AutoCloner

Multiple sequence alignment - TraesCS1D01G128500

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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	TraesCS1D01G128500	chr1D	100.000	4991	0	0	1872	6862	141710459	141705469	0.000000e+00	9217.0
1	TraesCS1D01G128500	chr1D	100.000	1578	0	0	1	1578	141712330	141710753	0.000000e+00	2915.0
2	TraesCS1D01G128500	chr1D	100.000	452	0	0	7229	7680	141705102	141704651	0.000000e+00	835.0
3	TraesCS1D01G128500	chr1D	91.981	212	17	0	156	367	453231701	453231912	1.620000e-76	298.0
4	TraesCS1D01G128500	chr1D	91.667	72	3	3	6192	6262	440050456	440050387	6.340000e-16	97.1
5	TraesCS1D01G128500	chr1B	98.091	4976	61	11	1872	6840	195595665	195590717	0.000000e+00	8632.0
6	TraesCS1D01G128500	chr1B	97.098	896	14	7	691	1578	195596583	195595692	0.000000e+00	1500.0
7	TraesCS1D01G128500	chr1B	95.796	333	10	1	7352	7680	195590456	195590124	1.130000e-147	534.0
8	TraesCS1D01G128500	chr1A	95.960	4381	128	21	1872	6211	148954499	148958871	0.000000e+00	7064.0
9	TraesCS1D01G128500	chr1A	96.633	891	17	7	700	1578	148953551	148954440	0.000000e+00	1467.0
10	TraesCS1D01G128500	chr1A	97.822	597	13	0	6266	6862	148958885	148959481	0.000000e+00	1031.0
11	TraesCS1D01G128500	chr1A	91.960	398	22	7	7290	7680	148959827	148960221	4.050000e-152	549.0
12	TraesCS1D01G128500	chr1A	84.848	198	21	2	232	420	584838800	584838997	2.830000e-44	191.0
13	TraesCS1D01G128500	chr1A	84.146	164	17	3	145	299	581293978	581293815	4.800000e-32	150.0
14	TraesCS1D01G128500	chr1A	82.031	128	20	2	340	465	144563314	144563440	1.050000e-18	106.0
15	TraesCS1D01G128500	chr2D	96.110	617	17	2	1	616	516394617	516395227	0.000000e+00	1000.0
16	TraesCS1D01G128500	chr2D	96.852	540	10	2	1	539	305943181	305943714	0.000000e+00	896.0
17	TraesCS1D01G128500	chr7B	90.123	648	43	8	1	636	614225092	614224454	0.000000e+00	822.0
18	TraesCS1D01G128500	chr7B	96.923	65	2	0	6199	6263	661996385	661996449	8.150000e-20	110.0
19	TraesCS1D01G128500	chr4A	92.632	475	26	4	1	475	419970915	419970450	0.000000e+00	675.0
20	TraesCS1D01G128500	chr4A	91.789	475	30	3	1	475	46438041	46438506	0.000000e+00	652.0
21	TraesCS1D01G128500	chr4B	84.431	501	50	11	157	630	349116662	349117161	1.170000e-127	468.0
22	TraesCS1D01G128500	chr4B	81.124	498	57	9	157	621	42544322	42544815	1.570000e-96	364.0
23	TraesCS1D01G128500	chr4B	92.405	79	6	0	4388	4466	16428892	16428970	6.300000e-21	113.0
24	TraesCS1D01G128500	chr4B	92.405	79	6	0	4388	4466	229683064	229682986	6.300000e-21	113.0
25	TraesCS1D01G128500	chr4B	100.000	28	0	0	601	628	467924108	467924081	1.400000e-02	52.8
26	TraesCS1D01G128500	chr2B	84.000	500	53	10	156	629	651323350	651323848	9.090000e-124	455.0
27	TraesCS1D01G128500	chr2B	83.832	501	52	12	156	629	480011294	480010796	4.230000e-122	449.0
28	TraesCS1D01G128500	chr6B	83.806	494	52	11	156	622	480658749	480658257	1.970000e-120	444.0
29	TraesCS1D01G128500	chr6B	83.537	492	53	11	157	621	95581595	95581105	1.180000e-117	435.0
30	TraesCS1D01G128500	chr6B	94.318	88	5	0	6271	6358	278674697	278674610	1.340000e-27	135.0
31	TraesCS1D01G128500	chr6B	89.888	89	8	1	4379	4466	66015852	66015764	6.300000e-21	113.0
32	TraesCS1D01G128500	chr6B	91.667	72	5	1	6192	6263	6187699	6187629	1.760000e-16	99.0
33	TraesCS1D01G128500	chr4D	88.398	362	29	6	156	505	48514592	48514952	2.560000e-114	424.0
34	TraesCS1D01G128500	chr4D	89.773	88	9	0	6276	6363	231221874	231221787	6.300000e-21	113.0
35	TraesCS1D01G128500	chr5B	83.505	485	36	17	158	618	384517432	384517896	5.550000e-111	412.0
36	TraesCS1D01G128500	chr5B	86.207	116	16	0	350	465	617238980	617239095	8.090000e-25	126.0
37	TraesCS1D01G128500	chr5B	92.405	79	6	0	4388	4466	581597360	581597438	6.300000e-21	113.0
38	TraesCS1D01G128500	chr5B	92.857	70	4	1	6194	6263	546085305	546085373	4.900000e-17	100.0
39	TraesCS1D01G128500	chr5B	100.000	29	0	0	603	631	536581976	536582004	4.000000e-03	54.7
40	TraesCS1D01G128500	chr5A	81.299	508	60	18	156	628	622982986	622983493	5.620000e-101	379.0
41	TraesCS1D01G128500	chr6D	93.478	92	6	0	6271	6362	155602045	155601954	3.740000e-28	137.0
42	TraesCS1D01G128500	chr6D	95.000	80	4	0	6271	6350	13067041	13067120	8.090000e-25	126.0
43	TraesCS1D01G128500	chr6D	96.774	62	2	0	6202	6263	185090705	185090766	3.790000e-18	104.0
44	TraesCS1D01G128500	chr6A	93.478	92	6	0	6271	6362	209391425	209391334	3.740000e-28	137.0
45	TraesCS1D01G128500	chr3D	87.963	108	11	2	6266	6372	108916257	108916363	8.090000e-25	126.0
46	TraesCS1D01G128500	chr3D	92.222	90	6	1	6266	6355	523157382	523157470	8.090000e-25	126.0
47	TraesCS1D01G128500	chrUn	93.671	79	5	0	4388	4466	434714136	434714214	1.350000e-22	119.0
48	TraesCS1D01G128500	chrUn	92.405	79	6	0	4388	4466	392729878	392729956	6.300000e-21	113.0
49	TraesCS1D01G128500	chrUn	92.405	79	6	0	4388	4466	420601279	420601201	6.300000e-21	113.0
50	TraesCS1D01G128500	chr3B	96.923	65	0	2	6201	6263	802705159	802705095	2.930000e-19	108.0
51	TraesCS1D01G128500	chr3B	98.276	58	1	0	6206	6263	132527384	132527327	1.360000e-17	102.0
52	TraesCS1D01G128500	chr7D	88.462	78	8	1	6189	6266	575717784	575717708	8.210000e-15	93.5
53	TraesCS1D01G128500	chr2A	100.000	29	0	0	601	629	153035173	153035201	4.000000e-03	54.7

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	TraesCS1D01G128500	chr1D	141704651	141712330	7679	True	4322.333333	9217	100.00000	1	7680	3	chr1D.!!$R2	7679
1	TraesCS1D01G128500	chr1B	195590124	195596583	6459	True	3555.333333	8632	96.99500	691	7680	3	chr1B.!!$R1	6989
2	TraesCS1D01G128500	chr1A	148953551	148960221	6670	False	2527.750000	7064	95.59375	700	7680	4	chr1A.!!$F3	6980
3	TraesCS1D01G128500	chr2D	516394617	516395227	610	False	1000.000000	1000	96.11000	1	616	1	chr2D.!!$F2	615
4	TraesCS1D01G128500	chr2D	305943181	305943714	533	False	896.000000	896	96.85200	1	539	1	chr2D.!!$F1	538
5	TraesCS1D01G128500	chr7B	614224454	614225092	638	True	822.000000	822	90.12300	1	636	1	chr7B.!!$R1	635
6	TraesCS1D01G128500	chr5A	622982986	622983493	507	False	379.000000	379	81.29900	156	628	1	chr5A.!!$F1	472

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	Hairpin	End Stability	Orientation
664	709	0.034477	GGTGGACGATTTGGATGGGT	60.034	55.000	0.00	4.51	F
669	714	0.038166	ACGATTTGGATGGGTGCAGT	59.962	50.000	0.00	4.40	F
673	718	0.187117	TTTGGATGGGTGCAGTTGGA	59.813	50.000	0.00	3.53	F
683	728	0.321346	TGCAGTTGGATTCGCTCTCA	59.679	50.000	0.00	3.27	F
1017	1070	0.531200	GAATGGAGGACTCGAACGGT	59.469	55.000	0.00	4.83	F
2094	2153	0.884704	TGTGCTTTTCCGTCAGAGCC	60.885	55.000	34.30	4.70	F
2101	2160	2.529780	TTCCGTCAGAGCCGTTTTAA	57.470	45.000	0.00	1.52	F
2105	2164	2.739913	CCGTCAGAGCCGTTTTAATGAA	59.260	45.455	0.00	2.57	F
3575	3640	0.980231	AGAGTCTGGAGTGGGATGGC	60.980	60.000	0.00	4.40	F
4750	4839	4.972440	GGCTGATTCGTCAAATTATTCTGC	59.028	41.667	0.00	4.26	F
5538	5627	6.022163	AGAAATGTCAAGCTCAAAATGGAG	57.978	37.500	37.97	3.86	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2111	2170	0.599558	GGCAGCTGCACAGATTGAAA	59.400	50.000	37.63	0.00	44.36	2.69	R
2115	2174	0.677098	CTCTGGCAGCTGCACAGATT	60.677	55.000	37.65	0.00	42.78	2.40	R
2121	2180	0.958876	CAATGACTCTGGCAGCTGCA	60.959	55.000	37.63	23.01	44.36	4.41	R
2122	2181	0.959372	ACAATGACTCTGGCAGCTGC	60.959	55.000	30.88	30.88	41.14	5.25	R
2517	2576	1.831736	GCTGGTAGACTAAGGCTGGAA	59.168	52.381	0.00	0.00	0.00	3.53	R
2927	2987	1.923899	TGTGTGCATGCACTTTGTTG	58.076	45.000	41.43	0.00	46.30	3.33	R
3575	3640	2.690653	ATCCCCAACACACACCACCG	62.691	60.000	0.00	0.00	0.00	4.94	R
4059	4128	4.524802	TGGAAATATGGCTGTGGAATCT	57.475	40.909	0.00	0.00	0.00	2.40	R
4674	4763	7.175641	GGATAACTTGGCTGCATGATTAATACT	59.824	37.037	0.50	0.00	0.00	2.12	R
5925	6015	1.214424	AGTAAGCCACCCAACAAGTGT	59.786	47.619	0.00	0.00	33.20	3.55	R
6706	6805	3.216187	TCTTTGAATCCGTTGGTCCAA	57.784	42.857	0.00	0.00	0.00	3.53	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
426	448	1.457643	CGGAGGCTGGGTGGATCTA	60.458	63.158	0.00	0.00	0.00	1.98
504	526	3.882444	TCGGGAGAGAAAGAAGTATCGA	58.118	45.455	0.00	0.00	0.00	3.59
520	565	3.662759	ATCGAGGCCCAAAAATTAGGA	57.337	42.857	0.00	0.00	0.00	2.94
565	610	1.388837	GGTTGTTTCCCTTGTGCGGT	61.389	55.000	0.00	0.00	0.00	5.68
592	637	2.356673	GCCCGAGTTTTCGTCCGT	60.357	61.111	0.00	0.00	45.28	4.69
637	682	8.545229	TTAATAGTAGTGTAGATACGGAGAGC	57.455	38.462	0.00	0.00	0.00	4.09
638	683	3.391965	AGTAGTGTAGATACGGAGAGCG	58.608	50.000	0.00	0.00	0.00	5.03
639	684	1.595466	AGTGTAGATACGGAGAGCGG	58.405	55.000	0.00	0.00	0.00	5.52
640	685	1.140452	AGTGTAGATACGGAGAGCGGA	59.860	52.381	0.00	0.00	0.00	5.54
641	686	1.263752	GTGTAGATACGGAGAGCGGAC	59.736	57.143	0.00	0.00	0.00	4.79
642	687	0.512085	GTAGATACGGAGAGCGGACG	59.488	60.000	0.00	0.00	0.00	4.79
643	688	1.226686	TAGATACGGAGAGCGGACGC	61.227	60.000	8.91	8.91	42.33	5.19
655	700	4.446413	GGACGCGGGTGGACGATT	62.446	66.667	10.96	0.00	35.47	3.34
656	701	2.433664	GACGCGGGTGGACGATTT	60.434	61.111	10.96	0.00	35.47	2.17
657	702	2.736682	GACGCGGGTGGACGATTTG	61.737	63.158	10.96	0.00	35.47	2.32
658	703	3.496131	CGCGGGTGGACGATTTGG	61.496	66.667	0.00	0.00	35.47	3.28
659	704	2.046700	GCGGGTGGACGATTTGGA	60.047	61.111	0.00	0.00	35.47	3.53
660	705	1.451387	GCGGGTGGACGATTTGGAT	60.451	57.895	0.00	0.00	35.47	3.41
661	706	1.714899	GCGGGTGGACGATTTGGATG	61.715	60.000	0.00	0.00	35.47	3.51
662	707	1.095228	CGGGTGGACGATTTGGATGG	61.095	60.000	0.00	0.00	35.47	3.51
663	708	0.751643	GGGTGGACGATTTGGATGGG	60.752	60.000	0.00	0.00	0.00	4.00
664	709	0.034477	GGTGGACGATTTGGATGGGT	60.034	55.000	0.00	0.00	0.00	4.51
665	710	1.094785	GTGGACGATTTGGATGGGTG	58.905	55.000	0.00	0.00	0.00	4.61
666	711	0.679640	TGGACGATTTGGATGGGTGC	60.680	55.000	0.00	0.00	0.00	5.01
667	712	0.679640	GGACGATTTGGATGGGTGCA	60.680	55.000	0.00	0.00	0.00	4.57
668	713	0.734889	GACGATTTGGATGGGTGCAG	59.265	55.000	0.00	0.00	0.00	4.41
669	714	0.038166	ACGATTTGGATGGGTGCAGT	59.962	50.000	0.00	0.00	0.00	4.40
670	715	1.176527	CGATTTGGATGGGTGCAGTT	58.823	50.000	0.00	0.00	0.00	3.16
671	716	1.135315	CGATTTGGATGGGTGCAGTTG	60.135	52.381	0.00	0.00	0.00	3.16
672	717	1.205417	GATTTGGATGGGTGCAGTTGG	59.795	52.381	0.00	0.00	0.00	3.77
673	718	0.187117	TTTGGATGGGTGCAGTTGGA	59.813	50.000	0.00	0.00	0.00	3.53
674	719	0.409092	TTGGATGGGTGCAGTTGGAT	59.591	50.000	0.00	0.00	0.00	3.41
675	720	0.409092	TGGATGGGTGCAGTTGGATT	59.591	50.000	0.00	0.00	0.00	3.01
676	721	1.106285	GGATGGGTGCAGTTGGATTC	58.894	55.000	0.00	0.00	0.00	2.52
677	722	0.734889	GATGGGTGCAGTTGGATTCG	59.265	55.000	0.00	0.00	0.00	3.34
678	723	1.315257	ATGGGTGCAGTTGGATTCGC	61.315	55.000	0.00	0.00	0.00	4.70
679	724	1.675641	GGGTGCAGTTGGATTCGCT	60.676	57.895	0.00	0.00	0.00	4.93
680	725	1.648467	GGGTGCAGTTGGATTCGCTC	61.648	60.000	0.00	0.00	0.00	5.03
681	726	0.674895	GGTGCAGTTGGATTCGCTCT	60.675	55.000	0.00	0.00	0.00	4.09
682	727	0.723981	GTGCAGTTGGATTCGCTCTC	59.276	55.000	0.00	0.00	0.00	3.20
683	728	0.321346	TGCAGTTGGATTCGCTCTCA	59.679	50.000	0.00	0.00	0.00	3.27
684	729	1.270785	TGCAGTTGGATTCGCTCTCAA	60.271	47.619	0.00	0.00	0.00	3.02
685	730	2.012673	GCAGTTGGATTCGCTCTCAAT	58.987	47.619	0.00	0.00	0.00	2.57
686	731	2.421424	GCAGTTGGATTCGCTCTCAATT	59.579	45.455	0.00	0.00	0.00	2.32
687	732	3.623060	GCAGTTGGATTCGCTCTCAATTA	59.377	43.478	0.00	0.00	0.00	1.40
688	733	4.494855	GCAGTTGGATTCGCTCTCAATTAC	60.495	45.833	0.00	0.00	0.00	1.89
689	734	4.631377	CAGTTGGATTCGCTCTCAATTACA	59.369	41.667	0.00	0.00	0.00	2.41
697	742	3.192633	TCGCTCTCAATTACAGTGCAGTA	59.807	43.478	0.00	0.00	31.89	2.74
698	743	4.115516	CGCTCTCAATTACAGTGCAGTAT	58.884	43.478	0.00	0.00	31.89	2.12
774	821	3.476552	GAACAACAGACACATTCCCTGA	58.523	45.455	0.00	0.00	0.00	3.86
1017	1070	0.531200	GAATGGAGGACTCGAACGGT	59.469	55.000	0.00	0.00	0.00	4.83
1388	1441	4.384868	CCCCCATTTCGTTAACAGACCTAT	60.385	45.833	6.39	0.00	0.00	2.57
1390	1443	4.814771	CCCATTTCGTTAACAGACCTATCC	59.185	45.833	6.39	0.00	0.00	2.59
1402	1460	6.295719	ACAGACCTATCCTCGTTTAAATGT	57.704	37.500	7.28	0.00	0.00	2.71
1524	1582	3.120165	GCTCTTTTGGGTCGAAATCTGAC	60.120	47.826	0.00	0.00	35.60	3.51
2094	2153	0.884704	TGTGCTTTTCCGTCAGAGCC	60.885	55.000	0.00	0.00	34.30	4.70
2101	2160	2.529780	TTCCGTCAGAGCCGTTTTAA	57.470	45.000	0.00	0.00	0.00	1.52
2102	2161	2.754946	TCCGTCAGAGCCGTTTTAAT	57.245	45.000	0.00	0.00	0.00	1.40
2105	2164	2.739913	CCGTCAGAGCCGTTTTAATGAA	59.260	45.455	0.00	0.00	0.00	2.57
2113	2172	3.659786	GCCGTTTTAATGAAGGCCTTTT	58.340	40.909	21.54	13.67	41.81	2.27
2114	2173	3.678072	GCCGTTTTAATGAAGGCCTTTTC	59.322	43.478	21.54	8.70	41.81	2.29
2115	2174	4.797933	GCCGTTTTAATGAAGGCCTTTTCA	60.798	41.667	21.54	15.09	41.81	2.69
2116	2175	5.293560	CCGTTTTAATGAAGGCCTTTTCAA	58.706	37.500	21.54	5.94	40.21	2.69
2117	2176	5.931724	CCGTTTTAATGAAGGCCTTTTCAAT	59.068	36.000	21.54	9.93	40.21	2.57
2118	2177	6.090763	CCGTTTTAATGAAGGCCTTTTCAATC	59.909	38.462	21.54	6.14	40.21	2.67
2119	2178	6.868339	CGTTTTAATGAAGGCCTTTTCAATCT	59.132	34.615	21.54	5.93	40.21	2.40
2120	2179	7.148755	CGTTTTAATGAAGGCCTTTTCAATCTG	60.149	37.037	21.54	2.40	40.21	2.90
2121	2180	6.916360	TTAATGAAGGCCTTTTCAATCTGT	57.084	33.333	21.54	0.00	40.21	3.41
2122	2181	4.796038	ATGAAGGCCTTTTCAATCTGTG	57.204	40.909	21.54	0.00	40.21	3.66
2627	2686	7.183460	AGCCGGGACTCTCTTAACTATATATT	58.817	38.462	2.18	0.00	0.00	1.28
2812	2871	7.600752	GCTACCTGTCTTCATATCATTCTTACC	59.399	40.741	0.00	0.00	0.00	2.85
2927	2987	3.201290	CCAGAATGTCACATAGAGGCAC	58.799	50.000	0.00	0.00	0.00	5.01
3492	3557	8.072480	AGTATTGGATTACCCCTCTTTACTAGT	58.928	37.037	0.00	0.00	34.81	2.57
3575	3640	0.980231	AGAGTCTGGAGTGGGATGGC	60.980	60.000	0.00	0.00	0.00	4.40
4750	4839	4.972440	GGCTGATTCGTCAAATTATTCTGC	59.028	41.667	0.00	0.00	0.00	4.26
5472	5561	7.251704	ACAATATCTGTACATAAGCTTGCAC	57.748	36.000	9.86	2.05	36.10	4.57
5538	5627	6.022163	AGAAATGTCAAGCTCAAAATGGAG	57.978	37.500	0.00	0.00	37.97	3.86
5918	6008	6.862090	ACTAATTATCTAGCGCTCTTTAACCG	59.138	38.462	16.34	0.00	0.00	4.44
5925	6015	1.069500	GCGCTCTTTAACCGCTTTTGA	60.069	47.619	0.00	0.00	43.95	2.69
5960	6059	4.202010	TGGCTTACTTTGTTCTCTGTTTGC	60.202	41.667	0.00	0.00	0.00	3.68
6121	6220	6.822170	TGCCAAAATTTATTGCTGCATCATAA	59.178	30.769	1.84	2.75	0.00	1.90
6220	6319	2.237643	GTATTCTACTCCCTCCGTCCC	58.762	57.143	0.00	0.00	0.00	4.46
6705	6804	5.760131	CCCCATCTTCTTTCTTATTCCACT	58.240	41.667	0.00	0.00	0.00	4.00
6706	6805	6.190587	CCCCATCTTCTTTCTTATTCCACTT	58.809	40.000	0.00	0.00	0.00	3.16
6745	6846	9.767684	TTCAAAGAAGCAATAATATGTACAACG	57.232	29.630	0.00	0.00	0.00	4.10
6769	6870	5.798434	GTGAAACCGCATAATTTCTTACACC	59.202	40.000	0.00	0.00	36.09	4.16
7278	7379	9.846248	GATTAATTCAACTGCTATCTGTTTTGT	57.154	29.630	0.00	0.00	32.96	2.83
7279	7380	9.630098	ATTAATTCAACTGCTATCTGTTTTGTG	57.370	29.630	0.00	0.00	32.96	3.33
7280	7381	6.639632	ATTCAACTGCTATCTGTTTTGTGT	57.360	33.333	0.00	0.00	32.96	3.72
7281	7382	5.422666	TCAACTGCTATCTGTTTTGTGTG	57.577	39.130	0.00	0.00	32.96	3.82
7282	7383	5.122519	TCAACTGCTATCTGTTTTGTGTGA	58.877	37.500	0.00	0.00	32.96	3.58
7283	7384	5.588246	TCAACTGCTATCTGTTTTGTGTGAA	59.412	36.000	0.00	0.00	32.96	3.18
7284	7385	6.262944	TCAACTGCTATCTGTTTTGTGTGAAT	59.737	34.615	0.00	0.00	32.96	2.57
7285	7386	6.639632	ACTGCTATCTGTTTTGTGTGAATT	57.360	33.333	0.00	0.00	0.00	2.17
7286	7387	7.042797	ACTGCTATCTGTTTTGTGTGAATTT	57.957	32.000	0.00	0.00	0.00	1.82
7287	7388	8.165239	ACTGCTATCTGTTTTGTGTGAATTTA	57.835	30.769	0.00	0.00	0.00	1.40
7288	7389	8.796475	ACTGCTATCTGTTTTGTGTGAATTTAT	58.204	29.630	0.00	0.00	0.00	1.40
7350	7451	5.020795	GGAACAACCCCCAAACTGTTATAT	58.979	41.667	0.00	0.00	32.31	0.86
7495	7598	6.959361	ACTACAAAAAGCATCAACAGTACAG	58.041	36.000	0.00	0.00	0.00	2.74
7545	7653	6.839124	CTCATAGAGCTCTCCATTCATAGT	57.161	41.667	22.17	0.00	0.00	2.12
7575	7683	1.692519	ACAAAGCTCACTACGGGACTT	59.307	47.619	0.00	0.00	0.00	3.01
7636	7744	3.957508	AGGAGGACCCTAACTCTAGAC	57.042	52.381	0.00	0.00	45.48	2.59
7671	7779	3.137544	TCAGGTCCAAAAAGCAACTCCTA	59.862	43.478	0.00	0.00	0.00	2.94

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
214	216	1.002134	CGTGGAAGCCATTGGAGGT	60.002	57.895	6.95	0.00	35.28	3.85
415	426	0.722676	ACTTCCCCTAGATCCACCCA	59.277	55.000	0.00	0.00	0.00	4.51
426	448	2.227036	CCTCCTGTGCACTTCCCCT	61.227	63.158	19.41	0.00	0.00	4.79
504	526	2.833943	CAGCTTCCTAATTTTTGGGCCT	59.166	45.455	4.53	0.00	0.00	5.19
520	565	1.748122	CAGATTCCGCTGGCAGCTT	60.748	57.895	34.17	17.78	39.60	3.74
565	610	0.244450	AAACTCGGGCGTTCGTATGA	59.756	50.000	0.00	0.00	0.00	2.15
578	623	1.762419	TTCTGACGGACGAAAACTCG	58.238	50.000	0.00	0.00	39.31	4.18
638	683	3.945304	AAATCGTCCACCCGCGTCC	62.945	63.158	4.92	0.00	0.00	4.79
639	684	2.433664	AAATCGTCCACCCGCGTC	60.434	61.111	4.92	0.00	0.00	5.19
640	685	2.740826	CAAATCGTCCACCCGCGT	60.741	61.111	4.92	0.00	0.00	6.01
641	686	3.496131	CCAAATCGTCCACCCGCG	61.496	66.667	0.00	0.00	0.00	6.46
642	687	1.451387	ATCCAAATCGTCCACCCGC	60.451	57.895	0.00	0.00	0.00	6.13
643	688	1.095228	CCATCCAAATCGTCCACCCG	61.095	60.000	0.00	0.00	0.00	5.28
644	689	0.751643	CCCATCCAAATCGTCCACCC	60.752	60.000	0.00	0.00	0.00	4.61
645	690	0.034477	ACCCATCCAAATCGTCCACC	60.034	55.000	0.00	0.00	0.00	4.61
646	691	1.094785	CACCCATCCAAATCGTCCAC	58.905	55.000	0.00	0.00	0.00	4.02
647	692	0.679640	GCACCCATCCAAATCGTCCA	60.680	55.000	0.00	0.00	0.00	4.02
648	693	0.679640	TGCACCCATCCAAATCGTCC	60.680	55.000	0.00	0.00	0.00	4.79
649	694	0.734889	CTGCACCCATCCAAATCGTC	59.265	55.000	0.00	0.00	0.00	4.20
650	695	0.038166	ACTGCACCCATCCAAATCGT	59.962	50.000	0.00	0.00	0.00	3.73
651	696	1.135315	CAACTGCACCCATCCAAATCG	60.135	52.381	0.00	0.00	0.00	3.34
652	697	1.205417	CCAACTGCACCCATCCAAATC	59.795	52.381	0.00	0.00	0.00	2.17
653	698	1.203162	TCCAACTGCACCCATCCAAAT	60.203	47.619	0.00	0.00	0.00	2.32
654	699	0.187117	TCCAACTGCACCCATCCAAA	59.813	50.000	0.00	0.00	0.00	3.28
655	700	0.409092	ATCCAACTGCACCCATCCAA	59.591	50.000	0.00	0.00	0.00	3.53
656	701	0.409092	AATCCAACTGCACCCATCCA	59.591	50.000	0.00	0.00	0.00	3.41
657	702	1.106285	GAATCCAACTGCACCCATCC	58.894	55.000	0.00	0.00	0.00	3.51
658	703	0.734889	CGAATCCAACTGCACCCATC	59.265	55.000	0.00	0.00	0.00	3.51
659	704	1.315257	GCGAATCCAACTGCACCCAT	61.315	55.000	0.00	0.00	0.00	4.00
660	705	1.971167	GCGAATCCAACTGCACCCA	60.971	57.895	0.00	0.00	0.00	4.51
661	706	1.648467	GAGCGAATCCAACTGCACCC	61.648	60.000	0.00	0.00	0.00	4.61
662	707	0.674895	AGAGCGAATCCAACTGCACC	60.675	55.000	0.00	0.00	0.00	5.01
663	708	0.723981	GAGAGCGAATCCAACTGCAC	59.276	55.000	0.00	0.00	0.00	4.57
664	709	0.321346	TGAGAGCGAATCCAACTGCA	59.679	50.000	0.00	0.00	0.00	4.41
665	710	1.442769	TTGAGAGCGAATCCAACTGC	58.557	50.000	0.00	0.00	0.00	4.40
666	711	4.631377	TGTAATTGAGAGCGAATCCAACTG	59.369	41.667	0.00	0.00	0.00	3.16
667	712	4.832248	TGTAATTGAGAGCGAATCCAACT	58.168	39.130	0.00	0.00	0.00	3.16
668	713	4.631813	ACTGTAATTGAGAGCGAATCCAAC	59.368	41.667	0.00	0.00	0.00	3.77
669	714	4.631377	CACTGTAATTGAGAGCGAATCCAA	59.369	41.667	0.00	0.00	0.00	3.53
670	715	4.183865	CACTGTAATTGAGAGCGAATCCA	58.816	43.478	0.00	0.00	0.00	3.41
671	716	3.001736	GCACTGTAATTGAGAGCGAATCC	59.998	47.826	0.00	0.00	0.00	3.01
672	717	3.618594	TGCACTGTAATTGAGAGCGAATC	59.381	43.478	0.00	0.00	30.42	2.52
673	718	3.599343	TGCACTGTAATTGAGAGCGAAT	58.401	40.909	0.00	0.00	30.42	3.34
674	719	2.995939	CTGCACTGTAATTGAGAGCGAA	59.004	45.455	0.00	0.00	30.42	4.70
675	720	2.029020	ACTGCACTGTAATTGAGAGCGA	60.029	45.455	0.00	0.00	30.42	4.93
676	721	2.341257	ACTGCACTGTAATTGAGAGCG	58.659	47.619	0.00	0.00	30.42	5.03
677	722	5.111989	TCATACTGCACTGTAATTGAGAGC	58.888	41.667	0.00	0.00	0.00	4.09
678	723	7.306457	CGAATCATACTGCACTGTAATTGAGAG	60.306	40.741	0.00	0.00	0.00	3.20
679	724	6.476706	CGAATCATACTGCACTGTAATTGAGA	59.523	38.462	0.00	0.00	0.00	3.27
680	725	6.643845	CGAATCATACTGCACTGTAATTGAG	58.356	40.000	0.00	0.00	0.00	3.02
681	726	5.006649	GCGAATCATACTGCACTGTAATTGA	59.993	40.000	0.00	0.00	0.00	2.57
682	727	5.007039	AGCGAATCATACTGCACTGTAATTG	59.993	40.000	0.00	0.00	0.00	2.32
683	728	5.118990	AGCGAATCATACTGCACTGTAATT	58.881	37.500	0.00	0.00	0.00	1.40
684	729	4.697514	AGCGAATCATACTGCACTGTAAT	58.302	39.130	0.00	0.00	0.00	1.89
685	730	4.112634	GAGCGAATCATACTGCACTGTAA	58.887	43.478	0.00	0.00	0.00	2.41
686	731	3.381590	AGAGCGAATCATACTGCACTGTA	59.618	43.478	0.00	0.00	0.00	2.74
687	732	2.167281	AGAGCGAATCATACTGCACTGT	59.833	45.455	0.00	0.00	0.00	3.55
688	733	2.793790	GAGAGCGAATCATACTGCACTG	59.206	50.000	0.00	0.00	0.00	3.66
689	734	2.428530	TGAGAGCGAATCATACTGCACT	59.571	45.455	0.00	0.00	0.00	4.40
753	800	3.476552	TCAGGGAATGTGTCTGTTGTTC	58.523	45.455	0.00	0.00	0.00	3.18
1388	1441	6.228258	ACAGAGCTAAACATTTAAACGAGGA	58.772	36.000	0.00	0.00	0.00	3.71
1390	1443	6.234213	CGACAGAGCTAAACATTTAAACGAG	58.766	40.000	0.00	0.00	0.00	4.18
1402	1460	1.343142	TGAGCAACCGACAGAGCTAAA	59.657	47.619	0.00	0.00	37.48	1.85
1524	1582	5.228635	GCACGCATCAAAAACATATCTTCTG	59.771	40.000	0.00	0.00	0.00	3.02
2094	2153	6.868339	AGATTGAAAAGGCCTTCATTAAAACG	59.132	34.615	20.79	0.00	35.31	3.60
2101	2160	3.056322	GCACAGATTGAAAAGGCCTTCAT	60.056	43.478	20.79	11.30	35.31	2.57
2102	2161	2.297033	GCACAGATTGAAAAGGCCTTCA	59.703	45.455	20.79	11.27	33.48	3.02
2105	2164	1.891150	CTGCACAGATTGAAAAGGCCT	59.109	47.619	0.00	0.00	0.00	5.19
2109	2168	2.325761	GCAGCTGCACAGATTGAAAAG	58.674	47.619	33.36	0.00	41.59	2.27
2111	2170	0.599558	GGCAGCTGCACAGATTGAAA	59.400	50.000	37.63	0.00	44.36	2.69
2113	2172	0.958876	CTGGCAGCTGCACAGATTGA	60.959	55.000	35.00	13.88	44.36	2.57
2114	2173	0.958876	TCTGGCAGCTGCACAGATTG	60.959	55.000	35.92	22.53	40.67	2.67
2115	2174	0.677098	CTCTGGCAGCTGCACAGATT	60.677	55.000	37.65	0.00	42.78	2.40
2116	2175	1.078356	CTCTGGCAGCTGCACAGAT	60.078	57.895	37.65	0.00	42.78	2.90
2117	2176	2.346365	CTCTGGCAGCTGCACAGA	59.654	61.111	36.31	36.31	42.10	3.41
2118	2177	2.032223	ACTCTGGCAGCTGCACAG	59.968	61.111	37.63	35.27	44.36	3.66
2119	2178	2.031616	GACTCTGGCAGCTGCACA	59.968	61.111	37.63	29.43	44.36	4.57
2120	2179	0.959372	AATGACTCTGGCAGCTGCAC	60.959	55.000	37.63	26.73	44.36	4.57
2121	2180	0.958876	CAATGACTCTGGCAGCTGCA	60.959	55.000	37.63	23.01	44.36	4.41
2122	2181	0.959372	ACAATGACTCTGGCAGCTGC	60.959	55.000	30.88	30.88	41.14	5.25
2517	2576	1.831736	GCTGGTAGACTAAGGCTGGAA	59.168	52.381	0.00	0.00	0.00	3.53
2812	2871	6.722301	CACTGGATATACAATTTCAGCTGTG	58.278	40.000	14.67	7.08	0.00	3.66
2927	2987	1.923899	TGTGTGCATGCACTTTGTTG	58.076	45.000	41.43	0.00	46.30	3.33
3492	3557	8.328758	ACAAATCATCCAAGAGTAATAAGTGGA	58.671	33.333	0.00	0.00	42.38	4.02
3575	3640	2.690653	ATCCCCAACACACACCACCG	62.691	60.000	0.00	0.00	0.00	4.94
4059	4128	4.524802	TGGAAATATGGCTGTGGAATCT	57.475	40.909	0.00	0.00	0.00	2.40
4674	4763	7.175641	GGATAACTTGGCTGCATGATTAATACT	59.824	37.037	0.50	0.00	0.00	2.12
4750	4839	9.396022	ACCTTGAATACCTGTAAATATCAAGTG	57.604	33.333	10.59	5.97	32.65	3.16
5398	5487	7.617041	AATAGCATGGTTGAGAAAAGACTAC	57.383	36.000	1.12	0.00	0.00	2.73
5621	5711	9.199982	CATCATCCATATTAAAACCATGAAAGC	57.800	33.333	0.00	0.00	0.00	3.51
5918	6008	2.539476	CACCCAACAAGTGTCAAAAGC	58.461	47.619	0.00	0.00	0.00	3.51
5925	6015	1.214424	AGTAAGCCACCCAACAAGTGT	59.786	47.619	0.00	0.00	33.20	3.55
5960	6059	6.709643	CCGAGATGCTACTTTTATTGAACAG	58.290	40.000	0.00	0.00	0.00	3.16
6399	6498	7.530426	AAAGGAGATGATGTAAGCAAAGTTT	57.470	32.000	0.00	0.00	33.49	2.66
6705	6804	3.556999	TCTTTGAATCCGTTGGTCCAAA	58.443	40.909	5.69	0.00	0.00	3.28
6706	6805	3.216187	TCTTTGAATCCGTTGGTCCAA	57.784	42.857	0.00	0.00	0.00	3.53
6745	6846	5.798434	GGTGTAAGAAATTATGCGGTTTCAC	59.202	40.000	0.00	0.00	36.92	3.18
6769	6870	5.922544	AGATTTTCCAAGAAAGATTGTTGCG	59.077	36.000	0.00	0.00	33.01	4.85
7306	7407	7.505585	TGTTCCAACCAGATCTCTTGTAAAAAT	59.494	33.333	0.00	0.00	0.00	1.82
7307	7408	6.831353	TGTTCCAACCAGATCTCTTGTAAAAA	59.169	34.615	0.00	0.00	0.00	1.94
7308	7409	6.361433	TGTTCCAACCAGATCTCTTGTAAAA	58.639	36.000	0.00	0.00	0.00	1.52
7350	7451	8.668353	CAATCTAAGAGCAAATACAGCAGTTAA	58.332	33.333	0.00	0.00	0.00	2.01
7387	7488	5.694006	GCTTGCTCTAACATGATTCGATAGT	59.306	40.000	0.00	0.00	37.40	2.12
7545	7653	4.623932	AGTGAGCTTTGTATCTTCACCA	57.376	40.909	0.00	0.00	0.00	4.17
7636	7744	5.840243	TTGGACCTGATTGCAATCTTATG	57.160	39.130	33.23	22.22	36.39	1.90

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.