AutoCloner

Multiple sequence alignment - TraesCS1B01G217700

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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	TraesCS1B01G217700	chr1B	100.000	2879	0	0	1	2879	394894624	394891746	0.000000e+00	5317.0
1	TraesCS1B01G217700	chr1B	91.856	528	31	5	1	522	139086602	139087123	0.000000e+00	726.0
2	TraesCS1B01G217700	chr1B	91.635	526	33	5	1	521	573070206	573070725	0.000000e+00	717.0
3	TraesCS1B01G217700	chr1B	91.445	526	34	5	1	521	573065842	573066361	0.000000e+00	712.0
4	TraesCS1B01G217700	chr1B	88.657	335	38	0	2545	2879	428731500	428731166	2.670000e-110	409.0
5	TraesCS1B01G217700	chr1B	89.091	55	4	2	2291	2344	666870487	666870434	1.850000e-07	67.6
6	TraesCS1B01G217700	chr1B	100.000	30	0	0	2499	2528	7354797	7354826	4.010000e-04	56.5
7	TraesCS1B01G217700	chr1D	92.158	1798	72	29	522	2274	293615587	293613814	0.000000e+00	2475.0
8	TraesCS1B01G217700	chr1D	88.235	51	4	2	2292	2341	74289036	74289085	3.100000e-05	60.2
9	TraesCS1B01G217700	chr1D	86.538	52	7	0	2290	2341	165560158	165560209	1.110000e-04	58.4
10	TraesCS1B01G217700	chr1A	91.883	1774	73	35	530	2258	365619453	365617706	0.000000e+00	2412.0
11	TraesCS1B01G217700	chr1A	88.189	127	15	0	2290	2416	510360539	510360413	4.970000e-33	152.0
12	TraesCS1B01G217700	chr1A	87.273	55	5	2	2291	2344	574392188	574392135	8.610000e-06	62.1
13	TraesCS1B01G217700	chr7A	98.132	589	10	1	2291	2879	19863337	19862750	0.000000e+00	1026.0
14	TraesCS1B01G217700	chr7A	89.053	338	37	0	2542	2879	494193853	494194190	1.230000e-113	420.0
15	TraesCS1B01G217700	chr6B	97.449	588	14	1	2292	2879	416921138	416920552	0.000000e+00	1002.0
16	TraesCS1B01G217700	chr6B	91.667	528	31	6	1	521	132889123	132888602	0.000000e+00	719.0
17	TraesCS1B01G217700	chr6B	88.070	570	46	5	2310	2879	19505858	19505311	0.000000e+00	656.0
18	TraesCS1B01G217700	chr5A	96.599	588	7	3	2292	2879	627031489	627030915	0.000000e+00	963.0
19	TraesCS1B01G217700	chr5A	88.060	201	23	1	1008	1208	667197348	667197149	1.330000e-58	237.0
20	TraesCS1B01G217700	chr5A	96.875	32	1	0	2292	2323	359741535	359741504	1.000000e-03	54.7
21	TraesCS1B01G217700	chr7B	95.958	569	11	1	2290	2858	424562663	424562107	0.000000e+00	913.0
22	TraesCS1B01G217700	chr5D	92.720	522	34	2	1	522	297122978	297122461	0.000000e+00	750.0
23	TraesCS1B01G217700	chr5D	84.103	585	68	9	2296	2879	530378883	530378323	2.520000e-150	542.0
24	TraesCS1B01G217700	chr5D	89.106	358	39	0	2522	2879	466563918	466564275	2.040000e-121	446.0
25	TraesCS1B01G217700	chr4B	92.720	522	35	1	1	522	1177461	1176943	0.000000e+00	750.0
26	TraesCS1B01G217700	chr4B	88.557	201	22	1	1008	1208	621675778	621675579	2.870000e-60	243.0
27	TraesCS1B01G217700	chr3B	93.083	506	32	1	1	506	225234566	225234064	0.000000e+00	737.0
28	TraesCS1B01G217700	chr2B	92.176	524	34	5	1	522	653894785	653894267	0.000000e+00	734.0
29	TraesCS1B01G217700	chr2B	91.762	522	34	5	1	521	419325407	419325920	0.000000e+00	717.0
30	TraesCS1B01G217700	chr2B	89.552	335	35	0	2545	2879	359643617	359643283	2.650000e-115	425.0
31	TraesCS1B01G217700	chr2B	89.349	338	36	0	2542	2879	776650642	776650979	2.650000e-115	425.0
32	TraesCS1B01G217700	chr2B	88.281	128	13	2	2290	2416	159008981	159009107	4.970000e-33	152.0
33	TraesCS1B01G217700	chr3A	84.615	585	65	11	2296	2879	41433369	41432809	2.510000e-155	558.0
34	TraesCS1B01G217700	chr3A	84.507	71	11	0	2288	2358	344146055	344146125	1.430000e-08	71.3
35	TraesCS1B01G217700	chr3D	82.906	585	75	14	2296	2879	57320217	57320777	1.190000e-138	503.0
36	TraesCS1B01G217700	chr2A	89.053	338	36	1	2542	2879	554512738	554513074	4.440000e-113	418.0
37	TraesCS1B01G217700	chr2A	88.189	127	15	0	2290	2416	716910866	716910740	4.970000e-33	152.0
38	TraesCS1B01G217700	chr4A	88.955	335	37	0	2545	2879	559062197	559061863	5.740000e-112	414.0
39	TraesCS1B01G217700	chr4A	88.000	125	15	0	2292	2416	478065932	478066056	6.430000e-32	148.0
40	TraesCS1B01G217700	chr4A	83.871	62	8	2	2281	2341	613761430	613761490	1.110000e-04	58.4
41	TraesCS1B01G217700	chr7D	88.358	335	39	0	2545	2879	571239025	571239359	1.240000e-108	403.0
42	TraesCS1B01G217700	chr7D	87.164	335	43	0	2545	2879	54009233	54008899	5.820000e-102	381.0
43	TraesCS1B01G217700	chr7D	85.455	55	8	0	2290	2344	617507453	617507399	1.110000e-04	58.4
44	TraesCS1B01G217700	chr4D	88.557	201	22	1	1008	1208	486918669	486918470	2.870000e-60	243.0
45	TraesCS1B01G217700	chr6A	77.060	449	69	16	2381	2825	595010664	595011082	8.030000e-56	228.0
46	TraesCS1B01G217700	chr6A	79.137	139	12	10	1722	1858	596229566	596229443	2.380000e-11	80.5
47	TraesCS1B01G217700	chr6A	89.091	55	4	2	2291	2344	86412928	86412875	1.850000e-07	67.6
48	TraesCS1B01G217700	chr5B	88.095	126	14	1	2291	2416	254148891	254149015	6.430000e-32	148.0
49	TraesCS1B01G217700	chr6D	88.679	53	4	2	2290	2341	53683970	53684021	2.390000e-06	63.9

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	TraesCS1B01G217700	chr1B	394891746	394894624	2878	True	5317.0	5317	100.000	1	2879	1	chr1B.!!$R1	2878
1	TraesCS1B01G217700	chr1B	139086602	139087123	521	False	726.0	726	91.856	1	522	1	chr1B.!!$F2	521
2	TraesCS1B01G217700	chr1B	573065842	573070725	4883	False	714.5	717	91.540	1	521	2	chr1B.!!$F3	520
3	TraesCS1B01G217700	chr1D	293613814	293615587	1773	True	2475.0	2475	92.158	522	2274	1	chr1D.!!$R1	1752
4	TraesCS1B01G217700	chr1A	365617706	365619453	1747	True	2412.0	2412	91.883	530	2258	1	chr1A.!!$R1	1728
5	TraesCS1B01G217700	chr7A	19862750	19863337	587	True	1026.0	1026	98.132	2291	2879	1	chr7A.!!$R1	588
6	TraesCS1B01G217700	chr6B	416920552	416921138	586	True	1002.0	1002	97.449	2292	2879	1	chr6B.!!$R3	587
7	TraesCS1B01G217700	chr6B	132888602	132889123	521	True	719.0	719	91.667	1	521	1	chr6B.!!$R2	520
8	TraesCS1B01G217700	chr6B	19505311	19505858	547	True	656.0	656	88.070	2310	2879	1	chr6B.!!$R1	569
9	TraesCS1B01G217700	chr5A	627030915	627031489	574	True	963.0	963	96.599	2292	2879	1	chr5A.!!$R2	587
10	TraesCS1B01G217700	chr7B	424562107	424562663	556	True	913.0	913	95.958	2290	2858	1	chr7B.!!$R1	568
11	TraesCS1B01G217700	chr5D	297122461	297122978	517	True	750.0	750	92.720	1	522	1	chr5D.!!$R1	521
12	TraesCS1B01G217700	chr5D	530378323	530378883	560	True	542.0	542	84.103	2296	2879	1	chr5D.!!$R2	583
13	TraesCS1B01G217700	chr4B	1176943	1177461	518	True	750.0	750	92.720	1	522	1	chr4B.!!$R1	521
14	TraesCS1B01G217700	chr3B	225234064	225234566	502	True	737.0	737	93.083	1	506	1	chr3B.!!$R1	505
15	TraesCS1B01G217700	chr2B	653894267	653894785	518	True	734.0	734	92.176	1	522	1	chr2B.!!$R2	521
16	TraesCS1B01G217700	chr2B	419325407	419325920	513	False	717.0	717	91.762	1	521	1	chr2B.!!$F2	520
17	TraesCS1B01G217700	chr3A	41432809	41433369	560	True	558.0	558	84.615	2296	2879	1	chr3A.!!$R1	583
18	TraesCS1B01G217700	chr3D	57320217	57320777	560	False	503.0	503	82.906	2296	2879	1	chr3D.!!$F1	583

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
943	5334	0.607217	CCAGATCTGCCACACAGCAA	60.607	55.0	17.76	0.0	46.76	3.91	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2072	6498	0.034198	TCGACCGCAACATCAGGAAA	59.966	50.0	0.0	0.0	0.0	3.13	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)

Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Hairpin	End Stability
436	4809	3.389983	CCGACCCATATCTAAAACAGGGA	59.610	47.826	0.00	39.60	4.20
438	4811	4.101119	CGACCCATATCTAAAACAGGGAGT	59.899	45.833	0.00	39.60	3.85
528	4901	4.460382	CCATTGAAGTTGCTCTTGTGGTAT	59.540	41.667	0.00	36.40	2.73
782	5167	4.686091	ACGATATGATACATGTTCGCAAGG	59.314	41.667	13.71	38.47	3.61
868	5258	3.001406	ACCCTCCCGGCTACACAC	61.001	66.667	0.00	33.26	3.82
870	5260	2.683933	CCTCCCGGCTACACACCT	60.684	66.667	0.00	0.00	4.00
872	5262	1.218316	CTCCCGGCTACACACCTTC	59.782	63.158	0.00	0.00	3.46
873	5263	1.229082	TCCCGGCTACACACCTTCT	60.229	57.895	0.00	0.00	2.85
874	5264	1.079127	CCCGGCTACACACCTTCTG	60.079	63.158	0.00	0.00	3.02
875	5265	1.741770	CCGGCTACACACCTTCTGC	60.742	63.158	0.00	0.00	4.26
925	5316	1.875514	GACCGGTCCTAAACAACAACC	59.124	52.381	24.75	0.00	3.77
943	5334	0.607217	CCAGATCTGCCACACAGCAA	60.607	55.000	17.76	46.76	3.91
985	5376	2.357575	GGAGCAGCAGAGCAGAGGA	61.358	63.158	0.00	36.85	3.71
1101	5492	0.965866	TCGAGTTCCAGCTCATCCGT	60.966	55.000	0.00	35.33	4.69
1149	5540	1.222113	GCCCCAGTACCTCAAGCTC	59.778	63.158	0.00	0.00	4.09
1279	5671	4.963276	ATACGTTGATGAAATGTGTGGG	57.037	40.909	0.00	38.50	4.61
1283	5675	3.609175	CGTTGATGAAATGTGTGGGTGAC	60.609	47.826	0.00	0.00	3.67
1326	5718	1.047596	AGATCCTGAGGCACATCGCT	61.048	55.000	0.00	41.91	4.93
1881	6279	1.227350	CGAGGCGCCATTCTGATCA	60.227	57.895	31.54	0.00	2.92
1890	6288	2.651455	CCATTCTGATCACCATGCACT	58.349	47.619	0.00	0.00	4.40
1900	6298	2.433145	CATGCACTGTCGCCGTCT	60.433	61.111	0.00	0.00	4.18
1903	6323	4.057428	GCACTGTCGCCGTCTCCT	62.057	66.667	0.00	0.00	3.69
1905	6325	3.432588	ACTGTCGCCGTCTCCTCG	61.433	66.667	0.00	0.00	4.63
1930	6350	3.857309	GAAGGTGCTGCCCACTGCT	62.857	63.158	9.36	44.08	4.24
1934	6354	3.654143	TGCTGCCCACTGCTCCAT	61.654	61.111	0.00	41.07	3.41

Showing 1 to 25 of 52 entries

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Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
18	19	2.722487	CGGGCGCTCGTCTTCTAT	59.278	61.111	24.35	0.00	0.00	1.98
48	49	4.956075	ACCCTGAAACTGAAACACTTGATT	59.044	37.500	0.00	0.00	0.00	2.57
55	56	3.924114	TCTCACCCTGAAACTGAAACA	57.076	42.857	0.00	0.00	0.00	2.83
98	102	0.102300	ACTGTTCAAACTTTGCCGCC	59.898	50.000	0.00	0.00	0.00	6.13
528	4901	3.181462	ACAGACAGAGACAAGTCATGCAA	60.181	43.478	2.72	0.00	37.23	4.08
606	4986	6.929049	GGCTTTATGCTATGTATGTGACACTA	59.071	38.462	7.20	0.00	40.68	2.74
695	5075	0.035439	CTCCCCGCCATGTAAAGTGT	60.035	55.000	0.00	0.00	0.00	3.55
782	5167	4.811024	AGCAAAAACTAAAGAGCAAAAGCC	59.189	37.500	0.00	0.00	0.00	4.35
943	5334	2.186155	TCGTTGATCGATGGACGGT	58.814	52.632	22.45	0.00	44.01	4.83
967	5358	1.897225	TTCCTCTGCTCTGCTGCTCC	61.897	60.000	0.00	0.00	0.00	4.70
985	5376	1.738099	GCATCGTCGCTGGTCACTT	60.738	57.895	0.00	0.00	0.00	3.16
1101	5492	3.744719	CCGCGGAAGGAGTCGACA	61.745	66.667	24.07	0.00	0.00	4.35
1283	5675	4.415332	ACTCTACACCCACGCGCG	62.415	66.667	30.96	30.96	0.00	6.86
1295	5687	3.181449	CCTCAGGATCTTCCTCGACTCTA	60.181	52.174	0.00	0.00	45.66	2.43
1326	5718	1.347707	CCCTGCCTCTTGTACTTGTCA	59.652	52.381	0.00	0.00	0.00	3.58
1519	5917	4.531912	CTGCTGCATGGCTTCGCG	62.532	66.667	1.31	0.00	0.00	5.87
1520	5918	2.594119	CTTCTGCTGCATGGCTTCGC	62.594	60.000	1.31	0.00	0.00	4.70
1521	5919	1.428219	CTTCTGCTGCATGGCTTCG	59.572	57.895	1.31	0.00	0.00	3.79
1522	5920	1.139095	GCTTCTGCTGCATGGCTTC	59.861	57.895	1.31	0.00	36.03	3.86
1523	5921	1.595993	CTGCTTCTGCTGCATGGCTT	61.596	55.000	1.31	0.00	39.86	4.35
1524	5922	2.035155	TGCTTCTGCTGCATGGCT	59.965	55.556	1.31	0.00	40.48	4.75
1525	5923	2.490217	CTGCTTCTGCTGCATGGC	59.510	61.111	1.31	8.63	39.86	4.40
1531	5929	2.871099	CTGCTGCTGCTTCTGCTG	59.129	61.111	17.00	1.17	40.48	4.41
1532	5930	3.056938	GCTGCTGCTGCTTCTGCT	61.057	61.111	22.10	0.00	40.48	4.24
1533	5931	3.329688	CTGCTGCTGCTGCTTCTGC	62.330	63.158	27.67	14.65	40.48	4.26

Showing 1 to 25 of 51 entries

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Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.