AutoCloner

Multiple sequence alignment - TraesCS5B01G302700

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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	TraesCS5B01G302700	chr5B	100.000	3592	0	0	1	3592	487250434	487246843	0.000000e+00	6634.0
1	TraesCS5B01G302700	chr5B	100.000	84	0	0	786	869	487249615	487249532	4.800000e-34	156.0
2	TraesCS5B01G302700	chr5B	100.000	84	0	0	820	903	487249649	487249566	4.800000e-34	156.0
3	TraesCS5B01G302700	chr5B	100.000	50	0	0	786	835	487249581	487249532	3.820000e-15	93.5
4	TraesCS5B01G302700	chr5B	100.000	50	0	0	854	903	487249649	487249600	3.820000e-15	93.5
5	TraesCS5B01G302700	chr5A	92.456	2757	132	22	854	3592	511964798	511962100	0.000000e+00	3869.0
6	TraesCS5B01G302700	chr5A	89.032	155	16	1	1	154	512037130	512036976	1.320000e-44	191.0
7	TraesCS5B01G302700	chr5A	97.980	99	2	0	723	821	511964861	511964763	4.770000e-39	172.0
8	TraesCS5B01G302700	chr5A	88.660	97	5	2	691	787	512024652	512024562	2.930000e-21	113.0
9	TraesCS5B01G302700	chr5A	90.244	82	5	2	889	967	511964879	511964798	1.760000e-18	104.0
10	TraesCS5B01G302700	chr5A	100.000	36	0	0	820	855	511964798	511964763	2.310000e-07	67.6
11	TraesCS5B01G302700	chr5D	96.580	2105	66	5	854	2953	406352120	406350017	0.000000e+00	3483.0
12	TraesCS5B01G302700	chr5D	89.740	653	58	5	2945	3592	406346291	406345643	0.000000e+00	826.0
13	TraesCS5B01G302700	chr5D	88.182	440	40	7	398	835	406352499	406352070	6.880000e-142	514.0
14	TraesCS5B01G302700	chr5D	87.688	398	41	6	8	402	406352934	406352542	1.180000e-124	457.0
15	TraesCS5B01G302700	chr5D	79.793	193	25	9	3411	3592	423223837	423223648	1.050000e-25	128.0
16	TraesCS5B01G302700	chr5D	79.085	153	25	7	395	543	563904361	563904510	8.210000e-17	99.0
17	TraesCS5B01G302700	chr2A	85.258	1723	201	26	893	2583	21191505	21193206	0.000000e+00	1725.0
18	TraesCS5B01G302700	chr2A	85.194	1675	194	24	963	2592	21006723	21005058	0.000000e+00	1670.0
19	TraesCS5B01G302700	chr2A	84.316	1696	219	18	935	2593	21177283	21178968	0.000000e+00	1615.0
20	TraesCS5B01G302700	chr2A	85.183	1586	196	14	1035	2593	21148240	21149813	0.000000e+00	1591.0
21	TraesCS5B01G302700	chr2A	83.427	531	82	3	2063	2593	21180368	21180892	4.170000e-134	488.0
22	TraesCS5B01G302700	chr2A	86.813	182	20	2	2542	2722	10550276	10550454	2.190000e-47	200.0
23	TraesCS5B01G302700	chr2A	87.640	89	11	0	434	522	77201407	77201495	1.760000e-18	104.0
24	TraesCS5B01G302700	chr2B	85.767	1637	189	20	996	2599	33728328	33729953	0.000000e+00	1692.0
25	TraesCS5B01G302700	chr2B	84.360	1688	219	18	936	2588	33662956	33664633	0.000000e+00	1613.0
26	TraesCS5B01G302700	chr2B	85.874	538	69	3	2063	2599	33578994	33578463	1.870000e-157	566.0
27	TraesCS5B01G302700	chr2D	84.229	1674	214	18	958	2593	20324794	20323133	0.000000e+00	1583.0
28	TraesCS5B01G302700	chr2D	87.349	1328	129	14	1337	2632	10313566	10314886	0.000000e+00	1485.0
29	TraesCS5B01G302700	chr2D	86.988	1099	139	3	963	2058	20381027	20382124	0.000000e+00	1234.0
30	TraesCS5B01G302700	chr2D	85.299	551	72	5	2050	2599	20382145	20382687	8.710000e-156	560.0
31	TraesCS5B01G302700	chr2D	85.932	526	68	1	2063	2588	20315438	20314919	1.130000e-154	556.0
32	TraesCS5B01G302700	chr3D	83.243	185	28	3	401	583	536888293	536888110	2.220000e-37	167.0
33	TraesCS5B01G302700	chr3D	80.226	177	24	5	3395	3565	497513283	497513454	4.870000e-24	122.0
34	TraesCS5B01G302700	chr4B	80.233	172	24	5	399	568	637347465	637347628	1.750000e-23	121.0
35	TraesCS5B01G302700	chr7B	76.847	203	44	3	3061	3260	728629363	728629161	1.050000e-20	111.0
36	TraesCS5B01G302700	chr7D	71.935	310	69	13	3061	3363	627354260	627354558	1.380000e-09	75.0
37	TraesCS5B01G302700	chr1A	92.683	41	3	0	455	495	554879408	554879448	3.870000e-05	60.2
38	TraesCS5B01G302700	chr6B	80.519	77	12	3	493	567	213835648	213835573	5.010000e-04	56.5

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	TraesCS5B01G302700	chr5B	487246843	487250434	3591	True	1426.60	6634	100.0000	1	3592	5	chr5B.!!$R1	3591
1	TraesCS5B01G302700	chr5A	511962100	511964879	2779	True	1053.15	3869	95.1700	723	3592	4	chr5A.!!$R3	2869
2	TraesCS5B01G302700	chr5D	406345643	406352934	7291	True	1320.00	3483	90.5475	8	3592	4	chr5D.!!$R2	3584
3	TraesCS5B01G302700	chr2A	21191505	21193206	1701	False	1725.00	1725	85.2580	893	2583	1	chr2A.!!$F3	1690
4	TraesCS5B01G302700	chr2A	21005058	21006723	1665	True	1670.00	1670	85.1940	963	2592	1	chr2A.!!$R1	1629
5	TraesCS5B01G302700	chr2A	21148240	21149813	1573	False	1591.00	1591	85.1830	1035	2593	1	chr2A.!!$F2	1558
6	TraesCS5B01G302700	chr2A	21177283	21180892	3609	False	1051.50	1615	83.8715	935	2593	2	chr2A.!!$F5	1658
7	TraesCS5B01G302700	chr2B	33728328	33729953	1625	False	1692.00	1692	85.7670	996	2599	1	chr2B.!!$F2	1603
8	TraesCS5B01G302700	chr2B	33662956	33664633	1677	False	1613.00	1613	84.3600	936	2588	1	chr2B.!!$F1	1652
9	TraesCS5B01G302700	chr2B	33578463	33578994	531	True	566.00	566	85.8740	2063	2599	1	chr2B.!!$R1	536
10	TraesCS5B01G302700	chr2D	20323133	20324794	1661	True	1583.00	1583	84.2290	958	2593	1	chr2D.!!$R2	1635
11	TraesCS5B01G302700	chr2D	10313566	10314886	1320	False	1485.00	1485	87.3490	1337	2632	1	chr2D.!!$F1	1295
12	TraesCS5B01G302700	chr2D	20381027	20382687	1660	False	897.00	1234	86.1435	963	2599	2	chr2D.!!$F2	1636
13	TraesCS5B01G302700	chr2D	20314919	20315438	519	True	556.00	556	85.9320	2063	2588	1	chr2D.!!$R1	525

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
427	477	0.115349	AGAGACTGGGCCAGTGTAGT	59.885	55.0	42.11	25.55	45.44	2.73	F
491	541	0.246910	GGAAACGTCTCCTCCCACTC	59.753	60.0	0.00	0.00	32.21	3.51	F
497	547	0.966920	GTCTCCTCCCACTCAACGAA	59.033	55.0	0.00	0.00	0.00	3.85	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2115	2243	0.034896	TCGTTGGTGAGGGCTTTCTC	59.965	55.000	0.0	0.0	0.00	2.87	R
2447	2576	0.107831	TGCCACTTTGGTAGCTCGTT	59.892	50.000	0.0	0.0	40.46	3.85	R
2745	2877	8.348285	TGAAAACAGAAATCATTAGTTAGGGG	57.652	34.615	0.0	0.0	0.00	4.79	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
27	28	8.348983	AGTCGAAAATAAACTATGTGTATCGG	57.651	34.615	0.00	0.00	0.00	4.18
37	38	2.902705	TGTGTATCGGCCTACCAATC	57.097	50.000	0.00	0.00	34.57	2.67
68	70	7.296628	AGGAGTAGAGACATCAATGGTTATC	57.703	40.000	0.00	0.00	0.00	1.75
83	85	9.884636	TCAATGGTTATCGAGAAAAATCTTCTA	57.115	29.630	0.00	0.00	0.00	2.10
92	94	8.703604	TCGAGAAAAATCTTCTATGTGTAAGG	57.296	34.615	0.00	0.00	0.00	2.69
150	152	4.283978	AGTGATTGAATTCAATTGGCACCA	59.716	37.500	29.57	21.76	45.72	4.17
201	204	0.614294	TTGGGCGAACCGATCCTTTA	59.386	50.000	0.00	0.00	44.64	1.85
206	209	3.878699	GGGCGAACCGATCCTTTATTTAA	59.121	43.478	0.00	0.00	36.48	1.52
209	212	5.237779	GGCGAACCGATCCTTTATTTAATGA	59.762	40.000	0.00	0.00	0.00	2.57
233	236	2.951229	AAAAACATCACGGAGGAGGT	57.049	45.000	0.00	0.00	32.39	3.85
262	265	7.127032	TGGGATGTGGAGGCAAAAATAAATTAT	59.873	33.333	0.00	0.00	0.00	1.28
268	271	9.822185	GTGGAGGCAAAAATAAATTATGAAGAT	57.178	29.630	0.00	0.00	0.00	2.40
286	289	4.164822	AGATGAAAATGAACCAAGCGTG	57.835	40.909	0.00	0.00	0.00	5.34
303	306	3.400054	GCCGGCCTACCAACTCCT	61.400	66.667	18.11	0.00	34.57	3.69
308	311	1.003233	CGGCCTACCAACTCCTCTTTT	59.997	52.381	0.00	0.00	34.57	2.27
309	312	2.437413	GGCCTACCAACTCCTCTTTTG	58.563	52.381	0.00	0.00	35.26	2.44
406	456	4.584743	TCATTCACATATACGAGCACCTCT	59.415	41.667	0.00	0.00	0.00	3.69
409	459	3.565902	TCACATATACGAGCACCTCTGAG	59.434	47.826	0.00	0.00	0.00	3.35
416	466	0.817013	GAGCACCTCTGAGAGACTGG	59.183	60.000	11.82	0.00	0.00	4.00
419	469	1.305718	ACCTCTGAGAGACTGGGCC	60.306	63.158	11.82	0.00	0.00	5.80
420	470	1.305633	CCTCTGAGAGACTGGGCCA	60.306	63.158	11.82	5.85	0.00	5.36
421	471	1.329171	CCTCTGAGAGACTGGGCCAG	61.329	65.000	31.62	31.62	37.52	4.85
423	473	0.902048	TCTGAGAGACTGGGCCAGTG	60.902	60.000	42.11	26.06	45.44	3.66
427	477	0.115349	AGAGACTGGGCCAGTGTAGT	59.885	55.000	42.11	25.55	45.44	2.73
433	483	4.345257	AGACTGGGCCAGTGTAGTATATTG	59.655	45.833	42.11	11.59	45.44	1.90
439	489	6.101150	TGGGCCAGTGTAGTATATTGAGATTT	59.899	38.462	0.00	0.00	0.00	2.17
443	493	9.542462	GCCAGTGTAGTATATTGAGATTTTACA	57.458	33.333	0.00	0.00	0.00	2.41
456	506	9.778741	ATTGAGATTTTACAAAGTCACTACAGA	57.221	29.630	0.86	0.00	0.00	3.41
474	524	2.180769	CGCCTCACAATCGACGGA	59.819	61.111	0.00	0.00	0.00	4.69
477	527	0.442699	GCCTCACAATCGACGGAAAC	59.557	55.000	0.00	0.00	0.00	2.78
491	541	0.246910	GGAAACGTCTCCTCCCACTC	59.753	60.000	0.00	0.00	32.21	3.51
497	547	0.966920	GTCTCCTCCCACTCAACGAA	59.033	55.000	0.00	0.00	0.00	3.85
524	574	2.806244	CCGGAAGCCTGGAATAAATACG	59.194	50.000	0.00	0.00	41.53	3.06
527	577	4.065789	GGAAGCCTGGAATAAATACGAGG	58.934	47.826	0.00	0.00	35.60	4.63
535	585	6.878923	CCTGGAATAAATACGAGGATAATGCA	59.121	38.462	0.00	0.00	34.68	3.96
537	587	8.862325	TGGAATAAATACGAGGATAATGCAAT	57.138	30.769	0.00	0.00	0.00	3.56
541	591	6.560253	AAATACGAGGATAATGCAATCACC	57.440	37.500	0.00	0.00	0.00	4.02
543	593	3.884895	ACGAGGATAATGCAATCACCAA	58.115	40.909	0.00	0.00	0.00	3.67
555	605	6.698008	TGCAATCACCAATGTAAATCTAGG	57.302	37.500	0.00	0.00	0.00	3.02
556	606	6.422333	TGCAATCACCAATGTAAATCTAGGA	58.578	36.000	0.00	0.00	0.00	2.94
557	607	6.318648	TGCAATCACCAATGTAAATCTAGGAC	59.681	38.462	0.00	0.00	0.00	3.85
558	608	6.543831	GCAATCACCAATGTAAATCTAGGACT	59.456	38.462	0.00	0.00	0.00	3.85
559	609	7.067494	GCAATCACCAATGTAAATCTAGGACTT	59.933	37.037	0.00	0.00	0.00	3.01
560	610	8.400947	CAATCACCAATGTAAATCTAGGACTTG	58.599	37.037	0.00	0.00	0.00	3.16
568	618	7.801893	TGTAAATCTAGGACTTGAACCCTAA	57.198	36.000	0.00	0.00	34.86	2.69
570	620	9.496710	TGTAAATCTAGGACTTGAACCCTAATA	57.503	33.333	0.00	0.00	34.86	0.98
576	626	4.783227	AGGACTTGAACCCTAATAAGCTGA	59.217	41.667	0.00	0.00	0.00	4.26
577	627	5.250774	AGGACTTGAACCCTAATAAGCTGAA	59.749	40.000	0.00	0.00	0.00	3.02
582	632	8.718656	ACTTGAACCCTAATAAGCTGAAGATAT	58.281	33.333	0.00	0.00	0.00	1.63
600	650	9.552695	TGAAGATATATGACATTGTCCTCCTAT	57.447	33.333	14.05	8.37	0.00	2.57
603	653	5.667539	ATATGACATTGTCCTCCTATCCG	57.332	43.478	14.05	0.00	0.00	4.18
604	654	2.039418	TGACATTGTCCTCCTATCCGG	58.961	52.381	14.05	0.00	0.00	5.14
612	662	0.987294	CCTCCTATCCGGCCAATCAT	59.013	55.000	2.24	0.00	0.00	2.45
629	679	6.373774	GCCAATCATATTCATCTCCTACTTGG	59.626	42.308	0.00	0.00	33.17	3.61
645	695	5.362717	CCTACTTGGTTTGGGAAGAAACTTT	59.637	40.000	0.00	0.00	36.30	2.66
725	775	4.518970	GGTGAATTAGAACAAGCACCAAGA	59.481	41.667	0.00	0.00	43.87	3.02
745	795	7.178274	ACCAAGAAACTTCCATGCATGTAATTA	59.822	33.333	24.58	4.86	0.00	1.40
825	875	3.464111	TTTTCGAAACGGACTTCTCCT	57.536	42.857	10.79	0.00	33.79	3.69
826	876	4.589216	TTTTCGAAACGGACTTCTCCTA	57.411	40.909	10.79	0.00	33.79	2.94
827	877	3.565905	TTCGAAACGGACTTCTCCTAC	57.434	47.619	0.00	0.00	33.79	3.18
828	878	2.787994	TCGAAACGGACTTCTCCTACT	58.212	47.619	0.00	0.00	33.79	2.57
829	879	3.152341	TCGAAACGGACTTCTCCTACTT	58.848	45.455	0.00	0.00	33.79	2.24
830	880	3.057736	TCGAAACGGACTTCTCCTACTTG	60.058	47.826	0.00	0.00	33.79	3.16
831	881	3.057736	CGAAACGGACTTCTCCTACTTGA	60.058	47.826	0.00	0.00	33.79	3.02
832	882	4.380655	CGAAACGGACTTCTCCTACTTGAT	60.381	45.833	0.00	0.00	33.79	2.57
833	883	5.480205	GAAACGGACTTCTCCTACTTGATT	58.520	41.667	0.00	0.00	33.79	2.57
834	884	5.485209	AACGGACTTCTCCTACTTGATTT	57.515	39.130	0.00	0.00	33.79	2.17
835	885	5.485209	ACGGACTTCTCCTACTTGATTTT	57.515	39.130	0.00	0.00	33.79	1.82
836	886	6.600882	ACGGACTTCTCCTACTTGATTTTA	57.399	37.500	0.00	0.00	33.79	1.52
837	887	7.184067	ACGGACTTCTCCTACTTGATTTTAT	57.816	36.000	0.00	0.00	33.79	1.40
838	888	7.621796	ACGGACTTCTCCTACTTGATTTTATT	58.378	34.615	0.00	0.00	33.79	1.40
839	889	8.101419	ACGGACTTCTCCTACTTGATTTTATTT	58.899	33.333	0.00	0.00	33.79	1.40
840	890	8.947115	CGGACTTCTCCTACTTGATTTTATTTT	58.053	33.333	0.00	0.00	33.79	1.82
859	909	3.464111	TTTTCGAAACGGACTTCTCCT	57.536	42.857	10.79	0.00	33.79	3.69
860	910	4.589216	TTTTCGAAACGGACTTCTCCTA	57.411	40.909	10.79	0.00	33.79	2.94
861	911	3.565905	TTCGAAACGGACTTCTCCTAC	57.434	47.619	0.00	0.00	33.79	3.18
862	912	2.787994	TCGAAACGGACTTCTCCTACT	58.212	47.619	0.00	0.00	33.79	2.57
863	913	3.152341	TCGAAACGGACTTCTCCTACTT	58.848	45.455	0.00	0.00	33.79	2.24
864	914	3.057736	TCGAAACGGACTTCTCCTACTTG	60.058	47.826	0.00	0.00	33.79	3.16
865	915	3.057736	CGAAACGGACTTCTCCTACTTGA	60.058	47.826	0.00	0.00	33.79	3.02
866	916	4.380655	CGAAACGGACTTCTCCTACTTGAT	60.381	45.833	0.00	0.00	33.79	2.57
867	917	5.480205	GAAACGGACTTCTCCTACTTGATT	58.520	41.667	0.00	0.00	33.79	2.57
868	918	5.485209	AACGGACTTCTCCTACTTGATTT	57.515	39.130	0.00	0.00	33.79	2.17
869	919	5.485209	ACGGACTTCTCCTACTTGATTTT	57.515	39.130	0.00	0.00	33.79	1.82
870	920	6.600882	ACGGACTTCTCCTACTTGATTTTA	57.399	37.500	0.00	0.00	33.79	1.52
871	921	7.184067	ACGGACTTCTCCTACTTGATTTTAT	57.816	36.000	0.00	0.00	33.79	1.40
872	922	7.621796	ACGGACTTCTCCTACTTGATTTTATT	58.378	34.615	0.00	0.00	33.79	1.40
873	923	8.101419	ACGGACTTCTCCTACTTGATTTTATTT	58.899	33.333	0.00	0.00	33.79	1.40
874	924	8.947115	CGGACTTCTCCTACTTGATTTTATTTT	58.053	33.333	0.00	0.00	33.79	1.82
1073	1139	4.764172	TCATGGTTTGTTTCTTGGGTTTG	58.236	39.130	0.00	0.00	0.00	2.93
1077	1143	4.284746	TGGTTTGTTTCTTGGGTTTGTTCT	59.715	37.500	0.00	0.00	0.00	3.01
1110	1179	1.006102	CTTGCGTCGACCTCCAACT	60.006	57.895	10.58	0.00	0.00	3.16
1122	1191	1.402456	CCTCCAACTACACCGACTTCG	60.402	57.143	0.00	0.00	39.44	3.79
1264	1333	1.520120	CACCGCTCTGCATCGTGAT	60.520	57.895	0.00	0.00	0.00	3.06
1376	1445	2.043248	GGCCTCTCCTACCGGTCA	60.043	66.667	12.40	0.00	0.00	4.02
1668	1743	1.814527	GACGCCTACGGGAATCTGT	59.185	57.895	0.00	0.00	46.04	3.41
1915	2013	1.659098	CGTAGAAAATCGTCAGGCCAC	59.341	52.381	5.01	0.00	0.00	5.01
2283	2412	3.179830	CTCTACAACATCCAGTACGTGC	58.820	50.000	0.00	0.00	0.00	5.34
2745	2877	2.159379	GCCAACATAGCTGCAAAGGTAC	60.159	50.000	1.02	0.00	0.00	3.34
2996	6862	2.723273	TCTCGATCTTGGTAGCACAGA	58.277	47.619	0.00	1.74	0.00	3.41
3003	6869	4.302559	TCTTGGTAGCACAGACTCTCTA	57.697	45.455	0.00	0.00	0.00	2.43
3008	6874	3.510360	GGTAGCACAGACTCTCTAAACCA	59.490	47.826	0.00	0.00	0.00	3.67
3044	6910	2.758207	TTTCTTCCCCACACCGCCA	61.758	57.895	0.00	0.00	0.00	5.69
3099	6965	1.038681	TGTCGGCGGCAAGGATAGTA	61.039	55.000	13.70	0.00	0.00	1.82
3107	6973	1.694693	GGCAAGGATAGTAGGGACCCA	60.695	57.143	14.60	0.00	0.00	4.51
3142	7013	2.039348	TCTCCCTAGGTTTTGTTTCCCG	59.961	50.000	8.29	0.00	0.00	5.14
3145	7016	2.039348	CCCTAGGTTTTGTTTCCCGAGA	59.961	50.000	8.29	0.00	0.00	4.04
3148	7019	3.570912	AGGTTTTGTTTCCCGAGAGAA	57.429	42.857	0.00	0.00	0.00	2.87
3203	7074	2.617840	TAAGGTCCCTTCGGTCTCTT	57.382	50.000	0.89	0.00	37.47	2.85
3207	7078	1.341778	GGTCCCTTCGGTCTCTTCCTA	60.342	57.143	0.00	0.00	0.00	2.94
3222	7093	3.875727	TCTTCCTACCTCTACGATGTTCG	59.124	47.826	0.00	0.00	46.93	3.95
3227	7098	1.955080	ACCTCTACGATGTTCGATCCC	59.045	52.381	3.62	0.00	43.74	3.85
3271	7142	7.121463	GTGAGAGTTTGTGTCTCTAGATCCTAA	59.879	40.741	0.00	0.00	41.58	2.69
3300	7171	7.905604	ATTGACACGTTTCAGATCTTGATAA	57.094	32.000	4.36	0.00	35.27	1.75
3327	7198	1.960689	TGCCCTTTACAAAGAGCAACC	59.039	47.619	8.26	0.00	45.01	3.77
3371	7242	5.833406	TTTCAACATCTTCTGCAACTTGA	57.167	34.783	0.00	0.00	0.00	3.02
3409	7280	3.562176	CCTCTGCCTAAACCTGGACATTT	60.562	47.826	0.00	0.00	0.00	2.32
3415	7287	3.192633	CCTAAACCTGGACATTTTTCGGG	59.807	47.826	0.00	0.00	0.00	5.14
3416	7288	0.966179	AACCTGGACATTTTTCGGGC	59.034	50.000	0.00	0.00	0.00	6.13
3417	7289	0.898326	ACCTGGACATTTTTCGGGCC	60.898	55.000	0.00	0.00	0.00	5.80
3482	7829	0.607620	CCGGCCCAAAACACATGAAT	59.392	50.000	0.00	0.00	0.00	2.57
3484	7831	2.430332	CCGGCCCAAAACACATGAATAT	59.570	45.455	0.00	0.00	0.00	1.28
3585	8072	4.192317	CCATATTAGGGCTTATCTTCGGC	58.808	47.826	0.00	0.00	0.00	5.54
3586	8073	4.080863	CCATATTAGGGCTTATCTTCGGCT	60.081	45.833	0.00	0.00	0.00	5.52
3589	8076	2.333688	AGGGCTTATCTTCGGCTTTC	57.666	50.000	0.00	0.00	0.00	2.62
3590	8077	0.938008	GGGCTTATCTTCGGCTTTCG	59.062	55.000	0.00	0.00	40.90	3.46

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
1	2	8.477709	CCGATACACATAGTTTATTTTCGACTC	58.522	37.037	0.00	0.00	0.00	3.36
6	7	7.492352	AGGCCGATACACATAGTTTATTTTC	57.508	36.000	0.00	0.00	0.00	2.29
11	12	4.894705	TGGTAGGCCGATACACATAGTTTA	59.105	41.667	0.00	0.00	37.67	2.01
24	25	1.580059	AAAGAGGATTGGTAGGCCGA	58.420	50.000	0.00	0.00	37.67	5.54
55	57	9.443283	GAAGATTTTTCTCGATAACCATTGATG	57.557	33.333	0.00	0.00	0.00	3.07
68	70	8.383619	CACCTTACACATAGAAGATTTTTCTCG	58.616	37.037	0.00	0.00	0.00	4.04
83	85	8.641541	AGAATTTGAAAATCACACCTTACACAT	58.358	29.630	0.00	0.00	0.00	3.21
85	87	8.871686	AAGAATTTGAAAATCACACCTTACAC	57.128	30.769	0.00	0.00	0.00	2.90
130	132	4.812626	GGATGGTGCCAATTGAATTCAATC	59.187	41.667	29.08	19.05	45.06	2.67
139	141	4.497300	CTTAGTTTGGATGGTGCCAATTG	58.503	43.478	0.00	0.00	46.59	2.32
181	183	0.034477	AAAGGATCGGTTCGCCCAAT	60.034	50.000	0.00	0.00	0.00	3.16
183	185	0.834612	ATAAAGGATCGGTTCGCCCA	59.165	50.000	0.00	0.00	0.00	5.36
221	224	1.685765	CCCATCACCTCCTCCGTGA	60.686	63.158	0.00	0.00	44.00	4.35
222	225	1.050988	ATCCCATCACCTCCTCCGTG	61.051	60.000	0.00	0.00	0.00	4.94
223	226	1.050988	CATCCCATCACCTCCTCCGT	61.051	60.000	0.00	0.00	0.00	4.69
224	227	1.050988	ACATCCCATCACCTCCTCCG	61.051	60.000	0.00	0.00	0.00	4.63
230	233	1.639635	GCCTCCACATCCCATCACCT	61.640	60.000	0.00	0.00	0.00	4.00
232	235	0.034186	TTGCCTCCACATCCCATCAC	60.034	55.000	0.00	0.00	0.00	3.06
233	236	0.703488	TTTGCCTCCACATCCCATCA	59.297	50.000	0.00	0.00	0.00	3.07
235	238	2.323999	TTTTTGCCTCCACATCCCAT	57.676	45.000	0.00	0.00	0.00	4.00
262	265	4.278170	ACGCTTGGTTCATTTTCATCTTCA	59.722	37.500	0.00	0.00	0.00	3.02
268	271	1.269517	GGCACGCTTGGTTCATTTTCA	60.270	47.619	0.00	0.00	0.00	2.69
286	289	3.387225	GAGGAGTTGGTAGGCCGGC	62.387	68.421	21.18	21.18	37.67	6.13
385	388	4.584743	TCAGAGGTGCTCGTATATGTGAAT	59.415	41.667	0.00	0.00	35.36	2.57
394	397	1.279558	AGTCTCTCAGAGGTGCTCGTA	59.720	52.381	0.57	0.00	35.36	3.43
406	456	0.114364	TACACTGGCCCAGTCTCTCA	59.886	55.000	15.03	0.00	43.43	3.27
409	459	1.848652	TACTACACTGGCCCAGTCTC	58.151	55.000	15.03	0.00	43.43	3.36
416	466	8.989980	GTAAAATCTCAATATACTACACTGGCC	58.010	37.037	0.00	0.00	0.00	5.36
433	483	7.619571	GCGTCTGTAGTGACTTTGTAAAATCTC	60.620	40.741	0.00	0.00	35.00	2.75
439	489	3.319972	AGGCGTCTGTAGTGACTTTGTAA	59.680	43.478	0.00	0.00	35.00	2.41
443	493	1.961394	TGAGGCGTCTGTAGTGACTTT	59.039	47.619	8.06	0.00	35.00	2.66
447	497	1.324383	TTGTGAGGCGTCTGTAGTGA	58.676	50.000	8.06	0.00	0.00	3.41
451	501	1.135489	GTCGATTGTGAGGCGTCTGTA	60.135	52.381	8.06	0.00	0.00	2.74
456	506	2.126071	CCGTCGATTGTGAGGCGT	60.126	61.111	0.00	0.00	33.10	5.68
474	524	1.070289	GTTGAGTGGGAGGAGACGTTT	59.930	52.381	0.00	0.00	0.00	3.60
477	527	1.213013	CGTTGAGTGGGAGGAGACG	59.787	63.158	0.00	0.00	0.00	4.18
491	541	1.419922	CTTCCGGCGATGTTCGTTG	59.580	57.895	9.30	0.00	42.81	4.10
497	547	4.473520	CCAGGCTTCCGGCGATGT	62.474	66.667	9.30	0.00	42.94	3.06
524	574	5.779529	ACATTGGTGATTGCATTATCCTC	57.220	39.130	0.00	0.00	0.00	3.71
535	585	8.328758	TCAAGTCCTAGATTTACATTGGTGATT	58.671	33.333	0.00	0.00	0.00	2.57
537	587	7.252612	TCAAGTCCTAGATTTACATTGGTGA	57.747	36.000	0.00	0.00	0.00	4.02
541	591	7.112779	AGGGTTCAAGTCCTAGATTTACATTG	58.887	38.462	0.00	0.00	0.00	2.82
543	593	6.893020	AGGGTTCAAGTCCTAGATTTACAT	57.107	37.500	0.00	0.00	0.00	2.29
555	605	6.407202	TCTTCAGCTTATTAGGGTTCAAGTC	58.593	40.000	0.00	0.00	0.00	3.01
556	606	6.374417	TCTTCAGCTTATTAGGGTTCAAGT	57.626	37.500	0.00	0.00	0.00	3.16
568	618	9.664332	GGACAATGTCATATATCTTCAGCTTAT	57.336	33.333	15.86	0.00	33.68	1.73
570	620	7.743749	AGGACAATGTCATATATCTTCAGCTT	58.256	34.615	15.86	0.00	33.68	3.74
572	622	6.593382	GGAGGACAATGTCATATATCTTCAGC	59.407	42.308	15.86	0.00	33.68	4.26
576	626	8.986991	GGATAGGAGGACAATGTCATATATCTT	58.013	37.037	21.38	10.11	31.65	2.40
577	627	7.286546	CGGATAGGAGGACAATGTCATATATCT	59.713	40.741	21.38	9.06	31.65	1.98
582	632	3.832490	CCGGATAGGAGGACAATGTCATA	59.168	47.826	15.86	2.89	45.00	2.15
583	633	2.634940	CCGGATAGGAGGACAATGTCAT	59.365	50.000	15.86	8.19	45.00	3.06
584	634	2.039418	CCGGATAGGAGGACAATGTCA	58.961	52.381	15.86	0.00	45.00	3.58
585	635	1.270358	GCCGGATAGGAGGACAATGTC	60.270	57.143	5.05	4.51	45.00	3.06
586	636	0.759346	GCCGGATAGGAGGACAATGT	59.241	55.000	5.05	0.00	45.00	2.71
589	639	1.002403	TGGCCGGATAGGAGGACAA	59.998	57.895	5.05	0.00	43.72	3.18
600	650	3.307691	GGAGATGAATATGATTGGCCGGA	60.308	47.826	5.05	0.00	0.00	5.14
603	653	6.059787	AGTAGGAGATGAATATGATTGGCC	57.940	41.667	0.00	0.00	0.00	5.36
604	654	6.373774	CCAAGTAGGAGATGAATATGATTGGC	59.626	42.308	0.00	0.00	41.22	4.52
612	662	5.729229	TCCCAAACCAAGTAGGAGATGAATA	59.271	40.000	0.00	0.00	41.22	1.75
629	679	4.692228	TGCATGAAAGTTTCTTCCCAAAC	58.308	39.130	16.33	0.00	36.64	2.93
645	695	2.621055	GGCCGGTTAATTACATGCATGA	59.379	45.455	32.75	12.33	0.00	3.07
725	775	7.238486	TGGTTAATTACATGCATGGAAGTTT	57.762	32.000	27.96	20.18	33.38	2.66
1101	1167	1.617357	GAAGTCGGTGTAGTTGGAGGT	59.383	52.381	0.00	0.00	0.00	3.85
1122	1191	2.887568	CGTGGAGATGCAGCGGAC	60.888	66.667	0.00	0.00	0.00	4.79
1247	1316	1.520120	CATCACGATGCAGAGCGGT	60.520	57.895	10.49	0.00	34.48	5.68
1376	1445	3.241530	TCGCTGTTGGGGCAGACT	61.242	61.111	0.00	0.00	38.70	3.24
1406	1475	1.153549	GAGCTTGGCGAGGTCGATT	60.154	57.895	17.52	0.00	42.45	3.34
1668	1743	2.282180	GGCCTTCTTGTCCGCCAA	60.282	61.111	0.00	0.00	41.25	4.52
1730	1828	0.168788	ACAGCACGATGCCGAAATTG	59.831	50.000	6.39	1.22	46.52	2.32
1915	2013	0.175989	GAGGTACAGGGCTTCGAAGG	59.824	60.000	25.77	11.96	0.00	3.46
2115	2243	0.034896	TCGTTGGTGAGGGCTTTCTC	59.965	55.000	0.00	0.00	0.00	2.87
2283	2412	1.283793	CTTTGCCGTTCCAGTGCTG	59.716	57.895	0.00	0.00	0.00	4.41
2447	2576	0.107831	TGCCACTTTGGTAGCTCGTT	59.892	50.000	0.00	0.00	40.46	3.85
2745	2877	8.348285	TGAAAACAGAAATCATTAGTTAGGGG	57.652	34.615	0.00	0.00	0.00	4.79
2850	2982	3.431673	TGGCTATTGTCATCACCAACA	57.568	42.857	0.00	0.00	0.00	3.33
2996	6862	1.207329	GACGGCCATGGTTTAGAGAGT	59.793	52.381	14.67	2.18	0.00	3.24
3003	6869	2.740826	CGACGACGGCCATGGTTT	60.741	61.111	14.67	0.00	35.72	3.27
3044	6910	3.069318	GAGAAGGGGGAGCGACGT	61.069	66.667	0.00	0.00	0.00	4.34
3099	6965	1.698874	AAAAGGATGGATGGGTCCCT	58.301	50.000	10.00	0.00	44.41	4.20
3126	6997	4.267349	TCTCTCGGGAAACAAAACCTAG	57.733	45.455	0.00	0.00	0.00	3.02
3142	7013	3.181485	CCACCACCTAGTCGATTTCTCTC	60.181	52.174	0.00	0.00	0.00	3.20
3145	7016	1.207329	GCCACCACCTAGTCGATTTCT	59.793	52.381	0.00	0.00	0.00	2.52
3148	7019	1.515954	CGCCACCACCTAGTCGATT	59.484	57.895	0.00	0.00	0.00	3.34
3271	7142	5.794894	AGATCTGAAACGTGTCAATAGGTT	58.205	37.500	10.22	0.00	0.00	3.50
3300	7171	3.571590	TCTTTGTAAAGGGCACACCAAT	58.428	40.909	4.67	0.00	43.89	3.16
3327	7198	2.179018	CGCTTCAATGGCCAACCG	59.821	61.111	10.96	0.21	39.70	4.44
3565	8052	5.763876	AAGCCGAAGATAAGCCCTAATAT	57.236	39.130	0.00	0.00	0.00	1.28

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.