AutoCloner

Multiple sequence alignment - TraesCS5A01G070300

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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	TraesCS5A01G070300	chr5A	100.000	2318	0	0	1	2318	78473456	78475773	0.000000e+00	4281.0
1	TraesCS5A01G070300	chr5A	83.759	1176	133	35	486	1615	78426022	78427185	0.000000e+00	1061.0
2	TraesCS5A01G070300	chr5A	84.222	881	101	14	754	1604	78368722	78369594	0.000000e+00	822.0
3	TraesCS5A01G070300	chr5A	86.792	265	19	8	486	735	78368341	78368604	4.880000e-72	281.0
4	TraesCS5A01G070300	chr5A	91.391	151	8	3	342	487	78368158	78368308	3.910000e-48	202.0
5	TraesCS5A01G070300	chr5A	91.597	119	6	3	372	487	78425872	78425989	6.630000e-36	161.0
6	TraesCS5A01G070300	chr5A	81.250	160	18	9	95	242	78424699	78424858	4.050000e-23	119.0
7	TraesCS5A01G070300	chr5B	86.415	2304	189	65	1	2215	91107835	91110103	0.000000e+00	2407.0
8	TraesCS5A01G070300	chr5B	84.788	1157	97	30	486	1600	90987807	90988926	0.000000e+00	1088.0
9	TraesCS5A01G070300	chr5B	88.732	142	7	2	342	480	90987590	90987725	5.120000e-37	165.0
10	TraesCS5A01G070300	chr5D	93.355	1550	83	8	775	2318	84178047	84179582	0.000000e+00	2274.0
11	TraesCS5A01G070300	chr5D	92.848	783	48	4	1	776	84011016	84011797	0.000000e+00	1129.0
12	TraesCS5A01G070300	chr5D	74.364	511	84	29	486	979	84185144	84185624	8.510000e-40	174.0
13	TraesCS5A01G070300	chr2D	81.993	572	78	9	999	1550	547791256	547790690	1.620000e-126	462.0
14	TraesCS5A01G070300	chrUn	84.580	441	58	6	982	1414	248122688	248122250	1.650000e-116	429.0
15	TraesCS5A01G070300	chrUn	84.375	448	58	8	977	1414	281905676	281906121	1.650000e-116	429.0
16	TraesCS5A01G070300	chr2B	84.580	441	58	6	982	1414	654649253	654648815	1.650000e-116	429.0
17	TraesCS5A01G070300	chr2B	84.580	441	58	6	982	1414	654699376	654698938	1.650000e-116	429.0
18	TraesCS5A01G070300	chr2B	77.500	320	51	13	680	984	654546545	654546232	3.060000e-39	172.0
19	TraesCS5A01G070300	chr2B	75.728	206	35	12	664	857	654433848	654433646	3.170000e-14	89.8

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	TraesCS5A01G070300	chr5A	78473456	78475773	2317	False	4281.0	4281	100.000000	1	2318	1	chr5A.!!$F1	2317
1	TraesCS5A01G070300	chr5A	78424699	78427185	2486	False	447.0	1061	85.535333	95	1615	3	chr5A.!!$F3	1520
2	TraesCS5A01G070300	chr5A	78368158	78369594	1436	False	435.0	822	87.468333	342	1604	3	chr5A.!!$F2	1262
3	TraesCS5A01G070300	chr5B	91107835	91110103	2268	False	2407.0	2407	86.415000	1	2215	1	chr5B.!!$F1	2214
4	TraesCS5A01G070300	chr5B	90987590	90988926	1336	False	626.5	1088	86.760000	342	1600	2	chr5B.!!$F2	1258
5	TraesCS5A01G070300	chr5D	84178047	84179582	1535	False	2274.0	2274	93.355000	775	2318	1	chr5D.!!$F2	1543
6	TraesCS5A01G070300	chr5D	84011016	84011797	781	False	1129.0	1129	92.848000	1	776	1	chr5D.!!$F1	775
7	TraesCS5A01G070300	chr2D	547790690	547791256	566	True	462.0	462	81.993000	999	1550	1	chr2D.!!$R1	551

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
89	91	0.248743	GCCATCGGTCATGCATTGTG	60.249	55.0	0.0	0.0	0.0	3.33	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1813	3046	0.320771	ATGTCTTGTGCAGTCGGTCC	60.321	55.0	0.0	0.0	0.0	4.46	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
56	58	2.644212	CGACCTGCCTGAGCTCACT	61.644	63.158	13.74	0.00	40.80	3.41
86	88	3.424300	CGCCATCGGTCATGCATT	58.576	55.556	0.00	0.00	0.00	3.56
87	89	1.009335	CGCCATCGGTCATGCATTG	60.009	57.895	0.00	0.00	0.00	2.82
88	90	1.717791	CGCCATCGGTCATGCATTGT	61.718	55.000	0.00	0.00	0.00	2.71
89	91	0.248743	GCCATCGGTCATGCATTGTG	60.249	55.000	0.00	0.00	0.00	3.33
90	92	1.097232	CCATCGGTCATGCATTGTGT	58.903	50.000	0.00	0.00	0.00	3.72
91	93	1.064505	CCATCGGTCATGCATTGTGTC	59.935	52.381	0.00	0.00	0.00	3.67
122	132	1.474677	CCTGGGAGCATTACTGAGCTG	60.475	57.143	0.00	0.00	42.04	4.24
139	149	3.815401	GAGCTGAAGTCCACAAAAGCTAA	59.185	43.478	0.00	0.00	40.90	3.09
161	171	1.384525	AGCACCAAACAGCAAACGTA	58.615	45.000	0.00	0.00	0.00	3.57
194	214	7.846644	ATTCTGAAGAAAGTATCTCAAGCTG	57.153	36.000	0.00	0.00	37.42	4.24
659	1699	7.031975	GGGCAAATTGAAGAATCACTTTCTAG	58.968	38.462	0.00	0.00	44.09	2.43
663	1703	9.286946	CAAATTGAAGAATCACTTTCTAGCATC	57.713	33.333	0.00	0.00	44.09	3.91
706	1755	5.106038	CGGCATATCCTGATGTTGCATTATT	60.106	40.000	14.71	0.00	34.78	1.40
886	2036	3.738830	ATTGCTTGCTTGCTGAAGAAA	57.261	38.095	3.47	0.00	0.00	2.52
913	2063	5.887598	ACATTTCATGAACATAGCTGCCTTA	59.112	36.000	7.89	0.00	0.00	2.69
1038	2243	0.173029	TGGTTGCAACACTGTTGCTG	59.827	50.000	35.28	10.93	45.13	4.41
1054	2259	3.238497	TGGTCCTGGTGGTGTCCG	61.238	66.667	0.00	0.00	34.23	4.79
1176	2381	4.030452	GCTGAGTGTTGTGCCGCC	62.030	66.667	0.00	0.00	0.00	6.13
1234	2439	2.669569	GCATCGCCGGCATATGGT	60.670	61.111	29.83	9.67	0.00	3.55
1353	2562	6.017605	CACTATCCATAAGCATCAAACTGTCC	60.018	42.308	0.00	0.00	0.00	4.02
1358	2567	0.670546	AGCATCAAACTGTCCGTCGG	60.671	55.000	4.39	4.39	0.00	4.79
1359	2568	0.949105	GCATCAAACTGTCCGTCGGT	60.949	55.000	11.88	0.00	37.22	4.69
1362	2571	1.608055	TCAAACTGTCCGTCGGTCTA	58.392	50.000	11.88	0.00	34.09	2.59
1365	2574	3.949754	TCAAACTGTCCGTCGGTCTATAT	59.050	43.478	11.88	0.00	34.09	0.86
1407	2618	3.681594	CGGCTAAATAAGTGGAGGAGCAA	60.682	47.826	0.00	0.00	0.00	3.91
1408	2619	3.879892	GGCTAAATAAGTGGAGGAGCAAG	59.120	47.826	0.00	0.00	0.00	4.01
1428	2655	5.915196	GCAAGTGAAAGGTCTTATTGTTGTC	59.085	40.000	0.00	0.00	0.00	3.18
1623	2856	9.353999	AGTAAAAATTGATCGCAAGGTAATTTC	57.646	29.630	0.00	0.00	37.45	2.17
1675	2908	8.540388	GCCCATAGACATCCTTATAGTTGATTA	58.460	37.037	0.00	0.00	0.00	1.75
1773	3006	8.040132	TCCACATTGGTTGAAATATTTCCATTC	58.960	33.333	22.42	11.61	39.03	2.67
1813	3046	7.389330	TGTTGGTAAGTATCCACAACAACATAG	59.611	37.037	6.12	0.00	45.64	2.23
1827	3060	0.973632	ACATAGGACCGACTGCACAA	59.026	50.000	0.00	0.00	0.00	3.33
1828	3061	1.066858	ACATAGGACCGACTGCACAAG	60.067	52.381	0.00	0.00	0.00	3.16
1841	3075	3.244875	ACTGCACAAGACATATGGTTGGA	60.245	43.478	18.93	5.57	0.00	3.53
1899	3133	5.478332	ACTTTCCCTCTTCAAATCCATGAAC	59.522	40.000	0.00	0.00	35.55	3.18
2011	3250	6.561737	TTATTCACAGTTTATTGGCGTTCA	57.438	33.333	0.00	0.00	0.00	3.18
2050	3289	3.014304	TGCCTCTCTATACTTCACCGT	57.986	47.619	0.00	0.00	0.00	4.83
2106	3349	7.929941	TGTGCAAATACCAAGATGTACAATA	57.070	32.000	0.00	0.00	35.86	1.90
2137	3380	3.006217	CCAATAGATCGCCTCTCATGTCA	59.994	47.826	0.00	0.00	35.28	3.58
2159	3402	8.360390	TGTCATCATGTATATGTCCTTACTGAC	58.640	37.037	0.00	0.00	35.73	3.51
2185	3429	6.533819	TGTTCCTATTGTCTTGTGTTTACG	57.466	37.500	0.00	0.00	0.00	3.18
2244	3488	6.150140	GCTCATTTCCATTCTACAAGAACAGT	59.850	38.462	0.00	0.00	37.00	3.55
2246	3490	7.223584	TCATTTCCATTCTACAAGAACAGTGA	58.776	34.615	0.00	0.00	37.00	3.41
2294	3538	3.609853	TGCTGAGCCACTCGAATTTTAT	58.390	40.909	0.23	0.00	32.35	1.40
2298	3542	3.128589	TGAGCCACTCGAATTTTATTGCC	59.871	43.478	0.00	0.00	32.35	4.52

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
13	14	7.365741	GTGATTAGCATGATAACATTTCAGGG	58.634	38.462	5.38	0.00	34.15	4.45
86	88	0.976641	CAGGGGAACAGCTAGACACA	59.023	55.000	0.00	0.00	0.00	3.72
87	89	0.250513	CCAGGGGAACAGCTAGACAC	59.749	60.000	0.00	0.00	0.00	3.67
88	90	0.909610	CCCAGGGGAACAGCTAGACA	60.910	60.000	0.00	0.00	37.50	3.41
89	91	0.617820	TCCCAGGGGAACAGCTAGAC	60.618	60.000	5.33	0.00	42.05	2.59
90	92	0.325671	CTCCCAGGGGAACAGCTAGA	60.326	60.000	5.33	0.00	44.66	2.43
91	93	1.977293	GCTCCCAGGGGAACAGCTAG	61.977	65.000	5.33	0.00	44.66	3.42
122	132	5.284428	GCTAGTTAGCTTTTGTGGACTTC	57.716	43.478	0.00	0.00	45.62	3.01
139	149	1.333619	CGTTTGCTGTTTGGTGCTAGT	59.666	47.619	0.00	0.00	0.00	2.57
148	158	7.491048	AGAATTCACATTTTACGTTTGCTGTTT	59.509	29.630	8.44	0.00	0.00	2.83
194	214	0.953471	TTGACGCATGCACCCACTAC	60.953	55.000	19.57	0.00	0.00	2.73
242	263	8.629158	TGGCATGCTTCTCGTTAATTAATTATT	58.371	29.630	18.92	0.00	0.00	1.40
243	264	8.165239	TGGCATGCTTCTCGTTAATTAATTAT	57.835	30.769	18.92	0.00	0.00	1.28
264	290	2.076100	CTAAGTTCTGCGACATTGGCA	58.924	47.619	0.00	0.00	38.92	4.92
319	346	6.242508	TGCAGCTATTACTGAGATAGTACG	57.757	41.667	0.00	0.00	41.48	3.67
659	1699	1.012234	GACCAATTCGTCGCGATGC	60.012	57.895	23.40	4.92	35.23	3.91
663	1703	0.789383	GCAAAGACCAATTCGTCGCG	60.789	55.000	0.00	0.00	37.85	5.87
767	1916	7.065683	TGTTGAACGATAACGACTACCATAGTA	59.934	37.037	0.00	0.00	39.59	1.82
886	2036	5.404946	GCAGCTATGTTCATGAAATGTGTT	58.595	37.500	10.35	0.00	46.80	3.32
1038	2243	3.236003	GACGGACACCACCAGGACC	62.236	68.421	0.00	0.00	38.69	4.46
1151	2356	1.079819	CAACACTCAGCCGACGGAT	60.080	57.895	20.50	9.11	0.00	4.18
1353	2562	7.193595	TGTTGATGCATATATATAGACCGACG	58.806	38.462	0.00	0.00	0.00	5.12
1365	2574	9.660180	TTAGCCGTATTAATGTTGATGCATATA	57.340	29.630	0.00	0.00	0.00	0.86
1407	2618	5.236478	CACGACAACAATAAGACCTTTCACT	59.764	40.000	0.00	0.00	0.00	3.41
1408	2619	5.007332	ACACGACAACAATAAGACCTTTCAC	59.993	40.000	0.00	0.00	0.00	3.18
1428	2655	3.438087	AGGCAGAGAATTCAAATCACACG	59.562	43.478	8.44	0.00	0.00	4.49
1623	2856	6.733725	CGCGCTGATAGTTGATTACAATATTG	59.266	38.462	14.01	14.01	38.32	1.90
1645	2878	2.357517	GGATGTCTATGGGCCGCG	60.358	66.667	0.00	0.00	0.00	6.46
1773	3006	9.871238	ATACTTACCAACAATCTAGTACACTTG	57.129	33.333	0.00	0.00	0.00	3.16
1813	3046	0.320771	ATGTCTTGTGCAGTCGGTCC	60.321	55.000	0.00	0.00	0.00	4.46
1827	3060	7.237471	TGGTCATGTATATCCAACCATATGTCT	59.763	37.037	1.24	0.00	32.08	3.41
1828	3061	7.394016	TGGTCATGTATATCCAACCATATGTC	58.606	38.462	1.24	0.00	32.08	3.06
1899	3133	2.100631	GTGCGAAGATGACACCGGG	61.101	63.158	6.32	0.00	0.00	5.73
2011	3250	3.565482	GGCATGACAATGTACCAATCGAT	59.435	43.478	0.00	0.00	36.08	3.59
2075	3314	7.895759	ACATCTTGGTATTTGCACAACTTTAT	58.104	30.769	0.00	0.00	0.00	1.40
2076	3315	7.283625	ACATCTTGGTATTTGCACAACTTTA	57.716	32.000	0.00	0.00	0.00	1.85
2078	3317	5.789643	ACATCTTGGTATTTGCACAACTT	57.210	34.783	0.00	0.00	0.00	2.66
2080	3319	6.007936	TGTACATCTTGGTATTTGCACAAC	57.992	37.500	0.00	0.00	0.00	3.32
2081	3320	6.641169	TTGTACATCTTGGTATTTGCACAA	57.359	33.333	0.00	0.00	0.00	3.33
2106	3349	5.041191	AGGCGATCTATTGGTCTTTTCAT	57.959	39.130	0.00	0.00	0.00	2.57
2137	3380	7.855784	TGGTCAGTAAGGACATATACATGAT	57.144	36.000	0.00	0.00	39.59	2.45
2159	3402	5.964958	AACACAAGACAATAGGAACATGG	57.035	39.130	0.00	0.00	0.00	3.66
2244	3488	8.198778	CACCATTGGAAATTGATCATATTGTCA	58.801	33.333	10.37	0.43	0.00	3.58
2246	3490	6.987992	GCACCATTGGAAATTGATCATATTGT	59.012	34.615	10.37	0.00	0.00	2.71

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.