AutoCloner

Multiple sequence alignment - TraesCS1D01G230400

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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	TraesCS1D01G230400	chr1D	100.000	2288	0	0	1	2288	318516674	318514387	0.000000e+00	4226.0
1	TraesCS1D01G230400	chr1D	97.995	798	13	3	98	895	475311186	475311980	0.000000e+00	1382.0
2	TraesCS1D01G230400	chr1D	87.765	425	48	3	1724	2148	318562550	318562130	5.680000e-136	494.0
3	TraesCS1D01G230400	chr7D	98.494	797	12	0	98	894	595975745	595976541	0.000000e+00	1406.0
4	TraesCS1D01G230400	chr7D	98.243	797	13	1	98	893	590890604	590889808	0.000000e+00	1393.0
5	TraesCS1D01G230400	chr7D	97.519	806	18	2	98	902	172779303	172780107	0.000000e+00	1376.0
6	TraesCS1D01G230400	chr7D	94.041	839	45	5	893	1727	188555248	188554411	0.000000e+00	1267.0
7	TraesCS1D01G230400	chr7D	94.125	834	46	3	893	1724	433076818	433077650	0.000000e+00	1266.0
8	TraesCS1D01G230400	chr7D	100.000	73	0	0	1	73	19679408	19679336	3.960000e-28	135.0
9	TraesCS1D01G230400	chr7D	100.000	73	0	0	1	73	176464886	176464958	3.960000e-28	135.0
10	TraesCS1D01G230400	chr7D	100.000	29	0	0	72	100	158648642	158648670	1.000000e-03	54.7
11	TraesCS1D01G230400	chr5D	98.241	796	13	1	98	893	233278272	233279066	0.000000e+00	1391.0
12	TraesCS1D01G230400	chr5D	98.116	796	15	0	98	893	334650844	334650049	0.000000e+00	1387.0
13	TraesCS1D01G230400	chr5D	97.990	796	16	0	98	893	429183714	429184509	0.000000e+00	1382.0
14	TraesCS1D01G230400	chr5D	93.600	125	8	0	893	1017	494994568	494994692	1.080000e-43	187.0
15	TraesCS1D01G230400	chr5D	100.000	73	0	0	1	73	429182579	429182651	3.960000e-28	135.0
16	TraesCS1D01G230400	chr3D	98.116	796	13	2	98	893	49430409	49431202	0.000000e+00	1386.0
17	TraesCS1D01G230400	chr3D	97.997	799	15	1	98	896	455890267	455889470	0.000000e+00	1386.0
18	TraesCS1D01G230400	chr3D	95.694	836	35	1	893	1727	6288507	6289342	0.000000e+00	1343.0
19	TraesCS1D01G230400	chr3D	95.465	838	37	1	893	1729	81834264	81835101	0.000000e+00	1336.0
20	TraesCS1D01G230400	chr3A	94.405	840	45	2	893	1730	71155312	71156151	0.000000e+00	1290.0
21	TraesCS1D01G230400	chr3A	100.000	73	0	0	1	73	133546379	133546451	3.960000e-28	135.0
22	TraesCS1D01G230400	chr7A	94.272	838	46	2	893	1729	221705824	221706660	0.000000e+00	1280.0
23	TraesCS1D01G230400	chr6D	93.950	843	44	7	893	1731	275680556	275679717	0.000000e+00	1267.0
24	TraesCS1D01G230400	chr4D	94.005	834	45	5	893	1724	15239545	15238715	0.000000e+00	1258.0
25	TraesCS1D01G230400	chr4D	93.713	843	44	7	893	1728	56942439	56943279	0.000000e+00	1254.0
26	TraesCS1D01G230400	chr1B	90.625	576	36	8	1725	2286	430627565	430626994	0.000000e+00	749.0
27	TraesCS1D01G230400	chr1A	88.792	571	44	6	1725	2286	399829684	399829125	0.000000e+00	682.0
28	TraesCS1D01G230400	chr1A	100.000	73	0	0	1	73	359186457	359186385	3.960000e-28	135.0
29	TraesCS1D01G230400	chr1A	100.000	73	0	0	1	73	579044030	579044102	3.960000e-28	135.0
30	TraesCS1D01G230400	chr1A	100.000	72	0	0	1	72	579045355	579045426	1.430000e-27	134.0
31	TraesCS1D01G230400	chr2B	100.000	73	0	0	1	73	772925694	772925766	3.960000e-28	135.0
32	TraesCS1D01G230400	chr2B	100.000	29	0	0	72	100	218526608	218526636	1.000000e-03	54.7
33	TraesCS1D01G230400	chr2B	100.000	29	0	0	72	100	754439694	754439722	1.000000e-03	54.7
34	TraesCS1D01G230400	chr2A	100.000	73	0	0	1	73	687888010	687887938	3.960000e-28	135.0
35	TraesCS1D01G230400	chrUn	98.182	55	1	0	893	947	472760571	472760517	1.870000e-16	97.1
36	TraesCS1D01G230400	chr3B	92.683	41	1	1	70	108	693550956	693550916	8.830000e-05	58.4
37	TraesCS1D01G230400	chr7B	100.000	29	0	0	72	100	673866283	673866311	1.000000e-03	54.7
38	TraesCS1D01G230400	chr5A	100.000	29	0	0	72	100	241464715	241464743	1.000000e-03	54.7
39	TraesCS1D01G230400	chr4B	92.308	39	1	1	72	108	610012270	610012232	1.000000e-03	54.7
40	TraesCS1D01G230400	chr4B	100.000	29	0	0	72	100	614458188	614458216	1.000000e-03	54.7
41	TraesCS1D01G230400	chr4A	92.308	39	1	2	72	108	686717679	686717641	1.000000e-03	54.7

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	TraesCS1D01G230400	chr1D	318514387	318516674	2287	True	4226.0	4226	100.000	1	2288	1	chr1D.!!$R1	2287
1	TraesCS1D01G230400	chr1D	475311186	475311980	794	False	1382.0	1382	97.995	98	895	1	chr1D.!!$F1	797
2	TraesCS1D01G230400	chr7D	595975745	595976541	796	False	1406.0	1406	98.494	98	894	1	chr7D.!!$F5	796
3	TraesCS1D01G230400	chr7D	590889808	590890604	796	True	1393.0	1393	98.243	98	893	1	chr7D.!!$R3	795
4	TraesCS1D01G230400	chr7D	172779303	172780107	804	False	1376.0	1376	97.519	98	902	1	chr7D.!!$F2	804
5	TraesCS1D01G230400	chr7D	188554411	188555248	837	True	1267.0	1267	94.041	893	1727	1	chr7D.!!$R2	834
6	TraesCS1D01G230400	chr7D	433076818	433077650	832	False	1266.0	1266	94.125	893	1724	1	chr7D.!!$F4	831
7	TraesCS1D01G230400	chr5D	233278272	233279066	794	False	1391.0	1391	98.241	98	893	1	chr5D.!!$F1	795
8	TraesCS1D01G230400	chr5D	334650049	334650844	795	True	1387.0	1387	98.116	98	893	1	chr5D.!!$R1	795
9	TraesCS1D01G230400	chr5D	429182579	429184509	1930	False	758.5	1382	98.995	1	893	2	chr5D.!!$F3	892
10	TraesCS1D01G230400	chr3D	49430409	49431202	793	False	1386.0	1386	98.116	98	893	1	chr3D.!!$F2	795
11	TraesCS1D01G230400	chr3D	455889470	455890267	797	True	1386.0	1386	97.997	98	896	1	chr3D.!!$R1	798
12	TraesCS1D01G230400	chr3D	6288507	6289342	835	False	1343.0	1343	95.694	893	1727	1	chr3D.!!$F1	834
13	TraesCS1D01G230400	chr3D	81834264	81835101	837	False	1336.0	1336	95.465	893	1729	1	chr3D.!!$F3	836
14	TraesCS1D01G230400	chr3A	71155312	71156151	839	False	1290.0	1290	94.405	893	1730	1	chr3A.!!$F1	837
15	TraesCS1D01G230400	chr7A	221705824	221706660	836	False	1280.0	1280	94.272	893	1729	1	chr7A.!!$F1	836
16	TraesCS1D01G230400	chr6D	275679717	275680556	839	True	1267.0	1267	93.950	893	1731	1	chr6D.!!$R1	838
17	TraesCS1D01G230400	chr4D	15238715	15239545	830	True	1258.0	1258	94.005	893	1724	1	chr4D.!!$R1	831
18	TraesCS1D01G230400	chr4D	56942439	56943279	840	False	1254.0	1254	93.713	893	1728	1	chr4D.!!$F1	835
19	TraesCS1D01G230400	chr1B	430626994	430627565	571	True	749.0	749	90.625	1725	2286	1	chr1B.!!$R1	561
20	TraesCS1D01G230400	chr1A	399829125	399829684	559	True	682.0	682	88.792	1725	2286	1	chr1A.!!$R2	561

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
92	93	0.03759	TGGCTAATGGGCGTGAGTTT	59.962	50.0	0.00	0.00	44.11	2.66	F
797	1842	0.53646	GTTTGGAGCTCCCCGAACAA	60.536	55.0	29.95	13.48	45.65	2.83	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1055	2101	0.249911	GGAGCAGACGGTGTTGTTCT	60.250	55.0	0.0	0.0	0.00	3.01	R
1612	2665	0.854062	CTGCATGTTGTTTGGTTGCG	59.146	50.0	0.0	0.0	36.11	4.85	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
75	76	7.886629	ATACTAGGCCATATTTAATGCATGG	57.113	36.000	5.01	0.00	41.85	3.66
83	84	6.342906	CCATATTTAATGCATGGCTAATGGG	58.657	40.000	17.03	9.94	36.71	4.00
84	85	3.749665	TTTAATGCATGGCTAATGGGC	57.250	42.857	0.00	0.00	36.71	5.36
85	86	1.246649	TAATGCATGGCTAATGGGCG	58.753	50.000	0.00	0.00	44.11	6.13
86	87	0.756442	AATGCATGGCTAATGGGCGT	60.756	50.000	0.00	0.00	44.11	5.68
89	90	4.885426	ATGGCTAATGGGCGTGAG	57.115	55.556	0.00	0.00	44.11	3.51
90	91	1.915228	ATGGCTAATGGGCGTGAGT	59.085	52.632	0.00	0.00	44.11	3.41
91	92	0.255890	ATGGCTAATGGGCGTGAGTT	59.744	50.000	0.00	0.00	44.11	3.01
92	93	0.037590	TGGCTAATGGGCGTGAGTTT	59.962	50.000	0.00	0.00	44.11	2.66
95	96	1.135402	GCTAATGGGCGTGAGTTTTGG	60.135	52.381	0.00	0.00	0.00	3.28
96	97	0.885196	TAATGGGCGTGAGTTTTGGC	59.115	50.000	0.00	0.00	0.00	4.52
124	1163	3.754965	AGCAGCCAAGTGTTTGATTAGA	58.245	40.909	0.00	0.00	36.36	2.10
236	1276	3.629220	GGAGGAGCCTAGGTGGTAA	57.371	57.895	11.31	0.00	38.35	2.85
474	1514	4.542697	TGAACTAGGCAAGGAAGGTTTTT	58.457	39.130	0.00	0.00	0.00	1.94
634	1678	1.215655	GGCGCCTAGTCATAGCAACG	61.216	60.000	22.15	0.00	0.00	4.10
787	1832	5.188359	TCGTTATAGTTTAGGGTTTGGAGCT	59.812	40.000	0.00	0.00	0.00	4.09
797	1842	0.536460	GTTTGGAGCTCCCCGAACAA	60.536	55.000	29.95	13.48	45.65	2.83
1036	2082	1.301716	AAGCACTTCATCGCGGTGT	60.302	52.632	20.53	0.00	33.96	4.16
1067	2113	1.670811	CAAGCTCAAGAACAACACCGT	59.329	47.619	0.00	0.00	0.00	4.83
1106	2152	2.143122	GGTGAAGCTGATGAACGACAA	58.857	47.619	0.00	0.00	0.00	3.18
1179	2225	1.175654	TCGGCTACATGGTGACGTTA	58.824	50.000	13.69	0.00	0.00	3.18
1342	2393	7.594758	TCTGCTTTGAACTGTTTATGTTTATGC	59.405	33.333	0.00	0.00	0.00	3.14
1446	2498	4.063689	GCTCTGCTTATGATGTGTGCTAT	58.936	43.478	0.00	0.00	0.00	2.97
1466	2518	0.179032	ATGGTTGTGCCGAAGTGTGA	60.179	50.000	0.00	0.00	41.21	3.58
1508	2560	3.283751	CAAAGAGGTTACCACACACCAA	58.716	45.455	3.51	0.00	35.25	3.67
1588	2640	0.396435	CACCAGGCAGTGTGGTTCTA	59.604	55.000	2.70	0.00	46.73	2.10
1589	2641	1.003580	CACCAGGCAGTGTGGTTCTAT	59.996	52.381	2.70	0.00	46.73	1.98
1693	2747	2.295885	GAGAAGGCTATGCAATGCAGT	58.704	47.619	14.98	4.79	43.65	4.40
1738	2792	3.131400	ACACGCCCATAGTTGTTGTTTTT	59.869	39.130	0.00	0.00	0.00	1.94
1802	2856	2.296190	ACCTTCTCATTCCCGCAAAAAC	59.704	45.455	0.00	0.00	0.00	2.43
1805	2859	4.217550	CCTTCTCATTCCCGCAAAAACTAA	59.782	41.667	0.00	0.00	0.00	2.24
1806	2860	5.105756	CCTTCTCATTCCCGCAAAAACTAAT	60.106	40.000	0.00	0.00	0.00	1.73
1841	2895	5.247110	ACTTCTCAGGAAAGATCTACTGCAA	59.753	40.000	14.06	9.74	0.00	4.08
1843	2897	4.774726	TCTCAGGAAAGATCTACTGCAACT	59.225	41.667	14.06	0.00	0.00	3.16
1902	2956	2.105993	AGTTTTCCCCGCTAGTTTCAGT	59.894	45.455	0.00	0.00	0.00	3.41
1978	3041	5.108385	AGATTACTTCTTGCAACAAACGG	57.892	39.130	0.00	0.00	0.00	4.44
1982	3045	0.248296	TTCTTGCAACAAACGGCGAC	60.248	50.000	16.62	0.00	0.00	5.19
2008	3071	9.542462	CATCTAAGTTAAGAACCCGATGAAATA	57.458	33.333	0.00	0.00	34.49	1.40
2128	3191	5.895636	TTCACAAAAATCTACCGATGCAT	57.104	34.783	0.00	0.00	0.00	3.96
2145	3208	5.049818	CGATGCATAAAGATGGTTCTCTTCC	60.050	44.000	0.00	0.00	34.40	3.46
2195	3259	7.419518	CCCACTAGAACATAAGGACATCATCTT	60.420	40.741	0.00	0.00	0.00	2.40
2263	3327	1.625818	CCTACACAAAGCTCCTCCTGT	59.374	52.381	0.00	0.00	0.00	4.00
2286	3357	4.717233	AGAAACATGTTTGTGTCTTGCA	57.283	36.364	27.85	0.00	46.36	4.08
2287	3358	4.423732	AGAAACATGTTTGTGTCTTGCAC	58.576	39.130	27.85	9.55	46.36	4.57

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
73	74	0.037590	AAACTCACGCCCATTAGCCA	59.962	50.000	0.00	0.00	0.00	4.75
74	75	1.135402	CAAAACTCACGCCCATTAGCC	60.135	52.381	0.00	0.00	0.00	3.93
75	76	1.135402	CCAAAACTCACGCCCATTAGC	60.135	52.381	0.00	0.00	0.00	3.09
76	77	1.135402	GCCAAAACTCACGCCCATTAG	60.135	52.381	0.00	0.00	0.00	1.73
78	79	0.827507	AGCCAAAACTCACGCCCATT	60.828	50.000	0.00	0.00	0.00	3.16
80	81	2.192861	CAGCCAAAACTCACGCCCA	61.193	57.895	0.00	0.00	0.00	5.36
81	82	1.452145	TTCAGCCAAAACTCACGCCC	61.452	55.000	0.00	0.00	0.00	6.13
82	83	0.598065	ATTCAGCCAAAACTCACGCC	59.402	50.000	0.00	0.00	0.00	5.68
83	84	2.422276	AATTCAGCCAAAACTCACGC	57.578	45.000	0.00	0.00	0.00	5.34
84	85	3.492313	GCTAATTCAGCCAAAACTCACG	58.508	45.455	0.00	0.00	45.23	4.35
96	97	4.022935	TCAAACACTTGGCTGCTAATTCAG	60.023	41.667	0.00	0.00	37.15	3.02
124	1163	2.420967	GCCATGTACATTTCCCGTACCT	60.421	50.000	5.37	0.00	38.77	3.08
236	1276	7.688325	CCAGTGTGGTACTTTGCAAAGCAAT	62.688	44.000	33.72	21.14	39.70	3.56
474	1514	8.425703	TGGGTCATATCTTCGTCAAATATGTAA	58.574	33.333	0.00	0.00	35.69	2.41
634	1678	5.861787	GTCATAACCTTGTAAATTGTGGTGC	59.138	40.000	0.00	0.00	0.00	5.01
787	1832	1.064611	TGGTCAAAAGTTGTTCGGGGA	60.065	47.619	0.00	0.00	0.00	4.81
1036	2082	0.671796	TTGAGCTTGAACTCCGTCGA	59.328	50.000	0.00	0.00	35.72	4.20
1055	2101	0.249911	GGAGCAGACGGTGTTGTTCT	60.250	55.000	0.00	0.00	0.00	3.01
1067	2113	0.895530	CGTTACCTTCCAGGAGCAGA	59.104	55.000	0.00	0.00	37.67	4.26
1083	2129	1.148310	CGTTCATCAGCTTCACCGTT	58.852	50.000	0.00	0.00	0.00	4.44
1179	2225	0.832135	TGTCGGGAGTGAGGAGCTTT	60.832	55.000	0.00	0.00	0.00	3.51
1342	2393	8.110612	CACTTCATAACAGTTCTACGCATAAAG	58.889	37.037	0.00	0.00	0.00	1.85
1411	2463	7.555965	TCATAAGCAGAGCAGAGTATAAACAA	58.444	34.615	0.00	0.00	0.00	2.83
1446	2498	1.070914	TCACACTTCGGCACAACCATA	59.929	47.619	0.00	0.00	39.03	2.74
1588	2640	1.455217	GCCTCTTGCCTGCATGGAT	60.455	57.895	6.40	0.00	38.35	3.41
1589	2641	2.044650	GCCTCTTGCCTGCATGGA	60.045	61.111	6.40	0.00	38.35	3.41
1612	2665	0.854062	CTGCATGTTGTTTGGTTGCG	59.146	50.000	0.00	0.00	36.11	4.85
1693	2747	1.515081	GTTGCCGTAGCCAACAGTAA	58.485	50.000	0.00	0.00	38.69	2.24
1782	2836	2.558359	AGTTTTTGCGGGAATGAGAAGG	59.442	45.455	0.00	0.00	0.00	3.46
1828	2882	5.746990	AACACCTAGTTGCAGTAGATCTT	57.253	39.130	0.00	0.00	39.49	2.40
1841	2895	4.891992	AGTAGCATCAACAACACCTAGT	57.108	40.909	0.00	0.00	0.00	2.57
1843	2897	5.995565	AGTAGTAGCATCAACAACACCTA	57.004	39.130	0.00	0.00	0.00	3.08
1852	2906	8.144478	GTCAGATCCATTTAGTAGTAGCATCAA	58.856	37.037	0.00	0.00	0.00	2.57
1969	3032	2.478894	ACTTAGATGTCGCCGTTTGTTG	59.521	45.455	0.00	0.00	0.00	3.33
1975	3038	4.171754	GTTCTTAACTTAGATGTCGCCGT	58.828	43.478	0.00	0.00	0.00	5.68
1978	3041	3.550678	CGGGTTCTTAACTTAGATGTCGC	59.449	47.826	0.00	0.00	0.00	5.19
1982	3045	7.843490	TTTCATCGGGTTCTTAACTTAGATG	57.157	36.000	12.14	12.14	37.58	2.90
2008	3071	9.710900	GTATTCAAAATTCTTTTGGATGAAGGT	57.289	29.630	13.82	0.00	45.88	3.50
2115	3178	5.489792	ACCATCTTTATGCATCGGTAGAT	57.510	39.130	0.19	4.78	37.65	1.98
2120	3183	4.384056	AGAGAACCATCTTTATGCATCGG	58.616	43.478	0.19	0.00	35.54	4.18
2121	3184	5.049818	GGAAGAGAACCATCTTTATGCATCG	60.050	44.000	0.19	0.00	39.63	3.84
2128	3191	7.554959	AGTACTTGGAAGAGAACCATCTTTA	57.445	36.000	0.00	0.00	39.63	1.85
2195	3259	9.830975	TGACGGAATTTCATATGATTCTTAAGA	57.169	29.630	15.37	0.00	33.75	2.10
2231	3295	4.157840	GCTTTGTGTAGGAATTTACCCCAG	59.842	45.833	0.00	0.00	0.00	4.45
2263	3327	6.201226	TGCAAGACACAAACATGTTTCTTA	57.799	33.333	20.85	5.20	36.89	2.10

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.