AutoCloner

Multiple sequence alignment - TraesCS7A01G307900

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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	TraesCS7A01G307900	chr7A	100.000	2573	0	0	1	2573	435828403	435825831	0.000000e+00	4752.0
1	TraesCS7A01G307900	chr7A	96.019	854	26	3	670	1517	435865562	435864711	0.000000e+00	1382.0
2	TraesCS7A01G307900	chr7A	93.157	453	25	5	19	467	182393341	182393791	0.000000e+00	660.0
3	TraesCS7A01G307900	chr7A	93.333	285	18	1	1	284	78124377	78124093	1.100000e-113	420.0
4	TraesCS7A01G307900	chr2A	95.558	1058	46	1	1517	2573	739468948	739467891	0.000000e+00	1692.0
5	TraesCS7A01G307900	chr7B	94.806	1059	53	1	1517	2573	710961331	710962389	0.000000e+00	1650.0
6	TraesCS7A01G307900	chr7B	93.519	864	40	9	667	1516	380856637	380855776	0.000000e+00	1271.0
7	TraesCS7A01G307900	chr7B	92.940	864	43	4	667	1517	380864227	380863369	0.000000e+00	1242.0
8	TraesCS7A01G307900	chr7B	97.143	35	1	0	613	647	380856673	380856639	2.760000e-05	60.2
9	TraesCS7A01G307900	chr2B	94.806	1059	54	1	1516	2573	680236660	680235602	0.000000e+00	1650.0
10	TraesCS7A01G307900	chr2B	93.762	1058	61	3	1517	2573	546952428	546953481	0.000000e+00	1583.0
11	TraesCS7A01G307900	chr1D	94.167	1063	60	2	1512	2573	93444437	93443376	0.000000e+00	1618.0
12	TraesCS7A01G307900	chr1D	94.859	992	51	0	1517	2508	57124865	57123874	0.000000e+00	1550.0
13	TraesCS7A01G307900	chr1D	95.745	47	2	0	564	610	451769783	451769829	2.750000e-10	76.8
14	TraesCS7A01G307900	chr3A	94.151	1060	55	5	1517	2573	102313461	102314516	0.000000e+00	1607.0
15	TraesCS7A01G307900	chr6B	93.424	1034	60	7	1531	2562	564064008	564065035	0.000000e+00	1526.0
16	TraesCS7A01G307900	chr6B	94.118	51	3	0	563	613	173653801	173653851	7.630000e-11	78.7
17	TraesCS7A01G307900	chr6B	89.831	59	5	1	467	524	156239298	156239356	9.870000e-10	75.0
18	TraesCS7A01G307900	chrUn	92.720	1044	76	0	1530	2573	70408603	70409646	0.000000e+00	1507.0
19	TraesCS7A01G307900	chr7D	92.640	856	47	5	667	1517	386563667	386562823	0.000000e+00	1218.0
20	TraesCS7A01G307900	chr4A	94.454	559	26	3	1	558	572221844	572221290	0.000000e+00	856.0
21	TraesCS7A01G307900	chr5B	98.000	50	1	0	564	613	540345331	540345282	1.270000e-13	87.9
22	TraesCS7A01G307900	chr6D	96.000	50	2	0	564	613	368992021	368992070	5.900000e-12	82.4
23	TraesCS7A01G307900	chr6D	95.745	47	2	0	564	610	394682056	394682102	2.750000e-10	76.8
24	TraesCS7A01G307900	chr2D	94.340	53	1	2	565	616	87998853	87998904	2.120000e-11	80.5
25	TraesCS7A01G307900	chr3D	95.745	47	2	0	564	610	322909655	322909701	2.750000e-10	76.8
26	TraesCS7A01G307900	chr5D	93.878	49	3	0	567	615	239560457	239560409	9.870000e-10	75.0
27	TraesCS7A01G307900	chr3B	93.750	48	3	0	566	613	64872071	64872118	3.550000e-09	73.1

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	TraesCS7A01G307900	chr7A	435825831	435828403	2572	True	4752.0	4752	100.000	1	2573	1	chr7A.!!$R2	2572
1	TraesCS7A01G307900	chr7A	435864711	435865562	851	True	1382.0	1382	96.019	670	1517	1	chr7A.!!$R3	847
2	TraesCS7A01G307900	chr2A	739467891	739468948	1057	True	1692.0	1692	95.558	1517	2573	1	chr2A.!!$R1	1056
3	TraesCS7A01G307900	chr7B	710961331	710962389	1058	False	1650.0	1650	94.806	1517	2573	1	chr7B.!!$F1	1056
4	TraesCS7A01G307900	chr7B	380863369	380864227	858	True	1242.0	1242	92.940	667	1517	1	chr7B.!!$R1	850
5	TraesCS7A01G307900	chr7B	380855776	380856673	897	True	665.6	1271	95.331	613	1516	2	chr7B.!!$R2	903
6	TraesCS7A01G307900	chr2B	680235602	680236660	1058	True	1650.0	1650	94.806	1516	2573	1	chr2B.!!$R1	1057
7	TraesCS7A01G307900	chr2B	546952428	546953481	1053	False	1583.0	1583	93.762	1517	2573	1	chr2B.!!$F1	1056
8	TraesCS7A01G307900	chr1D	93443376	93444437	1061	True	1618.0	1618	94.167	1512	2573	1	chr1D.!!$R2	1061
9	TraesCS7A01G307900	chr1D	57123874	57124865	991	True	1550.0	1550	94.859	1517	2508	1	chr1D.!!$R1	991
10	TraesCS7A01G307900	chr3A	102313461	102314516	1055	False	1607.0	1607	94.151	1517	2573	1	chr3A.!!$F1	1056
11	TraesCS7A01G307900	chr6B	564064008	564065035	1027	False	1526.0	1526	93.424	1531	2562	1	chr6B.!!$F3	1031
12	TraesCS7A01G307900	chrUn	70408603	70409646	1043	False	1507.0	1507	92.720	1530	2573	1	chrUn.!!$F1	1043
13	TraesCS7A01G307900	chr7D	386562823	386563667	844	True	1218.0	1218	92.640	667	1517	1	chr7D.!!$R1	850
14	TraesCS7A01G307900	chr4A	572221290	572221844	554	True	856.0	856	94.454	1	558	1	chr4A.!!$R1	557

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
806	808	0.041312	ACAACGCGTGAGTCAAATGC	60.041	50.0	14.98	0.0	0.0	3.56	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2390	2427	0.600255	GCCGCTACGCCTGTTGATAT	60.6	55.0	0.0	0.0	0.0	1.63	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
26	27	2.837291	GGCATTAATGGCGGGGCA	60.837	61.111	24.24	0.0	43.58	5.36
129	130	2.567049	GTCCACCCGTCTCTGTCG	59.433	66.667	0.00	0.0	0.00	4.35
145	146	0.452585	GTCGACGGAAGAGGAAGGAG	59.547	60.000	0.00	0.0	0.00	3.69
148	149	1.679336	CGACGGAAGAGGAAGGAGAGA	60.679	57.143	0.00	0.0	0.00	3.10
152	153	0.744281	GAAGAGGAAGGAGAGAGCGG	59.256	60.000	0.00	0.0	0.00	5.52
192	193	0.185901	TGGACTTGAGCCTGCCTTTT	59.814	50.000	0.00	0.0	0.00	2.27
199	200	0.884514	GAGCCTGCCTTTTCCAGAAC	59.115	55.000	0.00	0.0	32.03	3.01
241	243	4.070552	GAGGAGAGGTGGCGCGTT	62.071	66.667	8.43	0.0	0.00	4.84
329	331	2.997315	CACGGAGAGACCAGCCCA	60.997	66.667	0.00	0.0	38.90	5.36
333	335	2.801631	GGAGAGACCAGCCCATCCG	61.802	68.421	0.00	0.0	38.79	4.18
529	531	2.046700	GGACGGAATGGCCAACGA	60.047	61.111	27.49	0.0	35.94	3.85
532	534	4.160635	CGGAATGGCCAACGACGC	62.161	66.667	10.96	0.0	35.94	5.19
558	560	3.636231	CTGGGGCACACGAAGGGA	61.636	66.667	0.00	0.0	0.00	4.20
559	561	3.612247	CTGGGGCACACGAAGGGAG	62.612	68.421	0.00	0.0	0.00	4.30
560	562	3.319198	GGGGCACACGAAGGGAGA	61.319	66.667	0.00	0.0	0.00	3.71
561	563	2.047179	GGGCACACGAAGGGAGAC	60.047	66.667	0.00	0.0	0.00	3.36
576	578	2.753247	GGAGACCCTGGACTTAGATGT	58.247	52.381	0.00	0.0	0.00	3.06
577	579	2.432510	GGAGACCCTGGACTTAGATGTG	59.567	54.545	0.00	0.0	0.00	3.21
578	580	3.366396	GAGACCCTGGACTTAGATGTGA	58.634	50.000	0.00	0.0	0.00	3.58
579	581	3.769844	GAGACCCTGGACTTAGATGTGAA	59.230	47.826	0.00	0.0	0.00	3.18
580	582	4.168101	AGACCCTGGACTTAGATGTGAAA	58.832	43.478	0.00	0.0	0.00	2.69
581	583	4.785376	AGACCCTGGACTTAGATGTGAAAT	59.215	41.667	0.00	0.0	0.00	2.17
582	584	5.964477	AGACCCTGGACTTAGATGTGAAATA	59.036	40.000	0.00	0.0	0.00	1.40
583	585	6.443849	AGACCCTGGACTTAGATGTGAAATAA	59.556	38.462	0.00	0.0	0.00	1.40
584	586	6.653989	ACCCTGGACTTAGATGTGAAATAAG	58.346	40.000	0.00	0.0	33.63	1.73
585	587	6.215636	ACCCTGGACTTAGATGTGAAATAAGT	59.784	38.462	0.00	0.0	41.28	2.24
586	588	7.402071	ACCCTGGACTTAGATGTGAAATAAGTA	59.598	37.037	0.00	0.0	39.28	2.24
587	589	8.432805	CCCTGGACTTAGATGTGAAATAAGTAT	58.567	37.037	0.00	0.0	39.28	2.12
588	590	9.838339	CCTGGACTTAGATGTGAAATAAGTATT	57.162	33.333	0.00	0.0	39.28	1.89
647	649	2.851263	TGTAACGGTTGAAGCATCCT	57.149	45.000	3.07	0.0	0.00	3.24
648	650	3.965379	TGTAACGGTTGAAGCATCCTA	57.035	42.857	3.07	0.0	0.00	2.94
649	651	4.481368	TGTAACGGTTGAAGCATCCTAT	57.519	40.909	3.07	0.0	0.00	2.57
650	652	4.839121	TGTAACGGTTGAAGCATCCTATT	58.161	39.130	3.07	0.0	0.00	1.73
651	653	5.979993	TGTAACGGTTGAAGCATCCTATTA	58.020	37.500	3.07	0.0	0.00	0.98
652	654	6.588204	TGTAACGGTTGAAGCATCCTATTAT	58.412	36.000	3.07	0.0	0.00	1.28
653	655	7.051623	TGTAACGGTTGAAGCATCCTATTATT	58.948	34.615	3.07	0.0	0.00	1.40
654	656	8.205512	TGTAACGGTTGAAGCATCCTATTATTA	58.794	33.333	3.07	0.0	0.00	0.98
655	657	9.216117	GTAACGGTTGAAGCATCCTATTATTAT	57.784	33.333	3.07	0.0	0.00	1.28
656	658	8.691661	AACGGTTGAAGCATCCTATTATTATT	57.308	30.769	0.00	0.0	0.00	1.40
657	659	9.787435	AACGGTTGAAGCATCCTATTATTATTA	57.213	29.630	0.00	0.0	0.00	0.98
658	660	9.959721	ACGGTTGAAGCATCCTATTATTATTAT	57.040	29.630	0.00	0.0	0.00	1.28
700	702	7.251281	CAGTACGTATGTATGGAATCGATCAT	58.749	38.462	0.00	1.2	32.11	2.45
748	750	3.006940	TGATTATTCAACGAGCCCACAC	58.993	45.455	0.00	0.0	0.00	3.82
759	761	3.945285	ACGAGCCCACACTTTAATTATGG	59.055	43.478	0.00	0.0	0.00	2.74
763	765	4.654091	CCCACACTTTAATTATGGGCTG	57.346	45.455	7.92	0.0	43.51	4.85
806	808	0.041312	ACAACGCGTGAGTCAAATGC	60.041	50.000	14.98	0.0	0.00	3.56
807	809	0.235665	CAACGCGTGAGTCAAATGCT	59.764	50.000	14.98	0.0	0.00	3.79
948	965	4.056740	CCTCGATCATCTCAACATTCCAG	58.943	47.826	0.00	0.0	0.00	3.86
1221	1252	0.399949	TGGTGGAGGTGACCAAGACT	60.400	55.000	3.63	0.0	40.65	3.24
1434	1465	1.987704	GCACACAGACAACGCCACAA	61.988	55.000	0.00	0.0	0.00	3.33
1470	1501	2.665000	GCTGGTGCTGAGCCTGTA	59.335	61.111	0.23	0.0	36.03	2.74
1508	1539	2.743928	CCTCGTGGCTGGCTTGAC	60.744	66.667	2.00	0.0	0.00	3.18
1536	1567	4.148079	TCTGTATGTTGTTGGGATTGCAA	58.852	39.130	0.00	0.0	0.00	4.08
1589	1620	9.148879	GTATATATGATGTATAAGAGGTGGGCT	57.851	37.037	0.00	0.0	0.00	5.19
1590	1621	4.630644	ATGATGTATAAGAGGTGGGCTG	57.369	45.455	0.00	0.0	0.00	4.85
1664	1697	5.245531	CACAACACATATACTCAACACCCT	58.754	41.667	0.00	0.0	0.00	4.34
1714	1750	1.792949	CAAAGACTGGACCGAAACTCG	59.207	52.381	0.00	0.0	40.07	4.18
1744	1780	1.303317	CGTAGGCAAGCCCTTGGTT	60.303	57.895	7.62	0.0	43.06	3.67
1782	1818	1.549203	TGGGAAGTAGGGACGTGTAC	58.451	55.000	0.00	0.0	0.00	2.90
1923	1959	1.133790	GTAGACCACCGTAGCACGATT	59.866	52.381	9.75	0.0	46.05	3.34
2085	2121	3.307762	GGTCCAAGGAAGACACAATAGCT	60.308	47.826	0.00	0.0	35.89	3.32
2239	2275	2.045926	GCGGCCCAGTGAACATCT	60.046	61.111	0.00	0.0	0.00	2.90
2241	2277	1.296392	CGGCCCAGTGAACATCTCA	59.704	57.895	0.00	0.0	0.00	3.27
2300	2336	1.202582	ACTGAATCTCCGGTCGAGTTG	59.797	52.381	0.00	0.0	39.84	3.16
2356	2393	0.393402	AGAATGCAGCATCCGAAGCA	60.393	50.000	8.77	0.0	41.73	3.91
2390	2427	1.002868	GCAGAGAGCTTGGCCTTCA	60.003	57.895	3.32	0.0	41.15	3.02

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
125	126	0.251033	TCCTTCCTCTTCCGTCGACA	60.251	55.000	17.16	0.00	0.00	4.35
129	130	2.021457	CTCTCTCCTTCCTCTTCCGTC	58.979	57.143	0.00	0.00	0.00	4.79
132	133	0.744281	CGCTCTCTCCTTCCTCTTCC	59.256	60.000	0.00	0.00	0.00	3.46
145	146	2.130426	TGCCATCTCCTCCGCTCTC	61.130	63.158	0.00	0.00	0.00	3.20
148	149	2.293318	TTGTGCCATCTCCTCCGCT	61.293	57.895	0.00	0.00	0.00	5.52
294	296	3.173240	GCCTCGTCTCGCGTCAAC	61.173	66.667	5.77	1.87	42.13	3.18
307	309	2.680352	TGGTCTCTCCGTGGCCTC	60.680	66.667	3.32	0.00	39.52	4.70
333	335	1.153588	TTAAATCCGCCGGTCCGTC	60.154	57.895	11.06	0.00	0.00	4.79
348	350	2.047655	CGTGGCCGCTCCTGTTAA	60.048	61.111	15.69	0.00	35.26	2.01
384	386	4.519437	CGGCAGCGCTGGATCTGA	62.519	66.667	36.47	0.00	32.26	3.27
509	511	4.418328	TTGGCCATTCCGTCCGGG	62.418	66.667	6.09	0.00	37.80	5.73
510	512	3.131478	GTTGGCCATTCCGTCCGG	61.131	66.667	6.09	0.00	37.80	5.14
511	513	3.496131	CGTTGGCCATTCCGTCCG	61.496	66.667	6.09	0.00	37.80	4.79
514	516	2.740826	CGTCGTTGGCCATTCCGT	60.741	61.111	6.09	0.00	37.80	4.69
532	534	4.748144	GTGCCCCAGCCCTTCCTG	62.748	72.222	0.00	0.00	38.69	3.86
557	559	3.366396	TCACATCTAAGTCCAGGGTCTC	58.634	50.000	0.00	0.00	0.00	3.36
558	560	3.474798	TCACATCTAAGTCCAGGGTCT	57.525	47.619	0.00	0.00	0.00	3.85
559	561	4.553330	TTTCACATCTAAGTCCAGGGTC	57.447	45.455	0.00	0.00	0.00	4.46
560	562	6.215636	ACTTATTTCACATCTAAGTCCAGGGT	59.784	38.462	0.00	0.00	31.72	4.34
561	563	6.653989	ACTTATTTCACATCTAAGTCCAGGG	58.346	40.000	0.00	0.00	31.72	4.45
562	564	9.838339	AATACTTATTTCACATCTAAGTCCAGG	57.162	33.333	0.00	0.00	37.07	4.45
611	613	9.465985	AACCGTTACATTTTTATGTTCGAAATT	57.534	25.926	0.00	0.00	36.08	1.82
616	618	7.408921	GCTTCAACCGTTACATTTTTATGTTCG	60.409	37.037	0.00	0.00	36.08	3.95
700	702	0.176680	GAAGCTGCTAGCCTACTGCA	59.823	55.000	13.29	0.00	43.77	4.41
748	750	8.912988	TCTGGAAATTACAGCCCATAATTAAAG	58.087	33.333	0.00	0.00	35.94	1.85
759	761	2.872858	GGTCGATCTGGAAATTACAGCC	59.127	50.000	0.00	0.00	35.94	4.85
763	765	3.175109	ACGGGTCGATCTGGAAATTAC	57.825	47.619	9.81	0.00	0.00	1.89
806	808	7.430793	CGTCATACAGACTCTGTCAAATTAGAG	59.569	40.741	15.20	2.07	41.21	2.43
807	809	7.251281	CGTCATACAGACTCTGTCAAATTAGA	58.749	38.462	15.20	0.00	41.21	2.10
964	981	4.260170	TCGAGGGACTAGTAGTTGAGAAC	58.740	47.826	3.85	0.00	41.55	3.01
1221	1252	1.667830	GCTGCAGTTGTCGTAGGCA	60.668	57.895	16.64	0.00	45.30	4.75
1492	1523	3.114616	CGTCAAGCCAGCCACGAG	61.115	66.667	0.00	0.00	34.06	4.18
1508	1539	2.416547	CCCAACAACATACAGAGAAGCG	59.583	50.000	0.00	0.00	0.00	4.68
1589	1620	4.400529	TCATTTTATAGCTGAGGTCGCA	57.599	40.909	0.00	0.00	0.00	5.10
1590	1621	4.811557	AGTTCATTTTATAGCTGAGGTCGC	59.188	41.667	0.00	0.00	0.00	5.19
1605	1636	1.285078	GGCCCACCTCCTAGTTCATTT	59.715	52.381	0.00	0.00	0.00	2.32
1608	1639	0.714180	TAGGCCCACCTCCTAGTTCA	59.286	55.000	0.00	0.00	46.34	3.18
1626	1657	7.622893	ATGTGTTGTGCATATGTGTGTATTA	57.377	32.000	4.29	0.00	0.00	0.98
1635	1666	7.852454	GTGTTGAGTATATGTGTTGTGCATATG	59.148	37.037	0.00	0.00	39.19	1.78
1714	1750	1.713830	GCCTACGGCGTCATTTGAC	59.286	57.895	19.21	0.46	39.62	3.18
1744	1780	7.560991	ACTTCCCAACAATTTGCAGATATCATA	59.439	33.333	5.32	0.00	0.00	2.15
1782	1818	1.405105	CCCTTGGCCATATTCGTGTTG	59.595	52.381	6.09	0.00	0.00	3.33
1875	1911	1.716826	CGTCTCGGCTGTCTACCTCC	61.717	65.000	0.00	0.00	0.00	4.30
1923	1959	1.203112	AGGAGCTCTCTTGTCCTGTGA	60.203	52.381	14.64	0.00	39.36	3.58
2085	2121	3.125573	CTCGTCGCTCCACCTCGA	61.126	66.667	0.00	0.00	0.00	4.04
2179	2215	1.153289	CTGCGGCACTATGGAGCTT	60.153	57.895	0.00	0.00	0.00	3.74
2239	2275	4.132336	GTCTTCATATGCATGCTCCTTGA	58.868	43.478	20.33	13.27	31.73	3.02
2241	2277	3.881688	GTGTCTTCATATGCATGCTCCTT	59.118	43.478	20.33	3.81	31.73	3.36
2300	2336	2.360801	GTGCTCTCCAGTATCTCACTCC	59.639	54.545	0.00	0.00	34.26	3.85
2356	2393	1.306141	TGCCTCGGATGGTTCTCCT	60.306	57.895	0.00	0.00	32.77	3.69
2390	2427	0.600255	GCCGCTACGCCTGTTGATAT	60.600	55.000	0.00	0.00	0.00	1.63

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.