AutoCloner

Multiple sequence alignment - TraesCS5A01G518500

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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	TraesCS5A01G518500	chr5A	100.000	3416	0	0	1	3416	680697809	680694394	0.000000e+00	6309.0
1	TraesCS5A01G518500	chr5A	90.591	1828	156	10	754	2571	680748867	680750688	0.000000e+00	2409.0
2	TraesCS5A01G518500	chr5A	86.070	402	43	5	2928	3327	680752330	680752720	1.470000e-113	420.0
3	TraesCS5A01G518500	chr5A	76.859	834	100	56	215	987	680663612	680662811	5.350000e-103	385.0
4	TraesCS5A01G518500	chr5A	81.879	447	46	18	2134	2571	680662802	680662382	9.080000e-91	344.0
5	TraesCS5A01G518500	chr5A	83.880	366	48	4	2966	3330	680661731	680661376	4.220000e-89	339.0
6	TraesCS5A01G518500	chr5A	85.635	181	20	4	353	531	680748498	680748674	5.820000e-43	185.0
7	TraesCS5A01G518500	chr5A	94.118	85	4	1	207	291	680748410	680748493	9.950000e-26	128.0
8	TraesCS5A01G518500	chr4D	94.939	2055	75	5	545	2571	499713362	499711309	0.000000e+00	3192.0
9	TraesCS5A01G518500	chr4D	90.154	1757	162	6	818	2568	499694324	499696075	0.000000e+00	2276.0
10	TraesCS5A01G518500	chr4D	86.263	1849	161	32	659	2432	499702219	499700389	0.000000e+00	1921.0
11	TraesCS5A01G518500	chr4D	95.137	473	21	2	2945	3416	499710556	499710085	0.000000e+00	745.0
12	TraesCS5A01G518500	chr4D	91.171	521	42	2	1675	2192	499830833	499831352	0.000000e+00	704.0
13	TraesCS5A01G518500	chr4D	89.770	479	33	7	2944	3416	499676863	499677331	1.750000e-167	599.0
14	TraesCS5A01G518500	chr4D	87.719	456	29	8	1	434	499714043	499713593	1.090000e-139	507.0
15	TraesCS5A01G518500	chr4D	86.544	379	46	5	2171	2546	499833646	499834022	2.450000e-111	412.0
16	TraesCS5A01G518500	chr4D	85.063	395	53	4	1875	2265	499844655	499845047	6.870000e-107	398.0
17	TraesCS5A01G518500	chr4D	84.699	366	45	4	2963	3327	499696663	499697018	4.190000e-94	355.0
18	TraesCS5A01G518500	chr4D	90.706	269	19	3	263	529	499713596	499713332	1.510000e-93	353.0
19	TraesCS5A01G518500	chr4D	85.467	289	39	3	2928	3215	499834977	499835263	7.170000e-77	298.0
20	TraesCS5A01G518500	chr4D	87.405	262	16	3	1418	1679	499794184	499794428	5.580000e-73	285.0
21	TraesCS5A01G518500	chr4D	79.767	257	32	11	2330	2571	499845057	499845308	5.860000e-38	169.0
22	TraesCS5A01G518500	chr4D	97.059	34	1	0	2928	2961	499710714	499710681	1.320000e-04	58.4
23	TraesCS5A01G518500	chr4B	89.040	1688	155	18	754	2421	642963569	642965246	0.000000e+00	2065.0
24	TraesCS5A01G518500	chr4B	88.157	1731	176	12	818	2536	642750862	642749149	0.000000e+00	2034.0
25	TraesCS5A01G518500	chr4B	93.583	1013	30	4	673	1652	642781119	642780109	0.000000e+00	1478.0
26	TraesCS5A01G518500	chr4B	94.880	918	47	0	1636	2553	642779700	642778783	0.000000e+00	1435.0
27	TraesCS5A01G518500	chr4B	92.992	528	26	7	2892	3416	642778051	642777532	0.000000e+00	760.0
28	TraesCS5A01G518500	chr4B	88.652	282	29	3	36	317	642781649	642781371	1.170000e-89	340.0
29	TraesCS5A01G518500	chr4B	88.672	256	24	3	149	403	486974116	486974367	1.190000e-79	307.0
30	TraesCS5A01G518500	chr4B	83.014	365	32	14	207	554	642751819	642751468	1.540000e-78	303.0
31	TraesCS5A01G518500	chr4B	88.703	239	16	2	381	617	642781350	642781121	7.220000e-72	281.0
32	TraesCS5A01G518500	chr4B	88.718	195	17	3	339	531	642963222	642963413	2.050000e-57	233.0
33	TraesCS5A01G518500	chr4B	92.547	161	12	0	686	846	486974373	486974533	7.370000e-57	231.0
34	TraesCS5A01G518500	chr4B	81.250	176	24	2	3137	3312	642961460	642961626	2.140000e-27	134.0
35	TraesCS5A01G518500	chr4B	90.722	97	6	3	207	302	642963129	642963223	3.580000e-25	126.0
36	TraesCS5A01G518500	chr3D	83.125	160	20	7	207	364	578589857	578590011	4.600000e-29	139.0

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	TraesCS5A01G518500	chr5A	680694394	680697809	3415	True	6309.000000	6309	100.000000	1	3416	1	chr5A.!!$R1	3415
1	TraesCS5A01G518500	chr5A	680748410	680752720	4310	False	785.500000	2409	89.103500	207	3327	4	chr5A.!!$F1	3120
2	TraesCS5A01G518500	chr5A	680661376	680663612	2236	True	356.000000	385	80.872667	215	3330	3	chr5A.!!$R2	3115
3	TraesCS5A01G518500	chr4D	499700389	499702219	1830	True	1921.000000	1921	86.263000	659	2432	1	chr4D.!!$R1	1773
4	TraesCS5A01G518500	chr4D	499694324	499697018	2694	False	1315.500000	2276	87.426500	818	3327	2	chr4D.!!$F3	2509
5	TraesCS5A01G518500	chr4D	499710085	499714043	3958	True	971.080000	3192	93.112000	1	3416	5	chr4D.!!$R2	3415
6	TraesCS5A01G518500	chr4D	499830833	499835263	4430	False	471.333333	704	87.727333	1675	3215	3	chr4D.!!$F4	1540
7	TraesCS5A01G518500	chr4D	499844655	499845308	653	False	283.500000	398	82.415000	1875	2571	2	chr4D.!!$F5	696
8	TraesCS5A01G518500	chr4B	642749149	642751819	2670	True	1168.500000	2034	85.585500	207	2536	2	chr4B.!!$R1	2329
9	TraesCS5A01G518500	chr4B	642777532	642781649	4117	True	858.800000	1478	91.762000	36	3416	5	chr4B.!!$R2	3380
10	TraesCS5A01G518500	chr4B	642961460	642965246	3786	False	639.500000	2065	87.432500	207	3312	4	chr4B.!!$F2	3105

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
314	1778	0.248907	TACGCTATGCTCCGAACTGC	60.249	55.0	0.00	0.0	0.00	4.40	F
707	2736	0.529378	GGAGCACTGGCCATTTTCTG	59.471	55.0	5.51	0.0	42.56	3.02	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1509	3623	1.002366	GCACATCGAAGCTACCAGTG	58.998	55.0	0.0	0.0	0.0	3.66	R
2586	7694	0.973496	TAGGGTGGCATCGCAGTGTA	60.973	55.0	0.0	0.0	0.0	2.90	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
67	69	5.943349	TTATACAGATTGGTTTCGAGGGA	57.057	39.130	0.00	0.00	0.00	4.20
78	95	0.828762	TTCGAGGGAGGTCGGTTGAA	60.829	55.000	0.00	0.00	40.49	2.69
83	100	2.747989	GAGGGAGGTCGGTTGAATTTTC	59.252	50.000	0.00	0.00	0.00	2.29
84	101	2.375509	AGGGAGGTCGGTTGAATTTTCT	59.624	45.455	0.00	0.00	0.00	2.52
85	102	2.747989	GGGAGGTCGGTTGAATTTTCTC	59.252	50.000	0.00	0.00	0.00	2.87
102	119	4.640771	TTCTCAGGTTTCAGTTATGGCT	57.359	40.909	0.00	0.00	0.00	4.75
141	158	8.682936	AAAAGTATCCACTCCATCAATATCAC	57.317	34.615	0.00	0.00	32.29	3.06
184	209	7.394359	TCGAACCGTATATATACCCTTTAGCTT	59.606	37.037	15.70	0.00	0.00	3.74
307	1771	3.312828	CTTGACAGATACGCTATGCTCC	58.687	50.000	0.00	0.00	0.00	4.70
309	1773	1.535896	GACAGATACGCTATGCTCCGA	59.464	52.381	0.00	0.00	0.00	4.55
311	1775	2.287668	ACAGATACGCTATGCTCCGAAC	60.288	50.000	0.00	0.00	0.00	3.95
312	1776	2.030717	CAGATACGCTATGCTCCGAACT	60.031	50.000	0.00	0.00	0.00	3.01
313	1777	2.030717	AGATACGCTATGCTCCGAACTG	60.031	50.000	0.00	0.00	0.00	3.16
314	1778	0.248907	TACGCTATGCTCCGAACTGC	60.249	55.000	0.00	0.00	0.00	4.40
315	1779	1.227089	CGCTATGCTCCGAACTGCT	60.227	57.895	0.00	0.00	0.00	4.24
316	1780	1.485838	CGCTATGCTCCGAACTGCTG	61.486	60.000	0.00	0.00	0.00	4.41
342	1824	5.419788	TCAAGTTCGGGCTAGTTGAATACTA	59.580	40.000	0.00	0.00	38.33	1.82
383	1868	0.752054	TTGGCAGCAAAGAACCAAGG	59.248	50.000	0.00	0.00	37.26	3.61
419	2072	3.844577	AGTCTGTTTGATTGATGCAGC	57.155	42.857	0.00	0.00	0.00	5.25
511	2179	1.070758	AGATACATGGTGATGGTCCGC	59.929	52.381	0.00	0.00	33.39	5.54
602	2631	3.439129	GTGTTGTACCTGCCATTAGGAAC	59.561	47.826	0.00	0.00	40.42	3.62
609	2638	2.092212	CCTGCCATTAGGAACCAGTCAT	60.092	50.000	0.00	0.00	40.42	3.06
633	2662	9.069078	CATGTCTATGTGATAAAGCAACAAAAG	57.931	33.333	0.00	0.00	0.00	2.27
650	2679	3.636282	AAAGTTGCAACCCGATACAAC	57.364	42.857	25.62	0.00	42.08	3.32
699	2728	1.544825	TAGTGAGTGGAGCACTGGCC	61.545	60.000	0.00	0.00	45.44	5.36
707	2736	0.529378	GGAGCACTGGCCATTTTCTG	59.471	55.000	5.51	0.00	42.56	3.02
1075	3183	4.138290	TGGCTTAGAGAGGATTCTACTCG	58.862	47.826	0.00	0.00	39.90	4.18
1276	3384	5.633182	GTGTCCAAATTTCGTTATGCACAAT	59.367	36.000	0.00	0.00	0.00	2.71
1305	3413	2.974489	CTCCAGCGGCAACAGCAAG	61.974	63.158	1.45	0.00	38.34	4.01
1509	3623	2.606308	CCTTCTGTGCACACAATCTTGC	60.606	50.000	17.42	0.00	41.33	4.01
1527	3650	1.002366	GCACTGGTAGCTTCGATGTG	58.998	55.000	0.00	0.00	0.00	3.21
1601	3724	2.551032	TCTGCGAAGACGAAAGAGTACA	59.449	45.455	0.00	0.00	42.66	2.90
1680	4228	0.107993	CCGCTTTGAGAGGCAGATGA	60.108	55.000	0.00	0.00	0.00	2.92
1690	4238	0.547075	AGGCAGATGAGCAGCAAGAT	59.453	50.000	0.00	0.00	35.83	2.40
1792	4343	0.038251	TTGCCGACAGAGCACTACAG	60.038	55.000	0.00	0.00	40.69	2.74
2041	4596	7.429340	GTGTATTGAGAGCCAATTTTAACATCG	59.571	37.037	0.00	0.00	42.55	3.84
2085	4640	3.190849	CGACGAGGGTGCATGCAG	61.191	66.667	23.41	11.76	0.00	4.41
2138	4693	5.305585	GTGTGAACTTCTCAGTGGGAATAA	58.694	41.667	5.75	0.00	33.60	1.40
2255	7125	3.848272	AATGGCCGTAGATGTTTTGTG	57.152	42.857	0.00	0.00	0.00	3.33
2423	7308	8.726988	TGGTATTAGACATGTTTAGTTTTGCTC	58.273	33.333	0.00	0.00	0.00	4.26
2449	7334	5.646793	TGTAAGTCGTCTATACTCTTGTGCT	59.353	40.000	0.00	0.00	0.00	4.40
2556	7476	5.734855	TTCTTCAGAGTGTAACAAGTTGC	57.265	39.130	1.81	0.00	41.43	4.17
2561	7481	1.082366	GTGTAACAAGTTGCGCCCG	60.082	57.895	4.18	0.00	36.32	6.13
2571	7495	0.596341	GTTGCGCCCGTTTGTTTGAT	60.596	50.000	4.18	0.00	0.00	2.57
2573	7497	0.596083	TGCGCCCGTTTGTTTGATTG	60.596	50.000	4.18	0.00	0.00	2.67
2574	7498	0.596341	GCGCCCGTTTGTTTGATTGT	60.596	50.000	0.00	0.00	0.00	2.71
2584	7685	6.088883	CCGTTTGTTTGATTGTTATAAGCACC	59.911	38.462	0.00	0.00	0.00	5.01
2586	7694	5.950758	TGTTTGATTGTTATAAGCACCGT	57.049	34.783	0.00	0.00	0.00	4.83
2642	8346	9.827411	GATTCCTTCATTTACTGTTGAAACTAC	57.173	33.333	0.00	0.00	31.85	2.73
2684	8429	6.150474	GCCAAGCCTCTATGTAACTACAAAAA	59.850	38.462	0.00	0.00	39.99	1.94
2751	8641	9.342308	GATCTCATGGGTTTTCTGTTATTGATA	57.658	33.333	0.00	0.00	0.00	2.15
2755	8645	8.058235	TCATGGGTTTTCTGTTATTGATATCCA	58.942	33.333	0.00	0.00	0.00	3.41
2801	8808	8.693120	ATCACTCTTATTCTCGGTAAGTATGA	57.307	34.615	0.00	0.00	33.26	2.15
2814	8821	3.610040	AAGTATGAATGTGGAGTCGCA	57.390	42.857	0.00	0.00	37.83	5.10
2887	9483	5.013391	AGTTAATACTCCTTCCGTCCCAAAA	59.987	40.000	0.00	0.00	0.00	2.44
2889	9485	5.703730	AATACTCCTTCCGTCCCAAAATA	57.296	39.130	0.00	0.00	0.00	1.40
3222	10220	2.899900	ACCCATTCTTCTTTCCAAAGGC	59.100	45.455	0.00	0.00	36.67	4.35
3338	10336	1.442769	ACAGCCTGTAACAGATTGCG	58.557	50.000	0.00	0.00	32.44	4.85
3344	10342	3.002791	CCTGTAACAGATTGCGACACAT	58.997	45.455	0.00	0.00	32.44	3.21

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
57	59	0.669625	CAACCGACCTCCCTCGAAAC	60.670	60.000	0.00	0.00	35.58	2.78
61	63	0.249398	AATTCAACCGACCTCCCTCG	59.751	55.000	0.00	0.00	0.00	4.63
67	69	3.181443	ACCTGAGAAAATTCAACCGACCT	60.181	43.478	0.00	0.00	0.00	3.85
78	95	6.012745	AGCCATAACTGAAACCTGAGAAAAT	58.987	36.000	0.00	0.00	0.00	1.82
83	100	3.942829	TGAGCCATAACTGAAACCTGAG	58.057	45.455	0.00	0.00	0.00	3.35
84	101	4.574674	ATGAGCCATAACTGAAACCTGA	57.425	40.909	0.00	0.00	0.00	3.86
85	102	4.201851	CGAATGAGCCATAACTGAAACCTG	60.202	45.833	0.00	0.00	0.00	4.00
184	209	6.985188	AAGCGCATATTTAGTTCTCAAAGA	57.015	33.333	11.47	0.00	0.00	2.52
309	1773	1.308998	CCCGAACTTGAACAGCAGTT	58.691	50.000	0.00	0.00	41.64	3.16
311	1775	0.886490	AGCCCGAACTTGAACAGCAG	60.886	55.000	0.00	0.00	0.00	4.24
312	1776	0.394938	TAGCCCGAACTTGAACAGCA	59.605	50.000	0.00	0.00	0.00	4.41
313	1777	1.079503	CTAGCCCGAACTTGAACAGC	58.920	55.000	0.00	0.00	0.00	4.40
314	1778	2.457366	ACTAGCCCGAACTTGAACAG	57.543	50.000	0.00	0.00	0.00	3.16
315	1779	2.103432	TCAACTAGCCCGAACTTGAACA	59.897	45.455	0.00	0.00	0.00	3.18
316	1780	2.762745	TCAACTAGCCCGAACTTGAAC	58.237	47.619	0.00	0.00	0.00	3.18
342	1824	6.600822	CCAACACTTCATTATCATCTGAACCT	59.399	38.462	0.00	0.00	0.00	3.50
343	1825	6.678900	GCCAACACTTCATTATCATCTGAACC	60.679	42.308	0.00	0.00	0.00	3.62
344	1826	6.127925	TGCCAACACTTCATTATCATCTGAAC	60.128	38.462	0.00	0.00	0.00	3.18
345	1827	5.945191	TGCCAACACTTCATTATCATCTGAA	59.055	36.000	0.00	0.00	0.00	3.02
347	1829	5.732528	GCTGCCAACACTTCATTATCATCTG	60.733	44.000	0.00	0.00	0.00	2.90
348	1830	4.337555	GCTGCCAACACTTCATTATCATCT	59.662	41.667	0.00	0.00	0.00	2.90
349	1831	4.096833	TGCTGCCAACACTTCATTATCATC	59.903	41.667	0.00	0.00	0.00	2.92
350	1832	4.018490	TGCTGCCAACACTTCATTATCAT	58.982	39.130	0.00	0.00	0.00	2.45
383	1868	3.134458	CAGACTTGACTGAGAACCAACC	58.866	50.000	0.00	0.00	39.94	3.77
419	2072	5.639757	TGAAGCATCACCACATATTTTTCG	58.360	37.500	0.00	0.00	0.00	3.46
511	2179	5.997746	TGACTAACTCTTGGATCTTTGTTGG	59.002	40.000	0.00	0.00	0.00	3.77
602	2631	6.051074	TGCTTTATCACATAGACATGACTGG	58.949	40.000	8.00	2.91	35.96	4.00
609	2638	8.165239	ACTTTTGTTGCTTTATCACATAGACA	57.835	30.769	0.00	0.00	0.00	3.41
633	2662	0.167251	CCGTTGTATCGGGTTGCAAC	59.833	55.000	21.59	21.59	45.88	4.17
650	2679	1.152694	ATTCCATGCACCCCATCCG	60.153	57.895	0.00	0.00	29.71	4.18
1276	3384	2.346541	CGCTGGAGAGACAGAGCCA	61.347	63.158	0.00	0.00	40.97	4.75
1305	3413	3.542712	TCAAGCGCTTCTGATGTTTTC	57.457	42.857	22.21	0.00	0.00	2.29
1509	3623	1.002366	GCACATCGAAGCTACCAGTG	58.998	55.000	0.00	0.00	0.00	3.66
1601	3724	5.324832	AATAATCTGGGGGAAACGATCAT	57.675	39.130	0.00	0.00	0.00	2.45
1656	4204	2.167861	GCCTCTCAAAGCGGCTACG	61.168	63.158	1.35	0.00	42.61	3.51
1680	4228	7.677892	TCTCATTATTCTCATATCTTGCTGCT	58.322	34.615	0.00	0.00	0.00	4.24
1690	4238	9.872721	GATCAGCAATCTCTCATTATTCTCATA	57.127	33.333	0.00	0.00	0.00	2.15
1792	4343	8.129211	GCTTGTGATAATGATTTTACTACCACC	58.871	37.037	0.00	0.00	0.00	4.61
2041	4596	2.229784	CCAGAACCTTGCACCAGAAATC	59.770	50.000	0.00	0.00	0.00	2.17
2085	4640	2.485814	CCCAAACTTACAGAGCTGCTTC	59.514	50.000	2.53	0.00	0.00	3.86
2138	4693	4.695455	CCATTCGTTGAAGATACACAGGTT	59.305	41.667	0.00	0.00	0.00	3.50
2255	7125	2.514824	GAGGCCTGGCGATTCCAC	60.515	66.667	12.00	0.00	40.72	4.02
2423	7308	6.415280	GCACAAGAGTATAGACGACTTACATG	59.585	42.308	0.00	0.00	0.00	3.21
2449	7334	9.613428	AGTTATACAACATAGCAGAAAATAGCA	57.387	29.630	0.00	0.00	37.10	3.49
2536	7455	3.604772	GCGCAACTTGTTACACTCTGAAG	60.605	47.826	0.30	0.00	0.00	3.02
2556	7476	1.846541	AACAATCAAACAAACGGGCG	58.153	45.000	0.00	0.00	0.00	6.13
2561	7481	6.639279	ACGGTGCTTATAACAATCAAACAAAC	59.361	34.615	0.00	0.00	0.00	2.93
2571	7495	3.680937	GCAGTGTACGGTGCTTATAACAA	59.319	43.478	11.10	0.00	36.71	2.83
2573	7497	2.280708	CGCAGTGTACGGTGCTTATAAC	59.719	50.000	15.12	0.00	37.55	1.89
2574	7498	2.164017	TCGCAGTGTACGGTGCTTATAA	59.836	45.455	15.12	0.00	37.55	0.98
2584	7685	2.452813	GGTGGCATCGCAGTGTACG	61.453	63.158	0.00	0.00	0.00	3.67
2586	7694	0.973496	TAGGGTGGCATCGCAGTGTA	60.973	55.000	0.00	0.00	0.00	2.90
2642	8346	3.251479	TGGCACTATGTTGTGAGCTAG	57.749	47.619	0.00	0.00	40.12	3.42
2684	8429	5.762218	CAGTGGAAGAAAAAGATCACTCTGT	59.238	40.000	0.00	0.00	33.80	3.41
2731	8479	8.281531	TCTGGATATCAATAACAGAAAACCCAT	58.718	33.333	4.83	0.00	35.45	4.00
2801	8808	1.153369	CGGGATGCGACTCCACATT	60.153	57.895	6.10	0.00	37.01	2.71
3054	10052	2.880443	ACGGACTCTTGTGGGTTAGTA	58.120	47.619	0.00	0.00	0.00	1.82
3222	10220	2.015227	AACAGTTGCCACCTTTGCCG	62.015	55.000	0.00	0.00	0.00	5.69

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.