AutoCloner

Multiple sequence alignment - TraesCS2A01G137100

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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	TraesCS2A01G137100	chr2A	100.000	3764	0	0	1	3764	82806819	82803056	0.000000e+00	6951
1	TraesCS2A01G137100	chr6B	94.951	2832	126	13	947	3764	103259219	103262047	0.000000e+00	4421
2	TraesCS2A01G137100	chr6B	86.854	426	46	8	1	418	711533651	711533228	5.690000e-128	468
3	TraesCS2A01G137100	chr6B	86.905	420	47	5	1	418	456581340	456580927	7.360000e-127	464
4	TraesCS2A01G137100	chr6B	85.986	421	49	8	1	418	456580040	456579627	3.450000e-120	442
5	TraesCS2A01G137100	chr7A	96.328	2669	93	5	1100	3764	517128076	517130743	0.000000e+00	4381
6	TraesCS2A01G137100	chr7A	94.545	990	36	7	1	975	517126391	517127377	0.000000e+00	1513
7	TraesCS2A01G137100	chr7A	95.887	924	23	4	1	910	151405581	151404659	0.000000e+00	1482
8	TraesCS2A01G137100	chr7A	94.913	924	32	5	1	910	103916468	103917390	0.000000e+00	1432
9	TraesCS2A01G137100	chr5B	95.159	1735	83	1	979	2712	553580197	553578463	0.000000e+00	2737
10	TraesCS2A01G137100	chrUn	94.697	1735	81	7	979	2712	184899702	184901426	0.000000e+00	2684
11	TraesCS2A01G137100	chrUn	93.364	1733	103	5	981	2712	227524376	227526097	0.000000e+00	2553
12	TraesCS2A01G137100	chrUn	95.451	1231	55	1	1376	2605	218749864	218748634	0.000000e+00	1962
13	TraesCS2A01G137100	chrUn	94.519	1186	53	5	1528	2712	343092480	343091306	0.000000e+00	1820
14	TraesCS2A01G137100	chrUn	94.519	1186	53	5	1528	2712	343094944	343093770	0.000000e+00	1820
15	TraesCS2A01G137100	chrUn	87.591	548	37	19	979	1526	286785026	286785542	1.160000e-169	606
16	TraesCS2A01G137100	chr2B	94.746	1732	80	7	982	2712	755391765	755390044	0.000000e+00	2684
17	TraesCS2A01G137100	chr2B	87.294	425	46	3	1	418	680919170	680918747	2.630000e-131	479
18	TraesCS2A01G137100	chr3D	97.517	1047	24	2	2719	3764	501322095	501321050	0.000000e+00	1788
19	TraesCS2A01G137100	chr3D	97.421	1047	26	1	2719	3764	98584418	98583372	0.000000e+00	1783
20	TraesCS2A01G137100	chr3D	97.230	1047	27	2	2719	3764	583552551	583551506	0.000000e+00	1772
21	TraesCS2A01G137100	chr7D	97.421	1047	26	1	2719	3764	543342211	543341165	0.000000e+00	1783
22	TraesCS2A01G137100	chr7D	97.135	1047	29	1	2719	3764	40629113	40628067	0.000000e+00	1766
23	TraesCS2A01G137100	chr5D	96.961	1053	31	1	2713	3764	551209707	551210759	0.000000e+00	1766
24	TraesCS2A01G137100	chr2D	97.135	1047	29	1	2719	3764	60313166	60312120	0.000000e+00	1766
25	TraesCS2A01G137100	chr2D	87.381	420	47	5	1	418	50836262	50835847	9.460000e-131	477
26	TraesCS2A01G137100	chr2D	87.351	419	48	4	1	418	50833631	50833217	3.400000e-130	475
27	TraesCS2A01G137100	chr5A	95.747	964	26	4	1	951	3479459	3478498	0.000000e+00	1539
28	TraesCS2A01G137100	chr5A	95.016	923	32	4	1	910	702051887	702050966	0.000000e+00	1437
29	TraesCS2A01G137100	chr5A	94.982	837	28	4	88	910	541376028	541375192	0.000000e+00	1301
30	TraesCS2A01G137100	chr3B	95.445	922	26	3	1	910	767185585	767186502	0.000000e+00	1456
31	TraesCS2A01G137100	chr3B	91.592	559	46	1	947	1504	406134835	406134277	0.000000e+00	771
32	TraesCS2A01G137100	chr3B	92.308	169	11	2	967	1133	796733365	796733533	4.860000e-59	239
33	TraesCS2A01G137100	chr1B	95.135	925	30	4	1	910	683655696	683656620	0.000000e+00	1445
34	TraesCS2A01G137100	chr1B	93.774	514	28	4	415	928	626128226	626127717	0.000000e+00	769
35	TraesCS2A01G137100	chr1B	90.840	393	33	3	936	1327	441139273	441139663	1.200000e-144	523
36	TraesCS2A01G137100	chr1B	85.514	428	55	3	1	422	52305742	52305316	1.240000e-119	440
37	TraesCS2A01G137100	chr4B	91.008	923	30	5	1	910	341435597	341436479	0.000000e+00	1195
38	TraesCS2A01G137100	chr4D	86.905	420	53	2	1	418	480485982	480485563	1.580000e-128	470
39	TraesCS2A01G137100	chr4A	86.313	358	38	9	626	979	238130709	238130359	2.740000e-101	379

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	TraesCS2A01G137100	chr2A	82803056	82806819	3763	True	6951	6951	100.0000	1	3764	1	chr2A.!!$R1	3763
1	TraesCS2A01G137100	chr6B	103259219	103262047	2828	False	4421	4421	94.9510	947	3764	1	chr6B.!!$F1	2817
2	TraesCS2A01G137100	chr6B	456579627	456581340	1713	True	453	464	86.4455	1	418	2	chr6B.!!$R2	417
3	TraesCS2A01G137100	chr7A	517126391	517130743	4352	False	2947	4381	95.4365	1	3764	2	chr7A.!!$F2	3763
4	TraesCS2A01G137100	chr7A	151404659	151405581	922	True	1482	1482	95.8870	1	910	1	chr7A.!!$R1	909
5	TraesCS2A01G137100	chr7A	103916468	103917390	922	False	1432	1432	94.9130	1	910	1	chr7A.!!$F1	909
6	TraesCS2A01G137100	chr5B	553578463	553580197	1734	True	2737	2737	95.1590	979	2712	1	chr5B.!!$R1	1733
7	TraesCS2A01G137100	chrUn	184899702	184901426	1724	False	2684	2684	94.6970	979	2712	1	chrUn.!!$F1	1733
8	TraesCS2A01G137100	chrUn	227524376	227526097	1721	False	2553	2553	93.3640	981	2712	1	chrUn.!!$F2	1731
9	TraesCS2A01G137100	chrUn	218748634	218749864	1230	True	1962	1962	95.4510	1376	2605	1	chrUn.!!$R1	1229
10	TraesCS2A01G137100	chrUn	343091306	343094944	3638	True	1820	1820	94.5190	1528	2712	2	chrUn.!!$R2	1184
11	TraesCS2A01G137100	chrUn	286785026	286785542	516	False	606	606	87.5910	979	1526	1	chrUn.!!$F3	547
12	TraesCS2A01G137100	chr2B	755390044	755391765	1721	True	2684	2684	94.7460	982	2712	1	chr2B.!!$R2	1730
13	TraesCS2A01G137100	chr3D	501321050	501322095	1045	True	1788	1788	97.5170	2719	3764	1	chr3D.!!$R2	1045
14	TraesCS2A01G137100	chr3D	98583372	98584418	1046	True	1783	1783	97.4210	2719	3764	1	chr3D.!!$R1	1045
15	TraesCS2A01G137100	chr3D	583551506	583552551	1045	True	1772	1772	97.2300	2719	3764	1	chr3D.!!$R3	1045
16	TraesCS2A01G137100	chr7D	543341165	543342211	1046	True	1783	1783	97.4210	2719	3764	1	chr7D.!!$R2	1045
17	TraesCS2A01G137100	chr7D	40628067	40629113	1046	True	1766	1766	97.1350	2719	3764	1	chr7D.!!$R1	1045
18	TraesCS2A01G137100	chr5D	551209707	551210759	1052	False	1766	1766	96.9610	2713	3764	1	chr5D.!!$F1	1051
19	TraesCS2A01G137100	chr2D	60312120	60313166	1046	True	1766	1766	97.1350	2719	3764	1	chr2D.!!$R1	1045
20	TraesCS2A01G137100	chr2D	50833217	50836262	3045	True	476	477	87.3660	1	418	2	chr2D.!!$R2	417
21	TraesCS2A01G137100	chr5A	3478498	3479459	961	True	1539	1539	95.7470	1	951	1	chr5A.!!$R1	950
22	TraesCS2A01G137100	chr5A	702050966	702051887	921	True	1437	1437	95.0160	1	910	1	chr5A.!!$R3	909
23	TraesCS2A01G137100	chr5A	541375192	541376028	836	True	1301	1301	94.9820	88	910	1	chr5A.!!$R2	822
24	TraesCS2A01G137100	chr3B	767185585	767186502	917	False	1456	1456	95.4450	1	910	1	chr3B.!!$F1	909
25	TraesCS2A01G137100	chr3B	406134277	406134835	558	True	771	771	91.5920	947	1504	1	chr3B.!!$R1	557
26	TraesCS2A01G137100	chr1B	683655696	683656620	924	False	1445	1445	95.1350	1	910	1	chr1B.!!$F2	909
27	TraesCS2A01G137100	chr1B	626127717	626128226	509	True	769	769	93.7740	415	928	1	chr1B.!!$R2	513
28	TraesCS2A01G137100	chr4B	341435597	341436479	882	False	1195	1195	91.0080	1	910	1	chr4B.!!$F1	909

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
945	2590	1.227556	CCTACGCACCCATAGCCAC	60.228	63.158	0.00	0.00	0.0	5.01	F
1242	3511	0.032017	ACCTCGGCATCTACCTCCTT	60.032	55.000	0.00	0.00	0.0	3.36	F
2332	7110	0.746063	TTTTGCTGTTGTCCTGCTGG	59.254	50.000	2.58	2.58	38.7	4.85	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2332	7110	1.242076	ATTCACAAGGTCTGCAGCAC	58.758	50.000	9.47	8.27	0.00	4.40	R
2696	7497	1.800805	ATGCAACTCACTCGGACAAG	58.199	50.000	0.00	0.00	0.00	3.16	R
3276	8078	1.820906	GGCAGCGAGGCATGAATGA	60.821	57.895	0.00	0.00	43.51	2.57	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
139	788	5.126869	TCAGCAGGAATTTGTCTTTTTCACA	59.873	36.000	0.00	0.00	0.00	3.58
324	987	9.076596	CAAAGAAAATAAAAGATTCCTTAGGCG	57.923	33.333	0.00	0.00	31.15	5.52
834	2474	1.948145	CTACGGTAGGCGATCTGAACT	59.052	52.381	7.30	0.00	0.00	3.01
839	2479	1.476891	GTAGGCGATCTGAACTGTCCA	59.523	52.381	0.00	0.00	0.00	4.02
849	2489	2.496070	CTGAACTGTCCAATCGTCCCTA	59.504	50.000	0.00	0.00	0.00	3.53
861	2501	2.313317	TCGTCCCTAATCTAACGGCAT	58.687	47.619	0.00	0.00	35.89	4.40
922	2567	2.626780	CGCACCACTCGTCCTCTCA	61.627	63.158	0.00	0.00	0.00	3.27
942	2587	2.426023	CCCCTACGCACCCATAGC	59.574	66.667	0.00	0.00	0.00	2.97
943	2588	2.426023	CCCTACGCACCCATAGCC	59.574	66.667	0.00	0.00	0.00	3.93
944	2589	2.439960	CCCTACGCACCCATAGCCA	61.440	63.158	0.00	0.00	0.00	4.75
945	2590	1.227556	CCTACGCACCCATAGCCAC	60.228	63.158	0.00	0.00	0.00	5.01
997	2643	2.445155	GCAACCAATCCCCCACCT	59.555	61.111	0.00	0.00	0.00	4.00
1011	2657	2.284699	ACCTCACCCTTCCTCCCG	60.285	66.667	0.00	0.00	0.00	5.14
1221	3490	3.158676	GGGCTTCTACATCGTCTCCTAT	58.841	50.000	0.00	0.00	0.00	2.57
1223	3492	3.821600	GGCTTCTACATCGTCTCCTATGA	59.178	47.826	0.00	0.00	0.00	2.15
1242	3511	0.032017	ACCTCGGCATCTACCTCCTT	60.032	55.000	0.00	0.00	0.00	3.36
1325	3595	3.020647	CCCCATGCTACCCACCCA	61.021	66.667	0.00	0.00	0.00	4.51
1400	3670	5.714333	TCTGGTATATCCATCTCTTCTGCTC	59.286	44.000	0.00	0.00	46.12	4.26
1440	3711	5.893687	TGATTGCGTGAAATTGATGCTAAT	58.106	33.333	0.00	0.00	0.00	1.73
1443	3714	7.972832	TGATTGCGTGAAATTGATGCTAATTTA	59.027	29.630	0.00	0.00	39.60	1.40
1468	3739	3.845781	TCAGATGCAATACCCTTCTCC	57.154	47.619	0.00	0.00	0.00	3.71
1613	3922	3.368739	GCCTTGCTAATTCATGTGCCTTT	60.369	43.478	0.00	0.00	0.00	3.11
1622	3931	1.350684	TCATGTGCCTTTCCAGCTACA	59.649	47.619	0.00	0.00	0.00	2.74
1874	4185	5.243207	TGCTAACTGCTTTTACTTCCCTAC	58.757	41.667	0.00	0.00	43.37	3.18
2087	4399	9.933723	GGTGTTCTTTTAGTGGTATTTAGTCTA	57.066	33.333	0.00	0.00	0.00	2.59
2303	7081	9.273016	TGACTTTGAGGATTTTTACTAACTGAG	57.727	33.333	0.00	0.00	0.00	3.35
2332	7110	0.746063	TTTTGCTGTTGTCCTGCTGG	59.254	50.000	2.58	2.58	38.70	4.85
2434	7234	2.532843	ACATGCTCCTTTTCTGGCATT	58.467	42.857	0.00	0.00	42.49	3.56
2448	7248	1.596934	GCATTCCACGAGGTCCAGA	59.403	57.895	0.00	0.00	35.89	3.86
2481	7282	3.496875	TTTTTGCCATGCACGCGCT	62.497	52.632	5.73	0.00	38.71	5.92
2650	7451	5.651172	TTTTGTGTGTTACTCATCTGTCG	57.349	39.130	0.00	0.00	0.00	4.35
2696	7497	2.477754	GAGCTTGCTTCAAAACATTGCC	59.522	45.455	0.00	0.00	0.00	4.52
2856	7657	3.904339	ACCTACAGTGTCAATCAGGTCTT	59.096	43.478	8.60	0.00	0.00	3.01
3260	8062	0.739462	CTCTGTTACGGCCGATGCAA	60.739	55.000	35.90	16.74	40.13	4.08
3264	8066	2.395360	TTACGGCCGATGCAACAGC	61.395	57.895	35.90	0.00	40.13	4.40
3276	8078	1.242076	GCAACAGCAACTCAGGACAT	58.758	50.000	0.00	0.00	0.00	3.06
3367	8169	6.526526	TGGTACTTGTTGCTGTTGTATTCTA	58.473	36.000	0.00	0.00	0.00	2.10
3384	8186	7.691213	TGTATTCTAATTACTTGTTGGGACCA	58.309	34.615	0.00	0.00	0.00	4.02
3483	8465	8.462811	TCAAACAAATTTTGAGTACTTGCACTA	58.537	29.630	15.81	0.00	33.90	2.74
3554	8536	5.237048	TGCGTAGGTTTAAAAATACTCCGT	58.763	37.500	8.59	0.00	0.00	4.69
3665	8837	8.643324	GGTGATCTGATTAGGAAGTGTAAGTAT	58.357	37.037	0.00	0.00	0.00	2.12

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
60	709	3.613299	GCTACCTCGTAGTTTGCTCTTTC	59.387	47.826	1.11	0.00	38.30	2.62
139	788	7.417456	GGTGTAAAAAGTTTTGATCCACCTCTT	60.417	37.037	20.61	0.99	35.50	2.85
178	827	8.924511	ACTAGGCTATATACAATGCACAATTT	57.075	30.769	0.00	0.00	0.00	1.82
324	987	4.270245	TCCTGGAATGGCAAACAATTTC	57.730	40.909	0.00	0.00	0.00	2.17
468	1339	5.361135	TTTGCATTGTGTGATCTAGTGTG	57.639	39.130	0.00	0.00	0.00	3.82
834	2474	4.202080	CGTTAGATTAGGGACGATTGGACA	60.202	45.833	0.00	0.00	37.69	4.02
839	2479	2.696707	TGCCGTTAGATTAGGGACGATT	59.303	45.455	0.00	0.00	37.69	3.34
849	2489	3.433173	GGGGTCAAGTATGCCGTTAGATT	60.433	47.826	0.00	0.00	0.00	2.40
861	2501	0.901580	GAGACGGTGGGGGTCAAGTA	60.902	60.000	0.00	0.00	36.87	2.24
958	2603	1.608154	TCGAGGAGAGGTCGATGGT	59.392	57.895	0.00	0.00	41.41	3.55
997	2643	2.683933	GAGCGGGAGGAAGGGTGA	60.684	66.667	0.00	0.00	0.00	4.02
1177	3446	3.204827	GTAGTAGACCCGCGGCGA	61.205	66.667	25.92	0.00	0.00	5.54
1221	3490	0.755698	GGAGGTAGATGCCGAGGTCA	60.756	60.000	0.00	0.00	0.00	4.02
1223	3492	0.032017	AAGGAGGTAGATGCCGAGGT	60.032	55.000	0.00	0.00	0.00	3.85
1242	3511	1.120530	GGAAGCCGATGAGGAGGTTA	58.879	55.000	0.00	0.00	45.00	2.85
1312	3582	4.109675	GCCGTGGGTGGGTAGCAT	62.110	66.667	0.00	0.00	0.00	3.79
1317	3587	4.130554	TTGTTGCCGTGGGTGGGT	62.131	61.111	0.00	0.00	0.00	4.51
1325	3595	0.655733	CTTGAACTCGTTGTTGCCGT	59.344	50.000	1.75	0.00	39.30	5.68
1360	3630	2.464157	CAGAACTTGGACTCAGGGAC	57.536	55.000	0.00	0.00	0.00	4.46
1440	3711	6.753913	AGGGTATTGCATCTGATCTCTAAA	57.246	37.500	0.00	0.00	0.00	1.85
1443	3714	4.906664	AGAAGGGTATTGCATCTGATCTCT	59.093	41.667	0.00	0.00	0.00	3.10
1468	3739	4.450419	GCTATTCGATCAAATCTGGGTCTG	59.550	45.833	0.00	0.00	0.00	3.51
1613	3922	3.508402	TCACATCTAACGTTGTAGCTGGA	59.492	43.478	11.99	0.86	0.00	3.86
1622	3931	4.811969	TGGGTGTATCACATCTAACGTT	57.188	40.909	5.88	5.88	35.86	3.99
2087	4399	9.920946	AGGATCAAAATGTTACCATATAACAGT	57.079	29.630	5.79	0.44	40.27	3.55
2164	4477	2.165998	GCAGCAAGGAAACAGAGGAAT	58.834	47.619	0.00	0.00	0.00	3.01
2274	7052	8.568794	AGTTAGTAAAAATCCTCAAAGTCAAGC	58.431	33.333	0.00	0.00	0.00	4.01
2332	7110	1.242076	ATTCACAAGGTCTGCAGCAC	58.758	50.000	9.47	8.27	0.00	4.40
2696	7497	1.800805	ATGCAACTCACTCGGACAAG	58.199	50.000	0.00	0.00	0.00	3.16
3260	8062	3.244665	TGAATGATGTCCTGAGTTGCTGT	60.245	43.478	0.00	0.00	0.00	4.40
3264	8066	3.066342	GGCATGAATGATGTCCTGAGTTG	59.934	47.826	0.00	0.00	34.14	3.16
3276	8078	1.820906	GGCAGCGAGGCATGAATGA	60.821	57.895	0.00	0.00	43.51	2.57
3367	8169	6.548321	TCAATACTGGTCCCAACAAGTAATT	58.452	36.000	0.00	0.00	43.57	1.40
3384	8186	5.105997	GCAACCAGCAAAATCTCTCAATACT	60.106	40.000	0.00	0.00	44.79	2.12
3483	8465	6.394345	ACCAGGAGTATTTCAATCCTTTCT	57.606	37.500	0.00	0.00	41.60	2.52
3554	8536	5.449862	GCTTGTTGGTTTCATCACAAGTACA	60.450	40.000	11.45	0.00	37.48	2.90
3665	8837	5.610982	AGCCCAATTACCTACCAGATCATTA	59.389	40.000	0.00	0.00	0.00	1.90

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.