AutoCloner

Multiple sequence alignment - TraesCS5B01G221500

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	TraesCS5B01G221500	chr5B	100.000	3256	0	0	1	3256	395920695	395923950	0.000000e+00	6013
1	TraesCS5B01G221500	chr5D	95.958	2573	81	12	703	3256	337301335	337303903	0.000000e+00	4154
2	TraesCS5B01G221500	chr5D	95.562	721	21	5	1	719	337300593	337301304	0.000000e+00	1144
3	TraesCS5B01G221500	chr5A	94.083	2535	103	27	763	3256	438471510	438474038	0.000000e+00	3807
4	TraesCS5B01G221500	chr5A	87.973	582	48	8	1	575	438470695	438471261	0.000000e+00	667
5	TraesCS5B01G221500	chr1A	85.741	533	76	0	1113	1645	256827668	256827136	6.100000e-157	564
6	TraesCS5B01G221500	chr1A	83.569	353	53	3	1783	2134	256827014	256826666	3.130000e-85	326
7	TraesCS5B01G221500	chr1A	81.944	144	24	2	3112	3254	256825578	256825436	1.590000e-23	121
8	TraesCS5B01G221500	chr1D	85.178	533	79	0	1113	1645	202570177	202569645	6.140000e-152	547
9	TraesCS5B01G221500	chr1D	82.927	369	58	3	1767	2134	202569537	202569173	8.710000e-86	327
10	TraesCS5B01G221500	chr1D	84.722	144	20	2	3112	3254	202568096	202567954	3.390000e-30	143
11	TraesCS5B01G221500	chr1B	85.283	530	78	0	1116	1645	296502657	296502128	6.140000e-152	547
12	TraesCS5B01G221500	chr1B	82.927	369	58	3	1767	2134	296502020	296501656	8.710000e-86	327
13	TraesCS5B01G221500	chr1B	83.333	144	22	2	3112	3254	296500543	296500401	7.330000e-27	132
14	TraesCS5B01G221500	chr6A	81.949	554	90	5	1079	1627	47903013	47902465	8.230000e-126	460
15	TraesCS5B01G221500	chr3B	79.563	504	97	4	1134	1637	525611941	525611444	4.000000e-94	355
16	TraesCS5B01G221500	chr7D	74.541	436	98	12	1149	1576	14880463	14880893	9.280000e-41	178
17	TraesCS5B01G221500	chr7A	74.201	438	98	14	1148	1576	14189538	14189969	5.590000e-38	169

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	TraesCS5B01G221500	chr5B	395920695	395923950	3255	False	6013.000000	6013	100.000000	1	3256	1	chr5B.!!$F1	3255
1	TraesCS5B01G221500	chr5D	337300593	337303903	3310	False	2649.000000	4154	95.760000	1	3256	2	chr5D.!!$F1	3255
2	TraesCS5B01G221500	chr5A	438470695	438474038	3343	False	2237.000000	3807	91.028000	1	3256	2	chr5A.!!$F1	3255
3	TraesCS5B01G221500	chr1A	256825436	256827668	2232	True	337.000000	564	83.751333	1113	3254	3	chr1A.!!$R1	2141
4	TraesCS5B01G221500	chr1D	202567954	202570177	2223	True	339.000000	547	84.275667	1113	3254	3	chr1D.!!$R1	2141
5	TraesCS5B01G221500	chr1B	296500401	296502657	2256	True	335.333333	547	83.847667	1116	3254	3	chr1B.!!$R1	2138
6	TraesCS5B01G221500	chr6A	47902465	47903013	548	True	460.000000	460	81.949000	1079	1627	1	chr6A.!!$R1	548

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
287	290	0.176910	GTGCACTTCTAGCCCCTCTC	59.823	60.0	10.32	0.0	0.00	3.20	F
712	825	0.799534	GCGGCTGCTGTAATGCAAAG	60.800	55.0	11.21	0.0	42.83	2.77	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1760	1939	0.108992	CGCCGGTCAGTGCTAGTAAA	60.109	55.0	1.9	0.0	0.0	2.01	R
2484	2896	0.037303	CAGGGGAAGCACACACTGAT	59.963	55.0	0.0	0.0	0.0	2.90	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
26	27	4.044065	TCCAGATGAATTAACAACCTGGGT	59.956	41.667	0.00	0.00	0.00	4.51
121	123	2.423538	ACTGTGCAAACAGACAAGGAAC	59.576	45.455	12.57	0.00	39.99	3.62
148	150	7.739043	CCGTAGAGAAGAAATAACAAAACGAAC	59.261	37.037	0.00	0.00	0.00	3.95
162	164	8.703823	AACAAAACGAACGAGTATTAAACATC	57.296	30.769	0.14	0.00	0.00	3.06
181	183	2.825836	CCCTGCCGATCAAGGTGC	60.826	66.667	5.60	0.00	0.00	5.01
285	288	1.486211	TAGTGCACTTCTAGCCCCTC	58.514	55.000	27.06	0.00	0.00	4.30
286	289	0.252467	AGTGCACTTCTAGCCCCTCT	60.252	55.000	15.25	0.00	0.00	3.69
287	290	0.176910	GTGCACTTCTAGCCCCTCTC	59.823	60.000	10.32	0.00	0.00	3.20
288	291	0.978146	TGCACTTCTAGCCCCTCTCC	60.978	60.000	0.00	0.00	0.00	3.71
289	292	1.691195	GCACTTCTAGCCCCTCTCCC	61.691	65.000	0.00	0.00	0.00	4.30
290	293	1.051556	CACTTCTAGCCCCTCTCCCC	61.052	65.000	0.00	0.00	0.00	4.81
318	321	7.119709	CCCCCTCTTTTAGTTTCTTTTCAAA	57.880	36.000	0.00	0.00	0.00	2.69
465	468	3.061831	CAGATTTTGTAGCTGTGCTCTCG	59.938	47.826	0.00	0.00	40.44	4.04
618	627	6.072618	GGTGGATATCAGAATTCTGCTTCATG	60.073	42.308	27.45	6.44	43.46	3.07
712	825	0.799534	GCGGCTGCTGTAATGCAAAG	60.800	55.000	11.21	0.00	42.83	2.77
757	924	6.119536	TGATGGTTTGGTGAATACTGGTATC	58.880	40.000	0.00	0.00	0.00	2.24
761	928	5.497474	GTTTGGTGAATACTGGTATCCTGT	58.503	41.667	4.00	4.00	39.06	4.00
779	947	7.921041	ATCCTGTTTATCCTCAGTCTGAATA	57.079	36.000	3.67	0.00	0.00	1.75
790	958	8.740123	TCCTCAGTCTGAATACTACTCTTAAG	57.260	38.462	3.67	0.00	0.00	1.85
821	989	6.346518	CGTTCAAAAATCAAGTAAATGCACCC	60.347	38.462	0.00	0.00	0.00	4.61
825	993	3.848272	ATCAAGTAAATGCACCCGTTG	57.152	42.857	0.00	0.00	0.00	4.10
878	1046	3.868619	AACTTACCAGCTACCCACAAA	57.131	42.857	0.00	0.00	0.00	2.83
1014	1188	7.710044	ACAAAACATAGCATGAACAAAACATCA	59.290	29.630	0.00	0.00	0.00	3.07
1076	1250	6.545504	TGCACAATCTTCAGAACTCTTAAC	57.454	37.500	0.00	0.00	0.00	2.01
1753	1932	2.604912	AGGAGGACAAATGGGGAAAC	57.395	50.000	0.00	0.00	0.00	2.78
1754	1933	2.073776	AGGAGGACAAATGGGGAAACT	58.926	47.619	0.00	0.00	0.00	2.66
1755	1934	3.265489	AGGAGGACAAATGGGGAAACTA	58.735	45.455	0.00	0.00	0.00	2.24
1756	1935	3.267031	AGGAGGACAAATGGGGAAACTAG	59.733	47.826	0.00	0.00	0.00	2.57
1757	1936	3.017442	GAGGACAAATGGGGAAACTAGC	58.983	50.000	0.00	0.00	0.00	3.42
1758	1937	2.649816	AGGACAAATGGGGAAACTAGCT	59.350	45.455	0.00	0.00	0.00	3.32
1759	1938	2.755103	GGACAAATGGGGAAACTAGCTG	59.245	50.000	0.00	0.00	0.00	4.24
1760	1939	3.421844	GACAAATGGGGAAACTAGCTGT	58.578	45.455	0.00	0.00	0.00	4.40
1761	1940	3.826729	GACAAATGGGGAAACTAGCTGTT	59.173	43.478	0.00	0.00	41.29	3.16
1997	2255	1.046472	ACACCTGGTTGAGACGGTCA	61.046	55.000	11.27	0.00	0.00	4.02
2128	2386	0.979187	GACCCGTAGATCCACCCCAA	60.979	60.000	0.00	0.00	0.00	4.12
2166	2430	4.494091	AGGAACACAGATCATTACTGGG	57.506	45.455	0.00	0.00	43.49	4.45
2180	2444	5.964477	TCATTACTGGGAGTCTGGAACTATT	59.036	40.000	0.00	0.00	38.74	1.73
2378	2790	3.589654	CTGCCCGAACCGCTTCTCA	62.590	63.158	0.00	0.00	0.00	3.27
2442	2854	2.617532	CCTGGAGAGCCAAAGAGGAAAG	60.618	54.545	0.00	0.00	45.41	2.62
2484	2896	4.497340	GCGACTGAACTGAAACCAAAATGA	60.497	41.667	0.00	0.00	0.00	2.57
2681	3162	1.201647	CATCCTGTTCCGACGTACACT	59.798	52.381	0.00	0.00	0.00	3.55
2693	3174	0.828022	CGTACACTGGCCCTTGGATA	59.172	55.000	0.00	0.00	0.00	2.59
2714	3195	0.251916	CGTCCAGCCCCTTCATGTTA	59.748	55.000	0.00	0.00	0.00	2.41
2734	3215	8.824781	CATGTTAATCTGATCACCAAGAACTAG	58.175	37.037	0.00	0.00	0.00	2.57
2735	3216	7.907389	TGTTAATCTGATCACCAAGAACTAGT	58.093	34.615	0.00	0.00	0.00	2.57
2746	3227	8.367660	TCACCAAGAACTAGTAATCTCAGATT	57.632	34.615	4.98	4.98	0.00	2.40
2765	3246	5.538053	CAGATTCATGGCTCTCCTAGACTAA	59.462	44.000	0.00	0.00	32.57	2.24
2766	3247	6.041409	CAGATTCATGGCTCTCCTAGACTAAA	59.959	42.308	0.00	0.00	32.57	1.85
2767	3248	6.613271	AGATTCATGGCTCTCCTAGACTAAAA	59.387	38.462	0.00	0.00	32.57	1.52
2785	3266	9.601217	AGACTAAAACATAATGTAGGTGTGATC	57.399	33.333	0.00	0.00	0.00	2.92
2790	3278	5.357257	ACATAATGTAGGTGTGATCGAACC	58.643	41.667	8.28	8.28	36.66	3.62
2794	3282	2.819019	TGTAGGTGTGATCGAACCGTAA	59.181	45.455	10.15	0.00	41.61	3.18
3063	3571	3.938963	TGAGCAAGAAACGTTCTGAGTTT	59.061	39.130	0.00	0.00	43.60	2.66

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
3	4	4.044065	ACCCAGGTTGTTAATTCATCTGGA	59.956	41.667	10.85	0.00	39.32	3.86
121	123	6.366877	TCGTTTTGTTATTTCTTCTCTACGGG	59.633	38.462	0.00	0.00	0.00	5.28
148	150	3.139077	GCAGGGGGATGTTTAATACTCG	58.861	50.000	0.00	0.00	0.00	4.18
181	183	2.674852	AGTTGTTATCTGCACAGCATCG	59.325	45.455	0.00	0.00	38.13	3.84
318	321	2.291605	GGAAAAGAATGGGGCACTACCT	60.292	50.000	0.00	0.00	39.10	3.08
386	389	9.061435	CCATATCTTTCAGTATCTTTTTCCCTC	57.939	37.037	0.00	0.00	0.00	4.30
465	468	1.958579	GGGGTTGGTTAAGGTGACAAC	59.041	52.381	0.00	0.00	41.71	3.32
585	594	7.069085	CAGAATTCTGATATCCACCAAACCATT	59.931	37.037	28.13	0.00	46.59	3.16
618	627	6.280643	ACTTTAAACTTGGAACTGGAAATGC	58.719	36.000	0.00	0.00	0.00	3.56
624	633	7.095695	TCAAAGACTTTAAACTTGGAACTGG	57.904	36.000	0.00	0.00	0.00	4.00
695	808	1.135286	GGACTTTGCATTACAGCAGCC	60.135	52.381	0.00	0.00	46.54	4.85
712	825	9.520204	CCATCATAAATGTACAATTCAAAGGAC	57.480	33.333	0.00	0.00	0.00	3.85
757	924	7.118496	AGTATTCAGACTGAGGATAAACAGG	57.882	40.000	5.10	0.00	0.00	4.00
761	928	9.702253	AAGAGTAGTATTCAGACTGAGGATAAA	57.298	33.333	5.10	0.00	0.00	1.40
779	947	8.652810	TTTTGAACGTAAAGCTTAAGAGTAGT	57.347	30.769	6.67	0.00	0.00	2.73
790	958	9.777843	CATTTACTTGATTTTTGAACGTAAAGC	57.222	29.630	0.00	0.00	31.48	3.51
806	974	2.577700	ACAACGGGTGCATTTACTTGA	58.422	42.857	0.00	0.00	0.00	3.02
821	989	5.109903	AGCCTAATGTAGCTAAGAACAACG	58.890	41.667	0.00	0.00	37.64	4.10
825	993	7.793927	ATCAAAGCCTAATGTAGCTAAGAAC	57.206	36.000	0.00	0.00	38.74	3.01
878	1046	4.136796	TGTGTTTTAGCTGTGATTGCTCT	58.863	39.130	0.00	0.00	41.46	4.09
1096	1270	1.595382	GCCTGACGTGAAGCAGTGT	60.595	57.895	0.00	0.00	0.00	3.55
1753	1932	4.425520	GGTCAGTGCTAGTAAACAGCTAG	58.574	47.826	0.00	0.00	39.83	3.42
1754	1933	3.119602	CGGTCAGTGCTAGTAAACAGCTA	60.120	47.826	0.00	0.00	39.83	3.32
1755	1934	2.352814	CGGTCAGTGCTAGTAAACAGCT	60.353	50.000	0.00	0.00	39.83	4.24
1756	1935	1.993370	CGGTCAGTGCTAGTAAACAGC	59.007	52.381	0.00	0.00	39.56	4.40
1757	1936	2.607187	CCGGTCAGTGCTAGTAAACAG	58.393	52.381	0.00	0.00	0.00	3.16
1758	1937	1.337447	GCCGGTCAGTGCTAGTAAACA	60.337	52.381	1.90	0.00	0.00	2.83
1759	1938	1.356938	GCCGGTCAGTGCTAGTAAAC	58.643	55.000	1.90	0.00	0.00	2.01
1760	1939	0.108992	CGCCGGTCAGTGCTAGTAAA	60.109	55.000	1.90	0.00	0.00	2.01
1761	1940	1.509463	CGCCGGTCAGTGCTAGTAA	59.491	57.895	1.90	0.00	0.00	2.24
1762	1941	2.412323	CCGCCGGTCAGTGCTAGTA	61.412	63.158	1.90	0.00	0.00	1.82
1763	1942	3.760035	CCGCCGGTCAGTGCTAGT	61.760	66.667	1.90	0.00	0.00	2.57
1823	2081	4.135153	CCGCTGCTCGCCTACTGT	62.135	66.667	0.00	0.00	36.73	3.55
1978	2236	1.046472	TGACCGTCTCAACCAGGTGT	61.046	55.000	0.00	0.00	37.07	4.16
1997	2255	2.125512	GCGCCGATCAACCTGTCT	60.126	61.111	0.00	0.00	0.00	3.41
2144	2402	4.536090	TCCCAGTAATGATCTGTGTTCCTT	59.464	41.667	0.00	0.00	0.00	3.36
2166	2430	7.010923	CAGCTTCACATAAATAGTTCCAGACTC	59.989	40.741	0.00	0.00	39.86	3.36
2180	2444	4.202357	ACCACTTCAGACAGCTTCACATAA	60.202	41.667	0.00	0.00	0.00	1.90
2321	2733	0.392998	CCACGTTCATGGAGGAAGGG	60.393	60.000	0.00	0.00	43.02	3.95
2378	2790	5.191426	CAGATGATGTCCCAGATGAACTTT	58.809	41.667	0.00	0.00	0.00	2.66
2442	2854	2.735134	CGCTTAGTACAGGTTGGTGAAC	59.265	50.000	0.00	0.00	0.00	3.18
2484	2896	0.037303	CAGGGGAAGCACACACTGAT	59.963	55.000	0.00	0.00	0.00	2.90
2681	3162	3.316029	GACGGTATCCAAGGGCCA	58.684	61.111	6.18	0.00	0.00	5.36
2693	3174	2.610859	ATGAAGGGGCTGGACGGT	60.611	61.111	0.00	0.00	0.00	4.83
2714	3195	8.986991	AGATTACTAGTTCTTGGTGATCAGATT	58.013	33.333	0.00	0.00	36.23	2.40
2734	3215	5.011943	AGGAGAGCCATGAATCTGAGATTAC	59.988	44.000	7.82	3.03	36.29	1.89
2735	3216	5.153675	AGGAGAGCCATGAATCTGAGATTA	58.846	41.667	7.82	0.00	36.29	1.75
2746	3227	5.023452	TGTTTTAGTCTAGGAGAGCCATGA	58.977	41.667	0.00	0.00	36.29	3.07
2765	3246	6.315393	GGTTCGATCACACCTACATTATGTTT	59.685	38.462	2.23	0.00	0.00	2.83
2766	3247	5.815740	GGTTCGATCACACCTACATTATGTT	59.184	40.000	2.23	0.00	0.00	2.71
2767	3248	5.357257	GGTTCGATCACACCTACATTATGT	58.643	41.667	2.58	2.58	0.00	2.29
2794	3282	2.943993	GTCTTCTTCGACGTAAGCCTT	58.056	47.619	0.00	0.00	45.62	4.35
3063	3571	3.190744	AGAGCTTCGTCGTAAATGTCAGA	59.809	43.478	0.00	0.00	0.00	3.27

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.