AutoCloner

Multiple sequence alignment - TraesCS2B01G087100

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	TraesCS2B01G087100	chr2B	100.000	2754	0	0	1	2754	49284696	49287449	0.000000e+00	5086
1	TraesCS2B01G087100	chr2B	92.936	1911	128	7	293	2201	48216863	48214958	0.000000e+00	2774
2	TraesCS2B01G087100	chr2B	91.837	1911	152	4	293	2201	48181531	48179623	0.000000e+00	2662
3	TraesCS2B01G087100	chr2B	94.508	1566	82	3	3	1567	48149351	48147789	0.000000e+00	2412
4	TraesCS2B01G087100	chr2B	92.453	1219	88	4	297	1514	48305448	48304233	0.000000e+00	1738
5	TraesCS2B01G087100	chr2B	93.144	773	36	9	1987	2754	48147778	48147018	0.000000e+00	1118
6	TraesCS2B01G087100	chr2B	92.057	705	54	1	1499	2201	48304214	48303510	0.000000e+00	990
7	TraesCS2B01G087100	chr2B	89.841	502	44	5	2203	2700	49255718	49256216	2.990000e-179	638
8	TraesCS2B01G087100	chr2B	91.416	233	20	0	1	233	48181759	48181527	1.230000e-83	320
9	TraesCS2B01G087100	chr2D	96.129	2015	72	5	745	2754	29885608	29883595	0.000000e+00	3284
10	TraesCS2B01G087100	chr2D	90.314	1466	114	13	748	2201	30097587	30096138	0.000000e+00	1895
11	TraesCS2B01G087100	chr2D	89.917	1448	119	10	766	2201	30238813	30237381	0.000000e+00	1840
12	TraesCS2B01G087100	chr2D	96.267	750	24	3	1	746	29886327	29885578	0.000000e+00	1227
13	TraesCS2B01G087100	chr2D	91.187	556	43	4	2203	2754	30047587	30047034	0.000000e+00	750
14	TraesCS2B01G087100	chr2D	93.111	450	29	2	297	746	30098007	30097560	0.000000e+00	658
15	TraesCS2B01G087100	chr2D	87.207	555	55	10	2205	2751	30165210	30164664	3.900000e-173	617
16	TraesCS2B01G087100	chr2D	87.027	555	56	8	2205	2751	30121362	30120816	1.810000e-171	612
17	TraesCS2B01G087100	chr2D	86.667	555	58	10	2205	2751	30237220	30236674	3.920000e-168	601
18	TraesCS2B01G087100	chr2A	92.519	1965	115	20	266	2201	32101742	32099781	0.000000e+00	2785
19	TraesCS2B01G087100	chr2A	93.176	1187	78	2	1015	2201	32017857	32016674	0.000000e+00	1740
20	TraesCS2B01G087100	chr2A	92.612	934	62	4	1	927	32094632	32093699	0.000000e+00	1336
21	TraesCS2B01G087100	chr2A	93.740	655	38	2	1227	1881	32018521	32017870	0.000000e+00	979
22	TraesCS2B01G087100	chr2A	94.468	470	22	3	1045	1514	32026994	32026529	0.000000e+00	721
23	TraesCS2B01G087100	chr2A	93.277	476	31	1	426	900	32027521	32027046	0.000000e+00	701
24	TraesCS2B01G087100	chr2A	90.519	443	37	2	1	443	32020561	32020124	5.110000e-162	580
25	TraesCS2B01G087100	chr2A	88.986	345	33	3	2408	2748	32097431	32097088	3.280000e-114	422
26	TraesCS2B01G087100	chrUn	90.191	1468	118	11	745	2201	311531205	311532657	0.000000e+00	1890
27	TraesCS2B01G087100	chrUn	90.023	1323	106	12	748	2059	338699404	338698097	0.000000e+00	1688
28	TraesCS2B01G087100	chrUn	86.667	555	58	10	2205	2751	295795826	295796372	3.920000e-168	601
29	TraesCS2B01G087100	chrUn	84.912	285	34	7	2205	2484	379449941	379449661	2.090000e-71	279

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	TraesCS2B01G087100	chr2B	49284696	49287449	2753	False	5086.000000	5086	100.000000	1	2754	1	chr2B.!!$F2	2753
1	TraesCS2B01G087100	chr2B	48214958	48216863	1905	True	2774.000000	2774	92.936000	293	2201	1	chr2B.!!$R1	1908
2	TraesCS2B01G087100	chr2B	48147018	48149351	2333	True	1765.000000	2412	93.826000	3	2754	2	chr2B.!!$R2	2751
3	TraesCS2B01G087100	chr2B	48179623	48181759	2136	True	1491.000000	2662	91.626500	1	2201	2	chr2B.!!$R3	2200
4	TraesCS2B01G087100	chr2B	48303510	48305448	1938	True	1364.000000	1738	92.255000	297	2201	2	chr2B.!!$R4	1904
5	TraesCS2B01G087100	chr2D	29883595	29886327	2732	True	2255.500000	3284	96.198000	1	2754	2	chr2D.!!$R4	2753
6	TraesCS2B01G087100	chr2D	30096138	30098007	1869	True	1276.500000	1895	91.712500	297	2201	2	chr2D.!!$R5	1904
7	TraesCS2B01G087100	chr2D	30236674	30238813	2139	True	1220.500000	1840	88.292000	766	2751	2	chr2D.!!$R6	1985
8	TraesCS2B01G087100	chr2D	30047034	30047587	553	True	750.000000	750	91.187000	2203	2754	1	chr2D.!!$R1	551
9	TraesCS2B01G087100	chr2D	30164664	30165210	546	True	617.000000	617	87.207000	2205	2751	1	chr2D.!!$R3	546
10	TraesCS2B01G087100	chr2D	30120816	30121362	546	True	612.000000	612	87.027000	2205	2751	1	chr2D.!!$R2	546
11	TraesCS2B01G087100	chr2A	32093699	32101742	8043	True	1514.333333	2785	91.372333	1	2748	3	chr2A.!!$R3	2747
12	TraesCS2B01G087100	chr2A	32016674	32020561	3887	True	1099.666667	1740	92.478333	1	2201	3	chr2A.!!$R1	2200
13	TraesCS2B01G087100	chr2A	32026529	32027521	992	True	711.000000	721	93.872500	426	1514	2	chr2A.!!$R2	1088
14	TraesCS2B01G087100	chrUn	311531205	311532657	1452	False	1890.000000	1890	90.191000	745	2201	1	chrUn.!!$F2	1456
15	TraesCS2B01G087100	chrUn	338698097	338699404	1307	True	1688.000000	1688	90.023000	748	2059	1	chrUn.!!$R1	1311
16	TraesCS2B01G087100	chrUn	295795826	295796372	546	False	601.000000	601	86.667000	2205	2751	1	chrUn.!!$F1	546

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
608	613	0.686441	TACGAGGCATACCAGCACCT	60.686	55.0	0.0	0.0	39.06	4.00	F
1573	3659	0.874390	TTGCTCGACAGGCAATTGTC	59.126	50.0	0.5	0.5	43.50	3.18	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1622	3708	1.002773	CTCCATGGCATGATCATCGGA	59.997	52.381	28.43	13.98	0.00	4.55	R
2484	6731	2.639839	CCTCCCTTGTTCAAGAAGGAGA	59.360	50.000	25.25	9.16	42.44	3.71	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
136	137	3.573598	TGGCATTTTACAATGAAGTGCG	58.426	40.909	5.78	0.00	42.35	5.34
163	164	5.048573	TGGTGACATTGTCAATCTCAACATG	60.049	40.000	20.57	0.00	44.49	3.21
232	233	1.971357	CGCCTTCATAGGGGTGAGTAT	59.029	52.381	0.00	0.00	46.58	2.12
243	244	2.486548	GGGGTGAGTATGTGTGTGTGTT	60.487	50.000	0.00	0.00	0.00	3.32
244	245	2.548057	GGGTGAGTATGTGTGTGTGTTG	59.452	50.000	0.00	0.00	0.00	3.33
245	246	2.032030	GGTGAGTATGTGTGTGTGTTGC	60.032	50.000	0.00	0.00	0.00	4.17
246	247	2.611751	GTGAGTATGTGTGTGTGTTGCA	59.388	45.455	0.00	0.00	0.00	4.08
255	260	4.082517	TGTGTGTGTGTTGCAAGTTTATGT	60.083	37.500	0.00	0.00	0.00	2.29
552	557	3.199946	GTGGAGATAGGTTGTCCATTGGA	59.800	47.826	0.00	0.00	42.34	3.53
608	613	0.686441	TACGAGGCATACCAGCACCT	60.686	55.000	0.00	0.00	39.06	4.00
814	900	5.163269	CCATGAGAATGTTAGAGGTGGATCA	60.163	44.000	0.00	0.00	0.00	2.92
1102	3122	9.497030	TGTTTCATTATGTTATGCGATGTTTAC	57.503	29.630	0.00	0.00	0.00	2.01
1401	3421	3.766545	TGATTTGTTCCTTGAGGGGAAG	58.233	45.455	0.00	0.00	44.83	3.46
1573	3659	0.874390	TTGCTCGACAGGCAATTGTC	59.126	50.000	0.50	0.50	43.50	3.18
1622	3708	3.230976	GTGAAGATGGTTGGGGTTTCTT	58.769	45.455	0.00	0.00	0.00	2.52
1749	3835	5.048504	TCAACAAGAAGAAGAATGACATGGC	60.049	40.000	0.00	0.00	0.00	4.40
1785	3871	2.315925	TGCTTAAGCGATGGAGGAAG	57.684	50.000	21.97	0.00	45.83	3.46
1799	3885	9.601217	GCGATGGAGGAAGTAATAATGTATAAT	57.399	33.333	0.00	0.00	0.00	1.28
2209	4522	7.923878	AGTTAAATTAACTTGCCACGACATTTT	59.076	29.630	12.24	0.00	46.27	1.82
2246	4559	4.357947	GCCTCGCTGGTGTCGACA	62.358	66.667	15.76	15.76	38.35	4.35
2322	4635	1.211457	AGGAGCATTGTGTCATCTCCC	59.789	52.381	3.23	0.00	43.21	4.30
2365	4678	2.158623	ACATGCCATACATCCAATCGGT	60.159	45.455	0.00	0.00	36.64	4.69
2391	4705	1.270358	GCAGAAGAAAGAGGGACGTGT	60.270	52.381	0.00	0.00	0.00	4.49
2405	4719	1.798223	GACGTGTGAGCTGCATAAACA	59.202	47.619	1.02	0.00	0.00	2.83
2484	6731	6.498538	AGGGATCTATTATCTCGTTGAGGAT	58.501	40.000	0.00	0.00	0.00	3.24
2508	6755	2.290577	CCTTCTTGAACAAGGGAGGAGG	60.291	54.545	21.53	14.26	40.94	4.30
2552	6799	1.381851	CTGCCCCAAAGAGCCTTCT	59.618	57.895	0.00	0.00	34.29	2.85
2595	6842	5.955959	TCTGGCCTCTACTTGAACTATTACA	59.044	40.000	3.32	0.00	0.00	2.41
2602	6849	7.976734	CCTCTACTTGAACTATTACAACTGGAG	59.023	40.741	0.00	0.00	0.00	3.86
2679	6930	9.225436	TGCATAGCATAATCGGATATTACAAAA	57.775	29.630	0.00	0.00	31.71	2.44
2721	6972	2.609459	GACATGATAACCAGCGGAAGTG	59.391	50.000	0.00	0.00	0.00	3.16

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
11	12	2.091555	TGAACCCTGGGTAAGCTTGTTT	60.092	45.455	20.91	0.00	33.12	2.83
19	20	3.975312	TGTAGAACTTGAACCCTGGGTAA	59.025	43.478	20.91	9.98	33.12	2.85
136	137	3.814842	TGAGATTGACAATGTCACCACAC	59.185	43.478	20.77	9.28	42.60	3.82
163	164	7.065085	AGCAGTTATGTGATGTTGAGTCAATAC	59.935	37.037	9.18	7.12	0.00	1.89
232	233	4.082517	ACATAAACTTGCAACACACACACA	60.083	37.500	0.00	0.00	0.00	3.72
243	244	5.163744	ACACGTTACAACACATAAACTTGCA	60.164	36.000	0.00	0.00	0.00	4.08
244	245	5.267776	ACACGTTACAACACATAAACTTGC	58.732	37.500	0.00	0.00	0.00	4.01
245	246	6.711579	AGACACGTTACAACACATAAACTTG	58.288	36.000	0.00	0.00	0.00	3.16
246	247	6.759827	AGAGACACGTTACAACACATAAACTT	59.240	34.615	0.00	0.00	0.00	2.66
255	260	7.773864	TTATTTTGAGAGACACGTTACAACA	57.226	32.000	0.00	0.00	0.00	3.33
552	557	4.724279	AGATGGGAAAAGGTAAGTGTGT	57.276	40.909	0.00	0.00	0.00	3.72
814	900	8.159229	GGATAATTCCACCCTATACTGGTATT	57.841	38.462	0.00	0.00	42.12	1.89
862	2330	8.400186	TGCTAACAACAACATGATGAAGATATG	58.600	33.333	10.29	2.01	0.00	1.78
985	2995	7.233348	TCCCATATTCATTCCTTTTTCTATGGC	59.767	37.037	0.00	0.00	35.24	4.40
986	2996	8.710749	TCCCATATTCATTCCTTTTTCTATGG	57.289	34.615	0.00	0.00	35.97	2.74
1031	3041	4.355437	ACAATGACAGAGAACGATCGATC	58.645	43.478	24.34	20.21	0.00	3.69
1374	3394	4.501400	CCCTCAAGGAACAAATCAACAACC	60.501	45.833	0.00	0.00	38.24	3.77
1401	3421	6.862944	TCGAACAAAACAATGTCAAACTTC	57.137	33.333	0.00	0.00	31.81	3.01
1474	3494	7.528996	ACATGCCAAATACTTGCATATACAT	57.471	32.000	0.00	0.00	31.96	2.29
1573	3659	1.140852	TCCCCCATAGCACGAATCTTG	59.859	52.381	0.00	0.00	0.00	3.02
1622	3708	1.002773	CTCCATGGCATGATCATCGGA	59.997	52.381	28.43	13.98	0.00	4.55
1749	3835	2.396160	GCAAGATGAATTGCGCTAGG	57.604	50.000	9.73	0.00	45.43	3.02
1805	3891	5.127194	ACGGAGACTGAAGCAAACATAGATA	59.873	40.000	0.00	0.00	0.00	1.98
1877	3963	6.475504	TGGATAATGATGTCTCGCCATTAAT	58.524	36.000	0.00	0.00	36.65	1.40
2104	4191	4.034048	CGGTGATGGATTAATAATAGCGGC	59.966	45.833	0.00	0.00	0.00	6.53
2201	4514	1.017387	GGGGCTAGAGCAAAATGTCG	58.983	55.000	3.54	0.00	44.36	4.35
2209	4522	3.089874	AATGGCGGGGCTAGAGCA	61.090	61.111	3.54	0.00	44.36	4.26
2234	4547	3.581755	TGTATAACTTGTCGACACCAGC	58.418	45.455	19.90	5.77	0.00	4.85
2322	4635	6.276091	TGTCGATCTCAATCATTGGAAGTAG	58.724	40.000	0.00	0.00	31.76	2.57
2365	4678	2.104111	TCCCTCTTTCTTCTGCGTGAAA	59.896	45.455	0.00	0.00	33.79	2.69
2484	6731	2.639839	CCTCCCTTGTTCAAGAAGGAGA	59.360	50.000	25.25	9.16	42.44	3.71
2508	6755	2.772691	CCCTACCTCGCTCGTGGAC	61.773	68.421	16.04	0.00	33.41	4.02
2544	6791	4.586841	AGTGACATAGATGGTAGAAGGCTC	59.413	45.833	0.00	0.00	0.00	4.70
2552	6799	4.039609	CCAGATGCAGTGACATAGATGGTA	59.960	45.833	0.00	0.00	0.00	3.25
2595	6842	9.959721	ATATGTAGTGTATTTTTCACTCCAGTT	57.040	29.630	1.82	0.00	43.76	3.16
2679	6930	6.288294	TGTCTATGTAAGCTTTGTGTTGTCT	58.712	36.000	3.20	0.00	0.00	3.41
2721	6972	4.377022	CCATAGTTACCGATTTATGCACGC	60.377	45.833	0.00	0.00	0.00	5.34

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.