AutoCloner

Multiple sequence alignment - TraesCS4B01G024000

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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	TraesCS4B01G024000	chr4B	100.000	9678	0	0	1	9678	17228197	17237874	0.000000e+00	17872.0
1	TraesCS4B01G024000	chr4B	94.789	4682	171	27	2176	6826	20086027	20081388	0.000000e+00	7227.0
2	TraesCS4B01G024000	chr4B	91.469	1430	75	17	725	2138	20087425	20086027	0.000000e+00	1921.0
3	TraesCS4B01G024000	chr4B	90.097	1444	116	18	7609	9040	20080351	20078923	0.000000e+00	1849.0
4	TraesCS4B01G024000	chr4B	96.048	582	23	0	3066	3647	20072769	20073350	0.000000e+00	948.0
5	TraesCS4B01G024000	chr4B	85.204	784	70	33	6868	7624	20081193	20080429	0.000000e+00	763.0
6	TraesCS4B01G024000	chr4B	91.111	405	21	4	415	807	17228212	17228613	1.430000e-147	534.0
7	TraesCS4B01G024000	chr4B	91.111	405	21	4	16	417	17228611	17229003	1.430000e-147	534.0
8	TraesCS4B01G024000	chr4B	81.918	365	39	14	2	340	20087825	20087462	5.720000e-72	283.0
9	TraesCS4B01G024000	chr4B	88.696	230	19	2	416	638	20087806	20087577	3.440000e-69	274.0
10	TraesCS4B01G024000	chr4B	84.158	202	24	5	7	203	20088626	20088428	1.280000e-43	189.0
11	TraesCS4B01G024000	chr4B	83.938	193	24	4	415	602	20088618	20088428	2.780000e-40	178.0
12	TraesCS4B01G024000	chr4B	84.507	142	22	0	1460	1601	20011301	20011160	3.640000e-29	141.0
13	TraesCS4B01G024000	chr4D	96.471	8189	178	34	725	8871	10754287	10746168	0.000000e+00	13418.0
14	TraesCS4B01G024000	chr4D	80.887	586	104	6	9095	9676	85674851	85675432	1.150000e-123	455.0
15	TraesCS4B01G024000	chr4D	81.918	365	39	15	2	340	10754687	10754324	5.720000e-72	283.0
16	TraesCS4B01G024000	chr4D	88.696	230	19	2	416	638	10754668	10754439	3.440000e-69	274.0
17	TraesCS4B01G024000	chr4D	85.990	207	23	3	2	203	10755494	10755289	5.890000e-52	217.0
18	TraesCS4B01G024000	chr4D	85.492	193	22	3	415	602	10755480	10755289	7.670000e-46	196.0
19	TraesCS4B01G024000	chr4D	85.211	142	21	0	1460	1601	10690359	10690218	7.830000e-31	147.0
20	TraesCS4B01G024000	chr4A	94.791	5203	164	34	1655	6801	593193320	593198471	0.000000e+00	8008.0
21	TraesCS4B01G024000	chr4A	91.648	2263	135	32	6868	9093	593198652	593200897	0.000000e+00	3083.0
22	TraesCS4B01G024000	chr4A	92.432	370	18	5	1284	1645	593189245	593189612	4.010000e-143	520.0
23	TraesCS4B01G024000	chr4A	85.507	345	35	8	2	337	593188684	593189022	7.190000e-91	346.0
24	TraesCS4B01G024000	chr4A	93.617	188	12	0	724	911	593189060	593189247	2.060000e-71	281.0
25	TraesCS4B01G024000	chr4A	92.727	165	12	0	724	888	591450660	591450496	1.260000e-58	239.0
26	TraesCS4B01G024000	chr4A	92.727	165	12	0	724	888	592893309	592893473	1.260000e-58	239.0
27	TraesCS4B01G024000	chr4A	92.121	165	13	0	724	888	592604189	592604353	5.840000e-57	233.0
28	TraesCS4B01G024000	chr4A	92.121	165	13	0	724	888	593164779	593164943	5.840000e-57	233.0
29	TraesCS4B01G024000	chr4A	91.515	165	14	0	724	888	592266771	592266935	2.720000e-55	228.0
30	TraesCS4B01G024000	chr4A	85.714	140	20	0	1462	1601	593278620	593278759	2.180000e-31	148.0
31	TraesCS4B01G024000	chr5B	85.274	584	84	1	9095	9678	526522455	526521874	1.390000e-167	601.0
32	TraesCS4B01G024000	chr5B	85.714	147	20	1	1459	1605	641560180	641560325	4.680000e-33	154.0
33	TraesCS4B01G024000	chr5B	83.824	68	8	3	2504	2570	617247187	617247252	2.920000e-05	62.1
34	TraesCS4B01G024000	chr7D	89.931	437	42	1	9242	9678	262631481	262631915	6.560000e-156	562.0
35	TraesCS4B01G024000	chr7D	88.889	153	14	2	3904	4053	457148949	457148797	1.660000e-42	185.0
36	TraesCS4B01G024000	chr7B	82.646	582	96	4	9095	9675	19014926	19014349	2.410000e-140	510.0
37	TraesCS4B01G024000	chr7B	88.858	359	36	4	9321	9678	241115237	241114882	1.150000e-118	438.0
38	TraesCS4B01G024000	chr7B	92.941	85	6	0	9242	9326	241123885	241123801	3.670000e-24	124.0
39	TraesCS4B01G024000	chr7B	94.737	38	2	0	9056	9093	732432625	732432588	1.050000e-04	60.2
40	TraesCS4B01G024000	chr1B	82.333	583	100	2	9095	9676	148223459	148222879	4.030000e-138	503.0
41	TraesCS4B01G024000	chr7A	89.571	326	34	0	9353	9678	285568795	285569120	1.940000e-111	414.0
42	TraesCS4B01G024000	chr7A	81.067	375	60	6	9255	9626	202179956	202179590	1.230000e-73	289.0
43	TraesCS4B01G024000	chr7A	88.889	153	14	2	3904	4053	130229695	130229543	1.660000e-42	185.0
44	TraesCS4B01G024000	chr2D	77.490	502	74	26	1689	2165	142675283	142675770	2.070000e-66	265.0
45	TraesCS4B01G024000	chr2D	88.889	153	14	2	3904	4053	86086117	86085965	1.660000e-42	185.0
46	TraesCS4B01G024000	chr2D	88.889	153	14	2	3904	4053	556055658	556055810	1.660000e-42	185.0
47	TraesCS4B01G024000	chr2D	100.000	28	0	0	9053	9080	70525548	70525575	1.800000e-02	52.8
48	TraesCS4B01G024000	chrUn	89.610	154	13	2	3903	4053	95996575	95996422	9.920000e-45	193.0
49	TraesCS4B01G024000	chr3B	88.889	153	14	2	3904	4053	14466836	14466988	1.660000e-42	185.0
50	TraesCS4B01G024000	chr2B	78.832	137	20	8	2488	2618	47643601	47643734	6.230000e-12	84.2
51	TraesCS4B01G024000	chr2B	100.000	28	0	0	9053	9080	106941227	106941254	1.800000e-02	52.8
52	TraesCS4B01G024000	chr3A	97.059	34	1	0	2121	2154	19498677	19498644	3.780000e-04	58.4
53	TraesCS4B01G024000	chr2A	100.000	28	0	0	9053	9080	70030298	70030325	1.800000e-02	52.8

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	TraesCS4B01G024000	chr4B	17228197	17237874	9677	False	17872.0	17872	100.000000	1	9678	1	chr4B.!!$F1	9677
1	TraesCS4B01G024000	chr4B	20078923	20088626	9703	True	1585.5	7227	87.533625	2	9040	8	chr4B.!!$R2	9038
2	TraesCS4B01G024000	chr4B	20072769	20073350	581	False	948.0	948	96.048000	3066	3647	1	chr4B.!!$F2	581
3	TraesCS4B01G024000	chr4B	17228212	17229003	791	False	534.0	534	91.111000	16	807	2	chr4B.!!$F3	791
4	TraesCS4B01G024000	chr4D	10746168	10755494	9326	True	2877.6	13418	87.713400	2	8871	5	chr4D.!!$R2	8869
5	TraesCS4B01G024000	chr4D	85674851	85675432	581	False	455.0	455	80.887000	9095	9676	1	chr4D.!!$F1	581
6	TraesCS4B01G024000	chr4A	593188684	593200897	12213	False	2447.6	8008	91.599000	2	9093	5	chr4A.!!$F6	9091
7	TraesCS4B01G024000	chr5B	526521874	526522455	581	True	601.0	601	85.274000	9095	9678	1	chr5B.!!$R1	583
8	TraesCS4B01G024000	chr7B	19014349	19014926	577	True	510.0	510	82.646000	9095	9675	1	chr7B.!!$R1	580
9	TraesCS4B01G024000	chr1B	148222879	148223459	580	True	503.0	503	82.333000	9095	9676	1	chr1B.!!$R1	581

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
934	1493	0.179073	CCGCTTCCAACCTCATCGAT	60.179	55.000	0.00	0.00	0.00	3.59	F
984	1543	0.250038	TGCTGCCACTTCACTCTGTC	60.250	55.000	0.00	0.00	0.00	3.51	F
2087	6376	0.687354	TTCTCTCCAGCGGCTTCTTT	59.313	50.000	0.00	0.00	0.00	2.52	F
2736	7055	2.900122	ATGCGGTGAAAACTGAATCG	57.100	45.000	0.00	0.00	0.00	3.34	F
3292	7616	4.990426	CCACTGCCATTTAAAACCAAAGAG	59.010	41.667	0.00	0.00	0.00	2.85	F
3994	8320	5.468746	AGTGAACATGCGTACTAAAATGTGT	59.531	36.000	0.00	0.00	33.65	3.72	F
4706	9060	4.222124	GACAAGGGTATCAGTTGTCCAT	57.778	45.455	8.59	0.00	42.79	3.41	F
5641	10008	3.808728	TGTGGTCTCTTAAGGCATATGC	58.191	45.455	19.79	19.79	41.14	3.14	F
6884	11415	2.629617	AGCATGGGTTTGAGAAAGGTTG	59.370	45.455	0.00	0.00	0.00	3.77	F
7505	12068	4.371786	CTTTGTTGTCTGTACTGAGAGCA	58.628	43.478	11.27	11.27	0.00	4.26	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1973	6262	0.331278	CTTAGGCATGTTGGGGGTGA	59.669	55.000	0.00	0.00	0.00	4.02	R
2802	7125	1.337635	GGCCAATGTGCCGAAATTTCA	60.338	47.619	17.99	0.00	42.54	2.69	R
3075	7399	5.496556	TCAACCGGTGTCATGAGATAAAAT	58.503	37.500	8.52	0.00	0.00	1.82	R
4295	8639	4.414182	ACCCCGGATGTTAAGATATTCCAA	59.586	41.667	0.73	0.00	0.00	3.53	R
4435	8783	5.546526	ACAAAGCAGAAAAGGACAAAACAA	58.453	33.333	0.00	0.00	0.00	2.83	R
5388	9744	3.708403	ATTTCATGAGGAGACACTGCA	57.292	42.857	0.00	0.00	0.00	4.41	R
6530	10906	1.657094	CGAAGCAATGCATTTTCCAGC	59.343	47.619	9.83	9.90	0.00	4.85	R
7296	11859	3.272574	ACAGACACTGGCATATCCAAG	57.727	47.619	0.00	0.00	46.01	3.61	R
8023	12679	0.032678	AGATGCGCCAGTAAGGATCG	59.967	55.000	4.18	0.00	39.67	3.69	R
9471	14142	0.248565	GAAGAACCGGGACTGGTACC	59.751	60.000	6.32	4.43	42.89	3.34	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
891	1450	1.413767	CGTCCATCCGCGAAACTGAG	61.414	60.000	8.23	0.00	0.00	3.35
933	1492	1.218047	CCGCTTCCAACCTCATCGA	59.782	57.895	0.00	0.00	0.00	3.59
934	1493	0.179073	CCGCTTCCAACCTCATCGAT	60.179	55.000	0.00	0.00	0.00	3.59
935	1494	1.212616	CGCTTCCAACCTCATCGATC	58.787	55.000	0.00	0.00	0.00	3.69
936	1495	1.212616	GCTTCCAACCTCATCGATCG	58.787	55.000	9.36	9.36	0.00	3.69
948	1507	2.918230	ATCGATCGGCCGGTGGTTTC	62.918	60.000	27.83	4.29	0.00	2.78
950	1509	1.376812	GATCGGCCGGTGGTTTCTT	60.377	57.895	27.83	0.00	0.00	2.52
951	1510	1.366854	GATCGGCCGGTGGTTTCTTC	61.367	60.000	27.83	0.00	0.00	2.87
952	1511	1.838073	ATCGGCCGGTGGTTTCTTCT	61.838	55.000	27.83	0.00	0.00	2.85
953	1512	1.599797	CGGCCGGTGGTTTCTTCTT	60.600	57.895	20.10	0.00	0.00	2.52
954	1513	1.852067	CGGCCGGTGGTTTCTTCTTG	61.852	60.000	20.10	0.00	0.00	3.02
955	1514	1.524008	GGCCGGTGGTTTCTTCTTGG	61.524	60.000	1.90	0.00	0.00	3.61
980	1539	0.880278	TTCGTGCTGCCACTTCACTC	60.880	55.000	0.00	0.00	39.86	3.51
981	1540	1.301244	CGTGCTGCCACTTCACTCT	60.301	57.895	0.00	0.00	39.86	3.24
982	1541	1.563435	CGTGCTGCCACTTCACTCTG	61.563	60.000	0.00	0.00	39.86	3.35
983	1542	0.533755	GTGCTGCCACTTCACTCTGT	60.534	55.000	0.00	0.00	38.93	3.41
984	1543	0.250038	TGCTGCCACTTCACTCTGTC	60.250	55.000	0.00	0.00	0.00	3.51
1689	5953	4.039124	GGTTTTGAGCTTTCAAGGGATTGA	59.961	41.667	0.00	0.00	0.00	2.57
1694	5958	3.615155	AGCTTTCAAGGGATTGACTAGC	58.385	45.455	12.77	12.77	38.30	3.42
1943	6230	4.832608	CCCTCTAACCGCGGCCAC	62.833	72.222	28.58	0.00	0.00	5.01
1973	6262	3.387947	CCGGCGAACCTACACCCT	61.388	66.667	9.30	0.00	0.00	4.34
2076	6365	2.499289	GACTGCATCTTCCTTCTCTCCA	59.501	50.000	0.00	0.00	0.00	3.86
2087	6376	0.687354	TTCTCTCCAGCGGCTTCTTT	59.313	50.000	0.00	0.00	0.00	2.52
2131	6424	6.017440	CGACTGACCCAAAAACTATTTTCAGA	60.017	38.462	0.00	0.00	36.62	3.27
2198	6491	4.021807	TGGCTATCATTGGCAATGCATTAG	60.022	41.667	30.62	27.03	38.77	1.73
2389	6683	4.875544	TGAGTTTTGAGTTCCTGTTTCG	57.124	40.909	0.00	0.00	0.00	3.46
2535	6841	8.732746	ATTTCTATGTACTACCGAAATTGCTT	57.267	30.769	0.00	0.00	32.19	3.91
2589	6897	8.356657	TCAGTGTACCGAAATGAATGAAATTTT	58.643	29.630	0.00	0.00	36.07	1.82
2703	7022	6.031471	CAGTGGTTACCAAAATATTTACGGC	58.969	40.000	5.33	0.00	34.18	5.68
2736	7055	2.900122	ATGCGGTGAAAACTGAATCG	57.100	45.000	0.00	0.00	0.00	3.34
2802	7125	8.791327	AAAGGTTGAATTTTTGTCAGTCAAAT	57.209	26.923	0.00	0.00	44.15	2.32
3292	7616	4.990426	CCACTGCCATTTAAAACCAAAGAG	59.010	41.667	0.00	0.00	0.00	2.85
3994	8320	5.468746	AGTGAACATGCGTACTAAAATGTGT	59.531	36.000	0.00	0.00	33.65	3.72
4595	8949	8.918202	ATTTGTTACCTCTTTTGTACTCATCA	57.082	30.769	0.00	0.00	0.00	3.07
4629	8983	8.289440	AGTTGCATCGCATTTCATTTATTATG	57.711	30.769	0.00	0.00	38.76	1.90
4658	9012	8.101654	TGCCATACTCTTACGTAATTTTGTTT	57.898	30.769	8.76	0.00	0.00	2.83
4706	9060	4.222124	GACAAGGGTATCAGTTGTCCAT	57.778	45.455	8.59	0.00	42.79	3.41
4818	9172	6.436218	GCCTATGGAGGTTTCCTTTTTCTTTA	59.564	38.462	0.00	0.00	45.78	1.85
5641	10008	3.808728	TGTGGTCTCTTAAGGCATATGC	58.191	45.455	19.79	19.79	41.14	3.14
6689	11065	7.256286	TCTTTGTACTTTCTCTTATAGCGTCC	58.744	38.462	0.00	0.00	0.00	4.79
6692	11068	6.359804	TGTACTTTCTCTTATAGCGTCCCTA	58.640	40.000	0.00	0.00	0.00	3.53
6760	11137	6.772770	TTTTTCATCATTGAAGTGCATGTG	57.227	33.333	0.00	0.00	42.60	3.21
6801	11178	6.672147	AGCAAATGTATTCTTGTCAACTGAC	58.328	36.000	2.78	2.78	44.97	3.51
6839	11216	7.967854	TGTTCACACATGACTTAAGAAAAACTG	59.032	33.333	10.09	0.00	33.38	3.16
6840	11217	6.494842	TCACACATGACTTAAGAAAAACTGC	58.505	36.000	10.09	0.00	0.00	4.40
6844	11221	8.682710	ACACATGACTTAAGAAAAACTGCTTTA	58.317	29.630	10.09	0.00	0.00	1.85
6845	11222	9.173939	CACATGACTTAAGAAAAACTGCTTTAG	57.826	33.333	10.09	0.00	0.00	1.85
6881	11412	5.665916	ATAAAGCATGGGTTTGAGAAAGG	57.334	39.130	3.86	0.00	34.94	3.11
6884	11415	2.629617	AGCATGGGTTTGAGAAAGGTTG	59.370	45.455	0.00	0.00	0.00	3.77
7109	11672	6.155827	GGCATATTTTTGTTCTTGCACTGTA	58.844	36.000	0.00	0.00	0.00	2.74
7505	12068	4.371786	CTTTGTTGTCTGTACTGAGAGCA	58.628	43.478	11.27	11.27	0.00	4.26
8023	12679	1.376609	CCGGCATTCAGGTAACAGCC	61.377	60.000	0.00	0.00	37.94	4.85
8039	12698	2.499205	CCGATCCTTACTGGCGCA	59.501	61.111	10.83	0.00	35.26	6.09
8040	12699	1.069765	CCGATCCTTACTGGCGCAT	59.930	57.895	10.83	0.00	35.26	4.73
8099	12759	6.597562	ACACTTTAGTACCCTTTCACATTGA	58.402	36.000	0.00	0.00	0.00	2.57
8176	12836	2.167281	ACCATGTCCTCTTCGATGACAG	59.833	50.000	11.51	1.94	39.66	3.51
8275	12935	5.126061	ACTGCAACCCTCTGCTAAAAATATG	59.874	40.000	0.00	0.00	43.07	1.78
8390	13051	8.915871	ATGTGTAATTTTGCATTGTCTGATAC	57.084	30.769	0.00	0.00	0.00	2.24
8413	13074	0.535102	CCTTTTGCCTGAGTGTCCGT	60.535	55.000	0.00	0.00	0.00	4.69
8506	13168	4.226761	GTTGCAAATTAACAGTTCCTCCG	58.773	43.478	0.00	0.00	0.00	4.63
8587	13249	5.709594	TCTGATCAGGGATCATCTTCTGTA	58.290	41.667	22.42	0.00	46.16	2.74
8619	13281	2.730934	ATGCATGATCAAGCTGTCCT	57.269	45.000	22.26	1.46	0.00	3.85
8694	13356	1.857217	CTGAAGACCGATCTCGCATTG	59.143	52.381	0.00	0.00	38.18	2.82
8745	13407	6.266558	ACCTGTGGAACTTGCAAATGTTATAA	59.733	34.615	0.00	0.00	38.04	0.98
8746	13408	6.586082	CCTGTGGAACTTGCAAATGTTATAAC	59.414	38.462	8.75	8.75	38.04	1.89
8754	13416	7.505258	ACTTGCAAATGTTATAACCCAAAACT	58.495	30.769	13.01	0.00	0.00	2.66
8872	13537	9.294030	CATTACTCAAATTGCCAATCTAGTTTC	57.706	33.333	5.07	0.00	0.00	2.78
8898	13563	2.779506	TCTTCTTTTCGAAAGGGAGGC	58.220	47.619	23.75	0.00	0.00	4.70
8916	13581	0.743345	GCTAAAACCTCCGGCGATGT	60.743	55.000	9.30	0.00	0.00	3.06
8930	13595	3.483574	CGGCGATGTACATTCTTGTTGAC	60.484	47.826	10.30	0.00	37.28	3.18
8932	13597	4.154195	GGCGATGTACATTCTTGTTGACTT	59.846	41.667	10.30	0.00	37.28	3.01
8940	13605	8.826710	TGTACATTCTTGTTGACTTTTCTGTAG	58.173	33.333	0.00	0.00	37.28	2.74
8989	13655	7.093596	GGTGAACCATTACAAGGTACTAGTAGT	60.094	40.741	8.14	8.14	38.76	2.73
8994	13660	3.863142	ACAAGGTACTAGTAGTTGCCG	57.137	47.619	18.68	3.20	38.49	5.69
8995	13661	3.160269	ACAAGGTACTAGTAGTTGCCGT	58.840	45.455	18.68	7.11	38.49	5.68
8999	13665	4.625816	AGGTACTAGTAGTTGCCGTTGCA	61.626	47.826	8.40	0.00	42.20	4.08
9067	13736	4.948004	TGTCACACATATACTCTCTCCGTT	59.052	41.667	0.00	0.00	0.00	4.44
9075	13744	8.141909	CACATATACTCTCTCCGTTCCAAAATA	58.858	37.037	0.00	0.00	0.00	1.40
9076	13745	8.871125	ACATATACTCTCTCCGTTCCAAAATAT	58.129	33.333	0.00	0.00	0.00	1.28
9151	13820	5.564651	GCTTTCAAGAAATGTCGGGATTGAA	60.565	40.000	0.00	0.00	35.50	2.69
9161	13830	9.849166	GAAATGTCGGGATTGAAAATAAACTTA	57.151	29.630	0.00	0.00	0.00	2.24
9206	13875	2.588620	GGATACATCACGGAGGAGTCT	58.411	52.381	0.00	0.00	0.00	3.24
9212	13881	0.693622	TCACGGAGGAGTCTCTGAGT	59.306	55.000	4.32	0.00	46.72	3.41
9242	13911	6.037172	CCAATCGACTTAATTGTTGACTAGGG	59.963	42.308	0.00	0.00	33.65	3.53
9333	14002	6.180472	CCTACTATGTCCAAGGTTCAACATT	58.820	40.000	0.00	0.00	34.39	2.71
9385	14054	1.296715	CAAGGCTGCGAGGGTAGTT	59.703	57.895	0.00	0.00	0.00	2.24
9399	14068	5.561679	GAGGGTAGTTTTGATCAACTCCTT	58.438	41.667	7.89	4.35	38.07	3.36
9471	14142	2.172082	TCTTCCATCAGGAGATTGCCAG	59.828	50.000	0.00	0.00	46.74	4.85
9491	14162	0.971386	GTACCAGTCCCGGTTCTTCA	59.029	55.000	0.00	0.00	40.67	3.02
9585	14256	2.250924	CAGCCTTGGGTTCATTTCCTT	58.749	47.619	0.00	0.00	0.00	3.36
9601	14272	3.071874	TCCTTCAAGCGGATGAACATT	57.928	42.857	0.00	0.00	35.55	2.71
9608	14279	2.936202	AGCGGATGAACATTGCCTTAT	58.064	42.857	8.54	0.00	0.00	1.73
9643	14315	0.445043	GGCGTATTGAAACCGGTGAC	59.555	55.000	8.52	6.03	0.00	3.67

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
891	1450	1.838077	AGGCGGGGAATATATACAGGC	59.162	52.381	0.00	0.00	0.00	4.85
933	1492	1.376812	GAAGAAACCACCGGCCGAT	60.377	57.895	30.73	6.36	0.00	4.18
934	1493	2.031465	GAAGAAACCACCGGCCGA	59.969	61.111	30.73	0.00	0.00	5.54
935	1494	1.599797	AAGAAGAAACCACCGGCCG	60.600	57.895	21.04	21.04	0.00	6.13
936	1495	1.524008	CCAAGAAGAAACCACCGGCC	61.524	60.000	0.00	0.00	0.00	6.13
948	1507	1.676006	AGCACGAAACCAACCAAGAAG	59.324	47.619	0.00	0.00	0.00	2.85
950	1509	1.021202	CAGCACGAAACCAACCAAGA	58.979	50.000	0.00	0.00	0.00	3.02
951	1510	0.594796	GCAGCACGAAACCAACCAAG	60.595	55.000	0.00	0.00	0.00	3.61
952	1511	1.435515	GCAGCACGAAACCAACCAA	59.564	52.632	0.00	0.00	0.00	3.67
953	1512	2.485795	GGCAGCACGAAACCAACCA	61.486	57.895	0.00	0.00	0.00	3.67
954	1513	2.335011	GGCAGCACGAAACCAACC	59.665	61.111	0.00	0.00	0.00	3.77
955	1514	1.299089	GTGGCAGCACGAAACCAAC	60.299	57.895	0.00	0.00	33.03	3.77
1689	5953	2.232452	CAGTTACCTGACAGCTGCTAGT	59.768	50.000	15.27	9.03	41.50	2.57
1891	6170	4.341502	CAACAAGGCGGCGGTTGG	62.342	66.667	29.01	17.12	38.52	3.77
1892	6171	4.999939	GCAACAAGGCGGCGGTTG	63.000	66.667	30.90	30.90	43.53	3.77
1919	6206	2.444256	GCGGTTAGAGGGATGGCCT	61.444	63.158	3.32	0.00	0.00	5.19
1973	6262	0.331278	CTTAGGCATGTTGGGGGTGA	59.669	55.000	0.00	0.00	0.00	4.02
2076	6365	1.611936	GGAAGGAAGAAAGAAGCCGCT	60.612	52.381	0.00	0.00	0.00	5.52
2087	6376	4.041691	AGTCGATTTTGGAAGGAAGGAAGA	59.958	41.667	0.00	0.00	0.00	2.87
2131	6424	6.758886	GCTCACAATAGCTACTTGTAAGTCAT	59.241	38.462	16.23	0.00	39.50	3.06
2198	6491	7.670559	TCCTATTCTCTACAAGCTATTAGGGAC	59.329	40.741	3.97	0.00	0.00	4.46
2389	6683	5.499139	TCAGCGATGACCAAAATATTTCC	57.501	39.130	0.00	0.00	0.00	3.13
2589	6897	5.509716	TCTCACTTTCAGTGTAGTTTCGA	57.490	39.130	3.87	0.00	46.03	3.71
2595	6914	8.553459	AATTATGGTTCTCACTTTCAGTGTAG	57.447	34.615	3.87	1.52	46.03	2.74
2703	7022	9.739786	GTTTTCACCGCATTTTATTTGATTAAG	57.260	29.630	0.00	0.00	0.00	1.85
2736	7055	3.780804	AAACAAATTAAGTTGGGCCCC	57.219	42.857	22.27	4.15	32.50	5.80
2802	7125	1.337635	GGCCAATGTGCCGAAATTTCA	60.338	47.619	17.99	0.00	42.54	2.69
2855	7178	9.739276	AACATAAGAATGAGAACAGGTAAATCA	57.261	29.630	0.00	0.00	36.54	2.57
3004	7328	5.711976	ACCCCAATACTGAGAAACAAATCTG	59.288	40.000	0.00	0.00	0.00	2.90
3075	7399	5.496556	TCAACCGGTGTCATGAGATAAAAT	58.503	37.500	8.52	0.00	0.00	1.82
3388	7712	6.071672	CCTTTTCCCTGAAAAAGAGAAGGATC	60.072	42.308	9.96	0.00	45.12	3.36
4295	8639	4.414182	ACCCCGGATGTTAAGATATTCCAA	59.586	41.667	0.73	0.00	0.00	3.53
4435	8783	5.546526	ACAAAGCAGAAAAGGACAAAACAA	58.453	33.333	0.00	0.00	0.00	2.83
4595	8949	6.867816	TGAAATGCGATGCAACTAAAGAAAAT	59.132	30.769	0.00	0.00	43.62	1.82
4629	8983	7.478520	AAATTACGTAAGAGTATGGCATGAC	57.521	36.000	14.25	0.00	43.62	3.06
4658	9012	6.147164	CGTCTAGGTCAAATCTGTAAAAAGCA	59.853	38.462	0.00	0.00	0.00	3.91
4818	9172	9.857656	TTTAAGCAATCAGATAGATCAGGATTT	57.142	29.630	0.00	0.00	35.39	2.17
5162	9517	5.643379	AAGCACAAGACAAGAACAGAAAA	57.357	34.783	0.00	0.00	0.00	2.29
5239	9594	6.198650	TCATCAATGCCATAGTTGTTTCTG	57.801	37.500	0.00	0.00	0.00	3.02
5376	9732	4.142381	GGAGACACTGCACTCAAAGTTTTT	60.142	41.667	4.64	0.00	35.17	1.94
5388	9744	3.708403	ATTTCATGAGGAGACACTGCA	57.292	42.857	0.00	0.00	0.00	4.41
5641	10008	9.751542	CCCTGACTAAGTATCAACTAATAAGTG	57.248	37.037	0.00	0.00	35.62	3.16
5706	10073	9.979578	AGATAATTACAATTGTCAGCAAAAACA	57.020	25.926	15.85	0.00	38.51	2.83
5981	10352	4.691860	ACAGCATTGTATTCTGAGTTGC	57.308	40.909	0.00	0.00	35.25	4.17
6022	10393	6.734104	AAGAAGAAAAAGATGGTCAGATCG	57.266	37.500	0.00	0.00	0.00	3.69
6031	10402	9.467258	TTGCTACATCAAAAGAAGAAAAAGATG	57.533	29.630	0.00	0.00	37.85	2.90
6530	10906	1.657094	CGAAGCAATGCATTTTCCAGC	59.343	47.619	9.83	9.90	0.00	4.85
6689	11065	7.227512	AGGTCTCGAGCAAAATAATTGAATAGG	59.772	37.037	7.81	0.00	0.00	2.57
6692	11068	7.770897	ACTAGGTCTCGAGCAAAATAATTGAAT	59.229	33.333	7.81	0.00	0.00	2.57
6787	11164	6.920817	ACAGATATACGTCAGTTGACAAGAA	58.079	36.000	12.33	0.00	44.99	2.52
6801	11178	7.063426	AGTCATGTGTGAACAAACAGATATACG	59.937	37.037	4.18	0.00	32.67	3.06
6844	11221	9.617523	CCCATGCTTTATAAAATGGATTTTTCT	57.382	29.630	22.54	0.00	41.84	2.52
6845	11222	9.394767	ACCCATGCTTTATAAAATGGATTTTTC	57.605	29.630	22.54	0.00	41.84	2.29
6881	11412	4.213482	AGCAAACGAGGTTTATCTCACAAC	59.787	41.667	0.00	0.00	33.70	3.32
6884	11415	3.746492	ACAGCAAACGAGGTTTATCTCAC	59.254	43.478	0.00	0.00	33.70	3.51
6898	11434	6.902341	TGAACTCATATTCTCAACAGCAAAC	58.098	36.000	0.00	0.00	0.00	2.93
7086	11649	6.863126	ACTACAGTGCAAGAACAAAAATATGC	59.137	34.615	0.00	0.00	0.00	3.14
7109	11672	8.747538	AACATTACTTTGTAGAAACTGGAACT	57.252	30.769	0.00	0.00	0.00	3.01
7296	11859	3.272574	ACAGACACTGGCATATCCAAG	57.727	47.619	0.00	0.00	46.01	3.61
7505	12068	5.068723	CCATCTCTGCAAGGAAAGCAAATAT	59.931	40.000	0.00	0.00	42.17	1.28
7916	12572	8.809066	ACCTGACAACAACATATGTAGTTAGTA	58.191	33.333	9.21	0.00	42.99	1.82
8023	12679	0.032678	AGATGCGCCAGTAAGGATCG	59.967	55.000	4.18	0.00	39.67	3.69
8039	12698	7.704359	AAGGAGAAAATAAGGATCTGGAGAT	57.296	36.000	0.00	0.00	37.51	2.75
8040	12699	7.182749	TCAAAGGAGAAAATAAGGATCTGGAGA	59.817	37.037	0.00	0.00	0.00	3.71
8099	12759	7.439056	GCATAAGCAATTGCCATTACATTACTT	59.561	33.333	26.45	11.90	43.38	2.24
8176	12836	3.526825	GCATCGGCGGTGAAATTAC	57.473	52.632	26.58	0.00	0.00	1.89
8275	12935	0.396060	GGCATCAGTGAGAGGGGATC	59.604	60.000	0.00	0.00	0.00	3.36
8390	13051	2.427506	GACACTCAGGCAAAAGGTAGG	58.572	52.381	0.00	0.00	0.00	3.18
8413	13074	1.344438	CATGGCTATAGGGAGCGACAA	59.656	52.381	1.04	0.00	43.83	3.18
8603	13265	2.414994	ACCAGGACAGCTTGATCATG	57.585	50.000	0.00	0.00	0.00	3.07
8694	13356	1.549170	ACCGTCCACTATTGTCCAGAC	59.451	52.381	0.00	0.00	0.00	3.51
8745	13407	5.187186	AGACATCATAGTACGAGTTTTGGGT	59.813	40.000	0.00	0.00	0.00	4.51
8746	13408	5.661458	AGACATCATAGTACGAGTTTTGGG	58.339	41.667	0.00	0.00	0.00	4.12
8754	13416	6.275494	TCCAAACAAGACATCATAGTACGA	57.725	37.500	0.00	0.00	0.00	3.43
8836	13501	5.870978	GCAATTTGAGTAATGCATTCAGGTT	59.129	36.000	16.86	4.38	0.00	3.50
8916	13581	9.261180	CTCTACAGAAAAGTCAACAAGAATGTA	57.739	33.333	0.00	0.00	39.40	2.29
8930	13595	9.314321	TCTCTTGTTTTGTACTCTACAGAAAAG	57.686	33.333	0.00	0.00	40.24	2.27
8932	13597	9.095065	GTTCTCTTGTTTTGTACTCTACAGAAA	57.905	33.333	0.00	0.00	40.24	2.52
8940	13605	6.935208	ACCCATAGTTCTCTTGTTTTGTACTC	59.065	38.462	0.00	0.00	0.00	2.59
8994	13660	3.758931	GATGGCCCCCGTTGCAAC	61.759	66.667	19.89	19.89	0.00	4.17
8999	13665	0.560688	AAATATGGATGGCCCCCGTT	59.439	50.000	10.82	2.35	0.00	4.44
9000	13666	0.560688	AAAATATGGATGGCCCCCGT	59.439	50.000	0.00	5.68	0.00	5.28
9001	13667	1.715785	AAAAATATGGATGGCCCCCG	58.284	50.000	0.00	0.00	0.00	5.73
9003	13669	7.553504	AACTATTAAAAATATGGATGGCCCC	57.446	36.000	0.00	0.00	0.00	5.80
9043	13712	4.335874	ACGGAGAGAGTATATGTGTGACAC	59.664	45.833	9.14	9.14	34.56	3.67
9044	13713	4.524053	ACGGAGAGAGTATATGTGTGACA	58.476	43.478	0.00	0.00	0.00	3.58
9045	13714	5.502153	AACGGAGAGAGTATATGTGTGAC	57.498	43.478	0.00	0.00	0.00	3.67
9046	13715	4.579340	GGAACGGAGAGAGTATATGTGTGA	59.421	45.833	0.00	0.00	0.00	3.58
9047	13716	4.338400	TGGAACGGAGAGAGTATATGTGTG	59.662	45.833	0.00	0.00	0.00	3.82
9048	13717	4.533815	TGGAACGGAGAGAGTATATGTGT	58.466	43.478	0.00	0.00	0.00	3.72
9049	13718	5.515797	TTGGAACGGAGAGAGTATATGTG	57.484	43.478	0.00	0.00	0.00	3.21
9050	13719	6.540438	TTTTGGAACGGAGAGAGTATATGT	57.460	37.500	0.00	0.00	0.00	2.29
9093	13762	7.234355	AGGAACTTAAGATGTTGAATGTCCTT	58.766	34.615	10.09	0.00	27.25	3.36
9151	13820	7.656137	TCACTTCGCTCTTCACTAAGTTTATTT	59.344	33.333	0.00	0.00	34.13	1.40
9161	13830	1.620819	ACCATCACTTCGCTCTTCACT	59.379	47.619	0.00	0.00	0.00	3.41
9206	13875	6.954487	TTAAGTCGATTGGCTATACTCAGA	57.046	37.500	0.00	0.00	0.00	3.27
9209	13878	7.948278	ACAATTAAGTCGATTGGCTATACTC	57.052	36.000	0.00	0.00	38.50	2.59
9212	13881	7.985184	AGTCAACAATTAAGTCGATTGGCTATA	59.015	33.333	0.00	0.00	38.50	1.31
9242	13911	5.764131	CCGAGATAAGTAGTCAGGAATGAC	58.236	45.833	0.06	0.06	39.00	3.06
9250	13919	2.035961	GGCATGCCGAGATAAGTAGTCA	59.964	50.000	23.48	0.00	0.00	3.41
9333	14002	0.397675	TTGCCATGTGGTTCAACCCA	60.398	50.000	3.42	1.86	37.50	4.51
9343	14012	2.259204	CAACGCCCTTGCCATGTG	59.741	61.111	0.00	0.00	0.00	3.21
9344	14013	2.990967	CCAACGCCCTTGCCATGT	60.991	61.111	0.00	0.00	0.00	3.21
9373	14042	3.071479	GTTGATCAAAACTACCCTCGCA	58.929	45.455	10.35	0.00	0.00	5.10
9385	14054	6.885918	TGCTAATCATGAAGGAGTTGATCAAA	59.114	34.615	10.35	0.00	30.03	2.69
9450	14121	2.172082	CTGGCAATCTCCTGATGGAAGA	59.828	50.000	0.00	0.00	42.66	2.87
9452	14123	1.213678	CCTGGCAATCTCCTGATGGAA	59.786	52.381	0.00	0.00	42.66	3.53
9471	14142	0.248565	GAAGAACCGGGACTGGTACC	59.751	60.000	6.32	4.43	42.89	3.34
9491	14162	3.341469	TATCACCCTTCCCCGCCCT	62.341	63.158	0.00	0.00	0.00	5.19
9496	14167	0.694444	TCTGCCTATCACCCTTCCCC	60.694	60.000	0.00	0.00	0.00	4.81
9575	14246	3.684908	TCATCCGCTTGAAGGAAATGAA	58.315	40.909	0.00	0.00	41.69	2.57
9585	14256	0.810648	GGCAATGTTCATCCGCTTGA	59.189	50.000	6.96	0.00	0.00	3.02
9620	14291	1.091537	CCGGTTTCAATACGCCACAT	58.908	50.000	0.00	0.00	0.00	3.21
9643	14315	1.524621	CTCAAGCCATAGCCCACCG	60.525	63.158	0.00	0.00	41.25	4.94
9646	14318	3.009473	GGATAATCTCAAGCCATAGCCCA	59.991	47.826	0.00	0.00	41.25	5.36
9652	14324	1.800805	CGCGGATAATCTCAAGCCAT	58.199	50.000	0.00	0.00	0.00	4.40

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.