGCAAACTATTCTA	59.737	43.478	0.00	0.00	0.00	2.10
618	6193	2.436417	TCCAGTGCCTGCAAACTATTC	58.564	47.619	0.00	0.00	0.00	1.75
619	6194	2.584835	TCCAGTGCCTGCAAACTATT	57.415	45.000	0.00	0.00	0.00	1.73
620	6195	2.814805	ATCCAGTGCCTGCAAACTAT	57.185	45.000	0.00	0.00	0.00	2.12
622	6197	1.251251	GAATCCAGTGCCTGCAAACT	58.749	50.000	0.00	0.00	0.00	2.66
623	6198	0.961019	TGAATCCAGTGCCTGCAAAC	59.039	50.000	0.00	0.00	0.00	2.93
625	6200	1.246056	GCTGAATCCAGTGCCTGCAA	61.246	55.000	0.00	0.00	42.35	4.08
626	6201	1.676635	GCTGAATCCAGTGCCTGCA	60.677	57.895	0.00	0.00	42.35	4.41
628	6203	3.915575	GGCTGAATCCAGTGCCTG	58.084	61.111	0.00	0.00	42.35	4.85
631	6206	0.607489	ACACAGGCTGAATCCAGTGC	60.607	55.000	23.66	0.00	44.51	4.40
632	6207	1.446907	GACACAGGCTGAATCCAGTG	58.553	55.000	23.66	9.55	45.64	3.66
633	6208	0.326264	GGACACAGGCTGAATCCAGT	59.674	55.000	26.42	13.99	42.35	4.00
672	6320	3.056107	GTGCTGGAACATATATCCCGCTA	60.056	47.826	18.01	7.44	44.64	4.26
685	6333	1.966451	CCCACGAAGGTGCTGGAAC	60.966	63.158	0.00	0.00	43.00	3.62
771	6422	1.143838	CACTTCCGCCATCGATCCA	59.856	57.895	0.00	0.00	38.10	3.41
774	6425	2.203070	GCCACTTCCGCCATCGAT	60.203	61.111	0.00	0.00	38.10	3.59
775	6426	3.700970	TGCCACTTCCGCCATCGA	61.701	61.111	0.00	0.00	38.10	3.59
777	6428	3.134127	GGTGCCACTTCCGCCATC	61.134	66.667	0.00	0.00	33.12	3.51
875	6663	5.811100	GCTAGCTAATCCGATGGGTAAATAC	59.189	44.000	7.70	0.00	33.83	1.89
954	6745	4.195416	GGGATGGAAATGAGAGTCAAGTC	58.805	47.826	0.00	0.00	0.00	3.01
955	6746	3.369892	CGGGATGGAAATGAGAGTCAAGT	60.370	47.826	0.00	0.00	0.00	3.16
956	6747	3.201290	CGGGATGGAAATGAGAGTCAAG	58.799	50.000	0.00	0.00	0.00	3.02
958	6749	1.486310	CCGGGATGGAAATGAGAGTCA	59.514	52.381	0.00	0.00	42.00	3.41
961	6752	0.471617	AGCCGGGATGGAAATGAGAG	59.528	55.000	2.18	0.00	42.00	3.20
962	6753	0.181114	CAGCCGGGATGGAAATGAGA	59.819	55.000	3.87	0.00	42.00	3.27
963	6754	1.450531	GCAGCCGGGATGGAAATGAG	61.451	60.000	15.01	0.00	42.00	2.90
977	6768	1.817099	CCGTGATTGAGGAGCAGCC	60.817	63.158	0.00	0.00	0.00	4.85
1142	6963	0.393537	ATTCCAAGAAGCTGGAGCGG	60.394	55.000	0.00	0.00	46.20	5.52
1143	6964	1.012841	GATTCCAAGAAGCTGGAGCG	58.987	55.000	0.00	0.00	46.20	5.03
1144	6965	2.119801	TGATTCCAAGAAGCTGGAGC	57.880	50.000	0.00	0.00	46.20	4.70
1297	7127	3.907260	CTGCTCGCTTCTTGGGCCA	62.907	63.158	0.00	0.00	0.00	5.36
1491	7321	1.207089	TCCATAGGGAAGTTGAGTGCG	59.793	52.381	0.00	0.00	41.32	5.34
1494	7324	1.482593	CGCTCCATAGGGAAGTTGAGT	59.517	52.381	0.00	0.00	44.38	3.41
1687	7517	4.436998	CAGCTCCACGACGGGACC	62.437	72.222	0.00	0.00	34.36	4.46
1752	7582	4.840271	AGTGTTATTGGTAAGCTGTACCC	58.160	43.478	17.26	4.11	36.79	3.69
1785	7617	3.441572	AGCTAGAACAACCGTACGTGTAT	59.558	43.478	15.21	7.96	0.00	2.29
1963	8125	4.985044	ATGCGGCATTACGAGTTAATAC	57.015	40.909	10.23	0.00	35.47	1.89
2117	9383	4.279671	GGTTCATGTCAATGGTGGTTGTTA	59.720	41.667	0.00	0.00	34.30	2.41
2122	9391	2.158475	AGTGGTTCATGTCAATGGTGGT	60.158	45.455	0.00	0.00	34.30	4.16
2123	9392	2.517959	AGTGGTTCATGTCAATGGTGG	58.482	47.619	0.00	0.00	34.30	4.61
2124	9393	4.326826	AGTAGTGGTTCATGTCAATGGTG	58.673	43.478	0.00	0.00	34.30	4.17
2521	10026	2.419159	GCTCCGTTTTACCCCTCGTATT	60.419	50.000	0.00	0.00	0.00	1.89
2618	10194	1.911766	GGTCAAGACGGGACAGGGA	60.912	63.158	0.00	0.00	37.00	4.20
2665	10242	2.187707	GCCAACATGAATGATCAACGC	58.812	47.619	0.00	0.00	39.49	4.84

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.