AutoCloner

Multiple sequence alignment - TraesCS1A01G059400

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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	TraesCS1A01G059400	chr1A	100.000	2438	0	0	1	2438	40279184	40281621	0.000000e+00	4503.0
1	TraesCS1A01G059400	chr3A	89.866	2467	208	19	1	2438	157348886	157346433	0.000000e+00	3133.0
2	TraesCS1A01G059400	chr3A	91.910	1607	122	3	1	1607	290707882	290709480	0.000000e+00	2241.0
3	TraesCS1A01G059400	chr3A	91.667	864	60	7	1586	2438	290709501	290710363	0.000000e+00	1186.0
4	TraesCS1A01G059400	chr6A	92.653	1606	114	2	1	1606	396917490	396919091	0.000000e+00	2309.0
5	TraesCS1A01G059400	chr6A	92.357	1413	105	1	1	1413	496086000	496084591	0.000000e+00	2008.0
6	TraesCS1A01G059400	chr6A	90.930	882	66	4	1570	2438	396919096	396919976	0.000000e+00	1173.0
7	TraesCS1A01G059400	chr6A	89.145	866	82	7	1582	2438	307921949	307922811	0.000000e+00	1068.0
8	TraesCS1A01G059400	chr1D	91.615	1288	84	10	341	1616	266178919	266177644	0.000000e+00	1759.0
9	TraesCS1A01G059400	chr1D	93.023	344	18	5	1	343	266181182	266180844	4.680000e-137	497.0
10	TraesCS1A01G059400	chr5A	89.440	1250	92	12	351	1588	1136094	1134873	0.000000e+00	1541.0
11	TraesCS1A01G059400	chr5A	89.017	865	81	8	1585	2438	213047454	213046593	0.000000e+00	1059.0
12	TraesCS1A01G059400	chr5A	94.231	260	14	1	1	259	1136346	1136087	1.760000e-106	396.0
13	TraesCS1A01G059400	chr3B	90.275	1018	73	11	430	1445	610990893	610991886	0.000000e+00	1308.0
14	TraesCS1A01G059400	chr3B	90.377	1008	63	11	450	1445	680396031	680395046	0.000000e+00	1293.0
15	TraesCS1A01G059400	chr3B	88.734	861	80	15	1585	2438	817687040	817686190	0.000000e+00	1037.0
16	TraesCS1A01G059400	chr3B	88.591	859	82	14	1586	2438	817709850	817709002	0.000000e+00	1029.0
17	TraesCS1A01G059400	chr3B	96.296	54	2	0	1545	1598	784351732	784351785	3.340000e-14	89.8
18	TraesCS1A01G059400	chr4B	89.293	1018	82	10	430	1445	29156361	29157353	0.000000e+00	1251.0
19	TraesCS1A01G059400	chr4B	89.627	964	62	15	430	1379	2417339	2416400	0.000000e+00	1192.0
20	TraesCS1A01G059400	chr4B	90.877	570	41	7	1	561	649114125	649113558	0.000000e+00	754.0
21	TraesCS1A01G059400	chr2B	89.126	1030	74	12	430	1445	697786165	697787170	0.000000e+00	1247.0
22	TraesCS1A01G059400	chr2B	89.780	998	64	12	430	1413	110633136	110632163	0.000000e+00	1243.0
23	TraesCS1A01G059400	chr2B	89.827	865	74	8	1585	2438	318193380	318192519	0.000000e+00	1098.0
24	TraesCS1A01G059400	chr7B	88.488	860	89	10	1585	2438	681953719	681952864	0.000000e+00	1031.0
25	TraesCS1A01G059400	chr4A	87.529	425	43	4	2023	2438	735843852	735843429	1.310000e-132	483.0
26	TraesCS1A01G059400	chr4A	81.452	124	9	10	1388	1511	158101753	158101644	3.340000e-14	89.8
27	TraesCS1A01G059400	chr6B	86.818	440	45	7	2009	2438	558485368	558484932	1.700000e-131	479.0
28	TraesCS1A01G059400	chr6B	86.199	442	47	7	2009	2438	546205450	546205889	1.320000e-127	466.0
29	TraesCS1A01G059400	chr1B	87.864	412	41	4	2035	2437	441138472	441138061	2.190000e-130	475.0
30	TraesCS1A01G059400	chr1B	90.476	126	12	0	1320	1445	685391798	685391923	1.500000e-37	167.0
31	TraesCS1A01G059400	chr3D	86.468	436	49	5	2012	2438	24270120	24270554	1.020000e-128	470.0
32	TraesCS1A01G059400	chr3D	96.850	127	4	0	1	127	181942696	181942822	1.900000e-51	213.0
33	TraesCS1A01G059400	chr2D	85.321	436	50	9	2015	2438	614127989	614127556	2.880000e-119	438.0
34	TraesCS1A01G059400	chr7D	96.850	127	4	0	1	127	48002091	48001965	1.900000e-51	213.0

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	TraesCS1A01G059400	chr1A	40279184	40281621	2437	False	4503.0	4503	100.0000	1	2438	1	chr1A.!!$F1	2437
1	TraesCS1A01G059400	chr3A	157346433	157348886	2453	True	3133.0	3133	89.8660	1	2438	1	chr3A.!!$R1	2437
2	TraesCS1A01G059400	chr3A	290707882	290710363	2481	False	1713.5	2241	91.7885	1	2438	2	chr3A.!!$F1	2437
3	TraesCS1A01G059400	chr6A	496084591	496086000	1409	True	2008.0	2008	92.3570	1	1413	1	chr6A.!!$R1	1412
4	TraesCS1A01G059400	chr6A	396917490	396919976	2486	False	1741.0	2309	91.7915	1	2438	2	chr6A.!!$F2	2437
5	TraesCS1A01G059400	chr6A	307921949	307922811	862	False	1068.0	1068	89.1450	1582	2438	1	chr6A.!!$F1	856
6	TraesCS1A01G059400	chr1D	266177644	266181182	3538	True	1128.0	1759	92.3190	1	1616	2	chr1D.!!$R1	1615
7	TraesCS1A01G059400	chr5A	213046593	213047454	861	True	1059.0	1059	89.0170	1585	2438	1	chr5A.!!$R1	853
8	TraesCS1A01G059400	chr5A	1134873	1136346	1473	True	968.5	1541	91.8355	1	1588	2	chr5A.!!$R2	1587
9	TraesCS1A01G059400	chr3B	610990893	610991886	993	False	1308.0	1308	90.2750	430	1445	1	chr3B.!!$F1	1015
10	TraesCS1A01G059400	chr3B	680395046	680396031	985	True	1293.0	1293	90.3770	450	1445	1	chr3B.!!$R1	995
11	TraesCS1A01G059400	chr3B	817686190	817687040	850	True	1037.0	1037	88.7340	1585	2438	1	chr3B.!!$R2	853
12	TraesCS1A01G059400	chr3B	817709002	817709850	848	True	1029.0	1029	88.5910	1586	2438	1	chr3B.!!$R3	852
13	TraesCS1A01G059400	chr4B	29156361	29157353	992	False	1251.0	1251	89.2930	430	1445	1	chr4B.!!$F1	1015
14	TraesCS1A01G059400	chr4B	2416400	2417339	939	True	1192.0	1192	89.6270	430	1379	1	chr4B.!!$R1	949
15	TraesCS1A01G059400	chr4B	649113558	649114125	567	True	754.0	754	90.8770	1	561	1	chr4B.!!$R2	560
16	TraesCS1A01G059400	chr2B	697786165	697787170	1005	False	1247.0	1247	89.1260	430	1445	1	chr2B.!!$F1	1015
17	TraesCS1A01G059400	chr2B	110632163	110633136	973	True	1243.0	1243	89.7800	430	1413	1	chr2B.!!$R1	983
18	TraesCS1A01G059400	chr2B	318192519	318193380	861	True	1098.0	1098	89.8270	1585	2438	1	chr2B.!!$R2	853
19	TraesCS1A01G059400	chr7B	681952864	681953719	855	True	1031.0	1031	88.4880	1585	2438	1	chr7B.!!$R1	853

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
906	2876	0.11456	AGAGACGAGAAGGGGGTCAA	59.885	55.0	0.0	0.0	33.18	3.18	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2340	4377	1.305213	AAAATGGCGGGCATGACCT	60.305	52.632	17.64	0.0	39.1	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
74	75	5.769662	ACCAGAAACACAAATAGAGCATCAA	59.230	36.000	0.00	0.00	37.82	2.57
214	216	0.394899	CACTTCAGGCAAGGGATCCC	60.395	60.000	24.59	24.59	37.81	3.85
274	277	5.046878	ACATGTACAACGACCTCAGGATTAA	60.047	40.000	0.00	0.00	0.00	1.40
317	320	2.286831	CCATGAATCGCATCAGTTGAGC	60.287	50.000	0.00	0.00	34.15	4.26
331	334	7.308229	GCATCAGTTGAGCTCTAGAAAAAGAAA	60.308	37.037	16.19	0.00	0.00	2.52
454	2380	8.196802	TCTAAATAGTGTCAACATACATGCAC	57.803	34.615	0.00	0.00	0.00	4.57
465	2391	8.853345	GTCAACATACATGCACTTTCTAAATTG	58.147	33.333	0.00	0.00	0.00	2.32
500	2426	3.096852	TGACCGTCCAATAGTCAGACAT	58.903	45.455	2.66	0.00	35.67	3.06
516	2450	2.798976	ACATGACAACAACATGGCAC	57.201	45.000	0.00	0.00	42.20	5.01
517	2451	2.030371	ACATGACAACAACATGGCACA	58.970	42.857	0.00	0.00	42.20	4.57
600	2534	0.312729	CAATGCTCAGCAACTGCACA	59.687	50.000	1.73	0.00	43.62	4.57
721	2691	0.179076	ATCAGATCCACATCGCGCAA	60.179	50.000	8.75	0.00	33.75	4.85
754	2724	0.971447	GAAGCAGGGGAGTAGGTCGT	60.971	60.000	0.00	0.00	0.00	4.34
765	2735	3.194116	GGAGTAGGTCGTTGTACCAATCA	59.806	47.826	0.00	0.00	42.40	2.57
835	2805	2.529744	GGTGTCCCTCCCAAGCAGT	61.530	63.158	0.00	0.00	0.00	4.40
841	2811	1.448540	CCTCCCAAGCAGTAGCACG	60.449	63.158	0.00	0.00	45.49	5.34
859	2829	3.584834	CACGACACATCACACCTTCATA	58.415	45.455	0.00	0.00	0.00	2.15
906	2876	0.114560	AGAGACGAGAAGGGGGTCAA	59.885	55.000	0.00	0.00	33.18	3.18
912	2882	1.608283	CGAGAAGGGGGTCAAACAGAC	60.608	57.143	0.00	0.00	46.83	3.51
990	2960	0.242825	CGGTTGGAGCTACTCGTTCA	59.757	55.000	0.00	0.00	0.00	3.18
1039	3009	2.035961	CCTGAGAAGAAGAACACGGACA	59.964	50.000	0.00	0.00	0.00	4.02
1080	3050	4.722535	AGGCAGGGGAGGAAGCGA	62.723	66.667	0.00	0.00	0.00	4.93
1131	3101	2.746697	GGACGGCATCCTGGATCTA	58.253	57.895	6.13	0.00	45.22	1.98
1148	3118	2.886913	TCTAGGAGGCAGAGATGATGG	58.113	52.381	0.00	0.00	0.00	3.51
1150	3120	2.419457	AGGAGGCAGAGATGATGGAT	57.581	50.000	0.00	0.00	0.00	3.41
1166	3136	5.745227	TGATGGATTGAGGAAGTTAGGAAC	58.255	41.667	0.00	0.00	0.00	3.62
1184	3154	1.040339	ACGGCTGTGAGGAGGAGATC	61.040	60.000	0.00	0.00	0.00	2.75
1289	3268	1.064134	CGCGTGATGGATCTCGACA	59.936	57.895	13.70	0.00	43.97	4.35
1311	3290	2.748058	GAACGCCAGCCTCCCAAAGA	62.748	60.000	0.00	0.00	0.00	2.52
1394	3379	2.430610	GCTCGATCCAGAGGCAGGT	61.431	63.158	0.00	0.00	38.63	4.00
1431	3416	0.909133	TACTGCTGGATCTGGCCACA	60.909	55.000	0.00	0.00	33.52	4.17
1532	3517	2.046700	GGGTTCGCGGGTGAATCA	60.047	61.111	6.13	0.00	30.33	2.57
1535	3520	1.024579	GGTTCGCGGGTGAATCATGT	61.025	55.000	6.13	0.00	0.00	3.21
1542	3527	0.096976	GGGTGAATCATGTTGCGTCG	59.903	55.000	0.00	0.00	0.00	5.12
1626	3653	0.461870	CGGCGGTGGATTCAGATCAA	60.462	55.000	0.00	0.00	33.77	2.57
1635	3662	5.884792	GGTGGATTCAGATCAAATCAGAGTT	59.115	40.000	17.58	0.00	35.30	3.01
1640	3667	6.627087	TTCAGATCAAATCAGAGTTAGGGT	57.373	37.500	0.00	0.00	0.00	4.34
1660	3687	2.043852	GGAGAGAGGGGCGTCAGA	60.044	66.667	0.00	0.00	0.00	3.27
1713	3740	3.300765	GACGTGGGTGAGACCGGT	61.301	66.667	6.92	6.92	39.83	5.28
1743	3770	2.016604	GCCGTTGGATCCAGCAACATA	61.017	52.381	26.00	2.55	0.00	2.29
1760	3788	5.334879	GCAACATATGACGGTGATTTATCCC	60.335	44.000	10.38	0.00	0.00	3.85
1768	3796	1.346722	GGTGATTTATCCCCGATCCGT	59.653	52.381	0.00	0.00	0.00	4.69
1799	3827	1.071542	TCTGGACCAATCAGAACGCAA	59.928	47.619	0.00	0.00	38.20	4.85
1873	3901	8.863872	AAAGTAAGGTGCTAAATCATGTTAGT	57.136	30.769	5.32	0.00	34.20	2.24
1927	3960	5.117355	ACTTCTCATTGTGTCAGCAAATG	57.883	39.130	0.00	0.00	31.63	2.32
1933	3966	3.696281	TTGTGTCAGCAAATGTGACTG	57.304	42.857	13.41	0.00	44.02	3.51
1941	3974	5.682862	GTCAGCAAATGTGACTGTAGTTTTG	59.317	40.000	7.06	3.66	41.05	2.44
2156	4193	5.043248	CCAAATGGTTGAGTGTCAAAAGAC	58.957	41.667	0.00	0.00	38.22	3.01
2207	4244	0.391130	CCGCCGATTCAGTTGGAAGA	60.391	55.000	0.00	0.00	39.30	2.87
2248	4285	4.156556	CAGCTGCCTCATAGTTTGCTTTTA	59.843	41.667	0.00	0.00	0.00	1.52
2249	4286	4.952335	AGCTGCCTCATAGTTTGCTTTTAT	59.048	37.500	0.00	0.00	0.00	1.40
2340	4377	6.173339	CAAGATTCAACCACTAGCTAGGAAA	58.827	40.000	24.35	9.35	0.00	3.13
2368	4405	0.801836	CCGCCATTTTGACCGCATTC	60.802	55.000	0.00	0.00	0.00	2.67

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
14	15	5.131142	CACATAGATGGGTCTCCCTAGTTTT	59.869	44.000	6.38	0.00	45.70	2.43
62	63	6.421485	ACCTGAAGTTGATTGATGCTCTATT	58.579	36.000	0.00	0.00	0.00	1.73
74	75	7.823745	AATTCACTGTAAACCTGAAGTTGAT	57.176	32.000	0.00	0.00	39.19	2.57
115	117	5.714047	TGTTGCAATGTGTTTCAGTTACAA	58.286	33.333	0.59	0.00	0.00	2.41
128	130	7.317842	TGTTTGAATTTGAATGTTGCAATGT	57.682	28.000	0.59	0.00	0.00	2.71
214	216	2.988570	AGCTCTTCAAATCTGCTGGAG	58.011	47.619	0.00	0.00	32.32	3.86
245	247	4.443621	TGAGGTCGTTGTACATGTTTTGA	58.556	39.130	2.30	0.00	0.00	2.69
274	277	3.182590	TTGCAAGCTCTCACCCGCT	62.183	57.895	0.00	0.00	38.30	5.52
317	320	8.383318	TCCATCTGTTGTTTCTTTTTCTAGAG	57.617	34.615	0.00	0.00	0.00	2.43
331	334	1.566298	GCCTCCCCTCCATCTGTTGT	61.566	60.000	0.00	0.00	0.00	3.32
465	2391	4.394920	TGGACGGTCAAAATAGAGATTTGC	59.605	41.667	10.76	0.00	37.62	3.68
500	2426	1.467920	TGTGTGCCATGTTGTTGTCA	58.532	45.000	0.00	0.00	0.00	3.58
625	2559	3.886505	GGTGTTTGTGGAGGTGATTTACA	59.113	43.478	0.00	0.00	0.00	2.41
706	2676	0.167908	TTTGTTGCGCGATGTGGATC	59.832	50.000	12.10	0.00	0.00	3.36
721	2691	4.956075	CCCCTGCTTCCTATGTTAATTTGT	59.044	41.667	0.00	0.00	0.00	2.83
765	2735	3.203040	CCCCTAACTCCATCAAGGTGATT	59.797	47.826	0.00	0.00	34.28	2.57
835	2805	0.966179	AGGTGTGATGTGTCGTGCTA	59.034	50.000	0.00	0.00	0.00	3.49
841	2811	4.130118	GGGATATGAAGGTGTGATGTGTC	58.870	47.826	0.00	0.00	0.00	3.67
859	2829	0.848735	CCAGGATGTCACCATGGGAT	59.151	55.000	18.09	1.90	0.00	3.85
906	2876	2.910688	TTCTTCTTCCGCTGTCTGTT	57.089	45.000	0.00	0.00	0.00	3.16
912	2882	2.404215	TCGTCTTTTCTTCTTCCGCTG	58.596	47.619	0.00	0.00	0.00	5.18
1060	3030	2.364317	CTTCCTCCCCTGCCTCGA	60.364	66.667	0.00	0.00	0.00	4.04
1131	3101	2.372504	CAATCCATCATCTCTGCCTCCT	59.627	50.000	0.00	0.00	0.00	3.69
1148	3118	2.937149	GCCGTTCCTAACTTCCTCAATC	59.063	50.000	0.00	0.00	0.00	2.67
1150	3120	1.975680	AGCCGTTCCTAACTTCCTCAA	59.024	47.619	0.00	0.00	0.00	3.02
1166	3136	1.739049	GATCTCCTCCTCACAGCCG	59.261	63.158	0.00	0.00	0.00	5.52
1184	3154	0.248661	CAGGTGCGTCCATCTACTCG	60.249	60.000	0.75	0.00	39.02	4.18
1307	3286	1.304713	TCTCTACCGGCGGGTCTTT	60.305	57.895	31.78	11.45	46.01	2.52
1369	3348	4.519437	CTGGATCGAGCAGGCGCA	62.519	66.667	10.83	0.00	42.27	6.09
1394	3379	2.595380	AGTAATCCCTCCTTCCCACCTA	59.405	50.000	0.00	0.00	0.00	3.08
1431	3416	2.293170	TCGACTCGATCTGCTCATCTT	58.707	47.619	0.00	0.00	0.00	2.40
1626	3653	4.017037	TCTCTCCTCACCCTAACTCTGATT	60.017	45.833	0.00	0.00	0.00	2.57
1635	3662	1.950748	GCCCCTCTCTCCTCACCCTA	61.951	65.000	0.00	0.00	0.00	3.53
1640	3667	2.043852	GACGCCCCTCTCTCCTCA	60.044	66.667	0.00	0.00	0.00	3.86
1660	3687	1.919600	GCACCCTTCTCTCCCATGCT	61.920	60.000	0.00	0.00	0.00	3.79
1760	3788	2.105128	GCCTCTCACACGGATCGG	59.895	66.667	0.00	0.00	0.00	4.18
1768	3796	1.610673	GGTCCAGAGGCCTCTCACA	60.611	63.158	33.06	16.15	42.34	3.58
1799	3827	9.866655	ATGGTCAAAATATCACACCTTGTATAT	57.133	29.630	0.00	0.00	0.00	0.86
1900	3930	5.581605	TGCTGACACAATGAGAAGTTTTTC	58.418	37.500	0.00	0.00	0.00	2.29
1927	3960	8.443937	GTGATTATTCCTCAAAACTACAGTCAC	58.556	37.037	0.00	0.00	0.00	3.67
2017	4051	5.476599	TCATTTTGGACACTCGGAAATGAAT	59.523	36.000	7.19	0.00	41.24	2.57
2114	4151	8.389603	CCATTTGGTCAATTGTGCATTAAATAC	58.610	33.333	5.13	0.00	0.00	1.89
2207	4244	3.897505	AGCTGCAGTTCAAATTTTACCCT	59.102	39.130	16.64	0.00	0.00	4.34
2340	4377	1.305213	AAAATGGCGGGCATGACCT	60.305	52.632	17.64	0.00	39.10	3.85
2389	4436	7.490000	TGCGAAGGTTTTCTAAATTTTTGGTA	58.510	30.769	0.00	0.00	0.00	3.25
2391	4438	6.836577	TGCGAAGGTTTTCTAAATTTTTGG	57.163	33.333	0.00	0.00	0.00	3.28
2392	4439	8.334632	ACAATGCGAAGGTTTTCTAAATTTTTG	58.665	29.630	0.00	0.00	0.00	2.44

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.