AutoCloner

Multiple sequence alignment - TraesCS4D01G016200

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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	TraesCS4D01G016200	chr4D	100.000	2707	0	0	1	2707	7408439	7411145	0.000000e+00	5000.0
1	TraesCS4D01G016200	chr4D	86.364	88	12	0	2521	2608	503564369	503564456	2.220000e-16	97.1
2	TraesCS4D01G016200	chr4B	88.821	1798	114	44	209	1971	13276621	13278366	0.000000e+00	2126.0
3	TraesCS4D01G016200	chr4B	86.697	218	20	4	1	215	13232617	13232828	1.620000e-57	233.0
4	TraesCS4D01G016200	chr4B	92.045	88	6	1	2611	2697	13278591	13278678	3.660000e-24	122.0
5	TraesCS4D01G016200	chr4A	86.439	1261	86	48	660	1887	596239568	596238360	0.000000e+00	1303.0
6	TraesCS4D01G016200	chr4A	89.734	1052	59	25	732	1757	596214781	596215809	0.000000e+00	1299.0
7	TraesCS4D01G016200	chr4A	90.972	720	51	11	660	1372	596207732	596208444	0.000000e+00	957.0
8	TraesCS4D01G016200	chr4A	90.972	720	51	11	660	1372	596211379	596212091	0.000000e+00	957.0
9	TraesCS4D01G016200	chr4A	89.971	678	41	12	700	1372	596204141	596204796	0.000000e+00	850.0
10	TraesCS4D01G016200	chr4A	94.048	252	10	3	285	531	596211027	596211278	7.070000e-101	377.0
11	TraesCS4D01G016200	chr4A	93.651	252	11	3	285	531	596207380	596207631	3.290000e-99	372.0
12	TraesCS4D01G016200	chr4A	88.281	256	25	2	6	257	596243065	596242811	4.380000e-78	302.0
13	TraesCS4D01G016200	chr4A	91.925	161	7	3	285	439	596239855	596239695	1.260000e-53	220.0
14	TraesCS4D01G016200	chr4A	80.723	166	24	5	2450	2614	484862151	484862309	3.660000e-24	122.0
15	TraesCS4D01G016200	chr4A	94.737	57	3	0	2554	2610	582438983	582438927	3.710000e-14	89.8
16	TraesCS4D01G016200	chr5B	83.523	176	22	4	2431	2606	680812475	680812307	1.000000e-34	158.0
17	TraesCS4D01G016200	chr2B	82.418	182	19	4	2441	2610	495146741	495146561	2.170000e-31	147.0
18	TraesCS4D01G016200	chr3D	77.510	249	48	8	2172	2415	67724699	67724454	2.810000e-30	143.0
19	TraesCS4D01G016200	chr3D	79.670	182	29	6	2170	2347	433564300	433564123	1.020000e-24	124.0
20	TraesCS4D01G016200	chr1A	82.927	164	23	5	2169	2330	523109704	523109864	2.810000e-30	143.0
21	TraesCS4D01G016200	chr6D	81.481	189	19	5	2437	2612	457640543	457640728	1.010000e-29	141.0
22	TraesCS4D01G016200	chr7B	85.106	141	15	4	2441	2575	679591159	679591299	3.630000e-29	139.0
23	TraesCS4D01G016200	chr3B	81.176	170	28	4	2172	2339	114100222	114100389	1.690000e-27	134.0
24	TraesCS4D01G016200	chr3B	80.606	165	17	6	2445	2608	796512115	796511965	2.200000e-21	113.0
25	TraesCS4D01G016200	chr2A	80.899	178	26	7	2174	2347	24118818	24118991	1.690000e-27	134.0
26	TraesCS4D01G016200	chr2A	80.469	128	19	4	2441	2562	12249014	12248887	2.870000e-15	93.5
27	TraesCS4D01G016200	chr2D	80.226	177	31	4	2173	2347	558801358	558801532	2.190000e-26	130.0
28	TraesCS4D01G016200	chr2D	77.439	164	23	7	2465	2618	112917402	112917561	4.800000e-13	86.1
29	TraesCS4D01G016200	chr6B	80.952	168	27	5	2174	2339	536831173	536831337	7.870000e-26	128.0
30	TraesCS4D01G016200	chr6B	80.000	175	33	2	2174	2347	634977504	634977677	7.870000e-26	128.0
31	TraesCS4D01G016200	chr6B	80.226	177	27	6	2167	2339	497258549	497258377	2.830000e-25	126.0
32	TraesCS4D01G016200	chr5A	78.155	206	28	8	2427	2618	469108042	469107840	6.120000e-22	115.0
33	TraesCS4D01G016200	chrUn	86.735	98	10	3	2427	2523	95294213	95294308	3.690000e-19	106.0
34	TraesCS4D01G016200	chrUn	88.095	84	9	1	2527	2609	126990304	126990221	6.170000e-17	99.0
35	TraesCS4D01G016200	chr5D	78.125	192	25	9	2437	2614	9531921	9531733	3.690000e-19	106.0
36	TraesCS4D01G016200	chr7D	87.209	86	9	2	2441	2525	595523637	595523553	2.220000e-16	97.1

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	TraesCS4D01G016200	chr4D	7408439	7411145	2706	False	5000.000000	5000	100.000000	1	2707	1	chr4D.!!$F1	2706
1	TraesCS4D01G016200	chr4B	13276621	13278678	2057	False	1124.000000	2126	90.433000	209	2697	2	chr4B.!!$F2	2488
2	TraesCS4D01G016200	chr4A	596204141	596215809	11668	False	802.000000	1299	91.558000	285	1757	6	chr4A.!!$F2	1472
3	TraesCS4D01G016200	chr4A	596238360	596243065	4705	True	608.333333	1303	88.881667	6	1887	3	chr4A.!!$R2	1881

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
783	7414	0.538057	CTCTGGGAAAAGCAGTGGCA	60.538	55.0	0.0	0.0	44.61	4.92	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2033	12039	0.030638	CTGTTTTGTGGCTTGTCGGG	59.969	55.0	0.0	0.0	0.0	5.14	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
27	28	6.527423	ACATGAGTTCTAAGTTTCGGGTTTA	58.473	36.000	0.00	0.00	0.00	2.01
30	31	6.527423	TGAGTTCTAAGTTTCGGGTTTACAT	58.473	36.000	0.00	0.00	0.00	2.29
105	106	7.865706	AGGTTAAAAGCTACATGAATCGATT	57.134	32.000	11.20	11.20	34.49	3.34
106	107	7.697691	AGGTTAAAAGCTACATGAATCGATTG	58.302	34.615	16.96	4.53	34.49	2.67
122	123	8.397906	TGAATCGATTGTTTGTCTTCCATTATC	58.602	33.333	16.96	0.00	0.00	1.75
123	124	7.864108	ATCGATTGTTTGTCTTCCATTATCA	57.136	32.000	0.00	0.00	0.00	2.15
166	167	5.930569	TGATGAATGAATTAGAGATCCAGCG	59.069	40.000	0.00	0.00	0.00	5.18
199	200	2.159382	CACCACTTCCCGCATAACTTT	58.841	47.619	0.00	0.00	0.00	2.66
200	201	2.556622	CACCACTTCCCGCATAACTTTT	59.443	45.455	0.00	0.00	0.00	2.27
201	202	3.754323	CACCACTTCCCGCATAACTTTTA	59.246	43.478	0.00	0.00	0.00	1.52
207	208	4.497291	TCCCGCATAACTTTTAGGTGAT	57.503	40.909	0.00	0.00	0.00	3.06
242	247	3.857052	TGTTAGCTCCACGAATTTCGAT	58.143	40.909	24.50	6.90	43.74	3.59
248	253	5.223382	AGCTCCACGAATTTCGATATACAG	58.777	41.667	24.50	11.60	43.74	2.74
262	267	0.678395	ATACAGAGGCTGAGGCGATG	59.322	55.000	10.94	10.94	39.81	3.84
355	6964	6.471233	AGAATAGAATTCGACCATGAGTCA	57.529	37.500	12.80	0.00	46.69	3.41
476	7091	1.934589	CACGACCTTGAGTCACACAA	58.065	50.000	0.00	0.00	46.69	3.33
541	7156	6.734532	TCCCTACTTCATTAGTACAGTACCA	58.265	40.000	7.13	0.00	38.33	3.25
713	7341	0.596083	CTCTGATGCACGATCCGTCC	60.596	60.000	0.00	0.00	38.32	4.79
720	7348	1.813859	CACGATCCGTCCCAGCTAA	59.186	57.895	0.00	0.00	38.32	3.09
783	7414	0.538057	CTCTGGGAAAAGCAGTGGCA	60.538	55.000	0.00	0.00	44.61	4.92
978	10937	4.660938	AAGCCCGGCCAGTTCACC	62.661	66.667	5.55	0.00	0.00	4.02
999	10962	0.469494	CGATCATCATCCACCCACCA	59.531	55.000	0.00	0.00	0.00	4.17
1005	10968	1.000739	CATCCACCCACCAATGGCT	59.999	57.895	0.00	0.00	45.76	4.75
1036	10999	3.621394	GCGGCATCTCGTTCTCGC	61.621	66.667	0.00	0.00	36.96	5.03
1170	11142	4.687215	GTGCAGGCCTCGCTGTCA	62.687	66.667	22.36	5.93	0.00	3.58

Showing 1 to 25 of 384 entries

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Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
0	1	4.562757	CCCGAAACTTAGAACTCATGTCCA	60.563	45.833	0.00	0.00	0.00	4.02
1	2	3.933332	CCCGAAACTTAGAACTCATGTCC	59.067	47.826	0.00	0.00	0.00	4.02
3	4	4.618920	ACCCGAAACTTAGAACTCATGT	57.381	40.909	0.00	0.00	0.00	3.21
4	5	5.941948	AAACCCGAAACTTAGAACTCATG	57.058	39.130	0.00	0.00	0.00	3.07
9	10	6.790285	TGATGTAAACCCGAAACTTAGAAC	57.210	37.500	0.00	0.00	0.00	3.01
27	28	4.447138	TTGGGAACTAGTTGGTTGATGT	57.553	40.909	14.14	0.00	0.00	3.06
30	31	4.237976	TGTTTGGGAACTAGTTGGTTGA	57.762	40.909	14.14	0.00	36.70	3.18
60	61	7.651229	ACCTACCTCCTCTGATAAGTAGTAT	57.349	40.000	0.00	0.00	0.00	2.12
138	139	9.373603	CTGGATCTCTAATTCATTCATCAGATC	57.626	37.037	0.00	0.00	36.03	2.75
143	144	6.162079	TCGCTGGATCTCTAATTCATTCATC	58.838	40.000	0.00	0.00	0.00	2.92
149	150	5.598416	TTCTTCGCTGGATCTCTAATTCA	57.402	39.130	0.00	0.00	0.00	2.57
232	237	5.461526	TCAGCCTCTGTATATCGAAATTCG	58.538	41.667	9.38	9.38	35.51	3.34
242	247	1.889170	CATCGCCTCAGCCTCTGTATA	59.111	52.381	0.00	0.00	34.57	1.47
248	253	2.279120	CGACATCGCCTCAGCCTC	60.279	66.667	0.00	0.00	34.57	4.70
262	267	6.196538	CACCTTTTACTTTTTGAGCTTTCGAC	59.803	38.462	0.00	0.00	0.00	4.20
355	6964	1.515954	CGTGTATGCCTCGGTCCTT	59.484	57.895	0.00	0.00	0.00	3.36
476	7091	1.348064	TGGACCTCTCCGTTCATTGT	58.652	50.000	0.00	0.00	39.88	2.71
713	7341	2.288213	TGAACTCGACACTGTTAGCTGG	60.288	50.000	0.00	0.00	0.00	4.85
720	7348	1.200252	CTCGGATGAACTCGACACTGT	59.800	52.381	0.00	0.00	0.00	3.55
768	7399	1.662044	CACTGCCACTGCTTTTCCC	59.338	57.895	0.00	0.00	38.71	3.97
978	10937	0.250467	GTGGGTGGATGATGATCGGG	60.250	60.000	0.00	0.00	0.00	5.14
1024	10987	4.554363	CGCGGGCGAGAACGAGAT	62.554	66.667	7.38	0.00	42.83	2.75
1170	11142	1.080705	GAAGTAGCTCACGCACGGT	60.081	57.895	0.00	0.00	39.10	4.83
1359	11331	6.210584	ATGTATATCATGTCATGGACGTACCA	59.789	38.462	12.90	8.81	43.28	3.25
1379	11351	7.497249	GCTCCATCTCAGTTTTTCTACATGTAT	59.503	37.037	5.91	0.00	0.00	2.29

Showing 1 to 25 of 357 entries

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Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.