AutoCloner

Multiple sequence alignment - TraesCS5B01G034200

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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	TraesCS5B01G034200	chr5B	100.000	6080	0	0	1	6080	37060794	37054715	0.000000e+00	11228.0
1	TraesCS5B01G034200	chr5B	92.125	3162	216	15	828	3964	55625385	55622232	0.000000e+00	4429.0
2	TraesCS5B01G034200	chr5B	91.801	683	30	7	4535	5211	55621707	55621045	0.000000e+00	928.0
3	TraesCS5B01G034200	chr5B	91.957	460	27	7	4093	4546	55622181	55621726	2.390000e-178	636.0
4	TraesCS5B01G034200	chr5B	96.113	283	9	2	5798	6080	87139205	87139485	1.540000e-125	460.0
5	TraesCS5B01G034200	chr5B	82.672	479	21	22	369	800	55626065	55625602	9.630000e-98	368.0
6	TraesCS5B01G034200	chr5B	91.286	241	18	2	5798	6037	655210811	655211049	5.880000e-85	326.0
7	TraesCS5B01G034200	chr5B	78.417	417	38	26	2	370	55626606	55626194	2.210000e-54	224.0
8	TraesCS5B01G034200	chr5B	92.701	137	6	3	5903	6037	333192191	333192057	1.730000e-45	195.0
9	TraesCS5B01G034200	chr5B	85.093	161	17	5	3599	3754	55622747	55622589	2.270000e-34	158.0
10	TraesCS5B01G034200	chr5B	89.216	102	9	2	3999	4099	140966020	140965920	6.400000e-25	126.0
11	TraesCS5B01G034200	chr5B	98.182	55	1	0	5744	5798	87139072	87139126	5.020000e-16	97.1
12	TraesCS5B01G034200	chr5B	98.182	55	1	0	5744	5798	655210677	655210731	5.020000e-16	97.1
13	TraesCS5B01G034200	chr5B	89.041	73	4	4	6008	6079	425181515	425181584	3.020000e-13	87.9
14	TraesCS5B01G034200	chr5B	93.220	59	2	2	6024	6080	333191934	333191876	1.090000e-12	86.1
15	TraesCS5B01G034200	chr5D	97.423	3104	75	3	830	3930	42555121	42558222	0.000000e+00	5284.0
16	TraesCS5B01G034200	chr5D	92.220	3162	213	16	828	3964	52617479	52614326	0.000000e+00	4446.0
17	TraesCS5B01G034200	chr5D	88.595	2718	242	30	834	3520	15352551	15355231	0.000000e+00	3240.0
18	TraesCS5B01G034200	chr5D	90.789	988	74	9	2556	3527	15128904	15129890	0.000000e+00	1304.0
19	TraesCS5B01G034200	chr5D	92.771	830	21	9	1	805	42554051	42554866	0.000000e+00	1164.0
20	TraesCS5B01G034200	chr5D	86.595	1022	131	3	1026	2044	15103070	15104088	0.000000e+00	1123.0
21	TraesCS5B01G034200	chr5D	95.827	647	18	2	4535	5181	42558766	42559403	0.000000e+00	1037.0
22	TraesCS5B01G034200	chr5D	94.797	615	22	6	3933	4543	42558127	42558735	0.000000e+00	950.0
23	TraesCS5B01G034200	chr5D	94.412	519	26	3	5226	5743	42231154	42230638	0.000000e+00	795.0
24	TraesCS5B01G034200	chr5D	92.996	514	36	0	2049	2562	15126696	15127209	0.000000e+00	750.0
25	TraesCS5B01G034200	chr5D	91.828	465	25	9	4093	4546	52614187	52613725	2.390000e-178	636.0
26	TraesCS5B01G034200	chr5D	91.195	477	22	7	4743	5211	52605600	52605136	1.110000e-176	630.0
27	TraesCS5B01G034200	chr5D	78.811	774	64	43	111	800	52618508	52617751	4.350000e-116	429.0
28	TraesCS5B01G034200	chr5D	95.055	182	7	2	4535	4715	52613706	52613526	9.970000e-73	285.0
29	TraesCS5B01G034200	chr5D	83.986	281	24	10	4947	5211	15216397	15216672	3.640000e-62	250.0
30	TraesCS5B01G034200	chr5D	85.714	161	16	5	3599	3754	52614841	52614683	4.880000e-36	163.0
31	TraesCS5B01G034200	chr5D	85.821	134	11	5	2	127	52618652	52618519	1.060000e-27	135.0
32	TraesCS5B01G034200	chr5D	88.571	105	10	2	3999	4102	128577678	128577575	6.400000e-25	126.0
33	TraesCS5B01G034200	chr5D	97.778	45	1	0	3963	4007	52614233	52614189	1.820000e-10	78.7
34	TraesCS5B01G034200	chr5D	93.478	46	2	1	3864	3909	52614233	52614189	3.930000e-07	67.6
35	TraesCS5B01G034200	chr5A	93.858	521	27	4	828	1347	41708705	41708189	0.000000e+00	780.0
36	TraesCS5B01G034200	chr5A	84.825	257	12	10	561	800	41709209	41708963	3.660000e-57	233.0
37	TraesCS5B01G034200	chr5A	94.624	93	5	0	478	570	41709322	41709230	1.770000e-30	145.0
38	TraesCS5B01G034200	chr1A	72.353	1483	337	53	1008	2446	392529817	392528364	3.410000e-107	399.0
39	TraesCS5B01G034200	chr1A	93.478	92	5	1	3999	4089	530756665	530756574	1.060000e-27	135.0
40	TraesCS5B01G034200	chr1A	100.000	28	0	0	3904	3931	323287937	323287964	1.100000e-02	52.8
41	TraesCS5B01G034200	chr1B	72.267	1482	340	51	1008	2446	423209932	423208479	1.590000e-105	394.0
42	TraesCS5B01G034200	chr1B	90.511	137	10	2	5902	6037	539601032	539601166	1.740000e-40	178.0
43	TraesCS5B01G034200	chr1D	72.132	1482	342	51	1008	2446	312973483	312972030	3.440000e-102	383.0
44	TraesCS5B01G034200	chr4B	90.041	241	21	2	5798	6037	440918859	440918621	5.920000e-80	309.0
45	TraesCS5B01G034200	chr2B	88.393	224	17	4	5816	6037	649944750	649944966	1.680000e-65	261.0
46	TraesCS5B01G034200	chr2B	94.915	59	1	2	6024	6080	649945091	649945149	2.330000e-14	91.6
47	TraesCS5B01G034200	chr2B	94.545	55	3	0	5744	5798	649944610	649944664	1.090000e-12	86.1
48	TraesCS5B01G034200	chr2B	93.103	58	2	2	6024	6079	773007100	773007157	3.910000e-12	84.2
49	TraesCS5B01G034200	chr2B	91.379	58	3	2	6024	6080	567982667	567982723	1.820000e-10	78.7
50	TraesCS5B01G034200	chr3D	75.785	446	102	6	2003	2445	432135149	432135591	2.850000e-53	220.0
51	TraesCS5B01G034200	chr3B	75.281	445	106	4	2003	2445	564319144	564319586	6.180000e-50	209.0
52	TraesCS5B01G034200	chr6B	89.855	138	10	2	5902	6038	6612713	6612847	2.250000e-39	174.0
53	TraesCS5B01G034200	chr6B	89.209	139	7	5	5902	6037	589049681	589049814	3.770000e-37	167.0
54	TraesCS5B01G034200	chr6B	89.051	137	10	3	5902	6037	6667837	6667705	1.360000e-36	165.0
55	TraesCS5B01G034200	chr6B	95.918	49	1	1	6024	6071	589049937	589049985	1.820000e-10	78.7
56	TraesCS5B01G034200	chr7D	91.089	101	8	1	4000	4099	167548415	167548515	1.060000e-27	135.0
57	TraesCS5B01G034200	chr7D	90.099	101	9	1	4000	4099	167548509	167548409	4.950000e-26	130.0
58	TraesCS5B01G034200	chr7D	96.774	31	1	0	3900	3930	604995492	604995522	1.100000e-02	52.8
59	TraesCS5B01G034200	chr6A	95.349	86	3	1	4004	4088	584511447	584511362	1.060000e-27	135.0
60	TraesCS5B01G034200	chr6A	96.226	53	2	0	5746	5798	615622999	615623051	3.020000e-13	87.9
61	TraesCS5B01G034200	chr2A	93.333	90	5	1	4000	4088	483604566	483604655	1.380000e-26	132.0
62	TraesCS5B01G034200	chr2A	94.545	55	3	0	5744	5798	10371751	10371697	1.090000e-12	86.1
63	TraesCS5B01G034200	chr2D	90.816	98	7	2	4003	4099	302248099	302248003	4.950000e-26	130.0
64	TraesCS5B01G034200	chr6D	96.364	55	2	0	5744	5798	83282810	83282756	2.330000e-14	91.6
65	TraesCS5B01G034200	chr6D	94.643	56	1	2	5744	5798	126628930	126628876	1.090000e-12	86.1
66	TraesCS5B01G034200	chr3A	96.364	55	2	0	5744	5798	767696	767750	2.330000e-14	91.6

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	TraesCS5B01G034200	chr5B	37054715	37060794	6079	True	11228.000000	11228	100.000000	1	6080	1	chr5B.!!$R1	6079
1	TraesCS5B01G034200	chr5B	55621045	55626606	5561	True	1123.833333	4429	87.010833	2	5211	6	chr5B.!!$R3	5209
2	TraesCS5B01G034200	chr5D	15352551	15355231	2680	False	3240.000000	3240	88.595000	834	3520	1	chr5D.!!$F3	2686
3	TraesCS5B01G034200	chr5D	42554051	42559403	5352	False	2108.750000	5284	95.204500	1	5181	4	chr5D.!!$F5	5180
4	TraesCS5B01G034200	chr5D	15103070	15104088	1018	False	1123.000000	1123	86.595000	1026	2044	1	chr5D.!!$F1	1018
5	TraesCS5B01G034200	chr5D	15126696	15129890	3194	False	1027.000000	1304	91.892500	2049	3527	2	chr5D.!!$F4	1478
6	TraesCS5B01G034200	chr5D	42230638	42231154	516	True	795.000000	795	94.412000	5226	5743	1	chr5D.!!$R1	517
7	TraesCS5B01G034200	chr5D	52613526	52618652	5126	True	780.037500	4446	90.088125	2	4715	8	chr5D.!!$R4	4713
8	TraesCS5B01G034200	chr5A	41708189	41709322	1133	True	386.000000	780	91.102333	478	1347	3	chr5A.!!$R1	869
9	TraesCS5B01G034200	chr1A	392528364	392529817	1453	True	399.000000	399	72.353000	1008	2446	1	chr1A.!!$R1	1438
10	TraesCS5B01G034200	chr1B	423208479	423209932	1453	True	394.000000	394	72.267000	1008	2446	1	chr1B.!!$R1	1438
11	TraesCS5B01G034200	chr1D	312972030	312973483	1453	True	383.000000	383	72.132000	1008	2446	1	chr1D.!!$R1	1438

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
187	238	0.179171	CGTACCCTGACTACGCACAG	60.179	60.000	0.00	0.00	31.32	3.66	F
805	1099	1.134788	ACCTTGCCGTATACTCAGCAC	60.135	52.381	10.52	0.00	34.37	4.40	F
1419	1953	0.248621	GATTACTGCGCAACATGGCC	60.249	55.000	13.05	0.00	0.00	5.36	F
1924	2477	0.704551	GCGTTTTGCTCATGCTTTCG	59.295	50.000	0.00	0.00	41.73	3.46	F
3288	5587	0.947244	GACAGGGAATATGCAAGGCG	59.053	55.000	0.00	0.00	0.00	5.52	F
3894	6198	0.110486	TGAGGAAAGGTTGGCAGACC	59.890	55.000	9.86	9.86	40.11	3.85	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Hairpin	End Stability	Orientation
1155	1689	1.065926	CCAGCAAGGTATCTGCACTCA	60.066	52.381	0.00	0.00	3.41	R
2748	5023	0.035317	ACAGCAACGCCTGAAGATCA	59.965	50.000	0.00	36.67	2.92	R
2848	5123	0.381801	ACACGGCAAAACTGAAGCAG	59.618	50.000	0.00	37.52	4.24	R
3875	6179	0.110486	GGTCTGCCAACCTTTCCTCA	59.890	55.000	0.00	36.32	3.86	R
4988	7455	0.034756	AACTGCAGCGTATGTCACCA	59.965	50.000	15.27	0.00	4.17	R
5826	8299	0.039978	CAGCAGTAGTCGATAGCCCG	60.040	60.000	0.00	0.00	6.13	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
22	23	0.253327	ACGGCATTCCTTCCTTCTCC	59.747	55.000	0.00	0.00	0.00	3.71
158	209	4.567857	AGGGCCTTCTGGTTATATACAGT	58.432	43.478	0.00	0.00	36.17	3.55
159	210	5.723355	AGGGCCTTCTGGTTATATACAGTA	58.277	41.667	0.00	0.00	36.17	2.74
160	211	6.331846	AGGGCCTTCTGGTTATATACAGTAT	58.668	40.000	0.00	0.00	36.17	2.12
161	212	6.440965	AGGGCCTTCTGGTTATATACAGTATC	59.559	42.308	0.00	0.00	36.17	2.24
164	215	9.203163	GGCCTTCTGGTTATATACAGTATCTAT	57.797	37.037	0.00	0.00	36.17	1.98
187	238	0.179171	CGTACCCTGACTACGCACAG	60.179	60.000	0.00	0.00	31.32	3.66
314	388	9.626045	CACCAAGGAATTTATTTACTTTCTCAC	57.374	33.333	0.00	0.00	0.00	3.51
470	697	8.531622	TTTTACATGTTGAAATAATGCACTGG	57.468	30.769	2.30	0.00	0.00	4.00
491	722	8.604035	CACTGGTCAAAGTATATATGTTGTGTC	58.396	37.037	0.00	0.00	0.00	3.67
605	868	4.191544	CACATAAAGGCTGTTAGCTAGCA	58.808	43.478	18.83	10.09	42.88	3.49
681	944	5.475719	TCAGTAAGTTCTTGGGTTACATCG	58.524	41.667	0.00	0.00	0.00	3.84
685	965	3.170717	AGTTCTTGGGTTACATCGGAGA	58.829	45.455	0.00	0.00	45.75	3.71
790	1070	5.457140	TGCATTTTTACGCTCTTTACCTTG	58.543	37.500	0.00	0.00	0.00	3.61
805	1099	1.134788	ACCTTGCCGTATACTCAGCAC	60.135	52.381	10.52	0.00	34.37	4.40
806	1100	1.134818	CCTTGCCGTATACTCAGCACA	60.135	52.381	10.52	4.06	34.37	4.57
807	1101	2.483714	CCTTGCCGTATACTCAGCACAT	60.484	50.000	10.52	0.00	34.37	3.21
809	1103	3.260475	TGCCGTATACTCAGCACATTT	57.740	42.857	7.71	0.00	0.00	2.32
810	1104	2.935849	TGCCGTATACTCAGCACATTTG	59.064	45.455	7.71	0.00	0.00	2.32
811	1105	2.936498	GCCGTATACTCAGCACATTTGT	59.064	45.455	0.56	0.00	0.00	2.83
812	1106	3.001330	GCCGTATACTCAGCACATTTGTC	59.999	47.826	0.56	0.00	0.00	3.18
813	1107	4.433615	CCGTATACTCAGCACATTTGTCT	58.566	43.478	0.56	0.00	0.00	3.41
815	1109	5.351465	CCGTATACTCAGCACATTTGTCTTT	59.649	40.000	0.56	0.00	0.00	2.52
816	1110	6.243551	CGTATACTCAGCACATTTGTCTTTG	58.756	40.000	0.56	0.00	0.00	2.77
817	1111	3.360249	ACTCAGCACATTTGTCTTTGC	57.640	42.857	0.00	0.00	35.08	3.68

Showing 1 to 25 of 298 entries

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Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
22	23	2.986534	ATATGCTTCTCCAATGGGGG	57.013	50.000	0.00	0.00	37.22	5.40
75	76	7.499232	ACTTTGGGTCTAATCTAATGCATGTAC	59.501	37.037	0.00	0.00	0.00	2.90
76	77	7.573710	ACTTTGGGTCTAATCTAATGCATGTA	58.426	34.615	0.00	0.00	0.00	2.29
77	78	6.426587	ACTTTGGGTCTAATCTAATGCATGT	58.573	36.000	0.00	0.00	0.00	3.21
158	209	6.980978	GCGTAGTCAGGGTACGTATATAGATA	59.019	42.308	0.00	0.00	44.14	1.98
159	210	5.814705	GCGTAGTCAGGGTACGTATATAGAT	59.185	44.000	0.00	0.00	44.14	1.98
160	211	5.171476	GCGTAGTCAGGGTACGTATATAGA	58.829	45.833	0.00	0.00	44.14	1.98
161	212	4.931601	TGCGTAGTCAGGGTACGTATATAG	59.068	45.833	0.00	0.00	44.14	1.31
164	215	2.872245	GTGCGTAGTCAGGGTACGTATA	59.128	50.000	0.00	0.00	44.14	1.47
460	687	9.845740	AACATATATACTTTGACCAGTGCATTA	57.154	29.630	0.00	0.00	0.00	1.90
470	697	9.084164	ACGAAGACACAACATATATACTTTGAC	57.916	33.333	10.70	4.23	0.00	3.18
484	715	0.782384	CCAGCGTACGAAGACACAAC	59.218	55.000	21.65	0.00	0.00	3.32
491	722	4.374707	GCGAAATAATACCAGCGTACGAAG	60.375	45.833	21.65	10.01	0.00	3.79
587	850	4.881850	GGATTTGCTAGCTAACAGCCTTTA	59.118	41.667	17.23	0.00	43.77	1.85
605	868	4.080299	GGTGACTAGGTGAGATTGGGATTT	60.080	45.833	0.00	0.00	0.00	2.17
681	944	5.819901	GCTGCATGGTCCTAATATAATCTCC	59.180	44.000	0.00	0.00	0.00	3.71
685	965	5.948162	CCAAGCTGCATGGTCCTAATATAAT	59.052	40.000	15.42	0.00	33.08	1.28
790	1070	2.936498	ACAAATGTGCTGAGTATACGGC	59.064	45.455	10.19	10.19	41.89	5.68
805	1099	9.976511	ATATAATCTCCAATGCAAAGACAAATG	57.023	29.630	0.00	0.00	0.00	2.32
1015	1549	5.598416	TCCTGAGCATCTTTTAGAATCGA	57.402	39.130	0.00	0.00	34.92	3.59
1155	1689	1.065926	CCAGCAAGGTATCTGCACTCA	60.066	52.381	0.00	0.00	0.00	3.41
1166	1700	1.565759	TCAGGATAATGCCAGCAAGGT	59.434	47.619	0.00	0.00	40.61	3.50
1187	1721	3.493767	ACTTTCCTTCCACAGAGTTCC	57.506	47.619	0.00	0.00	0.00	3.62
1419	1953	1.340399	TAGGAGATGCACCCTGCTGG	61.340	60.000	18.18	1.89	45.31	4.85
1488	2025	3.203716	GTCCTTGTCGAACCTCAAGTTT	58.796	45.455	11.27	0.00	39.40	2.66

Showing 1 to 25 of 293 entries

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Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.