AutoCloner

Multiple sequence alignment - TraesCS5B01G332800

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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	TraesCS5B01G332800	chr5B	100.000	1754	0	0	1	1754	517191615	517193368	0.000000e+00	3240.0
1	TraesCS5B01G332800	chr5B	95.159	599	26	3	1	598	568356414	568357010	0.000000e+00	942.0
2	TraesCS5B01G332800	chr5B	94.684	602	28	4	7	607	522034827	522035425	0.000000e+00	931.0
3	TraesCS5B01G332800	chr5B	100.000	441	0	0	1986	2426	517193600	517194040	0.000000e+00	815.0
4	TraesCS5B01G332800	chr5B	79.141	489	62	17	849	1307	517208917	517208439	3.920000e-78	302.0
5	TraesCS5B01G332800	chr5B	84.348	115	13	4	2057	2171	517207479	517207370	9.170000e-20	108.0
6	TraesCS5B01G332800	chr5B	82.069	145	9	6	1339	1473	517208438	517208301	9.170000e-20	108.0
7	TraesCS5B01G332800	chr5D	93.441	1052	37	12	599	1628	427519308	427520349	0.000000e+00	1531.0
8	TraesCS5B01G332800	chr5D	93.155	599	38	3	1	598	184875504	184876100	0.000000e+00	876.0
9	TraesCS5B01G332800	chr5D	88.839	448	39	5	1986	2426	427520596	427521039	7.630000e-150	540.0
10	TraesCS5B01G332800	chr5D	81.531	601	69	16	849	1438	427544914	427544345	7.910000e-125	457.0
11	TraesCS5B01G332800	chr5D	95.312	128	5	1	1627	1754	427520431	427520557	4.090000e-48	202.0
12	TraesCS5B01G332800	chr5A	92.715	1057	43	12	599	1628	541935423	541936472	0.000000e+00	1495.0
13	TraesCS5B01G332800	chr5A	91.136	361	27	3	2067	2426	541936735	541937091	3.630000e-133	484.0
14	TraesCS5B01G332800	chr5A	81.685	546	55	19	953	1473	542002130	542001605	1.740000e-111	412.0
15	TraesCS5B01G332800	chr5A	95.000	40	2	0	2201	2240	542000873	542000834	2.010000e-06	63.9
16	TraesCS5B01G332800	chr1B	97.000	600	17	1	1	599	615403275	615403874	0.000000e+00	1007.0
17	TraesCS5B01G332800	chr2B	96.167	600	19	4	1	599	755040275	755040871	0.000000e+00	977.0
18	TraesCS5B01G332800	chr2A	93.677	601	36	2	1	600	752762469	752761870	0.000000e+00	898.0
19	TraesCS5B01G332800	chrUn	93.012	601	39	3	1	600	41032784	41032186	0.000000e+00	874.0
20	TraesCS5B01G332800	chr6D	92.857	602	40	3	1	601	362177823	362177224	0.000000e+00	870.0
21	TraesCS5B01G332800	chr6A	92.988	599	38	4	1	597	28943999	28944595	0.000000e+00	870.0

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	TraesCS5B01G332800	chr5B	517191615	517194040	2425	False	2027.500000	3240	100.000000	1	2426	2	chr5B.!!$F3	2425
1	TraesCS5B01G332800	chr5B	568356414	568357010	596	False	942.000000	942	95.159000	1	598	1	chr5B.!!$F2	597
2	TraesCS5B01G332800	chr5B	522034827	522035425	598	False	931.000000	931	94.684000	7	607	1	chr5B.!!$F1	600
3	TraesCS5B01G332800	chr5D	184875504	184876100	596	False	876.000000	876	93.155000	1	598	1	chr5D.!!$F1	597
4	TraesCS5B01G332800	chr5D	427519308	427521039	1731	False	757.666667	1531	92.530667	599	2426	3	chr5D.!!$F2	1827
5	TraesCS5B01G332800	chr5D	427544345	427544914	569	True	457.000000	457	81.531000	849	1438	1	chr5D.!!$R1	589
6	TraesCS5B01G332800	chr5A	541935423	541937091	1668	False	989.500000	1495	91.925500	599	2426	2	chr5A.!!$F1	1827
7	TraesCS5B01G332800	chr5A	542000834	542002130	1296	True	237.950000	412	88.342500	953	2240	2	chr5A.!!$R1	1287
8	TraesCS5B01G332800	chr1B	615403275	615403874	599	False	1007.000000	1007	97.000000	1	599	1	chr1B.!!$F1	598
9	TraesCS5B01G332800	chr2B	755040275	755040871	596	False	977.000000	977	96.167000	1	599	1	chr2B.!!$F1	598
10	TraesCS5B01G332800	chr2A	752761870	752762469	599	True	898.000000	898	93.677000	1	600	1	chr2A.!!$R1	599
11	TraesCS5B01G332800	chrUn	41032186	41032784	598	True	874.000000	874	93.012000	1	600	1	chrUn.!!$R1	599
12	TraesCS5B01G332800	chr6D	362177224	362177823	599	True	870.000000	870	92.857000	1	601	1	chr6D.!!$R1	600
13	TraesCS5B01G332800	chr6A	28943999	28944595	596	False	870.000000	870	92.988000	1	597	1	chr6A.!!$F1	596

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
925	941	1.001181	CATCCACCCACAGCCAAAAAG	59.999	52.381	0.0	0.0	0.0	2.27	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2173	2487	1.469308	CCTGAGACACGTAGACAGACC	59.531	57.143	11.04	0.0	0.0	3.85	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
80	81	2.611473	CCTCTGCAGCTTTCTTCTTCGA	60.611	50.000	9.47	0.00	0.00	3.71
111	112	1.133450	ACGGCTATCCTTCTGCTCCTA	60.133	52.381	0.00	0.00	0.00	2.94
315	318	2.093658	GGAGCGATGTTCTTCCCTTGTA	60.094	50.000	0.00	0.00	0.00	2.41
433	436	1.953686	GACTCTACTAGCAGGGCTCTG	59.046	57.143	10.01	10.01	40.44	3.35
696	703	2.978010	CAGCCCGCCTCAACGTTT	60.978	61.111	0.00	0.00	0.00	3.60
894	908	2.436115	CTCCGGCCCGTTTCTTCC	60.436	66.667	0.85	0.00	0.00	3.46
925	941	1.001181	CATCCACCCACAGCCAAAAAG	59.999	52.381	0.00	0.00	0.00	2.27
931	947	3.622612	CACCCACAGCCAAAAAGAAAAAG	59.377	43.478	0.00	0.00	0.00	2.27
934	950	4.940654	CCCACAGCCAAAAAGAAAAAGAAA	59.059	37.500	0.00	0.00	0.00	2.52
1127	1150	2.115911	AGCTCAGCGTACTCGGAGG	61.116	63.158	13.68	0.00	37.56	4.30
1217	1252	1.304217	AGCGGGTCTTCGAGGAGAA	60.304	57.895	0.00	0.00	37.31	2.87
1262	1297	3.827898	GGACACGAGGGCGAGGAG	61.828	72.222	0.00	0.00	41.64	3.69
1310	1345	2.579787	CGACACGATCCCGCTGAC	60.580	66.667	0.00	0.00	39.95	3.51
1311	1346	2.579787	GACACGATCCCGCTGACG	60.580	66.667	0.00	0.00	39.95	4.35
1313	1348	2.579787	CACGATCCCGCTGACGTC	60.580	66.667	9.11	9.11	39.95	4.34
1314	1349	3.823330	ACGATCCCGCTGACGTCC	61.823	66.667	14.12	0.00	39.95	4.79
1315	1350	4.907034	CGATCCCGCTGACGTCCG	62.907	72.222	14.12	8.02	37.70	4.79
1479	1552	4.546829	TGTGTAATTACCGCCTCTCTTT	57.453	40.909	13.01	0.00	0.00	2.52
1544	1617	1.592669	CAGATGGTTAGCGCCTCCG	60.593	63.158	2.29	0.00	37.57	4.63
1545	1618	2.058595	AGATGGTTAGCGCCTCCGT	61.059	57.895	2.29	5.57	36.67	4.69
1587	1663	1.964608	CTGGCCTTCCGAGATCTGCA	61.965	60.000	3.32	0.00	34.14	4.41
1672	1972	6.092807	GCTCTGAATTTTCTTACCAAGTCGAT	59.907	38.462	0.00	0.00	0.00	3.59
1716	2024	8.643324	CCTTTTAATCCAGCTATGTACTCTAGT	58.357	37.037	0.00	0.00	0.00	2.57
1740	2048	1.886542	GCTCTTTCACGGGATTTTGGT	59.113	47.619	0.00	0.00	0.00	3.67
1742	2050	3.146066	CTCTTTCACGGGATTTTGGTCA	58.854	45.455	0.00	0.00	0.00	4.02
1746	2054	3.932545	TCACGGGATTTTGGTCAAATG	57.067	42.857	0.00	0.00	35.02	2.32
2019	2327	8.391106	GTCTAAATGTTCATCGCTACTTGAAAT	58.609	33.333	0.00	0.00	33.90	2.17
2031	2339	7.713750	TCGCTACTTGAAATACTAGCTATGTT	58.286	34.615	0.00	0.00	31.20	2.71
2088	2396	6.500684	TGATCTTATCTTGGCAAGTTGAAC	57.499	37.500	25.39	16.77	0.00	3.18
2093	2401	4.961438	ATCTTGGCAAGTTGAACCAATT	57.039	36.364	25.39	4.51	42.35	2.32
2171	2485	8.556517	AAGTTTTATGTTACTCGCACTTTTTC	57.443	30.769	0.00	0.00	0.00	2.29
2172	2486	7.699566	AGTTTTATGTTACTCGCACTTTTTCA	58.300	30.769	0.00	0.00	0.00	2.69
2173	2487	7.855904	AGTTTTATGTTACTCGCACTTTTTCAG	59.144	33.333	0.00	0.00	0.00	3.02
2176	2490	3.558418	TGTTACTCGCACTTTTTCAGGTC	59.442	43.478	0.00	0.00	0.00	3.85
2177	2491	2.622064	ACTCGCACTTTTTCAGGTCT	57.378	45.000	0.00	0.00	0.00	3.85
2178	2492	2.213499	ACTCGCACTTTTTCAGGTCTG	58.787	47.619	0.00	0.00	0.00	3.51
2179	2493	2.213499	CTCGCACTTTTTCAGGTCTGT	58.787	47.619	0.00	0.00	0.00	3.41
2181	2495	2.158957	TCGCACTTTTTCAGGTCTGTCT	60.159	45.455	0.00	0.00	0.00	3.41
2182	2496	3.069016	TCGCACTTTTTCAGGTCTGTCTA	59.931	43.478	0.00	0.00	0.00	2.59
2183	2497	3.184581	CGCACTTTTTCAGGTCTGTCTAC	59.815	47.826	0.00	0.00	0.00	2.59
2190	2505	2.424557	TCAGGTCTGTCTACGTGTCTC	58.575	52.381	0.00	0.00	36.77	3.36
2264	2668	2.222953	GCAATTAAGGCGACCGTTGTAG	60.223	50.000	0.00	0.00	0.00	2.74
2280	2684	4.093408	CGTTGTAGGGATCAACACTCAATG	59.907	45.833	8.98	0.00	43.40	2.82
2338	2742	2.493713	AACGCGTAGATGACATCCTC	57.506	50.000	14.46	4.83	0.00	3.71
2343	2747	4.218635	ACGCGTAGATGACATCCTCATATT	59.781	41.667	11.67	0.00	39.96	1.28
2353	2757	1.874129	TCCTCATATTGGTGGGACGT	58.126	50.000	0.00	0.00	0.00	4.34

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
5	6	0.612732	TCCAATGGCTGCAAGAAGGG	60.613	55.000	0.50	0.00	34.07	3.95
15	16	2.231380	AGGTCCCGTTCCAATGGCT	61.231	57.895	0.00	0.00	33.59	4.75
80	81	3.711059	ATAGCCGTCGGGAGGTCGT	62.711	63.158	14.38	0.00	34.06	4.34
111	112	0.396811	CCACCTCTCCCGAACAAACT	59.603	55.000	0.00	0.00	0.00	2.66
166	167	0.592247	GCAGACAAAGTGCACAACCG	60.592	55.000	21.04	6.82	40.86	4.44
315	318	1.141053	GTGAACTGTCTGAACCCAGGT	59.859	52.381	0.00	0.00	40.76	4.00
552	558	2.825532	GGAGCCCAGCTTTGAATTAACA	59.174	45.455	0.00	0.00	39.88	2.41
696	703	3.636313	GAATCGGTCCCGCGTCACA	62.636	63.158	4.92	0.00	39.59	3.58
894	908	2.903855	GTGGATGGCTGCGGATGG	60.904	66.667	0.00	0.00	0.00	3.51
950	970	2.922758	GCGACAGGATTAGCGAATCGAT	60.923	50.000	6.91	1.41	42.20	3.59
951	971	1.599667	GCGACAGGATTAGCGAATCGA	60.600	52.381	6.91	0.00	42.20	3.59
961	981	0.320771	AGTTGCTTCGCGACAGGATT	60.321	50.000	9.15	0.38	44.70	3.01
962	982	1.016130	CAGTTGCTTCGCGACAGGAT	61.016	55.000	9.15	0.00	44.70	3.24
1185	1220	3.827898	CGCTCCTCCACCTCGACC	61.828	72.222	0.00	0.00	0.00	4.79
1371	1406	2.501128	CATGACGATGACGCCCCT	59.499	61.111	0.00	0.00	43.96	4.79
1479	1552	4.141801	TGTCTTTTCCCGTTTCTTCTCTGA	60.142	41.667	0.00	0.00	0.00	3.27
1587	1663	6.421485	AGGTAATGATGAGCTCTGATGTTTT	58.579	36.000	16.19	2.62	0.00	2.43
1716	2024	3.695830	AAATCCCGTGAAAGAGCACTA	57.304	42.857	0.00	0.00	36.65	2.74
1997	2305	8.268850	AGTATTTCAAGTAGCGATGAACATTT	57.731	30.769	0.00	0.00	35.42	2.32
2019	2327	3.772572	TGGAACTGCCAACATAGCTAGTA	59.227	43.478	0.00	0.00	45.87	1.82
2143	2454	6.385537	AGTGCGAGTAACATAAAACTTACG	57.614	37.500	0.00	0.00	0.00	3.18
2171	2485	2.152016	TGAGACACGTAGACAGACCTG	58.848	52.381	0.00	0.00	0.00	4.00
2172	2486	2.428491	CTGAGACACGTAGACAGACCT	58.572	52.381	0.00	0.00	0.00	3.85
2173	2487	1.469308	CCTGAGACACGTAGACAGACC	59.531	57.143	11.04	0.00	0.00	3.85
2176	2490	4.442375	AAATCCTGAGACACGTAGACAG	57.558	45.455	0.00	0.00	0.00	3.51
2177	2491	5.008331	ACTAAATCCTGAGACACGTAGACA	58.992	41.667	0.00	0.00	0.00	3.41
2178	2492	5.354792	AGACTAAATCCTGAGACACGTAGAC	59.645	44.000	0.00	0.00	0.00	2.59
2179	2493	5.498393	AGACTAAATCCTGAGACACGTAGA	58.502	41.667	0.00	0.00	0.00	2.59
2181	2495	5.708697	TCAAGACTAAATCCTGAGACACGTA	59.291	40.000	0.00	0.00	0.00	3.57
2182	2496	4.523173	TCAAGACTAAATCCTGAGACACGT	59.477	41.667	0.00	0.00	0.00	4.49
2183	2497	5.060662	TCAAGACTAAATCCTGAGACACG	57.939	43.478	0.00	0.00	0.00	4.49
2280	2684	6.397272	TGAACTATCAATGCCCATTTTCAAC	58.603	36.000	3.75	0.00	30.99	3.18
2291	2695	6.364706	CCGTTCTCTCTATGAACTATCAATGC	59.635	42.308	0.00	0.00	40.95	3.56
2338	2742	1.872237	CGGCTACGTCCCACCAATATG	60.872	57.143	0.00	0.00	34.81	1.78
2393	2797	7.067129	ACAGAAGAAAAACTTTCCACTTAGACC	59.933	37.037	0.00	0.00	39.13	3.85

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.