AutoCloner

Multiple sequence alignment - TraesCS4A01G020200

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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	TraesCS4A01G020200	chr4A	100.000	3156	0	0	1	3156	13760297	13757142	0.000000e+00	5829.0
1	TraesCS4A01G020200	chr4A	100.000	693	0	0	3368	4060	13756930	13756238	0.000000e+00	1280.0
2	TraesCS4A01G020200	chr4D	98.063	1497	29	0	1581	3077	453319702	453321198	0.000000e+00	2604.0
3	TraesCS4A01G020200	chr4D	93.561	497	26	4	3380	3874	453321401	453321893	0.000000e+00	736.0
4	TraesCS4A01G020200	chr4D	95.977	174	7	0	3874	4047	453323537	453323710	2.390000e-72	283.0
5	TraesCS4A01G020200	chr4D	97.778	45	1	0	1	45	453315270	453315314	1.210000e-10	78.7
6	TraesCS4A01G020200	chr4B	94.362	1685	51	9	44	1702	566977256	566978922	0.000000e+00	2545.0
7	TraesCS4A01G020200	chr4B	97.321	1456	37	1	1701	3156	566979180	566980633	0.000000e+00	2471.0
8	TraesCS4A01G020200	chr4B	97.384	1338	33	1	1819	3156	566981810	566983145	0.000000e+00	2276.0
9	TraesCS4A01G020200	chr4B	92.972	683	35	8	3380	4060	566980719	566981390	0.000000e+00	983.0
10	TraesCS4A01G020200	chr4B	92.972	683	35	8	3380	4060	566983231	566983902	0.000000e+00	983.0
11	TraesCS4A01G020200	chr4B	97.778	45	1	0	1	45	566977151	566977195	1.210000e-10	78.7
12	TraesCS4A01G020200	chr3D	85.769	2108	211	47	1079	3137	611563922	611565989	0.000000e+00	2148.0
13	TraesCS4A01G020200	chr3D	86.667	90	11	1	3529	3617	611566194	611566283	9.290000e-17	99.0
14	TraesCS4A01G020200	chr3D	95.556	45	2	0	1	45	554073778	554073734	5.630000e-09	73.1
15	TraesCS4A01G020200	chr3A	90.254	1498	127	9	1667	3156	746355525	746354039	0.000000e+00	1940.0
16	TraesCS4A01G020200	chr3A	77.835	388	59	14	783	1146	746356483	746356099	8.840000e-52	215.0
17	TraesCS4A01G020200	chr3B	90.203	1480	126	8	1667	3137	829285235	829286704	0.000000e+00	1912.0
18	TraesCS4A01G020200	chr3B	75.505	396	49	22	775	1146	829284424	829284795	2.530000e-32	150.0
19	TraesCS4A01G020200	chr3B	86.667	90	11	1	3529	3617	829286849	829286938	9.290000e-17	99.0
20	TraesCS4A01G020200	chr1D	79.715	1262	242	14	1806	3060	182676759	182678013	0.000000e+00	900.0
21	TraesCS4A01G020200	chr1B	79.526	1265	241	18	1805	3060	259025456	259026711	0.000000e+00	885.0
22	TraesCS4A01G020200	chr5A	86.214	457	56	2	1952	2401	367617426	367616970	4.720000e-134	488.0
23	TraesCS4A01G020200	chr6B	82.840	169	23	4	963	1129	288948986	288949150	3.270000e-31	147.0
24	TraesCS4A01G020200	chr5D	97.674	43	1	0	44	86	508111896	508111938	1.570000e-09	75.0
25	TraesCS4A01G020200	chr5D	95.556	45	2	0	1	45	302885873	302885829	5.630000e-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	TraesCS4A01G020200	chr4A	13756238	13760297	4059	True	3554.500000	5829	100.000000	1	4060	2	chr4A.!!$R1	4059
1	TraesCS4A01G020200	chr4D	453319702	453323710	4008	False	1207.666667	2604	95.867000	1581	4047	3	chr4D.!!$F2	2466
2	TraesCS4A01G020200	chr4B	566977151	566983902	6751	False	1556.116667	2545	95.464833	1	4060	6	chr4B.!!$F1	4059
3	TraesCS4A01G020200	chr3D	611563922	611566283	2361	False	1123.500000	2148	86.218000	1079	3617	2	chr3D.!!$F1	2538
4	TraesCS4A01G020200	chr3A	746354039	746356483	2444	True	1077.500000	1940	84.044500	783	3156	2	chr3A.!!$R1	2373
5	TraesCS4A01G020200	chr3B	829284424	829286938	2514	False	720.333333	1912	84.125000	775	3617	3	chr3B.!!$F1	2842
6	TraesCS4A01G020200	chr1D	182676759	182678013	1254	False	900.000000	900	79.715000	1806	3060	1	chr1D.!!$F1	1254
7	TraesCS4A01G020200	chr1B	259025456	259026711	1255	False	885.000000	885	79.526000	1805	3060	1	chr1B.!!$F1	1255

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
59	122	0.908180	CCCCTACCCCAGAACGACTT	60.908	60.000	0.00	0.00	0.00	3.01	F
1027	1129	1.070134	TCTGGTTGTTTCTGGAGTCCG	59.930	52.381	4.30	0.00	0.00	4.79	F
1306	1436	0.312102	TAGGATCAGTGATCGCAGCG	59.688	55.000	23.56	9.06	39.72	5.18	F
1654	1901	3.368843	GGTACCAAGTGTTATTTCGACGG	59.631	47.826	7.15	0.00	0.00	4.79	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1301	1431	0.854705	CTTGTTTTGGCTTTCGCTGC	59.145	50.000	0.00	0.00	36.09	5.25	R
2225	2744	0.460311	CTTCCGAATACTCTGGCGGT	59.540	55.000	0.00	0.00	43.92	5.68	R
2228	2747	2.993539	GGCTTCCGAATACTCTGGC	58.006	57.895	0.00	0.00	0.00	4.85	R
3578	6658	1.478105	CCACATCCATGGACATGAGGG	60.478	57.143	18.99	15.02	43.02	4.30	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	118	2.064581	CCTCCCCTACCCCAGAACG	61.065	68.421	0.00	0.00	0.00	3.95
59	122	0.908180	CCCCTACCCCAGAACGACTT	60.908	60.000	0.00	0.00	0.00	3.01
109	172	2.075338	CTCAAGCACTGCTCTTTCTCC	58.925	52.381	3.40	0.00	38.25	3.71
117	180	4.836825	CACTGCTCTTTCTCCAGGATTAA	58.163	43.478	0.00	0.00	0.00	1.40
122	185	6.725364	TGCTCTTTCTCCAGGATTAATTCTT	58.275	36.000	0.00	0.00	0.00	2.52
130	193	9.672673	TTCTCCAGGATTAATTCTTAGAAGTTG	57.327	33.333	11.79	0.00	0.00	3.16
131	194	7.770897	TCTCCAGGATTAATTCTTAGAAGTTGC	59.229	37.037	0.00	0.00	0.00	4.17
183	246	6.239232	GCAAATGATCCAGGATATTTTCTGCT	60.239	38.462	0.32	0.00	0.00	4.24
213	276	4.744631	GTGTGTGTGATTTGGGTTTGAATC	59.255	41.667	0.00	0.00	33.83	2.52
215	278	3.005261	TGTGTGATTTGGGTTTGAATCGG	59.995	43.478	0.00	0.00	35.53	4.18
245	308	3.258228	AGGTTTGTTTTTGGAGTTTGCG	58.742	40.909	0.00	0.00	0.00	4.85
251	314	4.307432	TGTTTTTGGAGTTTGCGTTCAAA	58.693	34.783	0.00	0.00	39.67	2.69
266	329	3.126171	CGTTCAAATTATTGACGGGCAGA	59.874	43.478	0.00	0.00	45.01	4.26
393	456	1.856597	GCCGCATTGCATGAGAATTTC	59.143	47.619	9.69	0.00	31.20	2.17
402	465	6.976636	TTGCATGAGAATTTCGTATGTACA	57.023	33.333	0.00	0.00	0.00	2.90
442	506	2.151202	TGGAGTCGATGCTTTTGGTTC	58.849	47.619	0.00	0.00	0.00	3.62
632	710	5.835113	AGTGACATGTTAGTGTTGCTTTT	57.165	34.783	0.00	0.00	31.16	2.27
634	712	6.959361	AGTGACATGTTAGTGTTGCTTTTAG	58.041	36.000	0.00	0.00	31.16	1.85
742	820	7.709613	ACATTTGTGATAAAGAGACCGGTATAC	59.290	37.037	7.34	1.41	0.00	1.47
834	912	8.539770	TTAAGTGCTATTTTCTCAGTCAGAAG	57.460	34.615	0.00	0.00	42.37	2.85
914	1008	5.414454	TGGTTCATACTTATGGTCTTGCAAC	59.586	40.000	0.00	0.00	34.50	4.17
1027	1129	1.070134	TCTGGTTGTTTCTGGAGTCCG	59.930	52.381	4.30	0.00	0.00	4.79
1150	1260	5.013183	AGTGCTAATCCTTTGGTTAGTGACT	59.987	40.000	0.00	0.00	31.98	3.41
1231	1346	4.034510	GGTCTTCTTCGCATGGAATAGTTG	59.965	45.833	0.00	0.00	33.26	3.16
1246	1373	6.032094	GGAATAGTTGTGTCTGATGCATTTG	58.968	40.000	0.00	0.00	0.00	2.32
1301	1431	7.652727	TCTTTATCAGTTAGGATCAGTGATCG	58.347	38.462	23.56	11.12	39.72	3.69
1306	1436	0.312102	TAGGATCAGTGATCGCAGCG	59.688	55.000	23.56	9.06	39.72	5.18
1379	1612	6.292389	GTGCTAAATGCTCCTGTACTAATG	57.708	41.667	0.00	0.00	43.37	1.90
1398	1632	8.366671	ACTAATGTAATTCGAGTGCTAATTCC	57.633	34.615	0.00	0.00	37.87	3.01
1399	1633	8.204836	ACTAATGTAATTCGAGTGCTAATTCCT	58.795	33.333	0.00	0.00	37.87	3.36
1400	1634	7.865706	AATGTAATTCGAGTGCTAATTCCTT	57.134	32.000	0.00	0.00	0.00	3.36
1483	1720	9.710900	GTTTCAATGGAAAAAGAATATTCCTGT	57.289	29.630	11.92	0.00	44.18	4.00
1509	1746	6.360370	TCTAAGTTCTAAGCCAAGTCACAT	57.640	37.500	0.00	0.00	0.00	3.21
1537	1782	9.784531	CACTTGATCTTGTATCCATAGGTTATT	57.215	33.333	0.00	0.00	0.00	1.40
1538	1783	9.784531	ACTTGATCTTGTATCCATAGGTTATTG	57.215	33.333	0.00	0.00	0.00	1.90
1654	1901	3.368843	GGTACCAAGTGTTATTTCGACGG	59.631	47.826	7.15	0.00	0.00	4.79
1803	2322	8.019669	GCATCTTATATGATTGGTCAATGTGTC	58.980	37.037	0.43	0.00	38.01	3.67
2189	2708	4.660789	AATATCTTGGCATGCCTTTGAC	57.339	40.909	35.53	10.37	36.94	3.18
2228	2747	1.546961	AGTCACTTCCTCCAGTACCG	58.453	55.000	0.00	0.00	0.00	4.02
2318	2837	0.601311	GCAAAGACTCAGTGCGAGGT	60.601	55.000	0.00	0.00	46.98	3.85
2407	2926	2.547855	GGAAGCGGCATTTCTTTGGTTT	60.548	45.455	1.45	0.00	0.00	3.27
2696	3215	3.128589	GCTTACGGAATCCAAGCATTTCA	59.871	43.478	16.59	0.00	43.29	2.69
2793	3312	2.224523	TGGACAAGGTTCATGGACAGTC	60.225	50.000	6.44	10.30	0.00	3.51
2997	3519	2.364970	TCTTTCATGGCAAACTTGTGGG	59.635	45.455	0.00	0.00	0.00	4.61
3082	3604	2.700371	TGTGTCTGTCTGTCAAGTGGAT	59.300	45.455	0.00	0.00	0.00	3.41
3143	6215	6.676990	ATCAGATTTTGAAAGAAAGCCCTT	57.323	33.333	0.00	0.00	39.77	3.95
3393	6466	2.154462	ACCGCAAAATTCTCTGAGGTG	58.846	47.619	4.59	0.00	43.17	4.00
3395	6468	2.160417	CCGCAAAATTCTCTGAGGTGTC	59.840	50.000	4.59	0.00	0.00	3.67
3442	6519	2.037847	GGGGCCAGAGCAATGGTT	59.962	61.111	4.39	0.00	42.75	3.67
3481	6559	1.154197	GAACCTTCCGTAGCACCAAC	58.846	55.000	0.00	0.00	0.00	3.77
3499	6577	4.534401	GGTGTATCCGGAAGCACC	57.466	61.111	31.60	31.60	43.52	5.01
3519	6597	2.266554	CCGTGATCTTTCTGAGCTGAC	58.733	52.381	0.00	0.00	31.32	3.51
3603	6683	4.928263	TCATGTCCATGGATGTGGTTTTA	58.072	39.130	19.62	1.00	40.27	1.52
3609	6689	6.126409	GTCCATGGATGTGGTTTTATTCCTA	58.874	40.000	19.62	0.00	40.27	2.94
3640	6720	7.976175	GCATATGTATTGTAGCAGCAGACTATA	59.024	37.037	4.29	0.00	0.00	1.31
3648	6728	7.208225	TGTAGCAGCAGACTATATAGACTTG	57.792	40.000	16.79	11.94	0.00	3.16

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
35	36	0.691413	GTTCTGGGGTAGGGGAGGAG	60.691	65.000	0.00	0.00	0.00	3.69
109	172	6.316390	ACGGCAACTTCTAAGAATTAATCCTG	59.684	38.462	0.00	0.00	0.00	3.86
117	180	4.385825	TGAACACGGCAACTTCTAAGAAT	58.614	39.130	0.00	0.00	0.00	2.40
122	185	2.869801	CAACTGAACACGGCAACTTCTA	59.130	45.455	0.00	0.00	0.00	2.10
130	193	1.021968	AACTTCCAACTGAACACGGC	58.978	50.000	0.00	0.00	0.00	5.68
131	194	4.062293	TCATAACTTCCAACTGAACACGG	58.938	43.478	0.00	0.00	0.00	4.94
183	246	6.227298	ACCCAAATCACACACACATAAAAA	57.773	33.333	0.00	0.00	0.00	1.94
213	276	0.541063	AACAAACCTTAAGGGCCCCG	60.541	55.000	25.31	11.07	40.27	5.73
215	278	3.472652	CAAAAACAAACCTTAAGGGCCC	58.527	45.455	25.31	16.46	40.27	5.80
245	308	4.156008	AGTCTGCCCGTCAATAATTTGAAC	59.844	41.667	0.00	0.00	43.29	3.18
251	314	1.559682	ACCAGTCTGCCCGTCAATAAT	59.440	47.619	0.00	0.00	0.00	1.28
287	350	5.379706	AACCCAAATGATTTCCCAAAACA	57.620	34.783	0.00	0.00	0.00	2.83
393	456	8.882415	AATAACCCTAAGTCAATGTACATACG	57.118	34.615	9.21	3.79	0.00	3.06
402	465	6.674419	ACTCCAGAGAATAACCCTAAGTCAAT	59.326	38.462	0.70	0.00	0.00	2.57
481	545	7.420214	CCCTTGGAAGATAATAACTCTAAGCCA	60.420	40.741	0.00	0.00	0.00	4.75
491	555	5.045213	TGACTGCACCCTTGGAAGATAATAA	60.045	40.000	0.00	0.00	0.00	1.40
495	559	2.265367	TGACTGCACCCTTGGAAGATA	58.735	47.619	0.00	0.00	0.00	1.98
632	710	6.986817	GGAACTTGCACAATATCTCTAAGCTA	59.013	38.462	0.00	0.00	0.00	3.32
634	712	5.586243	TGGAACTTGCACAATATCTCTAAGC	59.414	40.000	0.00	0.00	0.00	3.09
735	813	8.339714	TCACAAAACAAAAAGAGAAGTATACCG	58.660	33.333	0.00	0.00	0.00	4.02
777	855	9.892130	ATCTATAAGCTTAAAGCAACACTAACT	57.108	29.630	10.85	0.00	45.56	2.24
834	912	9.226345	GCATACAAAATTCTCAAGTAATACTGC	57.774	33.333	0.00	0.00	0.00	4.40
914	1008	4.205065	TGCCCAAAAATGCCTTAATCAG	57.795	40.909	0.00	0.00	0.00	2.90
1130	1232	6.472887	TCCAAGTCACTAACCAAAGGATTAG	58.527	40.000	0.00	0.00	35.03	1.73
1150	1260	8.210265	TGTGTACTGCTCATATGATATTTCCAA	58.790	33.333	5.72	0.00	0.00	3.53
1185	1295	7.542025	ACCATGCAGAAAAGAGATGAAATTAC	58.458	34.615	0.00	0.00	0.00	1.89
1231	1346	3.302555	CACACACAAATGCATCAGACAC	58.697	45.455	0.00	0.00	0.00	3.67
1246	1373	3.660621	GCTCCTTCAGCCACACAC	58.339	61.111	0.00	0.00	43.17	3.82
1301	1431	0.854705	CTTGTTTTGGCTTTCGCTGC	59.145	50.000	0.00	0.00	36.09	5.25
1306	1436	2.602257	ACAGGCTTGTTTTGGCTTTC	57.398	45.000	0.00	0.00	38.29	2.62
1483	1720	5.989777	GTGACTTGGCTTAGAACTTAGAACA	59.010	40.000	0.00	0.00	0.00	3.18
1522	1759	7.448748	AAAATCGGCAATAACCTATGGATAC	57.551	36.000	0.00	0.00	0.00	2.24
1537	1782	8.128582	GTCATCTGTATTGAAATAAAATCGGCA	58.871	33.333	0.00	0.00	0.00	5.69
1538	1783	8.345565	AGTCATCTGTATTGAAATAAAATCGGC	58.654	33.333	0.00	0.00	0.00	5.54
1654	1901	7.023575	CACAACTTGTCCACTAGCAAAATATC	58.976	38.462	0.00	0.00	0.00	1.63
1710	2221	9.942850	CAAAACCAAAGGGAGTTATCATTTTAT	57.057	29.630	0.00	0.00	38.05	1.40
1720	2231	5.692115	ATGAAACAAAACCAAAGGGAGTT	57.308	34.783	0.00	0.00	38.05	3.01
1803	2322	2.499289	AGGACACAGATTCTACCTGCAG	59.501	50.000	6.78	6.78	35.14	4.41
2225	2744	0.460311	CTTCCGAATACTCTGGCGGT	59.540	55.000	0.00	0.00	43.92	5.68
2228	2747	2.993539	GGCTTCCGAATACTCTGGC	58.006	57.895	0.00	0.00	0.00	4.85
2318	2837	6.874664	TGTAAAATACAACACGCCTCATAGAA	59.125	34.615	0.00	0.00	35.38	2.10
2407	2926	4.887071	AGAGGCAGTTGTTTATGACACAAA	59.113	37.500	0.00	0.00	38.18	2.83
2696	3215	6.091713	CCACTGAATAAAGACGACCGTTAAAT	59.908	38.462	0.00	0.00	0.00	1.40
3367	6439	5.295431	TCAGAGAATTTTGCGGTAACATG	57.705	39.130	0.00	0.00	0.00	3.21
3368	6440	4.396166	CCTCAGAGAATTTTGCGGTAACAT	59.604	41.667	0.00	0.00	0.00	2.71
3369	6441	3.751175	CCTCAGAGAATTTTGCGGTAACA	59.249	43.478	0.00	0.00	0.00	2.41
3370	6442	3.751698	ACCTCAGAGAATTTTGCGGTAAC	59.248	43.478	0.00	0.00	31.01	2.50
3371	6443	3.751175	CACCTCAGAGAATTTTGCGGTAA	59.249	43.478	0.00	0.00	31.01	2.85
3372	6444	3.244422	ACACCTCAGAGAATTTTGCGGTA	60.244	43.478	0.00	0.00	31.01	4.02
3373	6445	2.154462	CACCTCAGAGAATTTTGCGGT	58.846	47.619	0.00	0.00	32.88	5.68
3374	6446	2.154462	ACACCTCAGAGAATTTTGCGG	58.846	47.619	0.00	0.00	0.00	5.69
3375	6447	2.807967	TGACACCTCAGAGAATTTTGCG	59.192	45.455	0.00	0.00	0.00	4.85
3376	6448	4.540824	GTTGACACCTCAGAGAATTTTGC	58.459	43.478	0.00	0.00	0.00	3.68
3377	6449	4.580167	TGGTTGACACCTCAGAGAATTTTG	59.420	41.667	0.00	0.00	44.61	2.44
3378	6450	4.792068	TGGTTGACACCTCAGAGAATTTT	58.208	39.130	0.00	0.00	44.61	1.82
3407	6480	4.023291	GCCCCCTCTTTGATAAACATCAA	58.977	43.478	0.00	0.00	38.64	2.57
3499	6577	2.266554	GTCAGCTCAGAAAGATCACGG	58.733	52.381	0.00	0.00	0.00	4.94
3506	6584	4.887748	TCCTAAAGTGTCAGCTCAGAAAG	58.112	43.478	0.00	0.00	0.00	2.62
3519	6597	4.698304	TCGGCTAACCAAAATCCTAAAGTG	59.302	41.667	0.00	0.00	34.57	3.16
3578	6658	1.478105	CCACATCCATGGACATGAGGG	60.478	57.143	18.99	15.02	43.02	4.30
3603	6683	8.960591	GCTACAATACATATGCCAAATAGGAAT	58.039	33.333	1.58	0.00	41.22	3.01
3609	6689	5.535783	TGCTGCTACAATACATATGCCAAAT	59.464	36.000	1.58	0.00	0.00	2.32
3669	6749	2.376808	TTGGCACAAACCAAACACTG	57.623	45.000	0.00	0.00	46.65	3.66
3695	6775	2.733956	CTAGCCAAATTTGGGGTAGCA	58.266	47.619	33.01	11.85	46.07	3.49
3836	6918	8.797350	TCCATTCAGAATATATAGCCACATTG	57.203	34.615	0.00	0.00	0.00	2.82
4007	8733	2.922955	TCCCAGGTCATTCCATAACCAA	59.077	45.455	0.00	0.00	39.02	3.67
4028	8754	1.900016	CCATGCACTGCACCACTGT	60.900	57.895	5.67	0.00	43.04	3.55

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.