AutoCloner

Multiple sequence alignment - TraesCS6D01G058600

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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	TraesCS6D01G058600	chr6D	100.000	3312	0	0	1	3312	27554204	27550893	0.000000e+00	6117.0
1	TraesCS6D01G058600	chr6D	85.187	1951	216	23	453	2338	27534761	27532819	0.000000e+00	1934.0
2	TraesCS6D01G058600	chr6D	86.030	995	109	16	2336	3312	27531249	27530267	0.000000e+00	1040.0
3	TraesCS6D01G058600	chr6D	81.447	1078	157	24	455	1503	27539059	27537996	0.000000e+00	843.0
4	TraesCS6D01G058600	chr6D	76.354	1108	200	43	455	1534	27708822	27707749	3.760000e-149	538.0
5	TraesCS6D01G058600	chr6D	75.821	1187	182	54	2206	3311	27665302	27664140	3.810000e-139	505.0
6	TraesCS6D01G058600	chr6D	85.321	218	30	2	1317	1533	15175832	15175616	1.200000e-54	224.0
7	TraesCS6D01G058600	chr6D	86.127	173	24	0	455	627	27729444	27729616	1.570000e-43	187.0
8	TraesCS6D01G058600	chr6D	70.566	1077	248	52	444	1481	28415947	28414901	5.680000e-38	169.0
9	TraesCS6D01G058600	chr6D	74.157	356	76	12	478	828	28305044	28304700	2.070000e-27	134.0
10	TraesCS6D01G058600	chr6D	74.474	380	59	14	2211	2559	15175434	15175062	2.680000e-26	130.0
11	TraesCS6D01G058600	chr6D	96.970	66	2	0	395	460	27539149	27539084	9.720000e-21	111.0
12	TraesCS6D01G058600	chr1A	95.350	3118	116	21	221	3312	536811590	536808476	0.000000e+00	4927.0
13	TraesCS6D01G058600	chr1A	94.886	176	7	2	1	175	536811766	536811592	1.170000e-69	274.0
14	TraesCS6D01G058600	chr6A	85.165	2811	300	49	302	3037	30455015	30457783	0.000000e+00	2772.0
15	TraesCS6D01G058600	chr6A	88.406	276	25	6	3038	3312	30457874	30458143	3.190000e-85	326.0
16	TraesCS6D01G058600	chr6A	76.328	659	106	33	2218	2848	30441369	30442005	1.150000e-79	307.0
17	TraesCS6D01G058600	chr6A	76.707	249	45	11	1238	1478	29472718	29472961	3.470000e-25	126.0
18	TraesCS6D01G058600	chr6A	76.585	205	32	11	95	294	30454430	30454623	7.560000e-17	99.0
19	TraesCS6D01G058600	chr6B	86.448	1675	166	34	1009	2630	51310944	51309278	0.000000e+00	1779.0
20	TraesCS6D01G058600	chr6B	86.360	1437	161	10	96	1503	51353510	51352080	0.000000e+00	1535.0
21	TraesCS6D01G058600	chr6B	80.914	1116	172	28	444	1529	54149064	54150168	0.000000e+00	843.0
22	TraesCS6D01G058600	chr6B	76.000	1100	226	30	455	1534	51423383	51422302	4.860000e-148	534.0
23	TraesCS6D01G058600	chr6B	84.112	535	61	11	2788	3312	51303211	51302691	2.300000e-136	496.0
24	TraesCS6D01G058600	chr6B	78.400	750	92	36	102	793	51311719	51310982	1.100000e-114	424.0
25	TraesCS6D01G058600	chr6B	73.369	1119	223	47	442	1534	45551941	45553010	2.450000e-91	346.0
26	TraesCS6D01G058600	chr6B	74.704	846	141	42	2206	3007	51422053	51421237	3.210000e-80	309.0
27	TraesCS6D01G058600	chr6B	81.560	282	34	10	3041	3312	51411956	51411683	2.000000e-52	217.0
28	TraesCS6D01G058600	chr6B	78.405	301	39	14	1670	1952	51352084	51351792	4.390000e-39	172.0
29	TraesCS6D01G058600	chrUn	81.965	865	133	14	453	1301	137812439	137813296	0.000000e+00	712.0
30	TraesCS6D01G058600	chrUn	76.610	885	146	38	679	1533	137670338	137671191	6.570000e-117	431.0
31	TraesCS6D01G058600	chrUn	83.491	424	65	4	1715	2136	137820036	137820456	1.110000e-104	390.0
32	TraesCS6D01G058600	chr3B	94.737	38	1	1	34	70	312144446	312144409	1.280000e-04	58.4

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	TraesCS6D01G058600	chr6D	27550893	27554204	3311	True	6117.000000	6117	100.000000	1	3312	1	chr6D.!!$R1	3311
1	TraesCS6D01G058600	chr6D	27530267	27539149	8882	True	982.000000	1934	87.408500	395	3312	4	chr6D.!!$R7	2917
2	TraesCS6D01G058600	chr6D	27707749	27708822	1073	True	538.000000	538	76.354000	455	1534	1	chr6D.!!$R3	1079
3	TraesCS6D01G058600	chr6D	27664140	27665302	1162	True	505.000000	505	75.821000	2206	3311	1	chr6D.!!$R2	1105
4	TraesCS6D01G058600	chr1A	536808476	536811766	3290	True	2600.500000	4927	95.118000	1	3312	2	chr1A.!!$R1	3311
5	TraesCS6D01G058600	chr6A	30454430	30458143	3713	False	1065.666667	2772	83.385333	95	3312	3	chr6A.!!$F3	3217
6	TraesCS6D01G058600	chr6A	30441369	30442005	636	False	307.000000	307	76.328000	2218	2848	1	chr6A.!!$F2	630
7	TraesCS6D01G058600	chr6B	51309278	51311719	2441	True	1101.500000	1779	82.424000	102	2630	2	chr6B.!!$R3	2528
8	TraesCS6D01G058600	chr6B	51351792	51353510	1718	True	853.500000	1535	82.382500	96	1952	2	chr6B.!!$R4	1856
9	TraesCS6D01G058600	chr6B	54149064	54150168	1104	False	843.000000	843	80.914000	444	1529	1	chr6B.!!$F2	1085
10	TraesCS6D01G058600	chr6B	51302691	51303211	520	True	496.000000	496	84.112000	2788	3312	1	chr6B.!!$R1	524
11	TraesCS6D01G058600	chr6B	51421237	51423383	2146	True	421.500000	534	75.352000	455	3007	2	chr6B.!!$R5	2552
12	TraesCS6D01G058600	chr6B	45551941	45553010	1069	False	346.000000	346	73.369000	442	1534	1	chr6B.!!$F1	1092
13	TraesCS6D01G058600	chrUn	137812439	137813296	857	False	712.000000	712	81.965000	453	1301	1	chrUn.!!$F2	848
14	TraesCS6D01G058600	chrUn	137670338	137671191	853	False	431.000000	431	76.610000	679	1533	1	chrUn.!!$F1	854

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
325	725	0.543749	GGCTTCAGTCTACAGCCCAT	59.456	55.0	9.53	0.0	46.55	4.0	F
1124	5948	0.609662	ATGCCAATGGGAAACACTGC	59.390	50.0	0.00	0.0	35.59	4.4	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1252	6076	2.260844	TCAACAGTTCTTCCCAGCAG	57.739	50.000	0.0	0.0	0.0	4.24	R
2770	9314	1.204467	ACACAAACCACAACAGCCAAG	59.796	47.619	0.0	0.0	0.0	3.61	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
39	40	5.189659	AGCGTTAGATCTCTTCCATGTAC	57.810	43.478	0.00	0.00	0.00	2.90
68	69	1.084370	GCGACCGACCCAATCTTCAG	61.084	60.000	0.00	0.00	0.00	3.02
200	203	6.740110	TGCCATTTATCACTACGTTGTTTTT	58.260	32.000	0.00	0.00	0.00	1.94
201	204	6.638873	TGCCATTTATCACTACGTTGTTTTTG	59.361	34.615	0.00	0.00	0.00	2.44
204	207	8.073768	CCATTTATCACTACGTTGTTTTTGAGT	58.926	33.333	0.00	0.00	0.00	3.41
325	725	0.543749	GGCTTCAGTCTACAGCCCAT	59.456	55.000	9.53	0.00	46.55	4.00
361	766	3.490348	CACCTCACTTCACCTTTCCAAT	58.510	45.455	0.00	0.00	0.00	3.16
562	1023	3.327404	GCCGAAACCCTCCCCTCA	61.327	66.667	0.00	0.00	0.00	3.86
577	1038	2.755876	TCATCGGCTGCCTCGTCT	60.756	61.111	17.92	0.00	0.00	4.18
753	1235	4.329545	CTGGTGTGGGACCCCGTG	62.330	72.222	8.45	0.00	45.45	4.94
806	1294	1.179174	GGGTTCGCCAAGAAAGCCTT	61.179	55.000	0.00	0.00	41.10	4.35
977	1489	1.084370	CCGTCCGAGAATTCTGGTGC	61.084	60.000	14.00	5.65	0.00	5.01
1043	1561	5.394553	GGGATTCCTTTTATTGGTTGCTCTG	60.395	44.000	2.01	0.00	0.00	3.35
1124	5948	0.609662	ATGCCAATGGGAAACACTGC	59.390	50.000	0.00	0.00	35.59	4.40
1202	6026	2.894126	TCGTCTTTCTGAGAGGCTTTCT	59.106	45.455	6.60	0.00	39.54	2.52
1252	6076	0.037975	CAAGGGTGTTGCTTCATGGC	60.038	55.000	0.00	0.00	0.00	4.40
1440	6276	2.749621	CCTTGAATCCAAGCACTGGTAC	59.250	50.000	4.89	0.00	46.42	3.34
1553	6413	5.506151	CGTTTTACCTGTTTACTTTGGGTCC	60.506	44.000	0.00	0.00	0.00	4.46
1615	6482	2.479566	TCTGAGGTGGATCAGCAAAC	57.520	50.000	0.00	0.00	45.25	2.93
1894	6785	9.099454	GATCTTGCTAGTAATATTAAATCCCCG	57.901	37.037	0.00	0.00	0.00	5.73
2111	7006	9.410556	TGTACCGACTTAAGTGTAATTTTAGAC	57.589	33.333	14.14	0.00	0.00	2.59
2295	7218	1.202927	TGGGCCATATGGAGCTAAAGC	60.203	52.381	26.47	6.85	37.39	3.51
2439	8964	5.149973	TGGTTGCTACATTGCATTGATTT	57.850	34.783	15.20	0.00	42.96	2.17
2495	9020	6.232581	AGGATGATTTGTTTGTTGTTCCAA	57.767	33.333	0.00	0.00	0.00	3.53
2497	9022	6.048509	GGATGATTTGTTTGTTGTTCCAACT	58.951	36.000	8.41	0.00	0.00	3.16
2567	9106	9.908152	AAACTTCCTTTATTAATAATATGCGCC	57.092	29.630	4.18	0.00	0.00	6.53
2770	9314	5.411781	AGTTCGTCTGATCCAAACTACATC	58.588	41.667	0.00	0.00	0.00	3.06
2889	9438	8.615211	GCATGACTAGATTCATATTGAACACAA	58.385	33.333	0.00	0.00	39.45	3.33
3121	9792	1.005215	CTGTTTCTCCATGAGCCCCTT	59.995	52.381	0.00	0.00	0.00	3.95
3289	9975	7.972277	CGCTACAAATTAACTGTCTTCCTACTA	59.028	37.037	0.00	0.00	0.00	1.82

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
132	134	3.446161	CCATTGCATGATCCAGAACTTGT	59.554	43.478	0.00	0.00	0.00	3.16
166	169	3.190535	GTGATAAATGGCAACCGTGTTCT	59.809	43.478	0.00	0.00	0.00	3.01
167	170	3.190535	AGTGATAAATGGCAACCGTGTTC	59.809	43.478	0.00	0.00	0.00	3.18
169	172	2.790433	AGTGATAAATGGCAACCGTGT	58.210	42.857	0.00	0.00	0.00	4.49
216	231	7.604657	TTCAGATAAAAACCCCTAAAAAGCA	57.395	32.000	0.00	0.00	0.00	3.91
224	239	4.217767	GCGACTTTTCAGATAAAAACCCCT	59.782	41.667	0.00	0.00	0.00	4.79
226	241	4.915667	GTGCGACTTTTCAGATAAAAACCC	59.084	41.667	0.00	0.00	0.00	4.11
325	725	1.601759	GGTGCAGCAGGCTCTCAAA	60.602	57.895	11.86	0.00	45.15	2.69
562	1023	0.823769	TCATAGACGAGGCAGCCGAT	60.824	55.000	5.55	0.00	0.00	4.18
577	1038	3.088532	AGCGAACCTGGCAAAAATCATA	58.911	40.909	0.00	0.00	0.00	2.15
697	1158	1.751924	GTGGAAGATGAGTACGAGGCT	59.248	52.381	0.00	0.00	0.00	4.58
753	1235	2.357517	CTGTGCTGGTCACCGGTC	60.358	66.667	2.59	0.00	45.03	4.79
832	1326	3.075882	TGGAAATGGTGGAAATCTCCTGT	59.924	43.478	0.00	0.00	42.94	4.00
834	1328	3.309410	CCTGGAAATGGTGGAAATCTCCT	60.309	47.826	0.00	0.00	42.94	3.69
886	1383	0.603707	GAGGCTACTGCTTGTGTGCA	60.604	55.000	0.00	0.00	41.05	4.57
942	1442	0.892755	ACGGAAGCGGTGTTGAGATA	59.107	50.000	0.00	0.00	0.00	1.98
977	1489	2.172717	CCCTAGTAAACCATGGTGGGAG	59.827	54.545	25.09	15.07	43.37	4.30
1043	1561	3.701664	AGGATTCCTTGTGAATTCCCAC	58.298	45.455	0.00	0.00	43.81	4.61
1124	5948	6.294010	CCAAATATTGCCATCTCTCATGTCTG	60.294	42.308	0.00	0.00	0.00	3.51
1202	6026	2.945008	CTCCTCTTCCATAATTGCGCAA	59.055	45.455	27.24	27.24	0.00	4.85
1252	6076	2.260844	TCAACAGTTCTTCCCAGCAG	57.739	50.000	0.00	0.00	0.00	4.24
1431	6258	4.336889	TGGATAATAGCTGTACCAGTGC	57.663	45.455	0.00	0.00	33.43	4.40
1440	6276	6.769822	AGACACCTTCAAATGGATAATAGCTG	59.230	38.462	0.00	0.00	0.00	4.24
1553	6413	7.147312	TCTTTCCATTGTTTTGTTCTATGCAG	58.853	34.615	0.00	0.00	0.00	4.41
1894	6785	5.622770	AAACATCAAACCTGGTCGTTATC	57.377	39.130	0.00	0.00	0.00	1.75
2111	7006	4.751767	AGCAGATAGGAAAGGAGAAGTG	57.248	45.455	0.00	0.00	0.00	3.16
2295	7218	7.919091	AGAAATCAGCTTACATATTGTGCAATG	59.081	33.333	7.60	0.00	32.50	2.82
2451	8976	5.302059	TCCTCGAACTTGATAGACCCATAAG	59.698	44.000	0.00	0.00	0.00	1.73
2497	9022	9.389755	TGCTGTTAGTTATCAACTATTTGCATA	57.610	29.630	12.22	0.00	43.09	3.14
2770	9314	1.204467	ACACAAACCACAACAGCCAAG	59.796	47.619	0.00	0.00	0.00	3.61
2826	9373	8.635877	TGCGTTCAGTACAAAAATTGTTAAAT	57.364	26.923	0.54	0.00	42.22	1.40
2889	9438	4.764823	CAGACAACTACTCCTGAAGAGAGT	59.235	45.833	0.00	0.00	46.50	3.24
3121	9792	9.866655	AACTTTCTTTCTTATCATGGGCATATA	57.133	29.630	0.00	0.00	0.00	0.86

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.