AutoCloner

Multiple sequence alignment - TraesCS7D01G093900

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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	TraesCS7D01G093900	chr7D	100.000	2441	0	0	1	2441	56234851	56237291	0.000000e+00	4508
1	TraesCS7D01G093900	chr7D	77.330	1191	238	18	267	1446	140321546	140320377	0.000000e+00	675
2	TraesCS7D01G093900	chr7D	74.765	531	121	11	920	1445	55015414	55015936	2.440000e-55	226
3	TraesCS7D01G093900	chr7D	83.007	153	22	4	89	239	55555766	55555916	4.230000e-28	135
4	TraesCS7D01G093900	chr7A	95.092	1895	79	6	3	1896	60638284	60640165	0.000000e+00	2972
5	TraesCS7D01G093900	chr7A	96.198	263	5	4	2179	2441	60643146	60643403	2.240000e-115	425
6	TraesCS7D01G093900	chr7A	87.869	305	14	5	1897	2179	60640218	60640521	1.080000e-88	337
7	TraesCS7D01G093900	chr4A	93.238	1819	101	17	3	1808	673028861	673030670	0.000000e+00	2658
8	TraesCS7D01G093900	chr4A	76.787	1469	294	35	7	1448	670986217	670984769	0.000000e+00	780
9	TraesCS7D01G093900	chr7B	77.979	1326	253	35	140	1446	105522935	105521630	0.000000e+00	795

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	TraesCS7D01G093900	chr7D	56234851	56237291	2440	False	4508.000000	4508	100.000	1	2441	1	chr7D.!!$F3	2440
1	TraesCS7D01G093900	chr7D	140320377	140321546	1169	True	675.000000	675	77.330	267	1446	1	chr7D.!!$R1	1179
2	TraesCS7D01G093900	chr7D	55015414	55015936	522	False	226.000000	226	74.765	920	1445	1	chr7D.!!$F1	525
3	TraesCS7D01G093900	chr7A	60638284	60643403	5119	False	1244.666667	2972	93.053	3	2441	3	chr7A.!!$F1	2438
4	TraesCS7D01G093900	chr4A	673028861	673030670	1809	False	2658.000000	2658	93.238	3	1808	1	chr4A.!!$F1	1805
5	TraesCS7D01G093900	chr4A	670984769	670986217	1448	True	780.000000	780	76.787	7	1448	1	chr4A.!!$R1	1441
6	TraesCS7D01G093900	chr7B	105521630	105522935	1305	True	795.000000	795	77.979	140	1446	1	chr7B.!!$R1	1306

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
669	680	0.316204	ACCACTCTGACCGTAAACCG	59.684	55.0	0.0	0.0	0.0	4.44	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1534	1560	0.913924	TCATGAGAAGCATCCAGGCA	59.086	50.0	0.0	0.0	34.15	4.75	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
265	273	3.190874	CGAACCCTATGTCTTCTCTTGC	58.809	50.000	0.00	0.00	0.00	4.01
298	306	0.533755	GGAGGCTGCAATGTATCGCT	60.534	55.000	0.00	0.00	0.00	4.93
420	428	3.430218	GCTCTAATAGTATGTTGCAGCCG	59.570	47.826	0.00	0.00	0.00	5.52
528	536	0.687427	AAGGTGCTTGTTGCCAAGGT	60.687	50.000	5.08	0.00	46.72	3.50
669	680	0.316204	ACCACTCTGACCGTAAACCG	59.684	55.000	0.00	0.00	0.00	4.44
874	885	1.530323	GAAGTTGTACGCATGGGGTT	58.470	50.000	14.94	0.00	0.00	4.11
897	908	1.019278	TCGGCCAGCTTTTCATCGTC	61.019	55.000	2.24	0.00	0.00	4.20
909	920	4.398549	TTTCATCGTCGATTTGGACAAC	57.601	40.909	4.63	0.00	36.73	3.32
1031	1045	1.940613	GTATCTCGTTGAATGTGGGGC	59.059	52.381	0.00	0.00	0.00	5.80
1062	1076	0.109532	TGGTGGCAAGATGGTTTCGA	59.890	50.000	0.00	0.00	0.00	3.71
1077	1091	4.147322	CGATGCACGCCACGTTCC	62.147	66.667	0.00	0.00	38.32	3.62
1169	1189	0.179000	CCTGGTCGATGGAGAAAGGG	59.821	60.000	0.00	0.00	0.00	3.95
1249	1269	2.940971	GCTGTGGAATGCAGTGGATACA	60.941	50.000	0.00	0.00	38.23	2.29
1290	1310	0.613260	TGTGTGACTATGTCTGGCCC	59.387	55.000	0.00	0.00	33.15	5.80
1534	1560	0.548682	AAGCTCTGTCATCCCACCCT	60.549	55.000	0.00	0.00	0.00	4.34
1541	1567	3.016971	CATCCCACCCTGCCTGGA	61.017	66.667	0.00	0.00	38.35	3.86
1592	1620	9.926751	CAATCTGCTACTGTGTTATCTTTATTG	57.073	33.333	0.00	0.00	0.00	1.90
1649	1677	9.553064	GGATGATCTTATATGGGATGTGTATTC	57.447	37.037	0.00	0.00	0.00	1.75
1683	1711	4.633126	TCTTCATGATAGCAACTTGTGAGC	59.367	41.667	0.00	0.00	0.00	4.26
1799	1828	5.948992	ACCAAGTTTTGCTCTGAACTATC	57.051	39.130	0.00	0.00	35.17	2.08
1872	1901	7.417612	GTCAAATTGTCTGCTTAAGAAGTGAA	58.582	34.615	10.41	5.08	36.40	3.18
1877	1906	4.816385	TGTCTGCTTAAGAAGTGAAGGTTG	59.184	41.667	10.41	0.00	36.40	3.77
1879	1908	5.527582	GTCTGCTTAAGAAGTGAAGGTTGAA	59.472	40.000	10.41	0.00	36.40	2.69
1910	1991	7.440856	GGTCTCAGATAATCAACTTTCTGATCC	59.559	40.741	2.28	5.15	42.57	3.36
1976	2057	5.304101	AGTTTGACTGCATACATTTTGGGAA	59.696	36.000	0.00	0.00	0.00	3.97
1984	2065	8.153550	ACTGCATACATTTTGGGAAAACATTTA	58.846	29.630	0.00	0.00	32.37	1.40
2029	2110	3.383505	GTGTTTTTCTAGGGGTGCAAACT	59.616	43.478	0.00	0.00	0.00	2.66
2046	2146	6.518736	GTGCAAACTAGTTGTATAAAACGAGC	59.481	38.462	9.34	7.62	39.63	5.03
2106	2206	5.501156	ACCCAGCTTTTAAAATCTCGAGAT	58.499	37.500	22.32	22.32	36.07	2.75
2122	2222	6.269315	TCTCGAGATGCTTTAGCTAGAAAAG	58.731	40.000	12.08	11.66	42.66	2.27
2123	2223	5.352284	TCGAGATGCTTTAGCTAGAAAAGG	58.648	41.667	15.71	2.40	42.66	3.11
2125	2225	5.233263	CGAGATGCTTTAGCTAGAAAAGGAC	59.767	44.000	15.71	9.96	37.15	3.85
2126	2226	6.306643	AGATGCTTTAGCTAGAAAAGGACT	57.693	37.500	15.71	11.37	37.15	3.85
2127	2227	6.716284	AGATGCTTTAGCTAGAAAAGGACTT	58.284	36.000	15.71	3.84	37.15	3.01
2128	2228	7.852263	AGATGCTTTAGCTAGAAAAGGACTTA	58.148	34.615	15.71	0.00	37.15	2.24
2164	2266	4.216257	AGTGTTGACAATGTGATTGCCTAC	59.784	41.667	0.00	0.00	43.98	3.18
2169	2271	5.953183	TGACAATGTGATTGCCTACAAATC	58.047	37.500	0.00	0.00	43.98	2.17
2173	2275	2.754552	TGTGATTGCCTACAAATCTGGC	59.245	45.455	0.00	0.00	46.26	4.85
2183	4910	5.008613	GCCTACAAATCTGGCGATTATTTGA	59.991	40.000	17.70	6.33	41.14	2.69
2365	5092	0.605589	GGGCTGTATCGATGGAGGAG	59.394	60.000	8.54	0.00	0.00	3.69

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
0	1	3.067742	GGTAATAACGGCTGCAGTAGAGA	59.932	47.826	16.64	0.00	0.00	3.10
1	2	3.181479	TGGTAATAACGGCTGCAGTAGAG	60.181	47.826	16.64	6.93	0.00	2.43
13	14	4.403453	GCTTCTTGCACTTGGTAATAACG	58.597	43.478	0.00	0.00	42.31	3.18
242	250	4.177026	CAAGAGAAGACATAGGGTTCGTG	58.823	47.826	0.00	0.00	0.00	4.35
265	273	3.464907	CAGCCTCCATCATACAAGTCTG	58.535	50.000	0.00	0.00	0.00	3.51
298	306	2.103094	CCGGCTGAAGATCTGACCAATA	59.897	50.000	0.00	0.00	0.00	1.90
420	428	1.821332	CGGGAATGGCAGAGGAAGC	60.821	63.158	0.00	0.00	0.00	3.86
528	536	4.016444	GGAATAGCCAGTTGTCAATGGAA	58.984	43.478	14.59	5.61	39.02	3.53
669	680	5.891451	GGCACCACCAACTTATAGAAAATC	58.109	41.667	0.00	0.00	38.86	2.17
874	885	0.895100	ATGAAAAGCTGGCCGAAGCA	60.895	50.000	16.78	0.20	46.08	3.91
897	908	2.410730	GGTACAGTCGTTGTCCAAATCG	59.589	50.000	0.00	0.00	41.29	3.34
913	924	4.201657	CAGCTGATGGATGAAATGGTACA	58.798	43.478	8.42	0.00	36.49	2.90
1062	1076	3.353836	GTGGAACGTGGCGTGCAT	61.354	61.111	1.94	0.00	39.99	3.96
1077	1091	4.211164	TGTTCAAAGACATCGTAGCTTGTG	59.789	41.667	0.00	0.00	0.00	3.33
1144	1158	3.147595	CCATCGACCAGGGCTCGA	61.148	66.667	4.71	4.71	43.94	4.04
1146	1160	1.330655	TTCTCCATCGACCAGGGCTC	61.331	60.000	0.00	0.00	0.00	4.70
1169	1189	2.985847	GGCCACCCAACTCACTGC	60.986	66.667	0.00	0.00	0.00	4.40
1290	1310	3.347077	AGAGGATTTGCAGAAGAGGTG	57.653	47.619	0.00	0.00	0.00	4.00
1459	1479	2.613977	CCTCCAACGCAACAGAAGAGAT	60.614	50.000	0.00	0.00	0.00	2.75
1463	1483	1.264288	GAACCTCCAACGCAACAGAAG	59.736	52.381	0.00	0.00	0.00	2.85
1534	1560	0.913924	TCATGAGAAGCATCCAGGCA	59.086	50.000	0.00	0.00	34.15	4.75
1541	1567	6.261826	GCTATGGTAAAAGTCATGAGAAGCAT	59.738	38.462	0.00	4.37	37.85	3.79
1592	1620	4.700268	TTGATGTGTACACAATCATGGC	57.300	40.909	31.01	14.77	45.41	4.40
1649	1677	1.001624	TCATGAAGACTGCGCATTCG	58.998	50.000	20.34	7.84	39.07	3.34
1683	1711	6.785191	AGTTTGTTCAAGTACATGACACAAG	58.215	36.000	18.81	0.00	34.72	3.16
1799	1828	6.879276	ATTTATCTCAGTTGCAGGATGATG	57.121	37.500	0.00	0.00	39.69	3.07
1872	1901	7.890127	TGATTATCTGAGACCAAAATTCAACCT	59.110	33.333	0.00	0.00	0.00	3.50
1879	1908	9.525826	AGAAAGTTGATTATCTGAGACCAAAAT	57.474	29.630	0.00	0.00	0.00	1.82
1931	2012	7.897575	AACTTCACAATCTCTTCACTCATAC	57.102	36.000	0.00	0.00	0.00	2.39
1984	2065	6.309009	CACGCTGCTATATTTCGTCTAATCAT	59.691	38.462	0.00	0.00	0.00	2.45
2004	2085	1.892209	CACCCCTAGAAAAACACGCT	58.108	50.000	0.00	0.00	0.00	5.07
2029	2110	5.106197	TGGACTCGCTCGTTTTATACAACTA	60.106	40.000	0.60	0.00	0.00	2.24
2100	2200	5.127194	TCCTTTTCTAGCTAAAGCATCTCGA	59.873	40.000	4.54	0.00	45.16	4.04
2106	2206	8.565416	GTTTTAAGTCCTTTTCTAGCTAAAGCA	58.435	33.333	4.54	0.00	45.16	3.91
2122	2222	8.999431	TCAACACTATTGAGATGTTTTAAGTCC	58.001	33.333	0.00	0.00	34.36	3.85
2123	2223	9.813080	GTCAACACTATTGAGATGTTTTAAGTC	57.187	33.333	0.00	0.00	34.36	3.01
2128	2228	8.632679	ACATTGTCAACACTATTGAGATGTTTT	58.367	29.630	10.50	0.00	35.04	2.43
2164	2266	6.473455	GGAAACTCAAATAATCGCCAGATTTG	59.527	38.462	0.00	0.00	44.11	2.32
2169	2271	4.963276	TGGAAACTCAAATAATCGCCAG	57.037	40.909	0.00	0.00	0.00	4.85
2173	2275	9.619316	TGTTTAACATGGAAACTCAAATAATCG	57.381	29.630	19.97	0.00	37.62	3.34
2350	5077	2.959030	CCTCAACTCCTCCATCGATACA	59.041	50.000	0.00	0.00	0.00	2.29
2365	5092	2.294512	CAGCTGAAAAAGGGACCTCAAC	59.705	50.000	8.42	0.00	0.00	3.18

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.