AutoCloner

Multiple sequence alignment - TraesCS1B01G303400

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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	TraesCS1B01G303400	chr1B	100.000	2333	0	0	1	2333	524407542	524409874	0.000000e+00	4309.0
1	TraesCS1B01G303400	chr1B	78.611	547	79	25	1813	2329	631951810	631952348	6.220000e-86	327.0
2	TraesCS1B01G303400	chr6B	91.293	1183	80	14	1	1176	364703244	364702078	0.000000e+00	1592.0
3	TraesCS1B01G303400	chr6B	86.374	1277	121	20	1082	2332	364702081	364700832	0.000000e+00	1345.0
4	TraesCS1B01G303400	chr5B	86.139	1277	124	20	1082	2332	642850086	642851335	0.000000e+00	1328.0
5	TraesCS1B01G303400	chr5B	94.604	278	12	1	899	1176	642849815	642850089	5.960000e-116	427.0
6	TraesCS1B01G303400	chr5B	84.375	96	15	0	2238	2333	248353800	248353895	6.860000e-16	95.3
7	TraesCS1B01G303400	chr5D	90.330	910	83	2	478	1387	91597593	91596689	0.000000e+00	1188.0
8	TraesCS1B01G303400	chr5D	82.403	824	92	29	1414	2231	91592293	91591517	0.000000e+00	669.0
9	TraesCS1B01G303400	chr5D	91.667	72	6	0	2261	2332	91591519	91591448	1.480000e-17	100.0
10	TraesCS1B01G303400	chr5D	82.895	76	5	1	918	993	16011686	16011753	6.960000e-06	62.1
11	TraesCS1B01G303400	chr4A	81.736	1440	185	37	923	2331	423450853	423452245	0.000000e+00	1131.0
12	TraesCS1B01G303400	chr6D	93.132	597	40	1	422	1018	282218800	282219395	0.000000e+00	874.0
13	TraesCS1B01G303400	chr6D	91.930	570	32	7	1775	2332	282231534	282232101	0.000000e+00	785.0
14	TraesCS1B01G303400	chr6D	95.612	433	13	4	1	427	282140389	282140821	0.000000e+00	689.0
15	TraesCS1B01G303400	chr6D	93.491	169	11	0	1278	1446	282221710	282221878	3.850000e-63	252.0
16	TraesCS1B01G303400	chr7B	81.391	1064	142	36	915	1960	16934892	16935917	0.000000e+00	817.0
17	TraesCS1B01G303400	chr7B	81.389	360	51	13	1979	2326	16935981	16936336	1.770000e-71	279.0
18	TraesCS1B01G303400	chr5A	83.440	779	91	24	967	1730	297639564	297640319	0.000000e+00	689.0
19	TraesCS1B01G303400	chr5A	81.690	355	54	4	1979	2323	297640610	297640963	3.790000e-73	285.0
20	TraesCS1B01G303400	chr2D	81.943	731	94	11	921	1642	360776810	360776109	3.340000e-163	584.0
21	TraesCS1B01G303400	chr2D	81.103	725	98	23	928	1642	361142056	361141361	5.670000e-151	544.0
22	TraesCS1B01G303400	chr2D	78.284	373	59	15	1963	2319	360946932	360946566	1.090000e-53	220.0
23	TraesCS1B01G303400	chr2D	75.936	374	51	23	1963	2322	360775863	360775515	3.100000e-34	156.0
24	TraesCS1B01G303400	chr2B	77.143	315	62	6	959	1273	83723137	83723441	8.570000e-40	174.0
25	TraesCS1B01G303400	chr4D	82.895	76	5	1	918	993	505787496	505787563	6.960000e-06	62.1
26	TraesCS1B01G303400	chr1D	82.895	76	5	1	918	993	478551555	478551622	6.960000e-06	62.1

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	TraesCS1B01G303400	chr1B	524407542	524409874	2332	False	4309.0	4309	100.0000	1	2333	1	chr1B.!!$F1	2332
1	TraesCS1B01G303400	chr1B	631951810	631952348	538	False	327.0	327	78.6110	1813	2329	1	chr1B.!!$F2	516
2	TraesCS1B01G303400	chr6B	364700832	364703244	2412	True	1468.5	1592	88.8335	1	2332	2	chr6B.!!$R1	2331
3	TraesCS1B01G303400	chr5B	642849815	642851335	1520	False	877.5	1328	90.3715	899	2332	2	chr5B.!!$F2	1433
4	TraesCS1B01G303400	chr5D	91596689	91597593	904	True	1188.0	1188	90.3300	478	1387	1	chr5D.!!$R1	909
5	TraesCS1B01G303400	chr5D	91591448	91592293	845	True	384.5	669	87.0350	1414	2332	2	chr5D.!!$R2	918
6	TraesCS1B01G303400	chr4A	423450853	423452245	1392	False	1131.0	1131	81.7360	923	2331	1	chr4A.!!$F1	1408
7	TraesCS1B01G303400	chr6D	282231534	282232101	567	False	785.0	785	91.9300	1775	2332	1	chr6D.!!$F2	557
8	TraesCS1B01G303400	chr6D	282218800	282221878	3078	False	563.0	874	93.3115	422	1446	2	chr6D.!!$F3	1024
9	TraesCS1B01G303400	chr7B	16934892	16936336	1444	False	548.0	817	81.3900	915	2326	2	chr7B.!!$F1	1411
10	TraesCS1B01G303400	chr5A	297639564	297640963	1399	False	487.0	689	82.5650	967	2323	2	chr5A.!!$F1	1356
11	TraesCS1B01G303400	chr2D	361141361	361142056	695	True	544.0	544	81.1030	928	1642	1	chr2D.!!$R2	714
12	TraesCS1B01G303400	chr2D	360775515	360776810	1295	True	370.0	584	78.9395	921	2322	2	chr2D.!!$R3	1401

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
153	158	0.034089	CCCTCGGCCTCTCCATTTTT	60.034	55.0	0.0	0.0	34.01	1.94	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1729	4014	0.535102	ACGACTTCAGCCCAGTTTGG	60.535	55.0	0.0	0.0	37.25	3.28	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
55	56	6.321821	ACTATGCTAAAGAACACCCCAATA	57.678	37.500	0.00	0.00	0.00	1.90
59	60	3.699038	GCTAAAGAACACCCCAATATGCA	59.301	43.478	0.00	0.00	0.00	3.96
69	70	3.259876	ACCCCAATATGCATGCATGATTC	59.740	43.478	37.43	13.12	37.82	2.52
153	158	0.034089	CCCTCGGCCTCTCCATTTTT	60.034	55.000	0.00	0.00	34.01	1.94
170	175	6.780031	TCCATTTTTCCACTTCCACTTATGAA	59.220	34.615	0.00	0.00	0.00	2.57
173	178	9.143631	CATTTTTCCACTTCCACTTATGAATTC	57.856	33.333	0.00	0.00	0.00	2.17
175	180	5.160607	TCCACTTCCACTTATGAATTCGT	57.839	39.130	5.33	5.33	0.00	3.85
194	199	8.880878	AATTCGTTTTACAAATATAATGGCCC	57.119	30.769	0.00	0.00	0.00	5.80
203	208	7.251321	ACAAATATAATGGCCCAACTTTTCA	57.749	32.000	0.00	0.00	0.00	2.69
287	292	8.518430	TTTATGCATGTATGTGTATGGACTTT	57.482	30.769	10.16	0.00	0.00	2.66
288	293	9.620259	TTTATGCATGTATGTGTATGGACTTTA	57.380	29.630	10.16	0.00	0.00	1.85
289	294	6.918892	TGCATGTATGTGTATGGACTTTAC	57.081	37.500	0.00	0.00	0.00	2.01
291	296	7.109501	TGCATGTATGTGTATGGACTTTACTT	58.890	34.615	0.00	0.00	0.00	2.24
374	380	5.009631	CCCTCTCAACATACAACATTTGGA	58.990	41.667	0.00	0.00	34.12	3.53
481	488	5.154222	GTTTGAACATAACTAGTTGCCAGC	58.846	41.667	18.56	5.65	0.00	4.85
591	599	3.206150	TGTCTCTTCCAAGTGCTTGTTC	58.794	45.455	10.56	0.00	38.85	3.18
696	704	2.371841	ACAGAGCATGGTAGGACAACAA	59.628	45.455	0.00	0.00	0.00	2.83
750	758	1.237285	CCTTTGGGGTCAGCAACTCG	61.237	60.000	0.00	0.00	0.00	4.18
765	773	1.080093	CTCGGAAGTGTAGGCGCAA	60.080	57.895	10.83	0.00	0.00	4.85
827	835	6.072175	AGCGACAAGAAAAATATGTTTGGCTA	60.072	34.615	0.00	0.00	31.34	3.93
903	911	1.134401	ACAGCGGTGCATAGTGCTTAT	60.134	47.619	15.82	0.00	45.31	1.73
910	918	5.812642	GCGGTGCATAGTGCTTATATTAGAT	59.187	40.000	3.41	0.00	45.31	1.98
911	919	6.313905	GCGGTGCATAGTGCTTATATTAGATT	59.686	38.462	3.41	0.00	45.31	2.40
974	984	6.318648	TCTCATAACCTCATAACCATGTTTGC	59.681	38.462	0.00	0.00	33.57	3.68
977	987	5.391312	AACCTCATAACCATGTTTGCTTC	57.609	39.130	0.00	0.00	33.57	3.86
1076	3176	1.710013	AAGGTTGTATCTGACGTGCG	58.290	50.000	0.00	0.00	0.00	5.34
1149	3340	2.275318	GTGCATGAGAGAACTAGTGGC	58.725	52.381	0.00	0.00	0.00	5.01
1256	3447	2.564504	AGGAATCAAAAGAAGCAAGGGC	59.435	45.455	0.00	0.00	41.61	5.19
1281	3472	6.463049	CCAGACAAGAAGAGGAGTACAAGAAA	60.463	42.308	0.00	0.00	0.00	2.52
1486	3682	3.327626	TGCATGCATTTTGTTCATGGAC	58.672	40.909	18.46	0.00	38.33	4.02
1638	3881	6.057533	TGGATCAGAACCTATATTGCTGTTG	58.942	40.000	0.00	0.00	0.00	3.33
1642	3885	8.839310	ATCAGAACCTATATTGCTGTTGATAC	57.161	34.615	0.00	0.00	0.00	2.24
1643	3886	8.023021	TCAGAACCTATATTGCTGTTGATACT	57.977	34.615	0.00	0.00	0.00	2.12
1644	3887	9.143155	TCAGAACCTATATTGCTGTTGATACTA	57.857	33.333	0.00	0.00	0.00	1.82
1645	3888	9.416794	CAGAACCTATATTGCTGTTGATACTAG	57.583	37.037	0.00	0.00	0.00	2.57
1677	3950	8.058847	AGTGGGATGGTTTAGAAGCAATATTTA	58.941	33.333	0.00	0.00	42.83	1.40
1691	3976	9.196552	GAAGCAATATTTAACTGTTTTGAGCTT	57.803	29.630	0.00	6.20	38.60	3.74
1692	3977	9.546428	AAGCAATATTTAACTGTTTTGAGCTTT	57.454	25.926	0.00	0.00	32.82	3.51
1709	3994	5.171339	AGCTTTGTTGATGATGGACTAGT	57.829	39.130	0.00	0.00	0.00	2.57
1727	4012	5.978814	ACTAGTACTGGGCTGAAATTAGTG	58.021	41.667	11.30	0.00	0.00	2.74
1729	4014	1.839424	ACTGGGCTGAAATTAGTGGC	58.161	50.000	0.00	0.00	0.00	5.01
1731	4016	3.281332	GGGCTGAAATTAGTGGCCA	57.719	52.632	0.00	0.00	44.04	5.36
1763	4082	6.020971	TGAAGTCGTACTGAAATAAGCAGA	57.979	37.500	0.00	0.00	36.86	4.26
1784	4104	7.549488	AGCAGACCTAAATTTGTGTACTATGTC	59.451	37.037	0.00	0.00	0.00	3.06
1798	4119	8.491134	TGTGTACTATGTCTAAAATAATGGGCT	58.509	33.333	0.00	0.00	0.00	5.19
1918	4269	0.247185	AATCAGGCCCAACAATTGCG	59.753	50.000	5.05	0.00	0.00	4.85
2081	4481	4.806286	GCTGAAAGTAGGAAGCCAAAGGTA	60.806	45.833	0.00	0.00	35.30	3.08
2138	4538	1.682740	CATGTCCATGCACATGCCTA	58.317	50.000	16.55	0.00	45.43	3.93
2185	4585	2.343758	GTCACAGAAGCTCGGGCA	59.656	61.111	11.40	0.00	41.70	5.36
2239	4639	0.608308	CGCTGATCCATGATGGCCAT	60.608	55.000	20.96	20.96	37.47	4.40
2250	4660	1.251251	GATGGCCATGGGTTAGCATC	58.749	55.000	26.56	0.43	0.00	3.91
2332	4742	5.209240	TGGTTTTCAAAAACGTCATCGATC	58.791	37.500	11.15	0.00	47.00	3.69

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
42	43	2.034124	GCATGCATATTGGGGTGTTCT	58.966	47.619	14.21	0.00	0.00	3.01
69	70	8.948631	TCTCAAGCACCAGTAATAATAAAGAG	57.051	34.615	0.00	0.00	0.00	2.85
97	98	0.674895	AGTAGCAAAGCAGCCTTCGG	60.675	55.000	0.00	0.00	34.23	4.30
98	99	1.160137	AAGTAGCAAAGCAGCCTTCG	58.840	50.000	0.00	0.00	34.23	3.79
99	100	3.650070	AAAAGTAGCAAAGCAGCCTTC	57.350	42.857	0.00	0.00	34.23	3.46
139	144	2.222227	AGTGGAAAAATGGAGAGGCC	57.778	50.000	0.00	0.00	37.10	5.19
140	145	2.493675	GGAAGTGGAAAAATGGAGAGGC	59.506	50.000	0.00	0.00	0.00	4.70
153	158	5.160607	ACGAATTCATAAGTGGAAGTGGA	57.839	39.130	6.22	0.00	0.00	4.02
170	175	8.012957	TGGGCCATTATATTTGTAAAACGAAT	57.987	30.769	0.00	0.00	36.28	3.34
173	178	7.262048	AGTTGGGCCATTATATTTGTAAAACG	58.738	34.615	7.26	0.00	0.00	3.60
187	192	4.436113	ACAATTGAAAAGTTGGGCCATT	57.564	36.364	13.59	0.00	0.00	3.16
194	199	7.775397	ATTGGTGAGAACAATTGAAAAGTTG	57.225	32.000	13.59	0.00	35.11	3.16
263	268	9.051679	GTAAAGTCCATACACATACATGCATAA	57.948	33.333	0.00	0.00	0.00	1.90
342	348	2.496899	TGTTGAGAGGGATTGAAGGC	57.503	50.000	0.00	0.00	0.00	4.35
374	380	7.701539	TGCATGTGTAGATTAAGGATTGTTT	57.298	32.000	0.00	0.00	0.00	2.83
591	599	4.788925	TCTGGGGATTACTTAATGTGGG	57.211	45.455	0.00	0.00	0.00	4.61
696	704	3.562973	GCTGCTACAGTGAATACATGCAT	59.437	43.478	0.00	0.00	33.43	3.96
701	709	4.578871	ACAATGCTGCTACAGTGAATACA	58.421	39.130	12.71	0.00	37.84	2.29
750	758	1.135689	CATTGTTGCGCCTACACTTCC	60.136	52.381	4.18	0.00	0.00	3.46
765	773	7.041303	TGCACATGAATTTATTGTTTGCATTGT	60.041	29.630	0.00	0.00	0.00	2.71
800	808	6.148948	CCAAACATATTTTTCTTGTCGCTGA	58.851	36.000	0.00	0.00	0.00	4.26
827	835	4.440802	GCTACATCACACGAAGAGGAGAAT	60.441	45.833	0.00	0.00	0.00	2.40
876	884	1.062002	CTATGCACCGCTGTTTTACCG	59.938	52.381	0.00	0.00	0.00	4.02
911	919	8.897752	CAAGACATAAAAACAAATGGGGAAAAA	58.102	29.630	0.00	0.00	0.00	1.94
974	984	3.439476	AGTCTAGCAATGCAAGCAAGAAG	59.561	43.478	8.35	8.06	0.00	2.85
977	987	2.745821	TGAGTCTAGCAATGCAAGCAAG	59.254	45.455	8.35	0.00	0.00	4.01
1076	3176	0.590195	CTTCTTGGTGTGCTGAGTGC	59.410	55.000	0.00	0.00	43.25	4.40
1149	3340	1.750778	AGTTGTGCTTCAAGGTTGGTG	59.249	47.619	0.00	0.00	36.66	4.17
1256	3447	4.524714	TCTTGTACTCCTCTTCTTGTCTGG	59.475	45.833	0.00	0.00	0.00	3.86
1281	3472	1.813513	CGTCCATCTCAGCCTGTTTT	58.186	50.000	0.00	0.00	0.00	2.43
1284	3475	0.684479	TAGCGTCCATCTCAGCCTGT	60.684	55.000	0.00	0.00	0.00	4.00
1287	3478	1.134670	AGTTTAGCGTCCATCTCAGCC	60.135	52.381	0.00	0.00	0.00	4.85
1290	3481	3.585862	GTCAAGTTTAGCGTCCATCTCA	58.414	45.455	0.00	0.00	0.00	3.27
1486	3682	2.429213	GCAAAATGCACGCATTCATG	57.571	45.000	17.06	18.09	44.86	3.07
1643	3886	8.594550	GCTTCTAAACCATCCCACTATTATCTA	58.405	37.037	0.00	0.00	0.00	1.98
1644	3887	7.072454	TGCTTCTAAACCATCCCACTATTATCT	59.928	37.037	0.00	0.00	0.00	1.98
1645	3888	7.224297	TGCTTCTAAACCATCCCACTATTATC	58.776	38.462	0.00	0.00	0.00	1.75
1648	3891	5.450818	TGCTTCTAAACCATCCCACTATT	57.549	39.130	0.00	0.00	0.00	1.73
1677	3950	5.964758	TCATCAACAAAGCTCAAAACAGTT	58.035	33.333	0.00	0.00	0.00	3.16
1691	3976	5.104941	CCCAGTACTAGTCCATCATCAACAA	60.105	44.000	0.00	0.00	0.00	2.83
1692	3977	4.405680	CCCAGTACTAGTCCATCATCAACA	59.594	45.833	0.00	0.00	0.00	3.33
1709	3994	2.356741	GGCCACTAATTTCAGCCCAGTA	60.357	50.000	0.00	0.00	37.66	2.74
1729	4014	0.535102	ACGACTTCAGCCCAGTTTGG	60.535	55.000	0.00	0.00	37.25	3.28
1731	4016	1.692519	AGTACGACTTCAGCCCAGTTT	59.307	47.619	0.00	0.00	0.00	2.66
2081	4481	1.841277	TGTAGTGACCGGCCCAATTAT	59.159	47.619	0.00	0.00	0.00	1.28
2138	4538	5.359194	ACCCGTCATAGAATTTCATGACT	57.641	39.130	23.85	13.04	45.76	3.41
2201	4601	1.599047	CTGAGCCCATCCAGTTCGT	59.401	57.895	0.00	0.00	0.00	3.85
2239	4639	4.661222	TCTTCACAAATGATGCTAACCCA	58.339	39.130	0.00	0.00	33.85	4.51

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.