AutoCloner

Multiple sequence alignment - TraesCS5A01G289700

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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	TraesCS5A01G289700	chr5A	100.000	3513	0	0	1	3513	496300861	496297349	0.000000e+00	6488
1	TraesCS5A01G289700	chr5A	94.958	476	23	1	3039	3513	496579520	496579045	0.000000e+00	745
2	TraesCS5A01G289700	chr5A	86.601	306	28	7	1385	1688	488629885	488629591	3.380000e-85	326
3	TraesCS5A01G289700	chr5A	94.798	173	8	1	1780	1951	496579712	496579540	5.780000e-68	268
4	TraesCS5A01G289700	chr5A	87.379	206	22	3	95	296	488631405	488631200	2.110000e-57	233
5	TraesCS5A01G289700	chr5B	92.083	1983	114	16	1	1951	474466146	474464175	0.000000e+00	2752
6	TraesCS5A01G289700	chr5B	93.313	1002	55	9	1	994	428840027	428841024	0.000000e+00	1469
7	TraesCS5A01G289700	chr5B	92.739	909	32	11	1070	1951	428841024	428841925	0.000000e+00	1282
8	TraesCS5A01G289700	chr5B	92.571	525	35	4	2992	3513	428841918	428842441	0.000000e+00	750
9	TraesCS5A01G289700	chr5B	84.501	671	88	13	1023	1686	464890217	464889556	0.000000e+00	649
10	TraesCS5A01G289700	chr5B	89.320	206	18	3	95	296	464892359	464892154	4.500000e-64	255
11	TraesCS5A01G289700	chr6D	94.350	1062	26	13	1952	2991	106483160	106484209	0.000000e+00	1598
12	TraesCS5A01G289700	chr4D	93.383	1073	28	15	1955	2993	402548067	402547004	0.000000e+00	1548
13	TraesCS5A01G289700	chr2A	93.047	1093	23	17	1952	2993	188604104	188605194	0.000000e+00	1548
14	TraesCS5A01G289700	chr2A	89.954	1085	44	20	1952	2991	205206248	205205184	0.000000e+00	1339
15	TraesCS5A01G289700	chr2A	86.473	207	6	5	2796	2991	26935960	26935765	1.280000e-49	207
16	TraesCS5A01G289700	chr1B	90.625	1056	39	26	1986	2992	608037645	608038689	0.000000e+00	1347
17	TraesCS5A01G289700	chr1B	87.595	395	37	7	1951	2342	461306032	461305647	6.920000e-122	448
18	TraesCS5A01G289700	chr6A	89.104	1083	52	24	1952	2991	581534975	581533916	0.000000e+00	1286
19	TraesCS5A01G289700	chr6A	93.878	196	9	2	2796	2991	32557209	32557017	3.430000e-75	292
20	TraesCS5A01G289700	chr5D	95.192	520	23	2	2995	3513	394593275	394592757	0.000000e+00	821
21	TraesCS5A01G289700	chr5D	94.175	515	28	2	2999	3513	394559402	394558890	0.000000e+00	784
22	TraesCS5A01G289700	chr5D	94.175	515	28	2	2999	3513	394562817	394562305	0.000000e+00	784
23	TraesCS5A01G289700	chr5D	93.992	516	29	2	2999	3513	394582894	394582380	0.000000e+00	780
24	TraesCS5A01G289700	chr5D	84.398	673	88	12	1023	1686	386861687	386861023	0.000000e+00	645
25	TraesCS5A01G289700	chr5D	95.294	170	7	1	1783	1951	394593440	394593271	5.780000e-68	268
26	TraesCS5A01G289700	chr5D	88.889	207	18	4	95	296	386863820	386863614	2.090000e-62	250
27	TraesCS5A01G289700	chrUn	94.175	515	28	2	2999	3513	211146997	211146485	0.000000e+00	784
28	TraesCS5A01G289700	chrUn	93.798	516	30	2	2999	3513	211167134	211166620	0.000000e+00	774
29	TraesCS5A01G289700	chrUn	93.499	523	26	2	2992	3513	300352640	300353155	0.000000e+00	771
30	TraesCS5A01G289700	chrUn	87.874	602	37	11	2400	2991	319569431	319568856	0.000000e+00	675
31	TraesCS5A01G289700	chrUn	87.874	602	37	11	2400	2991	387975004	387974429	0.000000e+00	675
32	TraesCS5A01G289700	chrUn	87.708	602	39	10	2400	2991	319586437	319585861	0.000000e+00	669
33	TraesCS5A01G289700	chrUn	92.965	398	23	1	1950	2342	319587008	319586611	3.040000e-160	575
34	TraesCS5A01G289700	chrUn	92.714	398	24	1	1950	2342	319570002	319569605	1.410000e-158	569
35	TraesCS5A01G289700	chrUn	94.798	173	8	1	1780	1951	300352475	300352647	5.780000e-68	268
36	TraesCS5A01G289700	chrUn	94.798	173	8	1	1780	1951	300357176	300357348	5.780000e-68	268
37	TraesCS5A01G289700	chrUn	94.798	173	8	1	1780	1951	313020854	313021026	5.780000e-68	268
38	TraesCS5A01G289700	chr3B	87.708	602	39	10	2400	2991	794693622	794693046	0.000000e+00	669
39	TraesCS5A01G289700	chr3B	92.965	398	23	1	1950	2342	794694193	794693796	3.040000e-160	575
40	TraesCS5A01G289700	chr7B	84.884	688	40	15	2340	2992	639056091	639056749	1.380000e-178	636
41	TraesCS5A01G289700	chr7B	94.656	393	20	1	1950	2342	639052999	639053390	3.000000e-170	608
42	TraesCS5A01G289700	chr6B	94.416	197	9	2	2796	2991	202605247	202605442	5.700000e-78	302
43	TraesCS5A01G289700	chr2B	84.112	321	24	11	2699	2996	364845055	364844739	5.740000e-73	285
44	TraesCS5A01G289700	chr4B	90.909	209	8	3	2796	2993	188184920	188185128	1.610000e-68	270
45	TraesCS5A01G289700	chr4B	90.385	208	9	3	2796	2992	599465187	599465394	2.690000e-66	263
46	TraesCS5A01G289700	chr4B	89.855	207	10	4	2796	2991	330790025	330789819	4.500000e-64	255

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	TraesCS5A01G289700	chr5A	496297349	496300861	3512	True	6488.0	6488	100.000000	1	3513	1	chr5A.!!$R1	3512
1	TraesCS5A01G289700	chr5A	496579045	496579712	667	True	506.5	745	94.878000	1780	3513	2	chr5A.!!$R3	1733
2	TraesCS5A01G289700	chr5A	488629591	488631405	1814	True	279.5	326	86.990000	95	1688	2	chr5A.!!$R2	1593
3	TraesCS5A01G289700	chr5B	474464175	474466146	1971	True	2752.0	2752	92.083000	1	1951	1	chr5B.!!$R1	1950
4	TraesCS5A01G289700	chr5B	428840027	428842441	2414	False	1167.0	1469	92.874333	1	3513	3	chr5B.!!$F1	3512
5	TraesCS5A01G289700	chr5B	464889556	464892359	2803	True	452.0	649	86.910500	95	1686	2	chr5B.!!$R2	1591
6	TraesCS5A01G289700	chr6D	106483160	106484209	1049	False	1598.0	1598	94.350000	1952	2991	1	chr6D.!!$F1	1039
7	TraesCS5A01G289700	chr4D	402547004	402548067	1063	True	1548.0	1548	93.383000	1955	2993	1	chr4D.!!$R1	1038
8	TraesCS5A01G289700	chr2A	188604104	188605194	1090	False	1548.0	1548	93.047000	1952	2993	1	chr2A.!!$F1	1041
9	TraesCS5A01G289700	chr2A	205205184	205206248	1064	True	1339.0	1339	89.954000	1952	2991	1	chr2A.!!$R2	1039
10	TraesCS5A01G289700	chr1B	608037645	608038689	1044	False	1347.0	1347	90.625000	1986	2992	1	chr1B.!!$F1	1006
11	TraesCS5A01G289700	chr6A	581533916	581534975	1059	True	1286.0	1286	89.104000	1952	2991	1	chr6A.!!$R2	1039
12	TraesCS5A01G289700	chr5D	394558890	394562817	3927	True	784.0	784	94.175000	2999	3513	2	chr5D.!!$R3	514
13	TraesCS5A01G289700	chr5D	394582380	394582894	514	True	780.0	780	93.992000	2999	3513	1	chr5D.!!$R1	514
14	TraesCS5A01G289700	chr5D	394592757	394593440	683	True	544.5	821	95.243000	1783	3513	2	chr5D.!!$R4	1730
15	TraesCS5A01G289700	chr5D	386861023	386863820	2797	True	447.5	645	86.643500	95	1686	2	chr5D.!!$R2	1591
16	TraesCS5A01G289700	chrUn	211146485	211146997	512	True	784.0	784	94.175000	2999	3513	1	chrUn.!!$R1	514
17	TraesCS5A01G289700	chrUn	211166620	211167134	514	True	774.0	774	93.798000	2999	3513	1	chrUn.!!$R2	514
18	TraesCS5A01G289700	chrUn	387974429	387975004	575	True	675.0	675	87.874000	2400	2991	1	chrUn.!!$R3	591
19	TraesCS5A01G289700	chrUn	319568856	319570002	1146	True	622.0	675	90.294000	1950	2991	2	chrUn.!!$R4	1041
20	TraesCS5A01G289700	chrUn	319585861	319587008	1147	True	622.0	669	90.336500	1950	2991	2	chrUn.!!$R5	1041
21	TraesCS5A01G289700	chrUn	300352475	300353155	680	False	519.5	771	94.148500	1780	3513	2	chrUn.!!$F3	1733
22	TraesCS5A01G289700	chr3B	794693046	794694193	1147	True	622.0	669	90.336500	1950	2991	2	chr3B.!!$R1	1041
23	TraesCS5A01G289700	chr7B	639052999	639056749	3750	False	622.0	636	89.770000	1950	2992	2	chr7B.!!$F1	1042

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
813	1499	0.603707	CAATGTGTCGGTGCTGAGGT	60.604	55.0	0.0	0.0	0.0	3.85	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2781	6939	0.106669	GGCCCATCAGGAAACCCTAC	60.107	60.0	0.0	0.0	38.24	3.18	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
58	59	5.594317	GGTGGACACATAAAGCAGGAAATAT	59.406	40.000	4.69	0.00	0.00	1.28
60	61	7.363793	GGTGGACACATAAAGCAGGAAATATTT	60.364	37.037	0.00	0.00	0.00	1.40
247	252	6.752335	AAAAACGTGTTCATCATTCATGTG	57.248	33.333	0.00	0.00	33.66	3.21
428	1107	9.425248	AATAAATGGTCACCAACTATCATGAAT	57.575	29.630	0.00	0.00	36.95	2.57
464	1145	2.233676	TCTTCGCTATTTGGACTGCTCA	59.766	45.455	0.00	0.00	0.00	4.26
501	1184	0.892358	CACCCATGAGCAACTGCACT	60.892	55.000	4.22	0.00	45.16	4.40
522	1205	6.458342	GCACTGTAGACATAAAATGGTTAGGC	60.458	42.308	0.00	0.00	33.60	3.93
532	1215	3.560636	AATGGTTAGGCGTTAGCTCAT	57.439	42.857	0.00	0.00	44.37	2.90
589	1272	4.878971	GCATCTGAGTAGAGTAGAGACACA	59.121	45.833	0.00	0.00	36.14	3.72
695	1381	3.685435	CCATTGGGCTTGTTCGCT	58.315	55.556	0.00	0.00	0.00	4.93
702	1388	2.434359	GCTTGTTCGCTACCGGCT	60.434	61.111	0.00	0.00	39.13	5.52
704	1390	1.215647	CTTGTTCGCTACCGGCTCT	59.784	57.895	0.00	0.00	39.13	4.09
718	1404	2.485795	GCTCTGGCTCTCGGACGAT	61.486	63.158	0.00	0.00	35.22	3.73
727	1413	1.141665	CTCGGACGATGCCACATGA	59.858	57.895	0.00	0.00	0.00	3.07
813	1499	0.603707	CAATGTGTCGGTGCTGAGGT	60.604	55.000	0.00	0.00	0.00	3.85
980	1671	1.841302	TTGCCACAAGAGCCTCGGAT	61.841	55.000	0.00	0.00	0.00	4.18
1017	1708	3.648067	CCACCATGTACTCCATCCATAGT	59.352	47.826	0.00	0.00	0.00	2.12
1115	2342	3.897141	TGCGTATATTCTGTTGGTGGA	57.103	42.857	0.00	0.00	0.00	4.02
1151	2380	9.970395	TGAAGTTCGTAAGTCTTTGATTACTTA	57.030	29.630	0.00	0.00	37.19	2.24
1261	2493	9.639601	TCTATATGTGTATGGCGAATCTTAAAG	57.360	33.333	0.00	0.00	0.00	1.85
1418	2653	7.068226	AGGTTATTGCGCTTGTAAATTATTCCT	59.932	33.333	9.73	4.25	0.00	3.36
1419	2654	8.347035	GGTTATTGCGCTTGTAAATTATTCCTA	58.653	33.333	9.73	0.00	0.00	2.94
1542	2777	8.612233	TTTTACAAAAAGCATTTGCACATTTC	57.388	26.923	13.13	0.00	45.16	2.17
1544	2779	6.439675	ACAAAAAGCATTTGCACATTTCTT	57.560	29.167	13.13	0.00	45.16	2.52
1545	2780	6.854778	ACAAAAAGCATTTGCACATTTCTTT	58.145	28.000	13.13	0.00	45.16	2.52
1715	2955	1.895020	TTTGGCGAGCTATGTCGGGT	61.895	55.000	0.00	0.00	40.44	5.28
1740	2980	2.314323	ACCTAAACGGTGTTGTTCGT	57.686	45.000	0.00	0.00	46.80	3.85
1755	2995	6.244883	GTGTTGTTCGTTGCAAATATACGTAC	59.755	38.462	0.00	5.68	36.52	3.67
1821	3086	1.176527	GCTGTTTGCTGATTGGCCTA	58.823	50.000	3.32	0.00	38.95	3.93
1850	3115	2.813908	GCGTAGGCCACAACTCCG	60.814	66.667	5.01	0.00	0.00	4.63
1869	3134	3.016736	CCGGGATGCTAAAATTGAGTGT	58.983	45.455	0.00	0.00	0.00	3.55
2036	3301	2.147436	TTCCAAAAACAGCCATTCGC	57.853	45.000	0.00	0.00	37.98	4.70
2574	6704	5.940470	TCTGAAGATTAAAAGTGGAAGAGGC	59.060	40.000	0.00	0.00	0.00	4.70
2678	6817	3.833645	CGCCGGTCGAATCCAGGA	61.834	66.667	12.11	0.00	41.67	3.86
2781	6939	2.093306	TATGTCGTGACCCTGCAAAG	57.907	50.000	0.00	0.00	0.00	2.77
2895	7082	4.957684	ATTCGAATTTCGGGGATACTCT	57.042	40.909	18.02	0.00	40.88	3.24
2906	7093	3.725490	GGGGATACTCTAAAATTCGCGT	58.275	45.455	5.77	0.00	0.00	6.01
2907	7094	4.557296	CGGGGATACTCTAAAATTCGCGTA	60.557	45.833	5.77	0.00	33.64	4.42
2908	7095	5.476614	GGGGATACTCTAAAATTCGCGTAT	58.523	41.667	5.77	0.00	0.00	3.06
2909	7096	5.575995	GGGGATACTCTAAAATTCGCGTATC	59.424	44.000	5.77	1.64	34.99	2.24
2910	7097	5.575995	GGGATACTCTAAAATTCGCGTATCC	59.424	44.000	5.77	10.98	46.34	2.59
2911	7098	5.575995	GGATACTCTAAAATTCGCGTATCCC	59.424	44.000	5.77	0.00	43.60	3.85
2912	7099	3.378339	ACTCTAAAATTCGCGTATCCCG	58.622	45.455	5.77	0.00	40.40	5.14
2913	7100	2.729882	CTCTAAAATTCGCGTATCCCGG	59.270	50.000	5.77	0.00	36.94	5.73
2914	7101	1.193874	CTAAAATTCGCGTATCCCGGC	59.806	52.381	5.77	0.00	36.94	6.13
2941	7140	2.570181	CGTATCCCCGTATCCCGC	59.430	66.667	0.00	0.00	34.38	6.13
2954	7153	2.971095	ATCCCGCCGTATCAGGACGA	62.971	60.000	0.00	0.00	45.82	4.20
2993	7192	0.948678	GTGTCCGTGCTTTTTAGGCA	59.051	50.000	0.00	0.00	37.36	4.75
3082	10716	0.734253	GTGAACAGCGACTCAGCGAT	60.734	55.000	0.00	0.00	43.00	4.58
3091	10725	2.271607	GACTCAGCGATGCCGTGAGA	62.272	60.000	13.06	2.06	41.73	3.27
3156	10793	3.621268	TGTATTATGTTGCTGACTTCCGC	59.379	43.478	0.00	0.00	0.00	5.54
3230	10867	6.359480	AGTTTTAGTTCTGTACTTGTGCAC	57.641	37.500	10.75	10.75	38.33	4.57

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
187	190	2.359478	CACACGGTAAGGCCCACC	60.359	66.667	13.20	13.20	0.00	4.61
380	471	3.800628	GGCAACTTGGCATGAAGAC	57.199	52.632	10.37	0.00	43.14	3.01
428	1107	8.908786	AATAGCGAAGAAGATGGATTTTATCA	57.091	30.769	0.00	0.00	0.00	2.15
501	1184	5.736813	ACGCCTAACCATTTTATGTCTACA	58.263	37.500	0.00	0.00	0.00	2.74
522	1205	4.548916	CGCATTTGACACTATGAGCTAACG	60.549	45.833	0.00	0.00	0.00	3.18
532	1215	2.284150	GCTAATCGCGCATTTGACACTA	59.716	45.455	8.75	0.00	0.00	2.74
589	1272	4.968719	TGACCACCTCATACTACATCCATT	59.031	41.667	0.00	0.00	0.00	3.16
695	1381	2.829003	CGAGAGCCAGAGCCGGTA	60.829	66.667	1.90	0.00	41.25	4.02
702	1388	2.775856	GCATCGTCCGAGAGCCAGA	61.776	63.158	5.83	0.00	0.00	3.86
704	1390	3.838271	GGCATCGTCCGAGAGCCA	61.838	66.667	22.99	0.00	43.95	4.75
708	1394	1.141665	CATGTGGCATCGTCCGAGA	59.858	57.895	0.00	0.00	0.00	4.04
718	1404	5.008980	TCAACACAAAGATATCATGTGGCA	58.991	37.500	29.71	18.02	46.67	4.92
813	1499	0.179076	ATTCCATCATGCGCAGACGA	60.179	50.000	18.32	12.99	43.93	4.20
860	1548	0.541863	CCTATGTTCAACGCCTCCCT	59.458	55.000	0.00	0.00	0.00	4.20
993	1684	0.179018	GGATGGAGTACATGGTGGCC	60.179	60.000	0.00	0.00	40.72	5.36
1062	2289	9.932207	AGCATGAAAACAAAATATTCATCTTCA	57.068	25.926	0.00	0.00	40.75	3.02
1115	2342	6.038271	AGACTTACGAACTTCATGCAAAGTTT	59.962	34.615	15.77	5.90	46.69	2.66
1236	2466	9.424319	ACTTTAAGATTCGCCATACACATATAG	57.576	33.333	0.00	0.00	0.00	1.31
1610	2847	8.153550	ACATCATAGATGACTTGAATTACCTCC	58.846	37.037	13.46	0.00	40.03	4.30
1740	2980	9.352784	ACTTAAAGTACGTACGTATATTTGCAA	57.647	29.630	31.15	23.30	32.82	4.08
1755	2995	6.248839	CGACTCAGCTTTAGACTTAAAGTACG	59.751	42.308	8.37	0.00	44.92	3.67
1821	3086	2.498481	TGGCCTACGCACATTAGTAACT	59.502	45.455	3.32	0.00	36.38	2.24
1850	3115	3.763897	ACCACACTCAATTTTAGCATCCC	59.236	43.478	0.00	0.00	0.00	3.85
1869	3134	0.604243	GGTTGTATGCGTGGTGACCA	60.604	55.000	0.00	0.00	0.00	4.02
2113	3381	6.652900	GGGCAATATTCTCTATTCTCAACTCC	59.347	42.308	0.00	0.00	0.00	3.85
2543	6666	6.151648	TCCACTTTTAATCTTCAGATGCTTGG	59.848	38.462	0.00	0.00	34.49	3.61
2574	6704	5.603596	CATCCTCTCCTCATTCTTCTTCAG	58.396	45.833	0.00	0.00	0.00	3.02
2781	6939	0.106669	GGCCCATCAGGAAACCCTAC	60.107	60.000	0.00	0.00	38.24	3.18
2895	7082	1.219646	GCCGGGATACGCGAATTTTA	58.780	50.000	15.93	0.00	42.31	1.52
2914	7101	2.570181	GGGATACGGCGGGATACG	59.430	66.667	13.24	0.00	42.19	3.06
2915	7102	2.976356	GGGGATACGGCGGGATAC	59.024	66.667	13.24	4.61	37.60	2.24
2941	7140	1.531264	CGAACTGTCGTCCTGATACGG	60.531	57.143	0.00	0.00	43.05	4.02
2954	7153	1.079127	CCAGGAATCGCCGAACTGT	60.079	57.895	13.29	0.00	43.43	3.55
2993	7192	1.478654	CCGTGCCCTAATGCCCTATTT	60.479	52.381	0.00	0.00	0.00	1.40
3082	10716	1.253593	ATCTGCTCACTCTCACGGCA	61.254	55.000	0.00	0.00	0.00	5.69
3091	10725	0.104487	CATCCGCTGATCTGCTCACT	59.896	55.000	20.58	2.25	0.00	3.41
3230	10867	5.814188	TGTGAGAGCACTAGAATAAATGCAG	59.186	40.000	0.00	0.00	45.36	4.41

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.