AutoCloner

Multiple sequence alignment - TraesCS6B01G154400

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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	TraesCS6B01G154400	chr6B	100.000	2195	0	0	1	2195	157910545	157912739	0.000000e+00	4054.0
1	TraesCS6B01G154400	chr6B	93.953	1356	71	6	739	2094	157780026	157778682	0.000000e+00	2039.0
2	TraesCS6B01G154400	chr6B	83.197	1101	169	10	998	2094	156418364	156417276	0.000000e+00	994.0
3	TraesCS6B01G154400	chr6B	90.805	609	36	15	99	699	157780613	157780017	0.000000e+00	797.0
4	TraesCS6B01G154400	chr6B	100.000	355	0	0	2471	2825	157913015	157913369	0.000000e+00	656.0
5	TraesCS6B01G154400	chr6B	75.059	1267	268	33	850	2094	157027486	157026246	1.910000e-151	545.0
6	TraesCS6B01G154400	chr6B	88.761	347	36	2	2479	2825	158160516	158160173	3.360000e-114	422.0
7	TraesCS6B01G154400	chr6A	94.861	1907	90	4	194	2094	99787667	99785763	0.000000e+00	2972.0
8	TraesCS6B01G154400	chr6A	83.272	1088	168	8	1010	2094	98242366	98241290	0.000000e+00	989.0
9	TraesCS6B01G154400	chr6A	98.077	52	1	0	99	150	99790142	99790091	1.080000e-14	91.6
10	TraesCS6B01G154400	chr6D	93.995	1682	86	11	422	2094	82965151	82963476	0.000000e+00	2532.0
11	TraesCS6B01G154400	chr6D	83.394	1090	164	9	1008	2094	81920686	81919611	0.000000e+00	994.0
12	TraesCS6B01G154400	chr6D	82.727	1100	176	10	998	2094	81750104	81749016	0.000000e+00	966.0
13	TraesCS6B01G154400	chr6D	74.922	1284	281	27	831	2094	82220587	82219325	1.480000e-152	549.0
14	TraesCS6B01G154400	chr6D	91.743	327	21	5	108	428	82970182	82969856	1.540000e-122	449.0
15	TraesCS6B01G154400	chr5D	87.225	1683	175	25	420	2094	372060831	372059181	0.000000e+00	1881.0
16	TraesCS6B01G154400	chr5D	89.324	281	25	4	98	375	372061104	372060826	5.790000e-92	348.0
17	TraesCS6B01G154400	chr5D	91.667	96	8	0	6	101	372061234	372061139	1.770000e-27	134.0
18	TraesCS6B01G154400	chr7B	94.085	355	21	0	2471	2825	423570617	423570263	8.900000e-150	540.0
19	TraesCS6B01G154400	chr7B	93.000	100	5	1	2098	2195	423570771	423570672	8.160000e-31	145.0
20	TraesCS6B01G154400	chr7B	87.629	97	6	6	2094	2187	15296711	15296804	1.070000e-19	108.0
21	TraesCS6B01G154400	chr2B	94.302	351	18	2	2473	2822	49300426	49300775	1.150000e-148	536.0
22	TraesCS6B01G154400	chr2B	90.265	339	33	0	2484	2822	385137290	385137628	7.180000e-121	444.0
23	TraesCS6B01G154400	chr3B	90.805	348	32	0	2475	2822	539563856	539564203	1.530000e-127	466.0
24	TraesCS6B01G154400	chr3B	90.141	355	31	3	2471	2825	386975546	386975196	2.560000e-125	459.0
25	TraesCS6B01G154400	chr3B	89.625	347	33	2	2479	2825	466660613	466660270	3.340000e-119	438.0
26	TraesCS6B01G154400	chr3B	86.000	100	11	3	2094	2190	539563695	539563794	1.380000e-18	104.0
27	TraesCS6B01G154400	chr5B	89.943	348	33	2	2478	2825	105756169	105755824	5.550000e-122	448.0
28	TraesCS6B01G154400	chr4B	90.323	341	28	2	2482	2822	436261481	436261816	2.580000e-120	442.0
29	TraesCS6B01G154400	chr4B	87.912	91	9	2	2094	2183	436261315	436261404	3.850000e-19	106.0
30	TraesCS6B01G154400	chr1B	89.130	92	9	1	2093	2183	562470537	562470628	2.300000e-21	113.0
31	TraesCS6B01G154400	chr1B	85.149	101	13	2	2085	2183	161379584	161379684	4.980000e-18	102.0
32	TraesCS6B01G154400	chr3A	88.172	93	8	3	2094	2183	583752811	583752903	1.070000e-19	108.0
33	TraesCS6B01G154400	chr5A	87.368	95	8	4	2094	2185	319147823	319147916	3.850000e-19	106.0
34	TraesCS6B01G154400	chr5A	86.598	97	10	3	2094	2189	618262564	618262470	1.380000e-18	104.0
35	TraesCS6B01G154400	chr7A	95.652	46	1	1	384	429	209401816	209401772	3.900000e-09	73.1
36	TraesCS6B01G154400	chr7D	93.478	46	2	1	384	429	199477131	199477087	1.820000e-07	67.6
37	TraesCS6B01G154400	chr7D	91.111	45	4	0	382	426	183775238	183775282	8.450000e-06	62.1
38	TraesCS6B01G154400	chr3D	97.059	34	1	0	396	429	337302591	337302624	1.090000e-04	58.4

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	TraesCS6B01G154400	chr6B	157910545	157913369	2824	False	2355.000000	4054	100.000000	1	2825	2	chr6B.!!$F1	2824
1	TraesCS6B01G154400	chr6B	157778682	157780613	1931	True	1418.000000	2039	92.379000	99	2094	2	chr6B.!!$R4	1995
2	TraesCS6B01G154400	chr6B	156417276	156418364	1088	True	994.000000	994	83.197000	998	2094	1	chr6B.!!$R1	1096
3	TraesCS6B01G154400	chr6B	157026246	157027486	1240	True	545.000000	545	75.059000	850	2094	1	chr6B.!!$R2	1244
4	TraesCS6B01G154400	chr6A	99785763	99790142	4379	True	1531.800000	2972	96.469000	99	2094	2	chr6A.!!$R2	1995
5	TraesCS6B01G154400	chr6A	98241290	98242366	1076	True	989.000000	989	83.272000	1010	2094	1	chr6A.!!$R1	1084
6	TraesCS6B01G154400	chr6D	82963476	82965151	1675	True	2532.000000	2532	93.995000	422	2094	1	chr6D.!!$R4	1672
7	TraesCS6B01G154400	chr6D	81919611	81920686	1075	True	994.000000	994	83.394000	1008	2094	1	chr6D.!!$R2	1086
8	TraesCS6B01G154400	chr6D	81749016	81750104	1088	True	966.000000	966	82.727000	998	2094	1	chr6D.!!$R1	1096
9	TraesCS6B01G154400	chr6D	82219325	82220587	1262	True	549.000000	549	74.922000	831	2094	1	chr6D.!!$R3	1263
10	TraesCS6B01G154400	chr5D	372059181	372061234	2053	True	787.666667	1881	89.405333	6	2094	3	chr5D.!!$R1	2088
11	TraesCS6B01G154400	chr7B	423570263	423570771	508	True	342.500000	540	93.542500	2098	2825	2	chr7B.!!$R1	727
12	TraesCS6B01G154400	chr3B	539563695	539564203	508	False	285.000000	466	88.402500	2094	2822	2	chr3B.!!$F1	728
13	TraesCS6B01G154400	chr4B	436261315	436261816	501	False	274.000000	442	89.117500	2094	2822	2	chr4B.!!$F1	728

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
156	198	0.257039	AGATGGCAACCACAGATCCC	59.743	55.0	0.0	0.0	35.8	3.85	F
1039	3487	0.257328	TCCCACCAGTTCTTGCACAA	59.743	50.0	0.0	0.0	0.0	3.33	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1190	3640	0.041684	CCCCTCAAGGCCCTTCAAAT	59.958	55.0	0.0	0.0	0.0	2.32	R
1866	4319	0.251341	GGCAACTCCCCTGACATGTT	60.251	55.0	0.0	0.0	0.0	2.71	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
47	48	1.351350	GCTGGTTCCACCCTAAAGACT	59.649	52.381	0.00	0.00	37.50	3.24
58	59	4.020573	CACCCTAAAGACTATGTCCACACA	60.021	45.833	0.00	0.00	36.78	3.72
61	62	5.046591	CCCTAAAGACTATGTCCACACAAGA	60.047	44.000	0.00	0.00	35.64	3.02
63	64	7.106239	CCTAAAGACTATGTCCACACAAGAAT	58.894	38.462	0.00	0.00	35.64	2.40
75	76	3.436015	CACACAAGAATCAGAGCTTCAGG	59.564	47.826	0.00	0.00	0.00	3.86
151	193	1.808945	GAGTTCAGATGGCAACCACAG	59.191	52.381	0.00	0.00	35.80	3.66
156	198	0.257039	AGATGGCAACCACAGATCCC	59.743	55.000	0.00	0.00	35.80	3.85
187	2606	1.078567	GCAAGTGGAGCCAGGAGAG	60.079	63.158	0.00	0.00	0.00	3.20
191	2610	2.284921	TGGAGCCAGGAGAGTGGG	60.285	66.667	0.00	0.00	38.14	4.61
192	2611	3.086600	GGAGCCAGGAGAGTGGGG	61.087	72.222	0.00	0.00	38.14	4.96
211	2633	3.110358	GGGAAACAACAGCAAACGTAAC	58.890	45.455	0.00	0.00	0.00	2.50
233	2655	3.120889	CCATCAGACAATAATAGTGCGCG	60.121	47.826	0.00	0.00	0.00	6.86
254	2676	2.159382	AGTGGGCAATTAAACACCTCG	58.841	47.619	0.00	0.00	34.50	4.63
466	2889	3.853623	GCCTTCAGCAACTGTTGTC	57.146	52.632	20.57	13.18	42.97	3.18
518	2948	5.712152	AAACTGCTTCCTTTACTTGGATG	57.288	39.130	0.00	0.00	33.09	3.51
701	3137	4.518970	AGATATGTTTTGCACGGTCAGTTT	59.481	37.500	0.00	0.00	0.00	2.66
721	3157	4.615588	TTTCAGGAAAAATGGGCGATTT	57.384	36.364	1.26	1.26	35.65	2.17
829	3265	5.069781	TCTGATTTCGTTGACCCCAATTTTT	59.930	36.000	0.00	0.00	34.39	1.94
890	3326	5.943416	CCATTCATGTCTTACCCAACTACAA	59.057	40.000	0.00	0.00	0.00	2.41
946	3382	1.878948	GCACAAAAACCATGCAGCCAT	60.879	47.619	0.00	0.00	39.23	4.40
958	3394	1.275856	TGCAGCCATTCCATTTTCCAC	59.724	47.619	0.00	0.00	0.00	4.02
1000	3448	8.744568	AAAATTAATTTTCTTTGCCCTTGTGA	57.255	26.923	18.40	0.00	35.18	3.58
1003	3451	4.961438	ATTTTCTTTGCCCTTGTGATGT	57.039	36.364	0.00	0.00	0.00	3.06
1039	3487	0.257328	TCCCACCAGTTCTTGCACAA	59.743	50.000	0.00	0.00	0.00	3.33
1068	3517	2.539081	GGGGTCCCTCCTGCAGTTT	61.539	63.158	13.81	0.00	36.25	2.66
1190	3640	3.618263	GCAGTCACAGATGTCTCATTGGA	60.618	47.826	0.00	0.00	0.00	3.53
1352	3802	2.970974	GCTTCAACCGCCTCAGTGC	61.971	63.158	0.00	0.00	0.00	4.40
1357	3807	3.865929	AACCGCCTCAGTGCAGACG	62.866	63.158	0.00	0.00	0.00	4.18
1535	3988	2.936202	ACCGGATAATTTCTGCAGCAT	58.064	42.857	9.46	0.00	0.00	3.79
1822	4275	4.330250	CGGCAAGATTCCAGATTCCATAT	58.670	43.478	0.00	0.00	0.00	1.78
1823	4276	5.491070	CGGCAAGATTCCAGATTCCATATA	58.509	41.667	0.00	0.00	0.00	0.86
1864	4317	5.376625	AGAAGAGTTGCATTTGGACTACAA	58.623	37.500	0.00	0.00	37.28	2.41
1865	4318	5.239525	AGAAGAGTTGCATTTGGACTACAAC	59.760	40.000	0.00	0.00	39.19	3.32
1866	4319	4.460263	AGAGTTGCATTTGGACTACAACA	58.540	39.130	6.91	0.00	42.32	3.33
1896	4352	1.751927	GAGTTGCCATCAGCCCTGG	60.752	63.158	0.00	0.00	42.71	4.45
1907	4363	2.361230	GCCCTGGGTTACTGCACC	60.361	66.667	15.56	0.00	35.88	5.01
1979	4435	1.821088	AGGTCAACTTCTCCACCCTT	58.179	50.000	0.00	0.00	0.00	3.95
2055	4511	4.010349	AGAAAGTTTGTATACCTGCAGCC	58.990	43.478	8.66	0.00	0.00	4.85
2063	4519	2.563261	ATACCTGCAGCCATCTGATG	57.437	50.000	8.66	10.71	42.95	3.07
2190	4649	4.782019	AACACACACACACAGTTCAAAT	57.218	36.364	0.00	0.00	0.00	2.32
2609	5070	1.453379	GACGTCCCGATCCTGAGGA	60.453	63.158	2.43	2.43	35.55	3.71
2822	5283	1.398692	GGAAGTTGGAGTTGCACCAA	58.601	50.000	3.24	3.24	43.84	3.67

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
4	5	0.443869	CAATACAGTGCACGGACTGC	59.556	55.000	24.13	0.80	46.28	4.40
7	8	0.673644	AGGCAATACAGTGCACGGAC	60.674	55.000	24.13	6.69	46.81	4.79
8	9	0.673333	CAGGCAATACAGTGCACGGA	60.673	55.000	24.13	10.04	46.81	4.69
9	10	1.796151	CAGGCAATACAGTGCACGG	59.204	57.895	15.82	15.82	46.81	4.94
10	11	1.135315	GCAGGCAATACAGTGCACG	59.865	57.895	12.01	9.15	46.81	5.34
11	12	0.169672	CAGCAGGCAATACAGTGCAC	59.830	55.000	9.40	9.40	46.81	4.57
47	48	4.223700	AGCTCTGATTCTTGTGTGGACATA	59.776	41.667	0.00	0.00	30.13	2.29
58	59	2.909006	TGGTCCTGAAGCTCTGATTCTT	59.091	45.455	0.00	0.00	0.00	2.52
61	62	2.617532	GCTTGGTCCTGAAGCTCTGATT	60.618	50.000	6.68	0.00	42.21	2.57
63	64	0.322975	GCTTGGTCCTGAAGCTCTGA	59.677	55.000	6.68	0.00	42.21	3.27
75	76	5.048083	TGGTTGAATCATTAGTTGCTTGGTC	60.048	40.000	0.00	0.00	0.00	4.02
151	193	5.009010	CACTTGCACACTATTATTGGGGATC	59.991	44.000	0.00	0.00	0.00	3.36
156	198	4.201950	GCTCCACTTGCACACTATTATTGG	60.202	45.833	0.00	0.00	0.00	3.16
187	2606	1.801025	CGTTTGCTGTTGTTTCCCCAC	60.801	52.381	0.00	0.00	0.00	4.61
191	2610	3.110358	GGTTACGTTTGCTGTTGTTTCC	58.890	45.455	0.00	0.00	0.00	3.13
192	2611	3.760537	TGGTTACGTTTGCTGTTGTTTC	58.239	40.909	0.00	0.00	0.00	2.78
211	2633	3.120889	CGCGCACTATTATTGTCTGATGG	60.121	47.826	8.75	0.00	0.00	3.51
233	2655	2.161609	CGAGGTGTTTAATTGCCCACTC	59.838	50.000	0.00	0.00	0.00	3.51
243	2665	3.842007	TCTTTGACCCGAGGTGTTTAA	57.158	42.857	0.00	0.00	35.25	1.52
254	2676	4.257731	GTCTCTTCCATCTTCTTTGACCC	58.742	47.826	0.00	0.00	0.00	4.46
408	2830	3.822940	CAAGATAGTACTCCCTCCGTCT	58.177	50.000	0.00	0.00	0.00	4.18
518	2948	4.413495	TGCTTAACAGGAAAATACGTGC	57.587	40.909	0.00	0.00	0.00	5.34
577	3007	8.803397	ACCACCTTCACTAAATAAATCTTACC	57.197	34.615	0.00	0.00	0.00	2.85
701	3137	4.770010	AGTAAATCGCCCATTTTTCCTGAA	59.230	37.500	0.00	0.00	36.09	3.02
721	3157	5.279506	GCCTGCTATACTCTAATGGCAAGTA	60.280	44.000	0.00	0.00	41.97	2.24
829	3265	6.838612	TGAAAGAGAAATGAGGGGAAAGAAAA	59.161	34.615	0.00	0.00	0.00	2.29
946	3382	3.066064	CACTTCGTGTGTGGAAAATGGAA	59.934	43.478	3.79	0.00	41.53	3.53
1000	3448	2.172293	GAGAGGCCAAGGAGATCAACAT	59.828	50.000	5.01	0.00	0.00	2.71
1003	3451	1.207791	GGAGAGGCCAAGGAGATCAA	58.792	55.000	5.01	0.00	36.34	2.57
1039	3487	0.498685	AGGGACCCCTTCTCCTTCTT	59.501	55.000	7.00	0.00	45.70	2.52
1068	3517	1.235281	CCGACGACAGACCACTGAGA	61.235	60.000	0.00	0.00	46.03	3.27
1190	3640	0.041684	CCCCTCAAGGCCCTTCAAAT	59.958	55.000	0.00	0.00	0.00	2.32
1535	3988	5.048294	TCAACTACAGCTAACAATGACGAGA	60.048	40.000	0.00	0.00	0.00	4.04
1792	4245	0.171231	GGAATCTTGCCGCTGAAACC	59.829	55.000	0.00	0.00	0.00	3.27
1822	4275	3.032459	TCTAGTCTCTCGAGCTCACCTA	58.968	50.000	15.40	2.68	0.00	3.08
1823	4276	1.834896	TCTAGTCTCTCGAGCTCACCT	59.165	52.381	15.40	1.58	0.00	4.00
1864	4317	1.819305	GCAACTCCCCTGACATGTTGT	60.819	52.381	0.00	0.00	39.81	3.32
1865	4318	0.883833	GCAACTCCCCTGACATGTTG	59.116	55.000	0.00	0.00	40.38	3.33
1866	4319	0.251341	GGCAACTCCCCTGACATGTT	60.251	55.000	0.00	0.00	0.00	2.71
1896	4352	4.941263	TGTTATCAGATTGGTGCAGTAACC	59.059	41.667	0.00	0.00	40.94	2.85
1979	4435	5.273208	ACATCTAGAGTTTTCAGCCTAGGA	58.727	41.667	14.75	0.00	31.88	2.94
2055	4511	1.007734	GCCGCAATGCCATCAGATG	60.008	57.895	3.04	3.04	0.00	2.90
2063	4519	2.912624	GCCAGATAGCCGCAATGCC	61.913	63.158	0.00	0.00	0.00	4.40
2558	5019	1.153823	CACCGACCTTCGATCGCTT	60.154	57.895	11.09	0.00	43.74	4.68
2575	5036	0.608130	CGTCATCAACACCCTCCTCA	59.392	55.000	0.00	0.00	0.00	3.86
2708	5169	0.944386	CTTGGACACTTTGGACGGTG	59.056	55.000	0.00	0.00	39.13	4.94

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.