AutoCloner

Multiple sequence alignment - TraesCS1B01G194000

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	TraesCS1B01G194000	chr1B	100.000	2804	0	0	1	2804	349350492	349347689	0.000000e+00	5179.0
1	TraesCS1B01G194000	chr1B	94.355	248	14	0	2557	2804	568717865	568718112	5.670000e-102	381.0
2	TraesCS1B01G194000	chr1B	93.927	247	15	0	2558	2804	354562414	354562168	9.480000e-100	374.0
3	TraesCS1B01G194000	chr1B	92.578	256	19	0	2549	2804	154882890	154883145	4.410000e-98	368.0
4	TraesCS1B01G194000	chr1B	80.000	315	55	7	1024	1334	348905759	348905449	2.810000e-55	226.0
5	TraesCS1B01G194000	chr1B	79.394	330	55	9	1011	1334	349564108	349563786	1.310000e-53	220.0
6	TraesCS1B01G194000	chr1B	88.136	118	13	1	2441	2557	647047641	647047758	3.770000e-29	139.0
7	TraesCS1B01G194000	chr1B	97.727	44	1	0	776	819	349349678	349349635	3.000000e-10	76.8
8	TraesCS1B01G194000	chr1B	97.727	44	1	0	815	858	349349717	349349674	3.000000e-10	76.8
9	TraesCS1B01G194000	chr1A	90.999	1311	71	20	503	1786	337630331	337629041	0.000000e+00	1724.0
10	TraesCS1B01G194000	chr1A	87.137	241	25	3	2106	2342	337629044	337628806	4.600000e-68	268.0
11	TraesCS1B01G194000	chr1A	79.299	314	59	6	1024	1334	337301739	337301429	6.080000e-52	215.0
12	TraesCS1B01G194000	chr1D	91.406	1152	61	16	642	1786	262341132	262342252	0.000000e+00	1544.0
13	TraesCS1B01G194000	chr1D	91.281	367	30	2	2	368	262336897	262337261	1.500000e-137	499.0
14	TraesCS1B01G194000	chr1D	88.546	227	20	6	2103	2327	262342246	262342468	1.280000e-68	270.0
15	TraesCS1B01G194000	chr1D	96.429	140	5	0	473	612	262340992	262341131	6.040000e-57	231.0
16	TraesCS1B01G194000	chr1D	80.317	315	54	8	1024	1334	263198930	263198620	6.040000e-57	231.0
17	TraesCS1B01G194000	chr1D	79.205	327	61	6	1011	1334	262252734	262253056	1.310000e-53	220.0
18	TraesCS1B01G194000	chr5B	94.190	327	18	1	1780	2106	322151875	322151550	5.390000e-137	497.0
19	TraesCS1B01G194000	chr5B	92.899	338	23	1	1769	2106	44770988	44771324	9.030000e-135	490.0
20	TraesCS1B01G194000	chr5B	93.750	320	20	0	1787	2106	478698825	478699144	5.430000e-132	481.0
21	TraesCS1B01G194000	chr5B	93.769	321	19	1	1787	2106	603888797	603888477	5.430000e-132	481.0
22	TraesCS1B01G194000	chr5B	83.929	112	18	0	2430	2541	711276928	711277039	1.060000e-19	108.0
23	TraesCS1B01G194000	chr5B	80.620	129	24	1	2430	2557	15003373	15003501	6.390000e-17	99.0
24	TraesCS1B01G194000	chr3B	94.118	323	19	0	1787	2109	369098415	369098093	2.510000e-135	492.0
25	TraesCS1B01G194000	chr3B	94.099	322	19	0	1787	2108	596965147	596964826	9.030000e-135	490.0
26	TraesCS1B01G194000	chr3B	93.353	331	21	1	1779	2109	344956726	344956397	3.250000e-134	488.0
27	TraesCS1B01G194000	chr3B	94.378	249	12	1	2558	2804	261927323	261927571	5.670000e-102	381.0
28	TraesCS1B01G194000	chr2B	94.118	323	18	1	1787	2109	789530259	789529938	9.030000e-135	490.0
29	TraesCS1B01G194000	chr2B	93.927	247	15	0	2558	2804	568061257	568061011	9.480000e-100	374.0
30	TraesCS1B01G194000	chr4B	93.293	328	22	0	1782	2109	481800329	481800002	4.200000e-133	484.0
31	TraesCS1B01G194000	chr4B	94.332	247	14	0	2558	2804	403396522	403396276	2.040000e-101	379.0
32	TraesCS1B01G194000	chr4B	92.913	254	17	1	2552	2804	607173581	607173328	4.410000e-98	368.0
33	TraesCS1B01G194000	chr4B	78.387	310	67	0	1031	1340	471776062	471775753	4.740000e-48	202.0
34	TraesCS1B01G194000	chr7B	95.181	249	10	2	2558	2804	43607145	43606897	2.620000e-105	392.0
35	TraesCS1B01G194000	chr7B	93.254	252	17	0	2553	2804	400562624	400562373	3.410000e-99	372.0
36	TraesCS1B01G194000	chr7D	80.195	308	57	3	1029	1334	579536264	579535959	7.810000e-56	228.0
37	TraesCS1B01G194000	chr7D	82.946	129	20	2	2423	2549	11657449	11657577	6.350000e-22	115.0
38	TraesCS1B01G194000	chr7A	80.065	306	61	0	1029	1334	671219687	671219382	7.810000e-56	228.0
39	TraesCS1B01G194000	chr7A	79.180	317	64	2	1019	1334	29165568	29165253	4.700000e-53	219.0
40	TraesCS1B01G194000	chr4D	78.916	332	68	2	1012	1342	384951441	384951111	1.010000e-54	224.0
41	TraesCS1B01G194000	chr4A	78.593	327	65	4	1009	1334	66559387	66559065	7.870000e-51	211.0
42	TraesCS1B01G194000	chr3D	77.399	323	64	7	1009	1330	8860948	8860634	1.720000e-42	183.0
43	TraesCS1B01G194000	chr3D	80.426	235	41	4	1100	1333	544277867	544277637	1.030000e-39	174.0
44	TraesCS1B01G194000	chr3D	78.481	237	46	3	1100	1335	544353522	544353754	1.740000e-32	150.0
45	TraesCS1B01G194000	chr6D	86.822	129	17	0	2430	2558	288075747	288075619	8.090000e-31	145.0

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	TraesCS1B01G194000	chr1B	349347689	349350492	2803	True	1777.533333	5179	98.484667	1	2804	3	chr1B.!!$R4	2803
1	TraesCS1B01G194000	chr1A	337628806	337630331	1525	True	996.000000	1724	89.068000	503	2342	2	chr1A.!!$R2	1839
2	TraesCS1B01G194000	chr1D	262336897	262342468	5571	False	636.000000	1544	91.915500	2	2327	4	chr1D.!!$F2	2325

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
669	4322	0.174162	TACCGGCGCTTTTCTCCTAC	59.826	55.0	7.64	0.0	0.0	3.18	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1821	5482	0.035317	TCCGATCCTACATGGCATGC	59.965	55.0	26.7	9.9	35.26	4.06	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
28	29	5.555017	ACTGCTTGTATGATTGTTCACTCT	58.445	37.500	0.00	0.00	33.85	3.24
29	30	6.000219	ACTGCTTGTATGATTGTTCACTCTT	59.000	36.000	0.00	0.00	33.85	2.85
30	31	6.488006	ACTGCTTGTATGATTGTTCACTCTTT	59.512	34.615	0.00	0.00	33.85	2.52
120	121	7.956420	AAAATCCGAAATTCAAAAGGGTAAC	57.044	32.000	0.00	0.00	0.00	2.50
122	123	4.387598	TCCGAAATTCAAAAGGGTAACGA	58.612	39.130	0.00	0.00	37.60	3.85
125	126	6.016108	TCCGAAATTCAAAAGGGTAACGAAAT	60.016	34.615	0.00	0.00	37.60	2.17
151	152	2.786777	ACCATACCGGAAACCAGAAAC	58.213	47.619	9.46	0.00	38.63	2.78
152	153	2.089201	CCATACCGGAAACCAGAAACC	58.911	52.381	9.46	0.00	36.56	3.27
153	154	1.735571	CATACCGGAAACCAGAAACCG	59.264	52.381	9.46	0.00	44.16	4.44
212	213	8.942924	CGGTTTTTCTGTTTGATTTTAAAATGC	58.057	29.630	17.98	10.00	0.00	3.56
223	224	8.523523	TTGATTTTAAAATGCAGAGTGATGTG	57.476	30.769	17.98	0.00	0.00	3.21
243	244	2.368548	TGGAATGTAGATGATGTCCCCG	59.631	50.000	0.00	0.00	0.00	5.73
254	255	5.707298	AGATGATGTCCCCGCAAAATATAAG	59.293	40.000	0.00	0.00	0.00	1.73
256	257	4.578516	TGATGTCCCCGCAAAATATAAGTG	59.421	41.667	0.00	0.00	0.00	3.16
297	298	6.558009	GGTAGTCTTGACACGTATTACATGA	58.442	40.000	0.00	0.00	0.00	3.07
298	299	7.031372	GGTAGTCTTGACACGTATTACATGAA	58.969	38.462	0.00	0.00	0.00	2.57
362	363	8.102676	TGATCTAAACCATTGATTCTTGAGACA	58.897	33.333	0.00	0.00	0.00	3.41
368	369	5.645497	ACCATTGATTCTTGAGACAGCTAAC	59.355	40.000	0.00	0.00	0.00	2.34
369	370	5.220548	CCATTGATTCTTGAGACAGCTAACG	60.221	44.000	0.00	0.00	0.00	3.18
370	371	4.521130	TGATTCTTGAGACAGCTAACGT	57.479	40.909	0.00	0.00	0.00	3.99
371	372	4.237724	TGATTCTTGAGACAGCTAACGTG	58.762	43.478	0.00	0.00	0.00	4.49
381	1464	3.527533	ACAGCTAACGTGACTTTGTCAA	58.472	40.909	1.73	0.00	44.49	3.18
405	1488	1.134007	TCAGTGCACATCCATCCATCC	60.134	52.381	21.04	0.00	0.00	3.51
413	1496	4.220724	CACATCCATCCATCCCAGATTTT	58.779	43.478	0.00	0.00	0.00	1.82
414	1497	4.652421	CACATCCATCCATCCCAGATTTTT	59.348	41.667	0.00	0.00	0.00	1.94

Showing 1 to 25 of 603 entries

Previous1 2 3 4 5…25Next

Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
0	1	6.255670	GTGAACAATCATACAAGCAGTCGATA	59.744	38.462	0.00	0.00	38.01	2.92
92	93	7.102993	ACCCTTTTGAATTTCGGATTTTATGG	58.897	34.615	0.00	0.00	0.00	2.74
100	101	4.387598	TCGTTACCCTTTTGAATTTCGGA	58.612	39.130	0.00	0.00	0.00	4.55
106	107	9.634163	GTATGAAATTTCGTTACCCTTTTGAAT	57.366	29.630	17.71	1.34	0.00	2.57
110	111	7.527568	TGGTATGAAATTTCGTTACCCTTTT	57.472	32.000	29.23	6.83	37.57	2.27
120	121	5.994887	TTCCGGTATGGTATGAAATTTCG	57.005	39.130	13.34	0.00	39.52	3.46
122	123	5.952947	TGGTTTCCGGTATGGTATGAAATTT	59.047	36.000	0.00	0.00	39.52	1.82
125	126	4.225492	TCTGGTTTCCGGTATGGTATGAAA	59.775	41.667	0.00	0.00	39.52	2.69
165	166	5.181622	ACCGCACCGAAAATAAACAGAATTA	59.818	36.000	0.00	0.00	0.00	1.40
167	168	3.504520	ACCGCACCGAAAATAAACAGAAT	59.495	39.130	0.00	0.00	0.00	2.40
171	172	3.712091	AAACCGCACCGAAAATAAACA	57.288	38.095	0.00	0.00	0.00	2.83
212	213	5.910614	TCATCTACATTCCACATCACTCTG	58.089	41.667	0.00	0.00	0.00	3.35
223	224	2.872038	GCGGGGACATCATCTACATTCC	60.872	54.545	0.00	0.00	0.00	3.01
254	255	7.174599	AGACTACCGACAGTATATAACATCCAC	59.825	40.741	0.00	0.00	0.00	4.02
256	257	7.684937	AGACTACCGACAGTATATAACATCC	57.315	40.000	0.00	0.00	0.00	3.51
272	273	4.973396	TGTAATACGTGTCAAGACTACCG	58.027	43.478	0.00	4.29	0.00	4.02
316	317	0.732571	AAATGAATAGGGCACGTGCG	59.267	50.000	32.35	0.65	43.26	5.34
362	363	3.131396	CCTTGACAAAGTCACGTTAGCT	58.869	45.455	0.00	0.00	42.60	3.32
368	369	3.185188	CACTGATCCTTGACAAAGTCACG	59.815	47.826	0.00	0.00	42.60	4.35
369	370	3.058639	GCACTGATCCTTGACAAAGTCAC	60.059	47.826	0.00	0.00	42.60	3.67
370	371	3.141398	GCACTGATCCTTGACAAAGTCA	58.859	45.455	0.00	0.00	41.09	3.41
371	372	3.058639	GTGCACTGATCCTTGACAAAGTC	60.059	47.826	10.32	0.00	0.00	3.01
381	1464	1.142465	GGATGGATGTGCACTGATCCT	59.858	52.381	27.46	17.44	39.23	3.24
435	1518	1.225376	TGACCGTTGAATCGTGTGGC	61.225	55.000	0.00	0.00	0.00	5.01
449	1533	6.305693	AGACAAAAGAGAAAAATCTGACCG	57.694	37.500	0.00	0.00	0.00	4.79

Showing 1 to 25 of 549 entries

Previous1 2 3 4 5…22Next

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.