AutoCloner

Multiple sequence alignment - TraesCS2B01G032400

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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	TraesCS2B01G032400	chr2B	100.000	2618	0	0	1	2618	15638470	15635853	0.000000e+00	4835
1	TraesCS2B01G032400	chr2B	91.998	2287	156	17	1	2266	15790085	15787805	0.000000e+00	3184
2	TraesCS2B01G032400	chr2B	91.965	2290	155	16	1	2266	15882840	15880556	0.000000e+00	3182
3	TraesCS2B01G032400	chr2B	91.951	2286	158	16	1	2266	15727018	15724739	0.000000e+00	3179
4	TraesCS2B01G032400	chr2B	93.804	2082	115	9	1	2075	15818363	15816289	0.000000e+00	3118
5	TraesCS2B01G032400	chr2B	93.756	2082	116	9	1	2075	15917334	15915260	0.000000e+00	3112
6	TraesCS2B01G032400	chr2B	93.612	2082	119	9	1	2075	15695057	15692983	0.000000e+00	3096
7	TraesCS2B01G032400	chr2B	89.568	556	53	5	2060	2614	15692700	15692149	0.000000e+00	701
8	TraesCS2B01G032400	chr2B	89.388	556	54	5	2060	2614	15914977	15914426	0.000000e+00	695
9	TraesCS2B01G032400	chr2B	89.209	556	55	5	2060	2614	15816006	15815455	0.000000e+00	689
10	TraesCS2B01G032400	chr2B	89.029	556	56	5	2060	2614	15755060	15754509	0.000000e+00	684
11	TraesCS2B01G032400	chr2A	93.103	2639	149	21	1	2618	11044944	11042318	0.000000e+00	3834
12	TraesCS2B01G032400	chr2A	91.892	2627	186	16	1	2618	11309674	11307066	0.000000e+00	3646
13	TraesCS2B01G032400	chr2A	90.426	376	34	2	2241	2616	11237978	11237605	6.510000e-136	494
14	TraesCS2B01G032400	chr2D	93.004	2630	127	12	1	2618	10800303	10797719	0.000000e+00	3784
15	TraesCS2B01G032400	chr2D	90.710	775	33	19	1573	2335	10250783	10251530	0.000000e+00	996
16	TraesCS2B01G032400	chrUn	92.865	1906	124	7	1	1894	339546927	339548832	0.000000e+00	2756
17	TraesCS2B01G032400	chrUn	92.666	1909	128	7	1	1897	339561116	339559208	0.000000e+00	2739
18	TraesCS2B01G032400	chrUn	91.243	354	28	3	2264	2616	258350418	258350769	1.820000e-131	479
19	TraesCS2B01G032400	chrUn	90.110	364	30	3	1909	2266	466055963	466056326	3.950000e-128	468

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	TraesCS2B01G032400	chr2B	15635853	15638470	2617	True	4835.0	4835	100.0000	1	2618	1	chr2B.!!$R1	2617
1	TraesCS2B01G032400	chr2B	15787805	15790085	2280	True	3184.0	3184	91.9980	1	2266	1	chr2B.!!$R4	2265
2	TraesCS2B01G032400	chr2B	15880556	15882840	2284	True	3182.0	3182	91.9650	1	2266	1	chr2B.!!$R5	2265
3	TraesCS2B01G032400	chr2B	15724739	15727018	2279	True	3179.0	3179	91.9510	1	2266	1	chr2B.!!$R2	2265
4	TraesCS2B01G032400	chr2B	15815455	15818363	2908	True	1903.5	3118	91.5065	1	2614	2	chr2B.!!$R7	2613
5	TraesCS2B01G032400	chr2B	15914426	15917334	2908	True	1903.5	3112	91.5720	1	2614	2	chr2B.!!$R8	2613
6	TraesCS2B01G032400	chr2B	15692149	15695057	2908	True	1898.5	3096	91.5900	1	2614	2	chr2B.!!$R6	2613
7	TraesCS2B01G032400	chr2B	15754509	15755060	551	True	684.0	684	89.0290	2060	2614	1	chr2B.!!$R3	554
8	TraesCS2B01G032400	chr2A	11042318	11044944	2626	True	3834.0	3834	93.1030	1	2618	1	chr2A.!!$R1	2617
9	TraesCS2B01G032400	chr2A	11307066	11309674	2608	True	3646.0	3646	91.8920	1	2618	1	chr2A.!!$R3	2617
10	TraesCS2B01G032400	chr2D	10797719	10800303	2584	True	3784.0	3784	93.0040	1	2618	1	chr2D.!!$R1	2617
11	TraesCS2B01G032400	chr2D	10250783	10251530	747	False	996.0	996	90.7100	1573	2335	1	chr2D.!!$F1	762
12	TraesCS2B01G032400	chrUn	339546927	339548832	1905	False	2756.0	2756	92.8650	1	1894	1	chrUn.!!$F2	1893
13	TraesCS2B01G032400	chrUn	339559208	339561116	1908	True	2739.0	2739	92.6660	1	1897	1	chrUn.!!$R1	1896

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
339	340	0.684535	TGTTGACATCCTTGCCTCGA	59.315	50.0	0.0	0.0	0.0	4.04	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1924	1947	1.271217	GGTAAGACGGGGTCAAAGCTT	60.271	52.381	0.0	0.0	34.6	3.74	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
126	127	3.875727	GGAGATGAACACAGACATCATGG	59.124	47.826	0.00	0.00	43.40	3.66
127	128	4.383444	GGAGATGAACACAGACATCATGGA	60.383	45.833	0.00	0.00	43.40	3.41
128	129	5.366460	GAGATGAACACAGACATCATGGAT	58.634	41.667	0.00	0.00	43.40	3.41
162	163	4.898320	AGCTACTCATGTCATTGTTGTGA	58.102	39.130	0.00	0.00	0.00	3.58
176	177	3.140623	TGTTGTGACATGTCCACAGATG	58.859	45.455	22.85	0.00	44.22	2.90
326	327	1.222115	GGCGTGTCCTCACTGTTGAC	61.222	60.000	0.00	0.00	41.89	3.18
339	340	0.684535	TGTTGACATCCTTGCCTCGA	59.315	50.000	0.00	0.00	0.00	4.04
389	390	3.350833	GAAAGAGGAGTACGACCACCTA	58.649	50.000	13.06	0.00	32.53	3.08
626	628	1.967319	ACAGCTTTTGTGTGTCCGAT	58.033	45.000	0.00	0.00	38.99	4.18
687	689	2.702270	AAAGGTTTCCAAGGATGCCT	57.298	45.000	6.26	6.26	33.87	4.75
770	772	3.499918	CCACTCTTGAGAAATGTGGTGAC	59.500	47.826	4.49	0.00	42.11	3.67
803	805	4.319177	CGAGAGACTTTTTGGACATCCTT	58.681	43.478	0.00	0.00	36.82	3.36
821	823	7.066766	GACATCCTTGTTCATCTTAAAGATGCT	59.933	37.037	0.00	0.00	42.92	3.79
895	898	7.011482	GGTTAGTATGTCACCTTAAGCTCAATG	59.989	40.741	0.00	0.00	0.00	2.82
896	899	4.878397	AGTATGTCACCTTAAGCTCAATGC	59.122	41.667	0.00	0.00	43.29	3.56
1179	1182	2.602257	ATCTCAAATCGTGCATCCGA	57.398	45.000	1.59	1.59	41.73	4.55
1336	1339	1.277557	AGATCTGGACTGAACCACTGC	59.722	52.381	0.00	0.00	35.91	4.40
1515	1518	0.537371	CTTGGACAAAGCTTCCCGGT	60.537	55.000	0.00	0.00	31.33	5.28
1518	1521	1.515521	GGACAAAGCTTCCCGGTGTG	61.516	60.000	5.48	0.00	34.46	3.82
1533	1536	3.193691	CCGGTGTGAAGAGTATCAGTCTT	59.806	47.826	0.00	0.00	40.38	3.01
1542	1545	5.930837	AGAGTATCAGTCTTCAAGAAGGG	57.069	43.478	9.73	1.39	36.92	3.95
1564	1567	2.900273	CGGGCCTTGCACTAGCTA	59.100	61.111	0.84	0.00	42.74	3.32
1700	1708	7.149973	GGACTAGTGTGTGTTACATGTTTCTA	58.850	38.462	2.30	0.00	42.24	2.10
1758	1766	4.919206	TGCATGTGTGTACAAACAAAGAG	58.081	39.130	22.41	13.36	40.84	2.85
1870	1893	5.292589	GCAAATAATCCTTGGAATTGCACAG	59.707	40.000	18.77	0.90	40.86	3.66
1924	1947	0.958091	GGCTGTACAATTGTGTGCCA	59.042	50.000	29.56	17.82	39.43	4.92
1987	2014	5.589855	TGATATGTTCTGTATTGCCAGTTGG	59.410	40.000	0.00	0.00	34.02	3.77
2001	2028	4.192317	GCCAGTTGGTCTATGAACTAAGG	58.808	47.826	0.00	0.00	37.57	2.69
2044	2073	6.059484	AGGGTTTCTTTTGTCGTGAGAAATA	58.941	36.000	0.00	0.00	45.01	1.40
2153	2489	2.606108	GCCATCGAAAAGGCGAAAAAT	58.394	42.857	10.55	0.00	44.22	1.82
2154	2490	3.765026	GCCATCGAAAAGGCGAAAAATA	58.235	40.909	10.55	0.00	44.22	1.40
2164	2500	6.480524	AAAGGCGAAAAATAAGAAAATGCC	57.519	33.333	0.00	0.00	40.22	4.40
2197	2535	1.620323	GCTCAAGGCCCTGTTCATTTT	59.380	47.619	0.00	0.00	34.27	1.82
2200	2538	1.276138	CAAGGCCCTGTTCATTTTCCC	59.724	52.381	0.00	0.00	0.00	3.97
2204	2542	1.338105	GCCCTGTTCATTTTCCCTTGC	60.338	52.381	0.00	0.00	0.00	4.01
2235	2573	0.034896	TTCTGAAGAACTGGACCGCC	59.965	55.000	0.00	0.00	0.00	6.13
2373	2711	8.755696	TTAATGAATTGTATTTTGCAGGACAC	57.244	30.769	0.00	0.00	0.00	3.67
2375	2713	7.701539	ATGAATTGTATTTTGCAGGACACTA	57.298	32.000	0.00	0.00	0.00	2.74
2389	2727	5.533482	CAGGACACTATATTGTCAGGCTAC	58.467	45.833	20.87	6.28	46.68	3.58
2395	2733	5.755375	CACTATATTGTCAGGCTACTGGTTG	59.245	44.000	0.00	0.00	44.99	3.77
2424	2762	9.974750	GTTGATAATGCTACAACTAAGTTCTTC	57.025	33.333	0.00	0.00	40.13	2.87
2510	2849	4.915667	CACTTCATTTCATCAGTGCAACAG	59.084	41.667	0.00	0.00	41.43	3.16
2525	2864	3.181497	TGCAACAGCAAAGACAGAAAGAC	60.181	43.478	0.00	0.00	34.85	3.01
2533	2872	7.702348	ACAGCAAAGACAGAAAGACAAATTTAC	59.298	33.333	0.00	0.00	0.00	2.01

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
176	177	1.760192	TTCGTAGTACCTCAGAGGCC	58.240	55.000	17.31	7.50	39.63	5.19
205	206	0.037160	GGGACGGGAGGCAAAAACTA	59.963	55.000	0.00	0.00	42.53	2.24
326	327	0.816825	CCATGGTCGAGGCAAGGATG	60.817	60.000	2.57	0.00	0.00	3.51
404	405	3.374745	CAAGTCGCTGCAATGAGTTTTT	58.625	40.909	0.00	0.00	0.00	1.94
583	585	2.441001	AGATGGTTGAGGGCTATGAAGG	59.559	50.000	0.00	0.00	0.00	3.46
626	628	2.408565	CCTATGAGGGCTGGGAAGTAA	58.591	52.381	0.00	0.00	0.00	2.24
687	689	1.135257	CAACCGGTTGAGTGTTTGCAA	60.135	47.619	38.61	0.00	42.93	4.08
770	772	3.311486	AAGTCTCTCGCCTCTTTCTTG	57.689	47.619	0.00	0.00	0.00	3.02
821	823	0.478072	ACAGCAATGGTTGTCCCTCA	59.522	50.000	0.00	0.00	32.53	3.86
895	898	7.467557	TCAAAGAACAATGAATGAACTTTGC	57.532	32.000	0.00	0.00	44.55	3.68
896	899	7.306983	GGCTCAAAGAACAATGAATGAACTTTG	60.307	37.037	0.00	0.00	45.24	2.77
1179	1182	1.522569	GTGTATGCGGAAGGCCTCT	59.477	57.895	5.23	0.00	42.61	3.69
1518	1521	6.153680	TCCCTTCTTGAAGACTGATACTCTTC	59.846	42.308	11.53	1.88	42.76	2.87
1533	1536	1.378514	GCCCGCATTCCCTTCTTGA	60.379	57.895	0.00	0.00	0.00	3.02
1542	1545	1.718757	CTAGTGCAAGGCCCGCATTC	61.719	60.000	19.54	8.70	42.32	2.67
1717	1725	5.878332	TGCAGTGTCATAACATTACAAGG	57.122	39.130	0.00	0.00	37.81	3.61
1894	1917	4.705110	ATTGTACAGCCAGGCATGTATA	57.295	40.909	15.80	14.06	34.60	1.47
1895	1918	3.582998	ATTGTACAGCCAGGCATGTAT	57.417	42.857	15.80	3.41	34.60	2.29
1896	1919	3.016031	CAATTGTACAGCCAGGCATGTA	58.984	45.455	15.80	15.81	0.00	2.29
1897	1920	1.820519	CAATTGTACAGCCAGGCATGT	59.179	47.619	15.80	16.83	0.00	3.21
1924	1947	1.271217	GGTAAGACGGGGTCAAAGCTT	60.271	52.381	0.00	0.00	34.60	3.74
2134	2468	5.636837	TCTTATTTTTCGCCTTTTCGATGG	58.363	37.500	0.00	0.00	38.37	3.51
2164	2500	2.813354	GCCTTGAGCCTGATTAGGATGG	60.813	54.545	7.93	0.00	44.35	3.51
2188	2524	4.187694	GTTGTTGCAAGGGAAAATGAACA	58.812	39.130	0.00	0.00	0.00	3.18
2197	2535	3.454082	AGAATTTTGGTTGTTGCAAGGGA	59.546	39.130	0.00	0.00	0.00	4.20
2200	2538	5.811613	TCTTCAGAATTTTGGTTGTTGCAAG	59.188	36.000	0.00	0.00	0.00	4.01
2204	2542	6.256321	CCAGTTCTTCAGAATTTTGGTTGTTG	59.744	38.462	0.00	0.00	36.33	3.33
2373	2711	5.918608	ACAACCAGTAGCCTGACAATATAG	58.081	41.667	0.00	0.00	41.50	1.31
2375	2713	4.844349	ACAACCAGTAGCCTGACAATAT	57.156	40.909	0.00	0.00	41.50	1.28
2389	2727	6.252967	TGTAGCATTATCAACAACAACCAG	57.747	37.500	0.00	0.00	0.00	4.00
2424	2762	4.576463	AGCTGAGAGTACAAACCAAACAAG	59.424	41.667	0.00	0.00	0.00	3.16
2510	2849	7.306225	GCAGTAAATTTGTCTTTCTGTCTTTGC	60.306	37.037	0.00	0.00	0.00	3.68
2525	2864	5.799936	CCCGTGTAATTCAGCAGTAAATTTG	59.200	40.000	0.00	0.00	0.00	2.32
2533	2872	1.164411	TTGCCCGTGTAATTCAGCAG	58.836	50.000	0.00	0.00	0.00	4.24

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.