AutoCloner

Multiple sequence alignment - TraesCS1B01G053200

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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	TraesCS1B01G053200	chr1B	100.000	2570	0	0	1	2570	33947773	33945204	0.000000e+00	4747.0
1	TraesCS1B01G053200	chr1B	87.423	970	76	30	1	926	33922559	33921592	0.000000e+00	1074.0
2	TraesCS1B01G053200	chr1B	84.995	1093	114	23	930	2012	33921619	33920567	0.000000e+00	1064.0
3	TraesCS1B01G053200	chr1B	78.627	641	92	27	996	1614	33857392	33856775	1.440000e-102	383.0
4	TraesCS1B01G053200	chr1B	89.552	201	9	5	449	645	33963062	33962870	7.100000e-61	244.0
5	TraesCS1B01G053200	chr1B	93.805	113	7	0	707	819	33962690	33962578	1.220000e-38	171.0
6	TraesCS1B01G053200	chr1B	89.535	86	9	0	816	901	33962299	33962214	2.700000e-20	110.0
7	TraesCS1B01G053200	chr1B	85.714	77	9	2	1120	1195	513538739	513538814	2.120000e-11	80.5
8	TraesCS1B01G053200	chr1D	89.855	2612	173	37	1	2567	20060888	20063452	0.000000e+00	3271.0
9	TraesCS1B01G053200	chr1D	81.215	1416	174	45	939	2328	20184941	20186290	0.000000e+00	1057.0
10	TraesCS1B01G053200	chr1D	89.024	492	21	18	466	926	20184478	20184967	1.710000e-161	579.0
11	TraesCS1B01G053200	chr1D	84.805	487	49	10	1	472	20182492	20182968	1.390000e-127	466.0
12	TraesCS1B01G053200	chr1D	79.360	625	92	22	998	1603	20193407	20194013	3.080000e-109	405.0
13	TraesCS1B01G053200	chr1A	86.454	2104	175	39	1	2063	22283982	22281948	0.000000e+00	2206.0
14	TraesCS1B01G053200	chr1A	79.274	661	85	29	997	1617	22271964	22271316	5.120000e-112	414.0
15	TraesCS1B01G053200	chr1A	79.950	399	47	19	1152	1547	22074513	22074145	1.960000e-66	263.0
16	TraesCS1B01G053200	chr1A	78.616	159	21	9	1000	1156	22076886	22076739	2.720000e-15	93.5
17	TraesCS1B01G053200	chr1A	87.179	78	7	3	1120	1195	483025252	483025328	4.560000e-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	TraesCS1B01G053200	chr1B	33945204	33947773	2569	True	4747.000000	4747	100.000000	1	2570	1	chr1B.!!$R2	2569
1	TraesCS1B01G053200	chr1B	33920567	33922559	1992	True	1069.000000	1074	86.209000	1	2012	2	chr1B.!!$R3	2011
2	TraesCS1B01G053200	chr1B	33856775	33857392	617	True	383.000000	383	78.627000	996	1614	1	chr1B.!!$R1	618
3	TraesCS1B01G053200	chr1D	20060888	20063452	2564	False	3271.000000	3271	89.855000	1	2567	1	chr1D.!!$F1	2566
4	TraesCS1B01G053200	chr1D	20182492	20186290	3798	False	700.666667	1057	85.014667	1	2328	3	chr1D.!!$F3	2327
5	TraesCS1B01G053200	chr1D	20193407	20194013	606	False	405.000000	405	79.360000	998	1603	1	chr1D.!!$F2	605
6	TraesCS1B01G053200	chr1A	22281948	22283982	2034	True	2206.000000	2206	86.454000	1	2063	1	chr1A.!!$R2	2062
7	TraesCS1B01G053200	chr1A	22271316	22271964	648	True	414.000000	414	79.274000	997	1617	1	chr1A.!!$R1	620

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
96	97	1.035139	GGCATTTGGAGTAGGCATGG	58.965	55.000	0.00	0.0	0.00	3.66	F
719	2299	1.273048	GAACCACTTGCATTGCATCCA	59.727	47.619	12.95	0.0	38.76	3.41	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1358	2985	1.129437	GTTTCTTGATCGCTGCTGTCC	59.871	52.381	0.0	0.0	0.0	4.02	R
1623	3269	2.057137	ACTGCCAAAGAGCACAAAGA	57.943	45.000	0.0	0.0	38.0	2.52	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	5.365021	AAGTGCAGAAGGTATTAGATGCT	57.635	39.130	0.00	0.00	34.80	3.79
27	28	4.804108	CAGAAGGTATTAGATGCTCCTCG	58.196	47.826	0.00	0.00	0.00	4.63
68	69	6.959639	ACAAGAAGAGATCCAGAGATACTC	57.040	41.667	0.00	0.00	30.90	2.59
88	89	3.499338	TCTTTCATGTGGCATTTGGAGT	58.501	40.909	0.00	0.00	0.00	3.85
96	97	1.035139	GGCATTTGGAGTAGGCATGG	58.965	55.000	0.00	0.00	0.00	3.66
166	167	7.169035	TCGGTGCGATACTAATTTAATTGTC	57.831	36.000	0.00	0.00	0.00	3.18
228	239	3.221771	CCAAAACTGATGGGACTGACAA	58.778	45.455	0.00	0.00	34.15	3.18
353	368	8.628882	AAAAAGGAATAGAAAGTTTTGACACG	57.371	30.769	0.00	0.00	0.00	4.49
381	407	6.990908	ACCATGTCATAATCTCATCTCAGA	57.009	37.500	0.00	0.00	0.00	3.27
392	418	5.833406	TCTCATCTCAGATCTCAACTGAC	57.167	43.478	0.00	0.00	39.10	3.51
396	422	3.360867	TCTCAGATCTCAACTGACCCTC	58.639	50.000	0.00	0.00	39.10	4.30
444	480	5.069251	ACTTCTTGATATCCTTCCTACCACG	59.931	44.000	0.00	0.00	0.00	4.94
448	484	6.608405	TCTTGATATCCTTCCTACCACGTTTA	59.392	38.462	0.00	0.00	0.00	2.01
461	497	5.108385	ACCACGTTTAAAAGATTCTGCTG	57.892	39.130	8.18	0.00	0.00	4.41
478	2030	4.889409	TCTGCTGTTGAAATTTTCAGTCCT	59.111	37.500	11.41	0.00	41.38	3.85
580	2134	2.755103	GTCAAACCTGAATAAGCCCCTG	59.245	50.000	0.00	0.00	31.88	4.45
604	2166	5.635700	GTGGTTGATCTGAACTGAACTACTC	59.364	44.000	0.00	0.00	0.00	2.59
719	2299	1.273048	GAACCACTTGCATTGCATCCA	59.727	47.619	12.95	0.00	38.76	3.41
798	2401	3.005367	AGTTGTGCATTTCTTTAACCGGG	59.995	43.478	6.32	0.00	0.00	5.73
881	2484	5.454062	TGGTGCAAATGGCCTATAAATACT	58.546	37.500	3.32	0.00	43.89	2.12
926	2529	6.357579	TCTTCATCAGCTTCTTCTTCTTCT	57.642	37.500	0.00	0.00	0.00	2.85
927	2530	6.767456	TCTTCATCAGCTTCTTCTTCTTCTT	58.233	36.000	0.00	0.00	0.00	2.52
928	2531	6.873076	TCTTCATCAGCTTCTTCTTCTTCTTC	59.127	38.462	0.00	0.00	0.00	2.87
929	2532	6.357579	TCATCAGCTTCTTCTTCTTCTTCT	57.642	37.500	0.00	0.00	0.00	2.85
930	2533	6.767456	TCATCAGCTTCTTCTTCTTCTTCTT	58.233	36.000	0.00	0.00	0.00	2.52
931	2534	7.222872	TCATCAGCTTCTTCTTCTTCTTCTTT	58.777	34.615	0.00	0.00	0.00	2.52
932	2535	7.718753	TCATCAGCTTCTTCTTCTTCTTCTTTT	59.281	33.333	0.00	0.00	0.00	2.27
933	2536	7.872113	TCAGCTTCTTCTTCTTCTTCTTTTT	57.128	32.000	0.00	0.00	0.00	1.94
934	2537	7.924940	TCAGCTTCTTCTTCTTCTTCTTTTTC	58.075	34.615	0.00	0.00	0.00	2.29
935	2538	7.772757	TCAGCTTCTTCTTCTTCTTCTTTTTCT	59.227	33.333	0.00	0.00	0.00	2.52
936	2539	8.404765	CAGCTTCTTCTTCTTCTTCTTTTTCTT	58.595	33.333	0.00	0.00	0.00	2.52
937	2540	8.620416	AGCTTCTTCTTCTTCTTCTTTTTCTTC	58.380	33.333	0.00	0.00	0.00	2.87
978	2581	6.629128	TCATCATCTTCAGAGTTTCAGAGAC	58.371	40.000	0.00	0.00	0.00	3.36
1061	2664	1.523484	TGCTTCTGCTTGTGTCGCA	60.523	52.632	0.00	0.00	40.48	5.10
1161	2782	4.353437	GACCGCGTGTTCCCGTCT	62.353	66.667	4.92	0.00	0.00	4.18
1377	3004	1.442769	GGACAGCAGCGATCAAGAAA	58.557	50.000	0.00	0.00	0.00	2.52
1396	3023	2.106131	ACAACGACAGCAGCGACA	59.894	55.556	0.00	0.00	0.00	4.35
1398	3025	0.880278	ACAACGACAGCAGCGACAAT	60.880	50.000	0.00	0.00	0.00	2.71
1461	3103	1.255667	ACCCACCTTGCGACGAGTAT	61.256	55.000	0.00	0.00	0.00	2.12
1592	3238	0.773700	CCCCATCTCCCCCTATTGCT	60.774	60.000	0.00	0.00	0.00	3.91
1617	3263	8.133024	TGGGATTTTGCAGAATAGTACAATTT	57.867	30.769	1.88	0.00	0.00	1.82
1680	3333	9.661563	TTAAACCCTTTTTCTTCTTCTTTTTCC	57.338	29.630	0.00	0.00	0.00	3.13
1738	3395	3.378512	AGATGAGTGCCTGGAAGACATA	58.621	45.455	0.00	0.00	34.07	2.29
1858	3527	4.776795	ATTTGTCCGGTTATTGTTGACC	57.223	40.909	0.00	0.00	0.00	4.02
1863	3532	4.401519	TGTCCGGTTATTGTTGACCAAAAA	59.598	37.500	0.00	0.00	36.44	1.94
1928	3597	6.421801	GGCTCAACATGTAATTATCCAATTGC	59.578	38.462	0.00	0.00	37.29	3.56
1974	3643	0.251916	TTATCAGTTGGTGGCCCGAG	59.748	55.000	0.00	0.00	0.00	4.63
1986	3655	1.446366	GCCCGAGGTCATCTTACCC	59.554	63.158	0.00	0.00	40.71	3.69
2006	3675	3.621715	CCCCTTTTAGTATGTGCTCGTTC	59.378	47.826	0.00	0.00	0.00	3.95
2067	3737	5.765677	TGGAACCAAAAATTATCGTGTGAGA	59.234	36.000	0.00	0.00	0.00	3.27
2076	3746	6.910536	AATTATCGTGTGAGATCCAAGTTC	57.089	37.500	0.00	0.00	32.39	3.01
2126	3797	8.433421	TCTACATTAAACCTGGAAATTCGATC	57.567	34.615	0.00	0.00	0.00	3.69
2127	3798	8.265055	TCTACATTAAACCTGGAAATTCGATCT	58.735	33.333	0.00	0.00	0.00	2.75
2128	3799	9.542462	CTACATTAAACCTGGAAATTCGATCTA	57.458	33.333	0.00	0.00	0.00	1.98
2219	3891	0.815095	GGCCTTCCAATAAACGGTGG	59.185	55.000	0.00	0.00	36.13	4.61
2252	3925	9.675464	TCAAATATTTAGGAAACGTAGGACATT	57.325	29.630	0.00	0.00	0.00	2.71
2395	4074	6.073447	TCTTTTAATTCTCTATGCCCCACA	57.927	37.500	0.00	0.00	0.00	4.17
2445	4124	1.072505	GACGAAGCCACCCTCCAAA	59.927	57.895	0.00	0.00	0.00	3.28
2450	4129	2.812613	CGAAGCCACCCTCCAAACTTTA	60.813	50.000	0.00	0.00	0.00	1.85
2451	4130	3.227614	GAAGCCACCCTCCAAACTTTAA	58.772	45.455	0.00	0.00	0.00	1.52
2455	4134	2.158370	CCACCCTCCAAACTTTAACCCT	60.158	50.000	0.00	0.00	0.00	4.34
2490	4169	6.459670	TTTTGTTCAAGTTAGGAGTTTCCC	57.540	37.500	0.00	0.00	37.19	3.97
2500	4179	3.502123	AGGAGTTTCCCGAACATGAAA	57.498	42.857	0.00	0.00	40.84	2.69
2533	4212	6.610075	AAAACAAGACATGGCTATGGATTT	57.390	33.333	15.11	6.29	38.66	2.17

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
22	23	6.372103	TGTTTTCCTTAATATTTTCGCGAGGA	59.628	34.615	9.59	6.36	0.00	3.71
27	28	9.620660	TCTTCTTGTTTTCCTTAATATTTTCGC	57.379	29.630	0.00	0.00	0.00	4.70
68	69	3.947910	ACTCCAAATGCCACATGAAAG	57.052	42.857	0.00	0.00	0.00	2.62
88	89	3.452990	TCTTATCAAACGTCCCATGCCTA	59.547	43.478	0.00	0.00	0.00	3.93
96	97	5.741388	AATGATGCTCTTATCAAACGTCC	57.259	39.130	0.00	0.00	40.21	4.79
228	239	5.471456	CACTGAATCCTGCAGAGTTTACTTT	59.529	40.000	17.39	0.00	36.86	2.66
288	299	2.366533	TGGTACTTTGTGCCAACGAAA	58.633	42.857	5.09	0.00	44.72	3.46
296	307	6.838198	TTATGACGATATGGTACTTTGTGC	57.162	37.500	0.00	0.00	0.00	4.57
339	354	5.473796	TGGTACTTCGTGTCAAAACTTTC	57.526	39.130	0.00	0.00	0.00	2.62
353	368	8.363390	TGAGATGAGATTATGACATGGTACTTC	58.637	37.037	0.00	0.00	0.00	3.01
381	407	3.073650	AGCAAAAGAGGGTCAGTTGAGAT	59.926	43.478	0.00	0.00	0.00	2.75
392	418	6.376581	ACTTCATATCAGAAAGCAAAAGAGGG	59.623	38.462	0.00	0.00	0.00	4.30
396	422	6.307318	GTGCACTTCATATCAGAAAGCAAAAG	59.693	38.462	10.32	0.00	39.05	2.27
424	451	4.939052	ACGTGGTAGGAAGGATATCAAG	57.061	45.455	4.83	0.00	0.00	3.02
448	484	8.721019	TGAAAATTTCAACAGCAGAATCTTTT	57.279	26.923	5.87	0.00	36.59	2.27
461	497	7.333174	TGTTTTGGAAGGACTGAAAATTTCAAC	59.667	33.333	9.85	6.90	39.58	3.18
478	2030	4.503714	AGAGTCCTGTCTTGTTTTGGAA	57.496	40.909	0.00	0.00	0.00	3.53
580	2134	5.542779	AGTAGTTCAGTTCAGATCAACCAC	58.457	41.667	0.00	0.00	0.00	4.16
694	2257	0.877071	CAATGCAAGTGGTTCGAGCT	59.123	50.000	0.00	0.00	0.00	4.09
719	2299	1.066587	GAGTATCGCTGCTCGCCTT	59.933	57.895	0.00	0.00	38.27	4.35
745	2348	6.160576	AGAGATAGATGAAGAAGGAAGCAC	57.839	41.667	0.00	0.00	0.00	4.40
753	2356	5.079998	TGGCCCTAGAGATAGATGAAGAA	57.920	43.478	0.00	0.00	0.00	2.52
881	2484	2.069465	AAACGCATCAAACCGCAGCA	62.069	50.000	0.00	0.00	0.00	4.41
933	2536	9.618890	TGATGAAGAAGAAGAAAAAGAAGAAGA	57.381	29.630	0.00	0.00	0.00	2.87
936	2539	9.790344	AGATGATGAAGAAGAAGAAAAAGAAGA	57.210	29.630	0.00	0.00	0.00	2.87
942	2545	9.217278	CTCTGAAGATGATGAAGAAGAAGAAAA	57.783	33.333	0.00	0.00	0.00	2.29
953	2556	7.095910	GTCTCTGAAACTCTGAAGATGATGAA	58.904	38.462	0.00	0.00	0.00	2.57
964	2567	3.857549	TGATCGGTCTCTGAAACTCTG	57.142	47.619	0.00	0.00	0.00	3.35
978	2581	1.672881	GCTCTGAACCCAATTGATCGG	59.327	52.381	7.12	7.58	0.00	4.18
1260	2881	1.447838	GCCGATGGCGAACTCAAGA	60.448	57.895	0.00	0.00	39.62	3.02
1358	2985	1.129437	GTTTCTTGATCGCTGCTGTCC	59.871	52.381	0.00	0.00	0.00	4.02
1377	3004	2.106131	TCGCTGCTGTCGTTGTGT	59.894	55.556	0.00	0.00	0.00	3.72
1410	3052	1.743623	CCACAGCCCGCGTTTCATA	60.744	57.895	4.92	0.00	0.00	2.15
1592	3238	7.716799	AATTGTACTATTCTGCAAAATCCCA	57.283	32.000	0.00	0.00	0.00	4.37
1623	3269	2.057137	ACTGCCAAAGAGCACAAAGA	57.943	45.000	0.00	0.00	38.00	2.52
1657	3310	7.496346	AGGAAAAAGAAGAAGAAAAAGGGTT	57.504	32.000	0.00	0.00	0.00	4.11
1713	3366	3.954904	GTCTTCCAGGCACTCATCTACTA	59.045	47.826	0.00	0.00	34.60	1.82
1738	3395	6.814954	AAGAGATGACTTATGTACCATGGT	57.185	37.500	23.55	23.55	0.00	3.55
1805	3470	2.921834	ACCTGAGGTAAGCTCTGGTA	57.078	50.000	0.07	0.00	46.55	3.25
1950	3619	3.299503	GGGCCACCAACTGATAAATCAT	58.700	45.455	4.39	0.00	34.67	2.45
1974	3643	6.766467	CACATACTAAAAGGGGTAAGATGACC	59.234	42.308	0.00	0.00	38.93	4.02
1986	3655	6.035758	GGTAAGAACGAGCACATACTAAAAGG	59.964	42.308	0.00	0.00	0.00	3.11
2136	3808	9.717942	CATGTTAAATGGTTTTAGAATTCCCAA	57.282	29.630	0.65	0.00	0.00	4.12
2169	3841	6.365520	ACAAATCACTCTTGGAAACTAGGTT	58.634	36.000	0.00	0.00	33.71	3.50
2365	4044	9.125026	GGGCATAGAGAATTAAAAGAAGATGAA	57.875	33.333	0.00	0.00	0.00	2.57
2366	4045	7.721399	GGGGCATAGAGAATTAAAAGAAGATGA	59.279	37.037	0.00	0.00	0.00	2.92
2370	4049	6.603201	TGTGGGGCATAGAGAATTAAAAGAAG	59.397	38.462	0.00	0.00	0.00	2.85
2373	4052	6.966534	ATGTGGGGCATAGAGAATTAAAAG	57.033	37.500	0.00	0.00	35.74	2.27
2379	4058	4.803329	AGAAATGTGGGGCATAGAGAAT	57.197	40.909	0.00	0.00	36.67	2.40
2418	4097	2.433436	GGTGGCTTCGTCTACCAAAAT	58.567	47.619	0.00	0.00	37.52	1.82
2450	4129	8.927675	TGAACAAAAATACTACATACAGGGTT	57.072	30.769	0.00	0.00	0.00	4.11
2451	4130	8.927675	TTGAACAAAAATACTACATACAGGGT	57.072	30.769	0.00	0.00	0.00	4.34
2506	4185	4.949856	CCATAGCCATGTCTTGTTTTAGGT	59.050	41.667	0.00	0.00	0.00	3.08
2507	4186	5.192927	TCCATAGCCATGTCTTGTTTTAGG	58.807	41.667	0.00	0.00	0.00	2.69
2519	4198	3.319972	CAGGTTCCAAATCCATAGCCATG	59.680	47.826	0.00	0.00	0.00	3.66

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.