AutoCloner

Multiple sequence alignment - TraesCS2A01G018200

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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	TraesCS2A01G018200	chr2A	100.000	3461	0	0	1	3461	8629960	8633420	0.000000e+00	6392.0
1	TraesCS2A01G018200	chr2A	82.020	1535	256	14	999	2525	9944092	9945614	0.000000e+00	1288.0
2	TraesCS2A01G018200	chr2A	81.614	1599	253	22	999	2580	7786500	7788074	0.000000e+00	1286.0
3	TraesCS2A01G018200	chr2A	91.392	546	46	1	2917	3461	196352756	196352211	0.000000e+00	747.0
4	TraesCS2A01G018200	chr2A	84.810	79	10	2	404	481	7515670	7515593	1.030000e-10	78.7
5	TraesCS2A01G018200	chr2D	93.811	1858	104	5	923	2770	9380369	9382225	0.000000e+00	2784.0
6	TraesCS2A01G018200	chr2D	86.934	1523	173	17	693	2210	9251738	9253239	0.000000e+00	1687.0
7	TraesCS2A01G018200	chr2D	82.064	1667	236	28	703	2360	8479618	8478006	0.000000e+00	1363.0
8	TraesCS2A01G018200	chr2D	87.528	890	61	20	99	954	9279544	9280417	0.000000e+00	983.0
9	TraesCS2A01G018200	chr2D	93.260	549	37	0	2913	3461	71394722	71395270	0.000000e+00	809.0
10	TraesCS2A01G018200	chr2D	85.551	526	34	13	2357	2848	9334202	9334719	2.380000e-141	512.0
11	TraesCS2A01G018200	chr2D	95.522	268	7	2	672	935	9373090	9373356	1.150000e-114	424.0
12	TraesCS2A01G018200	chr2D	80.769	104	11	6	613	713	9505951	9506048	4.790000e-09	73.1
13	TraesCS2A01G018200	chr2D	97.436	39	1	0	426	464	9778931	9778893	2.230000e-07	67.6
14	TraesCS2A01G018200	chr2D	100.000	34	0	0	2850	2883	9383015	9383048	2.880000e-06	63.9
15	TraesCS2A01G018200	chr2B	88.833	1603	156	11	319	1901	12928722	12930321	0.000000e+00	1947.0
16	TraesCS2A01G018200	chr2B	86.725	1484	174	12	730	2210	11725528	11724065	0.000000e+00	1628.0
17	TraesCS2A01G018200	chr2B	79.587	2033	300	70	530	2503	13059239	13057263	0.000000e+00	1349.0
18	TraesCS2A01G018200	chr2B	81.193	1643	274	24	874	2503	13131653	13130033	0.000000e+00	1290.0
19	TraesCS2A01G018200	chr2B	81.438	1600	254	25	999	2580	11400640	11402214	0.000000e+00	1269.0
20	TraesCS2A01G018200	chr2B	79.630	1566	263	31	998	2528	12995970	12994426	0.000000e+00	1074.0
21	TraesCS2A01G018200	chr2B	92.125	546	42	1	2917	3461	108227688	108228233	0.000000e+00	769.0
22	TraesCS2A01G018200	chr2B	85.927	739	68	15	2138	2848	11568741	11568011	0.000000e+00	756.0
23	TraesCS2A01G018200	chr2B	92.233	206	16	0	1	206	11557106	11556901	3.380000e-75	292.0
24	TraesCS2A01G018200	chr2B	90.291	206	20	0	1	206	12917025	12917230	1.580000e-68	270.0
25	TraesCS2A01G018200	chr2B	89.305	187	20	0	2179	2365	11724063	11723877	5.770000e-58	235.0
26	TraesCS2A01G018200	chr2B	81.461	178	28	4	2244	2417	11993482	11993658	1.300000e-29	141.0
27	TraesCS2A01G018200	chr2B	85.366	123	12	4	201	322	12928448	12928565	4.690000e-24	122.0
28	TraesCS2A01G018200	chr5D	92.661	545	40	0	2917	3461	432806739	432807283	0.000000e+00	785.0
29	TraesCS2A01G018200	chr7D	92.350	549	41	1	2914	3461	634563458	634564006	0.000000e+00	780.0
30	TraesCS2A01G018200	chr7D	96.078	102	4	0	1	102	354587906	354587805	2.140000e-37	167.0
31	TraesCS2A01G018200	chr5A	92.477	545	41	0	2917	3461	15228291	15228835	0.000000e+00	780.0
32	TraesCS2A01G018200	chr5A	91.927	545	44	0	2917	3461	15193292	15193836	0.000000e+00	763.0
33	TraesCS2A01G018200	chr3B	91.590	547	42	3	2917	3461	751203892	751203348	0.000000e+00	752.0
34	TraesCS2A01G018200	chr3B	100.000	28	0	0	259	286	12308944	12308917	6.000000e-03	52.8
35	TraesCS2A01G018200	chr6B	91.289	551	47	1	2912	3461	674929159	674928609	0.000000e+00	750.0
36	TraesCS2A01G018200	chrUn	96.078	102	4	0	1	102	300474447	300474548	2.140000e-37	167.0
37	TraesCS2A01G018200	chr7A	96.078	102	4	0	1	102	262642387	262642488	2.140000e-37	167.0
38	TraesCS2A01G018200	chr4D	96.078	102	4	0	1	102	340565037	340564936	2.140000e-37	167.0
39	TraesCS2A01G018200	chr4B	96.078	102	4	0	1	102	376496509	376496408	2.140000e-37	167.0
40	TraesCS2A01G018200	chr1A	96.078	102	4	0	1	102	153513022	153513123	2.140000e-37	167.0
41	TraesCS2A01G018200	chr1A	96.078	102	4	0	1	102	383407218	383407319	2.140000e-37	167.0
42	TraesCS2A01G018200	chr5B	100.000	28	0	0	259	286	307881778	307881751	6.000000e-03	52.8

These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

	query	scaffold	start	end	length	rev.comp	avg.bitscore	max.bitscore	avg.percent.identical	query.start	query.end	num_hsp	groupid	homo_length
0	TraesCS2A01G018200	chr2A	8629960	8633420	3460	False	6392.00	6392	100.0000	1	3461	1	chr2A.!!$F2	3460
1	TraesCS2A01G018200	chr2A	9944092	9945614	1522	False	1288.00	1288	82.0200	999	2525	1	chr2A.!!$F3	1526
2	TraesCS2A01G018200	chr2A	7786500	7788074	1574	False	1286.00	1286	81.6140	999	2580	1	chr2A.!!$F1	1581
3	TraesCS2A01G018200	chr2A	196352211	196352756	545	True	747.00	747	91.3920	2917	3461	1	chr2A.!!$R2	544
4	TraesCS2A01G018200	chr2D	9251738	9253239	1501	False	1687.00	1687	86.9340	693	2210	1	chr2D.!!$F1	1517
5	TraesCS2A01G018200	chr2D	9380369	9383048	2679	False	1423.95	2784	96.9055	923	2883	2	chr2D.!!$F7	1960
6	TraesCS2A01G018200	chr2D	8478006	8479618	1612	True	1363.00	1363	82.0640	703	2360	1	chr2D.!!$R1	1657
7	TraesCS2A01G018200	chr2D	9279544	9280417	873	False	983.00	983	87.5280	99	954	1	chr2D.!!$F2	855
8	TraesCS2A01G018200	chr2D	71394722	71395270	548	False	809.00	809	93.2600	2913	3461	1	chr2D.!!$F6	548
9	TraesCS2A01G018200	chr2D	9334202	9334719	517	False	512.00	512	85.5510	2357	2848	1	chr2D.!!$F3	491
10	TraesCS2A01G018200	chr2B	13057263	13059239	1976	True	1349.00	1349	79.5870	530	2503	1	chr2B.!!$R4	1973
11	TraesCS2A01G018200	chr2B	13130033	13131653	1620	True	1290.00	1290	81.1930	874	2503	1	chr2B.!!$R5	1629
12	TraesCS2A01G018200	chr2B	11400640	11402214	1574	False	1269.00	1269	81.4380	999	2580	1	chr2B.!!$F1	1581
13	TraesCS2A01G018200	chr2B	12994426	12995970	1544	True	1074.00	1074	79.6300	998	2528	1	chr2B.!!$R3	1530
14	TraesCS2A01G018200	chr2B	12928448	12930321	1873	False	1034.50	1947	87.0995	201	1901	2	chr2B.!!$F5	1700
15	TraesCS2A01G018200	chr2B	11723877	11725528	1651	True	931.50	1628	88.0150	730	2365	2	chr2B.!!$R6	1635
16	TraesCS2A01G018200	chr2B	108227688	108228233	545	False	769.00	769	92.1250	2917	3461	1	chr2B.!!$F4	544
17	TraesCS2A01G018200	chr2B	11568011	11568741	730	True	756.00	756	85.9270	2138	2848	1	chr2B.!!$R2	710
18	TraesCS2A01G018200	chr5D	432806739	432807283	544	False	785.00	785	92.6610	2917	3461	1	chr5D.!!$F1	544
19	TraesCS2A01G018200	chr7D	634563458	634564006	548	False	780.00	780	92.3500	2914	3461	1	chr7D.!!$F1	547
20	TraesCS2A01G018200	chr5A	15228291	15228835	544	False	780.00	780	92.4770	2917	3461	1	chr5A.!!$F2	544
21	TraesCS2A01G018200	chr5A	15193292	15193836	544	False	763.00	763	91.9270	2917	3461	1	chr5A.!!$F1	544
22	TraesCS2A01G018200	chr3B	751203348	751203892	544	True	752.00	752	91.5900	2917	3461	1	chr3B.!!$R2	544
23	TraesCS2A01G018200	chr6B	674928609	674929159	550	True	750.00	750	91.2890	2912	3461	1	chr6B.!!$R1	549

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	Hairpin	End Stability	Orientation
43	44	0.040603	GTCGAACCGCCGTCCTATAG	60.041	60.0	0.00	0.00	1.31	F
44	45	0.179048	TCGAACCGCCGTCCTATAGA	60.179	55.0	0.00	0.00	1.98	F
1099	1349	0.182061	GAGGCATGCCCAATCAGAGA	59.818	55.0	33.14	36.58	3.10	F

Position	MSA Position	Penalty	Sequence	TM	GC	Hairpin	End Stability	Orientation
1884	2175	0.885879	GGAAAATGGGGTTCACCGAC	59.114	55.000	41.6	4.79	R
1965	2256	1.003839	TGGATGTTCTGCACGGTCC	60.004	57.895	34.7	4.46	R
2839	3217	0.472471	AAAAGAAGGACAGTGCGGGA	59.528	50.000	0.0	5.14	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
21	22	2.489329	ACTCAGTGCCATACAACATTGC	59.511	45.455	0.00	0.00	0.00	3.56
22	23	1.468127	TCAGTGCCATACAACATTGCG	59.532	47.619	0.00	0.00	0.00	4.85
23	24	0.810648	AGTGCCATACAACATTGCGG	59.189	50.000	0.00	0.00	0.00	5.69
24	25	0.179140	GTGCCATACAACATTGCGGG	60.179	55.000	0.00	0.00	0.00	6.13
25	26	0.610509	TGCCATACAACATTGCGGGT	60.611	50.000	0.00	0.00	0.00	5.28
26	27	0.100503	GCCATACAACATTGCGGGTC	59.899	55.000	0.00	0.00	0.00	4.46
27	28	0.376852	CCATACAACATTGCGGGTCG	59.623	55.000	0.00	0.00	0.00	4.79
28	29	1.364721	CATACAACATTGCGGGTCGA	58.635	50.000	0.00	0.00	0.00	4.20
29	30	1.735018	CATACAACATTGCGGGTCGAA	59.265	47.619	0.00	0.00	0.00	3.71
30	31	1.149987	TACAACATTGCGGGTCGAAC	58.850	50.000	0.00	0.00	0.00	3.95
31	32	1.209127	CAACATTGCGGGTCGAACC	59.791	57.895	10.31	10.31	37.60	3.62
40	41	3.443045	GGTCGAACCGCCGTCCTA	61.443	66.667	0.00	0.00	35.44	2.94
41	42	2.779033	GGTCGAACCGCCGTCCTAT	61.779	63.158	0.00	0.00	35.44	2.57
42	43	1.447317	GGTCGAACCGCCGTCCTATA	61.447	60.000	0.00	0.00	35.44	1.31
43	44	0.040603	GTCGAACCGCCGTCCTATAG	60.041	60.000	0.00	0.00	0.00	1.31
44	45	0.179048	TCGAACCGCCGTCCTATAGA	60.179	55.000	0.00	0.00	0.00	1.98
45	46	0.664761	CGAACCGCCGTCCTATAGAA	59.335	55.000	0.00	0.00	0.00	2.10
46	47	1.598924	CGAACCGCCGTCCTATAGAAC	60.599	57.143	0.00	0.00	0.00	3.01
47	48	1.680207	GAACCGCCGTCCTATAGAACT	59.320	52.381	0.00	0.00	0.00	3.01
48	49	1.772836	ACCGCCGTCCTATAGAACTT	58.227	50.000	0.00	0.00	0.00	2.66
49	50	1.407979	ACCGCCGTCCTATAGAACTTG	59.592	52.381	0.00	0.00	0.00	3.16
50	51	1.488527	CGCCGTCCTATAGAACTTGC	58.511	55.000	0.00	0.00	0.00	4.01
51	52	1.867166	GCCGTCCTATAGAACTTGCC	58.133	55.000	0.00	0.00	0.00	4.52
52	53	1.413077	GCCGTCCTATAGAACTTGCCT	59.587	52.381	0.00	0.00	0.00	4.75
53	54	2.158943	GCCGTCCTATAGAACTTGCCTT	60.159	50.000	0.00	0.00	0.00	4.35
54	55	3.681874	GCCGTCCTATAGAACTTGCCTTT	60.682	47.826	0.00	0.00	0.00	3.11
55	56	4.514401	CCGTCCTATAGAACTTGCCTTTT	58.486	43.478	0.00	0.00	0.00	2.27
56	57	5.667466	CCGTCCTATAGAACTTGCCTTTTA	58.333	41.667	0.00	0.00	0.00	1.52
57	58	5.753921	CCGTCCTATAGAACTTGCCTTTTAG	59.246	44.000	0.00	0.00	0.00	1.85
58	59	5.234543	CGTCCTATAGAACTTGCCTTTTAGC	59.765	44.000	0.00	0.00	0.00	3.09
59	60	6.350103	GTCCTATAGAACTTGCCTTTTAGCT	58.650	40.000	0.00	0.00	0.00	3.32
60	61	6.824196	GTCCTATAGAACTTGCCTTTTAGCTT	59.176	38.462	0.00	0.00	0.00	3.74
61	62	7.337184	GTCCTATAGAACTTGCCTTTTAGCTTT	59.663	37.037	0.00	0.00	0.00	3.51
62	63	7.888546	TCCTATAGAACTTGCCTTTTAGCTTTT	59.111	33.333	0.00	0.00	0.00	2.27
63	64	7.970614	CCTATAGAACTTGCCTTTTAGCTTTTG	59.029	37.037	0.00	0.00	0.00	2.44
64	65	4.948847	AGAACTTGCCTTTTAGCTTTTGG	58.051	39.130	0.00	0.00	0.00	3.28
65	66	3.751479	ACTTGCCTTTTAGCTTTTGGG	57.249	42.857	0.00	0.00	0.00	4.12
66	67	3.038280	ACTTGCCTTTTAGCTTTTGGGT	58.962	40.909	0.00	0.00	0.00	4.51
67	68	3.069586	ACTTGCCTTTTAGCTTTTGGGTC	59.930	43.478	0.00	0.00	0.00	4.46
68	69	2.672098	TGCCTTTTAGCTTTTGGGTCA	58.328	42.857	0.00	0.00	0.00	4.02
69	70	2.364002	TGCCTTTTAGCTTTTGGGTCAC	59.636	45.455	0.00	0.00	0.00	3.67
70	71	2.628178	GCCTTTTAGCTTTTGGGTCACT	59.372	45.455	0.00	0.00	0.00	3.41
71	72	3.305403	GCCTTTTAGCTTTTGGGTCACTC	60.305	47.826	0.00	0.00	0.00	3.51
72	73	4.145052	CCTTTTAGCTTTTGGGTCACTCT	58.855	43.478	0.00	0.00	0.00	3.24
73	74	4.216472	CCTTTTAGCTTTTGGGTCACTCTC	59.784	45.833	0.00	0.00	0.00	3.20
74	75	4.706842	TTTAGCTTTTGGGTCACTCTCT	57.293	40.909	0.00	0.00	0.00	3.10
75	76	4.706842	TTAGCTTTTGGGTCACTCTCTT	57.293	40.909	0.00	0.00	0.00	2.85
76	77	2.856222	AGCTTTTGGGTCACTCTCTTG	58.144	47.619	0.00	0.00	0.00	3.02
77	78	2.173569	AGCTTTTGGGTCACTCTCTTGT	59.826	45.455	0.00	0.00	0.00	3.16
78	79	2.550180	GCTTTTGGGTCACTCTCTTGTC	59.450	50.000	0.00	0.00	0.00	3.18
79	80	3.808728	CTTTTGGGTCACTCTCTTGTCA	58.191	45.455	0.00	0.00	0.00	3.58
80	81	2.910688	TTGGGTCACTCTCTTGTCAC	57.089	50.000	0.00	0.00	0.00	3.67
81	82	1.788229	TGGGTCACTCTCTTGTCACA	58.212	50.000	0.00	0.00	0.00	3.58
82	83	1.688735	TGGGTCACTCTCTTGTCACAG	59.311	52.381	0.00	0.00	0.00	3.66
83	84	1.964223	GGGTCACTCTCTTGTCACAGA	59.036	52.381	0.00	0.00	0.00	3.41
84	85	2.029470	GGGTCACTCTCTTGTCACAGAG	60.029	54.545	6.48	6.48	41.69	3.35
85	86	2.887783	GGTCACTCTCTTGTCACAGAGA	59.112	50.000	12.99	12.30	45.93	3.10
92	93	5.131594	TCTCTTGTCACAGAGAATGTCAG	57.868	43.478	10.49	0.00	45.28	3.51
93	94	4.829492	TCTCTTGTCACAGAGAATGTCAGA	59.171	41.667	10.49	0.00	45.28	3.27
94	95	5.302823	TCTCTTGTCACAGAGAATGTCAGAA	59.697	40.000	10.49	0.00	45.28	3.02
95	96	5.536260	TCTTGTCACAGAGAATGTCAGAAG	58.464	41.667	0.00	0.00	41.41	2.85
96	97	3.657634	TGTCACAGAGAATGTCAGAAGC	58.342	45.455	0.00	0.00	41.41	3.86
97	98	3.323115	TGTCACAGAGAATGTCAGAAGCT	59.677	43.478	0.00	0.00	41.41	3.74
145	146	9.899226	ATTAGAAAACAAGAAAGAGTTATGTGC	57.101	29.630	0.00	0.00	0.00	4.57
163	164	8.961092	GTTATGTGCAAATTATCATCATCACAC	58.039	33.333	0.00	0.00	36.26	3.82
176	177	2.493675	TCATCACACAGTCCAGACTAGC	59.506	50.000	0.00	0.00	40.20	3.42
228	232	3.664107	CTTATAAGCCCGCAATCAGCTA	58.336	45.455	0.00	0.00	42.61	3.32
275	298	6.464039	GGAAAAGCTATATACTCCCTCCGTTT	60.464	42.308	0.00	0.00	0.00	3.60
276	299	6.496144	AAAGCTATATACTCCCTCCGTTTT	57.504	37.500	0.00	0.00	0.00	2.43
290	313	6.315891	TCCCTCCGTTTTAAAATATAACGTGG	59.684	38.462	3.52	7.54	40.08	4.94
521	710	5.182570	AGCACAAGATAACTACTCACGTACA	59.817	40.000	0.00	0.00	0.00	2.90
526	715	7.821359	ACAAGATAACTACTCACGTACAGACTA	59.179	37.037	0.78	0.00	0.00	2.59
528	717	8.195617	AGATAACTACTCACGTACAGACTAAC	57.804	38.462	0.78	0.00	0.00	2.34
921	1167	8.055279	TGAGACTTTTCTATTTTGCCAATAGG	57.945	34.615	11.14	0.00	32.51	2.57
1044	1291	1.000506	GTAGGTGAACTCGTGAGCCAA	59.999	52.381	0.00	0.00	0.00	4.52
1099	1349	0.182061	GAGGCATGCCCAATCAGAGA	59.818	55.000	33.14	0.00	36.58	3.10
1111	1370	3.269178	CAATCAGAGAAGGAGAAGGTGC	58.731	50.000	0.00	0.00	0.00	5.01
1223	1482	1.173043	CTCAAGACGCTCTCAGAGGT	58.827	55.000	3.18	0.00	29.94	3.85
1286	1545	0.877743	GACCTCCAAGAAAGTGCAGC	59.122	55.000	0.00	0.00	0.00	5.25
1323	1585	5.999044	AGCATTAATGACTCATCTGGAAGT	58.001	37.500	19.73	0.00	33.76	3.01
1389	1678	1.073216	CACGCCTCGAGTCACATGAC	61.073	60.000	12.31	3.72	45.08	3.06
1571	1860	2.031163	GCAGCACAACGACCCTCT	59.969	61.111	0.00	0.00	0.00	3.69
1893	2184	2.255881	CCGGTTTGGGTCGGTGAAC	61.256	63.158	0.00	0.00	41.23	3.18
1965	2256	0.518636	CACTGGCATTCGGAAGTGTG	59.481	55.000	0.00	0.00	36.20	3.82
1989	2280	1.672030	TGCAGAACATCCACGGCTG	60.672	57.895	0.00	0.00	0.00	4.85
2106	2397	2.734606	CGATGTTCAGTTTTGGCGTAGA	59.265	45.455	0.00	0.00	0.00	2.59
2226	2554	1.369091	CGGACCTTGCTTTGGATCCG	61.369	60.000	7.39	14.06	39.68	4.18
2251	2579	7.043325	CGCTTAGTGTGAGACCTTATACAAATC	60.043	40.741	0.00	0.00	0.00	2.17
2445	2782	4.821589	CCAGGGAGGAAGCGACGC	62.822	72.222	13.03	13.03	41.22	5.19
2593	2936	8.085296	ACATTCGACTAAACATATGAGAGATCC	58.915	37.037	10.38	0.00	0.00	3.36
2598	2941	7.093988	CGACTAAACATATGAGAGATCCCAGAT	60.094	40.741	10.38	0.00	0.00	2.90
2622	2965	1.854743	CGGTTGAGATCACAGTATGCG	59.145	52.381	0.00	0.00	42.53	4.73
2702	3058	1.567357	GCCTCCCCAAAATTAGCCAA	58.433	50.000	0.00	0.00	0.00	4.52
2735	3091	9.594478	GAGAAGGAAACCAGTTTAAATTCAAAA	57.406	29.630	12.97	0.00	32.11	2.44
2761	3117	3.450817	TGAGGATATCGAAGAACTGGCAA	59.549	43.478	0.00	0.00	43.58	4.52
2839	3217	2.128226	AGCTCCCCTCCCACCATT	59.872	61.111	0.00	0.00	0.00	3.16
2848	3226	2.751436	CCCACCATTCCCGCACTG	60.751	66.667	0.00	0.00	0.00	3.66
2888	3954	9.859427	TCTTGTCATTCTTTAAAGCATTATTGG	57.141	29.630	10.51	0.00	0.00	3.16
2889	3955	8.477984	TTGTCATTCTTTAAAGCATTATTGGC	57.522	30.769	10.51	2.92	0.00	4.52
2890	3956	7.609960	TGTCATTCTTTAAAGCATTATTGGCA	58.390	30.769	10.51	5.28	0.00	4.92
2891	3957	8.259411	TGTCATTCTTTAAAGCATTATTGGCAT	58.741	29.630	10.51	0.00	0.00	4.40
2892	3958	8.758715	GTCATTCTTTAAAGCATTATTGGCATC	58.241	33.333	10.51	0.00	0.00	3.91
2893	3959	8.476447	TCATTCTTTAAAGCATTATTGGCATCA	58.524	29.630	10.51	0.00	0.00	3.07
2894	3960	9.100554	CATTCTTTAAAGCATTATTGGCATCAA	57.899	29.630	10.51	0.00	37.28	2.57
2895	3961	8.706492	TTCTTTAAAGCATTATTGGCATCAAG	57.294	30.769	10.51	0.00	36.19	3.02
2896	3962	7.267128	TCTTTAAAGCATTATTGGCATCAAGG	58.733	34.615	10.51	0.00	36.19	3.61
2897	3963	3.464111	AAGCATTATTGGCATCAAGGC	57.536	42.857	9.40	9.40	44.50	4.35
3024	4090	4.072088	GCGTCGCGGTCCTGTTTG	62.072	66.667	6.13	0.00	0.00	2.93
3104	4171	0.036952	CGGAGTTCACCACAGAGCAT	60.037	55.000	0.00	0.00	0.00	3.79
3125	4192	1.798223	GCGCCGAAGCATATCAATGTA	59.202	47.619	0.00	0.00	39.83	2.29
3218	4285	3.198853	AGAGGAGCCAAGAAGATAACCAC	59.801	47.826	0.00	0.00	0.00	4.16
3277	4344	2.742589	GTGGACGGAGATGAAAAAGACC	59.257	50.000	0.00	0.00	0.00	3.85
3371	4439	0.902531	CCAGTGGACATAGTTCCCGT	59.097	55.000	1.68	0.00	34.33	5.28
3433	4501	3.419759	GCGGACACAAACGGCGAT	61.420	61.111	16.62	0.00	0.00	4.58

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
1	2	2.476686	CGCAATGTTGTATGGCACTGAG	60.477	50.000	0.00	0.00	0.00	3.35
3	4	1.467883	CCGCAATGTTGTATGGCACTG	60.468	52.381	0.00	0.00	0.00	3.66
5	6	0.179140	CCCGCAATGTTGTATGGCAC	60.179	55.000	0.00	0.00	0.00	5.01
7	8	0.100503	GACCCGCAATGTTGTATGGC	59.899	55.000	0.00	0.00	0.00	4.40
8	9	0.376852	CGACCCGCAATGTTGTATGG	59.623	55.000	0.00	0.00	0.00	2.74
9	10	1.364721	TCGACCCGCAATGTTGTATG	58.635	50.000	0.00	0.00	0.00	2.39
10	11	1.735571	GTTCGACCCGCAATGTTGTAT	59.264	47.619	0.00	0.00	0.00	2.29
11	12	1.149987	GTTCGACCCGCAATGTTGTA	58.850	50.000	0.00	0.00	0.00	2.41
12	13	1.512156	GGTTCGACCCGCAATGTTGT	61.512	55.000	0.00	0.00	30.04	3.32
13	14	1.209127	GGTTCGACCCGCAATGTTG	59.791	57.895	0.00	0.00	30.04	3.33
14	15	2.322081	CGGTTCGACCCGCAATGTT	61.322	57.895	8.96	0.00	41.78	2.71
15	16	2.740826	CGGTTCGACCCGCAATGT	60.741	61.111	8.96	0.00	41.78	2.71
23	24	1.447317	TATAGGACGGCGGTTCGACC	61.447	60.000	13.24	4.68	43.27	4.79
24	25	0.040603	CTATAGGACGGCGGTTCGAC	60.041	60.000	13.24	0.00	0.00	4.20
25	26	0.179048	TCTATAGGACGGCGGTTCGA	60.179	55.000	13.24	0.00	0.00	3.71
26	27	0.664761	TTCTATAGGACGGCGGTTCG	59.335	55.000	13.24	0.00	0.00	3.95
27	28	1.680207	AGTTCTATAGGACGGCGGTTC	59.320	52.381	13.24	0.00	0.00	3.62
28	29	1.772836	AGTTCTATAGGACGGCGGTT	58.227	50.000	13.24	0.00	0.00	4.44
29	30	1.407979	CAAGTTCTATAGGACGGCGGT	59.592	52.381	13.24	0.00	0.00	5.68
30	31	1.868519	GCAAGTTCTATAGGACGGCGG	60.869	57.143	13.24	3.50	0.00	6.13
31	32	1.488527	GCAAGTTCTATAGGACGGCG	58.511	55.000	4.80	4.80	0.00	6.46
32	33	1.413077	AGGCAAGTTCTATAGGACGGC	59.587	52.381	17.73	17.73	0.00	5.68
33	34	3.821421	AAGGCAAGTTCTATAGGACGG	57.179	47.619	5.49	3.80	0.00	4.79
34	35	5.234543	GCTAAAAGGCAAGTTCTATAGGACG	59.765	44.000	5.49	0.00	0.00	4.79
35	36	6.350103	AGCTAAAAGGCAAGTTCTATAGGAC	58.650	40.000	2.58	2.58	34.17	3.85
36	37	6.561519	AGCTAAAAGGCAAGTTCTATAGGA	57.438	37.500	0.00	0.00	34.17	2.94
37	38	7.631717	AAAGCTAAAAGGCAAGTTCTATAGG	57.368	36.000	0.00	0.00	34.17	2.57
38	39	7.970614	CCAAAAGCTAAAAGGCAAGTTCTATAG	59.029	37.037	0.00	0.00	34.17	1.31
39	40	7.093945	CCCAAAAGCTAAAAGGCAAGTTCTATA	60.094	37.037	0.00	0.00	34.17	1.31
40	41	6.295292	CCCAAAAGCTAAAAGGCAAGTTCTAT	60.295	38.462	0.00	0.00	34.17	1.98
41	42	5.010617	CCCAAAAGCTAAAAGGCAAGTTCTA	59.989	40.000	0.00	0.00	34.17	2.10
42	43	4.202253	CCCAAAAGCTAAAAGGCAAGTTCT	60.202	41.667	0.00	0.00	34.17	3.01
43	44	4.058124	CCCAAAAGCTAAAAGGCAAGTTC	58.942	43.478	0.00	0.00	34.17	3.01
44	45	3.454447	ACCCAAAAGCTAAAAGGCAAGTT	59.546	39.130	0.00	0.00	34.17	2.66
45	46	3.038280	ACCCAAAAGCTAAAAGGCAAGT	58.962	40.909	0.00	0.00	34.17	3.16
46	47	3.069443	TGACCCAAAAGCTAAAAGGCAAG	59.931	43.478	0.00	0.00	34.17	4.01
47	48	3.034635	TGACCCAAAAGCTAAAAGGCAA	58.965	40.909	0.00	0.00	34.17	4.52
48	49	2.364002	GTGACCCAAAAGCTAAAAGGCA	59.636	45.455	0.00	0.00	34.17	4.75
49	50	2.628178	AGTGACCCAAAAGCTAAAAGGC	59.372	45.455	0.00	0.00	0.00	4.35
50	51	4.145052	AGAGTGACCCAAAAGCTAAAAGG	58.855	43.478	0.00	0.00	0.00	3.11
51	52	5.066593	AGAGAGTGACCCAAAAGCTAAAAG	58.933	41.667	0.00	0.00	0.00	2.27
52	53	5.048846	AGAGAGTGACCCAAAAGCTAAAA	57.951	39.130	0.00	0.00	0.00	1.52
53	54	4.706842	AGAGAGTGACCCAAAAGCTAAA	57.293	40.909	0.00	0.00	0.00	1.85
54	55	4.141482	ACAAGAGAGTGACCCAAAAGCTAA	60.141	41.667	0.00	0.00	0.00	3.09
55	56	3.391296	ACAAGAGAGTGACCCAAAAGCTA	59.609	43.478	0.00	0.00	0.00	3.32
56	57	2.173569	ACAAGAGAGTGACCCAAAAGCT	59.826	45.455	0.00	0.00	0.00	3.74
57	58	2.550180	GACAAGAGAGTGACCCAAAAGC	59.450	50.000	0.00	0.00	0.00	3.51
58	59	3.561725	GTGACAAGAGAGTGACCCAAAAG	59.438	47.826	0.00	0.00	0.00	2.27
59	60	3.054728	TGTGACAAGAGAGTGACCCAAAA	60.055	43.478	0.00	0.00	0.00	2.44
60	61	2.503765	TGTGACAAGAGAGTGACCCAAA	59.496	45.455	0.00	0.00	0.00	3.28
61	62	2.103094	CTGTGACAAGAGAGTGACCCAA	59.897	50.000	0.00	0.00	0.00	4.12
62	63	1.688735	CTGTGACAAGAGAGTGACCCA	59.311	52.381	0.00	0.00	0.00	4.51
63	64	1.964223	TCTGTGACAAGAGAGTGACCC	59.036	52.381	0.00	0.00	0.00	4.46
64	65	2.887783	TCTCTGTGACAAGAGAGTGACC	59.112	50.000	9.61	0.00	46.13	4.02
71	72	5.131594	TCTGACATTCTCTGTGACAAGAG	57.868	43.478	5.92	5.92	44.34	2.85
72	73	5.535753	TTCTGACATTCTCTGTGACAAGA	57.464	39.130	0.00	0.00	38.54	3.02
73	74	4.152045	GCTTCTGACATTCTCTGTGACAAG	59.848	45.833	0.00	0.00	38.54	3.16
74	75	4.060900	GCTTCTGACATTCTCTGTGACAA	58.939	43.478	0.00	0.00	38.54	3.18
75	76	3.323115	AGCTTCTGACATTCTCTGTGACA	59.677	43.478	0.00	0.00	38.54	3.58
76	77	3.924144	AGCTTCTGACATTCTCTGTGAC	58.076	45.455	0.00	0.00	38.54	3.67
77	78	4.313282	CAAGCTTCTGACATTCTCTGTGA	58.687	43.478	0.00	0.00	38.54	3.58
78	79	3.436015	CCAAGCTTCTGACATTCTCTGTG	59.564	47.826	0.00	0.00	38.54	3.66
79	80	3.672808	CCAAGCTTCTGACATTCTCTGT	58.327	45.455	0.00	0.00	42.15	3.41
80	81	2.419324	GCCAAGCTTCTGACATTCTCTG	59.581	50.000	0.00	0.00	0.00	3.35
81	82	2.305343	AGCCAAGCTTCTGACATTCTCT	59.695	45.455	0.00	0.00	33.89	3.10
82	83	2.709213	AGCCAAGCTTCTGACATTCTC	58.291	47.619	0.00	0.00	33.89	2.87
83	84	2.875094	AGCCAAGCTTCTGACATTCT	57.125	45.000	0.00	0.00	33.89	2.40
84	85	4.006319	AGTAAGCCAAGCTTCTGACATTC	58.994	43.478	4.87	0.00	46.77	2.67
85	86	4.026356	AGTAAGCCAAGCTTCTGACATT	57.974	40.909	4.87	0.00	46.77	2.71
86	87	3.710209	AGTAAGCCAAGCTTCTGACAT	57.290	42.857	4.87	0.00	46.77	3.06
87	88	4.617253	TTAGTAAGCCAAGCTTCTGACA	57.383	40.909	4.87	0.00	46.77	3.58
88	89	5.178797	TCATTAGTAAGCCAAGCTTCTGAC	58.821	41.667	4.87	0.00	46.77	3.51
89	90	5.420725	TCATTAGTAAGCCAAGCTTCTGA	57.579	39.130	4.87	1.23	46.77	3.27
90	91	6.072508	TGTTTCATTAGTAAGCCAAGCTTCTG	60.073	38.462	4.87	0.00	46.77	3.02
91	92	6.003950	TGTTTCATTAGTAAGCCAAGCTTCT	58.996	36.000	4.87	5.93	46.77	2.85
92	93	6.254281	TGTTTCATTAGTAAGCCAAGCTTC	57.746	37.500	4.87	0.00	46.77	3.86
94	95	7.938140	TTATGTTTCATTAGTAAGCCAAGCT	57.062	32.000	0.00	0.00	42.56	3.74
95	96	9.586435	AATTTATGTTTCATTAGTAAGCCAAGC	57.414	29.630	0.00	0.00	0.00	4.01
142	143	6.558009	ACTGTGTGATGATGATAATTTGCAC	58.442	36.000	0.00	0.00	0.00	4.57
145	146	7.281549	TCTGGACTGTGTGATGATGATAATTTG	59.718	37.037	0.00	0.00	0.00	2.32
163	164	6.868622	ACTTTAGTAATGCTAGTCTGGACTG	58.131	40.000	12.87	5.05	42.52	3.51
310	333	3.704566	TGGACTCCCATGTACATGAGTAC	59.295	47.826	32.72	27.66	43.14	2.73
328	351	1.478510	ACTCATCATCGTCACCTGGAC	59.521	52.381	0.00	0.00	43.36	4.02
516	699	3.909776	TGTCAGTGGTTAGTCTGTACG	57.090	47.619	0.00	0.00	33.89	3.67
521	710	7.873505	GTCTTTATCTTTGTCAGTGGTTAGTCT	59.126	37.037	0.00	0.00	0.00	3.24
526	715	4.755123	CGGTCTTTATCTTTGTCAGTGGTT	59.245	41.667	0.00	0.00	0.00	3.67
528	717	3.125316	GCGGTCTTTATCTTTGTCAGTGG	59.875	47.826	0.00	0.00	0.00	4.00
921	1167	4.069869	TGCCAAGTCTTGCAGAGC	57.930	55.556	7.09	5.90	32.77	4.09
1099	1349	1.274712	CTCTCCAGCACCTTCTCCTT	58.725	55.000	0.00	0.00	0.00	3.36
1223	1482	2.299013	GCACCATATCCTCGGTACATGA	59.701	50.000	0.00	0.00	32.98	3.07
1278	1537	1.373497	CTCGTCGAAGGCTGCACTT	60.373	57.895	0.50	2.32	0.00	3.16
1286	1545	2.295253	AATGCTAACCTCGTCGAAGG	57.705	50.000	1.40	1.40	42.55	3.46
1389	1678	4.376311	GCAATTTCTAAACTTTGCAAGGCG	60.376	41.667	8.71	0.00	43.00	5.52
1826	2117	1.076024	TGATCTTGCTTCCTTTGCCCT	59.924	47.619	0.00	0.00	0.00	5.19
1884	2175	0.885879	GGAAAATGGGGTTCACCGAC	59.114	55.000	0.00	0.00	41.60	4.79
1893	2184	4.536765	ACATAGCAGTAAGGAAAATGGGG	58.463	43.478	0.00	0.00	0.00	4.96
1896	2187	9.330063	TCATAAGACATAGCAGTAAGGAAAATG	57.670	33.333	0.00	0.00	0.00	2.32
1965	2256	1.003839	TGGATGTTCTGCACGGTCC	60.004	57.895	0.00	0.00	34.70	4.46
1989	2280	5.979517	GGCAAATTCATCTGCTATTTGTACC	59.020	40.000	0.00	0.00	39.97	3.34
2106	2397	3.336694	ACCTTGTCCCCTTGTCCAATATT	59.663	43.478	0.00	0.00	0.00	1.28
2226	2554	7.764443	TGATTTGTATAAGGTCTCACACTAAGC	59.236	37.037	0.00	0.00	0.00	3.09
2445	2782	7.035004	TCAATCAAAATTAAATTGGCTCTCCG	58.965	34.615	4.97	0.00	32.49	4.63
2655	2998	2.203209	GAAGGATCCCGGCGCATT	60.203	61.111	10.83	0.00	0.00	3.56
2735	3091	6.014242	TGCCAGTTCTTCGATATCCTCAATAT	60.014	38.462	0.00	0.00	33.03	1.28
2839	3217	0.472471	AAAAGAAGGACAGTGCGGGA	59.528	50.000	0.00	0.00	0.00	5.14
2848	3226	7.935520	AGAATGACAAGAAAGAAAAGAAGGAC	58.064	34.615	0.00	0.00	0.00	3.85
2903	3969	4.133373	CCTGACCATGGCCCCAGG	62.133	72.222	24.99	24.99	40.01	4.45
2904	3970	4.133373	CCCTGACCATGGCCCCAG	62.133	72.222	13.04	16.05	0.00	4.45
2906	3972	4.447342	CACCCTGACCATGGCCCC	62.447	72.222	13.04	1.64	0.00	5.80
2907	3973	4.447342	CCACCCTGACCATGGCCC	62.447	72.222	13.04	4.53	0.00	5.80
2908	3974	3.338250	TCCACCCTGACCATGGCC	61.338	66.667	13.04	0.00	33.20	5.36
2909	3975	2.044946	GTCCACCCTGACCATGGC	60.045	66.667	13.04	5.35	33.20	4.40
2910	3976	1.002134	GTGTCCACCCTGACCATGG	60.002	63.158	11.19	11.19	34.25	3.66
2911	3977	1.375908	CGTGTCCACCCTGACCATG	60.376	63.158	0.00	0.00	34.25	3.66
2912	3978	2.592993	CCGTGTCCACCCTGACCAT	61.593	63.158	0.00	0.00	34.25	3.55
2913	3979	3.238497	CCGTGTCCACCCTGACCA	61.238	66.667	0.00	0.00	34.25	4.02
2914	3980	3.236003	GACCGTGTCCACCCTGACC	62.236	68.421	0.00	0.00	34.25	4.02
2915	3981	2.342648	GACCGTGTCCACCCTGAC	59.657	66.667	0.00	0.00	35.77	3.51
3064	4130	3.740513	GGTCCAAACGAACCGCTT	58.259	55.556	0.00	0.00	0.00	4.68
3070	4136	4.992511	CCGGCCGGTCCAAACGAA	62.993	66.667	36.64	0.00	34.01	3.85
3104	4171	0.587768	CATTGATATGCTTCGGCGCA	59.412	50.000	10.83	0.00	45.37	6.09
3111	4178	3.245052	GCCCTCCCTACATTGATATGCTT	60.245	47.826	0.00	0.00	35.03	3.91
3117	4184	1.056700	AGCGCCCTCCCTACATTGAT	61.057	55.000	2.29	0.00	0.00	2.57
3118	4185	1.689233	AGCGCCCTCCCTACATTGA	60.689	57.895	2.29	0.00	0.00	2.57
3213	4280	1.446792	CGATGAGCTCGCTGTGGTT	60.447	57.895	9.64	0.00	41.14	3.67
3232	4299	0.718904	CGTCGTGCCAAATTCATCGA	59.281	50.000	0.00	0.00	0.00	3.59
3236	4303	2.950673	GCCGTCGTGCCAAATTCA	59.049	55.556	0.00	0.00	0.00	2.57
3303	4370	2.279650	AACGAACACGACGTGGGG	60.280	61.111	29.86	20.12	43.16	4.96
3423	4491	3.725010	GCTGAAGAAACTATCGCCGTTTG	60.725	47.826	0.00	0.00	34.94	2.93
3424	4492	2.415512	GCTGAAGAAACTATCGCCGTTT	59.584	45.455	0.00	0.00	37.30	3.60
3433	4501	1.298667	GCGGGGGCTGAAGAAACTA	59.701	57.895	0.00	0.00	0.00	2.24

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.