AutoCloner

Multiple sequence alignment - TraesCS3B01G114600

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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	TraesCS3B01G114600	chr3B	100.000	2759	0	0	1	2759	80660001	80657243	0.000000e+00	5096.0
1	TraesCS3B01G114600	chr3B	93.362	693	42	4	1	690	80203093	80202402	0.000000e+00	1022.0
2	TraesCS3B01G114600	chr3B	92.185	627	36	6	973	1588	80201469	80200845	0.000000e+00	874.0
3	TraesCS3B01G114600	chr3B	91.119	563	36	7	1073	1625	59323799	59324357	0.000000e+00	750.0
4	TraesCS3B01G114600	chr3B	84.641	612	42	13	2032	2593	80200556	80199947	1.860000e-156	562.0
5	TraesCS3B01G114600	chr3B	86.157	484	30	14	2295	2759	59327543	59328008	3.190000e-134	488.0
6	TraesCS3B01G114600	chr3B	87.624	404	32	6	1637	2036	59324414	59324803	1.160000e-123	453.0
7	TraesCS3B01G114600	chr3B	92.213	244	16	2	733	975	80201758	80201517	2.630000e-90	342.0
8	TraesCS3B01G114600	chr3B	83.379	367	51	9	38	397	811855430	811855793	5.700000e-87	331.0
9	TraesCS3B01G114600	chr3B	82.880	368	50	12	38	397	812011306	812011668	4.430000e-83	318.0
10	TraesCS3B01G114600	chr3B	86.500	200	21	4	795	993	59322513	59322707	5.980000e-52	215.0
11	TraesCS3B01G114600	chr3B	96.364	110	4	0	2085	2194	59327437	59327546	6.070000e-42	182.0
12	TraesCS3B01G114600	chr3B	89.231	130	11	2	795	923	59323424	59323551	2.840000e-35	159.0
13	TraesCS3B01G114600	chr3D	90.031	973	46	13	659	1625	50658855	50657928	0.000000e+00	1212.0
14	TraesCS3B01G114600	chr3D	86.456	1137	104	15	760	1856	36822109	36823235	0.000000e+00	1201.0
15	TraesCS3B01G114600	chr3D	84.530	724	40	20	2060	2759	36823975	36824650	0.000000e+00	651.0
16	TraesCS3B01G114600	chr3D	85.095	577	38	11	2032	2570	50656394	50655828	1.870000e-151	545.0
17	TraesCS3B01G114600	chr3D	93.103	232	14	2	413	643	50659511	50659281	3.400000e-89	339.0
18	TraesCS3B01G114600	chr3D	91.620	179	8	2	1862	2036	50657511	50657336	9.870000e-60	241.0
19	TraesCS3B01G114600	chr3D	94.268	157	5	1	1856	2008	36823377	36823533	1.280000e-58	237.0
20	TraesCS3B01G114600	chr3D	83.516	91	9	4	1950	2036	36592792	36592880	2.280000e-11	80.5
21	TraesCS3B01G114600	chr3A	89.077	888	71	13	759	1624	47046103	47046986	0.000000e+00	1079.0
22	TraesCS3B01G114600	chr3A	90.291	618	44	9	415	1019	63570018	63569404	0.000000e+00	795.0
23	TraesCS3B01G114600	chr3A	84.140	744	47	22	2060	2759	47047566	47048282	0.000000e+00	654.0
24	TraesCS3B01G114600	chrUn	95.581	430	18	1	1066	1495	69444467	69444039	0.000000e+00	688.0
25	TraesCS3B01G114600	chrUn	95.972	422	17	0	1064	1485	69362330	69362751	0.000000e+00	686.0
26	TraesCS3B01G114600	chr6B	94.305	439	25	0	1053	1491	101325635	101325197	0.000000e+00	673.0
27	TraesCS3B01G114600	chr6B	95.261	422	20	0	1064	1485	101167049	101167470	0.000000e+00	669.0
28	TraesCS3B01G114600	chr7B	81.236	874	89	32	795	1625	662311763	662310922	1.080000e-178	636.0
29	TraesCS3B01G114600	chr1D	82.007	578	34	29	2226	2759	460982002	460982553	7.060000e-116	427.0
30	TraesCS3B01G114600	chr1D	81.801	533	43	29	2226	2746	460995073	460995563	5.540000e-107	398.0
31	TraesCS3B01G114600	chr1D	84.533	375	50	8	37	405	239329593	239329221	5.620000e-97	364.0
32	TraesCS3B01G114600	chr1B	81.722	569	40	28	2226	2759	633260127	633260666	1.530000e-112	416.0
33	TraesCS3B01G114600	chr1B	82.192	365	47	9	44	397	593013336	593012979	5.780000e-77	298.0
34	TraesCS3B01G114600	chr4B	85.269	353	43	8	38	384	402094728	402094379	3.380000e-94	355.0
35	TraesCS3B01G114600	chr2D	86.624	314	36	6	38	346	9159186	9158874	2.630000e-90	342.0
36	TraesCS3B01G114600	chr4A	80.440	455	66	17	2311	2759	686579544	686579107	2.650000e-85	326.0
37	TraesCS3B01G114600	chr4A	80.467	471	42	24	2311	2756	642186180	642186625	5.740000e-82	315.0
38	TraesCS3B01G114600	chr4A	78.497	479	56	25	2295	2751	686573528	686573075	1.260000e-68	270.0
39	TraesCS3B01G114600	chr7A	79.870	462	61	15	2312	2759	37938462	37938019	2.670000e-80	309.0
40	TraesCS3B01G114600	chr7A	81.481	189	17	10	2435	2618	37354368	37354543	3.710000e-29	139.0
41	TraesCS3B01G114600	chr1A	79.727	513	33	23	2279	2759	552118862	552119335	3.450000e-79	305.0
42	TraesCS3B01G114600	chr2B	84.950	299	38	6	38	330	785211136	785210839	2.080000e-76	296.0
43	TraesCS3B01G114600	chr2B	84.615	299	39	6	38	330	677201521	677201224	9.670000e-75	291.0
44	TraesCS3B01G114600	chr7D	81.977	344	41	14	2410	2750	38204429	38204104	3.500000e-69	272.0
45	TraesCS3B01G114600	chr6D	85.350	157	11	8	2029	2173	27757963	27758119	4.760000e-33	152.0

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	TraesCS3B01G114600	chr3B	80657243	80660001	2758	True	5096.000000	5096	100.000000	1	2759	1	chr3B.!!$R1	2758
1	TraesCS3B01G114600	chr3B	80199947	80203093	3146	True	700.000000	1022	90.600250	1	2593	4	chr3B.!!$R2	2592
2	TraesCS3B01G114600	chr3B	59322513	59328008	5495	False	374.500000	750	89.499167	795	2759	6	chr3B.!!$F3	1964
3	TraesCS3B01G114600	chr3D	36822109	36824650	2541	False	696.333333	1201	88.418000	760	2759	3	chr3D.!!$F2	1999
4	TraesCS3B01G114600	chr3D	50655828	50659511	3683	True	584.250000	1212	89.962250	413	2570	4	chr3D.!!$R1	2157
5	TraesCS3B01G114600	chr3A	47046103	47048282	2179	False	866.500000	1079	86.608500	759	2759	2	chr3A.!!$F1	2000
6	TraesCS3B01G114600	chr3A	63569404	63570018	614	True	795.000000	795	90.291000	415	1019	1	chr3A.!!$R1	604
7	TraesCS3B01G114600	chr7B	662310922	662311763	841	True	636.000000	636	81.236000	795	1625	1	chr7B.!!$R1	830
8	TraesCS3B01G114600	chr1D	460982002	460982553	551	False	427.000000	427	82.007000	2226	2759	1	chr1D.!!$F1	533
9	TraesCS3B01G114600	chr1B	633260127	633260666	539	False	416.000000	416	81.722000	2226	2759	1	chr1B.!!$F1	533

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
161	163	1.075970	CCGTCAGAGGGGATGAGGA	60.076	63.158	0.63	0.0	35.15	3.71	F
888	1905	1.153369	CGCATCTGGGTCGTCCATT	60.153	57.895	0.04	0.0	46.01	3.16	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1467	3583	0.105964	CGGAGGTGAACTTGGTGACA	59.894	55.0	0.0	0.0	39.83	3.58	R
2231	7565	0.171455	GTCGTGACGGAGCAGAGATT	59.829	55.0	4.7	0.0	0.00	2.40	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	60	1.299773	GAGGAGCTTCGCCAGATCG	60.300	63.158	0.00	0.00	39.01	3.69
95	97	4.778415	GAGCGCGCGAGGAAGACA	62.778	66.667	37.18	0.00	0.00	3.41
102	104	4.452733	CGAGGAAGACACCGGGGC	62.453	72.222	1.73	0.00	34.73	5.80
143	145	4.821589	CAAGGAGGGGACGAGCGC	62.822	72.222	0.00	0.00	0.00	5.92
161	163	1.075970	CCGTCAGAGGGGATGAGGA	60.076	63.158	0.63	0.00	35.15	3.71
376	379	2.732016	GTTTTCCCCCGTGTTGCC	59.268	61.111	0.00	0.00	0.00	4.52
469	472	2.904434	GGTTAAGGAAGGTGGAGTGAGA	59.096	50.000	0.00	0.00	0.00	3.27
632	637	4.326278	TGATGTCGTGAATTAAGAGCGAAC	59.674	41.667	0.00	0.00	33.30	3.95
695	1110	6.600822	ACTCATGAAGTTGAACTATCCAATGG	59.399	38.462	0.00	0.00	33.03	3.16
710	1125	2.486592	CCAATGGTGGTTCGTTACTTCC	59.513	50.000	0.00	0.00	40.42	3.46
725	1142	6.044682	CGTTACTTCCGGGAAATATACAAGT	58.955	40.000	11.24	5.03	0.00	3.16
888	1905	1.153369	CGCATCTGGGTCGTCCATT	60.153	57.895	0.04	0.00	46.01	3.16
1011	2127	2.021457	CGTTTATCCACCACCATTCCC	58.979	52.381	0.00	0.00	0.00	3.97
1062	3160	2.120718	AGAGCACCTCTCCCCGTT	59.879	61.111	0.00	0.00	42.90	4.44
1218	3334	3.827302	AGAAGAAGTCCAAGAAGAGCGTA	59.173	43.478	0.00	0.00	0.00	4.42
1742	3939	8.633408	CAATTCTTAATTTCAGTTTCAGCGAAG	58.367	33.333	0.00	0.00	0.00	3.79
1852	4065	1.000590	AATGGCCATGATCCCCCAGA	61.001	55.000	21.63	0.00	0.00	3.86
1853	4066	1.000590	ATGGCCATGATCCCCCAGAA	61.001	55.000	20.04	0.00	0.00	3.02
1889	4245	4.851639	AATGGATCAGGCTTGTTCTAGT	57.148	40.909	6.82	0.00	0.00	2.57
1918	4274	8.700973	AGGAGAGGATGTTTATTTAGAGAAGAC	58.299	37.037	0.00	0.00	0.00	3.01
1999	4355	9.562583	TTCGCCACTTTTTGTAATAATGTAATC	57.437	29.630	0.00	0.00	0.00	1.75
2030	7325	3.838244	TCTTGGGAGTACATGGTATGC	57.162	47.619	0.00	0.00	0.00	3.14
2054	7349	0.315251	CTCTGCAGACAACGACTCCA	59.685	55.000	13.74	0.00	0.00	3.86
2105	7404	3.777106	TGAACTCTGAACTTGCAGGAT	57.223	42.857	1.40	0.00	36.55	3.24
2108	7407	4.040339	TGAACTCTGAACTTGCAGGATGTA	59.960	41.667	1.40	0.00	39.31	2.29
2160	7459	3.489180	AAGTGTCGGTATCTTCAGACG	57.511	47.619	0.00	0.00	35.82	4.18
2195	7522	1.168714	GGCTTTGATCGCCTGAAACT	58.831	50.000	3.09	0.00	44.17	2.66
2274	7613	5.918011	CGTCAAGCATTAAAAACCAAAGCTA	59.082	36.000	0.00	0.00	0.00	3.32
2318	7662	5.635417	AATTGGTTTCTTTCTAGCTCTGC	57.365	39.130	0.00	0.00	0.00	4.26
2372	7725	4.085619	GCACAAGTTAACAGCAAATGAACG	60.086	41.667	8.61	0.00	0.00	3.95
2596	7999	3.086600	GCCCTGCTCTAGCCTGGT	61.087	66.667	0.00	0.00	41.18	4.00
2605	8008	2.359107	TAGCCTGGTCGTCGTCGT	60.359	61.111	1.33	0.00	38.33	4.34
2606	8009	2.307137	CTAGCCTGGTCGTCGTCGTC	62.307	65.000	1.33	0.00	38.33	4.20
2607	8010	4.773117	GCCTGGTCGTCGTCGTCC	62.773	72.222	10.88	10.88	43.41	4.79
2608	8011	3.054503	CCTGGTCGTCGTCGTCCT	61.055	66.667	17.27	0.00	43.48	3.85
2609	8012	2.176055	CTGGTCGTCGTCGTCCTG	59.824	66.667	17.27	13.55	43.48	3.86
2610	8013	3.948086	CTGGTCGTCGTCGTCCTGC	62.948	68.421	17.27	0.00	43.48	4.85
2611	8014	3.735029	GGTCGTCGTCGTCCTGCT	61.735	66.667	10.58	0.00	40.85	4.24
2612	8015	2.502080	GTCGTCGTCGTCCTGCTG	60.502	66.667	1.33	0.00	38.33	4.41
2613	8016	4.400109	TCGTCGTCGTCCTGCTGC	62.400	66.667	1.33	0.00	38.33	5.25
2648	8051	4.834453	CTGCCGCTGCCAGGAGAG	62.834	72.222	0.00	0.00	36.33	3.20
2663	8066	4.400961	GAGCCGAGCCCAGCTGTT	62.401	66.667	13.81	0.00	39.88	3.16
2664	8067	4.711949	AGCCGAGCCCAGCTGTTG	62.712	66.667	13.81	4.44	39.88	3.33

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
7	8	2.728817	GGCTGATACGTCCTCCGG	59.271	66.667	0.00	0.00	42.24	5.14
114	116	4.830765	TCCTTGCCCGGATTCGCG	62.831	66.667	0.73	0.00	34.56	5.87
118	120	3.420482	CCCCTCCTTGCCCGGATT	61.420	66.667	0.73	0.00	31.43	3.01
125	127	4.821589	CGCTCGTCCCCTCCTTGC	62.822	72.222	0.00	0.00	0.00	4.01
143	145	0.687757	TTCCTCATCCCCTCTGACGG	60.688	60.000	0.00	0.00	0.00	4.79
148	150	1.764054	CGCCTTCCTCATCCCCTCT	60.764	63.158	0.00	0.00	0.00	3.69
170	172	2.415010	CATCGCGTCCCTCTCCAG	59.585	66.667	5.77	0.00	0.00	3.86
204	206	0.105658	CCTCCCCCAACCTCGATCTA	60.106	60.000	0.00	0.00	0.00	1.98
324	327	0.892358	AGTTCCGCTCTACACCGTCA	60.892	55.000	0.00	0.00	0.00	4.35
329	332	1.019805	GCCCAAGTTCCGCTCTACAC	61.020	60.000	0.00	0.00	0.00	2.90
355	358	1.830847	AACACGGGGGAAAACCAGC	60.831	57.895	0.00	0.00	42.91	4.85
403	406	3.084786	ACTTTGAGCATAAAGGAGCCAC	58.915	45.455	14.63	0.00	40.98	5.01
485	488	4.056740	AGTCTCAGCATCATAGCGAAATG	58.943	43.478	0.00	0.00	40.15	2.32
632	637	5.365605	TGGAGTTAATCTACTACATGTGGGG	59.634	44.000	14.25	6.17	34.05	4.96
695	1110	0.318120	TCCCGGAAGTAACGAACCAC	59.682	55.000	0.73	0.00	0.00	4.16
710	1125	6.920569	AAGCACTTACTTGTATATTTCCCG	57.079	37.500	0.00	0.00	0.00	5.14
725	1142	4.383850	TTTTTCTGCTGCAAAGCACTTA	57.616	36.364	3.02	0.00	40.23	2.24
757	1773	3.926527	GGCGGGAATTTGAGTTCAATTTC	59.073	43.478	15.82	15.82	41.65	2.17
837	1853	1.204312	GCTGACGTGGCGAAAGAAC	59.796	57.895	0.00	0.00	0.00	3.01
968	2003	0.321298	AGGGCGCGGCGAATTTATAT	60.321	50.000	28.54	0.00	0.00	0.86
1011	2127	2.125512	CTTCGCTCGAAGGTGGGG	60.126	66.667	20.67	0.00	45.60	4.96
1218	3334	6.824196	TGAAGATGTAGATCTTGTACGTCTCT	59.176	38.462	19.08	8.89	47.00	3.10
1467	3583	0.105964	CGGAGGTGAACTTGGTGACA	59.894	55.000	0.00	0.00	39.83	3.58
1742	3939	2.949644	ACTGAAACAGGGCACTAAACAC	59.050	45.455	0.00	0.00	35.51	3.32
1775	3973	6.768483	TGAGTTTGTCTGAAGATATCCACAA	58.232	36.000	0.00	0.00	31.39	3.33
1779	3977	7.604164	TGAAACTGAGTTTGTCTGAAGATATCC	59.396	37.037	16.25	0.00	35.77	2.59
1852	4065	2.498481	TCCATTAACCTCACGATCCGTT	59.502	45.455	0.00	0.00	38.32	4.44
1853	4066	2.104967	TCCATTAACCTCACGATCCGT	58.895	47.619	0.00	0.00	42.36	4.69
1889	4245	7.061054	TCTCTAAATAAACATCCTCTCCTCGA	58.939	38.462	0.00	0.00	0.00	4.04
1918	4274	4.613570	GCACAAGAAAAGTTTATGTGCG	57.386	40.909	25.36	8.91	45.51	5.34
1999	4355	4.578516	TGTACTCCCAAGAACAACAATGTG	59.421	41.667	0.00	0.00	40.46	3.21
2003	4359	4.141287	CCATGTACTCCCAAGAACAACAA	58.859	43.478	0.00	0.00	0.00	2.83
2004	4360	3.137544	ACCATGTACTCCCAAGAACAACA	59.862	43.478	0.00	0.00	0.00	3.33
2005	4361	3.751518	ACCATGTACTCCCAAGAACAAC	58.248	45.455	0.00	0.00	0.00	3.32
2030	7325	3.062763	AGTCGTTGTCTGCAGAGATTTG	58.937	45.455	18.89	8.83	0.00	2.32
2054	7349	2.039084	AGAGAAACATCTCTGCCGGTTT	59.961	45.455	1.90	0.00	44.63	3.27
2105	7404	4.422057	TGAAATAGACTCACCACCCTACA	58.578	43.478	0.00	0.00	0.00	2.74
2108	7407	3.521727	ACTGAAATAGACTCACCACCCT	58.478	45.455	0.00	0.00	0.00	4.34
2160	7459	4.451096	TCAAAGCCATCGAACTGAGTTTAC	59.549	41.667	0.00	0.00	0.00	2.01
2231	7565	0.171455	GTCGTGACGGAGCAGAGATT	59.829	55.000	4.70	0.00	0.00	2.40
2274	7613	6.713762	TTTCGCCATGATTATTTGGAGATT	57.286	33.333	0.00	0.00	40.76	2.40
2318	7662	0.179225	GCCGCGTGTTGTACAGAATG	60.179	55.000	4.92	0.00	46.00	2.67
2498	7901	3.598715	AGTCACCGCCGACGTTGA	61.599	61.111	3.74	0.00	38.49	3.18
2511	7914	0.400213	ACAAGGGGAAATCGCAGTCA	59.600	50.000	0.00	0.00	0.00	3.41
2564	7967	2.563427	GGCAAGACGGAAAGCAGC	59.437	61.111	0.00	0.00	0.00	5.25
2571	7974	1.304962	TAGAGCAGGGCAAGACGGA	60.305	57.895	0.00	0.00	0.00	4.69
2596	7999	4.400109	GCAGCAGGACGACGACGA	62.400	66.667	15.32	0.00	42.66	4.20
2613	8016	3.478274	GGGAGGAGGCTGCAGGAG	61.478	72.222	17.12	0.00	0.00	3.69

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.