AutoCloner

Multiple sequence alignment - TraesCS1D01G312400

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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	TraesCS1D01G312400	chr1D	100.000	2650	0	0	1	2650	408251210	408248561	0.000000e+00	4894
1	TraesCS1D01G312400	chr1B	94.611	1763	71	11	892	2650	548976149	548974407	0.000000e+00	2708
2	TraesCS1D01G312400	chr1B	92.822	404	23	1	490	893	548976609	548976212	4.920000e-162	580
3	TraesCS1D01G312400	chr2A	94.118	1530	57	11	892	2419	40830244	40828746	0.000000e+00	2296
4	TraesCS1D01G312400	chr2A	86.290	868	72	17	1805	2650	179296849	179297691	0.000000e+00	900
5	TraesCS1D01G312400	chr2A	91.787	414	21	3	480	893	40830704	40830304	4.950000e-157	564
6	TraesCS1D01G312400	chr2A	86.866	335	43	1	1252	1586	179270271	179269938	8.960000e-100	374
7	TraesCS1D01G312400	chr2A	94.894	235	6	3	2417	2650	40828665	40828436	1.940000e-96	363
8	TraesCS1D01G312400	chr2A	86.817	311	11	11	81	361	40832311	40832621	1.180000e-83	320
9	TraesCS1D01G312400	chr2A	97.561	82	2	0	1	82	40832126	40832207	9.890000e-30	141
10	TraesCS1D01G312400	chr1A	95.165	972	37	5	893	1862	504251284	504250321	0.000000e+00	1526
11	TraesCS1D01G312400	chr1A	93.297	910	36	12	1	893	504252249	504251348	0.000000e+00	1319
12	TraesCS1D01G312400	chr1A	91.627	836	31	6	1849	2650	504250303	504249473	0.000000e+00	1120
13	TraesCS1D01G312400	chr2D	86.290	868	69	23	1805	2650	170613338	170612499	0.000000e+00	898
14	TraesCS1D01G312400	chr2D	88.235	340	29	4	1223	1551	170626830	170627169	1.910000e-106	396
15	TraesCS1D01G312400	chr2B	85.421	878	68	23	1805	2650	226700511	226701360	0.000000e+00	857
16	TraesCS1D01G312400	chr2B	84.185	607	77	12	993	1586	226686523	226685923	2.960000e-159	571
17	TraesCS1D01G312400	chr7D	87.069	116	12	2	67	179	72938309	72938424	7.700000e-26	128

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	TraesCS1D01G312400	chr1D	408248561	408251210	2649	True	4894.000000	4894	100.000000	1	2650	1	chr1D.!!$R1	2649
1	TraesCS1D01G312400	chr1B	548974407	548976609	2202	True	1644.000000	2708	93.716500	490	2650	2	chr1B.!!$R1	2160
2	TraesCS1D01G312400	chr2A	40828436	40830704	2268	True	1074.333333	2296	93.599667	480	2650	3	chr2A.!!$R2	2170
3	TraesCS1D01G312400	chr2A	179296849	179297691	842	False	900.000000	900	86.290000	1805	2650	1	chr2A.!!$F1	845
4	TraesCS1D01G312400	chr1A	504249473	504252249	2776	True	1321.666667	1526	93.363000	1	2650	3	chr1A.!!$R1	2649
5	TraesCS1D01G312400	chr2D	170612499	170613338	839	True	898.000000	898	86.290000	1805	2650	1	chr2D.!!$R1	845
6	TraesCS1D01G312400	chr2B	226700511	226701360	849	False	857.000000	857	85.421000	1805	2650	1	chr2B.!!$F1	845
7	TraesCS1D01G312400	chr2B	226685923	226686523	600	True	571.000000	571	84.185000	993	1586	1	chr2B.!!$R1	593

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
113	114	0.251922	ATGTGGGCTGCACCATTCTT	60.252	50.0	12.03	0.0	43.59	2.52	F
964	1049	0.671251	GGTGTTCGTTCAATTGGCCA	59.329	50.0	0.00	0.0	0.00	5.36	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1113	1201	0.043940	AGCTTCACCTCCATCCTCCT	59.956	55.0	0.00	0.00	0.00	3.69	R
2039	2170	1.574702	GGAAGGCAGTACGGTTGTGC	61.575	60.0	5.98	5.98	36.42	4.57	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
27	28	9.760660	GCAATGTTTCTTTCTGTTGTATACTAG	57.239	33.333	4.17	0.72	0.00	2.57
98	99	4.270566	GCATCTAGCTGAGAACAGAATGTG	59.729	45.833	0.00	0.00	46.09	3.21
113	114	0.251922	ATGTGGGCTGCACCATTCTT	60.252	50.000	12.03	0.00	43.59	2.52
135	136	7.684670	TCTTATTATTGCTAAACTGTTCTGCG	58.315	34.615	11.25	0.00	0.00	5.18
149	150	4.183865	TGTTCTGCGATGTCTAAGGAATG	58.816	43.478	0.00	0.00	0.00	2.67
151	152	4.046938	TCTGCGATGTCTAAGGAATGTC	57.953	45.455	0.00	0.00	0.00	3.06
152	153	2.791560	CTGCGATGTCTAAGGAATGTCG	59.208	50.000	0.00	0.00	0.00	4.35
222	239	5.596845	TGTTCTGTAATTTTCAAACAGGGC	58.403	37.500	5.66	1.20	40.79	5.19
271	288	1.171308	GGCAGTGCATCATGTTGTCT	58.829	50.000	18.61	2.59	0.00	3.41
337	354	7.966753	ACATTGATTCATCTGTTCAAATTCGAG	59.033	33.333	0.00	0.00	33.45	4.04
338	355	6.426980	TGATTCATCTGTTCAAATTCGAGG	57.573	37.500	0.00	0.00	0.00	4.63
547	565	6.073819	CCATGATTTTCAAGTTCCCGTTTTTC	60.074	38.462	0.00	0.00	0.00	2.29
559	577	2.956333	CCCGTTTTTCCTTTCCAAGTCT	59.044	45.455	0.00	0.00	0.00	3.24
647	665	1.628340	TGAGTTGGTAGTGGTGGATGG	59.372	52.381	0.00	0.00	0.00	3.51
654	672	2.357154	GGTAGTGGTGGATGGAATTGCT	60.357	50.000	0.00	0.00	0.00	3.91
675	693	2.040464	GGATGGAGCAGGGGGAGA	60.040	66.667	0.00	0.00	0.00	3.71
676	694	1.463018	GGATGGAGCAGGGGGAGAT	60.463	63.158	0.00	0.00	0.00	2.75
728	746	1.066143	GGGTGATGTGGTTCGTCTGAT	60.066	52.381	0.00	0.00	33.55	2.90
729	747	2.002586	GGTGATGTGGTTCGTCTGATG	58.997	52.381	0.00	0.00	33.55	3.07
730	748	2.002586	GTGATGTGGTTCGTCTGATGG	58.997	52.381	0.00	0.00	33.55	3.51
731	749	1.899142	TGATGTGGTTCGTCTGATGGA	59.101	47.619	0.00	0.00	33.55	3.41
732	750	2.094026	TGATGTGGTTCGTCTGATGGAG	60.094	50.000	0.00	0.00	33.55	3.86
733	751	1.627864	TGTGGTTCGTCTGATGGAGA	58.372	50.000	0.00	0.00	0.00	3.71
734	752	2.179427	TGTGGTTCGTCTGATGGAGAT	58.821	47.619	0.00	0.00	31.63	2.75
760	778	0.678950	AACAAGGCCGGACAAAATGG	59.321	50.000	11.69	0.00	0.00	3.16
874	892	3.497031	GTTAACTCAGGCGGCGGC	61.497	66.667	27.24	27.24	38.90	6.53
887	905	2.709883	GGCGGCATAAAGGCAAGCA	61.710	57.895	3.07	0.00	44.47	3.91
912	997	3.153919	GTTTGGTTCTATTGCCTGGACA	58.846	45.455	0.00	0.00	0.00	4.02
916	1001	2.027192	GGTTCTATTGCCTGGACACTGA	60.027	50.000	0.00	0.00	0.00	3.41
932	1017	6.441924	TGGACACTGATCTAGAGATTTTCCTT	59.558	38.462	0.00	0.00	34.37	3.36
933	1018	7.619698	TGGACACTGATCTAGAGATTTTCCTTA	59.380	37.037	0.00	0.00	34.37	2.69
961	1046	3.371168	CACAAGGTGTTCGTTCAATTGG	58.629	45.455	5.42	0.00	0.00	3.16
964	1049	0.671251	GGTGTTCGTTCAATTGGCCA	59.329	50.000	0.00	0.00	0.00	5.36
1058	1146	4.009002	TGCAAATGTAGCTAGTTCATGCA	58.991	39.130	13.89	13.89	0.00	3.96
1199	1287	2.904866	GTGGTTGACAAGGCGCCA	60.905	61.111	31.54	3.61	0.00	5.69
1268	1356	4.357947	GTGGCTGACGAGACGGCA	62.358	66.667	8.43	0.00	45.13	5.69
1361	1449	3.318275	GTGGCATCTTCTCGTACCATAGA	59.682	47.826	0.00	0.00	0.00	1.98
1547	1635	0.607489	AAGTCTTCAAGCCGCTGCAT	60.607	50.000	2.05	0.00	41.13	3.96
1601	1699	9.230122	TCATTGTTGCTAAGTCTCATTAAATCA	57.770	29.630	0.00	0.00	0.00	2.57
1606	1704	9.604626	GTTGCTAAGTCTCATTAAATCATATGC	57.395	33.333	0.00	0.00	0.00	3.14
1607	1705	8.907222	TGCTAAGTCTCATTAAATCATATGCA	57.093	30.769	0.00	0.00	0.00	3.96
1608	1706	9.341078	TGCTAAGTCTCATTAAATCATATGCAA	57.659	29.630	0.00	0.00	0.00	4.08
1644	1742	5.806366	ACCGTGGTAGTAAATTATGCAAC	57.194	39.130	0.00	0.00	0.00	4.17
1686	1784	9.696917	AGTTTTGTATGCTTTCTCCTTAAAATG	57.303	29.630	0.00	0.00	0.00	2.32
1754	1852	4.586841	ACGGAGCTCATAGAAGATTTAGCT	59.413	41.667	17.19	0.00	42.70	3.32
1998	2129	2.568623	TTCCTTCTTGGCAGACTTCC	57.431	50.000	0.00	0.00	35.26	3.46
2089	2220	8.119226	GCAGTATTCATTCTACAAGTCATTGTC	58.881	37.037	0.00	0.00	46.90	3.18
2260	2452	6.402442	GCATGCAGTTTTTCTTTTGTTTCAGT	60.402	34.615	14.21	0.00	0.00	3.41
2317	2518	8.664079	AGTTGGATGGCTTATAATGTCTTCTAT	58.336	33.333	0.00	0.00	0.00	1.98
2468	2754	9.875691	GTTGACAGCATCCATATGTTCTATATA	57.124	33.333	1.24	0.00	35.38	0.86
2542	2839	6.463995	TCAAGTTTTGTTGCCTTCACTAAT	57.536	33.333	0.00	0.00	0.00	1.73
2543	2840	7.575414	TCAAGTTTTGTTGCCTTCACTAATA	57.425	32.000	0.00	0.00	0.00	0.98
2544	2841	7.422399	TCAAGTTTTGTTGCCTTCACTAATAC	58.578	34.615	0.00	0.00	0.00	1.89
2545	2842	6.952773	AGTTTTGTTGCCTTCACTAATACA	57.047	33.333	0.00	0.00	0.00	2.29
2546	2843	6.970484	AGTTTTGTTGCCTTCACTAATACAG	58.030	36.000	0.00	0.00	0.00	2.74

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
20	21	7.636036	AGCTCCTTCTAGTTCCTCTAGTATA	57.364	40.000	0.00	0.00	44.59	1.47
27	28	3.100671	TGGAAGCTCCTTCTAGTTCCTC	58.899	50.000	7.36	0.00	40.07	3.71
98	99	4.797275	GCAATAATAAGAATGGTGCAGCCC	60.797	45.833	14.36	0.00	36.04	5.19
113	114	7.279981	ACATCGCAGAACAGTTTAGCAATAATA	59.720	33.333	10.43	0.00	43.58	0.98
135	136	5.746245	CAGAAGACGACATTCCTTAGACATC	59.254	44.000	0.00	0.00	0.00	3.06
195	212	8.143835	CCCTGTTTGAAAATTACAGAACAGATT	58.856	33.333	22.66	0.00	43.95	2.40
222	239	4.005650	TGCACCTCAAAGATTGCTAGAAG	58.994	43.478	0.00	0.00	35.91	2.85
294	311	5.500234	TCAATGTCATTGAAAGGAGTAGGG	58.500	41.667	23.08	0.00	45.57	3.53
337	354	9.744468	AAGTACAAATGTGTTGTAAATTTCTCC	57.256	29.630	0.00	0.00	39.30	3.71
369	386	9.016438	TCTAACCAGGGTAATTTTCATGTTAAC	57.984	33.333	0.00	0.00	0.00	2.01
376	393	8.485578	AACAATTCTAACCAGGGTAATTTTCA	57.514	30.769	0.00	0.00	0.00	2.69
377	394	8.803235	AGAACAATTCTAACCAGGGTAATTTTC	58.197	33.333	0.00	2.93	38.49	2.29
427	445	4.380867	GCACCTTACCCAGACAATCAAATG	60.381	45.833	0.00	0.00	0.00	2.32
501	519	9.231297	TCATGGTTCCAAAATTGTAAAACAAAA	57.769	25.926	0.00	0.00	41.96	2.44
504	522	8.970859	AATCATGGTTCCAAAATTGTAAAACA	57.029	26.923	0.00	0.57	0.00	2.83
522	540	4.519540	AACGGGAACTTGAAAATCATGG	57.480	40.909	0.00	0.00	0.00	3.66
559	577	2.297880	TCAACTTCTACAACAGCCGCTA	59.702	45.455	0.00	0.00	0.00	4.26
647	665	2.883386	CTGCTCCATCCCTAAGCAATTC	59.117	50.000	0.00	0.00	44.79	2.17
654	672	1.385915	CCCCCTGCTCCATCCCTAA	60.386	63.158	0.00	0.00	0.00	2.69
675	693	0.393944	TCTAGCCCGAGACACGACAT	60.394	55.000	0.00	0.00	45.77	3.06
676	694	1.002990	TCTAGCCCGAGACACGACA	60.003	57.895	0.00	0.00	45.77	4.35
728	746	0.698238	CCTTGTTGGGTCCATCTCCA	59.302	55.000	0.00	0.00	0.00	3.86
729	747	0.681243	GCCTTGTTGGGTCCATCTCC	60.681	60.000	0.00	0.00	36.00	3.71
730	748	0.681243	GGCCTTGTTGGGTCCATCTC	60.681	60.000	0.00	0.00	36.00	2.75
731	749	1.384191	GGCCTTGTTGGGTCCATCT	59.616	57.895	0.00	0.00	36.00	2.90
732	750	2.046285	CGGCCTTGTTGGGTCCATC	61.046	63.158	0.00	0.00	36.00	3.51
733	751	2.035626	CGGCCTTGTTGGGTCCAT	59.964	61.111	0.00	0.00	36.00	3.41
734	752	4.278513	CCGGCCTTGTTGGGTCCA	62.279	66.667	0.00	0.00	36.00	4.02
760	778	2.660258	ATTGCGGCAGGATCGGTACC	62.660	60.000	0.16	0.16	0.00	3.34
874	892	2.704725	AACACGTGCTTGCCTTTATG	57.295	45.000	17.22	0.00	0.00	1.90
887	905	2.552315	CAGGCAATAGAACCAAACACGT	59.448	45.455	0.00	0.00	0.00	4.49
912	997	7.776030	TCGTCTAAGGAAAATCTCTAGATCAGT	59.224	37.037	0.00	0.00	32.75	3.41
916	1001	6.834451	TGGTCGTCTAAGGAAAATCTCTAGAT	59.166	38.462	0.00	0.00	36.07	1.98
932	1017	2.806608	GAACACCTTGTGGTCGTCTA	57.193	50.000	0.00	0.00	46.60	2.59
933	1018	3.680842	GAACACCTTGTGGTCGTCT	57.319	52.632	0.00	0.00	46.60	4.18
1058	1146	8.157476	AGATTTGTTGATAACCAGAGTAAGTGT	58.843	33.333	0.00	0.00	0.00	3.55
1113	1201	0.043940	AGCTTCACCTCCATCCTCCT	59.956	55.000	0.00	0.00	0.00	3.69
1268	1356	0.250901	ACAGAAGGAAATGCACCGCT	60.251	50.000	0.00	0.00	0.00	5.52
1314	1402	3.770040	CCGCACGATGTCCCCAGA	61.770	66.667	0.00	0.00	0.00	3.86
1388	1476	0.456221	TCTCCATTCGTCCTCGCTTC	59.544	55.000	0.00	0.00	36.96	3.86
1606	1704	4.873827	ACCACGGTTAGTATTGCACTATTG	59.126	41.667	0.00	0.00	39.51	1.90
1607	1705	5.093849	ACCACGGTTAGTATTGCACTATT	57.906	39.130	0.00	0.00	39.51	1.73
1608	1706	4.748277	ACCACGGTTAGTATTGCACTAT	57.252	40.909	0.00	0.00	39.51	2.12
1609	1707	4.706476	ACTACCACGGTTAGTATTGCACTA	59.294	41.667	0.00	0.00	38.80	2.74
1610	1708	3.512724	ACTACCACGGTTAGTATTGCACT	59.487	43.478	0.00	0.00	41.62	4.40
1611	1709	3.853475	ACTACCACGGTTAGTATTGCAC	58.147	45.455	0.00	0.00	0.00	4.57
1644	1742	4.096382	ACAAAACTCAGCAAGTGGTTAGTG	59.904	41.667	0.00	0.00	38.58	2.74
1686	1784	0.535335	TAGAACGATGGCCCAGTGAC	59.465	55.000	0.00	0.00	0.00	3.67
1754	1852	5.104109	ACAGCTTGGGATATACTTTTGGCTA	60.104	40.000	0.00	0.00	0.00	3.93
1998	2129	5.629079	AGAATAAGCCTTTTCAAGAACCG	57.371	39.130	0.00	0.00	0.00	4.44
2039	2170	1.574702	GGAAGGCAGTACGGTTGTGC	61.575	60.000	5.98	5.98	36.42	4.57
2260	2452	9.134734	GAATTGAATAAACTTGTTCGGCAATAA	57.865	29.630	0.00	0.00	36.36	1.40
2295	2488	6.881065	TGCATAGAAGACATTATAAGCCATCC	59.119	38.462	0.00	0.00	28.32	3.51
2317	2518	3.754965	AGTTAGAACAGGAATGCTTGCA	58.245	40.909	0.00	0.00	0.00	4.08
2468	2754	9.899661	TTGCATATACCAAGTTACTAACAGAAT	57.100	29.630	1.79	0.00	0.00	2.40

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.