AutoCloner

Multiple sequence alignment - TraesCS6D01G297400

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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	TraesCS6D01G297400	chr6D	100.000	4129	0	0	1	4129	408652182	408648054	0.000000e+00	7625.0
1	TraesCS6D01G297400	chr6D	81.913	669	83	15	1050	1700	450820072	450820720	7.860000e-147	531.0
2	TraesCS6D01G297400	chr6D	80.233	516	47	20	2048	2541	450821046	450821528	1.840000e-88	337.0
3	TraesCS6D01G297400	chr6D	85.000	80	10	2	1985	2063	450820953	450821031	3.420000e-11	80.5
4	TraesCS6D01G297400	chr6B	93.666	4089	153	40	1	4018	613112816	613108763	0.000000e+00	6019.0
5	TraesCS6D01G297400	chr6A	94.595	2812	104	20	1251	4022	554459223	554456420	0.000000e+00	4307.0
6	TraesCS6D01G297400	chr6A	93.031	1191	37	15	1	1168	554460381	554459214	0.000000e+00	1698.0
7	TraesCS6D01G297400	chr6A	79.368	1013	137	40	2608	3590	596341704	596342674	0.000000e+00	647.0
8	TraesCS6D01G297400	chr6A	76.585	1183	166	61	2571	3700	596363645	596364769	7.800000e-152	547.0
9	TraesCS6D01G297400	chr6A	84.802	329	23	10	2268	2577	596354783	596355103	5.190000e-79	305.0
10	TraesCS6D01G297400	chr6A	78.442	552	56	30	928	1455	596340607	596341119	6.710000e-78	302.0
11	TraesCS6D01G297400	chr6A	84.912	285	18	12	2263	2530	596341417	596341693	8.800000e-67	265.0
12	TraesCS6D01G297400	chr6A	94.017	117	6	1	1486	1602	596341117	596341232	4.240000e-40	176.0
13	TraesCS6D01G297400	chr3D	80.191	944	117	44	1891	2789	335629033	335629951	0.000000e+00	643.0
14	TraesCS6D01G297400	chr3D	81.796	401	48	17	1303	1695	335628609	335628992	3.100000e-81	313.0
15	TraesCS6D01G297400	chr3D	92.500	120	9	0	3012	3131	335630309	335630428	5.490000e-39	172.0
16	TraesCS6D01G297400	chr3D	83.529	85	14	0	1785	1869	370115798	370115714	3.420000e-11	80.5
17	TraesCS6D01G297400	chr3B	79.766	939	125	39	1890	2780	434048919	434049840	4.530000e-174	621.0
18	TraesCS6D01G297400	chr3B	81.095	402	49	20	1303	1695	434048498	434048881	3.120000e-76	296.0
19	TraesCS6D01G297400	chr3B	92.373	118	9	0	3012	3129	434050243	434050360	7.100000e-38	169.0
20	TraesCS6D01G297400	chr3A	78.963	694	90	29	2139	2789	453602231	453602911	4.940000e-114	422.0
21	TraesCS6D01G297400	chr3A	81.297	401	50	17	1303	1695	453601583	453601966	6.710000e-78	302.0
22	TraesCS6D01G297400	chr3A	88.966	145	12	4	3014	3156	453603270	453603412	4.240000e-40	176.0
23	TraesCS6D01G297400	chr3A	83.529	85	14	0	1785	1869	491189510	491189426	3.420000e-11	80.5
24	TraesCS6D01G297400	chr1D	88.889	90	8	1	1784	1873	149649710	149649797	4.360000e-20	110.0
25	TraesCS6D01G297400	chr4A	89.412	85	8	1	1785	1869	99009814	99009731	5.650000e-19	106.0
26	TraesCS6D01G297400	chr4A	83.871	93	13	2	1780	1871	99009725	99009816	2.040000e-13	87.9
27	TraesCS6D01G297400	chr4A	81.720	93	15	2	1794	1886	703430590	703430500	4.430000e-10	76.8
28	TraesCS6D01G297400	chr7B	88.000	75	9	0	1785	1859	713765819	713765893	5.690000e-14	89.8

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	TraesCS6D01G297400	chr6D	408648054	408652182	4128	True	7625.000000	7625	100.000000	1	4129	1	chr6D.!!$R1	4128
1	TraesCS6D01G297400	chr6D	450820072	450821528	1456	False	316.166667	531	82.382000	1050	2541	3	chr6D.!!$F1	1491
2	TraesCS6D01G297400	chr6B	613108763	613112816	4053	True	6019.000000	6019	93.666000	1	4018	1	chr6B.!!$R1	4017
3	TraesCS6D01G297400	chr6A	554456420	554460381	3961	True	3002.500000	4307	93.813000	1	4022	2	chr6A.!!$R1	4021
4	TraesCS6D01G297400	chr6A	596363645	596364769	1124	False	547.000000	547	76.585000	2571	3700	1	chr6A.!!$F2	1129
5	TraesCS6D01G297400	chr6A	596340607	596342674	2067	False	347.500000	647	84.184750	928	3590	4	chr6A.!!$F3	2662
6	TraesCS6D01G297400	chr3D	335628609	335630428	1819	False	376.000000	643	84.829000	1303	3131	3	chr3D.!!$F1	1828
7	TraesCS6D01G297400	chr3B	434048498	434050360	1862	False	362.000000	621	84.411333	1303	3129	3	chr3B.!!$F1	1826
8	TraesCS6D01G297400	chr3A	453601583	453603412	1829	False	300.000000	422	83.075333	1303	3156	3	chr3A.!!$F1	1853

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	Hairpin	End Stability	Orientation
883	907	0.750546	TCCGTGCCTAGTAGACGCAT	60.751	55.0	34.51	4.73	F
1241	1388	0.591659	TCCGTGTCTCTCTGTTGTCG	59.408	55.0	0.00	4.35	F
1636	1835	0.603707	TGCTGTTGCGGAGGAAGAAG	60.604	55.0	39.56	2.85	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2838	3371	0.892755	ATGACAATGGCCAACTGCTG	59.107	50.0	10.96	5.01	40.92	4.41	R
3111	3672	0.631753	AGCTACTCCTGGGCAGTAGA	59.368	55.0	20.85	0.00	44.30	2.59	R
3624	4217	0.768221	AGGCCCTTCTCACCACTTCA	60.768	55.0	0.00	0.00	0.00	3.02	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)

Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
124	125	1.069935	GAGGGGATTAGAGCGCCAC	59.930	63.158	2.29	0.00	40.52	5.01
181	182	4.155733	TGGTCGGCGCCACCTATG	62.156	66.667	33.43	17.43	34.66	2.23
608	621	0.825840	GACGAGAGCTAGATGCCCCT	60.826	60.000	0.00	0.00	44.23	4.79
685	698	2.366972	ATTGGGGTCTCCGGGGAG	60.367	66.667	2.77	8.48	43.21	4.30
801	816	1.609794	GACGGGAGGGAAGAGGTGT	60.610	63.158	0.00	0.00	0.00	4.16
810	825	1.298014	GAAGAGGTGTCTGGCCCTG	59.702	63.158	0.00	0.00	31.37	4.45
819	834	0.962356	GTCTGGCCCTGTGGAATGTG	60.962	60.000	0.00	0.00	0.00	3.21
843	867	5.697473	TTCCGTAAAACATGCATGAAAGA	57.303	34.783	32.75	15.08	0.00	2.52
850	874	7.478667	CGTAAAACATGCATGAAAGAGTACTTC	59.521	37.037	32.75	9.42	35.05	3.01
858	882	5.415221	CATGAAAGAGTACTTCACCTCTCC	58.585	45.833	0.00	0.00	35.05	3.71
883	907	0.750546	TCCGTGCCTAGTAGACGCAT	60.751	55.000	0.00	0.00	34.51	4.73
916	940	3.444916	TCTCTGAACACGTGTCTCAAAC	58.555	45.455	23.61	9.83	0.00	2.93
920	944	4.452795	TCTGAACACGTGTCTCAAACAAAA	59.547	37.500	23.61	3.68	40.31	2.44
1207	1354	1.571215	CCCCCGTTCGTTTTTCTCCG	61.571	60.000	0.00	0.00	0.00	4.63
1223	1370	2.159282	TCTCCGTTCCTGCTTACGAATC	60.159	50.000	0.00	0.00	40.03	2.52
1237	1384	2.638556	CGAATCCGTGTCTCTCTGTT	57.361	50.000	0.00	0.00	0.00	3.16
1238	1385	2.254459	CGAATCCGTGTCTCTCTGTTG	58.746	52.381	0.00	0.00	0.00	3.33
1240	1387	3.246619	GAATCCGTGTCTCTCTGTTGTC	58.753	50.000	0.00	0.00	0.00	3.18
1241	1388	0.591659	TCCGTGTCTCTCTGTTGTCG	59.408	55.000	0.00	0.00	0.00	4.35
1248	1400	5.031578	GTGTCTCTCTGTTGTCGTATCATC	58.968	45.833	0.00	0.00	0.00	2.92
1268	1420	1.377994	CTAGGCCATCCCCTGATGC	59.622	63.158	5.01	0.00	45.86	3.91
1298	1450	1.028868	GCTTGAGGCCACTGATCACC	61.029	60.000	5.01	0.00	34.27	4.02
1387	1549	7.487189	GTCTCATGCAATTCAAAGGATTTACAG	59.513	37.037	0.00	0.00	35.03	2.74
1441	1607	5.335269	GCTAGAGCAGGTTTTCTTTTCTTCC	60.335	44.000	0.00	0.00	41.59	3.46
1580	1779	0.622665	AGGGCATGGAAGGTGAAGAG	59.377	55.000	0.00	0.00	0.00	2.85

Showing 1 to 25 of 79 entries

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Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
124	125	0.041839	GCAACCATATTCTCGCGCTG	60.042	55.000	5.56	0.00	0.00	5.18
178	179	2.734591	GCCGTCATCCCGCTCATA	59.265	61.111	0.00	0.00	0.00	2.15
801	816	1.379916	CACATTCCACAGGGCCAGA	59.620	57.895	6.18	0.00	0.00	3.86
819	834	5.918011	TCTTTCATGCATGTTTTACGGAAAC	59.082	36.000	25.43	0.68	46.28	2.78
843	867	0.408700	ACGGGGAGAGGTGAAGTACT	59.591	55.000	0.00	0.00	0.00	2.73
883	907	1.825474	GTTCAGAGATGAGGGAACGGA	59.175	52.381	0.00	0.00	31.48	4.69
920	944	7.172361	GTGAAGCTTCTATGTTCAGACTCTTTT	59.828	37.037	26.09	0.00	30.94	2.27
924	948	4.867608	GGTGAAGCTTCTATGTTCAGACTC	59.132	45.833	26.09	4.72	30.94	3.36
926	950	4.629200	CAGGTGAAGCTTCTATGTTCAGAC	59.371	45.833	26.09	12.71	30.94	3.51
986	1022	0.250081	CTCCATCCCTAAGCTTCGGC	60.250	60.000	11.53	0.00	42.17	5.54
987	1023	0.394565	CCTCCATCCCTAAGCTTCGG	59.605	60.000	10.06	10.06	0.00	4.30
988	1024	0.394565	CCCTCCATCCCTAAGCTTCG	59.605	60.000	0.00	0.00	0.00	3.79
989	1025	0.767998	CCCCTCCATCCCTAAGCTTC	59.232	60.000	0.00	0.00	0.00	3.86
990	1026	1.356494	GCCCCTCCATCCCTAAGCTT	61.356	60.000	3.48	3.48	0.00	3.74
991	1027	1.772156	GCCCCTCCATCCCTAAGCT	60.772	63.158	0.00	0.00	0.00	3.74
992	1028	2.839836	GCCCCTCCATCCCTAAGC	59.160	66.667	0.00	0.00	0.00	3.09
1223	1370	0.311165	ACGACAACAGAGAGACACGG	59.689	55.000	0.00	0.00	0.00	4.94
1235	1382	3.181479	TGGCCTAGTGATGATACGACAAC	60.181	47.826	3.32	0.00	0.00	3.32
1237	1384	2.661718	TGGCCTAGTGATGATACGACA	58.338	47.619	3.32	0.00	0.00	4.35
1238	1385	3.367498	GGATGGCCTAGTGATGATACGAC	60.367	52.174	3.32	0.00	0.00	4.34
1240	1387	2.093973	GGGATGGCCTAGTGATGATACG	60.094	54.545	3.32	0.00	0.00	3.06
1241	1388	2.237392	GGGGATGGCCTAGTGATGATAC	59.763	54.545	3.32	0.00	0.00	2.24
1248	1400	0.399454	CATCAGGGGATGGCCTAGTG	59.601	60.000	3.32	0.00	45.84	2.74
1467	1666	6.938030	TCAACATAACCGGTCTTAATCAAGTT	59.062	34.615	8.04	0.21	33.20	2.66
1580	1779	0.387750	CTCAAGCCCTTTCGCAAAGC	60.388	55.000	3.86	0.00	37.18	3.51

Showing 1 to 25 of 77 entries

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Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.