AutoCloner

Multiple sequence alignment - TraesCS1D01G054800

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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	TraesCS1D01G054800	chr1D	100.000	2206	0	0	849	3054	36315606	36317811	0.000000e+00	4074.0
1	TraesCS1D01G054800	chr1D	94.260	906	44	6	1675	2576	36362365	36361464	0.000000e+00	1378.0
2	TraesCS1D01G054800	chr1D	93.233	798	54	0	849	1646	36363153	36362356	0.000000e+00	1175.0
3	TraesCS1D01G054800	chr1D	100.000	589	0	0	1	589	36314758	36315346	0.000000e+00	1088.0
4	TraesCS1D01G054800	chr1D	76.359	1214	240	34	1136	2337	24145146	24146324	2.600000e-170	608.0
5	TraesCS1D01G054800	chr1D	100.000	29	0	0	158	186	36314976	36315004	2.000000e-03	54.7
6	TraesCS1D01G054800	chr1A	92.130	2211	153	10	849	3054	35485998	35488192	0.000000e+00	3099.0
7	TraesCS1D01G054800	chr1A	92.680	1858	124	6	995	2849	35525788	35527636	0.000000e+00	2667.0
8	TraesCS1D01G054800	chr1A	91.854	1731	133	6	849	2576	35578649	35576924	0.000000e+00	2409.0
9	TraesCS1D01G054800	chr1A	89.298	1710	131	26	866	2559	35536206	35537879	0.000000e+00	2097.0
10	TraesCS1D01G054800	chr1A	89.706	476	41	5	2585	3054	35538510	35538983	4.360000e-168	601.0
11	TraesCS1D01G054800	chr1A	93.084	347	23	1	2599	2944	35576278	35575932	9.770000e-140	507.0
12	TraesCS1D01G054800	chr1A	89.655	290	28	2	198	486	35514660	35514948	4.810000e-98	368.0
13	TraesCS1D01G054800	chr1A	89.655	290	28	2	198	486	35535566	35535854	4.810000e-98	368.0
14	TraesCS1D01G054800	chr1A	89.078	293	25	4	198	487	35579157	35578869	1.040000e-94	357.0
15	TraesCS1D01G054800	chr1A	89.116	294	18	7	198	486	35485140	35485424	1.350000e-93	353.0
16	TraesCS1D01G054800	chr1A	96.226	159	4	1	1	157	35534993	35535151	3.020000e-65	259.0
17	TraesCS1D01G054800	chr1A	93.750	112	7	0	2943	3054	35575828	35575717	5.240000e-38	169.0
18	TraesCS1D01G054800	chr1A	89.600	125	10	2	1	123	35484569	35484692	4.080000e-34	156.0
19	TraesCS1D01G054800	chr1A	84.146	164	16	5	1	155	35514127	35514289	1.900000e-32	150.0
20	TraesCS1D01G054800	chr1A	90.000	100	5	1	490	589	35485482	35485576	1.150000e-24	124.0
21	TraesCS1D01G054800	chr1A	86.905	84	4	5	506	589	35578815	35578739	1.510000e-13	87.9
22	TraesCS1D01G054800	chr1A	100.000	29	0	0	158	186	35485161	35485189	2.000000e-03	54.7
23	TraesCS1D01G054800	chr1A	100.000	29	0	0	158	186	35514681	35514709	2.000000e-03	54.7
24	TraesCS1D01G054800	chr1A	100.000	29	0	0	158	186	35535587	35535615	2.000000e-03	54.7
25	TraesCS1D01G054800	chr1B	90.913	2168	142	13	849	3000	55977039	55979167	0.000000e+00	2861.0
26	TraesCS1D01G054800	chr1B	87.775	1636	160	28	849	2463	56016958	56018574	0.000000e+00	1877.0
27	TraesCS1D01G054800	chr1B	94.113	1206	66	4	860	2064	56140944	56139743	0.000000e+00	1829.0
28	TraesCS1D01G054800	chr1B	91.066	1220	97	7	849	2064	55998306	55999517	0.000000e+00	1639.0
29	TraesCS1D01G054800	chr1B	94.195	913	49	4	2092	3000	55999514	56000426	0.000000e+00	1389.0
30	TraesCS1D01G054800	chr1B	93.033	488	31	3	2092	2576	56139746	56139259	0.000000e+00	710.0
31	TraesCS1D01G054800	chr1B	92.616	474	33	2	2582	3054	56138631	56138159	0.000000e+00	680.0
32	TraesCS1D01G054800	chr1B	89.619	289	21	7	198	486	56016272	56016551	2.900000e-95	359.0
33	TraesCS1D01G054800	chr1B	88.356	292	27	4	198	486	56141651	56141364	8.110000e-91	344.0
34	TraesCS1D01G054800	chr1B	88.276	290	25	7	198	486	55976516	55976797	3.770000e-89	339.0
35	TraesCS1D01G054800	chr1B	88.353	249	26	3	2582	2829	56019017	56019263	2.300000e-76	296.0
36	TraesCS1D01G054800	chr1B	90.000	230	22	1	2825	3054	56056874	56057102	2.300000e-76	296.0
37	TraesCS1D01G054800	chr1B	91.729	133	5	2	1	127	55944214	55944346	2.420000e-41	180.0
38	TraesCS1D01G054800	chr1B	91.729	133	5	2	1	127	55955467	55955599	2.420000e-41	180.0
39	TraesCS1D01G054800	chr1B	84.270	178	22	4	309	486	55944841	55945012	5.240000e-38	169.0
40	TraesCS1D01G054800	chr1B	83.708	178	23	4	309	486	55956094	55956265	2.440000e-36	163.0
41	TraesCS1D01G054800	chr1B	93.590	78	5	0	198	275	55944764	55944841	1.920000e-22	117.0
42	TraesCS1D01G054800	chr1B	93.590	78	5	0	198	275	55956017	55956094	1.920000e-22	117.0
43	TraesCS1D01G054800	chrUn	80.083	482	66	10	2599	3054	333432	333909	6.310000e-87	331.0
44	TraesCS1D01G054800	chrUn	80.083	482	66	10	2599	3054	319351034	319350557	6.310000e-87	331.0

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	TraesCS1D01G054800	chr1D	36314758	36317811	3053	False	1738.90	4074	100.000000	1	3054	3	chr1D.!!$F2	3053
1	TraesCS1D01G054800	chr1D	36361464	36363153	1689	True	1276.50	1378	93.746500	849	2576	2	chr1D.!!$R1	1727
2	TraesCS1D01G054800	chr1D	24145146	24146324	1178	False	608.00	608	76.359000	1136	2337	1	chr1D.!!$F1	1201
3	TraesCS1D01G054800	chr1A	35525788	35527636	1848	False	2667.00	2667	92.680000	995	2849	1	chr1A.!!$F1	1854
4	TraesCS1D01G054800	chr1A	35484569	35488192	3623	False	757.34	3099	92.169200	1	3054	5	chr1A.!!$F2	3053
5	TraesCS1D01G054800	chr1A	35575717	35579157	3440	True	705.98	2409	90.934200	198	3054	5	chr1A.!!$R1	2856
6	TraesCS1D01G054800	chr1A	35534993	35538983	3990	False	675.94	2097	92.977000	1	3054	5	chr1A.!!$F4	3053
7	TraesCS1D01G054800	chr1B	55976516	55979167	2651	False	1600.00	2861	89.594500	198	3000	2	chr1B.!!$F4	2802
8	TraesCS1D01G054800	chr1B	55998306	56000426	2120	False	1514.00	1639	92.630500	849	3000	2	chr1B.!!$F5	2151
9	TraesCS1D01G054800	chr1B	56138159	56141651	3492	True	890.75	1829	92.029500	198	3054	4	chr1B.!!$R1	2856
10	TraesCS1D01G054800	chr1B	56016272	56019263	2991	False	844.00	1877	88.582333	198	2829	3	chr1B.!!$F6	2631

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
939	1592	0.107654	GTACCCTTCTCATTGCCGCT	60.108	55.0	0.0	0.0	0.0	5.52	F
1672	2335	0.625849	CCTTACATTCCAGCCCCTGT	59.374	55.0	0.0	0.0	0.0	4.00	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1868	2571	0.458889	CAATGGCAGCACCGAATTGG	60.459	55.0	0.0	0.0	43.94	3.16	R
2878	4451	2.979678	TCTACCATGATTTAGAGGGGCC	59.020	50.0	0.0	0.0	0.00	5.80	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
102	105	6.213195	TCCCCTTTTCATTGCTTTGACATAAT	59.787	34.615	0.00	0.00	0.00	1.28
157	175	0.627986	CAGGAAGCAGGAAAGGGGAT	59.372	55.000	0.00	0.00	0.00	3.85
158	176	0.922626	AGGAAGCAGGAAAGGGGATC	59.077	55.000	0.00	0.00	0.00	3.36
159	177	0.922626	GGAAGCAGGAAAGGGGATCT	59.077	55.000	0.00	0.00	0.00	2.75
160	178	1.286257	GGAAGCAGGAAAGGGGATCTT	59.714	52.381	0.00	0.00	37.28	2.40
161	179	2.509964	GGAAGCAGGAAAGGGGATCTTA	59.490	50.000	0.00	0.00	34.78	2.10
163	181	3.872459	AGCAGGAAAGGGGATCTTATG	57.128	47.619	0.00	0.00	34.78	1.90
164	182	3.397527	AGCAGGAAAGGGGATCTTATGA	58.602	45.455	0.00	0.00	34.78	2.15
165	183	3.393941	AGCAGGAAAGGGGATCTTATGAG	59.606	47.826	0.00	0.00	34.78	2.90
166	184	3.749226	CAGGAAAGGGGATCTTATGAGC	58.251	50.000	0.00	0.00	34.78	4.26
167	185	3.137176	CAGGAAAGGGGATCTTATGAGCA	59.863	47.826	0.00	0.00	34.78	4.26
169	187	4.077822	GGAAAGGGGATCTTATGAGCATG	58.922	47.826	0.00	0.00	34.78	4.06
170	188	3.803186	AAGGGGATCTTATGAGCATGG	57.197	47.619	0.00	0.00	33.14	3.66
171	189	2.711174	AGGGGATCTTATGAGCATGGT	58.289	47.619	0.00	0.00	0.00	3.55
172	190	3.059097	AGGGGATCTTATGAGCATGGTT	58.941	45.455	0.00	0.00	0.00	3.67
173	191	4.242811	AGGGGATCTTATGAGCATGGTTA	58.757	43.478	0.00	0.00	0.00	2.85
175	193	4.042187	GGGGATCTTATGAGCATGGTTACT	59.958	45.833	0.00	0.00	0.00	2.24
176	194	5.248477	GGGGATCTTATGAGCATGGTTACTA	59.752	44.000	0.00	0.00	0.00	1.82
177	195	6.069963	GGGGATCTTATGAGCATGGTTACTAT	60.070	42.308	0.00	0.00	0.00	2.12
178	196	7.125811	GGGGATCTTATGAGCATGGTTACTATA	59.874	40.741	0.00	0.00	0.00	1.31
179	197	8.709308	GGGATCTTATGAGCATGGTTACTATAT	58.291	37.037	0.00	0.00	0.00	0.86
180	198	9.757227	GGATCTTATGAGCATGGTTACTATATC	57.243	37.037	0.00	0.00	0.00	1.63
181	199	9.757227	GATCTTATGAGCATGGTTACTATATCC	57.243	37.037	0.00	0.00	0.00	2.59
182	200	8.664669	TCTTATGAGCATGGTTACTATATCCA	57.335	34.615	0.00	0.00	35.64	3.41
354	756	5.797434	GCTGTAGAATGAAGCTTTAAAGTGC	59.203	40.000	16.38	4.26	34.05	4.40
415	820	5.066375	GGTAATGTGTAGATCAGCATTGCAA	59.934	40.000	11.91	0.00	34.97	4.08
486	893	8.414778	AGTTTTAAAAACGGTGATCCATACAAA	58.585	29.630	1.31	0.00	0.00	2.83
919	1572	0.318441	CGTCCTCACCACATCACACT	59.682	55.000	0.00	0.00	0.00	3.55
939	1592	0.107654	GTACCCTTCTCATTGCCGCT	60.108	55.000	0.00	0.00	0.00	5.52
1010	1663	2.035626	CCCGGCCATGGTGAACTT	59.964	61.111	14.67	0.00	0.00	2.66
1194	1848	3.055719	CTGCGGTGCGTTCCCATT	61.056	61.111	0.00	0.00	0.00	3.16
1285	1939	2.359850	TACAGCTTGGCCTTGGCG	60.360	61.111	3.32	5.10	0.00	5.69
1672	2335	0.625849	CCTTACATTCCAGCCCCTGT	59.374	55.000	0.00	0.00	0.00	4.00
1708	2408	6.199376	AGGGACCCGTTTTTAATTCCATAAT	58.801	36.000	4.40	0.00	0.00	1.28
1709	2409	7.355890	AGGGACCCGTTTTTAATTCCATAATA	58.644	34.615	4.40	0.00	0.00	0.98
1710	2410	7.840210	AGGGACCCGTTTTTAATTCCATAATAA	59.160	33.333	4.40	0.00	0.00	1.40
1713	2413	9.857957	GACCCGTTTTTAATTCCATAATAAACA	57.142	29.630	0.00	0.00	0.00	2.83
1810	2510	1.609061	CGCTGACCCTGTCAACTCAAT	60.609	52.381	0.00	0.00	42.26	2.57
1868	2571	4.604843	TTCGCAGATCACAATTCACATC	57.395	40.909	0.00	0.00	35.04	3.06
1905	2608	6.777091	TGCCATTGTTAGCTACATAATCCATT	59.223	34.615	0.00	0.00	36.44	3.16
2041	2745	9.236006	AGTGATATTCATTTCCATAATAGCACC	57.764	33.333	15.23	3.17	46.22	5.01
2211	2990	1.927174	GTACCAGCTTCAGTGCATACG	59.073	52.381	0.00	0.00	34.99	3.06
2338	3119	2.832733	ACCAAAAGGTTTCGAAAACCCA	59.167	40.909	21.98	0.00	41.18	4.51
2594	4163	3.347077	TTTTTACGGGATTAAGCCGGA	57.653	42.857	22.50	3.44	32.99	5.14
2605	4174	6.428771	CGGGATTAAGCCGGATTATTTCTTTA	59.571	38.462	13.87	0.00	0.00	1.85
2729	4302	9.829507	CCTAATACTTTGATTCATCTCAAGTCT	57.170	33.333	5.04	0.00	36.55	3.24
2783	4356	8.681806	TCATAATAAATTTCCATGCAACTCGAA	58.318	29.630	0.00	0.00	0.00	3.71
2878	4451	7.964559	TCGCAAATGAATCAAACTTCTAATCTG	59.035	33.333	0.00	0.00	0.00	2.90

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
102	105	3.519510	ACTGGCTAGCTCTTGTATTTCCA	59.480	43.478	15.72	0.00	0.00	3.53
157	175	8.664669	TGGATATAGTAACCATGCTCATAAGA	57.335	34.615	0.00	0.00	0.00	2.10
158	176	8.535335	ACTGGATATAGTAACCATGCTCATAAG	58.465	37.037	0.00	0.00	33.08	1.73
159	177	8.435931	ACTGGATATAGTAACCATGCTCATAA	57.564	34.615	0.00	0.00	33.08	1.90
160	178	8.314021	CAACTGGATATAGTAACCATGCTCATA	58.686	37.037	0.00	0.00	33.08	2.15
161	179	6.942163	ACTGGATATAGTAACCATGCTCAT	57.058	37.500	0.00	0.00	33.08	2.90
163	181	5.934625	CCAACTGGATATAGTAACCATGCTC	59.065	44.000	0.00	0.00	37.39	4.26
164	182	5.606749	TCCAACTGGATATAGTAACCATGCT	59.393	40.000	0.00	0.00	39.78	3.79
165	183	5.865085	TCCAACTGGATATAGTAACCATGC	58.135	41.667	0.00	0.00	39.78	4.06
166	184	7.303182	TCTCCAACTGGATATAGTAACCATG	57.697	40.000	0.00	0.00	44.46	3.66
167	185	6.014156	GCTCTCCAACTGGATATAGTAACCAT	60.014	42.308	0.00	0.00	44.46	3.55
169	187	5.540719	AGCTCTCCAACTGGATATAGTAACC	59.459	44.000	0.00	0.00	44.46	2.85
170	188	6.658188	AGCTCTCCAACTGGATATAGTAAC	57.342	41.667	0.00	0.00	44.46	2.50
171	189	7.676683	AAAGCTCTCCAACTGGATATAGTAA	57.323	36.000	0.00	0.00	44.46	2.24
172	190	7.676683	AAAAGCTCTCCAACTGGATATAGTA	57.323	36.000	0.00	0.00	44.46	1.82
173	191	6.567602	AAAAGCTCTCCAACTGGATATAGT	57.432	37.500	0.00	0.00	44.46	2.12
323	725	7.559590	AAAGCTTCATTCTACAGCGAATATT	57.440	32.000	0.00	0.00	38.66	1.28
325	727	8.487313	TTTAAAGCTTCATTCTACAGCGAATA	57.513	30.769	0.00	0.00	38.66	1.75
415	820	3.945285	CGTAGGGGAAAAAGTGCATACAT	59.055	43.478	0.00	0.00	0.00	2.29
430	835	0.899720	TGTACCTTTCTGCGTAGGGG	59.100	55.000	0.00	3.79	35.79	4.79
858	1511	2.909965	GGGTGGGTTTGCTTGCGA	60.910	61.111	0.00	0.00	0.00	5.10
919	1572	0.392461	GCGGCAATGAGAAGGGTACA	60.392	55.000	0.00	0.00	0.00	2.90
939	1592	1.738432	CGCTCTAGATCTGGCTGCA	59.262	57.895	18.34	0.00	0.00	4.41
1230	1884	2.611225	ATTGCTGATTCGAGGAGGAC	57.389	50.000	0.00	0.00	0.00	3.85
1285	1939	2.202987	CGATGCCTCTGCCACCTC	60.203	66.667	0.00	0.00	36.33	3.85
1810	2510	2.349755	GTTGGGTGGAGGCGCTTA	59.650	61.111	7.64	0.00	0.00	3.09
1868	2571	0.458889	CAATGGCAGCACCGAATTGG	60.459	55.000	0.00	0.00	43.94	3.16
1905	2608	6.697395	TCTGACTCTTCGGAACAATTAATCA	58.303	36.000	0.00	0.00	33.90	2.57
1918	2621	4.442375	ACATACCAACTCTGACTCTTCG	57.558	45.455	0.00	0.00	0.00	3.79
2041	2745	3.375922	ACCAAAGTAACGAACAACCACTG	59.624	43.478	0.00	0.00	0.00	3.66
2189	2968	2.867109	ATGCACTGAAGCTGGTACTT	57.133	45.000	0.00	0.00	34.99	2.24
2279	3060	1.225376	CCAGCTACAACGCGACCAAA	61.225	55.000	15.93	0.00	34.40	3.28
2580	4149	4.324267	AGAAATAATCCGGCTTAATCCCG	58.676	43.478	1.18	7.52	45.17	5.14
2586	4155	9.498176	GGTAGAATAAAGAAATAATCCGGCTTA	57.502	33.333	0.00	0.00	0.00	3.09
2594	4163	9.262358	GTCGCTCTGGTAGAATAAAGAAATAAT	57.738	33.333	0.00	0.00	0.00	1.28
2605	4174	4.475345	AGGAATAGTCGCTCTGGTAGAAT	58.525	43.478	0.00	0.00	0.00	2.40
2783	4356	5.992217	GGAGATATGCTACGAATCTTTTGGT	59.008	40.000	0.00	0.00	30.19	3.67
2878	4451	2.979678	TCTACCATGATTTAGAGGGGCC	59.020	50.000	0.00	0.00	0.00	5.80
3011	4690	4.354893	TGCCAAAATTGAGGAAAAGCAT	57.645	36.364	0.79	0.00	0.00	3.79

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.