AutoCloner

Multiple sequence alignment - TraesCS2D01G272700

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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	TraesCS2D01G272700	chr2D	100.000	3567	0	0	1	3567	337922066	337925632	0.000000e+00	6588
1	TraesCS2D01G272700	chr2D	95.054	647	31	1	2921	3567	544172449	544173094	0.000000e+00	1016
2	TraesCS2D01G272700	chr2D	91.049	648	54	4	2921	3566	87832037	87832682	0.000000e+00	872
3	TraesCS2D01G272700	chr2B	95.381	1927	62	19	871	2774	405262175	405264097	0.000000e+00	3040
4	TraesCS2D01G272700	chr2B	91.204	648	56	1	2921	3567	387072092	387072739	0.000000e+00	880
5	TraesCS2D01G272700	chr2B	84.615	338	28	11	556	890	405261832	405262148	7.430000e-82	315
6	TraesCS2D01G272700	chr2B	81.818	286	29	10	131	393	405261479	405261764	6.000000e-53	219
7	TraesCS2D01G272700	chr2A	97.817	1008	22	0	1560	2567	448153688	448154695	0.000000e+00	1740
8	TraesCS2D01G272700	chr2A	92.781	1122	44	20	512	1608	448152588	448153697	0.000000e+00	1589
9	TraesCS2D01G272700	chr2A	78.222	776	143	23	1687	2449	448294184	448293422	1.160000e-129	473
10	TraesCS2D01G272700	chr2A	92.667	300	20	1	2625	2922	448154694	448154993	7.070000e-117	431
11	TraesCS2D01G272700	chr2A	87.500	256	23	8	269	516	448152099	448152353	1.620000e-73	287
12	TraesCS2D01G272700	chr2A	73.829	726	146	32	1692	2389	13004029	13003320	7.650000e-62	248
13	TraesCS2D01G272700	chr2A	95.238	147	7	0	132	278	448151496	448151642	2.140000e-57	233
14	TraesCS2D01G272700	chr2A	97.080	137	2	1	2	136	448151332	448151468	2.770000e-56	230
15	TraesCS2D01G272700	chr1A	82.274	1557	250	24	1022	2559	53997351	53995802	0.000000e+00	1323
16	TraesCS2D01G272700	chr1A	89.080	641	68	2	2927	3567	285520248	285519610	0.000000e+00	795
17	TraesCS2D01G272700	chr1B	80.259	1545	265	33	1022	2555	90544306	90542791	0.000000e+00	1127
18	TraesCS2D01G272700	chr1B	94.255	644	37	0	2922	3565	135237757	135237114	0.000000e+00	985
19	TraesCS2D01G272700	chr5B	79.027	1521	289	23	1017	2527	611868530	611870030	0.000000e+00	1014
20	TraesCS2D01G272700	chr5A	79.041	1522	286	26	1017	2527	619359815	619361314	0.000000e+00	1013
21	TraesCS2D01G272700	chr5D	78.900	1455	273	24	1022	2466	495290527	495291957	0.000000e+00	955
22	TraesCS2D01G272700	chr4D	91.499	647	54	1	2921	3567	43850484	43851129	0.000000e+00	889
23	TraesCS2D01G272700	chr1D	90.248	646	59	4	2923	3567	125140898	125140256	0.000000e+00	841
24	TraesCS2D01G272700	chr7D	88.872	647	69	3	2921	3566	335455413	335454769	0.000000e+00	793
25	TraesCS2D01G272700	chr3B	88.941	642	71	0	2926	3567	396027425	396028066	0.000000e+00	793
26	TraesCS2D01G272700	chrUn	78.916	1181	211	31	1385	2555	427096637	427097789	0.000000e+00	767
27	TraesCS2D01G272700	chr6B	81.828	919	147	17	1611	2519	674327781	674328689	0.000000e+00	754
28	TraesCS2D01G272700	chr6B	81.314	487	85	6	1023	1506	674327290	674327773	1.200000e-104	390
29	TraesCS2D01G272700	chr6D	83.112	829	126	12	1611	2432	446103372	446104193	0.000000e+00	743
30	TraesCS2D01G272700	chr6D	81.352	488	79	11	1025	1506	446102883	446103364	1.550000e-103	387
31	TraesCS2D01G272700	chr6A	81.692	863	142	14	1611	2465	592817924	592817070	0.000000e+00	704
32	TraesCS2D01G272700	chr6A	80.371	917	164	13	1611	2519	592813748	592812840	0.000000e+00	682

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	TraesCS2D01G272700	chr2D	337922066	337925632	3566	False	6588.000000	6588	100.000000	1	3567	1	chr2D.!!$F2	3566
1	TraesCS2D01G272700	chr2D	544172449	544173094	645	False	1016.000000	1016	95.054000	2921	3567	1	chr2D.!!$F3	646
2	TraesCS2D01G272700	chr2D	87832037	87832682	645	False	872.000000	872	91.049000	2921	3566	1	chr2D.!!$F1	645
3	TraesCS2D01G272700	chr2B	405261479	405264097	2618	False	1191.333333	3040	87.271333	131	2774	3	chr2B.!!$F2	2643
4	TraesCS2D01G272700	chr2B	387072092	387072739	647	False	880.000000	880	91.204000	2921	3567	1	chr2B.!!$F1	646
5	TraesCS2D01G272700	chr2A	448151332	448154993	3661	False	751.666667	1740	93.847167	2	2922	6	chr2A.!!$F1	2920
6	TraesCS2D01G272700	chr2A	448293422	448294184	762	True	473.000000	473	78.222000	1687	2449	1	chr2A.!!$R2	762
7	TraesCS2D01G272700	chr2A	13003320	13004029	709	True	248.000000	248	73.829000	1692	2389	1	chr2A.!!$R1	697
8	TraesCS2D01G272700	chr1A	53995802	53997351	1549	True	1323.000000	1323	82.274000	1022	2559	1	chr1A.!!$R1	1537
9	TraesCS2D01G272700	chr1A	285519610	285520248	638	True	795.000000	795	89.080000	2927	3567	1	chr1A.!!$R2	640
10	TraesCS2D01G272700	chr1B	90542791	90544306	1515	True	1127.000000	1127	80.259000	1022	2555	1	chr1B.!!$R1	1533
11	TraesCS2D01G272700	chr1B	135237114	135237757	643	True	985.000000	985	94.255000	2922	3565	1	chr1B.!!$R2	643
12	TraesCS2D01G272700	chr5B	611868530	611870030	1500	False	1014.000000	1014	79.027000	1017	2527	1	chr5B.!!$F1	1510
13	TraesCS2D01G272700	chr5A	619359815	619361314	1499	False	1013.000000	1013	79.041000	1017	2527	1	chr5A.!!$F1	1510
14	TraesCS2D01G272700	chr5D	495290527	495291957	1430	False	955.000000	955	78.900000	1022	2466	1	chr5D.!!$F1	1444
15	TraesCS2D01G272700	chr4D	43850484	43851129	645	False	889.000000	889	91.499000	2921	3567	1	chr4D.!!$F1	646
16	TraesCS2D01G272700	chr1D	125140256	125140898	642	True	841.000000	841	90.248000	2923	3567	1	chr1D.!!$R1	644
17	TraesCS2D01G272700	chr7D	335454769	335455413	644	True	793.000000	793	88.872000	2921	3566	1	chr7D.!!$R1	645
18	TraesCS2D01G272700	chr3B	396027425	396028066	641	False	793.000000	793	88.941000	2926	3567	1	chr3B.!!$F1	641
19	TraesCS2D01G272700	chrUn	427096637	427097789	1152	False	767.000000	767	78.916000	1385	2555	1	chrUn.!!$F1	1170
20	TraesCS2D01G272700	chr6B	674327290	674328689	1399	False	572.000000	754	81.571000	1023	2519	2	chr6B.!!$F1	1496
21	TraesCS2D01G272700	chr6D	446102883	446104193	1310	False	565.000000	743	82.232000	1025	2432	2	chr6D.!!$F1	1407
22	TraesCS2D01G272700	chr6A	592812840	592817924	5084	True	693.000000	704	81.031500	1611	2519	2	chr6A.!!$R1	908

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
415	950	0.035152	AGCTTGTCATGCATTCGGGA	60.035	50.000	12.76	0.0	0.0	5.14	F
1287	2147	1.002888	CTCTGCAACTCCACCATGACT	59.997	52.381	0.00	0.0	0.0	3.41	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1933	4625	0.695347	CCTGCTCCTTCCAGAGGTTT	59.305	55.0	0.0	0.0	46.39	3.27	R
2821	5522	0.250553	TGTCATCCCCGGTGTTCAAC	60.251	55.0	0.0	0.0	0.00	3.18	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
66	69	1.010935	CACTGCACCTGTCAGCTACG	61.011	60.000	0.00	0.00	35.04	3.51
150	185	2.237143	TCAAGCAACTGATCCAGGTAGG	59.763	50.000	0.00	0.00	35.51	3.18
176	211	3.807622	CAGCATCCATCCAATCAAAATGC	59.192	43.478	0.00	0.00	38.58	3.56
331	835	2.045708	GTGGCCGTGCATGGATGAA	61.046	57.895	29.54	7.16	0.00	2.57
393	905	1.757682	ACTGGAAGCAAAACGACCAA	58.242	45.000	0.00	0.00	37.60	3.67
407	942	1.135859	CGACCAAGAAGCTTGTCATGC	60.136	52.381	2.10	2.51	0.00	4.06
408	943	1.881973	GACCAAGAAGCTTGTCATGCA	59.118	47.619	2.10	0.00	0.00	3.96
409	944	2.490903	GACCAAGAAGCTTGTCATGCAT	59.509	45.455	2.10	0.00	0.00	3.96
410	945	2.895404	ACCAAGAAGCTTGTCATGCATT	59.105	40.909	2.10	4.72	0.00	3.56
411	946	3.057033	ACCAAGAAGCTTGTCATGCATTC	60.057	43.478	2.10	12.03	0.00	2.67
412	947	3.168963	CAAGAAGCTTGTCATGCATTCG	58.831	45.455	2.10	0.00	0.00	3.34
413	948	1.741706	AGAAGCTTGTCATGCATTCGG	59.258	47.619	2.10	0.00	0.00	4.30
415	950	0.035152	AGCTTGTCATGCATTCGGGA	60.035	50.000	12.76	0.00	0.00	5.14
417	952	1.406539	GCTTGTCATGCATTCGGGAAT	59.593	47.619	0.00	0.00	0.00	3.01
418	953	2.159198	GCTTGTCATGCATTCGGGAATT	60.159	45.455	0.00	0.00	0.00	2.17
419	954	3.676873	GCTTGTCATGCATTCGGGAATTT	60.677	43.478	0.00	0.00	0.00	1.82
420	955	3.507103	TGTCATGCATTCGGGAATTTG	57.493	42.857	0.00	0.00	0.00	2.32
421	956	2.195922	GTCATGCATTCGGGAATTTGC	58.804	47.619	0.00	1.11	0.00	3.68
422	957	1.136695	TCATGCATTCGGGAATTTGCC	59.863	47.619	0.00	0.00	0.00	4.52
423	958	1.134759	CATGCATTCGGGAATTTGCCA	60.135	47.619	7.77	0.00	0.00	4.92
424	959	1.193323	TGCATTCGGGAATTTGCCAT	58.807	45.000	7.77	0.00	0.00	4.40
425	960	1.134759	TGCATTCGGGAATTTGCCATG	60.135	47.619	7.77	5.47	0.00	3.66
476	1011	5.501715	ACGACATTATCAAGCGCTTTAATG	58.498	37.500	33.07	33.07	37.81	1.90
512	1048	9.822185	AAAGAAAGAGCATTATCAACAACTTTT	57.178	25.926	0.00	0.00	0.00	2.27
541	1315	1.696832	GCTGACTTTCGGGCGATCAC	61.697	60.000	0.00	0.00	0.00	3.06
636	1421	9.816354	ATGTAAATTAAAACTGTTCAAAGTGCT	57.184	25.926	0.00	0.00	0.00	4.40
718	1503	2.558617	TGCAGCGATGCAAGTGAAT	58.441	47.368	28.30	0.00	42.40	2.57
744	1529	1.198408	CGTCGTCACCACAAGCTAGTA	59.802	52.381	0.00	0.00	0.00	1.82
919	1757	1.665679	CATAAACGGTAGCCTGCACAG	59.334	52.381	0.00	0.00	0.00	3.66
1287	2147	1.002888	CTCTGCAACTCCACCATGACT	59.997	52.381	0.00	0.00	0.00	3.41
1497	2357	2.202987	CAGCTCATCGAGTGGGGC	60.203	66.667	0.00	0.00	31.39	5.80
1595	2495	3.773860	TGCTGTAACAAGTGTGGTTTG	57.226	42.857	0.00	0.00	0.00	2.93
2045	4737	0.179150	GATGACGAACGAGCAGCTCT	60.179	55.000	20.39	1.94	0.00	4.09
2622	5321	3.119173	TCAGTGAACAAACAAGCCCAAAG	60.119	43.478	0.00	0.00	0.00	2.77
2722	5421	9.632807	GGCAACTTGTATTTTGTATGTTTATCA	57.367	29.630	0.00	0.00	0.00	2.15
2783	5482	6.164876	TGTATTTTGCATGTTGATTCCCTTG	58.835	36.000	0.00	0.00	0.00	3.61
2799	5500	1.613437	CCTTGATGGAACCAAAGCGTT	59.387	47.619	0.00	0.00	38.35	4.84
2829	5530	5.659048	TTGTTGTTTTGTTGGTTGAACAC	57.341	34.783	0.00	0.00	44.53	3.32
2830	5531	4.058817	TGTTGTTTTGTTGGTTGAACACC	58.941	39.130	0.00	0.00	44.53	4.16
2838	5539	1.377229	GGTTGAACACCGGGGATGA	59.623	57.895	12.96	0.00	35.12	2.92
2862	5563	8.992073	TGACATTGATGTATACATGCATTCTAC	58.008	33.333	22.93	6.54	41.95	2.59
2865	5566	9.657419	CATTGATGTATACATGCATTCTACCTA	57.343	33.333	22.93	3.00	36.57	3.08
2879	5580	7.012327	TGCATTCTACCTAATCTGTATGCAAAC	59.988	37.037	0.00	0.00	38.20	2.93
2893	5594	4.924305	ATGCAAACCATACTATTGCCTG	57.076	40.909	7.19	0.00	46.74	4.85
2896	5597	4.769488	TGCAAACCATACTATTGCCTGAAA	59.231	37.500	7.19	0.00	46.74	2.69
2988	5690	5.785940	AGGTAGAAAGAGTACAAGGGTTGAT	59.214	40.000	0.00	0.00	0.00	2.57
3005	5707	3.562343	TGATGACTCCTAGCTCGTACT	57.438	47.619	0.00	0.00	0.00	2.73
3057	5759	2.514824	GAAGTGGGATGCTCGGCC	60.515	66.667	0.00	0.00	0.00	6.13
3267	5971	1.107538	CCTTCCGGAGCGATACTGGA	61.108	60.000	3.34	0.00	40.52	3.86
3373	6077	2.409870	CGGTGCCAAATCTCCCTGC	61.410	63.158	0.00	0.00	0.00	4.85
3383	6087	1.965754	ATCTCCCTGCAGAAGACGCC	61.966	60.000	17.39	0.00	0.00	5.68
3526	6230	5.049167	GCCACAAGAACATTTTGACATTGA	58.951	37.500	0.00	0.00	0.00	2.57
3527	6231	5.050837	GCCACAAGAACATTTTGACATTGAC	60.051	40.000	0.00	0.00	0.00	3.18
3555	6259	1.770658	CAGCCCTTCCATGTCATCCTA	59.229	52.381	0.00	0.00	0.00	2.94

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
66	69	2.234187	GAAACAAGACAAGATTCGCGC	58.766	47.619	0.00	0.00	0.00	6.86
150	185	3.204306	TGATTGGATGGATGCTGACTC	57.796	47.619	0.00	0.00	0.00	3.36
176	211	4.445718	CGATTTGTACGAGATTCCAGATGG	59.554	45.833	0.00	0.00	0.00	3.51
328	829	0.390340	CGGCAGTAGCAGCTTCTTCA	60.390	55.000	0.00	0.00	44.61	3.02
331	835	0.539051	ATTCGGCAGTAGCAGCTTCT	59.461	50.000	0.00	0.00	44.61	2.85
356	868	4.273969	TCCAGTTTTATTGGTGTTGTCGTC	59.726	41.667	0.00	0.00	37.02	4.20
393	905	1.741706	CCGAATGCATGACAAGCTTCT	59.258	47.619	0.00	0.00	0.00	2.85
407	942	1.807377	GCCATGGCAAATTCCCGAATG	60.807	52.381	32.08	0.00	41.49	2.67
408	943	0.465287	GCCATGGCAAATTCCCGAAT	59.535	50.000	32.08	0.00	41.49	3.34
409	944	1.612395	GGCCATGGCAAATTCCCGAA	61.612	55.000	36.56	0.00	44.11	4.30
410	945	2.057408	GGCCATGGCAAATTCCCGA	61.057	57.895	36.56	0.00	44.11	5.14
411	946	2.500646	GGCCATGGCAAATTCCCG	59.499	61.111	36.56	0.00	44.11	5.14
412	947	2.500646	CGGCCATGGCAAATTCCC	59.499	61.111	36.56	17.19	44.11	3.97
413	948	2.202919	GCGGCCATGGCAAATTCC	60.203	61.111	36.56	17.93	44.11	3.01
415	950	0.104671	GTATGCGGCCATGGCAAATT	59.895	50.000	36.56	20.65	44.66	1.82
417	952	2.422231	GGTATGCGGCCATGGCAAA	61.422	57.895	36.56	21.89	44.66	3.68
418	953	2.832661	GGTATGCGGCCATGGCAA	60.833	61.111	36.56	22.26	44.66	4.52
500	1036	6.426328	CAGCTCTCTCTACAAAAGTTGTTGAT	59.574	38.462	5.87	0.00	42.73	2.57
505	1041	5.537188	AGTCAGCTCTCTCTACAAAAGTTG	58.463	41.667	0.00	0.00	0.00	3.16
508	1044	5.344665	CGAAAGTCAGCTCTCTCTACAAAAG	59.655	44.000	0.00	0.00	0.00	2.27
512	1048	2.750166	CCGAAAGTCAGCTCTCTCTACA	59.250	50.000	0.00	0.00	0.00	2.74
543	1317	0.586319	AAGTCGTCGCCACAAATGTG	59.414	50.000	6.57	6.57	45.23	3.21
718	1503	2.734670	CTTGTGGTGACGACGACTTTA	58.265	47.619	0.00	0.00	32.30	1.85
744	1529	1.134580	CATGCGAGGGTCTTGTCATCT	60.135	52.381	0.00	0.00	0.00	2.90
919	1757	4.215827	AGCTAGTGCGTATGTAGTATGTCC	59.784	45.833	0.00	0.00	45.42	4.02
1287	2147	3.622263	AGGTGGGGGAGGCAGGTA	61.622	66.667	0.00	0.00	0.00	3.08
1449	2309	1.227556	GTAGCCCATGTACCCGCAG	60.228	63.158	0.00	0.00	0.00	5.18
1517	2377	9.558396	GTAGGAGCTAGTAGTAGAAATGTAGAA	57.442	37.037	8.87	0.00	0.00	2.10
1521	2381	8.936787	TCTAGTAGGAGCTAGTAGTAGAAATGT	58.063	37.037	8.87	0.00	39.60	2.71
1522	2382	9.953565	ATCTAGTAGGAGCTAGTAGTAGAAATG	57.046	37.037	17.42	0.00	39.60	2.32
1525	2385	7.451255	ACGATCTAGTAGGAGCTAGTAGTAGAA	59.549	40.741	17.42	7.09	39.60	2.10
1532	2393	4.840115	AGGTACGATCTAGTAGGAGCTAGT	59.160	45.833	0.00	0.00	39.44	2.57
1933	4625	0.695347	CCTGCTCCTTCCAGAGGTTT	59.305	55.000	0.00	0.00	46.39	3.27
2045	4737	4.323477	CCCCCACGCGAACTCCAA	62.323	66.667	15.93	0.00	0.00	3.53
2466	5165	1.805945	GTGGCTCTAACCGCACTCG	60.806	63.158	0.00	0.00	40.11	4.18
2622	5321	5.508489	CCCAACATGCATGTGGATAATTCTC	60.508	44.000	32.44	0.00	41.61	2.87
2693	5392	4.521256	ACATACAAAATACAAGTTGCCCGT	59.479	37.500	1.81	0.00	0.00	5.28
2799	5500	6.076981	ACCAACAAAACAACAATGCAAAAA	57.923	29.167	0.00	0.00	0.00	1.94
2821	5522	0.250553	TGTCATCCCCGGTGTTCAAC	60.251	55.000	0.00	0.00	0.00	3.18
2829	5530	2.928801	TACATCAATGTCATCCCCGG	57.071	50.000	0.00	0.00	41.97	5.73
2830	5531	4.893608	TGTATACATCAATGTCATCCCCG	58.106	43.478	0.08	0.00	41.97	5.73
2838	5539	8.159447	AGGTAGAATGCATGTATACATCAATGT	58.841	33.333	15.60	10.55	44.48	2.71
2862	5563	9.507329	AATAGTATGGTTTGCATACAGATTAGG	57.493	33.333	9.57	0.00	37.83	2.69
2865	5566	7.255590	GGCAATAGTATGGTTTGCATACAGATT	60.256	37.037	9.57	0.00	45.80	2.40
2879	5580	8.225603	AGTGTAATTTTCAGGCAATAGTATGG	57.774	34.615	0.00	0.00	0.00	2.74
2988	5690	3.008330	GTTGAGTACGAGCTAGGAGTCA	58.992	50.000	12.20	12.20	0.00	3.41
3005	5707	2.662596	CCTGGCACGCCTAGTTGA	59.337	61.111	9.92	0.00	36.94	3.18
3057	5759	4.565564	GCGATGTAAACCTACTGTAACTGG	59.434	45.833	0.00	0.00	0.00	4.00
3267	5971	0.461961	GAGACGCTACTGGCTCCATT	59.538	55.000	0.00	0.00	39.13	3.16

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.