AutoCloner

Multiple sequence alignment - TraesCS4A01G107300

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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	TraesCS4A01G107300	chr4A	100.000	2775	0	0	1	2775	123248633	123245859	0.000000e+00	5125
1	TraesCS4A01G107300	chr4A	89.542	153	15	1	123	274	729010293	729010445	2.820000e-45	193
2	TraesCS4A01G107300	chr4B	89.642	1815	104	38	853	2613	424721382	424723166	0.000000e+00	2233
3	TraesCS4A01G107300	chr4B	98.721	860	10	1	1	860	462772355	462771497	0.000000e+00	1526
4	TraesCS4A01G107300	chr4B	93.491	169	10	1	2605	2773	424723727	424723894	1.650000e-62	250
5	TraesCS4A01G107300	chr4D	93.916	1315	59	12	853	2159	342698554	342699855	0.000000e+00	1965
6	TraesCS4A01G107300	chr4D	94.059	404	19	1	2323	2726	342715244	342715642	2.360000e-170	608
7	TraesCS4A01G107300	chr1A	98.713	855	7	2	1	855	474159686	474160536	0.000000e+00	1515
8	TraesCS4A01G107300	chr1A	84.958	831	81	14	56	857	77787608	77786793	0.000000e+00	802
9	TraesCS4A01G107300	chr1A	79.012	162	30	4	1393	1552	42603672	42603513	1.050000e-19	108
10	TraesCS4A01G107300	chr5B	96.163	860	29	4	1	858	455493763	455494620	0.000000e+00	1402
11	TraesCS4A01G107300	chr7A	94.676	864	32	7	1	862	23754378	23753527	0.000000e+00	1328
12	TraesCS4A01G107300	chr7D	90.244	738	66	4	123	858	18028456	18027723	0.000000e+00	959
13	TraesCS4A01G107300	chr3A	89.204	741	76	3	123	862	506523679	506522942	0.000000e+00	922
14	TraesCS4A01G107300	chr2D	86.781	817	72	10	58	857	456547191	456546394	0.000000e+00	878
15	TraesCS4A01G107300	chr2D	78.395	162	31	4	1393	1552	4497188	4497347	4.890000e-18	102
16	TraesCS4A01G107300	chr6B	86.223	646	66	5	232	857	277269062	277268420	0.000000e+00	678
17	TraesCS4A01G107300	chr6B	87.500	232	18	7	56	276	430552462	430552231	9.860000e-65	257
18	TraesCS4A01G107300	chr6B	88.945	199	13	5	56	245	277269275	277269077	1.280000e-58	237
19	TraesCS4A01G107300	chr2A	80.376	479	70	16	399	857	44439328	44439802	2.650000e-90	342
20	TraesCS4A01G107300	chr3D	82.011	378	49	15	499	860	120279044	120278670	1.250000e-78	303
21	TraesCS4A01G107300	chr1B	79.012	162	30	4	1393	1552	63091253	63091094	1.050000e-19	108

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	TraesCS4A01G107300	chr4A	123245859	123248633	2774	True	5125.0	5125	100.0000	1	2775	1	chr4A.!!$R1	2774
1	TraesCS4A01G107300	chr4B	462771497	462772355	858	True	1526.0	1526	98.7210	1	860	1	chr4B.!!$R1	859
2	TraesCS4A01G107300	chr4B	424721382	424723894	2512	False	1241.5	2233	91.5665	853	2773	2	chr4B.!!$F1	1920
3	TraesCS4A01G107300	chr4D	342698554	342699855	1301	False	1965.0	1965	93.9160	853	2159	1	chr4D.!!$F1	1306
4	TraesCS4A01G107300	chr1A	474159686	474160536	850	False	1515.0	1515	98.7130	1	855	1	chr1A.!!$F1	854
5	TraesCS4A01G107300	chr1A	77786793	77787608	815	True	802.0	802	84.9580	56	857	1	chr1A.!!$R2	801
6	TraesCS4A01G107300	chr5B	455493763	455494620	857	False	1402.0	1402	96.1630	1	858	1	chr5B.!!$F1	857
7	TraesCS4A01G107300	chr7A	23753527	23754378	851	True	1328.0	1328	94.6760	1	862	1	chr7A.!!$R1	861
8	TraesCS4A01G107300	chr7D	18027723	18028456	733	True	959.0	959	90.2440	123	858	1	chr7D.!!$R1	735
9	TraesCS4A01G107300	chr3A	506522942	506523679	737	True	922.0	922	89.2040	123	862	1	chr3A.!!$R1	739
10	TraesCS4A01G107300	chr2D	456546394	456547191	797	True	878.0	878	86.7810	58	857	1	chr2D.!!$R1	799
11	TraesCS4A01G107300	chr6B	277268420	277269275	855	True	457.5	678	87.5840	56	857	2	chr6B.!!$R2	801

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
991	1092	2.125753	CCGTGTGCTCTGCTCTCC	60.126	66.667	0.0	0.0	0.0	3.71	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2090	2240	0.249868	GGGAAAAACAGCAGCAACCC	60.25	55.0	0.0	0.0	0.0	4.11	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
507	603	5.348724	CGTCATTCAATATATACCGCAAGCT	59.651	40.000	0.00	0.00	0.00	3.74
895	994	6.327365	TGCTCCATCTCAACTTGGAAGATATA	59.673	38.462	0.00	0.00	41.36	0.86
896	995	7.016957	TGCTCCATCTCAACTTGGAAGATATAT	59.983	37.037	0.00	0.00	41.36	0.86
991	1092	2.125753	CCGTGTGCTCTGCTCTCC	60.126	66.667	0.00	0.00	0.00	3.71
1026	1127	2.125512	AGCAACGAGGCCACGATC	60.126	61.111	29.67	15.95	37.03	3.69
1296	1397	1.661463	TCATCAAGCTCCTCCAGGTT	58.339	50.000	0.00	0.00	44.02	3.50
1301	1402	1.482593	CAAGCTCCTCCAGGTTCGTAT	59.517	52.381	0.00	0.00	41.09	3.06
1315	1416	4.876107	AGGTTCGTATGGAGCACATTTTAG	59.124	41.667	0.00	0.00	41.03	1.85
1319	1420	6.176975	TCGTATGGAGCACATTTTAGTTTG	57.823	37.500	0.00	0.00	41.03	2.93
1323	1424	6.594788	ATGGAGCACATTTTAGTTTGACAT	57.405	33.333	0.00	0.00	35.97	3.06
1341	1442	3.907481	TACGTGACGTGCGCTGCAT	62.907	57.895	22.16	0.00	41.91	3.96
1367	1468	2.823593	TGCGTGCAAGTGCTGTGT	60.824	55.556	4.69	0.00	42.66	3.72
1561	1662	4.096003	GCGCAGGCCAACCTCCTA	62.096	66.667	5.01	0.00	46.34	2.94
1621	1722	1.868997	CGTCGAGTTTGCTGCCAAT	59.131	52.632	0.00	0.00	0.00	3.16
1633	1734	3.195698	GCCAATCACCGAGGCGAC	61.196	66.667	0.00	0.00	38.86	5.19
1721	1822	2.484065	GCCATGTACCAACCGCTATACA	60.484	50.000	0.00	0.00	32.38	2.29
1885	2023	3.569701	AGATGTTCAACGGCAATGACTTT	59.430	39.130	0.00	0.00	0.00	2.66
1892	2030	4.111916	CAACGGCAATGACTTTGTCTTTT	58.888	39.130	0.00	0.00	37.81	2.27
1899	2037	5.679638	GCAATGACTTTGTCTTTTGGTGAGT	60.680	40.000	3.32	0.00	37.65	3.41
1924	2062	7.439655	GTCACCTTGGATCTAAATATCAGTGAC	59.560	40.741	0.00	13.64	37.22	3.67
1935	2073	2.765250	ATCAGTGACGAAGCCGCGTT	62.765	55.000	4.92	0.00	45.72	4.84
1952	2090	1.542915	CGTTGAGTTCGGGTAAGGAGA	59.457	52.381	0.00	0.00	0.00	3.71
2016	2162	0.397941	ATATGAGGGGCGATGGTGTG	59.602	55.000	0.00	0.00	0.00	3.82
2026	2172	1.404181	GCGATGGTGTGAAGCTACAGA	60.404	52.381	0.00	0.00	0.00	3.41
2028	2174	3.525537	CGATGGTGTGAAGCTACAGAAT	58.474	45.455	0.00	0.00	0.00	2.40
2090	2240	1.207593	CTTCGTGCAAAGAAGGCCG	59.792	57.895	19.79	4.34	46.59	6.13
2093	2243	2.597510	GTGCAAAGAAGGCCGGGT	60.598	61.111	2.18	0.00	0.00	5.28
2109	2259	0.249868	GGGTTGCTGCTGTTTTTCCC	60.250	55.000	0.00	0.00	0.00	3.97
2122	2272	3.759618	TGTTTTTCCCGTCTTGTCAAGTT	59.240	39.130	12.30	0.00	0.00	2.66
2132	2282	6.814644	CCCGTCTTGTCAAGTTAATATGTACA	59.185	38.462	12.30	0.00	0.00	2.90
2192	2349	9.736023	ATTATCATGAAAAGAAAATTACTCGGC	57.264	29.630	0.00	0.00	0.00	5.54
2193	2350	5.949735	TCATGAAAAGAAAATTACTCGGCC	58.050	37.500	0.00	0.00	0.00	6.13
2197	2354	2.973694	AGAAAATTACTCGGCCGCTA	57.026	45.000	23.51	9.49	0.00	4.26
2201	2358	0.388294	AATTACTCGGCCGCTAGGTC	59.612	55.000	23.51	0.00	40.50	3.85
2233	2390	4.473196	ACAATAGTGGATGGTGTACATGGA	59.527	41.667	0.00	0.00	40.72	3.41
2234	2391	4.689612	ATAGTGGATGGTGTACATGGAC	57.310	45.455	0.00	0.00	40.72	4.02
2235	2392	2.265367	AGTGGATGGTGTACATGGACA	58.735	47.619	6.68	6.68	40.72	4.02
2252	2409	6.263842	ACATGGACACATTGTGGATATTGATC	59.736	38.462	20.33	6.50	37.94	2.92
2274	2431	2.804931	GCAACCGCCACGATTTGC	60.805	61.111	9.46	9.46	38.03	3.68
2283	2440	1.019278	CCACGATTTGCGCTGTACCT	61.019	55.000	9.73	0.00	46.04	3.08
2297	2454	2.363680	CTGTACCTGGCAGATACTCCTG	59.636	54.545	19.51	4.43	36.12	3.86
2298	2455	2.292257	TGTACCTGGCAGATACTCCTGT	60.292	50.000	19.51	7.23	36.57	4.00
2365	2522	8.746052	ATTCAAATCTCGTTCCCATATTGTTA	57.254	30.769	0.00	0.00	0.00	2.41
2422	2579	0.028770	ACGAAACGTTGACGACCGTA	59.971	50.000	26.43	0.00	43.02	4.02
2446	2603	0.885879	TGTGACGTATCGGCTGAGTT	59.114	50.000	0.00	0.00	35.04	3.01
2447	2604	2.086094	TGTGACGTATCGGCTGAGTTA	58.914	47.619	0.00	0.00	35.04	2.24
2448	2605	2.159476	TGTGACGTATCGGCTGAGTTAC	60.159	50.000	0.00	1.43	35.04	2.50
2449	2606	2.097142	GTGACGTATCGGCTGAGTTACT	59.903	50.000	0.00	0.00	35.04	2.24
2450	2607	2.096980	TGACGTATCGGCTGAGTTACTG	59.903	50.000	0.00	0.00	35.04	2.74
2461	2618	4.811557	GGCTGAGTTACTGTAATTAGCAGG	59.188	45.833	22.85	7.60	38.22	4.85
2463	2620	4.430007	TGAGTTACTGTAATTAGCAGGCG	58.570	43.478	3.23	0.00	38.22	5.52
2580	2737	2.571653	TGGTGCTGTTGGCTAGAAGTAT	59.428	45.455	0.00	0.00	42.39	2.12
2622	3348	1.461127	CGACTTGCAAGCTTGAGTACC	59.539	52.381	30.39	12.13	0.00	3.34
2624	3350	2.222027	ACTTGCAAGCTTGAGTACCAC	58.778	47.619	30.39	10.65	0.00	4.16
2635	3361	4.323562	GCTTGAGTACCACCTAACCTGATT	60.324	45.833	0.00	0.00	0.00	2.57
2654	3380	3.889196	TTACCGGATGCAAAATATCGC	57.111	42.857	9.46	0.00	0.00	4.58
2660	3386	1.601903	GATGCAAAATATCGCGGGTCA	59.398	47.619	6.13	0.00	0.00	4.02
2673	3399	2.805671	CGCGGGTCATCAAATTAGCATA	59.194	45.455	0.00	0.00	0.00	3.14
2700	3426	0.107831	TGTTCGGGCTAAACAGCACT	59.892	50.000	0.00	0.00	35.75	4.40
2701	3427	0.796927	GTTCGGGCTAAACAGCACTC	59.203	55.000	0.00	0.00	35.75	3.51
2766	3492	8.158169	ACAGGAAGTAATATGTAACATGCATG	57.842	34.615	25.09	25.09	0.00	4.06

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
478	574	6.972901	TGCGGTATATATTGAATGACGAGATC	59.027	38.462	0.00	0.00	0.00	2.75
507	603	8.450964	GGAAATTTCTCATCGAAAGTGACATAA	58.549	33.333	17.42	0.00	44.29	1.90
895	994	3.794737	ATCGCTGTGATCTGGCAAT	57.205	47.368	0.00	0.00	28.49	3.56
921	1020	0.388649	CGAGGAGAGTGAAACACCGG	60.389	60.000	0.00	0.00	41.43	5.28
922	1021	1.009389	GCGAGGAGAGTGAAACACCG	61.009	60.000	0.00	0.00	41.43	4.94
923	1022	0.318762	AGCGAGGAGAGTGAAACACC	59.681	55.000	0.00	0.00	41.43	4.16
924	1023	1.423395	CAGCGAGGAGAGTGAAACAC	58.577	55.000	0.00	0.00	41.43	3.32
991	1092	2.296190	TGCTGTAGTCCATGGCGTATAG	59.704	50.000	6.96	9.43	0.00	1.31
1229	1330	4.966787	TGGTGAACTTGGCGGGCC	62.967	66.667	1.86	1.86	0.00	5.80
1296	1397	5.935206	TCAAACTAAAATGTGCTCCATACGA	59.065	36.000	0.00	0.00	31.97	3.43
1301	1402	6.348132	CGTATGTCAAACTAAAATGTGCTCCA	60.348	38.462	0.00	0.00	0.00	3.86
1315	1416	1.459624	CGCACGTCACGTATGTCAAAC	60.460	52.381	0.41	0.00	38.32	2.93
1319	1420	1.800315	AGCGCACGTCACGTATGTC	60.800	57.895	11.47	0.00	38.32	3.06
1323	1424	2.530465	TATGCAGCGCACGTCACGTA	62.530	55.000	11.47	0.00	43.04	3.57
1513	1614	1.302033	CACCTTGAGCTCGTTGGCT	60.302	57.895	9.64	0.63	46.11	4.75
1553	1654	2.237392	GTGTCTGGATGCTTAGGAGGTT	59.763	50.000	0.00	0.00	0.00	3.50
1561	1662	0.952497	CGTGCTGTGTCTGGATGCTT	60.952	55.000	0.00	0.00	0.00	3.91
1899	2037	7.500992	GTCACTGATATTTAGATCCAAGGTGA	58.499	38.462	0.00	0.00	0.00	4.02
1924	2062	2.470286	GAACTCAACGCGGCTTCG	59.530	61.111	12.47	0.00	0.00	3.79
1935	2073	3.095912	TCATCTCCTTACCCGAACTCA	57.904	47.619	0.00	0.00	0.00	3.41
1971	2109	5.187381	CCTCTGGCATCATCATAGTAGACAT	59.813	44.000	0.00	0.00	0.00	3.06
1991	2136	0.546267	ATCGCCCCTCATATGCCTCT	60.546	55.000	0.00	0.00	0.00	3.69
1999	2144	1.561769	TTCACACCATCGCCCCTCAT	61.562	55.000	0.00	0.00	0.00	2.90
2003	2148	2.252072	TAGCTTCACACCATCGCCCC	62.252	60.000	0.00	0.00	0.00	5.80
2016	2162	7.277981	TCAAGACCGAATAAATTCTGTAGCTTC	59.722	37.037	0.00	0.00	34.95	3.86
2056	2206	3.070018	ACGAAGAGAAACATCAGCCAAG	58.930	45.455	0.00	0.00	0.00	3.61
2057	2207	2.807967	CACGAAGAGAAACATCAGCCAA	59.192	45.455	0.00	0.00	0.00	4.52
2058	2208	2.416747	CACGAAGAGAAACATCAGCCA	58.583	47.619	0.00	0.00	0.00	4.75
2089	2239	0.597377	GGAAAAACAGCAGCAACCCG	60.597	55.000	0.00	0.00	0.00	5.28
2090	2240	0.249868	GGGAAAAACAGCAGCAACCC	60.250	55.000	0.00	0.00	0.00	4.11
2093	2243	0.383949	GACGGGAAAAACAGCAGCAA	59.616	50.000	0.00	0.00	0.00	3.91
2109	2259	9.083080	TCATGTACATATTAACTTGACAAGACG	57.917	33.333	21.95	0.00	0.00	4.18
2170	2327	5.391523	CGGCCGAGTAATTTTCTTTTCATGA	60.392	40.000	24.07	0.00	0.00	3.07
2171	2328	4.793216	CGGCCGAGTAATTTTCTTTTCATG	59.207	41.667	24.07	0.00	0.00	3.07
2179	2336	1.865340	CCTAGCGGCCGAGTAATTTTC	59.135	52.381	33.48	7.54	0.00	2.29
2180	2337	1.208776	ACCTAGCGGCCGAGTAATTTT	59.791	47.619	33.48	5.22	0.00	1.82
2182	2339	0.388294	GACCTAGCGGCCGAGTAATT	59.612	55.000	33.48	7.41	0.00	1.40
2183	2340	0.754217	TGACCTAGCGGCCGAGTAAT	60.754	55.000	33.48	10.85	0.00	1.89
2185	2342	2.117156	GTGACCTAGCGGCCGAGTA	61.117	63.158	33.48	18.46	0.00	2.59
2186	2343	3.450115	GTGACCTAGCGGCCGAGT	61.450	66.667	33.48	19.97	0.00	4.18
2187	2344	2.501223	TTTGTGACCTAGCGGCCGAG	62.501	60.000	33.48	18.99	0.00	4.63
2189	2346	2.047655	TTTGTGACCTAGCGGCCG	60.048	61.111	24.05	24.05	0.00	6.13
2192	2349	1.270094	TGTGAGTTTGTGACCTAGCGG	60.270	52.381	0.00	0.00	0.00	5.52
2193	2350	2.148916	TGTGAGTTTGTGACCTAGCG	57.851	50.000	0.00	0.00	0.00	4.26
2197	2354	4.102524	TCCACTATTGTGAGTTTGTGACCT	59.897	41.667	8.98	0.00	46.55	3.85
2201	2358	4.761739	ACCATCCACTATTGTGAGTTTGTG	59.238	41.667	8.98	0.00	46.55	3.33
2242	2399	4.662147	GCGGTTGCAGAGGATCAATATCC	61.662	52.174	0.00	0.00	45.84	2.59
2243	2400	2.481952	GCGGTTGCAGAGGATCAATATC	59.518	50.000	0.00	0.00	42.15	1.63
2252	2409	3.958147	ATCGTGGCGGTTGCAGAGG	62.958	63.158	0.00	0.00	45.35	3.69
2274	2431	0.747255	AGTATCTGCCAGGTACAGCG	59.253	55.000	17.06	0.00	35.04	5.18
2283	2440	1.476891	GACGAACAGGAGTATCTGCCA	59.523	52.381	0.00	0.00	38.26	4.92
2297	2454	2.240493	ATCGATCCCATTGGACGAAC	57.760	50.000	17.87	2.64	45.58	3.95
2298	2455	3.576550	TCATATCGATCCCATTGGACGAA	59.423	43.478	17.87	11.03	45.58	3.85
2337	2494	7.339212	ACAATATGGGAACGAGATTTGAATTCA	59.661	33.333	3.38	3.38	0.00	2.57
2365	2522	9.180678	GAATTATGTTCATCGCGGATTTTAAAT	57.819	29.630	6.13	0.00	0.00	1.40
2446	2603	4.178540	GTGAACGCCTGCTAATTACAGTA	58.821	43.478	11.58	0.00	33.09	2.74
2447	2604	3.000727	GTGAACGCCTGCTAATTACAGT	58.999	45.455	11.58	0.00	33.09	3.55
2448	2605	2.029244	CGTGAACGCCTGCTAATTACAG	59.971	50.000	7.63	7.63	34.82	2.74
2449	2606	1.996898	CGTGAACGCCTGCTAATTACA	59.003	47.619	0.00	0.00	0.00	2.41
2450	2607	2.264813	TCGTGAACGCCTGCTAATTAC	58.735	47.619	0.00	0.00	39.60	1.89
2461	2618	4.323751	CAATAGCTAAAACTCGTGAACGC	58.676	43.478	0.00	0.00	39.60	4.84
2463	2620	4.153475	TGGCAATAGCTAAAACTCGTGAAC	59.847	41.667	0.00	0.00	41.70	3.18
2548	2705	3.746492	CCAACAGCACCACTAGTAGAAAC	59.254	47.826	3.59	0.00	0.00	2.78
2551	2708	1.275291	GCCAACAGCACCACTAGTAGA	59.725	52.381	3.59	0.00	42.97	2.59
2563	2720	3.438297	TCGATACTTCTAGCCAACAGC	57.562	47.619	0.00	0.00	44.25	4.40
2580	2737	1.229428	ACTGAACCGTACGAGTTCGA	58.771	50.000	28.33	21.07	45.33	3.71
2622	3348	3.728845	CATCCGGTAATCAGGTTAGGTG	58.271	50.000	0.00	0.00	0.00	4.00
2624	3350	2.104111	TGCATCCGGTAATCAGGTTAGG	59.896	50.000	0.00	0.00	0.00	2.69
2635	3361	1.795872	CGCGATATTTTGCATCCGGTA	59.204	47.619	0.00	0.00	32.00	4.02
2654	3380	7.201732	GGGATTATATGCTAATTTGATGACCCG	60.202	40.741	0.00	0.00	0.00	5.28
2660	3386	8.950210	CGAACAGGGATTATATGCTAATTTGAT	58.050	33.333	0.00	0.00	0.00	2.57

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.