AutoCloner

Multiple sequence alignment - TraesCS6D01G307100

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	TraesCS6D01G307100	chr6D	100.000	3506	0	0	2420	5925	417897637	417894132	0.000000e+00	6475.0
1	TraesCS6D01G307100	chr6D	100.000	2167	0	0	1	2167	417900056	417897890	0.000000e+00	4002.0
2	TraesCS6D01G307100	chr6D	96.004	1126	37	5	4178	5302	417691143	417692261	0.000000e+00	1823.0
3	TraesCS6D01G307100	chr6D	85.413	521	48	11	5294	5810	417692293	417692789	3.170000e-142	516.0
4	TraesCS6D01G307100	chr6D	82.624	282	38	6	2493	2770	414460890	414461164	7.670000e-59	239.0
5	TraesCS6D01G307100	chr6D	88.514	148	12	2	4686	4833	417777857	417777715	2.190000e-39	174.0
6	TraesCS6D01G307100	chr6D	91.892	74	6	0	2093	2166	97717498	97717571	2.920000e-18	104.0
7	TraesCS6D01G307100	chr6D	93.333	60	4	0	5480	5539	417894518	417894577	8.180000e-14	89.8
8	TraesCS6D01G307100	chr6A	96.811	2822	74	9	2493	5302	560573564	560570747	0.000000e+00	4698.0
9	TraesCS6D01G307100	chr6A	92.206	1899	88	32	305	2167	560575784	560573910	0.000000e+00	2632.0
10	TraesCS6D01G307100	chr6A	94.612	798	36	1	4149	4946	560101616	560102406	0.000000e+00	1229.0
11	TraesCS6D01G307100	chr6A	88.872	647	37	13	5294	5925	560570615	560569989	0.000000e+00	763.0
12	TraesCS6D01G307100	chr6A	89.388	245	24	2	3	247	215633741	215633499	2.070000e-79	307.0
13	TraesCS6D01G307100	chr6A	96.471	85	3	0	5841	5925	560102414	560102498	2.230000e-29	141.0
14	TraesCS6D01G307100	chr6B	88.849	1677	97	46	282	1904	626893180	626891540	0.000000e+00	1978.0
15	TraesCS6D01G307100	chr6B	96.319	652	22	2	4653	5302	626887385	626886734	0.000000e+00	1070.0
16	TraesCS6D01G307100	chr6B	93.265	683	39	2	3169	3847	626608465	626609144	0.000000e+00	1000.0
17	TraesCS6D01G307100	chr6B	90.282	710	47	13	3169	3873	626891133	626890441	0.000000e+00	909.0
18	TraesCS6D01G307100	chr6B	88.752	729	48	16	5219	5925	626455072	626455788	0.000000e+00	861.0
19	TraesCS6D01G307100	chr6B	91.376	603	43	4	3985	4585	626888069	626887474	0.000000e+00	817.0
20	TraesCS6D01G307100	chr6B	87.665	681	48	12	2420	3087	626607809	626608466	0.000000e+00	760.0
21	TraesCS6D01G307100	chr6B	87.358	617	40	15	5294	5902	626886637	626886051	0.000000e+00	673.0
22	TraesCS6D01G307100	chr6B	90.054	372	16	10	5561	5925	626587718	626588075	4.180000e-126	462.0
23	TraesCS6D01G307100	chr6B	89.264	326	24	5	2552	2872	626891535	626891216	1.200000e-106	398.0
24	TraesCS6D01G307100	chr6B	91.026	234	21	0	3	236	194036753	194036520	3.450000e-82	316.0
25	TraesCS6D01G307100	chr6B	90.863	197	18	0	5027	5223	626643122	626643318	1.270000e-66	265.0
26	TraesCS6D01G307100	chr6B	80.412	194	22	6	2580	2770	624777234	624777414	3.730000e-27	134.0
27	TraesCS6D01G307100	chr6B	92.000	50	4	0	4583	4632	626887419	626887370	2.960000e-08	71.3
28	TraesCS6D01G307100	chr4B	95.110	409	19	1	2680	3087	608066393	608066801	1.390000e-180	643.0
29	TraesCS6D01G307100	chr4B	94.377	409	22	1	2680	3087	9935675	9935267	1.400000e-175	627.0
30	TraesCS6D01G307100	chr4B	98.220	337	6	0	3169	3505	9935268	9934932	1.840000e-164	590.0
31	TraesCS6D01G307100	chr4B	97.033	337	10	0	3169	3505	608066800	608067136	8.620000e-158	568.0
32	TraesCS6D01G307100	chr4B	91.064	235	21	0	3	237	494016369	494016603	9.580000e-83	318.0
33	TraesCS6D01G307100	chr4B	90.217	92	7	2	3080	3171	21938051	21937962	1.040000e-22	119.0
34	TraesCS6D01G307100	chr4B	93.333	75	4	1	2093	2167	32267281	32267208	6.280000e-20	110.0
35	TraesCS6D01G307100	chr2D	91.064	235	21	0	1	235	315859222	315858988	9.580000e-83	318.0
36	TraesCS6D01G307100	chr2D	85.938	64	7	1	5463	5526	107899866	107899805	3.830000e-07	67.6
37	TraesCS6D01G307100	chr3B	90.987	233	21	0	3	235	401219978	401220210	1.240000e-81	315.0
38	TraesCS6D01G307100	chr3B	95.946	74	2	1	2093	2166	425722682	425722610	1.040000e-22	119.0
39	TraesCS6D01G307100	chr3B	90.000	80	6	1	3092	3171	76488483	76488406	1.050000e-17	102.0
40	TraesCS6D01G307100	chr3B	85.714	70	7	2	5457	5526	798639380	798639446	2.960000e-08	71.3
41	TraesCS6D01G307100	chr3B	82.432	74	10	2	5452	5524	605277771	605277842	1.780000e-05	62.1
42	TraesCS6D01G307100	chr2A	90.638	235	22	0	3	237	562065405	562065171	4.460000e-81	313.0
43	TraesCS6D01G307100	chr2A	90.336	238	20	3	3	239	439199094	439198859	5.770000e-80	309.0
44	TraesCS6D01G307100	chr2A	89.388	245	24	2	3	247	498200851	498200609	2.070000e-79	307.0
45	TraesCS6D01G307100	chr2A	94.595	74	4	0	2093	2166	675456325	675456398	1.350000e-21	115.0
46	TraesCS6D01G307100	chr2A	87.368	95	9	3	3079	3170	613480727	613480633	8.120000e-19	106.0
47	TraesCS6D01G307100	chr2A	100.000	32	0	0	5495	5526	672626861	672626892	6.410000e-05	60.2
48	TraesCS6D01G307100	chr7A	90.598	234	22	0	3	236	163628548	163628315	1.600000e-80	311.0
49	TraesCS6D01G307100	chr7A	93.243	74	5	0	2093	2166	478042635	478042562	6.280000e-20	110.0
50	TraesCS6D01G307100	chr7A	85.507	69	8	2	5490	5557	513221066	513221133	2.960000e-08	71.3
51	TraesCS6D01G307100	chr4A	90.217	92	7	2	3080	3171	590662246	590662157	1.040000e-22	119.0
52	TraesCS6D01G307100	chr1D	88.421	95	10	1	3081	3175	77013457	77013364	4.850000e-21	113.0
53	TraesCS6D01G307100	chr1D	93.056	72	5	0	2093	2164	453421599	453421528	8.120000e-19	106.0
54	TraesCS6D01G307100	chr1D	85.938	64	7	1	5463	5526	3824268	3824207	3.830000e-07	67.6
55	TraesCS6D01G307100	chr7D	93.243	74	5	0	2093	2166	415950899	415950826	6.280000e-20	110.0
56	TraesCS6D01G307100	chr3D	93.333	75	4	1	2093	2166	328545732	328545658	6.280000e-20	110.0
57	TraesCS6D01G307100	chr5B	89.286	84	7	1	3084	3165	116684085	116684168	2.920000e-18	104.0
58	TraesCS6D01G307100	chr5B	86.765	68	3	5	5465	5530	215889768	215889705	2.960000e-08	71.3
59	TraesCS6D01G307100	chr4D	87.640	89	9	2	3080	3168	11860943	11861029	1.050000e-17	102.0
60	TraesCS6D01G307100	chr4D	83.333	72	10	1	5455	5526	254829816	254829885	1.380000e-06	65.8
61	TraesCS6D01G307100	chr2B	87.500	88	11	0	3085	3172	665188441	665188354	1.050000e-17	102.0
62	TraesCS6D01G307100	chr2B	84.286	70	7	3	5457	5526	162544204	162544269	1.380000e-06	65.8
63	TraesCS6D01G307100	chr1A	97.222	36	1	0	2420	2455	439991099	439991064	1.780000e-05	62.1

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	TraesCS6D01G307100	chr6D	417894132	417900056	5924	True	5238.500000	6475	100.000000	1	5925	2	chr6D.!!$R2	5924
1	TraesCS6D01G307100	chr6D	417691143	417692789	1646	False	1169.500000	1823	90.708500	4178	5810	2	chr6D.!!$F4	1632
2	TraesCS6D01G307100	chr6A	560569989	560575784	5795	True	2697.666667	4698	92.629667	305	5925	3	chr6A.!!$R2	5620
3	TraesCS6D01G307100	chr6A	560101616	560102498	882	False	685.000000	1229	95.541500	4149	5925	2	chr6A.!!$F1	1776
4	TraesCS6D01G307100	chr6B	626607809	626609144	1335	False	880.000000	1000	90.465000	2420	3847	2	chr6B.!!$F5	1427
5	TraesCS6D01G307100	chr6B	626455072	626455788	716	False	861.000000	861	88.752000	5219	5925	1	chr6B.!!$F2	706
6	TraesCS6D01G307100	chr6B	626886051	626893180	7129	True	845.185714	1978	90.778286	282	5902	7	chr6B.!!$R2	5620
7	TraesCS6D01G307100	chr4B	9934932	9935675	743	True	608.500000	627	96.298500	2680	3505	2	chr4B.!!$R3	825
8	TraesCS6D01G307100	chr4B	608066393	608067136	743	False	605.500000	643	96.071500	2680	3505	2	chr4B.!!$F2	825

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	Hairpin	End Stability	Orientation
297	298	0.030908	GAGGATGCGACCGGTAAGAG	59.969	60.000	7.34	34.73	2.85	F
820	879	0.108585	AGCGGCAAACAGAGGAGAAA	59.891	50.000	1.45	0.00	2.52	F
1601	1678	0.250234	CCGGAGAATGCAGGTGAAGA	59.750	55.000	0.00	0.00	2.87	F
1725	1802	0.531974	TCGTTGTTGCAGAGTCCACC	60.532	55.000	0.00	0.00	4.61	F
2016	2094	0.937699	TGCGCTACACTTGTCGTGAC	60.938	55.000	9.73	46.81	3.67	F
2453	2533	1.364626	CCATGAAGCTCCGTCACTGC	61.365	60.000	0.00	0.00	4.40	F
3924	4053	0.984230	AACACGAGTCCATGGTCCAT	59.016	50.000	12.58	0.00	3.41	F
4644	7130	1.616374	GACCCATTTTCCCGCAAAAGA	59.384	47.619	0.00	37.40	2.52	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1392	1469	0.666913	GCAACCTAGAGGCGACGATA	59.333	55.000	0.00	0.0	39.32	2.92	R
2438	2516	1.372997	TTCGCAGTGACGGAGCTTC	60.373	57.895	0.00	0.0	0.00	3.86	R
2447	2527	2.094700	GTCATGTAGAGGTTCGCAGTGA	60.095	50.000	0.00	0.0	0.00	3.41	R
3111	3223	4.516698	ACACTGCCACAGACTCTAAAAATG	59.483	41.667	0.78	0.0	35.18	2.32	R
3907	4036	0.250234	ACATGGACCATGGACTCGTG	59.750	55.000	32.82	18.5	45.16	4.35	R
4684	7170	8.237267	CACAACTCTGATATTAAGAAAACCACC	58.763	37.037	0.00	0.0	0.00	4.61	R
4848	7334	0.313987	CCGGTCCTTTTGGTTTGCTC	59.686	55.000	0.00	0.0	41.38	4.26	R
5486	8127	1.268352	TGAACTAAAACCACGGCATGC	59.732	47.619	9.90	9.9	0.00	4.06	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)

Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
30	31	5.712152	CTTTGGTCAAAGTCAAGCCTTAT	57.288	39.130	13.58	0.00	42.02	1.73
31	32	6.817765	CTTTGGTCAAAGTCAAGCCTTATA	57.182	37.500	13.58	0.00	42.02	0.98
32	33	7.214467	CTTTGGTCAAAGTCAAGCCTTATAA	57.786	36.000	13.58	0.00	42.02	0.98
33	34	7.589958	TTTGGTCAAAGTCAAGCCTTATAAA	57.410	32.000	0.00	0.00	0.00	1.40
34	35	6.569179	TGGTCAAAGTCAAGCCTTATAAAC	57.431	37.500	0.00	0.00	0.00	2.01
35	36	5.180492	TGGTCAAAGTCAAGCCTTATAAACG	59.820	40.000	0.00	0.00	0.00	3.60
36	37	5.180680	GGTCAAAGTCAAGCCTTATAAACGT	59.819	40.000	0.00	0.00	0.00	3.99
37	38	6.293790	GGTCAAAGTCAAGCCTTATAAACGTT	60.294	38.462	0.00	0.00	0.00	3.99
38	39	6.577427	GTCAAAGTCAAGCCTTATAAACGTTG	59.423	38.462	0.00	5.53	0.00	4.10
39	40	6.483974	TCAAAGTCAAGCCTTATAAACGTTGA	59.516	34.615	0.00	0.00	34.40	3.18
40	41	5.857822	AGTCAAGCCTTATAAACGTTGAC	57.142	39.130	17.72	17.72	42.59	3.18
41	42	4.387862	AGTCAAGCCTTATAAACGTTGACG	59.612	41.667	18.55	1.41	45.40	4.35
42	43	4.386652	GTCAAGCCTTATAAACGTTGACGA	59.613	41.667	10.87	0.00	43.02	4.20
43	44	4.989797	TCAAGCCTTATAAACGTTGACGAA	59.010	37.500	10.87	0.00	43.02	3.85
44	45	5.119588	TCAAGCCTTATAAACGTTGACGAAG	59.880	40.000	10.87	1.75	43.02	3.79
229	230	7.894376	TGTGTAGAGTAAATAAAAACGGAGG	57.106	36.000	0.00	0.00	0.00	4.30
230	231	7.669427	TGTGTAGAGTAAATAAAAACGGAGGA	58.331	34.615	0.00	0.00	0.00	3.71
231	232	8.149647	TGTGTAGAGTAAATAAAAACGGAGGAA	58.850	33.333	0.00	0.00	0.00	3.36
232	233	8.654215	GTGTAGAGTAAATAAAAACGGAGGAAG	58.346	37.037	0.00	0.00	0.00	3.46
233	234	8.370182	TGTAGAGTAAATAAAAACGGAGGAAGT	58.630	33.333	0.00	0.00	0.00	3.01
234	235	9.860898	GTAGAGTAAATAAAAACGGAGGAAGTA	57.139	33.333	0.00	0.00	0.00	2.24
236	237	9.955102	AGAGTAAATAAAAACGGAGGAAGTATT	57.045	29.630	0.00	0.00	0.00	1.89
241	242	9.524496	AAATAAAAACGGAGGAAGTATTTAGGT	57.476	29.630	0.00	0.00	0.00	3.08
243	244	7.912056	AAAAACGGAGGAAGTATTTAGGTAC	57.088	36.000	0.00	0.00	0.00	3.34
244	245	4.907879	ACGGAGGAAGTATTTAGGTACG	57.092	45.455	0.00	0.00	0.00	3.67

Showing 1 to 25 of 119 entries

Previous1 2 3 4 5Next

Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
9	10	7.430441	GTTTATAAGGCTTGACTTTGACCAAA	58.570	34.615	10.69	0.00	32.02	3.28
10	11	6.293735	CGTTTATAAGGCTTGACTTTGACCAA	60.294	38.462	10.69	0.00	32.02	3.67
11	12	5.180492	CGTTTATAAGGCTTGACTTTGACCA	59.820	40.000	10.69	0.00	32.02	4.02
12	13	5.180680	ACGTTTATAAGGCTTGACTTTGACC	59.819	40.000	10.69	0.00	32.02	4.02
13	14	6.237313	ACGTTTATAAGGCTTGACTTTGAC	57.763	37.500	10.69	0.00	32.02	3.18
14	15	6.483974	TCAACGTTTATAAGGCTTGACTTTGA	59.516	34.615	10.69	14.07	32.02	2.69
15	16	6.577427	GTCAACGTTTATAAGGCTTGACTTTG	59.423	38.462	10.69	12.27	36.10	2.77
16	17	6.565247	CGTCAACGTTTATAAGGCTTGACTTT	60.565	38.462	10.69	1.02	36.42	2.66
17	18	5.107220	CGTCAACGTTTATAAGGCTTGACTT	60.107	40.000	10.69	0.00	36.42	3.01
18	19	4.387862	CGTCAACGTTTATAAGGCTTGACT	59.612	41.667	10.69	0.00	36.42	3.41
19	20	4.386652	TCGTCAACGTTTATAAGGCTTGAC	59.613	41.667	10.69	15.01	40.80	3.18
20	21	4.558178	TCGTCAACGTTTATAAGGCTTGA	58.442	39.130	10.69	0.00	40.80	3.02
21	22	4.914312	TCGTCAACGTTTATAAGGCTTG	57.086	40.909	10.69	0.00	40.80	4.01
22	23	4.992951	ACTTCGTCAACGTTTATAAGGCTT	59.007	37.500	4.58	4.58	40.80	4.35
23	24	4.563061	ACTTCGTCAACGTTTATAAGGCT	58.437	39.130	0.00	0.00	40.80	4.58
24	25	4.916099	ACTTCGTCAACGTTTATAAGGC	57.084	40.909	0.00	0.00	40.80	4.35
30	31	9.979270	TTTGTTTATAAACTTCGTCAACGTTTA	57.021	25.926	24.81	1.51	39.59	2.01
31	32	8.892887	TTTGTTTATAAACTTCGTCAACGTTT	57.107	26.923	24.81	0.00	39.59	3.60
32	33	8.892887	TTTTGTTTATAAACTTCGTCAACGTT	57.107	26.923	24.81	0.00	39.59	3.99
33	34	8.892887	TTTTTGTTTATAAACTTCGTCAACGT	57.107	26.923	24.81	0.00	39.59	3.99
203	204	8.943002	CCTCCGTTTTTATTTACTCTACACATT	58.057	33.333	0.00	0.00	0.00	2.71
204	205	8.316214	TCCTCCGTTTTTATTTACTCTACACAT	58.684	33.333	0.00	0.00	0.00	3.21
205	206	7.669427	TCCTCCGTTTTTATTTACTCTACACA	58.331	34.615	0.00	0.00	0.00	3.72
206	207	8.538409	TTCCTCCGTTTTTATTTACTCTACAC	57.462	34.615	0.00	0.00	0.00	2.90
207	208	8.370182	ACTTCCTCCGTTTTTATTTACTCTACA	58.630	33.333	0.00	0.00	0.00	2.74

Showing 1 to 25 of 146 entries

Previous1 2 3 4 5 6Next

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.