AutoCloner

Multiple sequence alignment - TraesCS4A01G428500

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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	TraesCS4A01G428500	chr4A	100.000	5193	0	0	1	5193	699794645	699789453	0.000000e+00	9590.0
1	TraesCS4A01G428500	chr4A	89.342	638	34	9	3644	4279	700962021	700962626	0.000000e+00	771.0
2	TraesCS4A01G428500	chr4A	82.709	347	36	12	3939	4283	702574100	702573776	2.370000e-73	287.0
3	TraesCS4A01G428500	chr4A	82.709	347	36	12	3939	4283	702578911	702578587	2.370000e-73	287.0
4	TraesCS4A01G428500	chr4A	90.426	188	18	0	3717	3904	702574284	702574097	1.120000e-61	248.0
5	TraesCS4A01G428500	chr4A	90.426	188	18	0	3717	3904	702579095	702578908	1.120000e-61	248.0
6	TraesCS4A01G428500	chr4A	86.957	207	21	6	4096	4299	699582161	699581958	1.450000e-55	228.0
7	TraesCS4A01G428500	chr4A	87.952	166	20	0	3019	3184	700968150	700968315	4.100000e-46	196.0
8	TraesCS4A01G428500	chr4A	92.188	128	10	0	3054	3181	700663333	700663460	1.150000e-41	182.0
9	TraesCS4A01G428500	chr4A	88.028	142	16	1	2854	2994	702613325	702613184	3.220000e-37	167.0
10	TraesCS4A01G428500	chr4A	89.231	130	14	0	3054	3183	700543766	700543895	4.160000e-36	163.0
11	TraesCS4A01G428500	chr4A	80.392	102	18	2	2610	2710	477030391	477030291	5.580000e-10	76.8
12	TraesCS4A01G428500	chr7D	96.521	2357	72	6	2118	4472	29876984	29879332	0.000000e+00	3890.0
13	TraesCS4A01G428500	chr7D	87.104	1737	102	57	1	1684	29874283	29875950	0.000000e+00	1855.0
14	TraesCS4A01G428500	chr7D	86.499	874	80	16	4354	5193	29879348	29880217	0.000000e+00	926.0
15	TraesCS4A01G428500	chr7D	87.033	509	52	11	3785	4292	28789533	28789038	3.510000e-156	562.0
16	TraesCS4A01G428500	chr7D	91.842	380	25	5	1746	2119	29875949	29876328	4.610000e-145	525.0
17	TraesCS4A01G428500	chr7D	90.884	362	32	1	3931	4292	28827118	28826758	7.820000e-133	484.0
18	TraesCS4A01G428500	chr7D	93.249	237	15	1	3724	3959	28819026	28818790	1.070000e-91	348.0
19	TraesCS4A01G428500	chr7D	84.192	291	41	4	4644	4933	28822215	28821929	1.420000e-70	278.0
20	TraesCS4A01G428500	chr7D	90.840	131	12	0	3054	3184	28820015	28819885	5.340000e-40	176.0
21	TraesCS4A01G428500	chr7D	93.333	120	7	1	4081	4200	29110499	29110617	5.340000e-40	176.0
22	TraesCS4A01G428500	chr7D	83.140	172	20	4	3019	3184	28817260	28817092	1.170000e-31	148.0
23	TraesCS4A01G428500	chr7A	94.949	2356	107	4	2118	4472	30139004	30141348	0.000000e+00	3681.0
24	TraesCS4A01G428500	chr7A	89.208	1742	91	36	3	1705	30136250	30137933	0.000000e+00	2085.0
25	TraesCS4A01G428500	chr7A	88.603	895	74	10	3506	4389	29243689	29242812	0.000000e+00	1062.0
26	TraesCS4A01G428500	chr7A	93.601	672	40	3	3627	4297	29260554	29259885	0.000000e+00	1000.0
27	TraesCS4A01G428500	chr7A	91.379	406	28	4	1714	2119	30138014	30138412	2.730000e-152	549.0
28	TraesCS4A01G428500	chr7A	95.192	208	8	2	3335	3541	29260754	29260548	1.390000e-85	327.0
29	TraesCS4A01G428500	chr7A	89.091	165	18	0	3019	3183	29236775	29236611	6.820000e-49	206.0
30	TraesCS4A01G428500	chr7A	88.554	166	17	2	3019	3183	29258549	29258385	3.170000e-47	200.0
31	TraesCS4A01G428500	chr7A	82.667	225	16	8	4973	5177	30141656	30141877	1.490000e-40	178.0
32	TraesCS4A01G428500	chr7A	95.413	109	5	0	2894	3002	29260857	29260749	1.920000e-39	174.0
33	TraesCS4A01G428500	chr7A	85.000	160	23	1	2766	2925	327304368	327304210	1.500000e-35	161.0
34	TraesCS4A01G428500	chr1B	79.378	611	67	20	1091	1679	54000167	53999594	4.910000e-100	375.0
35	TraesCS4A01G428500	chr1B	90.099	101	8	2	2614	2713	354987530	354987431	4.220000e-26	130.0
36	TraesCS4A01G428500	chr1B	91.566	83	7	0	1744	1826	53999592	53999510	1.180000e-21	115.0
37	TraesCS4A01G428500	chr6B	85.855	304	31	7	1017	1318	456578445	456578152	3.900000e-81	313.0
38	TraesCS4A01G428500	chr6B	83.810	105	11	6	2615	2716	548119001	548118900	1.540000e-15	95.3
39	TraesCS4A01G428500	chrUn	88.235	238	27	1	1005	1242	231905162	231905398	3.060000e-72	283.0
40	TraesCS4A01G428500	chrUn	89.610	154	16	0	3019	3172	477902472	477902625	4.100000e-46	196.0
41	TraesCS4A01G428500	chr6A	91.279	172	14	1	1949	2119	611099434	611099263	3.130000e-57	233.0
42	TraesCS4A01G428500	chr3D	86.473	207	14	4	1080	1282	203918101	203918297	1.130000e-51	215.0
43	TraesCS4A01G428500	chr2B	92.308	143	11	0	1004	1146	102553021	102553163	2.450000e-48	204.0
44	TraesCS4A01G428500	chr5B	91.971	137	11	0	1010	1146	561795071	561794935	5.310000e-45	193.0
45	TraesCS4A01G428500	chr4B	90.210	143	14	0	1004	1146	610014902	610015044	2.470000e-43	187.0
46	TraesCS4A01G428500	chr4B	82.000	100	11	5	2613	2710	242704138	242704044	1.550000e-10	78.7
47	TraesCS4A01G428500	chr3B	90.210	143	14	0	1004	1146	604555170	604555028	2.470000e-43	187.0
48	TraesCS4A01G428500	chr5D	86.275	153	21	0	2766	2918	356985300	356985148	3.220000e-37	167.0
49	TraesCS4A01G428500	chr5D	91.000	100	9	0	2611	2710	553674827	553674728	9.070000e-28	135.0
50	TraesCS4A01G428500	chr1D	90.722	97	9	0	2614	2710	216018531	216018435	4.220000e-26	130.0
51	TraesCS4A01G428500	chr1D	89.320	103	10	1	2611	2713	258091960	258092061	1.520000e-25	128.0
52	TraesCS4A01G428500	chr4D	85.294	102	7	7	2613	2710	277378249	277378152	1.190000e-16	99.0

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	TraesCS4A01G428500	chr4A	699789453	699794645	5192	True	9590.00	9590	100.00000	1	5193	1	chr4A.!!$R3	5192
1	TraesCS4A01G428500	chr4A	700962021	700962626	605	False	771.00	771	89.34200	3644	4279	1	chr4A.!!$F3	635
2	TraesCS4A01G428500	chr4A	702573776	702574284	508	True	267.50	287	86.56750	3717	4283	2	chr4A.!!$R5	566
3	TraesCS4A01G428500	chr4A	702578587	702579095	508	True	267.50	287	86.56750	3717	4283	2	chr4A.!!$R6	566
4	TraesCS4A01G428500	chr7D	29874283	29880217	5934	False	1799.00	3890	90.49150	1	5193	4	chr7D.!!$F2	5192
5	TraesCS4A01G428500	chr7D	28817092	28822215	5123	True	237.50	348	87.85525	3019	4933	4	chr7D.!!$R3	1914
6	TraesCS4A01G428500	chr7A	30136250	30141877	5627	False	1623.25	3681	89.55075	3	5177	4	chr7A.!!$F1	5174
7	TraesCS4A01G428500	chr7A	29242812	29243689	877	True	1062.00	1062	88.60300	3506	4389	1	chr7A.!!$R2	883
8	TraesCS4A01G428500	chr7A	29258385	29260857	2472	True	425.25	1000	93.19000	2894	4297	4	chr7A.!!$R4	1403
9	TraesCS4A01G428500	chr1B	53999510	54000167	657	True	245.00	375	85.47200	1091	1826	2	chr1B.!!$R2	735

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	End Stability	Orientation
68	69	0.397675	AGATGATGGAGCTGGTCGGA	60.398	55.000	4.55	F
808	859	1.143073	AGAACCCAACGCCTTCTTCTT	59.857	47.619	2.52	F
1445	1516	0.317020	GTAGGCCGCAAAATCATCGC	60.317	55.000	4.58	F
1729	1882	0.613260	TGCTGAGTGGTGTGGGATAC	59.387	55.000	2.24	F
3201	4132	1.067669	TGCAGCTCGTCAGGACATATC	59.932	52.381	1.63	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Hairpin	End Stability	Orientation
1445	1516	0.178964	TTCCAGAGGGCCAAACAAGG	60.179	55.000	6.18	0.00	3.61	R
1711	1864	0.613260	TGTATCCCACACCACTCAGC	59.387	55.000	0.00	30.04	4.26	R
3201	4132	1.381872	ATCACCCTCTCGACCCCTG	60.382	63.158	0.00	0.00	4.45	R
3558	4813	2.526888	AGTCTTAGGTGGACGGATGA	57.473	50.000	0.00	38.58	2.92	R
5081	7880	0.038744	ATTTCCTGTGGCTCCCAGTG	59.961	55.000	0.00	32.34	3.66	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	1.583856	CTAATATAGCACGCGCCGATG	59.416	52.381	5.73	0.00	39.83	3.84
68	69	0.397675	AGATGATGGAGCTGGTCGGA	60.398	55.000	0.00	0.00	0.00	4.55
101	103	6.923508	TCACCTAATACTGAACAGCATATTCG	59.076	38.462	1.46	0.00	0.00	3.34
102	104	6.923508	CACCTAATACTGAACAGCATATTCGA	59.076	38.462	1.46	0.00	0.00	3.71
104	106	7.653713	ACCTAATACTGAACAGCATATTCGAAG	59.346	37.037	3.35	0.00	0.00	3.79
150	161	2.472723	CCGACAAAATAACCGCGTGTAC	60.473	50.000	4.92	0.00	0.00	2.90
162	173	2.066262	CGCGTGTACTTTCCAACAGAT	58.934	47.619	0.00	0.00	0.00	2.90
223	235	5.521906	TTGCTACTAGAGACAGGCATAAG	57.478	43.478	0.00	0.00	0.00	1.73
227	239	6.657117	TGCTACTAGAGACAGGCATAAGATAG	59.343	42.308	0.00	0.00	0.00	2.08
248	260	4.218312	AGTTAGCATTTCCCCCATTGATC	58.782	43.478	0.00	0.00	0.00	2.92
276	288	1.153568	CACCCACTGATCATCGCGT	60.154	57.895	5.77	0.00	0.00	6.01
322	354	1.679032	GCCCCAGTATCCAGTGTGTTC	60.679	57.143	0.00	0.00	0.00	3.18
324	356	2.305927	CCCCAGTATCCAGTGTGTTCTT	59.694	50.000	0.00	0.00	0.00	2.52
325	357	3.600388	CCCAGTATCCAGTGTGTTCTTC	58.400	50.000	0.00	0.00	0.00	2.87
326	358	3.261897	CCCAGTATCCAGTGTGTTCTTCT	59.738	47.826	0.00	0.00	0.00	2.85
329	361	5.419155	CCAGTATCCAGTGTGTTCTTCTCTA	59.581	44.000	0.00	0.00	0.00	2.43
348	380	2.743636	ATATAGCGTTGGGTGGATCG	57.256	50.000	0.00	0.00	0.00	3.69
441	478	2.511145	GCGGAAGAGGAGCAGCTG	60.511	66.667	10.11	10.11	0.00	4.24
442	479	2.511145	CGGAAGAGGAGCAGCTGC	60.511	66.667	31.53	31.53	42.49	5.25
721	771	3.213402	CGACCTCTCCGCTCCCTC	61.213	72.222	0.00	0.00	0.00	4.30
780	831	1.908299	CCTTTTGCCCCTGGGTCAC	60.908	63.158	12.71	1.08	37.65	3.67
808	859	1.143073	AGAACCCAACGCCTTCTTCTT	59.857	47.619	0.00	0.00	0.00	2.52
809	860	1.266989	GAACCCAACGCCTTCTTCTTG	59.733	52.381	0.00	0.00	0.00	3.02
816	867	1.692519	ACGCCTTCTTCTTGTACCACT	59.307	47.619	0.00	0.00	0.00	4.00
1285	1336	2.948720	GCCTCGGTTCCTGCTCTGT	61.949	63.158	0.00	0.00	0.00	3.41
1410	1481	5.874261	TGTCATGCAAAGATCGAGATTTGTA	59.126	36.000	20.12	17.63	38.41	2.41
1445	1516	0.317020	GTAGGCCGCAAAATCATCGC	60.317	55.000	0.00	0.00	0.00	4.58
1478	1549	5.536161	GCCCTCTGGAATGCTTAATTTGATA	59.464	40.000	0.00	0.00	0.00	2.15
1479	1550	6.040842	GCCCTCTGGAATGCTTAATTTGATAA	59.959	38.462	0.00	0.00	0.00	1.75
1496	1568	9.677567	AATTTGATAATTATCCGTGTTGTATGC	57.322	29.630	20.29	0.00	32.25	3.14
1506	1578	3.511699	CGTGTTGTATGCTTGCTCTCTA	58.488	45.455	0.00	0.00	0.00	2.43
1512	1584	7.116090	GTGTTGTATGCTTGCTCTCTAGATATG	59.884	40.741	0.00	0.00	0.00	1.78
1516	1588	3.831333	TGCTTGCTCTCTAGATATGGAGG	59.169	47.826	0.50	0.00	0.00	4.30
1527	1603	1.485066	GATATGGAGGTCGTTGTGGGT	59.515	52.381	0.00	0.00	0.00	4.51
1528	1604	1.354101	TATGGAGGTCGTTGTGGGTT	58.646	50.000	0.00	0.00	0.00	4.11
1572	1648	2.089854	GATGCCGTCGAATTGCTGT	58.910	52.632	0.00	0.00	0.00	4.40
1638	1719	4.656112	CCTCTAGGTGTCCTCCATTTATGT	59.344	45.833	0.00	0.00	34.61	2.29
1705	1786	4.706842	AGTAGTGGTTCAGTTGTGGAAT	57.293	40.909	0.00	0.00	0.00	3.01
1707	1788	1.956477	AGTGGTTCAGTTGTGGAATGC	59.044	47.619	0.00	0.00	0.00	3.56
1711	1864	2.287788	GGTTCAGTTGTGGAATGCAGTG	60.288	50.000	0.00	0.00	0.00	3.66
1712	1865	0.953727	TCAGTTGTGGAATGCAGTGC	59.046	50.000	8.58	8.58	0.00	4.40
1723	1876	0.887836	ATGCAGTGCTGAGTGGTGTG	60.888	55.000	17.60	0.00	0.00	3.82
1729	1882	0.613260	TGCTGAGTGGTGTGGGATAC	59.387	55.000	0.00	0.00	0.00	2.24
1736	1889	4.344968	TGAGTGGTGTGGGATACATATGAG	59.655	45.833	10.38	0.00	42.24	2.90
1839	1992	5.299279	CACACTTTGGTTGGTTCAGATAGTT	59.701	40.000	0.00	0.00	0.00	2.24
1840	1993	6.485313	CACACTTTGGTTGGTTCAGATAGTTA	59.515	38.462	0.00	0.00	0.00	2.24
1918	2072	4.442052	GCTGACCTGTTCATCTGTATGCTA	60.442	45.833	0.00	0.00	32.17	3.49
1944	2098	3.940852	TGCATTGATAACGCTTCATCTGT	59.059	39.130	0.00	0.00	0.00	3.41
2082	2240	4.590222	CCCATTCTAAATAAGCATGGCCTT	59.410	41.667	3.32	0.00	44.96	4.35
2100	2258	4.998033	GGCCTTATATTCTCTGTTACCTGC	59.002	45.833	0.00	0.00	0.00	4.85
2109	2267	3.388024	TCTCTGTTACCTGCTGACTGTTT	59.612	43.478	0.00	0.00	0.00	2.83
2112	2271	4.574828	TCTGTTACCTGCTGACTGTTTTTC	59.425	41.667	0.00	0.00	0.00	2.29
2119	2278	5.471456	ACCTGCTGACTGTTTTTCTCAATAG	59.529	40.000	0.00	0.00	0.00	1.73
2130	2965	7.054124	TGTTTTTCTCAATAGTTGTCCACTCT	58.946	34.615	0.00	0.00	36.88	3.24
2189	3025	5.351740	TGTTAAATGCATGCCATGACATTTG	59.648	36.000	29.54	3.41	41.92	2.32
2194	3030	3.935828	TGCATGCCATGACATTTGAAATG	59.064	39.130	16.68	15.82	0.00	2.32
2396	3232	6.706295	AGTATTAGCTCCCTCTTATTCATGC	58.294	40.000	0.00	0.00	0.00	4.06
2415	3251	8.424274	TTCATGCTACTACTATGTGAACATTG	57.576	34.615	0.47	2.34	37.76	2.82
2472	3308	5.488341	TCATTCTTAGTTTACCTGGAGCAC	58.512	41.667	0.00	0.00	0.00	4.40
2473	3309	5.248477	TCATTCTTAGTTTACCTGGAGCACT	59.752	40.000	0.00	1.10	0.00	4.40
2493	3329	9.118300	GAGCACTACTAGTAAAGTCACCTATAA	57.882	37.037	3.76	0.00	39.80	0.98
2542	3378	9.296400	TGTGAATAACTTTGCTTAAAACAGTTC	57.704	29.630	0.00	0.00	0.00	3.01
2550	3386	8.184848	ACTTTGCTTAAAACAGTTCTCTCTTTC	58.815	33.333	0.00	0.00	0.00	2.62
2568	3404	6.065976	TCTTTCTGAGATTTATGCCCTGAA	57.934	37.500	0.00	0.00	0.00	3.02
2574	3410	9.425248	TTCTGAGATTTATGCCCTGAATTATTT	57.575	29.630	0.00	0.00	0.00	1.40
2622	3458	6.506538	ACAGAAAATGCATATACTCCCTCT	57.493	37.500	0.00	0.00	0.00	3.69
2648	3484	6.603237	TCCATATTAATTGACGCTCACTTG	57.397	37.500	0.00	0.00	0.00	3.16
2698	3534	4.134563	AGTGGGCGTCAATTAATATGGAC	58.865	43.478	0.00	0.00	32.24	4.02
2881	3717	3.853475	CTTGGATCTTGTTGCCAAATCC	58.147	45.455	0.00	0.00	40.83	3.01
3089	4020	6.904463	TGACACTATACACTAAGGTCAACA	57.096	37.500	0.00	0.00	31.55	3.33
3201	4132	1.067669	TGCAGCTCGTCAGGACATATC	59.932	52.381	0.00	0.00	0.00	1.63
3220	4151	1.075896	AGGGGTCGAGAGGGTGATC	60.076	63.158	0.00	0.00	0.00	2.92
3558	4813	0.765510	AAAGAGTGGGAAGCTCGGTT	59.234	50.000	0.00	0.00	37.99	4.44
3754	5226	3.190079	TGCTCTGATGAAAGCATACGTC	58.810	45.455	0.00	0.00	43.30	4.34
3808	5280	2.669569	AAGCGTGCCAAGATGCGT	60.670	55.556	0.00	0.00	32.75	5.24
4132	5604	1.741770	GCGGCACCGTCTGAAGATT	60.742	57.895	11.27	0.00	42.09	2.40
4159	5631	0.034896	TGGAACTCAGCGAGGAAACC	59.965	55.000	9.75	7.60	33.35	3.27
4334	6408	2.032528	TTGGCCAAGGTCTCTGCG	59.967	61.111	16.05	0.00	0.00	5.18
4420	6525	4.663636	GGTGAACCGAATGAACTACAAG	57.336	45.455	0.00	0.00	0.00	3.16
4483	7236	6.851609	TGTGCAATGTCCTTAAATATGTGAC	58.148	36.000	0.00	0.00	0.00	3.67
4505	7258	6.880529	TGACATGAGCTGTGATGAAAGAATAA	59.119	34.615	0.00	0.00	38.54	1.40
4569	7330	1.661112	GGTACTCGAAAGTGCATCTGC	59.339	52.381	0.00	0.00	39.65	4.26
4593	7354	5.330455	AGACTCTGAATGCGTCTGAATTA	57.670	39.130	0.00	0.00	39.07	1.40
4629	7403	6.823182	TGAAGATCTGTCACAACTTTGAAAGA	59.177	34.615	12.53	0.00	42.84	2.52
4637	7411	8.824159	TGTCACAACTTTGAAAGAAAAATTGA	57.176	26.923	12.53	2.75	0.00	2.57
4645	7419	8.314021	ACTTTGAAAGAAAAATTGACACTTCCT	58.686	29.630	12.53	0.00	0.00	3.36
4664	7438	2.564062	CCTGGAAATCATTGTGCACCTT	59.436	45.455	15.69	0.00	0.00	3.50
4677	7451	4.148079	TGTGCACCTTGTGGAAATCATTA	58.852	39.130	15.69	0.00	35.32	1.90
4691	7465	1.847818	TCATTATTTCTCGCCCGTCG	58.152	50.000	0.00	0.00	40.15	5.12
4710	7487	4.259356	GTCGGGTCCTTTGCTAACTATTT	58.741	43.478	0.00	0.00	0.00	1.40
4737	7514	0.683412	ATCTGCGATATGGCTGCTCA	59.317	50.000	11.22	0.00	32.57	4.26
4744	7521	2.483106	CGATATGGCTGCTCATTGAAGG	59.517	50.000	8.53	0.00	0.00	3.46
4767	7544	4.767409	GGGTGAAGGAGATGCTTAAAACTT	59.233	41.667	0.00	0.00	0.00	2.66
4768	7545	5.335976	GGGTGAAGGAGATGCTTAAAACTTG	60.336	44.000	0.00	0.00	0.00	3.16
4791	7568	3.655777	TCAGGAATTTAGGGTTCAGTGGT	59.344	43.478	0.00	0.00	0.00	4.16
4813	7590	1.582461	GGCGTTTGGTTAATGGCGT	59.418	52.632	0.00	0.00	38.38	5.68
4892	7673	1.153958	GGGAACATTGCAGCTTCGC	60.154	57.895	0.00	0.00	0.00	4.70
4901	7682	2.979676	CAGCTTCGCAACTGCCCA	60.980	61.111	0.00	0.00	37.91	5.36
4935	7716	8.673711	TGAATAAATAGCAACACTACCAACATC	58.326	33.333	0.00	0.00	32.32	3.06
4940	7723	5.590530	AGCAACACTACCAACATCAAAAA	57.409	34.783	0.00	0.00	0.00	1.94
5003	7786	6.833839	CCATCATTTGGTGTTTAATGCAAAG	58.166	36.000	0.00	0.00	40.99	2.77
5036	7819	4.343526	AGCTGTATACCTTGTCATGGAGAG	59.656	45.833	11.60	0.00	0.00	3.20
5037	7820	4.342378	GCTGTATACCTTGTCATGGAGAGA	59.658	45.833	11.60	0.00	0.00	3.10
5038	7821	5.011533	GCTGTATACCTTGTCATGGAGAGAT	59.988	44.000	11.60	2.68	0.00	2.75
5041	7824	7.952671	TGTATACCTTGTCATGGAGAGATTAC	58.047	38.462	11.60	4.86	0.00	1.89
5081	7880	5.847670	AAGAACATACTTCTTCTCGTTGC	57.152	39.130	0.00	0.00	33.86	4.17
5082	7881	4.883083	AGAACATACTTCTTCTCGTTGCA	58.117	39.130	0.00	0.00	0.00	4.08
5084	7883	4.258702	ACATACTTCTTCTCGTTGCACT	57.741	40.909	0.00	0.00	0.00	4.40
5089	7888	0.318441	TCTTCTCGTTGCACTGGGAG	59.682	55.000	0.00	0.00	0.00	4.30
5090	7889	1.294659	CTTCTCGTTGCACTGGGAGC	61.295	60.000	0.00	0.00	0.00	4.70
5091	7890	2.731691	TTCTCGTTGCACTGGGAGCC	62.732	60.000	0.00	0.00	0.00	4.70
5095	7894	2.113774	TTGCACTGGGAGCCACAG	59.886	61.111	3.21	3.21	41.64	3.66
5122	7923	0.037326	TCCACATGCTCGGACTTGAC	60.037	55.000	0.00	0.00	0.00	3.18
5157	7958	4.965200	ACCATGATCTAGCCTTTAGTCC	57.035	45.455	0.00	0.00	0.00	3.85
5164	7965	3.182152	TCTAGCCTTTAGTCCCTGCTTT	58.818	45.455	0.00	0.00	33.63	3.51
5186	7987	2.099756	GGACTGCTGCTTTTGTGTTCTT	59.900	45.455	0.00	0.00	0.00	2.52

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
38	39	2.543012	CTCCATCATCTGTCATTCGTGC	59.457	50.000	0.00	0.00	0.00	5.34
68	69	8.893727	GCTGTTCAGTATTAGGTGATAAATGTT	58.106	33.333	1.78	0.00	0.00	2.71
101	103	3.130340	TGTTTTGTGGGAGCAGTTTCTTC	59.870	43.478	0.00	0.00	0.00	2.87
102	104	3.096092	TGTTTTGTGGGAGCAGTTTCTT	58.904	40.909	0.00	0.00	0.00	2.52
104	106	2.799562	GCTGTTTTGTGGGAGCAGTTTC	60.800	50.000	0.00	0.00	0.00	2.78
150	161	2.875296	TGGGGAACATCTGTTGGAAAG	58.125	47.619	0.00	0.00	38.56	2.62
162	173	1.281867	CAGTAGGAGCATTGGGGAACA	59.718	52.381	0.00	0.00	0.00	3.18
223	235	5.385198	TCAATGGGGGAAATGCTAACTATC	58.615	41.667	0.00	0.00	0.00	2.08
227	239	3.321968	GGATCAATGGGGGAAATGCTAAC	59.678	47.826	0.00	0.00	0.00	2.34
248	260	0.112218	TCAGTGGGTGTTTGGATGGG	59.888	55.000	0.00	0.00	0.00	4.00
276	288	0.595588	ATGGAATCAACGCAACGCAA	59.404	45.000	0.00	0.00	0.00	4.85
322	354	4.523173	TCCACCCAACGCTATATAGAGAAG	59.477	45.833	18.98	10.61	0.00	2.85
324	356	4.108501	TCCACCCAACGCTATATAGAGA	57.891	45.455	18.98	0.00	0.00	3.10
325	357	4.438880	CGATCCACCCAACGCTATATAGAG	60.439	50.000	14.16	12.76	0.00	2.43
326	358	3.442625	CGATCCACCCAACGCTATATAGA	59.557	47.826	14.16	0.00	0.00	1.98
329	361	1.337823	GCGATCCACCCAACGCTATAT	60.338	52.381	0.00	0.00	46.06	0.86
348	380	2.408835	CGCCCATTTCGGTGATGC	59.591	61.111	0.00	0.00	35.25	3.91
780	831	2.434359	GTTGGGTTCTCTCGGCGG	60.434	66.667	7.21	0.00	0.00	6.13
808	859	0.830444	AGTGGGCTTCGAGTGGTACA	60.830	55.000	0.00	0.00	0.00	2.90
809	860	0.108756	GAGTGGGCTTCGAGTGGTAC	60.109	60.000	0.00	0.00	0.00	3.34
910	961	1.918293	CCTCCACTAGCCACCACCA	60.918	63.158	0.00	0.00	0.00	4.17
1200	1251	4.228567	GGGCGGTAGAGCTCCTGC	62.229	72.222	10.93	12.58	37.29	4.85
1285	1336	3.845259	GCGGAGGGCATCACGGTA	61.845	66.667	0.08	0.00	42.87	4.02
1445	1516	0.178964	TTCCAGAGGGCCAAACAAGG	60.179	55.000	6.18	0.00	0.00	3.61
1478	1549	4.640201	AGCAAGCATACAACACGGATAATT	59.360	37.500	0.00	0.00	0.00	1.40
1479	1550	4.199310	AGCAAGCATACAACACGGATAAT	58.801	39.130	0.00	0.00	0.00	1.28
1493	1565	4.467082	CCTCCATATCTAGAGAGCAAGCAT	59.533	45.833	0.00	0.00	31.43	3.79
1496	1568	4.155826	CGACCTCCATATCTAGAGAGCAAG	59.844	50.000	0.00	0.00	31.43	4.01
1506	1578	1.762957	CCCACAACGACCTCCATATCT	59.237	52.381	0.00	0.00	0.00	1.98
1512	1584	1.395635	AAAAACCCACAACGACCTCC	58.604	50.000	0.00	0.00	0.00	4.30
1534	1610	5.578776	CATCGTTACACTAGCACATGACTA	58.421	41.667	0.00	0.00	0.00	2.59
1535	1611	4.424626	CATCGTTACACTAGCACATGACT	58.575	43.478	0.00	0.00	0.00	3.41
1536	1612	3.000322	GCATCGTTACACTAGCACATGAC	60.000	47.826	0.00	0.00	0.00	3.06
1538	1614	2.285220	GGCATCGTTACACTAGCACATG	59.715	50.000	0.00	0.00	0.00	3.21
1540	1616	1.734377	CGGCATCGTTACACTAGCACA	60.734	52.381	0.00	0.00	0.00	4.57
1541	1617	0.921347	CGGCATCGTTACACTAGCAC	59.079	55.000	0.00	0.00	0.00	4.40
1542	1618	3.339061	CGGCATCGTTACACTAGCA	57.661	52.632	0.00	0.00	0.00	3.49
1572	1648	4.590918	TCAACACTTACCCTTGTTTCACA	58.409	39.130	0.00	0.00	33.59	3.58
1638	1719	1.694150	CAACACTGGACAGAGGGAGAA	59.306	52.381	6.29	0.00	0.00	2.87
1705	1786	1.524393	CACACCACTCAGCACTGCA	60.524	57.895	3.30	0.00	0.00	4.41
1707	1788	1.598962	CCCACACCACTCAGCACTG	60.599	63.158	0.00	0.00	0.00	3.66
1711	1864	0.613260	TGTATCCCACACCACTCAGC	59.387	55.000	0.00	0.00	30.04	4.26
1712	1865	4.344968	TCATATGTATCCCACACCACTCAG	59.655	45.833	1.90	0.00	40.86	3.35
1723	1876	9.921637	TTGAAAAACAAAACTCATATGTATCCC	57.078	29.630	1.90	0.00	35.39	3.85
1736	1889	4.875536	AGGGCATGACTTGAAAAACAAAAC	59.124	37.500	0.00	0.00	38.08	2.43
1840	1993	9.927081	AGAAATGGAGTAAATCTATGGACAATT	57.073	29.630	0.00	0.00	0.00	2.32
1855	2008	3.009473	AGGCTTTCAGCAGAAATGGAGTA	59.991	43.478	4.61	0.00	44.75	2.59
1918	2072	3.073678	TGAAGCGTTATCAATGCAGTGT	58.926	40.909	14.62	4.33	45.82	3.55
1944	2098	9.528489	AGAAGCTAAAGGTAATTCATAAAACCA	57.472	29.630	0.00	0.00	34.29	3.67
2082	2240	6.607600	ACAGTCAGCAGGTAACAGAGAATATA	59.392	38.462	0.00	0.00	41.41	0.86
2087	2245	2.598565	ACAGTCAGCAGGTAACAGAGA	58.401	47.619	0.00	0.00	41.41	3.10
2100	2258	7.012327	TGGACAACTATTGAGAAAAACAGTCAG	59.988	37.037	0.00	0.00	0.00	3.51
2170	3006	3.897141	TCAAATGTCATGGCATGCATT	57.103	38.095	28.50	28.50	38.05	3.56
2189	3025	3.691118	TCAAGCAGTCATGGTAGCATTTC	59.309	43.478	4.25	1.49	35.69	2.17
2194	3030	2.099141	TGTCAAGCAGTCATGGTAGC	57.901	50.000	0.00	0.00	35.69	3.58
2247	3083	2.159099	CCAGCTAGTACGAAGCATTGGA	60.159	50.000	20.76	0.00	42.62	3.53
2396	3232	9.862371	AACTCTTCAATGTTCACATAGTAGTAG	57.138	33.333	0.00	0.00	35.10	2.57
2415	3251	2.673368	CGCCCATCAGTGTAAACTCTTC	59.327	50.000	0.00	0.00	0.00	2.87
2493	3329	6.096001	ACAAGAACTTGAGCAGTGAAAAGAAT	59.904	34.615	19.35	0.00	42.93	2.40
2550	3386	9.472361	CAAAATAATTCAGGGCATAAATCTCAG	57.528	33.333	0.00	0.00	0.00	3.35
2622	3458	6.524734	AGTGAGCGTCAATTAATATGGATCA	58.475	36.000	0.00	0.00	0.00	2.92
2698	3534	3.015675	GGGATATACTACTCCCTCCGG	57.984	57.143	0.00	0.00	46.55	5.14
2881	3717	3.574445	GCAGCAGCGATGCCTCTG	61.574	66.667	24.00	15.64	39.19	3.35
2899	3735	3.181485	GGAGGTCCATGAAGTACTTCTCG	60.181	52.174	30.47	21.98	36.93	4.04
3201	4132	1.381872	ATCACCCTCTCGACCCCTG	60.382	63.158	0.00	0.00	0.00	4.45
3220	4151	2.831333	CCATCCCTTGTCATCTCTTCG	58.169	52.381	0.00	0.00	0.00	3.79
3558	4813	2.526888	AGTCTTAGGTGGACGGATGA	57.473	50.000	0.00	0.00	38.58	2.92
3668	4923	3.452627	TCCTCTGTTTCCTTATCCTCTGC	59.547	47.826	0.00	0.00	0.00	4.26
3754	5226	2.768253	TGTCAAGCATACCCTCTGTG	57.232	50.000	0.00	0.00	0.00	3.66
3808	5280	1.079405	CGCGTTAAGCCTTCCTCCA	60.079	57.895	0.00	0.00	44.76	3.86
4132	5604	0.934496	CGCTGAGTTCCACGTTTTCA	59.066	50.000	0.00	0.00	0.00	2.69
4258	5731	4.201714	GGTTTTGCAGAAGAAAACAGCAAC	60.202	41.667	11.84	0.00	43.94	4.17
4302	6375	3.426615	TGGCCAACCGAAATAAATGTCT	58.573	40.909	0.61	0.00	39.70	3.41
4334	6408	0.804989	CAAAAGGACTCCGATGGTGC	59.195	55.000	0.00	0.00	0.00	5.01
4468	6573	6.539826	CACAGCTCATGTCACATATTTAAGGA	59.460	38.462	0.00	0.00	41.41	3.36
4483	7236	9.020813	CAAATTATTCTTTCATCACAGCTCATG	57.979	33.333	0.00	0.00	0.00	3.07
4529	7290	4.922206	ACCCAGTCACAATGTCACATAAT	58.078	39.130	0.00	0.00	0.00	1.28
4629	7403	7.123355	TGATTTCCAGGAAGTGTCAATTTTT	57.877	32.000	0.99	0.00	0.00	1.94
4637	7411	3.256631	GCACAATGATTTCCAGGAAGTGT	59.743	43.478	15.10	3.16	0.00	3.55
4645	7419	2.964464	ACAAGGTGCACAATGATTTCCA	59.036	40.909	23.10	0.00	0.00	3.53
4710	7487	3.381590	AGCCATATCGCAGATAATCGCTA	59.618	43.478	0.00	0.00	45.12	4.26
4728	7505	1.000521	CCCCTTCAATGAGCAGCCA	60.001	57.895	0.00	0.00	0.00	4.75
4737	7514	2.357569	GCATCTCCTTCACCCCTTCAAT	60.358	50.000	0.00	0.00	0.00	2.57
4744	7521	4.336280	AGTTTTAAGCATCTCCTTCACCC	58.664	43.478	0.00	0.00	0.00	4.61
4767	7544	4.506625	CCACTGAACCCTAAATTCCTGACA	60.507	45.833	0.00	0.00	0.00	3.58
4768	7545	4.010349	CCACTGAACCCTAAATTCCTGAC	58.990	47.826	0.00	0.00	0.00	3.51
4791	7568	0.039074	CCATTAACCAAACGCCGCAA	60.039	50.000	0.00	0.00	0.00	4.85
4813	7590	9.969001	AACCTTCCTTAACTAAAATATGTGCTA	57.031	29.630	0.00	0.00	0.00	3.49
4863	7643	4.092279	TGCAATGTTCCCAATACAATCCA	58.908	39.130	0.00	0.00	0.00	3.41
4892	7673	3.731652	TTCAGAATGTTTGGGCAGTTG	57.268	42.857	0.00	0.00	37.40	3.16
4943	7726	9.868277	TCACTCAACAGTTAACAAAATGAAATT	57.132	25.926	8.61	0.00	38.98	1.82
4945	7728	9.515020	GATCACTCAACAGTTAACAAAATGAAA	57.485	29.630	8.61	0.00	0.00	2.69
5003	7786	9.982651	TGACAAGGTATACAGCTTCTATTTATC	57.017	33.333	5.01	0.00	40.49	1.75
5081	7880	0.038744	ATTTCCTGTGGCTCCCAGTG	59.961	55.000	0.00	0.00	32.34	3.66
5082	7881	0.038744	CATTTCCTGTGGCTCCCAGT	59.961	55.000	0.00	0.00	32.34	4.00
5084	7883	1.002069	ATCATTTCCTGTGGCTCCCA	58.998	50.000	0.00	0.00	0.00	4.37
5089	7888	1.838112	TGTGGATCATTTCCTGTGGC	58.162	50.000	0.00	0.00	45.68	5.01
5090	7889	2.100252	GCATGTGGATCATTTCCTGTGG	59.900	50.000	0.00	0.00	45.68	4.17
5091	7890	3.021695	AGCATGTGGATCATTTCCTGTG	58.978	45.455	0.00	0.00	45.68	3.66
5095	7894	1.605710	CCGAGCATGTGGATCATTTCC	59.394	52.381	0.00	0.00	45.69	3.13
5122	7923	6.814506	AGATCATGGTTTTCACTCTGAAAG	57.185	37.500	0.00	0.00	45.77	2.62
5157	7958	1.177256	AAGCAGCAGTCCAAAGCAGG	61.177	55.000	0.00	0.00	0.00	4.85
5164	7965	1.405105	GAACACAAAAGCAGCAGTCCA	59.595	47.619	0.00	0.00	0.00	4.02

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.