AutoCloner

Multiple sequence alignment - TraesCS2D01G190600

Loading Multiple Alignment...

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	TraesCS2D01G190600	chr2D	100.000	7066	0	0	1	7066	134638673	134645738	0.000000e+00	13049.0
1	TraesCS2D01G190600	chr2D	91.549	284	15	6	6667	6948	567018967	567018691	4.000000e-102	383.0
2	TraesCS2D01G190600	chr2D	91.197	284	20	5	6667	6948	563965848	563966128	1.440000e-101	381.0
3	TraesCS2D01G190600	chr2B	93.051	3641	140	35	1	3607	191537040	191540601	0.000000e+00	5217.0
4	TraesCS2D01G190600	chr2B	95.117	2048	82	12	3726	5765	191540861	191542898	0.000000e+00	3212.0
5	TraesCS2D01G190600	chr2B	89.831	649	44	17	5942	6584	191543192	191543824	0.000000e+00	813.0
6	TraesCS2D01G190600	chr2B	92.818	181	12	1	5752	5931	191542926	191543106	1.960000e-65	261.0
7	TraesCS2D01G190600	chr2B	95.062	81	4	0	3592	3672	191540782	191540862	2.070000e-25	128.0
8	TraesCS2D01G190600	chr2B	96.491	57	2	0	3671	3727	695378390	695378446	2.100000e-15	95.3
9	TraesCS2D01G190600	chr2A	94.318	2288	105	14	596	2876	142683549	142685818	0.000000e+00	3482.0
10	TraesCS2D01G190600	chr2A	93.474	2222	112	19	3726	5936	142686667	142688866	0.000000e+00	3269.0
11	TraesCS2D01G190600	chr2A	94.273	873	25	3	2800	3672	142685821	142686668	0.000000e+00	1312.0
12	TraesCS2D01G190600	chr2A	90.333	600	42	10	5998	6584	142689028	142689624	0.000000e+00	773.0
13	TraesCS2D01G190600	chr2A	92.151	344	18	5	132	469	142682859	142683199	1.780000e-130	477.0
14	TraesCS2D01G190600	chr7D	93.262	282	14	5	6669	6948	630612534	630612812	1.830000e-110	411.0
15	TraesCS2D01G190600	chr7D	94.118	272	10	4	6667	6937	182599470	182599736	6.600000e-110	409.0
16	TraesCS2D01G190600	chr7D	98.165	109	2	0	6958	7066	182600192	182600300	2.600000e-44	191.0
17	TraesCS2D01G190600	chr7D	93.750	64	3	1	3664	3727	551735568	551735506	2.100000e-15	95.3
18	TraesCS2D01G190600	chr7A	92.419	277	15	6	6673	6948	725812921	725813192	2.390000e-104	390.0
19	TraesCS2D01G190600	chr7A	98.165	109	2	0	6958	7066	57806147	57806255	2.600000e-44	191.0
20	TraesCS2D01G190600	chr1D	92.674	273	14	6	6667	6937	334053230	334053498	8.600000e-104	388.0
21	TraesCS2D01G190600	chr6D	91.971	274	16	6	6667	6937	444087111	444086841	5.170000e-101	379.0
22	TraesCS2D01G190600	chr6D	91.135	282	18	6	6667	6947	417885517	417885242	6.690000e-100	375.0
23	TraesCS2D01G190600	chr6D	98.165	109	2	0	6958	7066	110655427	110655319	2.600000e-44	191.0
24	TraesCS2D01G190600	chr6D	96.491	57	2	0	3671	3727	284394950	284395006	2.100000e-15	95.3
25	TraesCS2D01G190600	chr4D	90.845	284	17	7	6667	6948	81327019	81327295	8.660000e-99	372.0
26	TraesCS2D01G190600	chr7B	98.165	109	2	0	6958	7066	670031455	670031563	2.600000e-44	191.0
27	TraesCS2D01G190600	chr7B	97.273	110	3	0	6957	7066	134504753	134504644	3.370000e-43	187.0
28	TraesCS2D01G190600	chr5A	98.165	109	2	0	6958	7066	52413575	52413467	2.600000e-44	191.0
29	TraesCS2D01G190600	chr3A	98.165	109	2	0	6958	7066	653964770	653964878	2.600000e-44	191.0
30	TraesCS2D01G190600	chr1B	98.165	109	2	0	6958	7066	120660708	120660816	2.600000e-44	191.0
31	TraesCS2D01G190600	chr1B	98.148	108	2	0	6958	7065	576146529	576146422	9.360000e-44	189.0
32	TraesCS2D01G190600	chr1B	93.151	73	4	1	3664	3736	656234053	656234124	9.690000e-19	106.0
33	TraesCS2D01G190600	chr1B	90.909	66	4	1	3662	3727	354922681	354922744	3.510000e-13	87.9
34	TraesCS2D01G190600	chr1A	91.429	70	3	1	3667	3733	363454147	363454216	7.550000e-15	93.5
35	TraesCS2D01G190600	chr3D	92.424	66	2	1	3665	3727	593276177	593276242	2.710000e-14	91.6
36	TraesCS2D01G190600	chr3D	89.855	69	7	0	3662	3730	42316868	42316936	9.760000e-14	89.8
37	TraesCS2D01G190600	chr6B	90.909	66	2	2	3662	3727	42432687	42432748	1.260000e-12	86.1
38	TraesCS2D01G190600	chr4B	95.238	42	1	1	773	813	468659356	468659315	1.650000e-06	65.8

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	TraesCS2D01G190600	chr2D	134638673	134645738	7065	False	13049.0	13049	100.0000	1	7066	1	chr2D.!!$F1	7065
1	TraesCS2D01G190600	chr2B	191537040	191543824	6784	False	1926.2	5217	93.1758	1	6584	5	chr2B.!!$F2	6583
2	TraesCS2D01G190600	chr2A	142682859	142689624	6765	False	1862.6	3482	92.9098	132	6584	5	chr2A.!!$F1	6452
3	TraesCS2D01G190600	chr7D	182599470	182600300	830	False	300.0	409	96.1415	6667	7066	2	chr7D.!!$F2	399

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
280	291	0.107654	GTCCATCCTCCCGTTGGAAG	60.108	60.000	0.00	0.0	41.16	3.46	F
384	409	0.326264	TCCTTTCCTCTGCTTGCTCC	59.674	55.000	0.00	0.0	0.00	4.70	F
572	602	0.672711	GGAAAAGGTCGCCGTAGCTT	60.673	55.000	0.00	0.0	38.80	3.74	F
901	1153	1.079543	CGGCAGTGAGGACCTTCAG	60.080	63.158	0.00	0.0	0.00	3.02	F
970	1222	1.193650	CCGTGTATGGTTTGACGTGTG	59.806	52.381	0.00	0.0	0.00	3.82	F
1168	1420	1.258676	GGTGGAGAAGAAGGACGACT	58.741	55.000	0.00	0.0	0.00	4.18	F
2798	3072	2.012673	GTCAAAGCCTCATTCGAGCAT	58.987	47.619	0.00	0.0	38.00	3.79	F
3353	3705	1.888215	CATCATGCGCCCTTACATCT	58.112	50.000	4.18	0.0	0.00	2.90	F
3932	4487	0.254178	GTCCAGTGGCATCATGTCCT	59.746	55.000	3.51	0.0	0.00	3.85	F
5046	5607	0.864455	GAACGCCATAGCAGAGATGC	59.136	55.000	0.00	0.0	39.83	3.91	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2243	2514	0.323957	AAGTTGTACGGAAGGAGGGC	59.676	55.000	0.00	0.0	0.00	5.19	R
2574	2848	1.231221	ACAACTCGGCAAATACGCAA	58.769	45.000	0.00	0.0	0.00	4.85	R
2754	3028	1.497309	CCCCAAAGAGCCCACACCTA	61.497	60.000	0.00	0.0	0.00	3.08	R
2788	3062	2.350484	GCATGACCATGATGCTCGAATG	60.350	50.000	13.67	0.0	42.52	2.67	R
2960	3312	3.243501	GGCAACAGTGAAAGCTCATTGAA	60.244	43.478	0.00	0.0	40.76	2.69	R
3353	3705	2.037641	CGCATGATGGGATCTTACCTCA	59.962	50.000	3.03	0.0	31.21	3.86	R
3674	4227	1.070758	CTGACATTATGGGACGGAGGG	59.929	57.143	0.00	0.0	0.00	4.30	R
5046	5607	0.179250	GTTGACACGTGCTACATGCG	60.179	55.000	17.22	0.0	46.63	4.73	R
6017	6701	0.176449	CACCAGGCGATCATCAGACA	59.824	55.000	0.00	0.0	0.00	3.41	R
6388	7105	0.168128	CTCAACGCAAACCCCGAATC	59.832	55.000	0.00	0.0	0.00	2.52	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)

Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
39	40	2.392181	CGCCGTTGCAAACCCGATA	61.392	57.895	0.00	0.00	46.28	2.92
41	42	1.798087	CCGTTGCAAACCCGATACC	59.202	57.895	0.00	0.00	46.28	2.73
47	48	0.655733	GCAAACCCGATACCGTCATG	59.344	55.000	0.00	0.00	0.00	3.07
49	50	2.833794	CAAACCCGATACCGTCATGAT	58.166	47.619	0.00	0.00	0.00	2.45
65	67	1.808411	TGATCCAAGGTTGAAGACGC	58.192	50.000	0.00	0.00	0.00	5.19
90	92	8.880768	CAAGATATGCAGTTGTTAGTTGTTAC	57.119	34.615	0.00	0.00	0.00	2.50
91	93	8.721478	CAAGATATGCAGTTGTTAGTTGTTACT	58.279	33.333	0.00	0.00	38.44	2.24
92	94	9.938280	AAGATATGCAGTTGTTAGTTGTTACTA	57.062	29.630	0.00	0.00	35.78	1.82
93	95	9.938280	AGATATGCAGTTGTTAGTTGTTACTAA	57.062	29.630	0.00	0.00	42.97	2.24
96	98	6.664515	TGCAGTTGTTAGTTGTTACTAATGC	58.335	36.000	11.54	11.54	45.80	3.56
97	99	6.485313	TGCAGTTGTTAGTTGTTACTAATGCT	59.515	34.615	16.15	7.49	45.80	3.79
98	100	6.797033	GCAGTTGTTAGTTGTTACTAATGCTG	59.203	38.462	11.32	13.16	45.80	4.41
99	101	7.298122	CAGTTGTTAGTTGTTACTAATGCTGG	58.702	38.462	0.00	0.00	45.80	4.85
100	102	5.873179	TGTTAGTTGTTACTAATGCTGGC	57.127	39.130	0.00	0.00	45.80	4.85
101	103	4.698304	TGTTAGTTGTTACTAATGCTGGCC	59.302	41.667	0.00	0.00	45.80	5.36
102	104	2.723273	AGTTGTTACTAATGCTGGCCC	58.277	47.619	0.00	0.00	31.21	5.80
103	105	1.749063	GTTGTTACTAATGCTGGCCCC	59.251	52.381	0.00	0.00	0.00	5.80
104	106	1.295020	TGTTACTAATGCTGGCCCCT	58.705	50.000	0.00	0.00	0.00	4.79
105	107	1.064758	TGTTACTAATGCTGGCCCCTG	60.065	52.381	0.00	0.00	0.00	4.45
106	108	1.064685	GTTACTAATGCTGGCCCCTGT	60.065	52.381	0.00	0.00	0.00	4.00
107	109	1.295020	TACTAATGCTGGCCCCTGTT	58.705	50.000	0.00	0.00	0.00	3.16
127	129	1.524863	TAGCTCCGCTAATCTCGCCC	61.525	60.000	0.00	0.00	38.27	6.13
130	132	2.658593	CCGCTAATCTCGCCCGTG	60.659	66.667	0.00	0.00	0.00	4.94
147	149	1.608025	CGTGCTACAAGAAGAAGGGCA	60.608	52.381	0.00	0.00	0.00	5.36
230	238	0.957888	AAGCAGAGGAGAAAAGCGCC	60.958	55.000	2.29	0.00	36.60	6.53

Showing 1 to 25 of 245 entries

Previous1 2 3 4 5…10Next

Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
23	24	1.798087	GGTATCGGGTTTGCAACGG	59.202	57.895	0.00	0.00	0.00	4.44
28	29	0.655733	CATGACGGTATCGGGTTTGC	59.344	55.000	0.00	0.00	41.39	3.68
36	37	3.753294	ACCTTGGATCATGACGGTATC	57.247	47.619	0.00	0.00	0.00	2.24
39	40	1.628340	TCAACCTTGGATCATGACGGT	59.372	47.619	0.00	0.00	0.00	4.83
41	42	3.372206	GTCTTCAACCTTGGATCATGACG	59.628	47.826	0.00	0.00	0.00	4.35
47	48	1.808411	TGCGTCTTCAACCTTGGATC	58.192	50.000	0.00	0.00	0.00	3.36
49	50	1.140052	TCTTGCGTCTTCAACCTTGGA	59.860	47.619	0.00	0.00	0.00	3.53
65	67	8.721478	AGTAACAACTAACAACTGCATATCTTG	58.279	33.333	0.00	0.00	0.00	3.02
78	80	4.698304	GGCCAGCATTAGTAACAACTAACA	59.302	41.667	0.00	0.00	35.34	2.41
82	84	2.620627	GGGGCCAGCATTAGTAACAACT	60.621	50.000	4.39	0.00	0.00	3.16
83	85	1.749063	GGGGCCAGCATTAGTAACAAC	59.251	52.381	4.39	0.00	0.00	3.32
85	87	1.064758	CAGGGGCCAGCATTAGTAACA	60.065	52.381	4.39	0.00	0.00	2.41
86	88	1.064685	ACAGGGGCCAGCATTAGTAAC	60.065	52.381	4.39	0.00	0.00	2.50
88	90	1.295020	AACAGGGGCCAGCATTAGTA	58.705	50.000	4.39	0.00	0.00	1.82
89	91	0.409484	AAACAGGGGCCAGCATTAGT	59.591	50.000	4.39	0.00	0.00	2.24
90	92	2.301346	CTAAACAGGGGCCAGCATTAG	58.699	52.381	4.39	4.98	0.00	1.73
91	93	1.684869	GCTAAACAGGGGCCAGCATTA	60.685	52.381	4.39	0.00	32.46	1.90
92	94	0.972471	GCTAAACAGGGGCCAGCATT	60.972	55.000	4.39	0.00	32.46	3.56
93	95	1.380380	GCTAAACAGGGGCCAGCAT	60.380	57.895	4.39	0.00	32.46	3.79
94	96	2.035626	GCTAAACAGGGGCCAGCA	59.964	61.111	4.39	0.00	32.46	4.41
95	97	1.750780	GAGCTAAACAGGGGCCAGC	60.751	63.158	4.39	4.20	0.00	4.85
96	98	1.077429	GGAGCTAAACAGGGGCCAG	60.077	63.158	4.39	0.00	0.00	4.85
97	99	2.966732	CGGAGCTAAACAGGGGCCA	61.967	63.158	4.39	0.00	0.00	5.36
98	100	2.124695	CGGAGCTAAACAGGGGCC	60.125	66.667	0.00	0.00	0.00	5.80
127	129	1.079503	GCCCTTCTTCTTGTAGCACG	58.920	55.000	0.00	0.00	0.00	5.34

Showing 1 to 25 of 251 entries

Previous1 2 3 4 5…11Next

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.