AutoCloner

Multiple sequence alignment - TraesCS5D01G493100

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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	TraesCS5D01G493100	chr5D	100.000	6382	0	0	1	6382	525979011	525972630	0.000000e+00	11786.0
1	TraesCS5D01G493100	chr5D	87.674	1939	167	32	948	2870	525977100	525975218	0.000000e+00	2191.0
2	TraesCS5D01G493100	chr5D	87.674	1939	167	32	1912	3794	525978064	525976142	0.000000e+00	2191.0
3	TraesCS5D01G493100	chr5D	88.889	990	57	19	951	1934	525976160	525975218	0.000000e+00	1170.0
4	TraesCS5D01G493100	chr5D	88.889	990	57	19	2852	3794	525978061	525977078	0.000000e+00	1170.0
5	TraesCS5D01G493100	chr5D	87.959	872	66	19	102	956	525977042	525976193	0.000000e+00	992.0
6	TraesCS5D01G493100	chr5D	87.959	872	66	19	1970	2819	525978910	525978056	0.000000e+00	992.0
7	TraesCS5D01G493100	chr5D	83.003	859	92	23	102	941	525976106	525975283	0.000000e+00	728.0
8	TraesCS5D01G493100	chr5D	83.003	859	92	23	2906	3729	525978910	525978071	0.000000e+00	728.0
9	TraesCS5D01G493100	chr5D	81.716	886	85	28	116	949	525977999	525977139	0.000000e+00	667.0
10	TraesCS5D01G493100	chr5D	81.716	886	85	28	1013	1873	525978896	525978063	0.000000e+00	667.0
11	TraesCS5D01G493100	chr5D	97.590	83	2	0	5131	5213	525973843	525973761	6.670000e-30	143.0
12	TraesCS5D01G493100	chr5D	97.590	83	2	0	5169	5251	525973881	525973799	6.670000e-30	143.0
13	TraesCS5D01G493100	chr5D	95.556	45	2	0	5131	5175	525973805	525973761	8.880000e-09	73.1
14	TraesCS5D01G493100	chr5D	95.556	45	2	0	5207	5251	525973881	525973837	8.880000e-09	73.1
15	TraesCS5D01G493100	chr5B	93.187	4315	203	38	948	5225	660661706	660657446	0.000000e+00	6255.0
16	TraesCS5D01G493100	chr5B	89.476	2841	204	40	1013	3794	660662605	660659801	0.000000e+00	3502.0
17	TraesCS5D01G493100	chr5B	88.471	1943	156	26	951	2870	660660764	660658867	0.000000e+00	2285.0
18	TraesCS5D01G493100	chr5B	85.813	1882	202	37	1970	3794	660662619	660660746	0.000000e+00	1936.0
19	TraesCS5D01G493100	chr5B	89.596	990	60	16	951	1934	660659819	660658867	0.000000e+00	1218.0
20	TraesCS5D01G493100	chr5B	87.980	990	75	18	1	949	660662729	660661743	0.000000e+00	1129.0
21	TraesCS5D01G493100	chr5B	86.866	868	73	20	102	950	660661648	660660803	0.000000e+00	933.0
22	TraesCS5D01G493100	chr5B	86.598	873	73	17	102	950	660660710	660659858	0.000000e+00	924.0
23	TraesCS5D01G493100	chr5B	84.101	868	93	20	102	950	660659765	660658924	0.000000e+00	797.0
24	TraesCS5D01G493100	chr5B	82.166	942	109	31	2906	3794	660662619	660661684	0.000000e+00	754.0
25	TraesCS5D01G493100	chr5B	86.022	465	26	11	5169	5599	660657540	660657081	4.510000e-126	462.0
26	TraesCS5D01G493100	chr5B	84.278	388	26	27	5870	6249	660656657	660656297	4.740000e-91	346.0
27	TraesCS5D01G493100	chr5B	89.655	58	4	2	5131	5187	660657502	660657446	8.880000e-09	73.1
28	TraesCS5D01G493100	chr5A	85.845	1971	159	48	17	1934	652668524	652666621	0.000000e+00	1984.0
29	TraesCS5D01G493100	chr5A	90.483	1387	112	11	2833	4207	652667590	652666212	0.000000e+00	1812.0
30	TraesCS5D01G493100	chr5A	87.703	984	107	10	1892	2870	652667595	652666621	0.000000e+00	1134.0
31	TraesCS5D01G493100	chr5A	88.744	613	54	9	4579	5187	652665569	652664968	0.000000e+00	736.0
32	TraesCS5D01G493100	chr5A	82.670	854	102	22	116	950	652667504	652666678	0.000000e+00	715.0
33	TraesCS5D01G493100	chr5A	86.207	696	46	19	5207	5861	652665024	652664338	0.000000e+00	708.0
34	TraesCS5D01G493100	chr5A	81.696	896	100	28	2874	3720	652668476	652667596	0.000000e+00	688.0
35	TraesCS5D01G493100	chr5A	84.283	579	64	16	1013	1568	652668431	652667857	2.020000e-149	540.0
36	TraesCS5D01G493100	chr5A	89.189	370	17	10	6019	6379	652663915	652663560	2.110000e-119	440.0
37	TraesCS5D01G493100	chr5A	88.591	298	20	6	4279	4574	652666050	652665765	3.660000e-92	350.0
38	TraesCS5D01G493100	chr5A	90.875	263	6	4	1608	1857	652667851	652667594	2.850000e-88	337.0
39	TraesCS5D01G493100	chr5A	90.816	98	7	1	5862	5957	652664298	652664201	5.190000e-26	130.0
40	TraesCS5D01G493100	chr5A	87.097	62	6	2	5165	5225	652665028	652664968	1.150000e-07	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	TraesCS5D01G493100	chr5D	525972630	525979011	6381	True	11786.000000	11786	100.000000	1	6382	1	chr5D.!!$R1	6381
1	TraesCS5D01G493100	chr5D	525973761	525978910	5149	True	852.014286	2191	88.912429	102	5251	14	chr5D.!!$R2	5149
2	TraesCS5D01G493100	chr5B	660656297	660661706	5409	True	2354.333333	6255	87.829000	948	6249	3	chr5B.!!$R1	5301
3	TraesCS5D01G493100	chr5B	660657446	660662729	5283	True	1355.110000	3502	87.072200	1	5187	10	chr5B.!!$R2	5186
4	TraesCS5D01G493100	chr5A	652663560	652668524	4964	True	741.800000	1984	87.246077	17	6379	13	chr5A.!!$R1	6362

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
1903	1973	8.912988	TCATTTCAGAAAATTACCAAGAGTGTT	58.087	29.630	0.00	0.00	32.69	3.32	F
1921	1991	7.253422	AGAGTGTTCATTTTGTTCAGAACTTG	58.747	34.615	14.51	7.18	40.62	3.16	F
5252	6606	5.693814	GGCAACTTATAGCAGTGAATATGC	58.306	41.667	0.00	0.00	44.18	3.14	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
5251	6605	1.815003	ACATAAAAGCCTCTGCACTGC	59.185	47.619	0.00	0.00	41.13	4.40	R
5252	6606	3.366679	CCAACATAAAAGCCTCTGCACTG	60.367	47.826	0.00	0.00	41.13	3.66	R
6249	8244	1.009222	GGAGGTCATACGTACGCCG	60.009	63.158	16.72	3.83	44.03	6.46	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
1903	1973	8.912988	TCATTTCAGAAAATTACCAAGAGTGTT	58.087	29.630	0.00	0.00	32.69	3.32
1921	1991	7.253422	AGAGTGTTCATTTTGTTCAGAACTTG	58.747	34.615	14.51	7.18	40.62	3.16
5252	6606	5.693814	GGCAACTTATAGCAGTGAATATGC	58.306	41.667	0.00	0.00	44.18	3.14
5331	6699	4.877773	TGACCCTGGCCAATTATACAAAT	58.122	39.130	7.01	0.00	0.00	2.32
5390	6768	4.698575	AGAGGAAGAAGTGAGTTGTTGAC	58.301	43.478	0.00	0.00	0.00	3.18
5429	6807	2.751259	AGTATAACTGACGGACGCTTCA	59.249	45.455	0.00	0.00	0.00	3.02
5468	6846	1.218316	GGTTCCCTCGCATCTCGTT	59.782	57.895	0.00	0.00	39.67	3.85
5472	6850	0.108804	TCCCTCGCATCTCGTTTCAC	60.109	55.000	0.00	0.00	39.67	3.18
5559	6950	5.537674	AGCAGTTTTGATCTGGTGATTTCTT	59.462	36.000	0.00	0.00	41.19	2.52
5620	7333	2.100916	ACTGGTATGCTGATGGTCGTAC	59.899	50.000	0.00	0.00	0.00	3.67
5633	7346	1.155042	GTCGTACACTCGTCTCCAGT	58.845	55.000	0.00	0.00	0.00	4.00
5659	7372	5.551233	TCAAGAATGAGAACCCAGTTGTAG	58.449	41.667	0.00	0.00	0.00	2.74
5681	7394	8.208224	TGTAGAATAACCACTGAAACTCTGAAA	58.792	33.333	0.00	0.00	0.00	2.69
5687	7400	2.106511	CACTGAAACTCTGAAAGGGGGA	59.893	50.000	0.00	0.00	40.48	4.81
5688	7401	2.989571	ACTGAAACTCTGAAAGGGGGAT	59.010	45.455	0.00	0.00	40.48	3.85
5689	7402	3.009584	ACTGAAACTCTGAAAGGGGGATC	59.990	47.826	0.00	0.00	40.48	3.36
5728	7446	1.099689	AACTAGAGGCGTCAGCTCTC	58.900	55.000	9.41	0.00	44.37	3.20
5732	7452	2.993840	AGGCGTCAGCTCTCTGCA	60.994	61.111	0.00	0.00	45.94	4.41
5736	7456	1.447314	CGTCAGCTCTCTGCATGCA	60.447	57.895	21.29	21.29	45.94	3.96
5778	7498	0.968901	TGTGCAGGTAGTACGAGGGG	60.969	60.000	0.00	0.00	35.35	4.79
5800	7520	2.004808	GAAAATGGCCGCACCCTAGC	62.005	60.000	0.00	0.00	37.83	3.42
5817	7537	3.357079	CCGTGTTCACCTGCTGGC	61.357	66.667	9.95	0.00	36.63	4.85
5830	7550	2.352229	CTGGCGCAACACAACACG	60.352	61.111	10.83	0.00	0.00	4.49
5836	7556	2.631428	CAACACAACACGGCGGAG	59.369	61.111	13.24	5.87	0.00	4.63
5908	7667	1.394917	CGAACAGAAAGATTCCAGGCG	59.605	52.381	0.00	0.00	0.00	5.52
5953	7712	3.086600	GCCCAGGACCAGCTAGCT	61.087	66.667	12.68	12.68	0.00	3.32
5954	7713	1.762460	GCCCAGGACCAGCTAGCTA	60.762	63.158	18.86	0.00	0.00	3.32
5955	7714	1.753368	GCCCAGGACCAGCTAGCTAG	61.753	65.000	18.86	16.84	0.00	3.42
6004	7764	0.109458	GGGAAACCGCCGAAATGAAC	60.109	55.000	0.00	0.00	43.64	3.18
6005	7765	0.109458	GGAAACCGCCGAAATGAACC	60.109	55.000	0.00	0.00	0.00	3.62
6006	7766	0.109458	GAAACCGCCGAAATGAACCC	60.109	55.000	0.00	0.00	0.00	4.11
6007	7767	1.858372	AAACCGCCGAAATGAACCCG	61.858	55.000	0.00	0.00	0.00	5.28
6008	7768	4.174129	CCGCCGAAATGAACCCGC	62.174	66.667	0.00	0.00	0.00	6.13
6009	7769	4.174129	CGCCGAAATGAACCCGCC	62.174	66.667	0.00	0.00	0.00	6.13
6010	7770	4.174129	GCCGAAATGAACCCGCCG	62.174	66.667	0.00	0.00	0.00	6.46
6011	7771	2.744709	CCGAAATGAACCCGCCGT	60.745	61.111	0.00	0.00	0.00	5.68
6072	8057	1.302033	GCCGGCCTATCCTGATGTG	60.302	63.158	18.11	0.00	0.00	3.21
6073	8058	1.302033	CCGGCCTATCCTGATGTGC	60.302	63.158	0.00	0.00	0.00	4.57
6075	8060	0.107456	CGGCCTATCCTGATGTGCTT	59.893	55.000	0.00	0.00	0.00	3.91
6076	8061	1.344438	CGGCCTATCCTGATGTGCTTA	59.656	52.381	0.00	0.00	0.00	3.09
6077	8062	2.772287	GGCCTATCCTGATGTGCTTAC	58.228	52.381	0.00	0.00	0.00	2.34
6078	8063	2.408050	GCCTATCCTGATGTGCTTACG	58.592	52.381	0.00	0.00	0.00	3.18
6184	8179	2.066700	TTGCATGGTCCAGTCCTGCA	62.067	55.000	12.84	12.84	38.65	4.41
6203	8198	2.903855	AGCCTGCACTGCACACAC	60.904	61.111	0.00	0.00	33.79	3.82
6204	8199	3.211245	GCCTGCACTGCACACACA	61.211	61.111	0.00	0.00	33.79	3.72
6294	8289	2.509336	CGGACCCTGCAGCGTAAG	60.509	66.667	8.66	0.00	43.44	2.34
6295	8290	2.663196	GGACCCTGCAGCGTAAGT	59.337	61.111	8.66	0.00	41.68	2.24
6296	8291	1.895238	GGACCCTGCAGCGTAAGTA	59.105	57.895	8.66	0.00	41.68	2.24
6297	8292	0.459759	GGACCCTGCAGCGTAAGTAC	60.460	60.000	8.66	0.00	41.68	2.73
6311	8306	3.546815	CGTAAGTACGTATGCGCTAGGTT	60.547	47.826	9.73	0.00	44.13	3.50
6317	8312	2.268298	CGTATGCGCTAGGTTTCAGTT	58.732	47.619	9.73	0.00	0.00	3.16
6318	8313	2.281762	CGTATGCGCTAGGTTTCAGTTC	59.718	50.000	9.73	0.00	0.00	3.01
6319	8314	2.472695	ATGCGCTAGGTTTCAGTTCA	57.527	45.000	9.73	0.00	0.00	3.18
6320	8315	1.508632	TGCGCTAGGTTTCAGTTCAC	58.491	50.000	9.73	0.00	0.00	3.18
6321	8316	1.070134	TGCGCTAGGTTTCAGTTCACT	59.930	47.619	9.73	0.00	0.00	3.41
6322	8317	1.461127	GCGCTAGGTTTCAGTTCACTG	59.539	52.381	0.00	0.02	45.08	3.66

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
14	15	1.794785	CGCAAGTGCAATGTCGCAG	60.795	57.895	3.87	0.00	44.05	5.18
1898	1968	7.156876	TCAAGTTCTGAACAAAATGAACACT	57.843	32.000	21.50	0.00	40.62	3.55
1899	1969	7.701924	TGATCAAGTTCTGAACAAAATGAACAC	59.298	33.333	21.50	14.11	40.62	3.32
1903	1973	6.016024	CCCTGATCAAGTTCTGAACAAAATGA	60.016	38.462	21.50	18.00	36.50	2.57
1921	1991	3.439129	CCAAACCGTAAACTTCCCTGATC	59.561	47.826	0.00	0.00	0.00	2.92
5251	6605	1.815003	ACATAAAAGCCTCTGCACTGC	59.185	47.619	0.00	0.00	41.13	4.40
5252	6606	3.366679	CCAACATAAAAGCCTCTGCACTG	60.367	47.826	0.00	0.00	41.13	3.66
5331	6699	3.367292	GCTCTGCGATTTTGGGATGAAAA	60.367	43.478	0.00	0.00	0.00	2.29
5364	6732	2.558795	CAACTCACTTCTTCCTCTCGGA	59.441	50.000	0.00	0.00	37.60	4.55
5390	6768	8.774586	AGTTATACTTTGCTACTTCAACACTTG	58.225	33.333	0.00	0.00	0.00	3.16
5468	6846	3.068732	TCAAATGCACAAAATCCGGTGAA	59.931	39.130	0.00	0.00	37.18	3.18
5472	6850	4.244066	TCAATCAAATGCACAAAATCCGG	58.756	39.130	0.00	0.00	0.00	5.14
5592	6985	3.562973	CCATCAGCATACCAGTTAAGCAG	59.437	47.826	0.00	0.00	0.00	4.24
5595	6988	3.804325	CGACCATCAGCATACCAGTTAAG	59.196	47.826	0.00	0.00	0.00	1.85
5620	7333	2.554462	TCTTGAGAACTGGAGACGAGTG	59.446	50.000	0.00	0.00	0.00	3.51
5659	7372	6.072452	CCCTTTCAGAGTTTCAGTGGTTATTC	60.072	42.308	0.00	0.00	0.00	1.75
5681	7394	2.000290	TTTCTTGGATGGATCCCCCT	58.000	50.000	17.98	0.57	46.59	4.79
5687	7400	4.515028	TCAGCAGATTTCTTGGATGGAT	57.485	40.909	0.00	0.00	0.00	3.41
5688	7401	4.305539	TTCAGCAGATTTCTTGGATGGA	57.694	40.909	0.00	0.00	0.00	3.41
5689	7402	4.461781	AGTTTCAGCAGATTTCTTGGATGG	59.538	41.667	0.00	0.00	0.00	3.51
5728	7446	1.296755	ACAGAAGCTCGTGCATGCAG	61.297	55.000	23.41	15.31	42.74	4.41
5732	7452	1.532868	GTGAAACAGAAGCTCGTGCAT	59.467	47.619	12.58	0.00	38.21	3.96
5736	7456	2.866762	GTTCAGTGAAACAGAAGCTCGT	59.133	45.455	7.25	0.00	43.21	4.18
5769	7489	1.379527	CCATTTTCAGCCCCTCGTAC	58.620	55.000	0.00	0.00	0.00	3.67
5778	7498	2.125952	GGTGCGGCCATTTTCAGC	60.126	61.111	2.24	0.00	37.17	4.26
5790	7510	2.813908	GAACACGGCTAGGGTGCG	60.814	66.667	0.00	0.00	36.01	5.34
5791	7511	2.033194	GTGAACACGGCTAGGGTGC	61.033	63.158	0.00	0.00	36.01	5.01
5800	7520	3.357079	GCCAGCAGGTGAACACGG	61.357	66.667	0.00	0.00	37.19	4.94
5817	7537	4.954680	CCGCCGTGTTGTGTTGCG	62.955	66.667	0.00	0.00	44.47	4.85
5858	7578	1.076533	ATCACATCGGTCGTGCGTTC	61.077	55.000	0.00	0.00	34.27	3.95
5893	7652	2.232941	TCGTTACGCCTGGAATCTTTCT	59.767	45.455	0.00	0.00	0.00	2.52
5908	7667	0.313705	CGGCGCGTACATTTCGTTAC	60.314	55.000	8.43	0.00	0.00	2.50
5957	7716	2.108976	CCGCCACTCACAGTGTGT	59.891	61.111	22.29	2.25	44.50	3.72
6073	8058	4.821412	CGCGCGCCGAAACGTAAG	62.821	66.667	27.72	2.72	40.02	2.34
6158	8153	3.443045	GGACCATGCAACGGCCAG	61.443	66.667	2.24	0.00	40.13	4.85
6184	8179	2.903855	GTGTGCAGTGCAGGCTGT	60.904	61.111	20.42	0.00	40.08	4.40
6203	8198	1.756538	AGGCAGGGTTTGTTTTGACTG	59.243	47.619	0.00	0.00	0.00	3.51
6204	8199	2.031870	GAGGCAGGGTTTGTTTTGACT	58.968	47.619	0.00	0.00	0.00	3.41
6249	8244	1.009222	GGAGGTCATACGTACGCCG	60.009	63.158	16.72	3.83	44.03	6.46
6250	8245	1.361632	GGGAGGTCATACGTACGCC	59.638	63.158	16.72	8.04	0.00	5.68
6251	8246	1.361632	GGGGAGGTCATACGTACGC	59.638	63.158	16.72	0.00	0.00	4.42
6294	8289	2.787680	CTGAAACCTAGCGCATACGTAC	59.212	50.000	11.47	0.00	42.83	3.67
6295	8290	2.424601	ACTGAAACCTAGCGCATACGTA	59.575	45.455	11.47	0.00	42.83	3.57
6296	8291	1.203994	ACTGAAACCTAGCGCATACGT	59.796	47.619	11.47	0.00	42.83	3.57
6297	8292	1.922570	ACTGAAACCTAGCGCATACG	58.077	50.000	11.47	0.00	44.07	3.06
6301	8296	1.070134	AGTGAACTGAAACCTAGCGCA	59.930	47.619	11.47	0.00	0.00	6.09
6311	8306	5.128827	ACTTGGTAAGTCTCAGTGAACTGAA	59.871	40.000	13.81	3.54	43.14	3.02
6329	8324	8.426489	TGTTATGTACTTGACTTAAGACTTGGT	58.574	33.333	10.09	6.41	39.76	3.67

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.