AutoCloner

Multiple sequence alignment - TraesCS2D01G252000

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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	TraesCS2D01G252000	chr2D	100.000	5396	0	0	1	5396	302241321	302246716	0.000000e+00	9965.0
1	TraesCS2D01G252000	chr2B	95.483	4251	133	18	923	5139	357913329	357917554	0.000000e+00	6732.0
2	TraesCS2D01G252000	chr2B	92.447	331	13	5	151	480	357911349	357911668	3.810000e-126	462.0
3	TraesCS2D01G252000	chr2B	94.942	257	7	4	5141	5396	357917643	357917894	1.090000e-106	398.0
4	TraesCS2D01G252000	chr2B	86.572	283	2	5	672	926	357912893	357913167	4.120000e-71	279.0
5	TraesCS2D01G252000	chr2B	95.455	110	5	0	1	110	357911239	357911348	5.550000e-40	176.0
6	TraesCS2D01G252000	chr2B	86.154	130	4	2	1151	1280	494372799	494372914	1.580000e-25	128.0
7	TraesCS2D01G252000	chr2A	95.547	3952	112	13	482	4401	379114880	379118799	0.000000e+00	6264.0
8	TraesCS2D01G252000	chr2A	92.254	426	5	7	4467	4892	379119023	379119420	3.620000e-161	579.0
9	TraesCS2D01G252000	chr2A	90.529	454	15	11	30	464	379114449	379114893	4.690000e-160	575.0
10	TraesCS2D01G252000	chr2A	95.082	366	10	3	5031	5396	379150318	379150675	2.180000e-158	569.0
11	TraesCS2D01G252000	chr2A	93.450	229	12	2	4893	5120	379150096	379150322	2.410000e-88	337.0
12	TraesCS2D01G252000	chr2A	91.753	97	3	3	4399	4491	379118881	379118976	4.390000e-26	130.0
13	TraesCS2D01G252000	chr2A	100.000	31	0	0	2	32	379094929	379094959	2.100000e-04	58.4
14	TraesCS2D01G252000	chr3A	95.897	780	28	3	4578	5356	730359817	730360593	0.000000e+00	1260.0
15	TraesCS2D01G252000	chr3A	95.897	780	27	4	4578	5356	102823110	102822335	0.000000e+00	1258.0
16	TraesCS2D01G252000	chr3A	95.006	781	33	5	4578	5356	696664582	696663806	0.000000e+00	1221.0
17	TraesCS2D01G252000	chr5B	85.350	157	11	3	1946	2099	669724879	669725026	9.360000e-33	152.0
18	TraesCS2D01G252000	chr5B	95.833	72	3	0	1095	1166	495820019	495819948	3.410000e-22	117.0
19	TraesCS2D01G252000	chr5B	84.746	118	4	2	1163	1280	495809893	495809790	7.390000e-19	106.0
20	TraesCS2D01G252000	chr5B	100.000	28	0	0	2120	2147	669725027	669725054	1.000000e-02	52.8
21	TraesCS2D01G252000	chr7B	83.007	153	14	3	1946	2095	157116377	157116520	1.580000e-25	128.0
22	TraesCS2D01G252000	chr7B	100.000	30	0	0	2118	2147	157116523	157116552	7.550000e-04	56.5

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	TraesCS2D01G252000	chr2D	302241321	302246716	5395	False	9965.0	9965	100.00000	1	5396	1	chr2D.!!$F1	5395
1	TraesCS2D01G252000	chr2B	357911239	357917894	6655	False	1609.4	6732	92.97980	1	5396	5	chr2B.!!$F2	5395
2	TraesCS2D01G252000	chr2A	379114449	379119420	4971	False	1887.0	6264	92.52075	30	4892	4	chr2A.!!$F2	4862
3	TraesCS2D01G252000	chr2A	379150096	379150675	579	False	453.0	569	94.26600	4893	5396	2	chr2A.!!$F3	503
4	TraesCS2D01G252000	chr3A	730359817	730360593	776	False	1260.0	1260	95.89700	4578	5356	1	chr3A.!!$F1	778
5	TraesCS2D01G252000	chr3A	102822335	102823110	775	True	1258.0	1258	95.89700	4578	5356	1	chr3A.!!$R1	778
6	TraesCS2D01G252000	chr3A	696663806	696664582	776	True	1221.0	1221	95.00600	4578	5356	1	chr3A.!!$R2	778

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
948	2229	0.105964	AGTAAGTGTTCCGCTGTGCA	59.894	50.000	0.00	4.57	F
2007	3307	0.461961	AGCTCGGCAAGATACAGACC	59.538	55.000	0.00	3.85	F
2704	4004	0.462759	CTTCACCGGCCTCATTCCTC	60.463	60.000	0.00	3.71	F
3114	4414	1.203100	AGCAGCAACTTCCTTGGGAAT	60.203	47.619	41.23	3.01	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Hairpin	End Stability	Orientation
2346	3646	0.603707	TCTTGCAAGCCTTCACTCCG	60.604	55.0	21.99	0.00	4.63	R
3161	4461	0.033366	TGCTTCACTGCTTGCGTAGA	59.967	50.0	0.00	0.00	2.59	R
3549	4849	0.890683	GCCTGACATTTCCAAGGGTG	59.109	55.0	0.00	0.00	4.61	R
4986	6456	2.517650	TTGGGCAAAACGAATGTTCC	57.482	45.0	0.00	37.31	3.62	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
115	116	3.435671	CCGGTGAAATAACTGAACCTGAC	59.564	47.826	0.00	0.00	0.00	3.51
192	198	5.932303	GGTTTCTTTTTGAAAAGGGGATAGC	59.068	40.000	14.33	4.41	45.10	2.97
195	201	8.195433	TTTCTTTTTGAAAAGGGGATAGCCCG	62.195	42.308	10.64	0.00	46.94	6.13
229	241	7.654568	CACTATTGTGATGCACATATCCAATT	58.345	34.615	0.50	0.00	44.16	2.32
290	302	6.929625	ACATCTGATGTATTCCTAGGATTCG	58.070	40.000	21.10	2.98	42.78	3.34
333	345	9.081204	ACCAAAATATGAATCATAGCATGCTTA	57.919	29.630	28.02	12.54	29.42	3.09
424	444	8.391106	CCTAAGAAATGAAAAAGGTACGAGATG	58.609	37.037	0.00	0.00	0.00	2.90
453	473	3.007614	ACGTAATCCTAGCCACAAAGTGT	59.992	43.478	0.00	0.00	0.00	3.55
560	1333	1.663730	CGATCCACACGAACACACGTA	60.664	52.381	0.00	0.00	44.76	3.57
561	1334	1.717645	GATCCACACGAACACACGTAC	59.282	52.381	0.00	0.00	44.76	3.67
562	1335	0.740149	TCCACACGAACACACGTACT	59.260	50.000	0.00	0.00	44.76	2.73
563	1336	1.126079	CCACACGAACACACGTACTC	58.874	55.000	0.00	0.00	44.76	2.59
564	1337	1.126079	CACACGAACACACGTACTCC	58.874	55.000	0.00	0.00	44.76	3.85
589	1362	5.221130	ACTTTACTGCGACAAGTCTACTTC	58.779	41.667	0.00	0.00	33.11	3.01
599	1372	6.073657	GCGACAAGTCTACTTCTATCGTCTAT	60.074	42.308	16.11	0.00	33.11	1.98
859	1975	2.594303	TGCTGTTTCCTGGTGGCG	60.594	61.111	0.00	0.00	0.00	5.69
948	2229	0.105964	AGTAAGTGTTCCGCTGTGCA	59.894	50.000	0.00	0.00	0.00	4.57
976	2264	0.555769	TCCTGCCTGAGTTTGGGTTT	59.444	50.000	0.00	0.00	0.00	3.27
1048	2336	6.623767	GCTCAAGATTTTTCTATTTGCCGTCT	60.624	38.462	0.00	0.00	0.00	4.18
1590	2890	3.667282	CGTCTCCGTGTGGTCCGT	61.667	66.667	0.00	0.00	36.30	4.69
1724	3024	1.078848	CCCGGCTCAAGAACCTCAG	60.079	63.158	0.00	0.00	0.00	3.35
2007	3307	0.461961	AGCTCGGCAAGATACAGACC	59.538	55.000	0.00	0.00	0.00	3.85
2295	3595	1.529010	CCTGTGCAGGCACCAGAAA	60.529	57.895	20.60	1.82	45.63	2.52
2346	3646	1.344763	CTCATCGGTAACATCCCTCCC	59.655	57.143	0.00	0.00	0.00	4.30
2547	3847	2.094390	TCTGTCGGGGAATTACTTCGTG	60.094	50.000	4.43	0.00	31.75	4.35
2550	3850	0.463116	CGGGGAATTACTTCGTGGGG	60.463	60.000	0.00	0.00	31.75	4.96
2583	3883	1.523154	GCATTGGCAACCTCACGGAA	61.523	55.000	0.00	0.00	40.72	4.30
2704	4004	0.462759	CTTCACCGGCCTCATTCCTC	60.463	60.000	0.00	0.00	0.00	3.71
2705	4005	2.202932	CACCGGCCTCATTCCTCG	60.203	66.667	0.00	0.00	0.00	4.63
2784	4084	1.337167	GGCACCATTCCTGCAAGTTTC	60.337	52.381	0.00	0.00	36.27	2.78
2835	4135	2.584391	GGGAGGCAACCGTCTGTCT	61.584	63.158	0.00	0.00	32.72	3.41
2838	4138	2.100879	GAGGCAACCGTCTGTCTGGT	62.101	60.000	0.00	0.00	41.20	4.00
2839	4139	1.668151	GGCAACCGTCTGTCTGGTC	60.668	63.158	0.00	0.00	37.54	4.02
2847	4147	1.459348	TCTGTCTGGTCCTGTGCCA	60.459	57.895	0.00	0.00	34.42	4.92
2889	4189	2.293170	GCCCTCCAGATTGCTCTAAAC	58.707	52.381	0.00	0.00	0.00	2.01
3114	4414	1.203100	AGCAGCAACTTCCTTGGGAAT	60.203	47.619	0.00	0.00	41.23	3.01
3126	4426	2.091665	CCTTGGGAATAATGGCCTCTGT	60.092	50.000	3.32	0.00	0.00	3.41
3184	4484	1.585006	GCAAGCAGTGAAGCAGCAT	59.415	52.632	0.00	0.00	37.62	3.79
3256	4556	4.028383	CGTCGTCATATTGGTTTCATTGC	58.972	43.478	0.00	0.00	0.00	3.56
3549	4849	0.597898	GCTTCCGAGCCGAGATAACC	60.598	60.000	0.00	0.00	43.29	2.85
4266	5566	4.726021	GCATTGTTCTGCACTAGTGAATCG	60.726	45.833	27.08	5.36	41.87	3.34
4338	5638	1.065854	AGGGCCTCTTCTTGTGATTCG	60.066	52.381	0.00	0.00	0.00	3.34
4359	5659	3.429960	CGTTCTCATCTCCAGCATCAGAA	60.430	47.826	0.00	0.00	0.00	3.02
4964	6434	7.575414	TTTCTTGCCAACTTACTGTGATAAA	57.425	32.000	0.00	0.00	0.00	1.40
4965	6435	7.575414	TTCTTGCCAACTTACTGTGATAAAA	57.425	32.000	0.00	0.00	0.00	1.52
5139	6688	2.263741	GGGTCAGCAAGGCACACTG	61.264	63.158	0.00	0.00	0.00	3.66
5231	6867	2.278854	GCCACAGCAAACAAACAACAT	58.721	42.857	0.00	0.00	39.53	2.71
5284	6921	4.164221	TCAGACTTTCTTTCCCAGACACTT	59.836	41.667	0.00	0.00	0.00	3.16
5320	6958	9.482627	TTTTTACCCAGTTTGCATAAACATAAG	57.517	29.630	4.19	0.00	46.76	1.73

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
115	116	1.205657	AAAGTATATGCGCACGACCG	58.794	50.000	14.90	0.00	0.00	4.79
196	202	1.596260	CATCACAATAGTGCAGAGGCG	59.404	52.381	0.00	0.00	45.49	5.52
273	285	8.980481	ATTTCAAACGAATCCTAGGAATACAT	57.020	30.769	17.30	0.00	0.00	2.29
290	302	6.993786	TTTTGGTTGGGAAGAATTTCAAAC	57.006	33.333	0.00	0.00	34.90	2.93
333	345	5.372373	GAGCTGGCCTCTTCAAAGTTATAT	58.628	41.667	3.32	0.00	37.60	0.86
340	352	0.320771	GACGAGCTGGCCTCTTCAAA	60.321	55.000	3.32	0.00	38.39	2.69
424	444	3.370061	GTGGCTAGGATTACGTGTGTTTC	59.630	47.826	0.00	0.00	0.00	2.78
480	500	3.991773	GAGGTGTCGTTAACATAAGCACA	59.008	43.478	6.39	0.00	40.80	4.57
481	501	4.243270	AGAGGTGTCGTTAACATAAGCAC	58.757	43.478	6.39	6.46	40.80	4.40
482	502	4.530710	AGAGGTGTCGTTAACATAAGCA	57.469	40.909	6.39	0.00	40.80	3.91
559	1332	4.763793	ACTTGTCGCAGTAAAGTAGGAGTA	59.236	41.667	0.00	0.00	33.88	2.59
560	1333	3.573110	ACTTGTCGCAGTAAAGTAGGAGT	59.427	43.478	0.00	0.00	33.88	3.85
561	1334	4.082679	AGACTTGTCGCAGTAAAGTAGGAG	60.083	45.833	0.00	0.00	35.24	3.69
562	1335	3.825014	AGACTTGTCGCAGTAAAGTAGGA	59.175	43.478	0.00	0.00	35.24	2.94
563	1336	4.175787	AGACTTGTCGCAGTAAAGTAGG	57.824	45.455	0.00	0.00	35.24	3.18
564	1337	5.940595	AGTAGACTTGTCGCAGTAAAGTAG	58.059	41.667	0.00	0.00	35.24	2.57
589	1362	3.156753	CACGATGACGCATAGACGATAG	58.843	50.000	0.00	0.00	43.96	2.08
599	1372	1.374125	CCCTGAACACGATGACGCA	60.374	57.895	0.00	0.00	43.96	5.24
859	1975	5.241949	CCACCCACTATGAGTCTATGACTAC	59.758	48.000	0.00	0.00	43.53	2.73
869	1985	1.584724	CTTCCCCACCCACTATGAGT	58.415	55.000	0.00	0.00	0.00	3.41
870	1986	0.839946	CCTTCCCCACCCACTATGAG	59.160	60.000	0.00	0.00	0.00	2.90
871	1987	0.419865	TCCTTCCCCACCCACTATGA	59.580	55.000	0.00	0.00	0.00	2.15
872	1988	0.839946	CTCCTTCCCCACCCACTATG	59.160	60.000	0.00	0.00	0.00	2.23
976	2264	1.219646	GTACGCGAGAAACAAACCCA	58.780	50.000	15.93	0.00	0.00	4.51
1033	2321	3.674997	AGCTCAAGACGGCAAATAGAAA	58.325	40.909	0.00	0.00	0.00	2.52
1048	2336	3.889134	CTGCCACAGCCGAGCTCAA	62.889	63.158	15.40	0.00	36.40	3.02
1575	2875	3.986006	GCACGGACCACACGGAGA	61.986	66.667	0.00	0.00	35.59	3.71
1724	3024	1.915614	CTGCCACAGGATCAACGTGC	61.916	60.000	0.00	0.00	37.84	5.34
1903	3203	1.821332	CGAGCTCCTTTGGGATGGC	60.821	63.158	8.47	0.00	41.36	4.40
2295	3595	1.558756	CCCAGGCTCAAGAAGATGAGT	59.441	52.381	6.22	0.00	46.85	3.41
2346	3646	0.603707	TCTTGCAAGCCTTCACTCCG	60.604	55.000	21.99	0.00	0.00	4.63
2490	3790	1.738099	CCTGAACTTGCCGACCTCG	60.738	63.158	0.00	0.00	39.44	4.63
2583	3883	5.934625	GGATGATATATTGAAGGCGACAAGT	59.065	40.000	0.00	0.00	0.00	3.16
2705	4005	4.767255	CCAGTGTGCCGAGCTCCC	62.767	72.222	8.47	0.00	0.00	4.30
2847	4147	2.057137	TGAGTTTGCCAAGCTCAACT	57.943	45.000	19.86	8.99	36.46	3.16
2889	4189	3.397482	GGATAGCATGTTGTAGCTGAGG	58.603	50.000	0.00	0.00	41.97	3.86
3126	4426	2.699846	ACAAGCTTTTCCTTTGATGCCA	59.300	40.909	0.00	0.00	0.00	4.92
3152	4452	3.187227	ACTGCTTGCGTAGACTGAATTTG	59.813	43.478	0.00	0.00	0.00	2.32
3161	4461	0.033366	TGCTTCACTGCTTGCGTAGA	59.967	50.000	0.00	0.00	0.00	2.59
3549	4849	0.890683	GCCTGACATTTCCAAGGGTG	59.109	55.000	0.00	0.00	0.00	4.61
4257	5557	3.557054	GCCTATCCAATGGCGATTCACTA	60.557	47.826	0.00	0.00	39.71	2.74
4338	5638	3.815856	TCTGATGCTGGAGATGAGAAC	57.184	47.619	0.00	0.00	0.00	3.01
4735	6195	6.366061	GCGCCTTGAATTATTTGTCTTCTTTT	59.634	34.615	0.00	0.00	0.00	2.27
4986	6456	2.517650	TTGGGCAAAACGAATGTTCC	57.482	45.000	0.00	0.00	37.31	3.62
5163	6799	2.260844	TCAACTGAACCTGCCTTCTG	57.739	50.000	0.00	0.00	0.00	3.02
5320	6958	8.351495	TCTTGTTTTTAAGCAAATGTGATGTC	57.649	30.769	0.00	0.00	0.00	3.06

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.