AutoCloner

Multiple sequence alignment - TraesCS4B01G061700

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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	TraesCS4B01G061700	chr4B	100.000	3257	0	0	1	3257	53074711	53071455	0.000000e+00	6015
1	TraesCS4B01G061700	chr4B	98.487	2314	27	7	1	2309	52864653	52866963	0.000000e+00	4072
2	TraesCS4B01G061700	chr4B	96.137	466	12	3	2391	2851	52866962	52867426	0.000000e+00	756
3	TraesCS4B01G061700	chr4B	96.437	449	16	0	2809	3257	52867426	52867874	0.000000e+00	741
4	TraesCS4B01G061700	chr3B	80.083	969	169	14	1260	2210	10291176	10290214	0.000000e+00	699
5	TraesCS4B01G061700	chr3B	96.689	151	5	0	1	151	273555622	273555772	5.390000e-63	252
6	TraesCS4B01G061700	chr3A	80.000	520	76	17	1703	2207	12404949	12405455	3.090000e-95	359
7	TraesCS4B01G061700	chr3A	95.364	151	7	0	1	151	1586201	1586351	1.170000e-59	241
8	TraesCS4B01G061700	chr7B	96.711	152	5	0	1	152	441433229	441433078	1.500000e-63	254
9	TraesCS4B01G061700	chr7B	93.617	94	5	1	2304	2396	649096756	649096663	4.380000e-29	139
10	TraesCS4B01G061700	chr7A	96.711	152	5	0	1	152	149500308	149500157	1.500000e-63	254
11	TraesCS4B01G061700	chr7A	91.837	98	7	1	2300	2397	210000867	210000963	5.670000e-28	135
12	TraesCS4B01G061700	chr6A	96.026	151	6	0	1	151	428844592	428844742	2.510000e-61	246
13	TraesCS4B01G061700	chr5A	96.026	151	6	0	1	151	7540787	7540937	2.510000e-61	246
14	TraesCS4B01G061700	chr5A	94.565	92	4	1	2307	2397	398722211	398722120	1.220000e-29	141
15	TraesCS4B01G061700	chr5A	91.837	98	7	1	2305	2402	598879645	598879741	5.670000e-28	135
16	TraesCS4B01G061700	chr2A	95.364	151	7	0	1	151	330489417	330489567	1.170000e-59	241
17	TraesCS4B01G061700	chr2A	94.382	89	4	1	2317	2405	755994915	755994828	5.670000e-28	135
18	TraesCS4B01G061700	chr1A	95.364	151	7	0	1	151	465688898	465689048	1.170000e-59	241
19	TraesCS4B01G061700	chr5B	81.466	232	30	10	2513	2739	317297199	317297422	9.290000e-41	178
20	TraesCS4B01G061700	chr6D	95.556	90	4	0	2308	2397	34809007	34808918	9.420000e-31	145
21	TraesCS4B01G061700	chr3D	94.681	94	3	2	2308	2400	68251739	68251647	9.420000e-31	145
22	TraesCS4B01G061700	chr3D	87.912	91	7	3	1262	1351	8513486	8513399	1.600000e-18	104
23	TraesCS4B01G061700	chr5D	95.556	90	3	1	2307	2396	547542611	547542523	3.390000e-30	143
24	TraesCS4B01G061700	chr7D	96.471	85	3	0	2308	2392	621487678	621487594	1.220000e-29	141

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	TraesCS4B01G061700	chr4B	53071455	53074711	3256	True	6015.000000	6015	100.000000	1	3257	1	chr4B.!!$R1	3256
1	TraesCS4B01G061700	chr4B	52864653	52867874	3221	False	1856.333333	4072	97.020333	1	3257	3	chr4B.!!$F1	3256
2	TraesCS4B01G061700	chr3B	10290214	10291176	962	True	699.000000	699	80.083000	1260	2210	1	chr3B.!!$R1	950
3	TraesCS4B01G061700	chr3A	12404949	12405455	506	False	359.000000	359	80.000000	1703	2207	1	chr3A.!!$F2	504

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
50	51	0.107361	GTATAGTTTGGGCTGGGCGT	60.107	55.0	0.00	0.00	0.00	5.68	F
212	213	0.173708	CTTTCTACGCCGCCTTCTCT	59.826	55.0	0.00	0.00	0.00	3.10	F
770	772	0.442699	GCAGTCGGATCCGTTTTCAC	59.557	55.0	32.15	22.36	40.74	3.18	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Hairpin	End Stability	Orientation
1430	1433	1.821753	CAAACACCTTGGTGTTGGTCA	59.178	47.619	31.10	45.64	4.02	R
1932	1941	2.549926	TGAATCCATTCATGACCGTCG	58.450	47.619	0.00	41.51	5.12	R
2391	2412	0.034574	TGGCCTGCGGTTACAATGAT	60.035	50.000	3.32	0.00	2.45	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
50	51	0.107361	GTATAGTTTGGGCTGGGCGT	60.107	55.000	0.00	0.00	0.00	5.68
98	99	5.667539	TGGTTTGGTTTCTGAAATGTCAA	57.332	34.783	6.06	8.75	31.88	3.18
126	127	3.020984	GGTTCAGTTCAGGTTTGGTTCA	58.979	45.455	0.00	0.00	0.00	3.18
151	152	2.026262	GCCCACCCACTCTCAGATTTAA	60.026	50.000	0.00	0.00	0.00	1.52
152	153	3.878778	CCCACCCACTCTCAGATTTAAG	58.121	50.000	0.00	0.00	0.00	1.85
158	159	6.098982	CACCCACTCTCAGATTTAAGTCCTAT	59.901	42.308	0.00	0.00	0.00	2.57
212	213	0.173708	CTTTCTACGCCGCCTTCTCT	59.826	55.000	0.00	0.00	0.00	3.10
310	311	0.878961	CCTACGCCACCGCCTTATTC	60.879	60.000	0.00	0.00	38.22	1.75
403	404	2.871022	CTGTGATACATGGAGAGCAAGC	59.129	50.000	0.00	0.00	0.00	4.01
408	409	1.822613	CATGGAGAGCAAGCGCCAT	60.823	57.895	2.29	10.04	41.61	4.40
563	564	2.850130	TGGCCTTGTACGGTGGGT	60.850	61.111	3.32	0.00	0.00	4.51
770	772	0.442699	GCAGTCGGATCCGTTTTCAC	59.557	55.000	32.15	22.36	40.74	3.18
805	807	2.124983	CTGCCTGGTGTCCGGATG	60.125	66.667	7.81	0.00	29.82	3.51
806	808	3.687321	CTGCCTGGTGTCCGGATGG	62.687	68.421	7.81	6.73	29.82	3.51
807	809	4.489771	GCCTGGTGTCCGGATGGG	62.490	72.222	7.81	7.09	35.24	4.00
928	931	5.895216	ATATATATGCACGCACATCGATG	57.105	39.130	23.68	23.68	41.67	3.84
1430	1433	1.889530	GACGGGCTTGTAGTGCTCCT	61.890	60.000	0.00	0.00	0.00	3.69
1847	1856	1.377725	AGTCATGCAAAGGGGAGCG	60.378	57.895	0.00	0.00	0.00	5.03
1932	1941	2.609427	TATGGATGCTGCACTCTGTC	57.391	50.000	3.57	0.00	0.00	3.51
2012	2027	6.171213	ACAAAACTTTATCGGTCCTTCCTAG	58.829	40.000	0.00	0.00	0.00	3.02
2147	2162	4.044065	TGGGTCCTTTGATTATGTTGGTCT	59.956	41.667	0.00	0.00	0.00	3.85
2153	2168	7.012421	GTCCTTTGATTATGTTGGTCTGGATAC	59.988	40.741	0.00	0.00	0.00	2.24
2313	2334	7.797038	TCAGTTTAGTTTGTCTTTTACTCCC	57.203	36.000	0.00	0.00	0.00	4.30
2314	2335	7.340256	TCAGTTTAGTTTGTCTTTTACTCCCA	58.660	34.615	0.00	0.00	0.00	4.37
2315	2336	7.830201	TCAGTTTAGTTTGTCTTTTACTCCCAA	59.170	33.333	0.00	0.00	0.00	4.12
2316	2337	8.630037	CAGTTTAGTTTGTCTTTTACTCCCAAT	58.370	33.333	0.00	0.00	0.00	3.16
2317	2338	8.630037	AGTTTAGTTTGTCTTTTACTCCCAATG	58.370	33.333	0.00	0.00	0.00	2.82
2318	2339	8.410912	GTTTAGTTTGTCTTTTACTCCCAATGT	58.589	33.333	0.00	0.00	0.00	2.71
2319	2340	9.629878	TTTAGTTTGTCTTTTACTCCCAATGTA	57.370	29.630	0.00	0.00	0.00	2.29
2320	2341	9.629878	TTAGTTTGTCTTTTACTCCCAATGTAA	57.370	29.630	0.00	0.00	0.00	2.41
2321	2342	8.528044	AGTTTGTCTTTTACTCCCAATGTAAA	57.472	30.769	0.00	0.00	37.88	2.01
2322	2343	8.410912	AGTTTGTCTTTTACTCCCAATGTAAAC	58.589	33.333	0.00	0.00	38.91	2.01
2323	2344	8.410912	GTTTGTCTTTTACTCCCAATGTAAACT	58.589	33.333	0.00	0.00	38.91	2.66
2324	2345	9.629878	TTTGTCTTTTACTCCCAATGTAAACTA	57.370	29.630	0.00	0.00	38.91	2.24
2325	2346	9.629878	TTGTCTTTTACTCCCAATGTAAACTAA	57.370	29.630	0.00	0.00	38.91	2.24
2326	2347	9.802039	TGTCTTTTACTCCCAATGTAAACTAAT	57.198	29.630	0.00	0.00	38.91	1.73
2386	2407	9.490379	AAATGCTCTTATATTAGTTTACGGAGG	57.510	33.333	0.00	0.00	0.00	4.30
2387	2408	6.989659	TGCTCTTATATTAGTTTACGGAGGG	58.010	40.000	0.00	0.00	0.00	4.30
2388	2409	6.779049	TGCTCTTATATTAGTTTACGGAGGGA	59.221	38.462	0.00	0.00	0.00	4.20
2389	2410	7.039923	TGCTCTTATATTAGTTTACGGAGGGAG	60.040	40.741	0.00	0.00	0.00	4.30
2390	2411	7.039853	GCTCTTATATTAGTTTACGGAGGGAGT	60.040	40.741	0.00	0.00	0.00	3.85
2391	2412	9.512588	CTCTTATATTAGTTTACGGAGGGAGTA	57.487	37.037	0.00	0.00	0.00	2.59
2537	2558	5.950544	ATTAGGCCCCTTTTATTTTGGTC	57.049	39.130	0.00	0.00	0.00	4.02
2572	2593	9.101971	GACCAAAAATTTTAATCAACGAAATGC	57.898	29.630	3.34	0.00	0.00	3.56
2589	2610	6.593770	ACGAAATGCAAACTATATGTCACAGA	59.406	34.615	0.00	0.00	0.00	3.41
2753	2776	7.144000	CGGAGGTAGTAGCGTATAATCTTTTT	58.856	38.462	0.00	0.00	0.00	1.94
2779	2802	6.823531	TGTTATAGGAAACGTTTTCATGACG	58.176	36.000	21.14	0.00	45.46	4.35
2783	2806	2.546789	GGAAACGTTTTCATGACGGACT	59.453	45.455	15.89	0.00	44.34	3.85
2800	2823	1.302431	CTGGTTGGTCACATGCGGA	60.302	57.895	0.00	0.00	0.00	5.54
2853	2921	7.681939	TTTTATTTATCGCTCAAAGTCTGGT	57.318	32.000	0.00	0.00	0.00	4.00
2880	2948	7.872483	CCAAAATACAAAGGAGCACAATAAACT	59.128	33.333	0.00	0.00	0.00	2.66
2919	2987	7.730364	AGCATATAGTCTTTTTCGTTATGGG	57.270	36.000	0.00	0.00	0.00	4.00
2948	3016	2.359107	ACAGGCCAGTCACATGCG	60.359	61.111	5.01	0.00	0.00	4.73
3014	3082	7.504924	TTTTTATCGTCTTCTTCCACAACAT	57.495	32.000	0.00	0.00	0.00	2.71
3031	3099	7.071196	TCCACAACATATCTTAGCCTTATCTGT	59.929	37.037	0.00	0.00	0.00	3.41
3070	3138	2.124695	GGTCCGTCATGGCTTCCC	60.125	66.667	0.00	0.00	37.80	3.97
3081	3149	4.847444	GCTTCCCCTGGCGAGCTC	62.847	72.222	2.73	2.73	31.93	4.09
3153	3221	1.411787	CGACCTCTTCCTCCCACCTAT	60.412	57.143	0.00	0.00	0.00	2.57
3162	3230	5.131142	TCTTCCTCCCACCTATCTCAAATTC	59.869	44.000	0.00	0.00	0.00	2.17
3184	3252	1.966451	GTTGTTGTCCCCGCTCCTG	60.966	63.158	0.00	0.00	0.00	3.86
3199	3267	2.429930	CTGACAACCAAGGGCGGA	59.570	61.111	0.00	0.00	0.00	5.54

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
50	51	2.208132	ACCCACGTAATTGGCATTGA	57.792	45.000	0.00	0.00	35.00	2.57
98	99	0.179056	CCTGAACTGAACCCACGTGT	60.179	55.000	15.65	0.00	0.00	4.49
126	127	1.770110	TGAGAGTGGGTGGGCAACT	60.770	57.895	0.00	0.00	0.00	3.16
177	178	2.314852	AGAAAGGGGTTGGAATTAGGGG	59.685	50.000	0.00	0.00	0.00	4.79
178	179	3.757947	AGAAAGGGGTTGGAATTAGGG	57.242	47.619	0.00	0.00	0.00	3.53
260	261	3.825160	AAGCGTTGGCAGAAGGCGA	62.825	57.895	6.71	0.00	46.16	5.54
408	409	6.259893	AGAAAGCTATGGCCAGATCTAGATA	58.740	40.000	13.05	0.00	39.73	1.98
563	564	6.920817	ACACGAAGTAACTTACATCATCAGA	58.079	36.000	1.79	0.00	41.61	3.27
701	703	0.391793	GCCAGCGGAAAGAGTAGCTT	60.392	55.000	0.00	0.00	37.94	3.74
770	772	3.729526	CAGGTAATCTGCTGTTTGACG	57.270	47.619	0.00	0.00	36.60	4.35
805	807	2.260743	GGTCGACAACTCGGACCC	59.739	66.667	18.91	0.00	40.58	4.46
806	808	2.126580	CGGTCGACAACTCGGACC	60.127	66.667	18.91	0.00	40.58	4.46
807	809	2.804090	GCGGTCGACAACTCGGAC	60.804	66.667	18.91	0.00	40.58	4.79
928	931	7.502895	TCTGGGTGAGAAACTATGTCTATAGAC	59.497	40.741	23.53	23.53	44.97	2.59
1290	1293	4.149598	GGATGTAGTTGGAAAAGGTGGTT	58.850	43.478	0.00	0.00	0.00	3.67
1430	1433	1.821753	CAAACACCTTGGTGTTGGTCA	59.178	47.619	31.10	0.00	45.64	4.02
1932	1941	2.549926	TGAATCCATTCATGACCGTCG	58.450	47.619	0.00	0.00	41.51	5.12
2147	2162	4.405680	ACATGTCGAAGATGAAGGTATCCA	59.594	41.667	11.65	0.00	40.67	3.41
2153	2168	5.611796	TGAAAACATGTCGAAGATGAAGG	57.388	39.130	11.65	0.00	40.67	3.46
2236	2254	8.473358	TTTCATCATCCATCTAATGCTTCATT	57.527	30.769	0.00	0.00	37.80	2.57
2360	2381	9.490379	CCTCCGTAAACTAATATAAGAGCATTT	57.510	33.333	0.00	0.00	0.00	2.32
2361	2382	8.095169	CCCTCCGTAAACTAATATAAGAGCATT	58.905	37.037	0.00	0.00	0.00	3.56
2362	2383	7.453752	TCCCTCCGTAAACTAATATAAGAGCAT	59.546	37.037	0.00	0.00	0.00	3.79
2363	2384	6.779049	TCCCTCCGTAAACTAATATAAGAGCA	59.221	38.462	0.00	0.00	0.00	4.26
2364	2385	7.039853	ACTCCCTCCGTAAACTAATATAAGAGC	60.040	40.741	0.00	0.00	0.00	4.09
2365	2386	8.406730	ACTCCCTCCGTAAACTAATATAAGAG	57.593	38.462	0.00	0.00	0.00	2.85
2368	2389	9.812347	TGATACTCCCTCCGTAAACTAATATAA	57.188	33.333	0.00	0.00	0.00	0.98
2369	2390	9.986157	ATGATACTCCCTCCGTAAACTAATATA	57.014	33.333	0.00	0.00	0.00	0.86
2370	2391	8.896722	ATGATACTCCCTCCGTAAACTAATAT	57.103	34.615	0.00	0.00	0.00	1.28
2371	2392	8.582437	CAATGATACTCCCTCCGTAAACTAATA	58.418	37.037	0.00	0.00	0.00	0.98
2372	2393	7.070821	ACAATGATACTCCCTCCGTAAACTAAT	59.929	37.037	0.00	0.00	0.00	1.73
2373	2394	6.381994	ACAATGATACTCCCTCCGTAAACTAA	59.618	38.462	0.00	0.00	0.00	2.24
2374	2395	5.895534	ACAATGATACTCCCTCCGTAAACTA	59.104	40.000	0.00	0.00	0.00	2.24
2375	2396	4.715297	ACAATGATACTCCCTCCGTAAACT	59.285	41.667	0.00	0.00	0.00	2.66
2376	2397	5.019785	ACAATGATACTCCCTCCGTAAAC	57.980	43.478	0.00	0.00	0.00	2.01
2377	2398	6.407299	GGTTACAATGATACTCCCTCCGTAAA	60.407	42.308	0.00	0.00	0.00	2.01
2378	2399	5.069516	GGTTACAATGATACTCCCTCCGTAA	59.930	44.000	0.00	0.00	0.00	3.18
2379	2400	4.586001	GGTTACAATGATACTCCCTCCGTA	59.414	45.833	0.00	0.00	0.00	4.02
2380	2401	3.387050	GGTTACAATGATACTCCCTCCGT	59.613	47.826	0.00	0.00	0.00	4.69
2381	2402	3.552273	CGGTTACAATGATACTCCCTCCG	60.552	52.174	0.00	0.00	0.00	4.63
2382	2403	3.802675	GCGGTTACAATGATACTCCCTCC	60.803	52.174	0.00	0.00	0.00	4.30
2383	2404	3.181469	TGCGGTTACAATGATACTCCCTC	60.181	47.826	0.00	0.00	0.00	4.30
2384	2405	2.769663	TGCGGTTACAATGATACTCCCT	59.230	45.455	0.00	0.00	0.00	4.20
2385	2406	3.131396	CTGCGGTTACAATGATACTCCC	58.869	50.000	0.00	0.00	0.00	4.30
2386	2407	3.131396	CCTGCGGTTACAATGATACTCC	58.869	50.000	0.00	0.00	0.00	3.85
2387	2408	2.544267	GCCTGCGGTTACAATGATACTC	59.456	50.000	0.00	0.00	0.00	2.59
2388	2409	2.561569	GCCTGCGGTTACAATGATACT	58.438	47.619	0.00	0.00	0.00	2.12
2389	2410	1.602377	GGCCTGCGGTTACAATGATAC	59.398	52.381	0.00	0.00	0.00	2.24
2390	2411	1.210722	TGGCCTGCGGTTACAATGATA	59.789	47.619	3.32	0.00	0.00	2.15
2391	2412	0.034574	TGGCCTGCGGTTACAATGAT	60.035	50.000	3.32	0.00	0.00	2.45
2561	2582	7.095017	TGTGACATATAGTTTGCATTTCGTTGA	60.095	33.333	0.00	0.00	0.00	3.18
2753	2776	7.799447	CGTCATGAAAACGTTTCCTATAACAAA	59.201	33.333	15.01	0.00	35.47	2.83
2754	2777	7.292292	CGTCATGAAAACGTTTCCTATAACAA	58.708	34.615	15.01	0.00	35.47	2.83
2761	2784	2.546789	GTCCGTCATGAAAACGTTTCCT	59.453	45.455	15.01	0.00	38.44	3.36
2779	2802	1.577328	CGCATGTGACCAACCAGTCC	61.577	60.000	0.00	0.00	35.83	3.85
2783	2806	1.599518	GTCCGCATGTGACCAACCA	60.600	57.895	8.11	0.00	0.00	3.67
2800	2823	0.944386	ATCGAAGCAAAACGCACAGT	59.056	45.000	0.00	0.00	46.13	3.55
2853	2921	7.531857	TTATTGTGCTCCTTTGTATTTTGGA	57.468	32.000	0.00	0.00	0.00	3.53
2871	2939	1.897802	ACCTCCGTCCGAGTTTATTGT	59.102	47.619	0.00	0.00	36.82	2.71
2880	2948	0.182061	ATGCTACTACCTCCGTCCGA	59.818	55.000	0.00	0.00	0.00	4.55
2919	2987	1.161563	TGGCCTGTCCGTCGTTTTTC	61.162	55.000	3.32	0.00	37.80	2.29
2957	3025	1.194547	TCAGCACGATCAAAGCGAAAC	59.805	47.619	0.00	0.00	0.00	2.78
3014	3082	5.473273	TGGGGAACAGATAAGGCTAAGATA	58.527	41.667	0.00	0.00	0.00	1.98
3031	3099	1.826720	GCAGCAAGAAATCATGGGGAA	59.173	47.619	0.00	0.00	0.00	3.97
3133	3201	0.033405	TAGGTGGGAGGAAGAGGTCG	60.033	60.000	0.00	0.00	0.00	4.79
3153	3221	4.280677	GGGACAACAACATGGAATTTGAGA	59.719	41.667	0.00	0.00	0.00	3.27
3162	3230	1.586154	GAGCGGGGACAACAACATGG	61.586	60.000	0.00	0.00	0.00	3.66
3184	3252	1.749258	GGATCCGCCCTTGGTTGTC	60.749	63.158	0.00	0.00	0.00	3.18
3199	3267	5.548056	CCTATACCAATGACCTTAGGTGGAT	59.452	44.000	9.39	0.00	35.25	3.41

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.