AutoCloner

Multiple sequence alignment - TraesCS5A01G230800

Loading Multiple Alignment...

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	TraesCS5A01G230800	chr5A	100.000	2388	0	0	1	2388	445673071	445670684	0.000000e+00	4410
1	TraesCS5A01G230800	chr5A	90.969	2115	142	18	270	2349	445768548	445766448	0.000000e+00	2802
2	TraesCS5A01G230800	chr5A	90.801	2098	148	11	271	2344	446024914	446022838	0.000000e+00	2763
3	TraesCS5A01G230800	chr5A	90.567	2099	161	13	269	2344	446039962	446037878	0.000000e+00	2745
4	TraesCS5A01G230800	chr5A	89.857	2100	150	16	270	2344	445810697	445812758	0.000000e+00	2639
5	TraesCS5A01G230800	chr5A	91.485	1327	102	6	1020	2344	446022161	446020844	0.000000e+00	1814
6	TraesCS5A01G230800	chr5A	95.349	258	12	0	8	265	445781069	445780812	6.140000e-111	411
7	TraesCS5A01G230800	chr5A	93.536	263	17	0	3	265	445698553	445698291	2.230000e-105	392
8	TraesCS5A01G230800	chr5A	93.411	258	17	0	8	265	446040705	446040448	1.340000e-102	383
9	TraesCS5A01G230800	chr5A	93.976	249	15	0	2	250	445809946	445810194	6.230000e-101	377
10	TraesCS5A01G230800	chr5A	93.651	252	16	0	14	265	446025654	446025403	6.230000e-101	377
11	TraesCS5A01G230800	chr5A	93.548	248	16	0	3	250	445834736	445834983	1.040000e-98	370
12	TraesCS5A01G230800	chr5D	92.827	2147	114	9	270	2388	345437528	345439662	0.000000e+00	3075
13	TraesCS5A01G230800	chr5D	93.444	1510	89	6	882	2388	345424254	345425756	0.000000e+00	2231
14	TraesCS5A01G230800	chr5D	89.571	700	42	13	383	1060	345358123	345358813	0.000000e+00	859
15	TraesCS5A01G230800	chr5D	91.139	237	21	0	272	508	296662567	296662331	2.960000e-84	322
16	TraesCS5A01G230800	chr2D	89.060	1106	94	10	553	1654	61272005	61273087	0.000000e+00	1347
17	TraesCS5A01G230800	chr2D	88.879	1106	81	24	553	1654	61299810	61300877	0.000000e+00	1323
18	TraesCS5A01G230800	chr2D	87.598	766	63	16	1648	2388	61268731	61269489	0.000000e+00	859
19	TraesCS5A01G230800	chr2A	88.969	1106	96	13	553	1654	61773216	61774299	0.000000e+00	1343
20	TraesCS5A01G230800	chr2B	88.718	1108	91	12	553	1654	95945600	95946679	0.000000e+00	1323
21	TraesCS5A01G230800	chr2B	87.300	1126	90	12	553	1654	95953857	95954953	0.000000e+00	1238
22	TraesCS5A01G230800	chr2B	91.845	233	19	0	275	507	484599979	484599747	2.290000e-85	326
23	TraesCS5A01G230800	chr5B	89.435	814	75	6	1578	2388	406400219	406399414	0.000000e+00	1016
24	TraesCS5A01G230800	chr5B	83.877	521	48	15	271	769	406406616	406406110	4.650000e-127	464
25	TraesCS5A01G230800	chr6D	93.182	264	18	0	2	265	402155387	402155124	2.880000e-104	388
26	TraesCS5A01G230800	chr6D	91.954	261	21	0	8	268	370695857	370695597	1.350000e-97	366
27	TraesCS5A01G230800	chr3B	92.045	264	21	0	2	265	411807115	411807378	2.900000e-99	372
28	TraesCS5A01G230800	chr6A	89.873	237	21	3	272	508	6997110	6997343	3.860000e-78	302

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	TraesCS5A01G230800	chr5A	445670684	445673071	2387	True	4410.000000	4410	100.0000	1	2388	1	chr5A.!!$R1	2387
1	TraesCS5A01G230800	chr5A	445766448	445768548	2100	True	2802.000000	2802	90.9690	270	2349	1	chr5A.!!$R3	2079
2	TraesCS5A01G230800	chr5A	446020844	446025654	4810	True	1651.333333	2763	91.9790	14	2344	3	chr5A.!!$R5	2330
3	TraesCS5A01G230800	chr5A	446037878	446040705	2827	True	1564.000000	2745	91.9890	8	2344	2	chr5A.!!$R6	2336
4	TraesCS5A01G230800	chr5A	445809946	445812758	2812	False	1508.000000	2639	91.9165	2	2344	2	chr5A.!!$F2	2342
5	TraesCS5A01G230800	chr5D	345437528	345439662	2134	False	3075.000000	3075	92.8270	270	2388	1	chr5D.!!$F3	2118
6	TraesCS5A01G230800	chr5D	345424254	345425756	1502	False	2231.000000	2231	93.4440	882	2388	1	chr5D.!!$F2	1506
7	TraesCS5A01G230800	chr5D	345358123	345358813	690	False	859.000000	859	89.5710	383	1060	1	chr5D.!!$F1	677
8	TraesCS5A01G230800	chr2D	61299810	61300877	1067	False	1323.000000	1323	88.8790	553	1654	1	chr2D.!!$F1	1101
9	TraesCS5A01G230800	chr2D	61268731	61273087	4356	False	1103.000000	1347	88.3290	553	2388	2	chr2D.!!$F2	1835
10	TraesCS5A01G230800	chr2A	61773216	61774299	1083	False	1343.000000	1343	88.9690	553	1654	1	chr2A.!!$F1	1101
11	TraesCS5A01G230800	chr2B	95945600	95946679	1079	False	1323.000000	1323	88.7180	553	1654	1	chr2B.!!$F1	1101
12	TraesCS5A01G230800	chr2B	95953857	95954953	1096	False	1238.000000	1238	87.3000	553	1654	1	chr2B.!!$F2	1101
13	TraesCS5A01G230800	chr5B	406399414	406400219	805	True	1016.000000	1016	89.4350	1578	2388	1	chr5B.!!$R1	810
14	TraesCS5A01G230800	chr5B	406406110	406406616	506	True	464.000000	464	83.8770	271	769	1	chr5B.!!$R2	498

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
258	259	0.033796	CTGGATGGCAATGGTCAGGT	60.034	55.0	0.0	0.0	28.09	4.0	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2164	4942	0.030101	ACCCGACATTTGCAACAACG	59.97	50.0	0.0	3.07	0.0	4.1	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
92	93	7.141363	CCCTAGAGTCAAAAACATTCAAAGTG	58.859	38.462	0.00	0.00	0.00	3.16
182	183	3.835978	TCCCAATTCCACTCGACTAAGAA	59.164	43.478	0.00	0.00	0.00	2.52
183	184	4.469945	TCCCAATTCCACTCGACTAAGAAT	59.530	41.667	0.00	0.00	0.00	2.40
258	259	0.033796	CTGGATGGCAATGGTCAGGT	60.034	55.000	0.00	0.00	28.09	4.00
265	266	0.598065	GCAATGGTCAGGTGTTCACC	59.402	55.000	13.45	13.45	0.00	4.02
286	770	1.870055	TTGACTGGAGCGTACGACCC	61.870	60.000	21.65	18.48	0.00	4.46
370	854	5.430886	AGGCTGGATTGATTTATTTTTGCC	58.569	37.500	0.00	0.00	36.11	4.52
391	875	7.111353	TGCCGCAAAACTATGTTTATTTTTC	57.889	32.000	0.00	0.00	0.00	2.29
396	880	7.113684	CGCAAAACTATGTTTATTTTTCGGTCA	59.886	33.333	0.00	0.00	0.00	4.02
531	1018	2.286595	GCACATGCGATCACCTGTATTG	60.287	50.000	0.00	0.00	0.00	1.90
565	3288	2.671963	GGTGCCAAGACGTTCCCC	60.672	66.667	0.00	0.00	0.00	4.81
686	3410	7.710044	AGCATTTCAGAGTGTAGATTCACATAG	59.290	37.037	0.00	0.00	40.37	2.23
975	3705	0.811219	CCGCCAAGCTTGATCGATCA	60.811	55.000	29.60	23.99	34.44	2.92
976	3706	1.224075	CGCCAAGCTTGATCGATCAT	58.776	50.000	27.75	11.48	36.56	2.45
1063	3793	1.016415	ACTCTCCCTAGGTTGGCCTA	58.984	55.000	8.29	0.00	44.90	3.93
1077	3812	4.202524	GGTTGGCCTATCTCTCTCTCTCTA	60.203	50.000	3.32	0.00	0.00	2.43
1148	3907	5.994668	TGATCTGTGCTTGTTTACATACACA	59.005	36.000	14.10	14.10	38.71	3.72
1153	3912	5.218885	GTGCTTGTTTACATACACAATGCA	58.781	37.500	0.00	0.00	39.39	3.96
1246	4005	4.124351	GTCGTCATCCGCGTCCCA	62.124	66.667	4.92	0.00	36.19	4.37
1390	4149	5.931441	TCTGCTCTTTTCTTTGCTAGTTC	57.069	39.130	0.00	0.00	0.00	3.01
1422	4181	7.202972	TGTATAAGGGTAGTAGCCAATGTTT	57.797	36.000	20.26	7.94	38.48	2.83
1427	4186	5.580022	AGGGTAGTAGCCAATGTTTTGATT	58.420	37.500	20.26	0.00	38.48	2.57
1627	4390	4.507710	AGCAAGAAACGAGCAGATGATAA	58.492	39.130	0.00	0.00	0.00	1.75
1657	4420	3.034635	CAGATCTAACACCTACCAGGCT	58.965	50.000	0.00	0.00	39.63	4.58
1744	4513	0.521242	CAAACGGTGCTTCGCATAGC	60.521	55.000	0.27	0.27	41.91	2.97
1797	4566	6.755461	ATAAGACATTTTAGATCAGCGACG	57.245	37.500	0.00	0.00	0.00	5.12
1824	4593	0.976641	ACCTCATCAAGCAAGGACGA	59.023	50.000	0.00	0.00	34.16	4.20
1881	4650	5.556355	ACGATGAGTCAATAGAACGTGTA	57.444	39.130	0.00	0.00	0.00	2.90
1916	4688	5.073311	TGAAGAAGGAGAAGATGTTACCG	57.927	43.478	0.00	0.00	0.00	4.02
2064	4841	8.584157	ACAAGATGTTGGAGTTGCAAATTATTA	58.416	29.630	0.00	0.00	38.07	0.98
2074	4851	7.315247	AGTTGCAAATTATTATCACGTGCTA	57.685	32.000	11.67	2.00	0.00	3.49
2143	4920	3.443329	TGTTTGTTTCACTGTGTGCATCT	59.557	39.130	7.79	0.00	32.98	2.90
2164	4942	5.575019	TCTTAAACGTCTTTTTGACTTGGC	58.425	37.500	0.00	0.00	43.25	4.52
2238	5016	3.516300	TGCCTCATCTTTGAATTTGGCAT	59.484	39.130	0.00	0.00	41.79	4.40
2239	5017	4.020039	TGCCTCATCTTTGAATTTGGCATT	60.020	37.500	0.00	0.00	41.79	3.56
2260	5038	5.468540	TTACATACATCTATGGCGAGCTT	57.531	39.130	0.00	0.00	34.96	3.74
2296	5076	7.762615	TCGTGGTGTAAATATCCTTTTAGAGTG	59.237	37.037	0.00	0.00	0.00	3.51
2297	5077	7.548075	CGTGGTGTAAATATCCTTTTAGAGTGT	59.452	37.037	0.00	0.00	0.00	3.55

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
0	1	5.163301	ACCCTAGGTACATGTCATTGTCATC	60.163	44.000	8.29	0.00	32.11	2.92
92	93	1.135199	TCAGTCGGTATCTTCGGTTGC	60.135	52.381	0.00	0.00	0.00	4.17
182	183	0.805614	CGTGAGGTCGAGTGACTCAT	59.194	55.000	13.67	0.00	44.83	2.90
183	184	2.244946	CGTGAGGTCGAGTGACTCA	58.755	57.895	13.67	5.29	44.83	3.41
258	259	0.108585	GCTCCAGTCAAGGGTGAACA	59.891	55.000	0.00	0.00	34.87	3.18
265	266	0.456312	GTCGTACGCTCCAGTCAAGG	60.456	60.000	11.24	0.00	0.00	3.61
303	787	3.208594	GAGATTACACTGCCATGCATGA	58.791	45.455	28.31	8.14	38.13	3.07
308	792	2.315925	ACGGAGATTACACTGCCATG	57.684	50.000	0.00	0.00	0.00	3.66
370	854	7.113684	TGACCGAAAAATAAACATAGTTTTGCG	59.886	33.333	0.03	3.81	41.32	4.85
391	875	5.118971	CACAATCAACAAATCCAAATGACCG	59.881	40.000	0.00	0.00	0.00	4.79
396	880	5.366460	TGCACACAATCAACAAATCCAAAT	58.634	33.333	0.00	0.00	0.00	2.32
432	916	0.541764	TTCAAAGAATGCCCGGCCTT	60.542	50.000	7.03	2.66	0.00	4.35
512	999	2.170397	TCCAATACAGGTGATCGCATGT	59.830	45.455	27.28	27.28	0.00	3.21
517	1004	7.912056	ATAATTCATCCAATACAGGTGATCG	57.088	36.000	0.00	0.00	0.00	3.69
531	1018	4.405358	TGGCACCAAAGGAATAATTCATCC	59.595	41.667	1.96	1.96	35.88	3.51
565	3288	6.673583	AGGGAGTCCTTTAATTATTCCCAAG	58.326	40.000	9.58	0.00	44.18	3.61
660	3384	5.798132	TGTGAATCTACACTCTGAAATGCT	58.202	37.500	0.00	0.00	40.87	3.79
798	3526	4.883585	TCTATTGCCGCATCTTCTCAATTT	59.116	37.500	0.00	0.00	0.00	1.82
811	3539	6.594159	ACATATGGTAAGTATTCTATTGCCGC	59.406	38.462	7.80	0.00	34.25	6.53
975	3705	1.076332	GTCGGCACTGCTTTTACGAT	58.924	50.000	0.00	0.00	32.73	3.73
976	3706	0.249531	TGTCGGCACTGCTTTTACGA	60.250	50.000	0.00	0.00	0.00	3.43
1148	3907	1.171308	GCCTGACACACTGATGCATT	58.829	50.000	0.00	0.00	0.00	3.56
1153	3912	1.188219	AGACCGCCTGACACACTGAT	61.188	55.000	0.00	0.00	0.00	2.90
1390	4149	6.929606	GGCTACTACCCTTATACATCAAGTTG	59.070	42.308	0.00	0.00	0.00	3.16
1422	4181	3.634448	TCTTCCGAGCCAAACAAAATCAA	59.366	39.130	0.00	0.00	0.00	2.57
1427	4186	5.776173	TTATTTCTTCCGAGCCAAACAAA	57.224	34.783	0.00	0.00	0.00	2.83
1627	4390	6.071840	GGTAGGTGTTAGATCTGAGCGATATT	60.072	42.308	5.18	0.00	30.84	1.28
1657	4420	1.703411	CTTCCTTTGTTTGGCCCTGA	58.297	50.000	0.00	0.00	0.00	3.86
1744	4513	7.832187	TGTTTATAGAGGGAGTATTTTTGGGTG	59.168	37.037	0.00	0.00	0.00	4.61
1792	4561	3.444916	TGATGAGGTTATCTTTCGTCGC	58.555	45.455	0.00	0.00	31.12	5.19
1794	4563	4.870426	TGCTTGATGAGGTTATCTTTCGTC	59.130	41.667	0.00	0.00	0.00	4.20
1797	4566	5.882557	TCCTTGCTTGATGAGGTTATCTTTC	59.117	40.000	0.00	0.00	32.33	2.62
1916	4688	4.638865	ACAACTTCTGTAAAGTGGACCAAC	59.361	41.667	0.00	0.00	36.10	3.77
2064	4841	1.917955	CGACGAACATTAGCACGTGAT	59.082	47.619	22.23	17.40	39.04	3.06
2074	4851	3.188254	TCAATTGTCATGCGACGAACATT	59.812	39.130	5.13	0.00	45.80	2.71
2164	4942	0.030101	ACCCGACATTTGCAACAACG	59.970	50.000	0.00	3.07	0.00	4.10
2238	5016	5.243954	AGAAGCTCGCCATAGATGTATGTAA	59.756	40.000	8.88	0.00	35.15	2.41
2239	5017	4.767409	AGAAGCTCGCCATAGATGTATGTA	59.233	41.667	8.88	0.00	35.15	2.29
2260	5038	8.308931	GGATATTTACACCACGACCAATATAGA	58.691	37.037	0.00	0.00	0.00	1.98
2296	5076	1.455383	CCAAGCTTGTCACCACCCAC	61.455	60.000	24.35	0.00	0.00	4.61
2297	5077	1.152777	CCAAGCTTGTCACCACCCA	60.153	57.895	24.35	0.00	0.00	4.51

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.