AutoCloner

Multiple sequence alignment - TraesCS3B01G190700

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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	TraesCS3B01G190700	chr3B	100.000	3166	0	0	1	3166	203611937	203615102	0.000000e+00	5847.0
1	TraesCS3B01G190700	chr3B	78.274	336	70	3	1283	1617	15177920	15177587	2.470000e-51	213.0
2	TraesCS3B01G190700	chr3B	86.747	83	11	0	2503	2585	443688221	443688139	3.360000e-15	93.5
3	TraesCS3B01G190700	chr4D	89.400	2585	189	37	8	2551	375115158	375117698	0.000000e+00	3177.0
4	TraesCS3B01G190700	chr4D	81.023	743	113	17	1283	2018	414328434	414327713	1.650000e-157	566.0
5	TraesCS3B01G190700	chr4D	88.148	135	16	0	1151	1285	414350004	414349870	9.090000e-36	161.0
6	TraesCS3B01G190700	chr4D	86.364	154	14	5	1134	1285	414365609	414365461	9.090000e-36	161.0
7	TraesCS3B01G190700	chr4D	86.000	150	21	0	1136	1285	414371368	414371219	9.090000e-36	161.0
8	TraesCS3B01G190700	chr4D	85.526	152	15	5	1136	1285	414337232	414337086	5.470000e-33	152.0
9	TraesCS3B01G190700	chr3A	87.537	2728	235	47	478	3161	160015926	160018592	0.000000e+00	3057.0
10	TraesCS3B01G190700	chr3A	89.299	1626	127	25	679	2280	159994937	159996539	0.000000e+00	1995.0
11	TraesCS3B01G190700	chr3A	79.534	601	77	13	2593	3161	160003587	160004173	1.380000e-103	387.0
12	TraesCS3B01G190700	chr3A	89.286	308	29	3	342	649	159994634	159994937	1.780000e-102	383.0
13	TraesCS3B01G190700	chr3A	81.548	336	62	0	1283	1618	17485259	17484924	8.650000e-71	278.0
14	TraesCS3B01G190700	chr3A	80.952	336	64	0	1283	1618	17433633	17433968	1.870000e-67	267.0
15	TraesCS3B01G190700	chr3D	89.328	1771	132	24	478	2221	141649958	141651698	0.000000e+00	2170.0
16	TraesCS3B01G190700	chr3D	89.922	774	57	11	2215	2980	141652494	141653254	0.000000e+00	977.0
17	TraesCS3B01G190700	chr3D	87.048	525	40	15	1	500	141451346	141451867	4.580000e-158	568.0
18	TraesCS3B01G190700	chr3D	90.419	334	23	6	482	810	141596788	141597117	6.270000e-117	431.0
19	TraesCS3B01G190700	chr3D	93.782	193	9	3	2971	3161	141653822	141654013	1.440000e-73	287.0
20	TraesCS3B01G190700	chr3D	84.444	90	13	1	2499	2587	343498126	343498037	1.560000e-13	87.9
21	TraesCS3B01G190700	chr4B	80.972	741	117	15	1283	2018	510434778	510434057	1.650000e-157	566.0
22	TraesCS3B01G190700	chr4B	79.079	717	124	16	1283	1995	510562431	510561737	1.330000e-128	470.0
23	TraesCS3B01G190700	chr4B	87.097	155	13	5	1133	1285	510482217	510482068	5.430000e-38	169.0
24	TraesCS3B01G190700	chr4A	80.972	741	111	19	1283	2018	49200043	49200758	7.670000e-156	560.0
25	TraesCS3B01G190700	chr2D	88.043	92	11	0	2496	2587	544207181	544207272	3.340000e-20	110.0
26	TraesCS3B01G190700	chr7A	84.946	93	13	1	2496	2587	204173421	204173329	3.360000e-15	93.5
27	TraesCS3B01G190700	chr6B	84.270	89	12	2	2500	2587	35374111	35374024	5.630000e-13	86.1
28	TraesCS3B01G190700	chr7D	89.231	65	7	0	2522	2586	185911153	185911217	7.280000e-12	82.4
29	TraesCS3B01G190700	chr1B	83.146	89	14	1	2498	2585	111915863	111915951	2.620000e-11	80.5

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	TraesCS3B01G190700	chr3B	203611937	203615102	3165	False	5847.000000	5847	100.000000	1	3166	1	chr3B.!!$F1	3165
1	TraesCS3B01G190700	chr4D	375115158	375117698	2540	False	3177.000000	3177	89.400000	8	2551	1	chr4D.!!$F1	2543
2	TraesCS3B01G190700	chr4D	414327713	414328434	721	True	566.000000	566	81.023000	1283	2018	1	chr4D.!!$R1	735
3	TraesCS3B01G190700	chr3A	160015926	160018592	2666	False	3057.000000	3057	87.537000	478	3161	1	chr3A.!!$F3	2683
4	TraesCS3B01G190700	chr3A	159994634	159996539	1905	False	1189.000000	1995	89.292500	342	2280	2	chr3A.!!$F4	1938
5	TraesCS3B01G190700	chr3A	160003587	160004173	586	False	387.000000	387	79.534000	2593	3161	1	chr3A.!!$F2	568
6	TraesCS3B01G190700	chr3D	141649958	141654013	4055	False	1144.666667	2170	91.010667	478	3161	3	chr3D.!!$F3	2683
7	TraesCS3B01G190700	chr3D	141451346	141451867	521	False	568.000000	568	87.048000	1	500	1	chr3D.!!$F1	499
8	TraesCS3B01G190700	chr4B	510434057	510434778	721	True	566.000000	566	80.972000	1283	2018	1	chr4B.!!$R1	735
9	TraesCS3B01G190700	chr4B	510561737	510562431	694	True	470.000000	470	79.079000	1283	1995	1	chr4B.!!$R3	712
10	TraesCS3B01G190700	chr4A	49200043	49200758	715	False	560.000000	560	80.972000	1283	2018	1	chr4A.!!$F1	735

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
344	371	0.601841	AAGACGTGCGACCCGAAAAT	60.602	50.0	0.0	0.0	0.0	1.82	F
1198	1275	0.032952	GTTCGTCTGCTGTGGGTGTA	59.967	55.0	0.0	0.0	0.0	2.90	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1411	1490	0.392863	CACCACATCGGATCTGCCAA	60.393	55.0	0.00	0.00	38.63	4.52	R
3080	4590	0.030638	CCGCCACAAAGTTTGGAGTG	59.969	55.0	19.45	15.03	36.02	3.51	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
103	104	6.803154	AAAGTAGCTAAGATTTGTGTGGTC	57.197	37.500	0.00	0.00	0.00	4.02
104	105	5.746990	AGTAGCTAAGATTTGTGTGGTCT	57.253	39.130	0.00	0.00	0.00	3.85
253	278	1.565156	GCTGGCACAACGAACGATCA	61.565	55.000	0.14	0.00	38.70	2.92
304	330	1.535462	CGCATTGAAGAAGAACGGGTT	59.465	47.619	0.00	0.00	0.00	4.11
314	340	1.179814	AGAACGGGTTGAGCGAGACT	61.180	55.000	0.00	0.00	0.00	3.24
330	357	1.597700	GACTGCGTGACGACAAGACG	61.598	60.000	10.10	0.00	39.31	4.18
344	371	0.601841	AAGACGTGCGACCCGAAAAT	60.602	50.000	0.00	0.00	0.00	1.82
361	388	5.278758	CCGAAAATGCACTAAAGGGAAAAGA	60.279	40.000	0.00	0.00	0.00	2.52
380	407	7.169813	GGAAAAGACCAAACAATCAACTGATTC	59.830	37.037	1.87	0.00	42.41	2.52
414	441	2.223112	CGGTGAGATCCGCAAAGAAATG	60.223	50.000	0.00	0.00	43.96	2.32
431	458	4.530553	AGAAATGGGACGGCCTAAAAATTT	59.469	37.500	7.57	6.21	0.00	1.82
434	461	3.436243	TGGGACGGCCTAAAAATTTGAT	58.564	40.909	7.57	0.00	0.00	2.57
455	482	6.995364	TGATCTGAAGCCAAATCAAAATCAA	58.005	32.000	0.00	0.00	0.00	2.57
457	484	8.098286	TGATCTGAAGCCAAATCAAAATCAATT	58.902	29.630	0.00	0.00	0.00	2.32
458	485	9.590451	GATCTGAAGCCAAATCAAAATCAATTA	57.410	29.630	0.00	0.00	0.00	1.40
526	554	3.487202	CGCCGTCGATGTTGTGGG	61.487	66.667	3.52	0.00	38.10	4.61
545	573	2.044555	CCAGGTGCAGTGCAGGATG	61.045	63.158	20.42	16.64	40.08	3.51
569	600	3.552541	CCGTACGATTCGAGGAACATAG	58.447	50.000	18.76	0.00	0.00	2.23
595	626	2.019807	TCCTTTCGTAGACAAGGGGT	57.980	50.000	0.00	0.00	41.63	4.95
627	658	1.523938	GACATCCCAAGGTAGGCGC	60.524	63.158	0.00	0.00	0.00	6.53
641	672	2.489938	AGGCGCCAAGAAAGTCAATA	57.510	45.000	31.54	0.00	0.00	1.90
642	673	3.004752	AGGCGCCAAGAAAGTCAATAT	57.995	42.857	31.54	0.00	0.00	1.28
696	727	5.082059	CGTCAAGCATACACATCTGAAAAC	58.918	41.667	0.00	0.00	0.00	2.43
811	845	8.807948	AAACAACCAGTGATATAATGCTAACT	57.192	30.769	0.00	0.00	0.00	2.24
813	847	8.438676	ACAACCAGTGATATAATGCTAACTTC	57.561	34.615	0.00	0.00	0.00	3.01
1027	1089	2.519771	AGCCATCAGAAGCAAATCCA	57.480	45.000	0.00	0.00	0.00	3.41
1061	1125	4.452455	ACGAACAAACAGATAGGCAAAGAG	59.548	41.667	0.00	0.00	0.00	2.85
1198	1275	0.032952	GTTCGTCTGCTGTGGGTGTA	59.967	55.000	0.00	0.00	0.00	2.90
1446	1525	1.891919	GTGCAAACCAGGCGTCTCA	60.892	57.895	0.00	0.00	0.00	3.27
1628	1711	3.758554	AGGTACACATGCATGAGTTTTCC	59.241	43.478	32.75	27.04	33.68	3.13
1739	1826	0.672401	GGGTGCGGTTCAAGATCGAA	60.672	55.000	0.00	0.00	0.00	3.71
1742	1829	1.019278	TGCGGTTCAAGATCGAAGGC	61.019	55.000	0.00	0.00	0.00	4.35
1775	1862	5.670792	TCAACCTAGTTACCGTGATGAAT	57.329	39.130	0.00	0.00	0.00	2.57
1832	1919	3.990469	TCAAGAGCTCTGATTCAAACGAC	59.010	43.478	19.06	0.00	0.00	4.34
1839	1926	4.248859	CTCTGATTCAAACGACTGGATGT	58.751	43.478	0.00	0.00	0.00	3.06
2040	2129	7.872993	TCTCCGGTGATCAATTTAGAATATGAC	59.127	37.037	0.00	0.00	0.00	3.06
2041	2130	6.934645	TCCGGTGATCAATTTAGAATATGACC	59.065	38.462	0.00	0.00	0.00	4.02
2053	2142	5.097742	AGAATATGACCGGTTCATGAACA	57.902	39.130	33.42	17.50	45.22	3.18
2061	2153	5.163248	TGACCGGTTCATGAACATACCATAT	60.163	40.000	33.42	13.86	42.85	1.78
2062	2154	5.690865	ACCGGTTCATGAACATACCATATT	58.309	37.500	33.42	9.37	42.85	1.28
2115	2207	2.666272	TTGTGCCCTGGTGTTCAATA	57.334	45.000	0.00	0.00	0.00	1.90
2205	2300	9.708222	CTTGTATGTGATTAACTTGTTCTATGC	57.292	33.333	0.00	0.00	0.00	3.14
2267	3164	5.462530	TGACTGATTCTACCGAGTTTCAA	57.537	39.130	0.00	0.00	0.00	2.69
2312	3210	8.646900	ACTTGTGGAAACCAACATTTATAACAT	58.353	29.630	0.00	0.00	34.18	2.71
2332	3230	6.047511	ACATTATAAGGCAAAATGGTTGCA	57.952	33.333	12.66	0.00	46.58	4.08
2481	3380	1.599071	CAACGGAATGTGATCGGATGG	59.401	52.381	0.00	0.00	0.00	3.51
2486	3385	3.242739	CGGAATGTGATCGGATGGTTTTC	60.243	47.826	0.00	0.00	0.00	2.29
2488	3387	4.035675	GGAATGTGATCGGATGGTTTTCTC	59.964	45.833	0.00	0.00	0.00	2.87
2490	3389	3.861840	TGTGATCGGATGGTTTTCTCTC	58.138	45.455	0.00	0.00	0.00	3.20
2515	3414	0.109723	CGAAAAGGAGGACAACCCCA	59.890	55.000	0.00	0.00	36.73	4.96
2553	3454	6.088719	CGGTGCGCACAATTATTTTTATTT	57.911	33.333	38.60	0.00	0.00	1.40
2554	3455	6.529696	CGGTGCGCACAATTATTTTTATTTT	58.470	32.000	38.60	0.00	0.00	1.82
2650	3556	7.076842	TGAGTTCAAGTTCTCACTTTTCTTG	57.923	36.000	0.00	0.00	40.66	3.02
2690	3596	4.771590	ATGTTGTCCACATAAAGCACAG	57.228	40.909	0.00	0.00	45.00	3.66
2704	3611	8.076178	ACATAAAGCACAGTACATCAGAAAAAC	58.924	33.333	0.00	0.00	0.00	2.43
2739	3646	6.616237	ATCCCAAAGAAAGCAAATCATCTT	57.384	33.333	0.00	0.00	33.73	2.40
2824	3738	9.631257	ACACACATATCTCATCCATTAAATCAA	57.369	29.630	0.00	0.00	0.00	2.57
2834	3748	9.941664	CTCATCCATTAAATCAACATAACTGTC	57.058	33.333	0.00	0.00	33.36	3.51
2967	3897	2.102252	GTCCAAGGTGGTCAAATGCAAA	59.898	45.455	0.00	0.00	39.03	3.68
2972	4479	5.337410	CCAAGGTGGTCAAATGCAAATATGA	60.337	40.000	0.00	0.00	31.35	2.15
3133	4645	5.661458	AGTGTACACGGGAGATAAATCAAG	58.339	41.667	19.93	0.00	36.20	3.02
3161	4673	9.344772	ACAAGACCTACAATACAACACAAAATA	57.655	29.630	0.00	0.00	0.00	1.40
3164	4676	9.959721	AGACCTACAATACAACACAAAATATCT	57.040	29.630	0.00	0.00	0.00	1.98
3165	4677	9.988350	GACCTACAATACAACACAAAATATCTG	57.012	33.333	0.00	0.00	0.00	2.90

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
116	117	2.834549	GAGGGAGGAGTGTCAGATTCAA	59.165	50.000	0.00	0.00	0.00	2.69
249	274	2.768834	GGAGAGGCCGTTGTTGATC	58.231	57.895	0.00	0.00	0.00	2.92
304	330	2.255554	GTCACGCAGTCTCGCTCA	59.744	61.111	0.00	0.00	41.61	4.26
314	340	1.942223	CACGTCTTGTCGTCACGCA	60.942	57.895	0.00	0.00	42.27	5.24
330	357	1.442017	GTGCATTTTCGGGTCGCAC	60.442	57.895	0.00	0.00	45.25	5.34
344	371	3.586470	TGGTCTTTTCCCTTTAGTGCA	57.414	42.857	0.00	0.00	0.00	4.57
361	388	5.106157	GGATCGAATCAGTTGATTGTTTGGT	60.106	40.000	11.81	0.00	44.14	3.67
380	407	3.478394	CACCGTGCACGTGGATCG	61.478	66.667	34.81	21.74	46.00	3.69
414	441	3.699538	AGATCAAATTTTTAGGCCGTCCC	59.300	43.478	0.00	0.00	0.00	4.46
431	458	6.593268	TGATTTTGATTTGGCTTCAGATCA	57.407	33.333	0.00	0.00	39.34	2.92
434	461	9.206870	GTTAATTGATTTTGATTTGGCTTCAGA	57.793	29.630	0.00	0.00	0.00	3.27
526	554	3.933048	ATCCTGCACTGCACCTGGC	62.933	63.158	0.00	0.00	45.13	4.85
545	573	0.379669	TTCCTCGAATCGTACGGCTC	59.620	55.000	16.52	11.08	0.00	4.70
569	600	4.425520	CTTGTCTACGAAAGGATGTCTCC	58.574	47.826	0.00	0.00	42.43	3.71
595	626	1.002257	ATGTCCATGTTCGGCTGCA	60.002	52.632	0.50	0.00	0.00	4.41
660	691	7.429920	GTGTATGCTTGACGTTTTCACTTTTAA	59.570	33.333	0.00	0.00	32.26	1.52
661	692	6.908284	GTGTATGCTTGACGTTTTCACTTTTA	59.092	34.615	0.00	0.00	32.26	1.52
663	694	5.163703	TGTGTATGCTTGACGTTTTCACTTT	60.164	36.000	0.00	0.00	32.26	2.66
664	695	4.334203	TGTGTATGCTTGACGTTTTCACTT	59.666	37.500	0.00	0.00	32.26	3.16
665	696	3.874543	TGTGTATGCTTGACGTTTTCACT	59.125	39.130	0.00	0.00	32.26	3.41
768	799	6.587608	GGTTGTTTATTGATCTTTGCTTCAGG	59.412	38.462	0.00	0.00	0.00	3.86
769	800	7.147312	TGGTTGTTTATTGATCTTTGCTTCAG	58.853	34.615	0.00	0.00	0.00	3.02
1027	1089	1.400494	GTTTGTTCGTGTGCTTCAGGT	59.600	47.619	0.00	0.00	34.10	4.00
1061	1125	0.321919	TGAATCTGGGAGCTGTGTGC	60.322	55.000	0.00	0.00	43.29	4.57
1198	1275	4.652131	TTTGTCCGCGGCCATGGT	62.652	61.111	23.51	0.00	0.00	3.55
1348	1425	1.154413	CATCGTTGAACAGCACCGC	60.154	57.895	0.00	0.00	31.87	5.68
1365	1442	4.262089	TGTCCACATGCCGCACCA	62.262	61.111	0.00	0.00	0.00	4.17
1411	1490	0.392863	CACCACATCGGATCTGCCAA	60.393	55.000	0.00	0.00	38.63	4.52
1446	1525	4.295119	GTGGCCGTCACCGTCACT	62.295	66.667	0.00	0.00	40.39	3.41
1524	1603	1.331214	CCATGTCAAAGTGTGGCCTT	58.669	50.000	3.32	0.00	0.00	4.35
1615	1698	7.288810	ACAATCTTTTAGGAAAACTCATGCA	57.711	32.000	0.00	0.00	0.00	3.96
1684	1771	2.397044	TGGGACCCTGCAGAAAAATT	57.603	45.000	17.39	0.00	0.00	1.82
1739	1826	1.628846	AGGTTGAAGTAATCGTGGCCT	59.371	47.619	3.32	0.00	0.00	5.19
1742	1829	5.809051	GGTAACTAGGTTGAAGTAATCGTGG	59.191	44.000	0.00	0.00	0.00	4.94
1832	1919	2.936498	GTTACGGGACATTGACATCCAG	59.064	50.000	0.00	0.00	36.65	3.86
2040	2129	6.633500	AAATATGGTATGTTCATGAACCGG	57.367	37.500	30.66	0.00	40.46	5.28
2041	2130	8.148807	TGTAAATATGGTATGTTCATGAACCG	57.851	34.615	30.66	0.00	40.46	4.44
2088	2180	4.972751	ACACCAGGGCACAAATAAATTT	57.027	36.364	0.00	0.00	0.00	1.82
2312	3210	4.874966	GCATGCAACCATTTTGCCTTATAA	59.125	37.500	14.21	0.00	44.32	0.98
2481	3380	5.774630	TCCTTTTCGAGAGAGAGAGAAAAC	58.225	41.667	0.00	0.00	43.69	2.43
2486	3385	3.377172	GTCCTCCTTTTCGAGAGAGAGAG	59.623	52.174	1.20	3.36	43.69	3.20
2488	3387	3.085533	TGTCCTCCTTTTCGAGAGAGAG	58.914	50.000	1.20	5.57	43.69	3.20
2490	3389	3.580731	GTTGTCCTCCTTTTCGAGAGAG	58.419	50.000	1.20	0.00	43.69	3.20
2681	3587	7.282224	AGTGTTTTTCTGATGTACTGTGCTTTA	59.718	33.333	0.00	0.00	0.00	1.85
2690	3596	7.421530	TTCTAGCAGTGTTTTTCTGATGTAC	57.578	36.000	0.00	0.00	35.20	2.90
2704	3611	5.964958	TTCTTTGGGATTTTCTAGCAGTG	57.035	39.130	0.00	0.00	0.00	3.66
2739	3646	5.733620	AAGAGTTTCTTGTATCCACGGTA	57.266	39.130	0.00	0.00	34.98	4.02
2764	3671	5.860941	AATGGTCATGGACTACTAGTGAG	57.139	43.478	5.39	1.88	32.47	3.51
2824	3738	8.918202	TTGTGATTTTCTAAGGACAGTTATGT	57.082	30.769	0.00	0.00	44.31	2.29
2830	3744	7.361542	CCAGTGATTGTGATTTTCTAAGGACAG	60.362	40.741	0.00	0.00	0.00	3.51
2834	3748	6.824305	ACCAGTGATTGTGATTTTCTAAGG	57.176	37.500	0.00	0.00	0.00	2.69
2967	3897	6.403636	GCTTTTCGTTGGTCATGAAGTCATAT	60.404	38.462	0.00	0.00	34.26	1.78
2972	4479	2.948979	TGCTTTTCGTTGGTCATGAAGT	59.051	40.909	0.00	0.00	31.71	3.01
3080	4590	0.030638	CCGCCACAAAGTTTGGAGTG	59.969	55.000	19.45	15.03	36.02	3.51
3133	4645	7.718272	TTGTGTTGTATTGTAGGTCTTGTAC	57.282	36.000	0.00	0.00	0.00	2.90

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.