AutoCloner

Multiple sequence alignment - TraesCS7D01G071000

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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	TraesCS7D01G071000	chr7D	100.000	3716	0	0	1	3716	41692173	41695888	0.000000e+00	6863.0
1	TraesCS7D01G071000	chr7D	77.955	440	63	22	2448	2876	82347884	82347468	1.030000e-60	244.0
2	TraesCS7D01G071000	chr7D	86.111	144	18	2	1892	2034	596015562	596015704	1.790000e-33	154.0
3	TraesCS7D01G071000	chr7D	86.232	138	18	1	1891	2028	596086567	596086703	8.320000e-32	148.0
4	TraesCS7D01G071000	chr4A	94.483	1287	64	6	741	2025	648880489	648881770	0.000000e+00	1977.0
5	TraesCS7D01G071000	chr4A	83.068	1193	74	42	2351	3537	648882189	648883259	0.000000e+00	966.0
6	TraesCS7D01G071000	chr4A	80.709	254	23	12	2107	2350	30778256	30778493	1.370000e-39	174.0
7	TraesCS7D01G071000	chr4A	92.623	122	8	1	3594	3715	648883259	648883379	1.370000e-39	174.0
8	TraesCS7D01G071000	chr4A	85.135	148	19	3	3081	3226	648765334	648765480	8.320000e-32	148.0
9	TraesCS7D01G071000	chr4A	79.464	112	13	8	477	585	652091747	652091643	1.850000e-08	71.3
10	TraesCS7D01G071000	chr4A	79.464	112	13	8	477	585	652103651	652103547	1.850000e-08	71.3
11	TraesCS7D01G071000	chr7A	83.026	1355	115	53	2160	3490	41422446	41423709	0.000000e+00	1122.0
12	TraesCS7D01G071000	chr7A	89.878	820	44	7	766	1583	41420578	41421360	0.000000e+00	1018.0
13	TraesCS7D01G071000	chr7A	92.892	408	29	0	1618	2025	41421356	41421763	8.890000e-166	593.0
14	TraesCS7D01G071000	chr7A	93.769	321	17	1	3	320	41420254	41420574	2.600000e-131	479.0
15	TraesCS7D01G071000	chr7A	80.420	429	54	14	2462	2876	84025714	84025302	2.170000e-77	300.0
16	TraesCS7D01G071000	chr7A	88.393	224	11	7	3493	3716	41423748	41423956	4.760000e-64	255.0
17	TraesCS7D01G071000	chr7A	94.643	56	1	2	2029	2083	41422146	41422200	6.610000e-13	86.1
18	TraesCS7D01G071000	chr2B	80.323	681	92	28	841	1508	55855925	55855274	9.340000e-131	477.0
19	TraesCS7D01G071000	chr2B	79.044	711	95	33	780	1467	55210409	55209730	4.410000e-119	438.0
20	TraesCS7D01G071000	chr2B	78.437	742	107	34	780	1508	55227648	55226947	5.700000e-118	435.0
21	TraesCS7D01G071000	chr2B	76.555	627	98	35	909	1503	55203587	55202978	7.800000e-77	298.0
22	TraesCS7D01G071000	chr2B	77.586	406	57	20	2413	2811	55512862	55512484	8.080000e-52	215.0
23	TraesCS7D01G071000	chr2B	77.551	392	54	21	2413	2798	55208566	55208203	4.860000e-49	206.0
24	TraesCS7D01G071000	chr2B	80.237	253	25	12	2107	2350	601734023	601734259	2.300000e-37	167.0
25	TraesCS7D01G071000	chr2B	79.921	254	25	12	2107	2350	675714186	675714423	2.970000e-36	163.0
26	TraesCS7D01G071000	chr2B	78.601	243	26	17	2906	3145	54785245	54785026	1.800000e-28	137.0
27	TraesCS7D01G071000	chr2B	90.217	92	9	0	1897	1988	122927759	122927850	1.810000e-23	121.0
28	TraesCS7D01G071000	chr2B	90.217	92	9	0	1897	1988	122993563	122993654	1.810000e-23	121.0
29	TraesCS7D01G071000	chr2B	82.759	87	14	1	496	581	785626661	785626575	3.980000e-10	76.8
30	TraesCS7D01G071000	chr2B	79.279	111	15	5	477	585	185816241	185816137	1.850000e-08	71.3
31	TraesCS7D01G071000	chr2A	78.890	739	121	20	780	1503	36392800	36392082	5.620000e-128	468.0
32	TraesCS7D01G071000	chr2A	81.373	306	39	12	838	1141	36203202	36202913	2.230000e-57	233.0
33	TraesCS7D01G071000	chr2A	75.817	459	71	27	2413	2860	36398570	36398141	2.930000e-46	196.0
34	TraesCS7D01G071000	chr2D	77.207	759	104	42	782	1503	33315527	33314801	2.710000e-101	379.0
35	TraesCS7D01G071000	chr2D	79.249	559	100	11	955	1508	33581073	33580526	3.500000e-100	375.0
36	TraesCS7D01G071000	chr2D	80.315	254	24	11	2107	2350	564470797	564471034	6.380000e-38	169.0
37	TraesCS7D01G071000	chr2D	77.160	324	42	18	2540	2860	33579234	33578940	3.840000e-35	159.0
38	TraesCS7D01G071000	chr2D	80.588	170	23	6	2107	2270	601807353	601807188	5.040000e-24	122.0
39	TraesCS7D01G071000	chr2D	89.130	92	10	0	1897	1988	79086245	79086336	8.430000e-22	115.0
40	TraesCS7D01G071000	chr6B	92.771	249	10	2	2351	2596	716938404	716938647	1.640000e-93	353.0
41	TraesCS7D01G071000	chr6B	76.276	333	60	10	2416	2745	718287688	718287372	3.840000e-35	159.0
42	TraesCS7D01G071000	chr6B	91.489	94	8	0	2503	2596	48047100	48047007	3.010000e-26	130.0
43	TraesCS7D01G071000	chr6B	83.333	102	7	7	3281	3381	637180054	637180146	6.610000e-13	86.1
44	TraesCS7D01G071000	chr1B	92.683	246	13	1	2351	2596	639176785	639176545	2.120000e-92	350.0
45	TraesCS7D01G071000	chr4B	91.870	246	15	1	2351	2596	613851375	613851615	4.600000e-89	339.0
46	TraesCS7D01G071000	chr4B	80.392	255	23	12	2107	2350	22447166	22446928	6.380000e-38	169.0
47	TraesCS7D01G071000	chr7B	77.108	581	100	21	842	1410	31448250	31447691	4.660000e-79	305.0
48	TraesCS7D01G071000	chr7B	76.936	581	101	21	842	1410	30766275	30765716	2.170000e-77	300.0
49	TraesCS7D01G071000	chr7B	82.955	88	14	1	495	581	512332649	512332562	1.110000e-10	78.7
50	TraesCS7D01G071000	chr7B	84.524	84	5	6	477	558	577675955	577676032	3.980000e-10	76.8
51	TraesCS7D01G071000	chr7B	79.817	109	12	8	477	582	9677757	9677656	1.850000e-08	71.3
52	TraesCS7D01G071000	chr3D	77.282	493	87	13	155	623	528606862	528606371	2.200000e-67	267.0
53	TraesCS7D01G071000	chr6A	80.709	254	23	11	2107	2350	561588513	561588276	1.370000e-39	174.0
54	TraesCS7D01G071000	chr6A	80.709	254	23	11	2107	2350	561601769	561601532	1.370000e-39	174.0
55	TraesCS7D01G071000	chr6A	81.778	225	22	8	2107	2321	561452125	561452340	1.770000e-38	171.0
56	TraesCS7D01G071000	chr5B	90.426	94	9	0	2503	2596	95839475	95839382	1.400000e-24	124.0
57	TraesCS7D01G071000	chr5B	84.337	83	4	4	477	558	690101514	690101588	5.150000e-09	73.1
58	TraesCS7D01G071000	chr5B	83.529	85	4	8	477	558	629689783	629689860	1.850000e-08	71.3

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	TraesCS7D01G071000	chr7D	41692173	41695888	3715	False	6863.000000	6863	100.0000	1	3716	1	chr7D.!!$F1	3715
1	TraesCS7D01G071000	chr4A	648880489	648883379	2890	False	1039.000000	1977	90.0580	741	3715	3	chr4A.!!$F3	2974
2	TraesCS7D01G071000	chr7A	41420254	41423956	3702	False	592.183333	1122	90.4335	3	3716	6	chr7A.!!$F1	3713
3	TraesCS7D01G071000	chr2B	55855274	55855925	651	True	477.000000	477	80.3230	841	1508	1	chr2B.!!$R5	667
4	TraesCS7D01G071000	chr2B	55226947	55227648	701	True	435.000000	435	78.4370	780	1508	1	chr2B.!!$R3	728
5	TraesCS7D01G071000	chr2B	55208203	55210409	2206	True	322.000000	438	78.2975	780	2798	2	chr2B.!!$R8	2018
6	TraesCS7D01G071000	chr2B	55202978	55203587	609	True	298.000000	298	76.5550	909	1503	1	chr2B.!!$R2	594
7	TraesCS7D01G071000	chr2A	36392082	36392800	718	True	468.000000	468	78.8900	780	1503	1	chr2A.!!$R2	723
8	TraesCS7D01G071000	chr2D	33314801	33315527	726	True	379.000000	379	77.2070	782	1503	1	chr2D.!!$R1	721
9	TraesCS7D01G071000	chr2D	33578940	33581073	2133	True	267.000000	375	78.2045	955	2860	2	chr2D.!!$R3	1905
10	TraesCS7D01G071000	chr7B	31447691	31448250	559	True	305.000000	305	77.1080	842	1410	1	chr7B.!!$R3	568
11	TraesCS7D01G071000	chr7B	30765716	30766275	559	True	300.000000	300	76.9360	842	1410	1	chr7B.!!$R2	568

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
738	742	0.033920	CAGCACAGTAGCACACAGGA	59.966	55.0	0.0	0.0	36.85	3.86	F
739	743	0.034059	AGCACAGTAGCACACAGGAC	59.966	55.0	0.0	0.0	36.85	3.85	F
2030	2144	0.334676	AGGTGCAGAGCCTCTCTACT	59.665	55.0	0.0	0.0	38.99	2.57	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2646	3852	1.068281	CGCAGCTCATGATAGACTGGT	59.932	52.381	13.71	0.0	0.00	4.00	R
2689	3896	1.068434	CTCCTGCTCCGATCTTTCTCC	59.932	57.143	0.00	0.0	0.00	3.71	R
3653	4921	0.249676	CTCAGGTGCTCAGCTCACAT	59.750	55.000	0.00	0.0	36.98	3.21	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
37	38	2.970324	TCTTTGTGGCGCGTGGAC	60.970	61.111	8.43	2.37	0.00	4.02
50	51	3.002862	GCGCGTGGACCATGAATATTTTA	59.997	43.478	18.32	0.00	0.00	1.52
58	59	7.981225	GTGGACCATGAATATTTTATGTGCTTT	59.019	33.333	0.00	0.00	0.00	3.51
66	67	7.502226	TGAATATTTTATGTGCTTTCCCGATCT	59.498	33.333	0.00	0.00	0.00	2.75
73	74	1.757118	TGCTTTCCCGATCTCGAATCT	59.243	47.619	0.22	0.00	43.02	2.40
92	93	1.876156	CTGCCAGAACAAACTGGTCTC	59.124	52.381	14.75	1.38	41.32	3.36
108	109	1.079819	CTCATCGGTGAACGGCACT	60.080	57.895	0.00	0.00	46.86	4.40
120	121	3.365265	GGCACTGGTTCCGCCTTG	61.365	66.667	0.00	0.00	42.78	3.61
142	143	1.663695	ACAACCACTTGTCCAGTTCG	58.336	50.000	0.00	0.00	35.57	3.95
147	148	1.143305	CACTTGTCCAGTTCGAGCAG	58.857	55.000	1.01	0.00	30.92	4.24
159	160	2.579738	GAGCAGGGTCGGAACCTC	59.420	66.667	12.78	7.50	45.66	3.85
202	203	2.032620	ACTAGTAGGACAATCGCCAGG	58.967	52.381	1.45	0.00	0.00	4.45
217	218	1.619654	CCAGGCATGGTTCTGAAACA	58.380	50.000	11.02	11.02	42.17	2.83
307	311	1.079612	CCTGATGCAGCTGTCGTCA	60.080	57.895	22.97	22.97	0.00	4.35
320	324	4.129737	CGTCATCGCCTCACCGGT	62.130	66.667	0.00	0.00	34.25	5.28
321	325	2.767445	CGTCATCGCCTCACCGGTA	61.767	63.158	6.87	0.00	34.25	4.02
322	326	1.065928	GTCATCGCCTCACCGGTAG	59.934	63.158	6.87	5.38	34.25	3.18
323	327	2.279517	CATCGCCTCACCGGTAGC	60.280	66.667	6.87	10.34	34.25	3.58
324	328	2.758327	ATCGCCTCACCGGTAGCA	60.758	61.111	19.77	9.90	34.25	3.49
325	329	3.077519	ATCGCCTCACCGGTAGCAC	62.078	63.158	19.77	5.68	34.25	4.40
326	330	4.814294	CGCCTCACCGGTAGCACC	62.814	72.222	19.77	3.43	34.25	5.01
327	331	4.468689	GCCTCACCGGTAGCACCC	62.469	72.222	6.87	0.00	33.75	4.61
335	339	3.961729	GGTAGCACCCGAACACAC	58.038	61.111	0.00	0.00	30.04	3.82
336	340	1.370064	GGTAGCACCCGAACACACT	59.630	57.895	0.00	0.00	30.04	3.55
337	341	0.604578	GGTAGCACCCGAACACACTA	59.395	55.000	0.00	0.00	30.04	2.74

Showing 1 to 25 of 436 entries

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Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
1	2	2.676471	ATGGGCTTGGGTGTTCGC	60.676	61.111	0.00	0.00	0.00	4.70
37	38	6.642131	CGGGAAAGCACATAAAATATTCATGG	59.358	38.462	12.29	5.27	0.00	3.66
50	51	0.824109	TCGAGATCGGGAAAGCACAT	59.176	50.000	1.91	0.00	40.29	3.21
58	59	0.755327	TGGCAGATTCGAGATCGGGA	60.755	55.000	1.91	0.00	40.29	5.14
66	67	2.807967	CAGTTTGTTCTGGCAGATTCGA	59.192	45.455	19.50	11.54	0.00	3.71
88	89	1.080093	TGCCGTTCACCGATGAGAC	60.080	57.895	0.00	0.00	39.56	3.36
92	93	2.390599	CCAGTGCCGTTCACCGATG	61.391	63.158	1.98	0.00	46.81	3.84
108	109	1.754621	TTGTTGCAAGGCGGAACCA	60.755	52.632	0.00	0.00	44.84	3.67
111	112	1.754621	TGGTTGTTGCAAGGCGGAA	60.755	52.632	0.00	0.00	0.00	4.30
202	203	4.504097	GTGAAGTTTGTTTCAGAACCATGC	59.496	41.667	0.00	0.00	37.72	4.06
207	208	7.148306	TGGAGTTAGTGAAGTTTGTTTCAGAAC	60.148	37.037	5.79	5.79	37.72	3.01
217	218	5.699458	CGTAATGGTGGAGTTAGTGAAGTTT	59.301	40.000	0.00	0.00	0.00	2.66
307	311	2.758327	TGCTACCGGTGAGGCGAT	60.758	61.111	19.93	0.00	46.52	4.58
320	324	1.913778	TCTAGTGTGTTCGGGTGCTA	58.086	50.000	0.00	0.00	0.00	3.49
321	325	1.204941	GATCTAGTGTGTTCGGGTGCT	59.795	52.381	0.00	0.00	0.00	4.40
322	326	1.204941	AGATCTAGTGTGTTCGGGTGC	59.795	52.381	0.00	0.00	0.00	5.01
323	327	2.492088	TCAGATCTAGTGTGTTCGGGTG	59.508	50.000	0.00	0.00	0.00	4.61
324	328	2.492484	GTCAGATCTAGTGTGTTCGGGT	59.508	50.000	0.00	0.00	0.00	5.28
325	329	2.492088	TGTCAGATCTAGTGTGTTCGGG	59.508	50.000	0.00	0.00	0.00	5.14
326	330	3.502920	GTGTCAGATCTAGTGTGTTCGG	58.497	50.000	0.00	0.00	0.00	4.30
327	331	3.502920	GGTGTCAGATCTAGTGTGTTCG	58.497	50.000	0.00	0.00	0.00	3.95
328	332	3.368531	GGGGTGTCAGATCTAGTGTGTTC	60.369	52.174	0.00	0.00	0.00	3.18
329	333	2.567615	GGGGTGTCAGATCTAGTGTGTT	59.432	50.000	0.00	0.00	0.00	3.32
330	334	2.180276	GGGGTGTCAGATCTAGTGTGT	58.820	52.381	0.00	0.00	0.00	3.72
331	335	2.179427	TGGGGTGTCAGATCTAGTGTG	58.821	52.381	0.00	0.00	0.00	3.82

Showing 1 to 25 of 456 entries

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Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.