AutoCloner

Multiple sequence alignment - TraesCS7A01G036300

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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	TraesCS7A01G036300	chr7A	100.000	3125	0	0	1	3125	16314823	16317947	0.000000e+00	5771.0
1	TraesCS7A01G036300	chr7A	95.280	2267	85	6	1	2254	16426924	16429181	0.000000e+00	3574.0
2	TraesCS7A01G036300	chr7A	92.700	2096	131	11	181	2257	15822539	15820447	0.000000e+00	3003.0
3	TraesCS7A01G036300	chr7A	94.246	504	24	2	2585	3087	16393882	16394381	0.000000e+00	765.0
4	TraesCS7A01G036300	chr7A	92.990	485	26	2	2610	3087	16429582	16430065	0.000000e+00	701.0
5	TraesCS7A01G036300	chr7A	87.079	534	33	13	2588	3087	15820071	15819540	3.500000e-159	571.0
6	TraesCS7A01G036300	chr7A	96.726	336	7	2	2254	2589	16429151	16429482	9.790000e-155	556.0
7	TraesCS7A01G036300	chr7A	94.643	336	17	1	2254	2589	15820481	15820147	1.280000e-143	520.0
8	TraesCS7A01G036300	chr7A	93.485	307	17	3	2254	2558	15791910	15791605	1.320000e-123	453.0
9	TraesCS7A01G036300	chr4A	94.660	2603	119	9	1	2589	717225445	717222849	0.000000e+00	4019.0
10	TraesCS7A01G036300	chr4A	94.165	2605	117	16	1	2589	717286902	717284317	0.000000e+00	3936.0
11	TraesCS7A01G036300	chr4A	95.769	2269	80	6	1	2254	717260545	717258278	0.000000e+00	3644.0
12	TraesCS7A01G036300	chr4A	94.888	2269	100	6	1	2254	717752962	717755229	0.000000e+00	3533.0
13	TraesCS7A01G036300	chr4A	94.881	2266	95	7	3	2254	717803782	717806040	0.000000e+00	3522.0
14	TraesCS7A01G036300	chr4A	89.711	554	42	10	2254	2804	717755199	717755740	0.000000e+00	693.0
15	TraesCS7A01G036300	chr4A	90.000	510	24	6	2585	3087	717257879	717257390	4.400000e-178	634.0
16	TraesCS7A01G036300	chr4A	95.337	386	17	1	2698	3083	717806523	717806907	2.060000e-171	612.0
17	TraesCS7A01G036300	chr4A	95.238	336	15	1	2254	2589	717806010	717806344	5.930000e-147	531.0
18	TraesCS7A01G036300	chr4A	92.834	307	14	2	2789	3087	717222519	717222213	3.700000e-119	438.0
19	TraesCS7A01G036300	chr4A	92.517	294	14	2	2789	3074	717755753	717756046	6.240000e-112	414.0
20	TraesCS7A01G036300	chr7D	96.205	2266	73	3	2	2254	16760755	16758490	0.000000e+00	3696.0
21	TraesCS7A01G036300	chr7D	95.240	2269	92	7	1	2254	17121863	17124130	0.000000e+00	3578.0
22	TraesCS7A01G036300	chr7D	97.172	495	13	1	2585	3078	16758082	16757588	0.000000e+00	835.0
23	TraesCS7A01G036300	chr7D	97.297	370	10	0	2709	3078	16996151	16996520	2.050000e-176	628.0
24	TraesCS7A01G036300	chr7D	97.619	336	7	1	2254	2589	16758520	16758186	2.700000e-160	575.0
25	TraesCS7A01G036300	chr7D	96.108	334	11	2	2254	2586	17124100	17124432	7.620000e-151	544.0
26	TraesCS7A01G036300	chr7D	96.617	266	9	0	2813	3078	17124730	17124995	2.860000e-120	442.0
27	TraesCS7A01G036300	chr7D	97.436	195	5	0	2585	2779	17124541	17124735	1.800000e-87	333.0
28	TraesCS7A01G036300	chr7D	96.842	95	3	0	2585	2679	16996062	16996156	3.230000e-35	159.0
29	TraesCS7A01G036300	chr7B	94.266	593	27	3	7	594	655808530	655809120	0.000000e+00	900.0
30	TraesCS7A01G036300	chr7B	88.716	514	43	6	2585	3087	655813578	655814087	5.730000e-172	614.0
31	TraesCS7A01G036300	chr7B	94.925	335	16	1	2255	2589	655813139	655813472	9.930000e-145	523.0
32	TraesCS7A01G036300	chr7B	100.000	40	0	0	3086	3125	478084503	478084542	1.200000e-09	75.0
33	TraesCS7A01G036300	chr7B	100.000	40	0	0	3086	3125	478086478	478086517	1.200000e-09	75.0
34	TraesCS7A01G036300	chr6B	100.000	41	0	0	3085	3125	577338680	577338640	3.340000e-10	76.8
35	TraesCS7A01G036300	chrUn	100.000	40	0	0	3086	3125	377558580	377558541	1.200000e-09	75.0
36	TraesCS7A01G036300	chr3B	100.000	40	0	0	3086	3125	737068187	737068148	1.200000e-09	75.0
37	TraesCS7A01G036300	chr3B	100.000	40	0	0	3086	3125	745467633	745467672	1.200000e-09	75.0
38	TraesCS7A01G036300	chr1A	100.000	40	0	0	3086	3125	203816796	203816757	1.200000e-09	75.0
39	TraesCS7A01G036300	chr1A	94.000	50	1	2	3077	3125	232104209	232104161	1.200000e-09	75.0
40	TraesCS7A01G036300	chr5B	97.674	43	0	1	3083	3125	711416628	711416669	4.320000e-09	73.1

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	TraesCS7A01G036300	chr7A	16314823	16317947	3124	False	5771.000000	5771	100.000000	1	3125	1	chr7A.!!$F1	3124
1	TraesCS7A01G036300	chr7A	16426924	16430065	3141	False	1610.333333	3574	94.998667	1	3087	3	chr7A.!!$F3	3086
2	TraesCS7A01G036300	chr7A	15819540	15822539	2999	True	1364.666667	3003	91.474000	181	3087	3	chr7A.!!$R2	2906
3	TraesCS7A01G036300	chr4A	717284317	717286902	2585	True	3936.000000	3936	94.165000	1	2589	1	chr4A.!!$R1	2588
4	TraesCS7A01G036300	chr4A	717222213	717225445	3232	True	2228.500000	4019	93.747000	1	3087	2	chr4A.!!$R2	3086
5	TraesCS7A01G036300	chr4A	717257390	717260545	3155	True	2139.000000	3644	92.884500	1	3087	2	chr4A.!!$R3	3086
6	TraesCS7A01G036300	chr4A	717803782	717806907	3125	False	1555.000000	3522	95.152000	3	3083	3	chr4A.!!$F2	3080
7	TraesCS7A01G036300	chr4A	717752962	717756046	3084	False	1546.666667	3533	92.372000	1	3074	3	chr4A.!!$F1	3073
8	TraesCS7A01G036300	chr7D	16757588	16760755	3167	True	1702.000000	3696	96.998667	2	3078	3	chr7D.!!$R1	3076
9	TraesCS7A01G036300	chr7D	17121863	17124995	3132	False	1224.250000	3578	96.350250	1	3078	4	chr7D.!!$F2	3077
10	TraesCS7A01G036300	chr7B	655808530	655809120	590	False	900.000000	900	94.266000	7	594	1	chr7B.!!$F1	587
11	TraesCS7A01G036300	chr7B	655813139	655814087	948	False	568.500000	614	91.820500	2255	3087	2	chr7B.!!$F3	832

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
188	195	0.179189	GCATGTCACGTGGCTTTAGC	60.179	55.000	22.43	15.23	41.14	3.09	F
387	394	1.964223	GTCAGACAGAGTTCTCCACCA	59.036	52.381	0.00	0.00	0.00	4.17	F
1246	1272	1.004745	CCTTAGGCAAGCTCTTCCCAA	59.995	52.381	0.00	0.00	0.00	4.12	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1163	1189	0.248784	GGCGATGAATGCAAGAAGGC	60.249	55.0	0.00	0.00	0.00	4.35	R
1466	1492	0.823356	GAAAGGTGGAGCTGCAACCA	60.823	55.0	20.79	15.53	36.37	3.67	R
2442	2518	0.445043	CATCTGACATGGTGCACACG	59.555	55.0	20.43	8.52	0.00	4.49	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
188	195	0.179189	GCATGTCACGTGGCTTTAGC	60.179	55.000	22.43	15.23	41.14	3.09
251	258	3.857052	AGTTCACGTGTTTGAGTCAAGA	58.143	40.909	16.51	0.00	0.00	3.02
387	394	1.964223	GTCAGACAGAGTTCTCCACCA	59.036	52.381	0.00	0.00	0.00	4.17
437	447	2.275089	CGCCATCACCCCATTGGA	59.725	61.111	3.62	0.00	38.00	3.53
474	484	2.036556	CGCTCATCGCACTTTTGTTT	57.963	45.000	0.00	0.00	39.08	2.83
491	501	7.338449	ACTTTTGTTTTTGTTAGCCTGACTCTA	59.662	33.333	0.00	0.00	0.00	2.43
624	634	9.140286	TCAGTGTAGAACAATCTTAGAATTTCG	57.860	33.333	0.00	0.00	37.10	3.46
676	689	7.025485	TGATGAAATTTATTGCGTATCTGCA	57.975	32.000	0.00	0.00	44.61	4.41
835	848	3.133691	GCTAGATGCACATTTCGATGGA	58.866	45.455	0.00	0.00	42.31	3.41
986	1012	9.686683	ATAGTTAACTCAAGTCCATTGCTAAAT	57.313	29.630	12.39	0.00	38.89	1.40
1186	1212	1.031571	TCTTGCATTCATCGCCACCC	61.032	55.000	0.00	0.00	0.00	4.61
1246	1272	1.004745	CCTTAGGCAAGCTCTTCCCAA	59.995	52.381	0.00	0.00	0.00	4.12
1264	1290	4.830600	TCCCAACTGTTATTTTCTGGAACC	59.169	41.667	0.00	0.00	0.00	3.62
1281	1307	2.029073	CGTGCCGACCAGACAAGT	59.971	61.111	0.00	0.00	0.00	3.16
1387	1413	5.939296	CCAAGTATTTTGGACAAAATGGCAT	59.061	36.000	25.32	12.89	46.80	4.40
1523	1549	9.540538	ACTATGCTACATAACCTTCATATCTCT	57.459	33.333	0.00	0.00	0.00	3.10
1529	1555	9.967451	CTACATAACCTTCATATCTCTAGAGGA	57.033	37.037	19.67	8.69	0.00	3.71
1873	1900	2.566833	ACCTGCAAAGTATGTGAGCA	57.433	45.000	0.00	0.00	0.00	4.26
1934	1961	1.335597	CGAGAAACGTACTGGACAGCA	60.336	52.381	0.00	0.00	37.22	4.41
1976	2003	3.265489	AGAGAATGGGTTTAAGGGGTGA	58.735	45.455	0.00	0.00	0.00	4.02
2004	2031	3.938963	TCTATCAGTTGGATGAAAACGCC	59.061	43.478	0.00	0.00	36.72	5.68
2183	2212	1.662044	GCTGCACTTGGGGACTTTG	59.338	57.895	0.00	0.00	0.00	2.77
2244	2281	9.832445	ACGGAGTACATCAAGATTTGTAATAAT	57.168	29.630	0.00	0.00	41.94	1.28
2416	2479	4.700213	TGAAACAATACTAGCTTCTTGGGC	59.300	41.667	0.00	0.00	0.00	5.36
2442	2518	7.914346	CCTTCATATCACTCTTCAGCATTTTTC	59.086	37.037	0.00	0.00	0.00	2.29
2480	2557	3.399440	TGTGCCTGGGCTTTTATTTTG	57.601	42.857	13.05	0.00	42.51	2.44
2491	2568	5.580691	GGGCTTTTATTTTGGTTATGTGCTC	59.419	40.000	0.00	0.00	0.00	4.26
2625	2893	2.158856	TGCTATGGACTTGCATCCTCAG	60.159	50.000	7.83	5.84	39.75	3.35
2640	2908	4.826274	TCCTCAGTCTAATTCTTGGTGG	57.174	45.455	0.00	0.00	0.00	4.61
3060	3392	1.992557	TCCTCCCACCAAAGCTGTATT	59.007	47.619	0.00	0.00	0.00	1.89
3066	3398	4.288626	TCCCACCAAAGCTGTATTAGAAGT	59.711	41.667	0.00	0.00	0.00	3.01
3078	3410	8.322091	AGCTGTATTAGAAGTTAATCACCAACT	58.678	33.333	0.00	0.00	37.85	3.16
3087	3419	0.185901	AATCACCAACTGCACCCACT	59.814	50.000	0.00	0.00	0.00	4.00
3088	3420	0.538057	ATCACCAACTGCACCCACTG	60.538	55.000	0.00	0.00	0.00	3.66
3089	3421	1.453745	CACCAACTGCACCCACTGT	60.454	57.895	0.00	0.00	0.00	3.55
3090	3422	1.152963	ACCAACTGCACCCACTGTC	60.153	57.895	0.00	0.00	0.00	3.51
3091	3423	1.152984	CCAACTGCACCCACTGTCA	60.153	57.895	0.00	0.00	0.00	3.58
3092	3424	0.751277	CCAACTGCACCCACTGTCAA	60.751	55.000	0.00	0.00	0.00	3.18
3093	3425	0.664761	CAACTGCACCCACTGTCAAG	59.335	55.000	0.00	0.00	0.00	3.02
3094	3426	0.466189	AACTGCACCCACTGTCAAGG	60.466	55.000	0.00	0.00	0.00	3.61
3099	3431	2.352805	CCCACTGTCAAGGGCCTC	59.647	66.667	6.46	0.00	38.44	4.70
3100	3432	2.046892	CCACTGTCAAGGGCCTCG	60.047	66.667	6.46	0.00	0.00	4.63
3101	3433	2.046892	CACTGTCAAGGGCCTCGG	60.047	66.667	6.46	1.47	0.00	4.63
3102	3434	2.526873	ACTGTCAAGGGCCTCGGT	60.527	61.111	6.46	2.26	0.00	4.69
3103	3435	2.046892	CTGTCAAGGGCCTCGGTG	60.047	66.667	6.46	0.81	0.00	4.94
3104	3436	4.329545	TGTCAAGGGCCTCGGTGC	62.330	66.667	6.46	0.00	0.00	5.01
3112	3444	4.329545	GCCTCGGTGCCCAAGACA	62.330	66.667	0.00	0.00	0.00	3.41
3113	3445	2.046892	CCTCGGTGCCCAAGACAG	60.047	66.667	0.00	0.00	0.00	3.51
3114	3446	2.743928	CTCGGTGCCCAAGACAGC	60.744	66.667	0.00	0.00	0.00	4.40
3115	3447	3.535629	CTCGGTGCCCAAGACAGCA	62.536	63.158	0.00	0.00	35.27	4.41
3116	3448	3.052082	CGGTGCCCAAGACAGCAG	61.052	66.667	0.00	0.00	40.28	4.24
3117	3449	2.674380	GGTGCCCAAGACAGCAGG	60.674	66.667	0.00	0.00	40.28	4.85
3118	3450	2.431683	GTGCCCAAGACAGCAGGA	59.568	61.111	0.00	0.00	40.28	3.86
3119	3451	1.968540	GTGCCCAAGACAGCAGGAC	60.969	63.158	0.00	0.00	40.28	3.85
3120	3452	2.360475	GCCCAAGACAGCAGGACC	60.360	66.667	0.00	0.00	0.00	4.46
3121	3453	2.900106	GCCCAAGACAGCAGGACCT	61.900	63.158	0.00	0.00	0.00	3.85
3122	3454	1.298014	CCCAAGACAGCAGGACCTC	59.702	63.158	0.00	0.00	0.00	3.85
3123	3455	1.079543	CCAAGACAGCAGGACCTCG	60.080	63.158	0.00	0.00	0.00	4.63
3124	3456	1.536073	CCAAGACAGCAGGACCTCGA	61.536	60.000	0.00	0.00	0.00	4.04

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
19	20	1.337167	GGCAATCACTCCAAAGTTGCC	60.337	52.381	11.12	11.12	45.11	4.52
333	340	4.181578	GCACCGGTCAGCGAATATATATT	58.818	43.478	2.59	7.72	0.00	1.28
437	447	2.752238	CGTCAGAGGAGGTCGCCT	60.752	66.667	0.00	0.00	42.17	5.52
474	484	4.323485	CCATGGTAGAGTCAGGCTAACAAA	60.323	45.833	2.57	0.00	38.87	2.83
491	501	2.793564	AGATCCCCAAATCATCCATGGT	59.206	45.455	12.58	0.00	32.13	3.55
624	634	9.910511	CATTTGAAATTAAGTGCAAGCAATATC	57.089	29.630	0.00	0.00	0.00	1.63
676	689	3.470888	CACCTCGATTCCGGGCCT	61.471	66.667	0.84	0.00	34.24	5.19
801	814	5.706833	TGTGCATCTAGCTCAAGAAAATTCA	59.293	36.000	0.00	0.00	43.16	2.57
815	828	5.739752	TTTCCATCGAAATGTGCATCTAG	57.260	39.130	0.00	0.00	32.96	2.43
816	829	6.992123	AGTATTTCCATCGAAATGTGCATCTA	59.008	34.615	8.38	0.00	46.07	1.98
986	1012	5.384336	TGAGGATCATGAAAGGACAACAAA	58.616	37.500	0.00	0.00	42.56	2.83
1163	1189	0.248784	GGCGATGAATGCAAGAAGGC	60.249	55.000	0.00	0.00	0.00	4.35
1186	1212	2.031163	GGCATACCAGCTAGGGCG	59.969	66.667	7.06	0.00	43.89	6.13
1246	1272	3.252458	GCACGGTTCCAGAAAATAACAGT	59.748	43.478	0.00	0.00	32.85	3.55
1281	1307	2.305635	TCCAATGTTAGAGCCAGCTGAA	59.694	45.455	17.39	0.00	0.00	3.02
1387	1413	6.622679	GCATGACCATAAGAACATTTGACGAA	60.623	38.462	0.00	0.00	0.00	3.85
1466	1492	0.823356	GAAAGGTGGAGCTGCAACCA	60.823	55.000	20.79	15.53	36.37	3.67
1523	1549	6.857848	AGATATGAATCTGGTGACTCCTCTA	58.142	40.000	0.00	0.00	41.08	2.43
1529	1555	8.708378	TGACAAATAGATATGAATCTGGTGACT	58.292	33.333	0.00	0.00	42.60	3.41
1873	1900	1.563410	CTTCAAGCCTCCCTCTTCCAT	59.437	52.381	0.00	0.00	0.00	3.41
1934	1961	3.228453	TCTGGGTTCACTAAGAGTCGTT	58.772	45.455	0.00	0.00	0.00	3.85
1976	2003	5.762179	TTCATCCAACTGATAGACAAGGT	57.238	39.130	0.00	0.00	30.56	3.50
2004	2031	6.401047	TCTACTGGGTATGAAAATACTCGG	57.599	41.667	3.52	3.52	39.27	4.63
2183	2212	4.373348	ACTAGAAGGAACATAGCGACAC	57.627	45.455	0.00	0.00	0.00	3.67
2242	2279	9.071276	ACAAATCTTGATGTACAAACAGAGATT	57.929	29.630	20.80	20.80	41.04	2.40
2243	2280	8.627208	ACAAATCTTGATGTACAAACAGAGAT	57.373	30.769	0.00	10.95	39.49	2.75
2244	2281	9.554395	TTACAAATCTTGATGTACAAACAGAGA	57.446	29.630	0.00	9.39	39.49	3.10
2328	2391	1.065401	CAAGGTTCAGCGAAAACAGCA	59.935	47.619	0.00	0.00	37.01	4.41
2416	2479	6.939132	AAATGCTGAAGAGTGATATGAAGG	57.061	37.500	0.00	0.00	0.00	3.46
2442	2518	0.445043	CATCTGACATGGTGCACACG	59.555	55.000	20.43	8.52	0.00	4.49
2480	2557	2.488153	GGACCAAACAGAGCACATAACC	59.512	50.000	0.00	0.00	0.00	2.85
2491	2568	7.630242	ACAAATAGATGTATGGACCAAACAG	57.370	36.000	0.00	0.00	0.00	3.16
2545	2622	1.522668	AACAGCTCTGCGTGCATTTA	58.477	45.000	0.00	0.00	0.00	1.40
2625	2893	2.164422	GCAAGGCCACCAAGAATTAGAC	59.836	50.000	5.01	0.00	0.00	2.59
2640	2908	1.514553	GGCTGGAGAATTGCAAGGC	59.485	57.895	4.94	0.00	0.00	4.35
3060	3392	5.001232	GGTGCAGTTGGTGATTAACTTCTA	58.999	41.667	0.00	0.00	36.29	2.10
3066	3398	2.158534	AGTGGGTGCAGTTGGTGATTAA	60.159	45.455	0.00	0.00	0.00	1.40
3078	3410	2.515398	CCCTTGACAGTGGGTGCA	59.485	61.111	7.28	0.00	38.65	4.57
3087	3419	4.329545	GCACCGAGGCCCTTGACA	62.330	66.667	0.00	0.00	0.00	3.58
3101	3433	1.968540	GTCCTGCTGTCTTGGGCAC	60.969	63.158	0.00	0.00	34.57	5.01
3102	3434	2.431683	GTCCTGCTGTCTTGGGCA	59.568	61.111	0.00	0.00	36.94	5.36
3103	3435	2.360475	GGTCCTGCTGTCTTGGGC	60.360	66.667	0.00	0.00	0.00	5.36
3104	3436	1.298014	GAGGTCCTGCTGTCTTGGG	59.702	63.158	0.00	0.00	0.00	4.12
3105	3437	1.079543	CGAGGTCCTGCTGTCTTGG	60.080	63.158	0.00	0.00	0.00	3.61
3106	3438	1.967535	TCGAGGTCCTGCTGTCTTG	59.032	57.895	0.00	0.00	0.00	3.02
3107	3439	4.521559	TCGAGGTCCTGCTGTCTT	57.478	55.556	0.00	0.00	0.00	3.01

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.