AutoCloner

Multiple sequence alignment - TraesCS6B01G016300

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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	TraesCS6B01G016300	chr6B	100.000	2714	0	0	1	2714	9928608	9931321	0.000000e+00	5012.0
1	TraesCS6B01G016300	chr6B	84.868	152	17	5	1753	1901	295982919	295982771	6.050000e-32	148.0
2	TraesCS6B01G016300	chr6B	82.609	161	27	1	2140	2300	135488369	135488210	1.010000e-29	141.0
3	TraesCS6B01G016300	chr1B	96.368	2726	72	7	4	2714	21537472	21534759	0.000000e+00	4460.0
4	TraesCS6B01G016300	chr4A	82.609	253	35	4	2404	2650	319817601	319817352	5.890000e-52	215.0
5	TraesCS6B01G016300	chr2A	81.716	268	37	6	2404	2660	189206852	189206586	2.120000e-51	213.0
6	TraesCS6B01G016300	chr2A	87.037	162	20	1	2140	2301	79315104	79315264	5.970000e-42	182.0
7	TraesCS6B01G016300	chr5A	81.783	258	37	5	2404	2652	343081665	343081409	9.850000e-50	207.0
8	TraesCS6B01G016300	chr5A	91.429	105	7	1	198	300	595917078	595916974	2.820000e-30	143.0
9	TraesCS6B01G016300	chr3A	79.767	257	44	3	2404	2654	602923441	602923187	2.150000e-41	180.0
10	TraesCS6B01G016300	chr3A	92.381	105	6	1	198	300	429624344	429624240	6.050000e-32	148.0
11	TraesCS6B01G016300	chr3A	84.810	79	11	1	1815	1893	681122789	681122866	8.060000e-11	78.7
12	TraesCS6B01G016300	chr5D	88.811	143	15	1	2140	2282	509138384	509138243	9.990000e-40	174.0
13	TraesCS6B01G016300	chr4D	79.681	251	39	4	2404	2647	479044960	479044715	1.290000e-38	171.0
14	TraesCS6B01G016300	chr2D	85.276	163	24	0	2140	2302	450377421	450377583	4.650000e-38	169.0
15	TraesCS6B01G016300	chr2D	82.317	164	24	4	2140	2301	539422876	539423036	1.310000e-28	137.0
16	TraesCS6B01G016300	chr7D	79.268	246	43	3	2404	2643	128859622	128859865	6.010000e-37	165.0
17	TraesCS6B01G016300	chr7B	83.333	162	27	0	2140	2301	697066095	697065934	1.680000e-32	150.0
18	TraesCS6B01G016300	chr6A	83.333	162	21	6	1734	1893	417629113	417628956	7.830000e-31	145.0
19	TraesCS6B01G016300	chr6A	82.353	170	24	5	2443	2608	495416470	495416637	2.820000e-30	143.0
20	TraesCS6B01G016300	chr7A	82.738	168	22	6	2136	2301	718252872	718253034	2.820000e-30	143.0
21	TraesCS6B01G016300	chr7A	89.524	105	9	1	198	300	50806493	50806597	6.100000e-27	132.0
22	TraesCS6B01G016300	chr6D	82.209	163	22	7	1734	1894	299902784	299902941	1.700000e-27	134.0
23	TraesCS6B01G016300	chr2B	80.982	163	31	0	2139	2301	119596862	119596700	2.190000e-26	130.0
24	TraesCS6B01G016300	chr3B	82.667	150	21	5	1737	1885	776039204	776039349	7.890000e-26	128.0
25	TraesCS6B01G016300	chr3B	79.167	192	30	5	2426	2608	128688228	128688418	1.020000e-24	124.0
26	TraesCS6B01G016300	chr3B	81.595	163	18	11	1734	1894	488316158	488316310	1.020000e-24	124.0

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	TraesCS6B01G016300	chr6B	9928608	9931321	2713	False	5012	5012	100.000	1	2714	1	chr6B.!!$F1	2713
1	TraesCS6B01G016300	chr1B	21534759	21537472	2713	True	4460	4460	96.368	4	2714	1	chr1B.!!$R1	2710

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
625	626	0.399376	TCTTGCCCCTCCCGCTTATA	60.399	55.0	0.0	0.0	0.0	0.98	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1801	1811	0.829333	ACACTCAGCCTCTGCATAGG	59.171	55.0	13.7	13.7	41.13	2.57	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
22	23	4.974368	ACAAAGATCGACCAACAAAACA	57.026	36.364	0.00	0.00	0.00	2.83
26	27	6.816140	ACAAAGATCGACCAACAAAACATTTT	59.184	30.769	0.00	0.00	0.00	1.82
133	134	3.365265	GGTGGTTGGCTCCTTGCG	61.365	66.667	1.63	0.00	44.05	4.85
187	188	3.687125	TCCCAACCAAATAATGCGTACA	58.313	40.909	0.00	0.00	0.00	2.90
191	192	6.377429	TCCCAACCAAATAATGCGTACATTTA	59.623	34.615	0.00	0.00	44.21	1.40
206	207	9.938670	TGCGTACATTTATTATCCATTTTGTAC	57.061	29.630	0.00	0.00	36.47	2.90
225	226	2.486472	CAGATGGTCTGGCTGAAACT	57.514	50.000	0.00	0.00	40.71	2.66
228	229	5.282055	CAGATGGTCTGGCTGAAACTATA	57.718	43.478	0.00	0.00	40.71	1.31
237	238	9.120538	GGTCTGGCTGAAACTATAATTATTTCA	57.879	33.333	2.68	7.75	39.42	2.69
300	301	5.452777	GCACTTGTGTTTTAGTCCATTCTC	58.547	41.667	2.61	0.00	0.00	2.87
301	302	5.008613	GCACTTGTGTTTTAGTCCATTCTCA	59.991	40.000	2.61	0.00	0.00	3.27
303	304	6.038161	CACTTGTGTTTTAGTCCATTCTCACA	59.962	38.462	0.00	0.00	33.71	3.58
304	305	6.038271	ACTTGTGTTTTAGTCCATTCTCACAC	59.962	38.462	0.00	0.00	34.96	3.82
305	306	5.432645	TGTGTTTTAGTCCATTCTCACACA	58.567	37.500	0.00	0.00	31.22	3.72
306	307	5.883115	TGTGTTTTAGTCCATTCTCACACAA	59.117	36.000	0.00	0.00	32.48	3.33
307	308	6.545666	TGTGTTTTAGTCCATTCTCACACAAT	59.454	34.615	0.00	0.00	32.48	2.71
308	309	6.857964	GTGTTTTAGTCCATTCTCACACAATG	59.142	38.462	0.00	0.00	0.00	2.82
309	310	6.545666	TGTTTTAGTCCATTCTCACACAATGT	59.454	34.615	0.00	0.00	30.40	2.71
374	375	3.146066	TGTCCTAACACAAAGTGATGGC	58.854	45.455	3.88	1.51	36.96	4.40
470	471	4.403113	TGACCACCATGCGTAGTAATAAGA	59.597	41.667	0.00	0.00	0.00	2.10
605	606	5.947228	TGGTTTCTTACTCTGCTGATTTG	57.053	39.130	0.00	0.00	0.00	2.32
625	626	0.399376	TCTTGCCCCTCCCGCTTATA	60.399	55.000	0.00	0.00	0.00	0.98
711	712	4.416505	ACTTCGTAGCCTGCGTATATAC	57.583	45.455	1.31	2.53	0.00	1.47
722	723	4.380550	CCTGCGTATATACATGGACATCGT	60.381	45.833	13.22	0.00	0.00	3.73
975	976	1.218316	GACTCCCCGGTGATGACAC	59.782	63.158	0.00	0.00	45.27	3.67
1153	1155	1.784062	CAGCTTCGAGAAAGTGCCG	59.216	57.895	0.00	0.00	37.31	5.69
1211	1213	1.185618	TCCATCGCTTATCCCTCCGG	61.186	60.000	0.00	0.00	0.00	5.14
1459	1461	4.884257	TATGTCGCCGCGGCTTCC	62.884	66.667	43.60	30.80	39.32	3.46
1601	1603	7.467131	CGATCACAGTTCCATATGCATGTTTAA	60.467	37.037	10.16	0.00	0.00	1.52
1656	1658	3.422796	TCTCAAGGTAGGTCAGTGAGAC	58.577	50.000	0.00	0.00	46.83	3.36
1663	1665	8.500238	TCAAGGTAGGTCAGTGAGACTATAATA	58.500	37.037	7.53	0.00	46.72	0.98
1757	1767	0.606401	TGACTTTGCTAGTGGCTGGC	60.606	55.000	0.00	0.00	42.39	4.85
1801	1811	1.879380	TGTTGGCTGTGTGCATCTTAC	59.121	47.619	0.00	0.00	45.15	2.34
1818	1828	2.461300	TACCTATGCAGAGGCTGAGT	57.539	50.000	27.20	9.97	40.65	3.41
1819	1829	0.829333	ACCTATGCAGAGGCTGAGTG	59.171	55.000	27.20	1.99	40.65	3.51
1920	1930	2.356135	GAGCTAGCAACCGAAATTGGA	58.644	47.619	18.83	0.00	0.00	3.53
1953	1963	1.967066	TGATTGCCAACGGAAAATGGT	59.033	42.857	0.00	0.00	39.00	3.55
1974	1984	1.440618	TCCAGTTTGGAGGTTAGGCA	58.559	50.000	0.00	0.00	42.67	4.75
1975	1985	1.992557	TCCAGTTTGGAGGTTAGGCAT	59.007	47.619	0.00	0.00	42.67	4.40
2037	2047	8.868522	ACTGGAACATATTTCTGAATTCTGAA	57.131	30.769	20.19	20.19	38.20	3.02
2044	2054	8.404000	ACATATTTCTGAATTCTGAACATCTGC	58.596	33.333	22.87	0.00	34.31	4.26
2126	2136	6.749118	GCATCCTTAGTTTTGTATTCAGCTTG	59.251	38.462	0.00	0.00	0.00	4.01
2142	2152	3.750130	CAGCTTGAGCACAAACATCTACT	59.250	43.478	5.70	0.00	45.16	2.57
2208	2218	4.988540	GGACTACATACGCAGCAATATGAA	59.011	41.667	17.01	0.00	33.73	2.57
2340	2350	5.258622	CAGCAATTAACGACAACTAGATGC	58.741	41.667	0.00	0.00	0.00	3.91
2360	2370	1.340308	CCAATGCCAGTGGAGTGATGA	60.340	52.381	15.20	0.00	38.54	2.92
2414	2424	9.730705	AAAACTTTGTCTAGAGATGATGATGAA	57.269	29.630	0.00	0.00	0.00	2.57
2430	2440	7.450903	TGATGATGAATGAATGAGTGCTCTAT	58.549	34.615	0.68	0.00	0.00	1.98
2432	2442	9.089601	GATGATGAATGAATGAGTGCTCTATAG	57.910	37.037	0.00	0.00	0.00	1.31
2472	2488	3.924922	CACTAGGGGTATCTAGGGTTGT	58.075	50.000	0.00	0.00	40.63	3.32
2519	2535	2.540515	ACATGCCGAATCTAACAGACG	58.459	47.619	0.00	0.00	0.00	4.18
2522	2538	3.853831	TGCCGAATCTAACAGACGTAA	57.146	42.857	0.00	0.00	0.00	3.18
2569	2585	0.619832	AAGCAGATGAGAGGCCTCCA	60.620	55.000	29.54	24.96	38.66	3.86
2579	2595	1.151810	AGGCCTCCAAAGTCCCTCA	60.152	57.895	0.00	0.00	0.00	3.86
2593	2609	3.117738	AGTCCCTCATCCTTAATTGGCTG	60.118	47.826	0.00	0.00	0.00	4.85
2650	2666	0.620410	CCCCCTAGTCCATGACACCA	60.620	60.000	0.00	0.00	34.60	4.17
2704	2720	4.140853	AGCCATTATGAAACCCTCCATCAT	60.141	41.667	0.00	0.00	37.54	2.45

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
0	1	6.627395	ATGTTTTGTTGGTCGATCTTTGTA	57.373	33.333	0.00	0.00	0.00	2.41
1	2	4.974368	TGTTTTGTTGGTCGATCTTTGT	57.026	36.364	0.00	0.00	0.00	2.83
2	3	6.826893	AAATGTTTTGTTGGTCGATCTTTG	57.173	33.333	0.00	0.00	0.00	2.77
26	27	8.713971	ACTGGTCATGTTAGGTCATTTATCATA	58.286	33.333	0.00	0.00	0.00	2.15
78	79	6.742926	GCCTGAACCTCTCCCTAATTTATCTC	60.743	46.154	0.00	0.00	0.00	2.75
162	163	2.920490	CGCATTATTTGGTTGGGAAACG	59.080	45.455	0.00	0.00	0.00	3.60
191	192	7.503566	CCAGACCATCTGTACAAAATGGATAAT	59.496	37.037	30.13	16.05	42.80	1.28
206	207	2.486472	AGTTTCAGCCAGACCATCTG	57.514	50.000	0.00	0.00	43.91	2.90
237	238	8.980596	ACATCCCACATTAATTATTCACAACAT	58.019	29.630	0.00	0.00	0.00	2.71
300	301	6.309251	ACGTAAGGAAAACAAAACATTGTGTG	59.691	34.615	0.00	0.00	46.39	3.82
301	302	6.391537	ACGTAAGGAAAACAAAACATTGTGT	58.608	32.000	0.00	0.00	46.39	3.72
303	304	6.183360	GCAACGTAAGGAAAACAAAACATTGT	60.183	34.615	0.00	0.00	46.39	2.71
304	305	6.181944	GCAACGTAAGGAAAACAAAACATTG	58.818	36.000	0.00	0.00	46.39	2.82
305	306	5.869888	TGCAACGTAAGGAAAACAAAACATT	59.130	32.000	0.00	0.00	46.39	2.71
306	307	5.411781	TGCAACGTAAGGAAAACAAAACAT	58.588	33.333	0.00	0.00	46.39	2.71
307	308	4.806330	TGCAACGTAAGGAAAACAAAACA	58.194	34.783	0.00	0.00	46.39	2.83
308	309	5.543716	GTTGCAACGTAAGGAAAACAAAAC	58.456	37.500	14.90	0.00	46.39	2.43
309	310	4.323868	CGTTGCAACGTAAGGAAAACAAAA	59.676	37.500	37.16	0.00	46.63	2.44
338	339	3.855689	AGGACAATACAGCAAACATGC	57.144	42.857	0.00	0.00	0.00	4.06
347	348	7.361201	CCATCACTTTGTGTTAGGACAATACAG	60.361	40.741	0.00	0.00	37.57	2.74
374	375	0.165944	GCGTTGTTGATCCGGTCTTG	59.834	55.000	0.00	0.00	0.00	3.02
427	428	2.045524	AGACCGAGCCAATCATCATCT	58.954	47.619	0.00	0.00	0.00	2.90
605	606	1.984288	ATAAGCGGGAGGGGCAAGAC	61.984	60.000	0.00	0.00	0.00	3.01
625	626	8.408601	CCGAGAAATTTATTCATTCCAGACAAT	58.591	33.333	0.00	0.00	0.00	2.71
711	712	5.812127	TGATGTTTCTAGAACGATGTCCATG	59.188	40.000	4.18	0.00	0.00	3.66
975	976	3.850098	AAGCCTGGGAACTGTGCGG	62.850	63.158	0.00	0.00	33.13	5.69
978	979	2.568623	AGTAAAGCCTGGGAACTGTG	57.431	50.000	0.00	0.00	0.00	3.66
1029	1031	4.873129	CCGACACCAGATCCGGCG	62.873	72.222	0.00	0.00	35.29	6.46
1136	1138	1.374758	CCGGCACTTTCTCGAAGCT	60.375	57.895	0.00	0.00	39.04	3.74
1153	1155	2.007608	GGGACTCGTACAATTTGCTCC	58.992	52.381	0.00	0.00	0.00	4.70
1167	1169	1.990614	GGTGGAGGACTGGGGACTC	60.991	68.421	0.00	0.00	0.00	3.36
1211	1213	7.231722	AGGCGGTATAGTTGGATCTGATATATC	59.768	40.741	5.73	5.73	0.00	1.63
1333	1335	0.396060	GCAGGATGATGGAGAGGGAC	59.604	60.000	0.00	0.00	39.69	4.46
1459	1461	4.749310	AGCTGCACCGAGCCGAAG	62.749	66.667	1.02	0.00	44.83	3.79
1467	1469	2.031516	CAGACCAAGAGCTGCACCG	61.032	63.158	1.02	0.00	0.00	4.94
1546	1548	5.129485	TCAGAGTCCATCCCAGAAGTAATTC	59.871	44.000	0.00	0.00	0.00	2.17
1681	1683	9.695526	CAATCATTCTTATTTGGAAACACAAGA	57.304	29.630	0.00	0.00	42.67	3.02
1749	1759	1.000717	ACATAAAAACACGCCAGCCAC	60.001	47.619	0.00	0.00	0.00	5.01
1757	1767	4.201359	CGAACACACACACATAAAAACACG	59.799	41.667	0.00	0.00	0.00	4.49
1801	1811	0.829333	ACACTCAGCCTCTGCATAGG	59.171	55.000	13.70	13.70	41.13	2.57
1818	1828	7.015584	AGGATACAGATACATAATGAGCACACA	59.984	37.037	0.00	0.00	41.41	3.72
1819	1829	7.382110	AGGATACAGATACATAATGAGCACAC	58.618	38.462	0.00	0.00	41.41	3.82
1972	1982	6.140303	TCTTAAAAGAATGGAGATGCATGC	57.860	37.500	11.82	11.82	30.73	4.06
1973	1983	9.031360	CAAATCTTAAAAGAATGGAGATGCATG	57.969	33.333	2.46	0.00	38.77	4.06
1974	1984	8.974238	TCAAATCTTAAAAGAATGGAGATGCAT	58.026	29.630	0.00	0.00	38.77	3.96
1975	1985	8.352137	TCAAATCTTAAAAGAATGGAGATGCA	57.648	30.769	0.00	0.00	38.77	3.96
2126	2136	3.526534	GAGGGAGTAGATGTTTGTGCTC	58.473	50.000	0.00	0.00	0.00	4.26
2142	2152	5.546499	AGGCGTATATTTAGAAATGGAGGGA	59.454	40.000	0.00	0.00	0.00	4.20
2340	2350	1.100510	CATCACTCCACTGGCATTGG	58.899	55.000	17.19	17.19	35.18	3.16
2360	2370	5.123502	GTGATCTCAAGACTTGCAACATCAT	59.876	40.000	10.50	0.00	0.00	2.45
2414	2424	8.364142	GGTTTAGTCTATAGAGCACTCATTCAT	58.636	37.037	1.64	0.00	0.00	2.57
2430	2440	9.750783	CTAGTGCCTATATAAGGGTTTAGTCTA	57.249	37.037	0.00	0.00	46.65	2.59
2432	2442	7.093421	CCCTAGTGCCTATATAAGGGTTTAGTC	60.093	44.444	6.74	0.00	46.65	2.59
2519	2535	4.689345	AGACTTGGCGTGTACTTCAATTAC	59.311	41.667	0.00	0.00	0.00	1.89
2522	2538	3.402628	AGACTTGGCGTGTACTTCAAT	57.597	42.857	0.00	0.00	0.00	2.57
2569	2585	4.017130	AGCCAATTAAGGATGAGGGACTTT	60.017	41.667	0.00	0.00	41.55	2.66
2579	2595	1.406903	GCTGCCAGCCAATTAAGGAT	58.593	50.000	5.06	0.00	34.48	3.24
2628	2644	0.686441	TGTCATGGACTAGGGGGTCG	60.686	60.000	0.00	0.00	37.12	4.79
2632	2648	1.417890	GATGGTGTCATGGACTAGGGG	59.582	57.143	0.00	0.00	32.98	4.79
2636	2652	2.093500	GCAGTGATGGTGTCATGGACTA	60.093	50.000	0.00	0.00	39.48	2.59
2650	2666	2.865119	TGGTGAACATGAGCAGTGAT	57.135	45.000	0.00	0.00	0.00	3.06

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.