AutoCloner

Multiple sequence alignment - TraesCS7D01G496400

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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	TraesCS7D01G496400	chr7D	100.000	3123	0	0	1	3123	603357622	603354500	0.000000e+00	5768
1	TraesCS7D01G496400	chr7D	84.077	1143	152	19	1886	3010	603284273	603283143	0.000000e+00	1075
2	TraesCS7D01G496400	chr7D	76.540	422	75	17	1374	1780	603269243	603268831	3.160000e-50	209
3	TraesCS7D01G496400	chr7D	87.027	185	16	5	562	745	603293050	603292873	5.280000e-48	202
4	TraesCS7D01G496400	chr7A	95.232	2370	74	16	349	2684	696019487	696017123	0.000000e+00	3714
5	TraesCS7D01G496400	chr7A	96.181	419	16	0	1	419	696019899	696019481	0.000000e+00	686
6	TraesCS7D01G496400	chr7A	96.277	188	7	0	2754	2941	696015192	696015005	3.020000e-80	309
7	TraesCS7D01G496400	chr7A	93.548	186	11	1	2938	3123	696014407	696014223	3.070000e-70	276
8	TraesCS7D01G496400	chr7B	94.014	1938	86	12	363	2282	684459746	684457821	0.000000e+00	2909
9	TraesCS7D01G496400	chr7B	94.562	331	18	0	1	331	684460076	684459746	2.150000e-141	512
10	TraesCS7D01G496400	chr7B	93.851	309	16	2	2817	3123	684440834	684440527	2.190000e-126	462
11	TraesCS7D01G496400	chr7B	96.457	254	8	1	2305	2557	684457828	684457575	4.820000e-113	418
12	TraesCS7D01G496400	chr7B	92.226	283	10	10	2552	2823	684457166	684456885	1.050000e-104	390
13	TraesCS7D01G496400	chr5D	88.056	1574	157	26	804	2360	416068137	416066578	0.000000e+00	1836
14	TraesCS7D01G496400	chr5D	84.441	752	95	9	1	750	416068995	416068264	0.000000e+00	721
15	TraesCS7D01G496400	chr5A	87.411	1549	163	27	804	2334	528559573	528558039	0.000000e+00	1751
16	TraesCS7D01G496400	chr5A	84.518	788	101	8	1	786	528560418	528559650	0.000000e+00	760
17	TraesCS7D01G496400	chr5B	84.451	656	80	19	1718	2360	502498948	502498302	7.350000e-176	627

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	TraesCS7D01G496400	chr7D	603354500	603357622	3122	True	5768.00	5768	100.00000	1	3123	1	chr7D.!!$R4	3122
1	TraesCS7D01G496400	chr7D	603283143	603284273	1130	True	1075.00	1075	84.07700	1886	3010	1	chr7D.!!$R2	1124
2	TraesCS7D01G496400	chr7A	696014223	696019899	5676	True	1246.25	3714	95.30950	1	3123	4	chr7A.!!$R1	3122
3	TraesCS7D01G496400	chr7B	684456885	684460076	3191	True	1057.25	2909	94.31475	1	2823	4	chr7B.!!$R2	2822
4	TraesCS7D01G496400	chr5D	416066578	416068995	2417	True	1278.50	1836	86.24850	1	2360	2	chr5D.!!$R1	2359
5	TraesCS7D01G496400	chr5A	528558039	528560418	2379	True	1255.50	1751	85.96450	1	2334	2	chr5A.!!$R1	2333
6	TraesCS7D01G496400	chr5B	502498302	502498948	646	True	627.00	627	84.45100	1718	2360	1	chr5B.!!$R1	642

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	Hairpin	End Stability	Orientation
283	285	0.741221	GGGAACACTCATCCGTCAGC	60.741	60.0	0.00	37.87	4.26	F
507	573	0.821517	TGATGACGCGGGTAGACAAT	59.178	50.0	12.47	0.00	2.71	F
1702	1851	0.453793	CAACCTTCGGCAACAACACA	59.546	50.0	0.00	0.00	3.72	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1303	1452	0.61585	TGATGCCCGACCACATACAA	59.384	50.0	0.00	0.00	0.00	2.41	R
1938	2087	0.82584	TGCACCCAAAACTAGCCACC	60.826	55.0	0.00	0.00	0.00	4.61	R
3094	6160	0.52218	ACGAGTGTCGACATGGAGTC	59.478	55.0	23.12	9.82	43.74	3.36	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
20	21	1.160946	ACAACATTGCCACGTACGCA	61.161	50.000	16.72	1.93	0.00	5.24
28	29	0.870307	GCCACGTACGCATAGGACAG	60.870	60.000	16.72	0.00	31.45	3.51
61	62	7.606073	TCCAATATTTGTACGATATCCCACATG	59.394	37.037	5.20	0.00	0.00	3.21
126	127	3.606886	CCATCGTACCACTATGGCC	57.393	57.895	0.00	0.00	42.67	5.36
255	257	6.898041	TCATCAGTTTTTGACTTGTTATCCG	58.102	36.000	0.00	0.00	38.99	4.18
268	270	2.027929	TGTTATCCGCGAAAAGAGGGAA	60.028	45.455	8.23	0.00	40.51	3.97
283	285	0.741221	GGGAACACTCATCCGTCAGC	60.741	60.000	0.00	0.00	37.87	4.26
386	388	1.403914	CGCTCTCTAGCCCATGCATAG	60.404	57.143	0.00	0.00	46.68	2.23
499	565	4.758251	TGCTGGTGATGACGCGGG	62.758	66.667	12.47	0.00	0.00	6.13
507	573	0.821517	TGATGACGCGGGTAGACAAT	59.178	50.000	12.47	0.00	0.00	2.71
558	624	2.037772	TCTCTCTTGGCTTGTGTCTTCC	59.962	50.000	0.00	0.00	0.00	3.46
559	625	1.768275	TCTCTTGGCTTGTGTCTTCCA	59.232	47.619	0.00	0.00	0.00	3.53
718	785	5.839262	TTGCAACGAAGTACTATGAGTTG	57.161	39.130	19.51	19.51	45.00	3.16
980	1126	6.374588	TGACCACTTTCCATTTTTACCCTTA	58.625	36.000	0.00	0.00	0.00	2.69
981	1127	6.839657	TGACCACTTTCCATTTTTACCCTTAA	59.160	34.615	0.00	0.00	0.00	1.85
987	1133	7.127493	ACTTTCCATTTTTACCCTTAAAACCCA	59.873	33.333	0.00	0.00	36.99	4.51
1025	1171	7.120923	TGGTCTATCTGTATTGGAAGTTACC	57.879	40.000	0.00	0.00	0.00	2.85
1099	1248	5.865552	GCTTATGTTGAAAATGCATGTCTGT	59.134	36.000	0.00	0.00	0.00	3.41
1159	1308	2.481952	GCTTGTTCTACCAGTGCTCTTG	59.518	50.000	0.00	0.00	0.00	3.02
1168	1317	0.954452	CAGTGCTCTTGGGGTTGTTC	59.046	55.000	0.00	0.00	0.00	3.18
1303	1452	6.566079	TCTTGGAATGAGAACATCCACTAT	57.434	37.500	0.00	0.00	35.30	2.12
1373	1522	1.956477	CAGTGCTAAACCTTGCCAACT	59.044	47.619	0.00	0.00	0.00	3.16
1566	1715	5.685511	CACTTACAAATTGTTCCAAACTCCG	59.314	40.000	3.17	0.00	0.00	4.63
1702	1851	0.453793	CAACCTTCGGCAACAACACA	59.546	50.000	0.00	0.00	0.00	3.72
1709	1858	4.214545	CCTTCGGCAACAACACATACTTAA	59.785	41.667	0.00	0.00	0.00	1.85
1789	1938	1.444933	TGCCGAATATGGGGGAGAAT	58.555	50.000	0.00	0.00	0.00	2.40
1795	1944	0.475632	ATATGGGGGAGAATCGGGCA	60.476	55.000	0.00	0.00	34.37	5.36
1897	2046	7.080353	ACCTAAGTATGAATAAGCTAAGGGGA	58.920	38.462	0.00	0.00	0.00	4.81
1938	2087	0.941463	AATCTATCTGCCGCGCTTCG	60.941	55.000	5.56	0.00	38.08	3.79
2099	2248	4.878397	AGTTATGGAAGCTTGATCTTTCCG	59.122	41.667	2.10	0.00	0.00	4.30
2242	2409	2.233271	CACCTTCCTGTTCTTGCATGT	58.767	47.619	0.00	0.00	0.00	3.21
2486	2656	6.078456	TGGTTGTATTGAGGGAGATGATTT	57.922	37.500	0.00	0.00	0.00	2.17
2630	3232	3.054655	GGGGCAGTCAAATAAGGTCTGTA	60.055	47.826	0.00	0.00	0.00	2.74
2644	3246	1.302511	CTGTAGTGTTGGCCCGCTT	60.303	57.895	0.00	0.00	0.00	4.68
2728	4455	2.883574	CGACGCCTCCTGTATTTTACA	58.116	47.619	0.00	0.00	37.13	2.41
2930	5395	4.409247	GGGATTAACTCAAGAAGGCCTAGA	59.591	45.833	5.16	0.75	0.00	2.43
2982	6048	2.084546	CCCTTGGGTCTTTCGATTCAC	58.915	52.381	0.00	0.00	0.00	3.18
3039	6105	2.487372	TGCAACATCTTAATGCGCTTCA	59.513	40.909	9.73	0.00	42.91	3.02
3055	6121	9.875691	AATGCGCTTCATGACTAAGATATATAA	57.124	29.630	9.73	0.00	35.13	0.98
3077	6143	5.559148	ACTTCTTCAGACTTCCATCAGTT	57.441	39.130	0.00	0.00	0.00	3.16
3083	6149	8.924511	TCTTCAGACTTCCATCAGTTAAATTT	57.075	30.769	0.00	0.00	0.00	1.82
3094	6160	3.678072	TCAGTTAAATTTGAGAGCGACGG	59.322	43.478	0.00	0.00	0.00	4.79

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
28	29	6.877611	ATCGTACAAATATTGGATGGGAAC	57.122	37.500	0.00	0.00	31.17	3.62
61	62	3.951655	CTTGCGCATGAACGGTGCC	62.952	63.158	17.78	0.00	40.93	5.01
126	127	5.063438	CACTTCATATAAGACGTGTTGTGGG	59.937	44.000	8.42	0.00	34.26	4.61
180	182	2.561858	GGACGGAAGACCAAGTCTAAGT	59.438	50.000	0.00	0.00	42.59	2.24
255	257	1.878953	TGAGTGTTCCCTCTTTTCGC	58.121	50.000	0.00	0.00	32.50	4.70
268	270	1.079543	GCAGCTGACGGATGAGTGT	60.080	57.895	20.43	0.00	32.28	3.55
283	285	9.956720	CTTATCCATAAATACTTTTTCAGGCAG	57.043	33.333	0.00	0.00	0.00	4.85
424	490	0.816825	CCAGCACAGCAGAAGTGTGT	60.817	55.000	5.11	0.00	45.95	3.72
499	565	8.383619	CGGATTTGCTAAGCATATATTGTCTAC	58.616	37.037	0.00	0.00	38.76	2.59
507	573	6.384258	TTTTGCGGATTTGCTAAGCATATA	57.616	33.333	0.00	0.00	38.76	0.86
542	608	1.972872	ACTGGAAGACACAAGCCAAG	58.027	50.000	0.00	0.00	37.43	3.61
718	785	2.118313	AACGTAGCCAAATACCCACC	57.882	50.000	0.00	0.00	0.00	4.61
816	959	4.951094	CCGGGAAAACACCTATTTATGGAA	59.049	41.667	0.00	0.00	0.00	3.53
1025	1171	5.003214	GTGCATACTACGTCACTTTTACTCG	59.997	44.000	0.00	0.00	0.00	4.18
1133	1282	2.875672	GCACTGGTAGAACAAGCATGGA	60.876	50.000	0.00	0.00	0.00	3.41
1159	1308	2.290960	ACTTGCTCCATAGAACAACCCC	60.291	50.000	0.00	0.00	0.00	4.95
1168	1317	6.204359	GCAATTAATGTCACTTGCTCCATAG	58.796	40.000	2.67	0.00	40.55	2.23
1216	1365	2.621338	TCAAGCAGTGAACGATGATCC	58.379	47.619	0.00	0.00	31.51	3.36
1222	1371	4.261155	CCTTTGAAATCAAGCAGTGAACGA	60.261	41.667	0.00	0.00	40.50	3.85
1303	1452	0.615850	TGATGCCCGACCACATACAA	59.384	50.000	0.00	0.00	0.00	2.41
1373	1522	1.888512	GATTTGGCCTGTCAAGCTCAA	59.111	47.619	3.32	0.00	0.00	3.02
1496	1645	7.706100	ACAAGTTGTTTTGTAAGTAAAGGGA	57.294	32.000	1.64	0.00	39.40	4.20
1497	1646	7.201487	GCAACAAGTTGTTTTGTAAGTAAAGGG	60.201	37.037	18.59	3.86	38.77	3.95
1510	1659	1.859302	TCCCCTGCAACAAGTTGTTT	58.141	45.000	18.59	1.89	38.77	2.83
1566	1715	7.703197	GCATGTTAGAAGAGAGGTCTAGTAAAC	59.297	40.741	0.00	0.00	30.45	2.01
1702	1851	7.123247	TGGGTAAGTCGTAGCTCTTTTAAGTAT	59.877	37.037	0.00	0.00	0.00	2.12
1709	1858	2.895404	TGTGGGTAAGTCGTAGCTCTTT	59.105	45.455	0.00	0.00	0.00	2.52
1789	1938	2.342279	CCGAGAAACACTGCCCGA	59.658	61.111	0.00	0.00	0.00	5.14
1795	1944	3.368531	GCCTATTCTGACCGAGAAACACT	60.369	47.826	0.00	0.00	44.11	3.55
1938	2087	0.825840	TGCACCCAAAACTAGCCACC	60.826	55.000	0.00	0.00	0.00	4.61
1939	2088	1.036707	TTGCACCCAAAACTAGCCAC	58.963	50.000	0.00	0.00	0.00	5.01
2099	2248	9.884465	GTGCTACCAACTATCAAAATGATTATC	57.116	33.333	0.00	0.00	38.26	1.75
2242	2409	3.785486	CTGACAGAAAGTGTGACACAGA	58.215	45.455	18.95	0.00	40.56	3.41
2298	2466	8.154856	ACCGCTAAGGAAAAGAAGCAATATATA	58.845	33.333	0.00	0.00	45.00	0.86
2299	2467	6.998673	ACCGCTAAGGAAAAGAAGCAATATAT	59.001	34.615	0.00	0.00	45.00	0.86
2300	2468	6.354130	ACCGCTAAGGAAAAGAAGCAATATA	58.646	36.000	0.00	0.00	45.00	0.86
2301	2469	5.193679	ACCGCTAAGGAAAAGAAGCAATAT	58.806	37.500	0.00	0.00	45.00	1.28
2310	2478	7.803279	AATATAGGAAACCGCTAAGGAAAAG	57.197	36.000	0.00	0.00	45.00	2.27
2630	3232	2.912025	CCAAAGCGGGCCAACACT	60.912	61.111	4.39	0.00	0.00	3.55
2712	4439	7.602753	ACTCAAAAATGTAAAATACAGGAGGC	58.397	34.615	0.00	0.00	42.77	4.70
2728	4455	5.811399	TTCTTGTGTCACGACTCAAAAAT	57.189	34.783	13.76	0.00	42.08	1.82
2930	5395	9.696917	GAAAATCAATTTGGAACTAAGACACAT	57.303	29.630	0.00	0.00	0.00	3.21
2959	6025	1.358152	ATCGAAAGACCCAAGGGACA	58.642	50.000	13.15	0.00	46.97	4.02
3022	6088	4.194640	AGTCATGAAGCGCATTAAGATGT	58.805	39.130	11.47	0.00	34.15	3.06
3055	6121	5.559148	AACTGATGGAAGTCTGAAGAAGT	57.441	39.130	0.00	0.00	0.00	3.01
3066	6132	6.092670	TCGCTCTCAAATTTAACTGATGGAAG	59.907	38.462	0.00	0.00	0.00	3.46
3077	6143	3.508762	GAGTCCGTCGCTCTCAAATTTA	58.491	45.455	9.09	0.00	0.00	1.40
3083	6149	1.378646	ATGGAGTCCGTCGCTCTCA	60.379	57.895	4.30	5.76	33.73	3.27
3094	6160	0.522180	ACGAGTGTCGACATGGAGTC	59.478	55.000	23.12	9.82	43.74	3.36

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.