AutoCloner

Multiple sequence alignment - TraesCS7D01G306900

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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	TraesCS7D01G306900	chr7D	100.000	5736	0	0	1	5736	388690941	388696676	0.000000e+00	10593.0
1	TraesCS7D01G306900	chr7D	89.508	305	19	6	1568	1860	636296751	636297054	1.950000e-99	374.0
2	TraesCS7D01G306900	chr7D	89.298	299	13	5	1571	1860	635714668	635714380	1.970000e-94	357.0
3	TraesCS7D01G306900	chr7B	95.032	5676	186	39	3	5627	383727281	383732911	0.000000e+00	8831.0
4	TraesCS7D01G306900	chr7B	92.308	91	3	4	5612	5698	639489917	639489827	6.030000e-25	126.0
5	TraesCS7D01G306900	chr7A	96.000	4225	115	24	1445	5627	438850266	438854478	0.000000e+00	6817.0
6	TraesCS7D01G306900	chr7A	95.789	760	30	2	598	1356	438849291	438850049	0.000000e+00	1225.0
7	TraesCS7D01G306900	chr7A	88.682	592	34	12	65	650	438848746	438849310	0.000000e+00	691.0
8	TraesCS7D01G306900	chr7A	91.753	291	13	3	1571	1860	471737806	471737526	1.500000e-105	394.0
9	TraesCS7D01G306900	chr7A	88.031	259	19	5	5378	5627	438854813	438855068	4.350000e-76	296.0
10	TraesCS7D01G306900	chr7A	83.415	205	28	3	1098	1296	575558772	575558976	9.810000e-43	185.0
11	TraesCS7D01G306900	chr7A	91.111	90	3	5	5614	5698	32013226	32013137	3.630000e-22	117.0
12	TraesCS7D01G306900	chr5B	83.630	2975	345	70	1945	4840	540254245	540251334	0.000000e+00	2665.0
13	TraesCS7D01G306900	chr5B	85.057	261	34	4	1001	1260	540255348	540255092	1.590000e-65	261.0
14	TraesCS7D01G306900	chr5B	76.757	185	40	3	3128	3311	540252888	540253070	3.660000e-17	100.0
15	TraesCS7D01G306900	chr5A	84.301	2325	286	39	2571	4839	559809530	559807229	0.000000e+00	2198.0
16	TraesCS7D01G306900	chr5A	87.023	262	29	4	1001	1261	559811399	559811142	2.020000e-74	291.0
17	TraesCS7D01G306900	chr5A	75.543	184	41	4	3098	3278	559808757	559808939	2.850000e-13	87.9
18	TraesCS7D01G306900	chr5D	85.322	1458	167	22	3412	4839	443636059	443634619	0.000000e+00	1463.0
19	TraesCS7D01G306900	chr5D	88.713	443	47	3	2571	3012	443636498	443636058	6.540000e-149	538.0
20	TraesCS7D01G306900	chr5D	82.596	339	45	8	1001	1328	443638476	443638141	2.620000e-73	287.0
21	TraesCS7D01G306900	chr5D	81.466	232	33	7	1101	1328	233275734	233275509	1.270000e-41	182.0
22	TraesCS7D01G306900	chr5D	91.765	85	5	2	5616	5698	402773365	402773449	3.630000e-22	117.0
23	TraesCS7D01G306900	chr5D	84.496	129	9	6	5110	5236	443634428	443634309	3.630000e-22	117.0
24	TraesCS7D01G306900	chr6A	90.258	1006	76	7	1976	2979	92339607	92340592	0.000000e+00	1295.0
25	TraesCS7D01G306900	chr3A	90.075	937	74	11	1860	2792	725009892	725008971	0.000000e+00	1197.0
26	TraesCS7D01G306900	chr3A	92.077	366	28	1	2146	2511	555513064	555512700	1.100000e-141	514.0
27	TraesCS7D01G306900	chr3A	86.780	295	14	6	1568	1861	343110874	343111144	7.220000e-79	305.0
28	TraesCS7D01G306900	chr3A	92.417	211	12	3	1655	1861	725010799	725010589	1.210000e-76	298.0
29	TraesCS7D01G306900	chr3A	82.069	290	48	2	4527	4813	697454942	697455230	1.600000e-60	244.0
30	TraesCS7D01G306900	chr3A	92.941	85	3	2	5626	5707	274756458	274756542	2.810000e-23	121.0
31	TraesCS7D01G306900	chr3A	91.765	85	4	2	5623	5705	274756535	274756452	1.310000e-21	115.0
32	TraesCS7D01G306900	chr3A	83.951	81	13	0	3623	3703	697454144	697454224	1.710000e-10	78.7
33	TraesCS7D01G306900	chr3A	100.000	30	0	0	4836	4865	697455323	697455352	8.030000e-04	56.5
34	TraesCS7D01G306900	chr4A	91.339	762	52	11	2035	2792	730355523	730356274	0.000000e+00	1029.0
35	TraesCS7D01G306900	chr4A	94.915	295	14	1	1568	1861	730354790	730355084	1.460000e-125	460.0
36	TraesCS7D01G306900	chr4A	78.182	110	21	3	3170	3279	37789799	37789905	3.710000e-07	67.6
37	TraesCS7D01G306900	chr3B	87.919	745	63	12	1964	2704	202532	203253	0.000000e+00	852.0
38	TraesCS7D01G306900	chr3B	86.395	294	21	4	1568	1860	448408021	448408296	2.600000e-78	303.0
39	TraesCS7D01G306900	chr3B	79.839	124	21	2	4023	4146	749022429	749022548	2.850000e-13	87.9
40	TraesCS7D01G306900	chr3B	81.944	72	13	0	4836	4907	749023536	749023607	1.730000e-05	62.1
41	TraesCS7D01G306900	chr2A	90.778	553	46	5	2187	2737	560574525	560575074	0.000000e+00	734.0
42	TraesCS7D01G306900	chr2A	92.784	291	10	3	1571	1860	312040117	312039837	1.490000e-110	411.0
43	TraesCS7D01G306900	chr1B	89.944	537	46	5	1976	2511	292422696	292423225	0.000000e+00	686.0
44	TraesCS7D01G306900	chr1B	89.572	537	48	5	1976	2511	292348370	292348899	0.000000e+00	675.0
45	TraesCS7D01G306900	chr1B	93.333	375	23	2	2607	2979	292348896	292349270	2.340000e-153	553.0
46	TraesCS7D01G306900	chr1B	93.333	375	22	3	2607	2979	292423222	292423595	8.400000e-153	551.0
47	TraesCS7D01G306900	chrUn	92.246	374	28	1	2607	2979	49575793	49575420	3.940000e-146	529.0
48	TraesCS7D01G306900	chrUn	88.514	296	28	3	1976	2271	49576264	49575975	2.540000e-93	353.0
49	TraesCS7D01G306900	chr4D	92.440	291	11	3	1571	1860	289466603	289466323	6.920000e-109	405.0
50	TraesCS7D01G306900	chr4D	93.902	82	3	1	5619	5698	43548864	43548945	7.800000e-24	122.0
51	TraesCS7D01G306900	chr3D	84.681	235	32	3	4582	4813	561709165	561709398	1.240000e-56	231.0
52	TraesCS7D01G306900	chr3D	83.333	228	38	0	4351	4578	561708809	561709036	1.620000e-50	211.0
53	TraesCS7D01G306900	chr3D	81.944	72	13	0	4836	4907	561709491	561709562	1.730000e-05	62.1
54	TraesCS7D01G306900	chr6D	94.872	78	3	1	5626	5702	63834806	63834729	2.810000e-23	121.0
55	TraesCS7D01G306900	chr6B	94.872	78	2	2	5623	5698	629435922	629435999	2.810000e-23	121.0
56	TraesCS7D01G306900	chr2B	93.827	81	1	4	5623	5699	614917138	614917218	1.010000e-22	119.0

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	TraesCS7D01G306900	chr7D	388690941	388696676	5735	False	10593.00	10593	100.00000	1	5736	1	chr7D.!!$F1	5735
1	TraesCS7D01G306900	chr7B	383727281	383732911	5630	False	8831.00	8831	95.03200	3	5627	1	chr7B.!!$F1	5624
2	TraesCS7D01G306900	chr7A	438848746	438855068	6322	False	2257.25	6817	92.12550	65	5627	4	chr7A.!!$F2	5562
3	TraesCS7D01G306900	chr5B	540251334	540255348	4014	True	1463.00	2665	84.34350	1001	4840	2	chr5B.!!$R1	3839
4	TraesCS7D01G306900	chr5A	559807229	559811399	4170	True	1244.50	2198	85.66200	1001	4839	2	chr5A.!!$R1	3838
5	TraesCS7D01G306900	chr5D	443634309	443638476	4167	True	601.25	1463	85.28175	1001	5236	4	chr5D.!!$R2	4235
6	TraesCS7D01G306900	chr6A	92339607	92340592	985	False	1295.00	1295	90.25800	1976	2979	1	chr6A.!!$F1	1003
7	TraesCS7D01G306900	chr3A	725008971	725010799	1828	True	747.50	1197	91.24600	1655	2792	2	chr3A.!!$R3	1137
8	TraesCS7D01G306900	chr4A	730354790	730356274	1484	False	744.50	1029	93.12700	1568	2792	2	chr4A.!!$F2	1224
9	TraesCS7D01G306900	chr3B	202532	203253	721	False	852.00	852	87.91900	1964	2704	1	chr3B.!!$F1	740
10	TraesCS7D01G306900	chr2A	560574525	560575074	549	False	734.00	734	90.77800	2187	2737	1	chr2A.!!$F1	550
11	TraesCS7D01G306900	chr1B	292422696	292423595	899	False	618.50	686	91.63850	1976	2979	2	chr1B.!!$F2	1003
12	TraesCS7D01G306900	chr1B	292348370	292349270	900	False	614.00	675	91.45250	1976	2979	2	chr1B.!!$F1	1003
13	TraesCS7D01G306900	chrUn	49575420	49576264	844	True	441.00	529	90.38000	1976	2979	2	chrUn.!!$R1	1003

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	End Stability	Orientation
896	940	0.250640	CAAGGGCTTCTCTGCTGTGT	60.251	55.000	0.00	3.72	F
2028	3102	3.489355	ACAGTTTGGCAAGATGTGATGA	58.511	40.909	15.84	2.92	F
3019	4314	6.260936	ACTTATTAAGCTGATGTGGATTTCGG	59.739	38.462	3.28	4.30	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Hairpin	End Stability	Orientation
2723	4017	2.807967	CGTCAACCATTCTCAGCTTCAA	59.192	45.455	0.00	0.00	2.69	R
3464	4782	1.798813	GTCAAACGCCAAGTCAGTAGG	59.201	52.381	0.00	0.00	3.18	R
4861	6276	1.040893	ACCGGTGATGATACTCGGCA	61.041	55.000	6.12	43.96	5.69	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
24	25	2.770164	GCTAGAGTTGGAGCCAAAGA	57.230	50.000	3.05	0.00	37.70	2.52
32	33	2.200373	TGGAGCCAAAGAGCTTTACC	57.800	50.000	0.00	0.00	45.15	2.85
48	49	3.665745	TTACCAACTGTTACCCGAGAC	57.334	47.619	0.00	0.00	0.00	3.36
53	54	2.479566	ACTGTTACCCGAGACGTAGA	57.520	50.000	0.00	0.00	0.00	2.59
55	56	1.063764	CTGTTACCCGAGACGTAGAGC	59.936	57.143	0.00	0.00	0.00	4.09
65	66	3.120269	CGAGACGTAGAGCTTGTAGTTGT	60.120	47.826	0.00	0.00	0.00	3.32
69	70	3.069158	ACGTAGAGCTTGTAGTTGTTGGT	59.931	43.478	0.00	0.00	0.00	3.67
169	170	4.444388	CCGTCGATGAAATGATACGTGATT	59.556	41.667	6.11	0.00	0.00	2.57
225	231	5.538433	AGTGTACTTTGCAAACCCACATATT	59.462	36.000	22.84	10.36	0.00	1.28
298	304	3.170991	AGAGTGCCCACTTGACTAGTA	57.829	47.619	0.00	0.00	42.66	1.82
327	333	2.169832	AAGTTGCATGCTACACTCGT	57.830	45.000	29.37	9.71	0.00	4.18
366	373	8.902540	ACTACATTTCAAACATCAGAACTACA	57.097	30.769	0.00	0.00	0.00	2.74
367	374	9.507329	ACTACATTTCAAACATCAGAACTACAT	57.493	29.630	0.00	0.00	0.00	2.29
408	415	3.126171	CAGGTTTGCCAAATGATGCATTG	59.874	43.478	0.00	0.00	37.33	2.82
411	418	2.388310	TGCCAAATGATGCATTGTGG	57.612	45.000	0.00	1.32	36.29	4.17
412	419	1.900486	TGCCAAATGATGCATTGTGGA	59.100	42.857	11.24	0.00	35.80	4.02
413	420	2.302157	TGCCAAATGATGCATTGTGGAA	59.698	40.909	11.24	0.00	35.80	3.53
417	424	5.618195	GCCAAATGATGCATTGTGGAAAAAG	60.618	40.000	11.24	0.00	35.80	2.27
459	468	8.424918	TCTTGAAAGTTTTGCATATTTTGGGTA	58.575	29.630	0.00	0.00	0.00	3.69
492	501	5.288472	GTGAAGCAAGGTTGTTTGTAAACTG	59.712	40.000	8.74	0.42	39.59	3.16
511	520	9.925268	GTAAACTGTTCTTTTAAACGAGAATCA	57.075	29.630	5.79	5.64	34.68	2.57
527	536	5.294552	CGAGAATCAGATCAAGGTAAAACCC	59.705	44.000	0.00	0.00	34.71	4.11
561	570	4.782116	CATGCGTCGCGTGTGCAG	62.782	66.667	27.44	5.35	42.65	4.41
709	752	3.758931	GCCAAATGTGGGCCCGTC	61.759	66.667	19.37	13.77	46.09	4.79
896	940	0.250640	CAAGGGCTTCTCTGCTGTGT	60.251	55.000	0.00	0.00	0.00	3.72
1311	1370	5.334414	GGTCCAAAATTGAGCGCTATATCTG	60.334	44.000	11.50	7.93	0.00	2.90
1364	1527	5.068198	GGCTAAATGGATGCAATTCTTCAGA	59.932	40.000	0.00	0.00	0.00	3.27
1369	1532	8.937634	AAATGGATGCAATTCTTCAGAATAAC	57.062	30.769	2.41	0.00	43.41	1.89
1419	1602	4.312443	TGATTTTCTCCTAACGTGTGTCC	58.688	43.478	0.00	0.00	0.00	4.02
1743	1983	4.571369	TCCTCGAGTAGTATATGGGAGG	57.429	50.000	12.31	0.00	40.67	4.30
2028	3102	3.489355	ACAGTTTGGCAAGATGTGATGA	58.511	40.909	15.84	0.00	0.00	2.92
2723	4017	6.585695	AAGAACAGATTGAAATGCTGACAT	57.414	33.333	0.00	0.00	38.49	3.06
3019	4314	6.260936	ACTTATTAAGCTGATGTGGATTTCGG	59.739	38.462	3.28	0.00	0.00	4.30
3231	4536	6.371389	GTTCGTATTTGAAAGAGGTTTCCAG	58.629	40.000	0.00	0.00	41.37	3.86
3464	4782	3.062774	GCTCGTTCAACTAAATCCAGCTC	59.937	47.826	0.00	0.00	0.00	4.09
3896	5217	1.455786	CGGTAACTCAGTTGAAGCGTG	59.544	52.381	0.00	0.00	0.00	5.34
4052	5373	5.701224	TGGTAAGAAAGGACAGACCAAATT	58.299	37.500	0.00	0.00	42.04	1.82
4180	5504	3.153919	GGTTGATGGTGGTAGAAAAGCA	58.846	45.455	0.00	0.00	0.00	3.91
4279	5609	1.675801	TGCAAGTGAGCAGAGGGAG	59.324	57.895	0.00	0.00	40.11	4.30
4292	5625	3.376546	GCAGAGGGAGAAAACATCATCAC	59.623	47.826	0.00	0.00	0.00	3.06
4414	5750	1.993370	GATGAGAACGTGAACCGGAAG	59.007	52.381	9.46	0.00	42.24	3.46
4489	5825	1.741706	CGAGTCTGCCAAATGCTCAAT	59.258	47.619	0.00	0.00	42.00	2.57
4610	5955	2.832129	GACAATGGACACTCTCAGGGTA	59.168	50.000	0.00	0.00	27.47	3.69
4830	6188	3.261643	TGAGAAGAGCACTAGCATTGGAA	59.738	43.478	0.00	0.00	45.49	3.53
4861	6276	6.951971	ACAATCATGTAGAGCTAAGGAACTT	58.048	36.000	0.00	0.00	45.58	2.66
4877	6293	2.604046	ACTTGCCGAGTATCATCACC	57.396	50.000	0.00	0.00	36.65	4.02
5011	6445	8.398878	TGTAAAAGATGGTAAGTAAAACCCTG	57.601	34.615	0.00	0.00	36.06	4.45
5038	6478	3.883830	TTTTTCCTTTTGCAGCAGTGA	57.116	38.095	0.00	0.00	0.00	3.41
5039	6479	3.883830	TTTTCCTTTTGCAGCAGTGAA	57.116	38.095	0.00	0.00	0.00	3.18
5041	6481	1.032014	TCCTTTTGCAGCAGTGAACC	58.968	50.000	0.00	0.00	0.00	3.62
5131	6571	0.321564	ACTGCGTGGCTCATTTGCTA	60.322	50.000	0.00	0.00	0.00	3.49
5328	6770	2.989639	TGGATTCCTCCCACTGCG	59.010	61.111	3.95	0.00	41.29	5.18
5468	6914	2.908940	GCGCCATATGCCTGCCTT	60.909	61.111	0.00	0.00	36.24	4.35
5488	7526	1.837538	CGTCGGCATTGTTCCGTTGT	61.838	55.000	1.22	0.00	46.49	3.32
5604	7651	2.159720	TCACACTATTGCGTTCAATGCG	60.160	45.455	0.00	0.00	42.50	4.73
5613	7660	0.795698	CGTTCAATGCGACATGTCCA	59.204	50.000	20.03	17.86	0.00	4.02
5627	7674	6.262601	CGACATGTCCACCCATAAAAATTAC	58.737	40.000	20.03	0.00	0.00	1.89
5628	7675	6.094881	CGACATGTCCACCCATAAAAATTACT	59.905	38.462	20.03	0.00	0.00	2.24
5629	7676	7.404671	ACATGTCCACCCATAAAAATTACTC	57.595	36.000	0.00	0.00	0.00	2.59
5630	7677	6.379988	ACATGTCCACCCATAAAAATTACTCC	59.620	38.462	0.00	0.00	0.00	3.85
5631	7678	5.265989	TGTCCACCCATAAAAATTACTCCC	58.734	41.667	0.00	0.00	0.00	4.30
5632	7679	5.015817	TGTCCACCCATAAAAATTACTCCCT	59.984	40.000	0.00	0.00	0.00	4.20
5633	7680	5.593095	GTCCACCCATAAAAATTACTCCCTC	59.407	44.000	0.00	0.00	0.00	4.30
5634	7681	4.893524	CCACCCATAAAAATTACTCCCTCC	59.106	45.833	0.00	0.00	0.00	4.30
5635	7682	4.578928	CACCCATAAAAATTACTCCCTCCG	59.421	45.833	0.00	0.00	0.00	4.63
5636	7683	4.228895	ACCCATAAAAATTACTCCCTCCGT	59.771	41.667	0.00	0.00	0.00	4.69
5637	7684	4.820173	CCCATAAAAATTACTCCCTCCGTC	59.180	45.833	0.00	0.00	0.00	4.79
5638	7685	4.820173	CCATAAAAATTACTCCCTCCGTCC	59.180	45.833	0.00	0.00	0.00	4.79
5639	7686	3.361281	AAAAATTACTCCCTCCGTCCC	57.639	47.619	0.00	0.00	0.00	4.46
5640	7687	1.961133	AAATTACTCCCTCCGTCCCA	58.039	50.000	0.00	0.00	0.00	4.37
5641	7688	2.191981	AATTACTCCCTCCGTCCCAT	57.808	50.000	0.00	0.00	0.00	4.00
5642	7689	3.339713	AATTACTCCCTCCGTCCCATA	57.660	47.619	0.00	0.00	0.00	2.74
5643	7690	2.852714	TTACTCCCTCCGTCCCATAA	57.147	50.000	0.00	0.00	0.00	1.90
5644	7691	3.339713	TTACTCCCTCCGTCCCATAAT	57.660	47.619	0.00	0.00	0.00	1.28
5645	7692	1.424638	ACTCCCTCCGTCCCATAATG	58.575	55.000	0.00	0.00	0.00	1.90
5646	7693	1.344087	ACTCCCTCCGTCCCATAATGT	60.344	52.381	0.00	0.00	0.00	2.71
5647	7694	2.090943	ACTCCCTCCGTCCCATAATGTA	60.091	50.000	0.00	0.00	0.00	2.29
5648	7695	2.969950	CTCCCTCCGTCCCATAATGTAA	59.030	50.000	0.00	0.00	0.00	2.41
5649	7696	2.969950	TCCCTCCGTCCCATAATGTAAG	59.030	50.000	0.00	0.00	0.00	2.34
5650	7697	2.969950	CCCTCCGTCCCATAATGTAAGA	59.030	50.000	0.00	0.00	0.00	2.10
5651	7698	3.244112	CCCTCCGTCCCATAATGTAAGAC	60.244	52.174	0.00	0.00	0.00	3.01
5653	7700	3.025978	TCCGTCCCATAATGTAAGACGT	58.974	45.455	9.63	0.00	46.62	4.34
5654	7701	3.448301	TCCGTCCCATAATGTAAGACGTT	59.552	43.478	9.63	0.00	46.62	3.99
5655	7702	4.081531	TCCGTCCCATAATGTAAGACGTTT	60.082	41.667	9.63	0.00	46.62	3.60
5656	7703	4.632688	CCGTCCCATAATGTAAGACGTTTT	59.367	41.667	9.63	0.00	46.62	2.43
5657	7704	5.122711	CCGTCCCATAATGTAAGACGTTTTT	59.877	40.000	9.63	0.00	46.62	1.94
5690	7737	3.720949	CGTCTTACATTATGGGACGGA	57.279	47.619	20.50	2.30	43.69	4.69
5691	7738	3.639538	CGTCTTACATTATGGGACGGAG	58.360	50.000	20.50	2.74	43.69	4.63
5692	7739	3.552273	CGTCTTACATTATGGGACGGAGG	60.552	52.174	20.50	5.87	43.69	4.30
5693	7740	2.969950	TCTTACATTATGGGACGGAGGG	59.030	50.000	0.00	0.00	0.00	4.30
5694	7741	2.779429	TACATTATGGGACGGAGGGA	57.221	50.000	0.00	0.00	0.00	4.20
5695	7742	1.424638	ACATTATGGGACGGAGGGAG	58.575	55.000	0.00	0.00	0.00	4.30
5696	7743	1.344087	ACATTATGGGACGGAGGGAGT	60.344	52.381	0.00	0.00	0.00	3.85
5697	7744	2.090943	ACATTATGGGACGGAGGGAGTA	60.091	50.000	0.00	0.00	0.00	2.59
5698	7745	3.173965	CATTATGGGACGGAGGGAGTAT	58.826	50.000	0.00	0.00	0.00	2.12
5699	7746	3.339713	TTATGGGACGGAGGGAGTATT	57.660	47.619	0.00	0.00	0.00	1.89
5700	7747	4.474303	TTATGGGACGGAGGGAGTATTA	57.526	45.455	0.00	0.00	0.00	0.98
5701	7748	2.852714	TGGGACGGAGGGAGTATTAA	57.147	50.000	0.00	0.00	0.00	1.40
5702	7749	2.391678	TGGGACGGAGGGAGTATTAAC	58.608	52.381	0.00	0.00	0.00	2.01
5703	7750	2.023695	TGGGACGGAGGGAGTATTAACT	60.024	50.000	0.00	0.00	39.21	2.24
5704	7751	3.036819	GGGACGGAGGGAGTATTAACTT	58.963	50.000	0.00	0.00	35.56	2.66
5705	7752	4.218312	GGGACGGAGGGAGTATTAACTTA	58.782	47.826	0.00	0.00	35.56	2.24
5706	7753	4.038522	GGGACGGAGGGAGTATTAACTTAC	59.961	50.000	0.00	0.00	35.56	2.34
5707	7754	4.038522	GGACGGAGGGAGTATTAACTTACC	59.961	50.000	0.00	0.00	35.56	2.85
5708	7755	4.876580	ACGGAGGGAGTATTAACTTACCT	58.123	43.478	3.32	3.32	42.67	3.08
5713	7760	7.764141	GAGGGAGTATTAACTTACCTCTAGG	57.236	44.000	16.60	0.00	46.41	3.02
5714	7761	6.076653	AGGGAGTATTAACTTACCTCTAGGC	58.923	44.000	0.00	0.00	38.36	3.93
5715	7762	6.076653	GGGAGTATTAACTTACCTCTAGGCT	58.923	44.000	0.00	0.00	35.57	4.58
5716	7763	6.015265	GGGAGTATTAACTTACCTCTAGGCTG	60.015	46.154	0.00	0.00	35.57	4.85
5717	7764	6.776603	GGAGTATTAACTTACCTCTAGGCTGA	59.223	42.308	0.00	0.00	35.57	4.26
5718	7765	7.040271	GGAGTATTAACTTACCTCTAGGCTGAG	60.040	44.444	0.00	1.96	35.57	3.35
5719	7766	6.778559	AGTATTAACTTACCTCTAGGCTGAGG	59.221	42.308	23.16	23.16	45.32	3.86
5723	7770	4.796408	CCTCTAGGCTGAGGTGGT	57.204	61.111	19.03	0.00	46.33	4.16
5724	7771	2.510664	CCTCTAGGCTGAGGTGGTC	58.489	63.158	19.03	0.00	46.33	4.02
5725	7772	1.388065	CCTCTAGGCTGAGGTGGTCG	61.388	65.000	19.03	0.38	46.33	4.79
5726	7773	0.394488	CTCTAGGCTGAGGTGGTCGA	60.394	60.000	0.00	0.00	0.00	4.20
5727	7774	0.259065	TCTAGGCTGAGGTGGTCGAT	59.741	55.000	0.00	0.00	0.00	3.59
5728	7775	0.387202	CTAGGCTGAGGTGGTCGATG	59.613	60.000	0.00	0.00	0.00	3.84
5729	7776	1.676678	TAGGCTGAGGTGGTCGATGC	61.677	60.000	0.00	0.00	0.00	3.91
5730	7777	2.512515	GCTGAGGTGGTCGATGCC	60.513	66.667	0.00	0.00	0.00	4.40
5731	7778	2.202797	CTGAGGTGGTCGATGCCG	60.203	66.667	0.00	0.00	37.07	5.69
5732	7779	4.451150	TGAGGTGGTCGATGCCGC	62.451	66.667	0.00	0.00	38.26	6.53

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
0	1	2.501492	GCTCCAACTCTAGCCCGTA	58.499	57.895	0.00	0.00	32.40	4.02
1	2	3.300013	GCTCCAACTCTAGCCCGT	58.700	61.111	0.00	0.00	32.40	5.28
7	8	2.260822	AGCTCTTTGGCTCCAACTCTA	58.739	47.619	0.00	0.00	38.24	2.43
24	25	2.369532	TCGGGTAACAGTTGGTAAAGCT	59.630	45.455	0.00	0.00	39.74	3.74
32	33	2.485426	TCTACGTCTCGGGTAACAGTTG	59.515	50.000	0.00	0.00	39.74	3.16
48	49	3.650139	ACCAACAACTACAAGCTCTACG	58.350	45.455	0.00	0.00	0.00	3.51
53	54	2.618709	GCTCAACCAACAACTACAAGCT	59.381	45.455	0.00	0.00	0.00	3.74
55	56	3.952535	GTGCTCAACCAACAACTACAAG	58.047	45.455	0.00	0.00	0.00	3.16
69	70	3.181501	CGAACAAGAAAACAGGTGCTCAA	60.182	43.478	0.00	0.00	0.00	3.02
78	79	2.223479	GCTTGAGGCGAACAAGAAAACA	60.223	45.455	19.89	0.00	44.92	2.83
79	80	2.385315	GCTTGAGGCGAACAAGAAAAC	58.615	47.619	19.89	4.82	44.92	2.43
114	115	4.986034	CGACAAAACCACATACACACTCTA	59.014	41.667	0.00	0.00	0.00	2.43
125	126	0.249531	TAGCGAGCGACAAAACCACA	60.250	50.000	0.00	0.00	0.00	4.17
130	131	1.735198	CGGGTAGCGAGCGACAAAA	60.735	57.895	10.26	0.00	0.00	2.44
228	234	6.176975	CAGAAAAGTTTTTGTGGGTTTTCC	57.823	37.500	1.64	0.00	37.66	3.13
280	286	4.910458	AATTACTAGTCAAGTGGGCACT	57.090	40.909	0.00	0.00	44.94	4.40
349	356	8.681806	TGTTTGAAATGTAGTTCTGATGTTTGA	58.318	29.630	0.00	0.00	0.00	2.69
350	357	8.854979	TGTTTGAAATGTAGTTCTGATGTTTG	57.145	30.769	0.00	0.00	0.00	2.93
351	358	9.683069	GATGTTTGAAATGTAGTTCTGATGTTT	57.317	29.630	0.00	0.00	0.00	2.83
352	359	8.849168	TGATGTTTGAAATGTAGTTCTGATGTT	58.151	29.630	0.00	0.00	0.00	2.71
353	360	8.394971	TGATGTTTGAAATGTAGTTCTGATGT	57.605	30.769	0.00	0.00	0.00	3.06
354	361	8.724229	TCTGATGTTTGAAATGTAGTTCTGATG	58.276	33.333	0.00	0.00	0.00	3.07
355	362	8.853077	TCTGATGTTTGAAATGTAGTTCTGAT	57.147	30.769	0.00	0.00	0.00	2.90
356	363	8.559536	GTTCTGATGTTTGAAATGTAGTTCTGA	58.440	33.333	0.00	0.00	0.00	3.27
357	364	8.562892	AGTTCTGATGTTTGAAATGTAGTTCTG	58.437	33.333	0.00	0.00	0.00	3.02
358	365	8.682936	AGTTCTGATGTTTGAAATGTAGTTCT	57.317	30.769	0.00	0.00	0.00	3.01
359	366	8.017946	GGAGTTCTGATGTTTGAAATGTAGTTC	58.982	37.037	0.00	0.00	0.00	3.01
360	367	7.040409	GGGAGTTCTGATGTTTGAAATGTAGTT	60.040	37.037	0.00	0.00	0.00	2.24
361	368	6.431234	GGGAGTTCTGATGTTTGAAATGTAGT	59.569	38.462	0.00	0.00	0.00	2.73
362	369	6.430925	TGGGAGTTCTGATGTTTGAAATGTAG	59.569	38.462	0.00	0.00	0.00	2.74
363	370	6.303054	TGGGAGTTCTGATGTTTGAAATGTA	58.697	36.000	0.00	0.00	0.00	2.29
364	371	5.139727	TGGGAGTTCTGATGTTTGAAATGT	58.860	37.500	0.00	0.00	0.00	2.71
365	372	5.336213	CCTGGGAGTTCTGATGTTTGAAATG	60.336	44.000	0.00	0.00	0.00	2.32
366	373	4.768968	CCTGGGAGTTCTGATGTTTGAAAT	59.231	41.667	0.00	0.00	0.00	2.17
367	374	4.144297	CCTGGGAGTTCTGATGTTTGAAA	58.856	43.478	0.00	0.00	0.00	2.69
368	375	3.138283	ACCTGGGAGTTCTGATGTTTGAA	59.862	43.478	0.00	0.00	0.00	2.69
455	464	2.156098	TGCTTCACCGTTTCATTACCC	58.844	47.619	0.00	0.00	0.00	3.69
459	468	2.306847	ACCTTGCTTCACCGTTTCATT	58.693	42.857	0.00	0.00	0.00	2.57
492	501	9.535270	CTTGATCTGATTCTCGTTTAAAAGAAC	57.465	33.333	5.35	1.87	34.52	3.01
511	520	3.365472	GCCATGGGTTTTACCTTGATCT	58.635	45.455	15.13	0.00	38.64	2.75
527	536	1.391933	ATGTGCTGCTCATGGCCATG	61.392	55.000	35.76	35.76	40.92	3.66
561	570	0.881118	TGGTTTCGAGCTTGCATTCC	59.119	50.000	0.00	0.00	0.00	3.01
708	751	4.429212	CCGACGTGGATGGCGTGA	62.429	66.667	0.00	0.00	43.04	4.35
770	813	2.546373	GCCTGTTATATACGCCAACCGA	60.546	50.000	0.00	0.00	41.02	4.69
878	922	0.475906	AACACAGCAGAGAAGCCCTT	59.524	50.000	0.00	0.00	34.23	3.95
896	940	4.668118	GACCAACCCGGCGTCGAA	62.668	66.667	12.93	0.00	39.03	3.71
936	980	1.927174	CAGACACCGCCGATAGAAAAG	59.073	52.381	0.00	0.00	39.76	2.27
1311	1370	1.004277	TGGTAATGGCCAGAACCAGAC	59.996	52.381	29.40	12.23	44.71	3.51
1364	1527	6.657541	TCCTAAATTTCAGTTCCGCAGTTATT	59.342	34.615	0.00	0.00	0.00	1.40
1369	1532	3.375299	CCTCCTAAATTTCAGTTCCGCAG	59.625	47.826	0.00	0.00	0.00	5.18
1432	1615	6.468319	GCACTAACTGTTATCACTAGTACACG	59.532	42.308	0.00	0.00	0.00	4.49
1743	1983	2.991250	TCAAAGCTACTGCATCCTTCC	58.009	47.619	0.00	0.00	42.74	3.46
2046	3127	4.944930	CCTGTTACAGCTACTAGTGAGACT	59.055	45.833	6.88	0.00	0.00	3.24
2662	3953	4.380531	TCTGGTTCAACACAGACAAGATC	58.619	43.478	5.00	0.00	38.71	2.75
2723	4017	2.807967	CGTCAACCATTCTCAGCTTCAA	59.192	45.455	0.00	0.00	0.00	2.69
3019	4314	8.858003	TTTCAAGAGAATACGATCATGTCTAC	57.142	34.615	0.00	0.00	32.89	2.59
3053	4349	7.817418	TCTTACAAATAGCACCAAAAAGAGT	57.183	32.000	0.00	0.00	0.00	3.24
3097	4399	6.516194	CGTGTATATTTGAACGGAGGGAGTAT	60.516	42.308	0.00	0.00	32.55	2.12
3231	4536	5.424757	TGTATGCCATAAGAGTTACACCAC	58.575	41.667	0.00	0.00	0.00	4.16
3464	4782	1.798813	GTCAAACGCCAAGTCAGTAGG	59.201	52.381	0.00	0.00	0.00	3.18
4052	5373	4.198530	TGAACTTGATTCTGTGTGCTGAA	58.801	39.130	0.00	0.00	38.25	3.02
4180	5504	1.611419	CTCCACCATGTCAGCCCAT	59.389	57.895	0.00	0.00	0.00	4.00
4279	5609	5.947443	CCTTGAGAAGGTGATGATGTTTTC	58.053	41.667	0.00	0.00	43.95	2.29
4489	5825	4.509230	GCTTTCTCATTGAGATGCATCGTA	59.491	41.667	24.74	11.11	38.56	3.43
4610	5955	2.351276	GGCCTCCGTGTGATTGGT	59.649	61.111	0.00	0.00	0.00	3.67
4621	5966	2.267961	CACCGGTTAGTGGCCTCC	59.732	66.667	2.97	0.00	33.95	4.30
4650	5995	3.923864	ACGGTCTTGTGCTCGCCA	61.924	61.111	0.00	0.00	0.00	5.69
4830	6188	4.267536	AGCTCTACATGATTGTTGCACAT	58.732	39.130	0.00	0.00	37.28	3.21
4861	6276	1.040893	ACCGGTGATGATACTCGGCA	61.041	55.000	6.12	0.00	43.96	5.69
4867	6282	9.095065	GTTAATAATATGGACCGGTGATGATAC	57.905	37.037	14.63	0.00	0.00	2.24
4877	6293	7.659799	TCATGGACTTGTTAATAATATGGACCG	59.340	37.037	0.00	0.00	0.00	4.79
5011	6445	3.364920	GCTGCAAAAGGAAAAATCGTAGC	59.635	43.478	0.00	0.00	0.00	3.58
5038	6478	0.967380	GCATGGTAAGCAGCAGGGTT	60.967	55.000	0.00	0.00	40.94	4.11
5039	6479	1.379044	GCATGGTAAGCAGCAGGGT	60.379	57.895	0.00	0.00	34.62	4.34
5041	6481	1.971481	TATGCATGGTAAGCAGCAGG	58.029	50.000	10.16	0.00	46.36	4.85
5131	6571	1.603802	CACGAGAAACCACATGTGCTT	59.396	47.619	20.81	14.90	0.00	3.91
5455	6897	1.224069	CCGACGAAGGCAGGCATATG	61.224	60.000	0.00	0.00	0.00	1.78
5488	7526	2.170166	GGATGAATTGGTTGGAGCACA	58.830	47.619	0.00	0.00	0.00	4.57
5546	7592	3.521529	ATTAGGGCTAGCTGCGGCG	62.522	63.158	15.72	0.51	44.05	6.46
5580	7627	4.092821	GCATTGAACGCAATAGTGTGACTA	59.907	41.667	11.19	2.10	42.66	2.59
5581	7628	3.120199	GCATTGAACGCAATAGTGTGACT	60.120	43.478	11.19	0.00	42.66	3.41
5604	7651	7.404671	AGTAATTTTTATGGGTGGACATGTC	57.595	36.000	17.91	17.91	32.39	3.06
5613	7660	4.228895	ACGGAGGGAGTAATTTTTATGGGT	59.771	41.667	0.00	0.00	0.00	4.51
5627	7674	1.424638	ACATTATGGGACGGAGGGAG	58.575	55.000	0.00	0.00	0.00	4.30
5628	7675	2.779429	TACATTATGGGACGGAGGGA	57.221	50.000	0.00	0.00	0.00	4.20
5629	7676	2.969950	TCTTACATTATGGGACGGAGGG	59.030	50.000	0.00	0.00	0.00	4.30
5630	7677	3.552273	CGTCTTACATTATGGGACGGAGG	60.552	52.174	20.50	5.87	43.69	4.30
5631	7678	3.639538	CGTCTTACATTATGGGACGGAG	58.360	50.000	20.50	2.74	43.69	4.63
5632	7679	3.720949	CGTCTTACATTATGGGACGGA	57.279	47.619	20.50	2.30	43.69	4.69
5665	7712	5.122711	CCGTCCCATAATGTAAGACGTTTTT	59.877	40.000	9.63	0.00	46.62	1.94
5666	7713	4.632688	CCGTCCCATAATGTAAGACGTTTT	59.367	41.667	9.63	0.00	46.62	2.43
5667	7714	4.081531	TCCGTCCCATAATGTAAGACGTTT	60.082	41.667	9.63	0.00	46.62	3.60
5668	7715	3.448301	TCCGTCCCATAATGTAAGACGTT	59.552	43.478	9.63	0.00	46.62	3.99
5669	7716	3.025978	TCCGTCCCATAATGTAAGACGT	58.974	45.455	9.63	0.00	46.62	4.34
5671	7718	3.244112	CCCTCCGTCCCATAATGTAAGAC	60.244	52.174	0.00	0.00	0.00	3.01
5672	7719	2.969950	CCCTCCGTCCCATAATGTAAGA	59.030	50.000	0.00	0.00	0.00	2.10
5673	7720	2.969950	TCCCTCCGTCCCATAATGTAAG	59.030	50.000	0.00	0.00	0.00	2.34
5674	7721	2.969950	CTCCCTCCGTCCCATAATGTAA	59.030	50.000	0.00	0.00	0.00	2.41
5675	7722	2.090943	ACTCCCTCCGTCCCATAATGTA	60.091	50.000	0.00	0.00	0.00	2.29
5676	7723	1.344087	ACTCCCTCCGTCCCATAATGT	60.344	52.381	0.00	0.00	0.00	2.71
5677	7724	1.424638	ACTCCCTCCGTCCCATAATG	58.575	55.000	0.00	0.00	0.00	1.90
5678	7725	3.562108	ATACTCCCTCCGTCCCATAAT	57.438	47.619	0.00	0.00	0.00	1.28
5679	7726	3.339713	AATACTCCCTCCGTCCCATAA	57.660	47.619	0.00	0.00	0.00	1.90
5680	7727	4.140853	AGTTAATACTCCCTCCGTCCCATA	60.141	45.833	0.00	0.00	0.00	2.74
5681	7728	2.970640	GTTAATACTCCCTCCGTCCCAT	59.029	50.000	0.00	0.00	0.00	4.00
5682	7729	2.023695	AGTTAATACTCCCTCCGTCCCA	60.024	50.000	0.00	0.00	0.00	4.37
5683	7730	2.675583	AGTTAATACTCCCTCCGTCCC	58.324	52.381	0.00	0.00	0.00	4.46
5684	7731	4.038522	GGTAAGTTAATACTCCCTCCGTCC	59.961	50.000	0.00	0.00	31.99	4.79
5685	7732	4.892345	AGGTAAGTTAATACTCCCTCCGTC	59.108	45.833	0.00	0.00	32.87	4.79
5686	7733	4.876580	AGGTAAGTTAATACTCCCTCCGT	58.123	43.478	0.00	0.00	32.87	4.69
5687	7734	5.139001	AGAGGTAAGTTAATACTCCCTCCG	58.861	45.833	15.07	0.00	45.13	4.63
5688	7735	6.720748	CCTAGAGGTAAGTTAATACTCCCTCC	59.279	46.154	15.07	0.00	45.13	4.30
5689	7736	6.209192	GCCTAGAGGTAAGTTAATACTCCCTC	59.791	46.154	12.53	12.53	44.76	4.30
5690	7737	6.076653	GCCTAGAGGTAAGTTAATACTCCCT	58.923	44.000	0.00	0.00	37.98	4.20
5691	7738	6.015265	CAGCCTAGAGGTAAGTTAATACTCCC	60.015	46.154	0.00	0.00	37.57	4.30
5692	7739	6.776603	TCAGCCTAGAGGTAAGTTAATACTCC	59.223	42.308	0.00	0.00	37.57	3.85
5693	7740	7.820578	TCAGCCTAGAGGTAAGTTAATACTC	57.179	40.000	0.00	3.51	37.57	2.59
5694	7741	7.826918	CTCAGCCTAGAGGTAAGTTAATACT	57.173	40.000	0.00	0.00	37.57	2.12
5707	7754	0.394488	TCGACCACCTCAGCCTAGAG	60.394	60.000	0.00	0.00	35.39	2.43
5708	7755	0.259065	ATCGACCACCTCAGCCTAGA	59.741	55.000	0.00	0.00	0.00	2.43
5709	7756	0.387202	CATCGACCACCTCAGCCTAG	59.613	60.000	0.00	0.00	0.00	3.02
5710	7757	1.676678	GCATCGACCACCTCAGCCTA	61.677	60.000	0.00	0.00	0.00	3.93
5711	7758	3.023949	GCATCGACCACCTCAGCCT	62.024	63.158	0.00	0.00	0.00	4.58
5712	7759	2.512515	GCATCGACCACCTCAGCC	60.513	66.667	0.00	0.00	0.00	4.85
5713	7760	2.512515	GGCATCGACCACCTCAGC	60.513	66.667	0.00	0.00	0.00	4.26
5714	7761	2.202797	CGGCATCGACCACCTCAG	60.203	66.667	0.00	0.00	39.00	3.35
5715	7762	4.451150	GCGGCATCGACCACCTCA	62.451	66.667	0.00	0.00	39.00	3.86

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.