AutoCloner

Multiple sequence alignment - TraesCS6B01G349200

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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	TraesCS6B01G349200	chr6B	100.000	3232	0	0	1	3232	614126422	614129653	0.000000e+00	5969.0
1	TraesCS6B01G349200	chr6B	85.563	1323	107	48	107	1405	613609295	613610557	0.000000e+00	1308.0
2	TraesCS6B01G349200	chr6B	92.484	785	45	3	1460	2244	613610567	613611337	0.000000e+00	1110.0
3	TraesCS6B01G349200	chr6A	95.321	2586	85	12	1	2570	554786272	554788837	0.000000e+00	4072.0
4	TraesCS6B01G349200	chr6A	86.735	2254	166	69	52	2244	554715001	554717182	0.000000e+00	2383.0
5	TraesCS6B01G349200	chr6A	91.446	643	36	17	2599	3232	554788829	554789461	0.000000e+00	865.0
6	TraesCS6B01G349200	chr6D	94.673	1821	70	10	1419	3232	409288306	409290106	0.000000e+00	2800.0
7	TraesCS6B01G349200	chr6D	88.129	2165	160	48	101	2244	408944635	408946723	0.000000e+00	2484.0
8	TraesCS6B01G349200	chr6D	93.015	1088	43	17	334	1405	409287253	409288323	0.000000e+00	1557.0
9	TraesCS6B01G349200	chr6D	94.362	337	16	3	1	336	409286795	409287129	6.180000e-142	514.0
10	TraesCS6B01G349200	chr7B	78.462	390	71	10	1493	1876	97192582	97192964	3.220000e-60	243.0
11	TraesCS6B01G349200	chr7A	78.351	388	71	10	1495	1876	134491662	134492042	4.170000e-59	239.0
12	TraesCS6B01G349200	chr7D	77.577	388	74	10	1495	1876	135357778	135358158	4.200000e-54	222.0
13	TraesCS6B01G349200	chr2D	85.484	124	12	5	1245	1365	627974070	627974190	1.220000e-24	124.0
14	TraesCS6B01G349200	chr2B	86.275	102	12	2	1245	1345	771043285	771043385	3.410000e-20	110.0
15	TraesCS6B01G349200	chr1B	79.661	118	24	0	1497	1614	615744798	615744681	5.750000e-13	86.1

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	TraesCS6B01G349200	chr6B	614126422	614129653	3231	False	5969.000000	5969	100.000000	1	3232	1	chr6B.!!$F1	3231
1	TraesCS6B01G349200	chr6B	613609295	613611337	2042	False	1209.000000	1308	89.023500	107	2244	2	chr6B.!!$F2	2137
2	TraesCS6B01G349200	chr6A	554786272	554789461	3189	False	2468.500000	4072	93.383500	1	3232	2	chr6A.!!$F2	3231
3	TraesCS6B01G349200	chr6A	554715001	554717182	2181	False	2383.000000	2383	86.735000	52	2244	1	chr6A.!!$F1	2192
4	TraesCS6B01G349200	chr6D	408944635	408946723	2088	False	2484.000000	2484	88.129000	101	2244	1	chr6D.!!$F1	2143
5	TraesCS6B01G349200	chr6D	409286795	409290106	3311	False	1623.666667	2800	94.016667	1	3232	3	chr6D.!!$F2	3231

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
660	880	1.066716	GCTGAATGCTGATTGCCCAAA	60.067	47.619	0.00	42.00	3.28	F
1190	1433	0.744414	GATGCCGTGGCTAGCTTTGA	60.744	55.000	15.72	42.51	2.69	F
1491	1747	1.682854	ACAAACTGGGTTGTGCTGATG	59.317	47.619	3.02	40.22	3.07	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Hairpin	End Stability	Orientation
1793	2049	0.545309	TGCTGGAGCTGGGACTAGTT	60.545	55.000	0.00	42.66	2.24	R
2103	2359	2.026542	GGTTGGAAATAGGGAAGTCGGT	60.027	50.000	0.00	0.00	4.69	R
2999	3262	2.158325	TCCCTCTTTTGACAGGGCAAAT	60.158	45.455	0.38	41.24	2.32	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
153	157	7.326454	CAACATGTACTATGATATCCCAGGAG	58.674	42.308	0.00	0.00	0.00	3.69
188	218	2.438411	TGTTGACATGCATGCAGATGA	58.562	42.857	26.69	7.82	0.00	2.92
272	302	4.148348	GTCGCCAATACAATATCGACAGAC	59.852	45.833	7.57	0.00	43.74	3.51
279	313	6.716934	ATACAATATCGACAGACCTTGAGT	57.283	37.500	0.00	0.00	0.00	3.41
356	516	8.950210	AGTTATGTCTTTGGAATTGATACAGTG	58.050	33.333	0.00	0.00	0.00	3.66
387	548	3.318275	GGAACCCACTTCTGAAACCTTTC	59.682	47.826	0.00	0.00	37.69	2.62
660	880	1.066716	GCTGAATGCTGATTGCCCAAA	60.067	47.619	0.00	0.00	42.00	3.28
734	954	2.041216	GTGGAGGACACCAATACCCTTT	59.959	50.000	0.00	0.00	44.49	3.11
739	959	1.639108	GACACCAATACCCTTTCCCCT	59.361	52.381	0.00	0.00	0.00	4.79
810	1035	5.479306	CAGATTAGTCCTTTCCACTCGAAA	58.521	41.667	0.00	0.00	38.16	3.46
1011	1242	2.118403	TCCTATCAATGGGGAGGTCC	57.882	55.000	0.00	0.00	0.00	4.46
1145	1377	0.874390	CTTGCAGGTACGCAACACAT	59.126	50.000	4.30	0.00	46.61	3.21
1190	1433	0.744414	GATGCCGTGGCTAGCTTTGA	60.744	55.000	15.72	0.00	42.51	2.69
1491	1747	1.682854	ACAAACTGGGTTGTGCTGATG	59.317	47.619	3.02	0.00	40.22	3.07
1610	1866	2.577059	GGCTTCGACCCGATGACA	59.423	61.111	6.46	0.00	38.62	3.58
1907	2163	2.968574	GCTGTCATCTCCAAGGATCCTA	59.031	50.000	16.55	0.00	0.00	2.94
1979	2235	7.069986	TCCAGATACCTAGTAGCTCATTCTTT	58.930	38.462	0.00	0.00	32.11	2.52
2103	2359	1.262640	GGACTCCCTTCCGCCACTTA	61.263	60.000	0.00	0.00	0.00	2.24
2314	2570	6.471233	TCTTACCTCTTATCTGTGATGTGG	57.529	41.667	0.00	0.00	0.00	4.17
2478	2734	3.180980	CAGCTTGAATTTTGTGCGACTTG	59.819	43.478	0.00	0.00	0.00	3.16
2479	2735	3.115554	GCTTGAATTTTGTGCGACTTGT	58.884	40.909	0.00	0.00	0.00	3.16
2480	2736	3.551485	GCTTGAATTTTGTGCGACTTGTT	59.449	39.130	0.00	0.00	0.00	2.83
2481	2737	4.032786	GCTTGAATTTTGTGCGACTTGTTT	59.967	37.500	0.00	0.00	0.00	2.83
2482	2738	5.445806	GCTTGAATTTTGTGCGACTTGTTTT	60.446	36.000	0.00	0.00	0.00	2.43
2483	2739	6.473397	TTGAATTTTGTGCGACTTGTTTTT	57.527	29.167	0.00	0.00	0.00	1.94
2550	2806	4.036518	AGACTGGGATCTTGCTCACTAAT	58.963	43.478	0.00	0.00	0.00	1.73
2551	2807	4.472833	AGACTGGGATCTTGCTCACTAATT	59.527	41.667	0.00	0.00	0.00	1.40
2552	2808	5.663106	AGACTGGGATCTTGCTCACTAATTA	59.337	40.000	0.00	0.00	0.00	1.40
2553	2809	6.156949	AGACTGGGATCTTGCTCACTAATTAA	59.843	38.462	0.00	0.00	0.00	1.40
2605	2861	5.636903	ATGACAGGCCTGTGAATAGTATT	57.363	39.130	42.40	15.13	45.05	1.89
2793	3050	0.319900	GAGTTGCAGAACAGCGGAGA	60.320	55.000	0.00	0.00	37.31	3.71
2806	3063	7.115520	CAGAACAGCGGAGAATACATGTATTAG	59.884	40.741	27.01	19.37	36.02	1.73
2810	3067	4.857588	GCGGAGAATACATGTATTAGACCG	59.142	45.833	34.98	34.98	41.95	4.79
2995	3258	4.443621	GAGGCAGTTATAGGAAGTTGACC	58.556	47.826	0.00	0.00	0.00	4.02
2999	3262	5.475564	GGCAGTTATAGGAAGTTGACCAAAA	59.524	40.000	0.00	0.00	0.00	2.44
3092	3355	9.212641	CATATGCTGCTGTCACTACTAATATTT	57.787	33.333	0.00	0.00	0.00	1.40
3096	3359	9.261180	TGCTGCTGTCACTACTAATATTTAATC	57.739	33.333	0.00	0.00	0.00	1.75
3158	3421	4.002982	TGCTAGTGTTTTGCCATAGTCAG	58.997	43.478	0.00	0.00	0.00	3.51
3161	3424	5.390991	GCTAGTGTTTTGCCATAGTCAGTTC	60.391	44.000	0.00	0.00	0.00	3.01
3212	3475	6.265196	ACATCTCACAGCTTCAAACCATTTAA	59.735	34.615	0.00	0.00	0.00	1.52

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
35	38	8.141909	TGAGACCGTCCTAATAACTATCAAATG	58.858	37.037	0.00	0.00	0.00	2.32
41	44	5.769162	GGACTGAGACCGTCCTAATAACTAT	59.231	44.000	2.11	0.00	45.87	2.12
153	157	7.691430	CATGTCAACATGTAGATGACTAGAC	57.309	40.000	23.06	8.77	46.71	2.59
272	302	4.521130	TGTAGTTGTAGCAGACTCAAGG	57.479	45.455	0.00	0.00	0.00	3.61
279	313	5.246203	AGTCTTGGAATGTAGTTGTAGCAGA	59.754	40.000	0.00	0.00	0.00	4.26
356	516	3.056328	GTGGGTTCCTGGAAGCGC	61.056	66.667	26.93	20.85	40.44	5.92
387	548	6.072673	GGCCTGTTATTCCGTATAAAATGAGG	60.073	42.308	0.00	0.00	30.70	3.86
660	880	1.689273	ACTTAAGGCGCTAGCTGCTAT	59.311	47.619	23.86	17.28	44.37	2.97
673	893	6.016360	TGTTGATCCATGTTGTTGACTTAAGG	60.016	38.462	7.53	0.00	0.00	2.69
739	959	3.442167	GCACATGTCATGCGCCCA	61.442	61.111	13.78	0.00	32.40	5.36
810	1035	6.848562	AAACCCAGGTCAGGATTAGATTAT	57.151	37.500	0.00	0.00	0.00	1.28
1011	1242	1.448540	ATTCTCGTCGCAGCAAGGG	60.449	57.895	0.00	0.00	0.00	3.95
1145	1377	0.319555	CGAGACAGAAAACGGAGGCA	60.320	55.000	0.00	0.00	0.00	4.75
1190	1433	2.138320	CGCATGAGCTACATTTCGGAT	58.862	47.619	0.00	0.00	37.07	4.18
1369	1617	5.065914	GCAAGAGATTTGATAGGTATGCCA	58.934	41.667	1.54	0.00	37.19	4.92
1535	1791	4.984785	CAGAAGTTCTTGATCTCGTTGTCA	59.015	41.667	1.56	0.00	0.00	3.58
1610	1866	4.648626	TCGGTCCTCGGTCGGTGT	62.649	66.667	0.00	0.00	39.77	4.16
1703	1959	4.648626	AGCTGGCTGGCGCTTTGA	62.649	61.111	7.64	0.00	37.29	2.69
1736	1992	3.036783	CTCGAGCTTTGCTGCCTGC	62.037	63.158	0.00	0.00	39.88	4.85
1793	2049	0.545309	TGCTGGAGCTGGGACTAGTT	60.545	55.000	0.00	0.00	42.66	2.24
1907	2163	2.173569	GTCTTGGCCATTGATACCCTCT	59.826	50.000	6.09	0.00	0.00	3.69
1979	2235	5.101648	TGATGATAGGCTGTTCATGTTCA	57.898	39.130	16.54	8.89	32.84	3.18
2103	2359	2.026542	GGTTGGAAATAGGGAAGTCGGT	60.027	50.000	0.00	0.00	0.00	4.69
2304	2560	4.761739	ACTACAATGGAAACCACATCACAG	59.238	41.667	0.00	0.00	35.80	3.66
2314	2570	4.003648	AGCTACAGCACTACAATGGAAAC	58.996	43.478	3.70	0.00	45.16	2.78
2450	2706	3.737774	GCACAAAATTCAAGCTGGAAGAC	59.262	43.478	9.90	0.00	34.07	3.01
2452	2708	2.727798	CGCACAAAATTCAAGCTGGAAG	59.272	45.455	9.90	0.00	0.00	3.46
2513	2769	2.354259	CAGTCTCCCATGAAGCACTTC	58.646	52.381	3.37	3.37	39.91	3.01
2832	3089	9.294614	AGCTTTTCTCTTAAAAAGATCACATCT	57.705	29.630	12.06	0.00	45.12	2.90
2833	3090	9.905171	AAGCTTTTCTCTTAAAAAGATCACATC	57.095	29.630	12.06	0.00	45.12	3.06
2839	3102	9.305925	CAACACAAGCTTTTCTCTTAAAAAGAT	57.694	29.630	12.06	4.03	45.12	2.40
2995	3258	4.512571	CCTCTTTTGACAGGGCAAATTTTG	59.487	41.667	0.38	4.72	37.57	2.44
2999	3262	2.158325	TCCCTCTTTTGACAGGGCAAAT	60.158	45.455	0.38	0.00	41.24	2.32
3158	3421	2.932614	CCGACAAGGACATGATGAGAAC	59.067	50.000	0.00	0.00	45.00	3.01
3161	3424	2.428530	TCTCCGACAAGGACATGATGAG	59.571	50.000	0.00	0.00	45.98	2.90

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.