AutoCloner

Multiple sequence alignment - TraesCS1B01G122300

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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	TraesCS1B01G122300	chr1B	100.000	7372	0	0	1	7372	146789952	146797323	0.000000e+00	13614.0
1	TraesCS1B01G122300	chr1B	85.185	432	41	11	1	409	598908775	598908344	8.840000e-114	422.0
2	TraesCS1B01G122300	chr1B	82.864	426	52	12	1	405	621995736	621995311	5.440000e-96	363.0
3	TraesCS1B01G122300	chr1B	90.047	211	19	2	507	716	643042824	643043033	9.420000e-69	272.0
4	TraesCS1B01G122300	chr1B	85.000	140	16	3	7164	7299	384651988	384652126	3.590000e-28	137.0
5	TraesCS1B01G122300	chr1B	77.000	200	26	13	6570	6752	72701526	72701722	6.090000e-16	97.1
6	TraesCS1B01G122300	chr1D	94.225	5316	227	22	1284	6538	92254069	92259365	0.000000e+00	8043.0
7	TraesCS1B01G122300	chr1D	95.714	560	20	1	720	1279	92253473	92254028	0.000000e+00	898.0
8	TraesCS1B01G122300	chr1D	81.535	417	42	18	1	402	470488815	470489211	2.000000e-80	311.0
9	TraesCS1B01G122300	chr1D	94.505	91	5	0	7000	7090	468312443	468312533	2.770000e-29	141.0
10	TraesCS1B01G122300	chr1D	92.553	94	7	0	7000	7093	203866292	203866199	1.290000e-27	135.0
11	TraesCS1B01G122300	chr1D	93.056	72	4	1	438	509	92253411	92253481	3.640000e-18	104.0
12	TraesCS1B01G122300	chr1A	95.299	4446	166	13	1283	5703	88346282	88350709	0.000000e+00	7012.0
13	TraesCS1B01G122300	chr1A	93.884	654	34	2	5798	6445	88351033	88351686	0.000000e+00	981.0
14	TraesCS1B01G122300	chr1A	95.018	562	25	3	720	1279	88345679	88346239	0.000000e+00	880.0
15	TraesCS1B01G122300	chr1A	93.089	246	14	2	6755	6999	138025398	138025641	2.530000e-94	357.0
16	TraesCS1B01G122300	chr1A	96.000	50	2	0	460	509	88345638	88345687	1.700000e-11	82.4
17	TraesCS1B01G122300	chr6B	86.936	421	36	10	1	402	103265869	103266289	8.720000e-124	455.0
18	TraesCS1B01G122300	chr6B	85.511	421	30	17	1	402	509522173	509521765	1.910000e-110	411.0
19	TraesCS1B01G122300	chr6B	82.578	419	48	14	1	405	346712168	346711761	5.480000e-91	346.0
20	TraesCS1B01G122300	chr6B	89.831	59	5	1	6690	6747	606006548	606006490	2.850000e-09	75.0
21	TraesCS1B01G122300	chr2B	85.613	424	39	11	1	402	373988471	373988894	6.840000e-115	425.0
22	TraesCS1B01G122300	chr2B	85.579	423	38	14	1	402	687249881	687249461	8.840000e-114	422.0
23	TraesCS1B01G122300	chr2B	91.549	213	14	4	510	719	27548138	27547927	2.600000e-74	291.0
24	TraesCS1B01G122300	chr2B	90.141	213	19	2	509	720	627773017	627772806	7.290000e-70	276.0
25	TraesCS1B01G122300	chr2B	80.000	400	49	17	20	402	746719897	746719512	4.380000e-67	267.0
26	TraesCS1B01G122300	chr3B	84.296	433	42	10	3	409	723473049	723472617	4.140000e-107	399.0
27	TraesCS1B01G122300	chr3B	90.698	215	18	2	504	716	171801016	171801230	1.210000e-72	285.0
28	TraesCS1B01G122300	chr3B	87.552	241	20	10	510	742	247502411	247502173	3.390000e-68	270.0
29	TraesCS1B01G122300	chr4D	92.941	255	14	3	6750	7003	322861064	322861315	1.170000e-97	368.0
30	TraesCS1B01G122300	chr4D	93.548	248	13	2	6753	6999	36536168	36535923	4.200000e-97	366.0
31	TraesCS1B01G122300	chr4D	92.339	248	16	2	6755	7001	356179865	356179620	4.230000e-92	350.0
32	TraesCS1B01G122300	chr4D	95.402	87	4	0	7000	7086	282512366	282512452	9.970000e-29	139.0
33	TraesCS1B01G122300	chr4D	90.909	99	8	1	6994	7091	415104171	415104269	1.670000e-26	132.0
34	TraesCS1B01G122300	chr4D	86.486	74	10	0	6670	6743	499105529	499105456	1.700000e-11	82.4
35	TraesCS1B01G122300	chr4A	92.520	254	16	2	6749	7001	680772431	680772180	1.960000e-95	361.0
36	TraesCS1B01G122300	chr4A	92.400	250	15	3	6752	6999	470874556	470874803	3.270000e-93	353.0
37	TraesCS1B01G122300	chr2A	93.089	246	14	2	6755	6999	521239293	521239536	2.530000e-94	357.0
38	TraesCS1B01G122300	chr2A	90.278	216	19	2	507	721	710461216	710461430	1.570000e-71	281.0
39	TraesCS1B01G122300	chr2A	75.773	194	29	13	6570	6747	738117148	738116957	1.700000e-11	82.4
40	TraesCS1B01G122300	chr7D	92.369	249	16	2	6752	6999	33195687	33195933	1.180000e-92	351.0
41	TraesCS1B01G122300	chr7D	83.436	163	21	5	7158	7316	623389520	623389360	5.960000e-31	147.0
42	TraesCS1B01G122300	chr7D	81.319	182	26	7	6907	7086	262095155	262095330	2.770000e-29	141.0
43	TraesCS1B01G122300	chr6A	92.369	249	16	2	6752	6999	47959091	47959337	1.180000e-92	351.0
44	TraesCS1B01G122300	chr6A	85.714	147	17	3	7164	7306	615379182	615379036	1.280000e-32	152.0
45	TraesCS1B01G122300	chr6A	88.750	80	3	4	7233	7307	56251057	56251135	7.880000e-15	93.5
46	TraesCS1B01G122300	chr4B	83.168	404	44	19	1	389	40871281	40870887	1.520000e-91	348.0
47	TraesCS1B01G122300	chr4B	85.938	256	17	7	1	237	630366449	630366704	9.490000e-64	255.0
48	TraesCS1B01G122300	chr4B	96.552	87	3	0	7000	7086	199147339	199147253	2.140000e-30	145.0
49	TraesCS1B01G122300	chr5B	91.080	213	16	3	510	721	51012923	51012713	1.210000e-72	285.0
50	TraesCS1B01G122300	chr5B	89.041	73	4	3	7233	7301	26326319	26326391	3.660000e-13	87.9
51	TraesCS1B01G122300	chr7B	90.610	213	15	5	510	720	1850249	1850458	2.030000e-70	278.0
52	TraesCS1B01G122300	chr7B	90.278	216	16	3	509	719	733770766	733770551	2.030000e-70	278.0
53	TraesCS1B01G122300	chr6D	79.512	410	58	18	2	402	82231401	82231793	1.220000e-67	268.0
54	TraesCS1B01G122300	chr6D	77.612	201	24	15	6573	6755	211509928	211509731	1.310000e-17	102.0
55	TraesCS1B01G122300	chr5A	77.887	407	57	17	4	402	318811122	318811503	9.630000e-54	222.0
56	TraesCS1B01G122300	chr5A	80.124	161	19	10	7174	7325	130083270	130083426	2.810000e-19	108.0
57	TraesCS1B01G122300	chr3D	94.565	92	5	0	7000	7091	283613205	283613114	7.710000e-30	143.0
58	TraesCS1B01G122300	chr3D	85.714	140	15	3	7159	7293	578075483	578075622	7.710000e-30	143.0
59	TraesCS1B01G122300	chr3D	82.692	156	23	2	7168	7319	552287325	552287170	1.290000e-27	135.0
60	TraesCS1B01G122300	chr3A	95.402	87	4	0	7000	7086	714779719	714779805	9.970000e-29	139.0
61	TraesCS1B01G122300	chr3A	91.837	98	7	1	6994	7090	744550734	744550831	1.290000e-27	135.0
62	TraesCS1B01G122300	chr2D	77.835	194	25	14	6569	6747	558254779	558254969	3.640000e-18	104.0
63	TraesCS1B01G122300	chrUn	92.754	69	2	3	7254	7319	11766703	11766771	6.090000e-16	97.1
64	TraesCS1B01G122300	chr7A	84.146	82	12	1	7168	7248	727220429	727220348	2.210000e-10	78.7

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	TraesCS1B01G122300	chr1B	146789952	146797323	7371	False	13614.00	13614	100.000000	1	7372	1	chr1B.!!$F2	7371
1	TraesCS1B01G122300	chr1D	92253411	92259365	5954	False	3015.00	8043	94.331667	438	6538	3	chr1D.!!$F3	6100
2	TraesCS1B01G122300	chr1A	88345638	88351686	6048	False	2238.85	7012	95.050250	460	6445	4	chr1A.!!$F2	5985

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
322	323	0.027586	ATTTTAGAATGCGGACGCGC	59.972	50.000	5.73	0.00	45.51	6.86	F
717	718	0.033504	TGGAACAGACAAGTCTCGCC	59.966	55.000	0.00	3.12	37.98	5.54	F
890	891	0.606401	TTCACTACCAGCTGCTTGCC	60.606	55.000	8.66	0.00	44.23	4.52	F
1742	1792	1.073284	GGAGGCCAAAGAGGTGTAACA	59.927	52.381	5.01	0.00	39.98	2.41	F
3199	3276	0.685660	TGCATTTTCAGCATTGGCCA	59.314	45.000	0.00	0.00	42.56	5.36	F
3502	3582	0.115547	TACCACAGGTCTGGCTGGTA	59.884	55.000	13.27	13.27	39.63	3.25	F
4716	4818	0.248377	GCCACTGAAGCAATCATCGC	60.248	55.000	0.00	0.00	37.44	4.58	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1139	1142	0.251474	TGCTGATCCAAGCTTTGCCT	60.251	50.000	0.00	0.00	43.90	4.75	R
1740	1790	1.067364	TGATGTGGTCGTAACACGTGT	59.933	47.619	17.22	17.22	43.14	4.49	R
2504	2574	1.684450	TCACGAGGAATAGGCGCATAA	59.316	47.619	10.83	0.00	0.00	1.90	R
3381	3461	1.958205	GATGAGCGGCCGAGGATTG	60.958	63.158	33.48	0.00	0.00	2.67	R
5134	5236	0.106149	GTGAAGTCCAACCCAGACGT	59.894	55.000	0.00	0.00	39.31	4.34	R
5220	5322	0.322098	TGTGATTTCCCCGTCGCATT	60.322	50.000	0.00	0.00	30.55	3.56	R
6487	6857	0.366871	CGAGGCGAAATCACGTTCTG	59.633	55.000	0.00	0.00	35.59	3.02	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
19	20	4.488136	TGGCAGCATACCAGGCGG	62.488	66.667	0.00	0.00	36.08	6.13
22	23	4.838152	CAGCATACCAGGCGGCGT	62.838	66.667	9.37	0.00	36.08	5.68
23	24	4.096003	AGCATACCAGGCGGCGTT	62.096	61.111	9.37	0.00	36.08	4.84
24	25	3.573491	GCATACCAGGCGGCGTTC	61.573	66.667	9.37	0.91	34.57	3.95
25	26	3.261951	CATACCAGGCGGCGTTCG	61.262	66.667	9.37	0.00	42.76	3.95
26	27	4.524318	ATACCAGGCGGCGTTCGG	62.524	66.667	9.37	8.96	39.69	4.30
48	49	2.681778	CAGACCCTGCTCCCGTCT	60.682	66.667	0.00	0.00	37.34	4.18
49	50	2.120718	AGACCCTGCTCCCGTCTT	59.879	61.111	0.00	0.00	33.01	3.01
50	51	1.985116	AGACCCTGCTCCCGTCTTC	60.985	63.158	0.00	0.00	33.01	2.87
51	52	2.203788	ACCCTGCTCCCGTCTTCA	60.204	61.111	0.00	0.00	0.00	3.02
52	53	1.613630	ACCCTGCTCCCGTCTTCAT	60.614	57.895	0.00	0.00	0.00	2.57
53	54	1.144936	CCCTGCTCCCGTCTTCATC	59.855	63.158	0.00	0.00	0.00	2.92
54	55	1.227089	CCTGCTCCCGTCTTCATCG	60.227	63.158	0.00	0.00	0.00	3.84
55	56	1.667154	CCTGCTCCCGTCTTCATCGA	61.667	60.000	0.00	0.00	0.00	3.59
56	57	0.526524	CTGCTCCCGTCTTCATCGAC	60.527	60.000	0.00	0.00	0.00	4.20
57	58	1.227002	GCTCCCGTCTTCATCGACC	60.227	63.158	0.00	0.00	0.00	4.79
58	59	1.668101	GCTCCCGTCTTCATCGACCT	61.668	60.000	0.00	0.00	0.00	3.85
59	60	0.382515	CTCCCGTCTTCATCGACCTC	59.617	60.000	0.00	0.00	0.00	3.85
60	61	0.323087	TCCCGTCTTCATCGACCTCA	60.323	55.000	0.00	0.00	0.00	3.86
61	62	0.179134	CCCGTCTTCATCGACCTCAC	60.179	60.000	0.00	0.00	0.00	3.51
62	63	0.811915	CCGTCTTCATCGACCTCACT	59.188	55.000	0.00	0.00	0.00	3.41
63	64	1.468224	CCGTCTTCATCGACCTCACTG	60.468	57.143	0.00	0.00	0.00	3.66
64	65	1.468224	CGTCTTCATCGACCTCACTGG	60.468	57.143	0.00	0.00	42.93	4.00
65	66	0.532573	TCTTCATCGACCTCACTGGC	59.467	55.000	0.00	0.00	40.22	4.85
66	67	0.803768	CTTCATCGACCTCACTGGCG	60.804	60.000	0.00	0.00	40.22	5.69

Showing 1 to 25 of 706 entries

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Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
2	3	4.488136	CCGCCTGGTATGCTGCCA	62.488	66.667	0.00	0.00	34.42	4.92
5	6	4.838152	ACGCCGCCTGGTATGCTG	62.838	66.667	0.00	0.00	37.67	4.41
6	7	4.096003	AACGCCGCCTGGTATGCT	62.096	61.111	0.00	0.00	37.67	3.79
7	8	3.573491	GAACGCCGCCTGGTATGC	61.573	66.667	0.00	0.00	37.67	3.14
8	9	3.261951	CGAACGCCGCCTGGTATG	61.262	66.667	0.00	0.00	37.67	2.39
9	10	4.524318	CCGAACGCCGCCTGGTAT	62.524	66.667	0.00	0.00	37.67	2.73
31	32	2.232298	GAAGACGGGAGCAGGGTCTG	62.232	65.000	0.00	0.00	40.67	3.51
32	33	1.985116	GAAGACGGGAGCAGGGTCT	60.985	63.158	0.00	0.00	42.52	3.85
33	34	1.617947	ATGAAGACGGGAGCAGGGTC	61.618	60.000	0.00	0.00	0.00	4.46
34	35	1.613630	ATGAAGACGGGAGCAGGGT	60.614	57.895	0.00	0.00	0.00	4.34
35	36	1.144936	GATGAAGACGGGAGCAGGG	59.855	63.158	0.00	0.00	0.00	4.45
36	37	1.227089	CGATGAAGACGGGAGCAGG	60.227	63.158	0.00	0.00	0.00	4.85
37	38	0.526524	GTCGATGAAGACGGGAGCAG	60.527	60.000	0.00	0.00	0.00	4.24
38	39	1.511305	GTCGATGAAGACGGGAGCA	59.489	57.895	0.00	0.00	0.00	4.26
39	40	1.227002	GGTCGATGAAGACGGGAGC	60.227	63.158	0.00	0.00	41.81	4.70
40	41	0.382515	GAGGTCGATGAAGACGGGAG	59.617	60.000	0.00	0.00	41.81	4.30
41	42	0.323087	TGAGGTCGATGAAGACGGGA	60.323	55.000	0.00	0.00	41.81	5.14
42	43	0.179134	GTGAGGTCGATGAAGACGGG	60.179	60.000	0.00	0.00	41.81	5.28
43	44	0.811915	AGTGAGGTCGATGAAGACGG	59.188	55.000	0.00	0.00	41.81	4.79
44	45	1.468224	CCAGTGAGGTCGATGAAGACG	60.468	57.143	0.00	0.00	41.81	4.18
45	46	1.737363	GCCAGTGAGGTCGATGAAGAC	60.737	57.143	0.00	0.00	40.61	3.01
46	47	0.532573	GCCAGTGAGGTCGATGAAGA	59.467	55.000	0.00	0.00	40.61	2.87
47	48	0.803768	CGCCAGTGAGGTCGATGAAG	60.804	60.000	0.00	0.00	38.60	3.02
48	49	1.215382	CGCCAGTGAGGTCGATGAA	59.785	57.895	0.00	0.00	38.60	2.57
49	50	1.677633	TCGCCAGTGAGGTCGATGA	60.678	57.895	0.00	0.00	39.72	2.92

Showing 1 to 25 of 629 entries

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Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.