AutoCloner

Multiple sequence alignment - TraesCS2D01G240300

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	TraesCS2D01G240300	chr2D	100.000	2372	0	0	1	2372	258371671	258369300	0.000000	4381.0
1	TraesCS2D01G240300	chr2D	94.781	2376	90	18	1	2372	383980866	383983211	0.000000	3670.0
2	TraesCS2D01G240300	chr2D	94.611	2375	99	20	1	2372	133502706	133505054	0.000000	3650.0
3	TraesCS2D01G240300	chr2D	94.187	2374	106	19	1	2372	262767790	262765447	0.000000	3591.0
4	TraesCS2D01G240300	chr2D	93.732	2377	118	24	1	2372	287276941	287274591	0.000000	3535.0
5	TraesCS2D01G240300	chr5D	94.777	2374	101	18	1	2372	308548010	308545658	0.000000	3675.0
6	TraesCS2D01G240300	chr5D	94.620	2379	98	22	1	2372	179674960	179672605	0.000000	3657.0
7	TraesCS2D01G240300	chr5D	93.554	1148	53	14	1	1147	305570397	305569270	0.000000	1690.0
8	TraesCS2D01G240300	chr5D	100.000	30	0	0	302	331	179674595	179674566	0.000329	56.5
9	TraesCS2D01G240300	chr5D	100.000	30	0	0	302	331	305570031	305570002	0.000329	56.5
10	TraesCS2D01G240300	chr1D	94.608	2374	101	18	1	2372	343046360	343048708	0.000000	3650.0
11	TraesCS2D01G240300	chr1D	100.000	30	0	0	302	331	81831291	81831320	0.000329	56.5
12	TraesCS2D01G240300	chr1D	100.000	30	0	0	302	331	343046727	343046756	0.000329	56.5
13	TraesCS2D01G240300	chr6D	94.437	2373	108	17	1	2372	223789007	223786658	0.000000	3629.0
14	TraesCS2D01G240300	chr4D	94.398	2374	107	18	1	2371	176590219	176592569	0.000000	3624.0
15	TraesCS2D01G240300	chr4D	94.063	2375	115	19	1	2372	267030789	267033140	0.000000	3581.0
16	TraesCS2D01G240300	chr4D	100.000	30	0	0	302	331	176590585	176590614	0.000329	56.5
17	TraesCS2D01G240300	chr3D	94.187	2374	113	17	1	2372	12959760	12962110	0.000000	3596.0
18	TraesCS2D01G240300	chr3D	100.000	30	0	0	302	331	12960125	12960154	0.000329	56.5
19	TraesCS2D01G240300	chrUn	100.000	30	0	0	302	331	27761156	27761185	0.000329	56.5
20	TraesCS2D01G240300	chr6A	100.000	30	0	0	302	331	266236575	266236604	0.000329	56.5
21	TraesCS2D01G240300	chr2B	97.059	34	0	1	302	335	374605535	374605567	0.000329	56.5

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	TraesCS2D01G240300	chr2D	258369300	258371671	2371	True	4381.00	4381	100.0000	1	2372	1	chr2D.!!$R1	2371
1	TraesCS2D01G240300	chr2D	383980866	383983211	2345	False	3670.00	3670	94.7810	1	2372	1	chr2D.!!$F2	2371
2	TraesCS2D01G240300	chr2D	133502706	133505054	2348	False	3650.00	3650	94.6110	1	2372	1	chr2D.!!$F1	2371
3	TraesCS2D01G240300	chr2D	262765447	262767790	2343	True	3591.00	3591	94.1870	1	2372	1	chr2D.!!$R2	2371
4	TraesCS2D01G240300	chr2D	287274591	287276941	2350	True	3535.00	3535	93.7320	1	2372	1	chr2D.!!$R3	2371
5	TraesCS2D01G240300	chr5D	308545658	308548010	2352	True	3675.00	3675	94.7770	1	2372	1	chr5D.!!$R1	2371
6	TraesCS2D01G240300	chr5D	179672605	179674960	2355	True	1856.75	3657	97.3100	1	2372	2	chr5D.!!$R2	2371
7	TraesCS2D01G240300	chr5D	305569270	305570397	1127	True	873.25	1690	96.7770	1	1147	2	chr5D.!!$R3	1146
8	TraesCS2D01G240300	chr1D	343046360	343048708	2348	False	1853.25	3650	97.3040	1	2372	2	chr1D.!!$F2	2371
9	TraesCS2D01G240300	chr6D	223786658	223789007	2349	True	3629.00	3629	94.4370	1	2372	1	chr6D.!!$R1	2371
10	TraesCS2D01G240300	chr4D	267030789	267033140	2351	False	3581.00	3581	94.0630	1	2372	1	chr4D.!!$F1	2371
11	TraesCS2D01G240300	chr4D	176590219	176592569	2350	False	1840.25	3624	97.1990	1	2371	2	chr4D.!!$F2	2370
12	TraesCS2D01G240300	chr3D	12959760	12962110	2350	False	1826.25	3596	97.0935	1	2372	2	chr3D.!!$F1	2371

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
306	309	0.027455	TTGTCAGCGTTCGTTTGCAG	59.973	50.0	0.0	0.0	0.0	4.41	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1719	1738	0.456221	AGCATCCCGAACACGACTAG	59.544	55.0	0.0	0.0	0.0	2.57	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
93	94	2.026262	GCAAGGTGGATCTAGGGTTTCA	60.026	50.000	0.00	0.00	0.00	2.69
306	309	0.027455	TTGTCAGCGTTCGTTTGCAG	59.973	50.000	0.00	0.00	0.00	4.41
308	311	0.654472	GTCAGCGTTCGTTTGCAGTG	60.654	55.000	0.00	0.00	0.00	3.66
309	312	2.005537	CAGCGTTCGTTTGCAGTGC	61.006	57.895	8.58	8.58	0.00	4.40
311	314	1.722507	GCGTTCGTTTGCAGTGCTC	60.723	57.895	17.60	6.10	0.00	4.26
312	315	1.641140	CGTTCGTTTGCAGTGCTCA	59.359	52.632	17.60	0.00	0.00	4.26
313	316	0.235665	CGTTCGTTTGCAGTGCTCAT	59.764	50.000	17.60	0.00	0.00	2.90
314	317	1.459209	CGTTCGTTTGCAGTGCTCATA	59.541	47.619	17.60	0.00	0.00	2.15
315	318	2.096466	CGTTCGTTTGCAGTGCTCATAA	60.096	45.455	17.60	0.00	0.00	1.90
316	319	3.424829	CGTTCGTTTGCAGTGCTCATAAT	60.425	43.478	17.60	0.00	0.00	1.28
317	320	3.745332	TCGTTTGCAGTGCTCATAATG	57.255	42.857	17.60	10.42	0.00	1.90
318	321	3.333804	TCGTTTGCAGTGCTCATAATGA	58.666	40.909	17.60	12.37	0.00	2.57
320	323	5.115480	TCGTTTGCAGTGCTCATAATGATA	58.885	37.500	17.60	0.00	0.00	2.15
321	324	5.006649	TCGTTTGCAGTGCTCATAATGATAC	59.993	40.000	17.60	0.00	0.00	2.24
322	325	5.220643	CGTTTGCAGTGCTCATAATGATACA	60.221	40.000	17.60	0.00	0.00	2.29
323	326	5.739752	TTGCAGTGCTCATAATGATACAC	57.260	39.130	17.60	0.00	35.08	2.90
324	327	4.129380	TGCAGTGCTCATAATGATACACC	58.871	43.478	17.60	0.00	35.30	4.16
325	328	4.129380	GCAGTGCTCATAATGATACACCA	58.871	43.478	8.18	0.00	35.30	4.17
326	329	4.576053	GCAGTGCTCATAATGATACACCAA	59.424	41.667	8.18	0.00	35.30	3.67
328	331	6.238842	GCAGTGCTCATAATGATACACCAATT	60.239	38.462	8.18	0.00	35.30	2.32
329	332	7.136772	CAGTGCTCATAATGATACACCAATTG	58.863	38.462	0.00	0.00	35.30	2.32
330	333	6.263842	AGTGCTCATAATGATACACCAATTGG	59.736	38.462	23.31	23.31	35.30	3.16
342	345	2.064573	CCAATTGGTTTCAGCGTTCC	57.935	50.000	16.90	0.00	0.00	3.62
343	346	1.613437	CCAATTGGTTTCAGCGTTCCT	59.387	47.619	16.90	0.00	0.00	3.36
344	347	2.035832	CCAATTGGTTTCAGCGTTCCTT	59.964	45.455	16.90	0.00	0.00	3.36
345	348	3.052036	CAATTGGTTTCAGCGTTCCTTG	58.948	45.455	0.00	0.00	0.00	3.61
346	349	0.383949	TTGGTTTCAGCGTTCCTTGC	59.616	50.000	0.00	0.00	0.00	4.01
347	350	0.749818	TGGTTTCAGCGTTCCTTGCA	60.750	50.000	0.00	0.00	33.85	4.08
348	351	0.598065	GGTTTCAGCGTTCCTTGCAT	59.402	50.000	0.00	0.00	33.85	3.96
349	352	1.000274	GGTTTCAGCGTTCCTTGCATT	60.000	47.619	0.00	0.00	33.85	3.56
390	397	6.509418	TTTTAATCCAGTAGGTGATTGCAC	57.491	37.500	0.00	0.00	44.39	4.57
483	491	3.680642	AGTGAATTCGCCGATTGAATG	57.319	42.857	15.29	0.00	36.24	2.67
520	528	0.181350	CCCCTCCTTCTGGTATGTGC	59.819	60.000	0.00	0.00	34.23	4.57
702	712	7.224362	TGAACTGCATTGTTGTTTTATTCAAGG	59.776	33.333	0.00	0.00	0.00	3.61
797	809	4.329528	TGCATTTGTTCTTTTTGTGCACTC	59.670	37.500	19.41	0.00	36.33	3.51
857	869	3.884704	TTTTCCATGCTGGGGCGCT	62.885	57.895	7.64	0.00	42.25	5.92
1074	1086	5.818136	TGAGGTTTGAAAGTGACTCAAAG	57.182	39.130	0.88	0.00	42.03	2.77
1098	1115	0.396435	TTGCGGAGAAGGAGAAGCAA	59.604	50.000	0.00	0.00	41.48	3.91
1099	1116	0.615331	TGCGGAGAAGGAGAAGCAAT	59.385	50.000	0.00	0.00	0.00	3.56
1352	1369	4.325028	TTGTGCTTGCTGATTTTGTGAT	57.675	36.364	0.00	0.00	0.00	3.06
1355	1372	2.028839	TGCTTGCTGATTTTGTGATGGG	60.029	45.455	0.00	0.00	0.00	4.00
1426	1443	0.394762	AGCGTGCCCATGATGATGTT	60.395	50.000	0.00	0.00	0.00	2.71
1496	1513	3.366052	AGGTTTGTTGAAGTGGACTGT	57.634	42.857	0.00	0.00	0.00	3.55
1613	1632	7.107639	AGGAAGAAGTCTAGTAAGAGCAATC	57.892	40.000	0.00	0.00	30.45	2.67
1659	1678	7.887996	GAGATGATTCTCGATTTAGCAAGAT	57.112	36.000	0.00	0.00	39.14	2.40
1692	1711	1.402787	CTTCCCACTGTTTGCAAGGT	58.597	50.000	0.00	0.00	0.00	3.50
1705	1724	2.596875	CAAGGTTGCTGCTTTGTGC	58.403	52.632	0.00	0.00	43.25	4.57
1791	1810	2.031245	AGAAAAATGTGTCGCGCATTCA	60.031	40.909	8.75	0.00	42.66	2.57
1868	1887	0.984230	TGGCAGGGTTCTTCGAATCT	59.016	50.000	0.00	0.00	0.00	2.40
2138	2159	1.896660	GGGCCTGCAGTTCGTTTGA	60.897	57.895	13.81	0.00	0.00	2.69
2194	2215	1.670406	GGCTATGGCGCAGATGGAG	60.670	63.158	10.83	0.00	39.81	3.86
2229	2250	3.057969	TGTTGATGAGTTGTAGGCAGG	57.942	47.619	0.00	0.00	0.00	4.85
2300	2321	0.324552	TGCCATTGTCCCCCTGATTG	60.325	55.000	0.00	0.00	0.00	2.67
2311	2332	3.455910	TCCCCCTGATTGTGTATCTTGAG	59.544	47.826	0.00	0.00	34.17	3.02
2353	2374	2.827652	TCAGTTATGCACACGTTGACA	58.172	42.857	0.00	0.00	0.00	3.58

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
93	94	4.414852	CAACAAAATCGGCGAAATCTGAT	58.585	39.130	15.93	1.01	33.70	2.90
306	309	6.441274	CCAATTGGTGTATCATTATGAGCAC	58.559	40.000	16.90	18.02	36.30	4.40
323	326	1.613437	AGGAACGCTGAAACCAATTGG	59.387	47.619	23.31	23.31	42.17	3.16
324	327	3.052036	CAAGGAACGCTGAAACCAATTG	58.948	45.455	0.00	0.00	0.00	2.32
325	328	2.545742	GCAAGGAACGCTGAAACCAATT	60.546	45.455	0.00	0.00	0.00	2.32
326	329	1.000274	GCAAGGAACGCTGAAACCAAT	60.000	47.619	0.00	0.00	0.00	3.16
328	331	0.749818	TGCAAGGAACGCTGAAACCA	60.750	50.000	0.00	0.00	0.00	3.67
329	332	0.598065	ATGCAAGGAACGCTGAAACC	59.402	50.000	0.00	0.00	0.00	3.27
330	333	2.422276	AATGCAAGGAACGCTGAAAC	57.578	45.000	0.00	0.00	0.00	2.78
331	334	4.782019	AATAATGCAAGGAACGCTGAAA	57.218	36.364	0.00	0.00	0.00	2.69
332	335	4.458989	AGAAATAATGCAAGGAACGCTGAA	59.541	37.500	0.00	0.00	0.00	3.02
333	336	4.009675	AGAAATAATGCAAGGAACGCTGA	58.990	39.130	0.00	0.00	0.00	4.26
334	337	4.100529	CAGAAATAATGCAAGGAACGCTG	58.899	43.478	0.00	0.00	0.00	5.18
335	338	3.758554	ACAGAAATAATGCAAGGAACGCT	59.241	39.130	0.00	0.00	0.00	5.07
336	339	4.096732	ACAGAAATAATGCAAGGAACGC	57.903	40.909	0.00	0.00	0.00	4.84
337	340	6.306356	CAGAAACAGAAATAATGCAAGGAACG	59.694	38.462	0.00	0.00	0.00	3.95
338	341	6.587608	CCAGAAACAGAAATAATGCAAGGAAC	59.412	38.462	0.00	0.00	0.00	3.62
339	342	6.267471	ACCAGAAACAGAAATAATGCAAGGAA	59.733	34.615	0.00	0.00	0.00	3.36
340	343	5.774690	ACCAGAAACAGAAATAATGCAAGGA	59.225	36.000	0.00	0.00	0.00	3.36
341	344	6.029346	ACCAGAAACAGAAATAATGCAAGG	57.971	37.500	0.00	0.00	0.00	3.61
342	345	7.951530	AAACCAGAAACAGAAATAATGCAAG	57.048	32.000	0.00	0.00	0.00	4.01
343	346	8.729805	AAAAACCAGAAACAGAAATAATGCAA	57.270	26.923	0.00	0.00	0.00	4.08
390	397	6.675026	CCAATTGGTGTATCATTATGAGCAG	58.325	40.000	16.90	0.00	0.00	4.24
483	491	1.682087	GGGCCACACTTATGGGAGAAC	60.682	57.143	4.39	0.00	40.43	3.01
520	528	7.953173	CAGCATACACAAAATAAACAAAGCATG	59.047	33.333	0.00	0.00	0.00	4.06
797	809	7.416154	TGAAGTTTGACTATGGTCGTTAAAG	57.584	36.000	4.63	0.00	44.83	1.85
857	869	3.050089	TGAGTAACCTCCTCAAACCCAA	58.950	45.455	0.00	0.00	36.07	4.12
947	959	4.717233	ACAGACTGCAATTGTGTTTCAA	57.283	36.364	7.40	0.00	40.53	2.69
979	991	5.104527	CCATCCAATCCTGTGTAACTTCCTA	60.105	44.000	0.00	0.00	38.04	2.94
1074	1086	0.608640	TCTCCTTCTCCGCAAACTCC	59.391	55.000	0.00	0.00	0.00	3.85
1098	1115	0.180642	CACCATCTGCAGCTCTCCAT	59.819	55.000	9.47	0.00	0.00	3.41
1099	1116	1.600638	CACCATCTGCAGCTCTCCA	59.399	57.895	9.47	0.00	0.00	3.86
1352	1369	3.383505	CGTCTACCAGTATGAACATCCCA	59.616	47.826	0.00	0.00	39.69	4.37
1355	1372	4.041740	TGCGTCTACCAGTATGAACATC	57.958	45.455	0.00	0.00	39.69	3.06
1426	1443	3.076621	GTCAGCACCAACATCTTCATCA	58.923	45.455	0.00	0.00	0.00	3.07
1613	1632	1.938577	CTCGGCATCATCTTCAGTTGG	59.061	52.381	0.00	0.00	0.00	3.77
1653	1672	1.524391	GCGACAAACGTACGATCTTGC	60.524	52.381	24.41	14.04	44.60	4.01
1659	1678	0.664166	GGGAAGCGACAAACGTACGA	60.664	55.000	24.41	0.00	44.60	3.43
1719	1738	0.456221	AGCATCCCGAACACGACTAG	59.544	55.000	0.00	0.00	0.00	2.57
1791	1810	5.089434	TCACTCCCATCAGATAGCACATAT	58.911	41.667	0.00	0.00	0.00	1.78
2002	2023	1.211703	TCAAGCAAGTCCTTGACACCA	59.788	47.619	11.12	0.00	44.49	4.17
2092	2113	6.389906	GCACAGCAAATTCTGGTAAAGTATT	58.610	36.000	0.00	0.00	38.36	1.89
2138	2159	2.867109	ACCATTGCAGCAACTCTACT	57.133	45.000	10.85	0.00	0.00	2.57
2194	2215	2.615869	TCAACAACAAGCTGGCAAAAC	58.384	42.857	0.00	0.00	0.00	2.43
2229	2250	1.034838	TGTTTGCCACCTCACCACAC	61.035	55.000	0.00	0.00	0.00	3.82
2300	2321	3.999663	AGCTTCAAGCACTCAAGATACAC	59.000	43.478	13.10	0.00	45.56	2.90
2353	2374	1.080093	CAGGTATGACGCACGTGGT	60.080	57.895	18.88	13.45	0.00	4.16

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.