AutoCloner

Multiple sequence alignment - TraesCS7D01G443900

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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	TraesCS7D01G443900	chr7D	100.000	3530	0	0	1	3530	564532400	564535929	0.000000e+00	6519.0
1	TraesCS7D01G443900	chr7D	100.000	850	0	0	2641	3490	564563410	564564259	0.000000e+00	1570.0
2	TraesCS7D01G443900	chr7D	86.486	592	54	14	1264	1848	242336807	242336235	8.320000e-176	627.0
3	TraesCS7D01G443900	chr7D	96.899	258	8	0	3273	3530	339113613	339113356	1.950000e-117	433.0
4	TraesCS7D01G443900	chr7D	98.374	246	3	1	3264	3508	564563168	564563413	7.000000e-117	431.0
5	TraesCS7D01G443900	chr7B	88.874	1528	117	24	1	1496	614296612	614295106	0.000000e+00	1831.0
6	TraesCS7D01G443900	chr7B	89.892	1395	70	35	1502	2864	614294986	614293631	0.000000e+00	1729.0
7	TraesCS7D01G443900	chr7B	83.908	870	98	21	1474	2308	404520615	404521477	0.000000e+00	793.0
8	TraesCS7D01G443900	chr7B	87.937	315	25	7	2959	3270	614293562	614293258	3.350000e-95	359.0
9	TraesCS7D01G443900	chr5A	85.735	1367	141	33	980	2308	614168871	614167521	0.000000e+00	1395.0
10	TraesCS7D01G443900	chr5A	82.988	482	63	14	2268	2733	533281449	533281927	5.450000e-113	418.0
11	TraesCS7D01G443900	chr5A	78.112	233	34	14	2300	2529	606050071	606049853	7.950000e-27	132.0
12	TraesCS7D01G443900	chr4B	84.953	1369	150	33	980	2308	359900543	359899191	0.000000e+00	1336.0
13	TraesCS7D01G443900	chr4B	83.784	74	7	5	3461	3530	86708931	86709003	8.180000e-07	65.8
14	TraesCS7D01G443900	chr6A	84.931	1367	149	34	980	2308	304901084	304899737	0.000000e+00	1330.0
15	TraesCS7D01G443900	chr6A	86.978	407	46	4	1489	1891	606002394	606001991	5.370000e-123	451.0
16	TraesCS7D01G443900	chr6A	86.019	422	51	5	1474	1891	575002337	575001920	2.500000e-121	446.0
17	TraesCS7D01G443900	chr6A	85.579	423	52	6	1474	1891	583750710	583751128	5.410000e-118	435.0
18	TraesCS7D01G443900	chr6A	87.382	317	21	13	291	588	207162072	207162388	2.610000e-91	346.0
19	TraesCS7D01G443900	chr6A	86.154	65	5	4	917	978	571020091	571020154	2.270000e-07	67.6
20	TraesCS7D01G443900	chr7A	90.178	957	82	10	1892	2842	649478112	649477162	0.000000e+00	1236.0
21	TraesCS7D01G443900	chr7A	85.122	1230	137	33	1621	2834	649800103	649798904	0.000000e+00	1216.0
22	TraesCS7D01G443900	chr7A	82.933	1248	156	38	668	1892	649479352	649478139	0.000000e+00	1072.0
23	TraesCS7D01G443900	chr7A	81.948	1119	121	39	1	1072	649801874	649800790	0.000000e+00	872.0
24	TraesCS7D01G443900	chr7A	85.545	422	54	4	1474	1891	17541341	17541759	5.410000e-118	435.0
25	TraesCS7D01G443900	chr7A	84.532	278	32	10	841	1112	649426691	649426419	7.510000e-67	265.0
26	TraesCS7D01G443900	chr7A	77.157	197	21	14	2961	3150	649476952	649476773	3.750000e-15	93.5
27	TraesCS7D01G443900	chr1A	84.597	844	84	28	1498	2308	562697574	562698404	0.000000e+00	797.0
28	TraesCS7D01G443900	chr1A	85.915	355	43	5	980	1333	562697227	562697575	4.300000e-99	372.0
29	TraesCS7D01G443900	chr1A	86.885	61	4	4	3473	3530	13750049	13749990	8.180000e-07	65.8
30	TraesCS7D01G443900	chr1A	83.784	74	7	5	3461	3530	516384451	516384523	8.180000e-07	65.8
31	TraesCS7D01G443900	chr5D	83.026	760	87	24	1988	2738	418430206	418430932	0.000000e+00	651.0
32	TraesCS7D01G443900	chr5D	75.620	242	44	11	2292	2529	484413555	484413325	4.820000e-19	106.0
33	TraesCS7D01G443900	chr5B	83.196	726	75	30	1988	2695	505770382	505771078	3.870000e-174	621.0
34	TraesCS7D01G443900	chr5B	77.778	234	34	13	2300	2529	595622522	595622303	1.030000e-25	128.0
35	TraesCS7D01G443900	chr6D	84.122	592	68	13	1264	1848	76997857	76997285	1.850000e-152	549.0
36	TraesCS7D01G443900	chr3B	89.696	427	36	7	1886	2308	615276560	615276982	4.010000e-149	538.0
37	TraesCS7D01G443900	chr2A	86.019	422	52	4	1474	1891	197933873	197934291	2.500000e-121	446.0
38	TraesCS7D01G443900	chr2A	86.458	384	31	11	293	665	532362622	532362995	5.490000e-108	401.0
39	TraesCS7D01G443900	chr2A	83.784	74	7	5	3461	3530	43663355	43663427	8.180000e-07	65.8
40	TraesCS7D01G443900	chr3D	85.782	422	53	4	1474	1891	482118683	482119101	1.160000e-119	440.0
41	TraesCS7D01G443900	chr3D	87.597	387	29	9	291	667	318682524	318682147	7.000000e-117	431.0
42	TraesCS7D01G443900	chr3D	85.294	238	30	5	3295	3530	347611983	347612217	1.270000e-59	241.0
43	TraesCS7D01G443900	chr3D	85.204	196	26	3	3295	3490	347624908	347625100	7.730000e-47	198.0
44	TraesCS7D01G443900	chr3A	88.068	352	23	8	326	667	725550032	725550374	1.970000e-107	399.0
45	TraesCS7D01G443900	chr3A	87.500	352	25	6	326	667	725592564	725592906	4.270000e-104	388.0
46	TraesCS7D01G443900	chr3A	87.500	352	25	8	326	667	725633557	725633899	4.270000e-104	388.0
47	TraesCS7D01G443900	chrUn	88.525	61	3	3	3473	3530	325526604	325526663	1.760000e-08	71.3
48	TraesCS7D01G443900	chr2B	88.525	61	3	3	3473	3530	359503936	359503877	1.760000e-08	71.3

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	TraesCS7D01G443900	chr7D	564532400	564535929	3529	False	6519.000000	6519	100.000000	1	3530	1	chr7D.!!$F1	3529
1	TraesCS7D01G443900	chr7D	564563168	564564259	1091	False	1000.500000	1570	99.187000	2641	3508	2	chr7D.!!$F2	867
2	TraesCS7D01G443900	chr7D	242336235	242336807	572	True	627.000000	627	86.486000	1264	1848	1	chr7D.!!$R1	584
3	TraesCS7D01G443900	chr7B	614293258	614296612	3354	True	1306.333333	1831	88.901000	1	3270	3	chr7B.!!$R1	3269
4	TraesCS7D01G443900	chr7B	404520615	404521477	862	False	793.000000	793	83.908000	1474	2308	1	chr7B.!!$F1	834
5	TraesCS7D01G443900	chr5A	614167521	614168871	1350	True	1395.000000	1395	85.735000	980	2308	1	chr5A.!!$R2	1328
6	TraesCS7D01G443900	chr4B	359899191	359900543	1352	True	1336.000000	1336	84.953000	980	2308	1	chr4B.!!$R1	1328
7	TraesCS7D01G443900	chr6A	304899737	304901084	1347	True	1330.000000	1330	84.931000	980	2308	1	chr6A.!!$R1	1328
8	TraesCS7D01G443900	chr7A	649798904	649801874	2970	True	1044.000000	1216	83.535000	1	2834	2	chr7A.!!$R3	2833
9	TraesCS7D01G443900	chr7A	649476773	649479352	2579	True	800.500000	1236	83.422667	668	3150	3	chr7A.!!$R2	2482
10	TraesCS7D01G443900	chr1A	562697227	562698404	1177	False	584.500000	797	85.256000	980	2308	2	chr1A.!!$F2	1328
11	TraesCS7D01G443900	chr5D	418430206	418430932	726	False	651.000000	651	83.026000	1988	2738	1	chr5D.!!$F1	750
12	TraesCS7D01G443900	chr5B	505770382	505771078	696	False	621.000000	621	83.196000	1988	2695	1	chr5B.!!$F1	707
13	TraesCS7D01G443900	chr6D	76997285	76997857	572	True	549.000000	549	84.122000	1264	1848	1	chr6D.!!$R1	584

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
315	361	0.117340	AGGGAGGGCAAGTGTCTAGT	59.883	55.0	0.00	0.00	2.57	F
1022	1101	0.246910	GTGAGTTTCCTCTCCCCGAC	59.753	60.0	0.00	38.61	4.79	F
1675	2139	1.517238	TGGATTAGGGCTGGCATACA	58.483	50.0	2.88	0.00	2.29	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1856	2326	0.172578	GGGGCGTGGAAAATTGCTAC	59.827	55.000	0.00	0.00	0.00	3.58	R
1870	2340	0.243636	GTGTTTGATTCCAAGGGGCG	59.756	55.000	0.00	0.00	33.23	6.13	R
2555	3100	1.541588	GGGAAGTTCTGGCACAACATC	59.458	52.381	8.35	5.45	38.70	3.06	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
147	161	9.816354	AAATTAAGTACTGAAACAATTTGCTGT	57.184	25.926	0.00	0.00	0.00	4.40
160	174	0.836606	TTGCTGTCAGACCCTCACAA	59.163	50.000	3.32	0.00	0.00	3.33
211	225	4.843220	AAAAATCAAGTGCCTGTCAGAG	57.157	40.909	0.00	0.00	0.00	3.35
214	228	0.972134	TCAAGTGCCTGTCAGAGAGG	59.028	55.000	9.41	9.41	0.00	3.69
216	230	0.178921	AAGTGCCTGTCAGAGAGGGA	60.179	55.000	15.42	9.88	0.00	4.20
217	231	0.614415	AGTGCCTGTCAGAGAGGGAG	60.614	60.000	15.42	0.00	30.44	4.30
218	232	1.305633	TGCCTGTCAGAGAGGGAGG	60.306	63.158	15.42	0.00	0.00	4.30
219	233	2.063378	GCCTGTCAGAGAGGGAGGG	61.063	68.421	15.42	0.00	0.00	4.30
220	234	1.390125	CCTGTCAGAGAGGGAGGGT	59.610	63.158	5.64	0.00	0.00	4.34
221	235	0.631753	CCTGTCAGAGAGGGAGGGTA	59.368	60.000	5.64	0.00	0.00	3.69
224	238	1.717077	TGTCAGAGAGGGAGGGTAAGT	59.283	52.381	0.00	0.00	0.00	2.24
226	240	1.717077	TCAGAGAGGGAGGGTAAGTGT	59.283	52.381	0.00	0.00	0.00	3.55
227	241	2.104170	CAGAGAGGGAGGGTAAGTGTC	58.896	57.143	0.00	0.00	0.00	3.67
228	242	2.004589	AGAGAGGGAGGGTAAGTGTCT	58.995	52.381	0.00	0.00	0.00	3.41
229	243	2.384029	AGAGAGGGAGGGTAAGTGTCTT	59.616	50.000	0.00	0.00	0.00	3.01
230	244	2.761767	GAGAGGGAGGGTAAGTGTCTTC	59.238	54.545	0.00	0.00	0.00	2.87
231	245	2.384029	AGAGGGAGGGTAAGTGTCTTCT	59.616	50.000	0.00	0.00	0.00	2.85
232	246	2.498078	GAGGGAGGGTAAGTGTCTTCTG	59.502	54.545	0.00	0.00	0.00	3.02
233	247	2.111972	AGGGAGGGTAAGTGTCTTCTGA	59.888	50.000	0.00	0.00	0.00	3.27
234	248	2.904434	GGGAGGGTAAGTGTCTTCTGAA	59.096	50.000	0.00	0.00	0.00	3.02
235	249	3.519913	GGGAGGGTAAGTGTCTTCTGAAT	59.480	47.826	0.00	0.00	0.00	2.57
283	297	9.905171	TCGATCTTCTGAATATCATCTACAAAG	57.095	33.333	13.91	0.00	0.00	2.77
304	350	0.980231	ACATGTCAGAGAGGGAGGGC	60.980	60.000	0.00	0.00	0.00	5.19
306	352	0.252881	ATGTCAGAGAGGGAGGGCAA	60.253	55.000	0.00	0.00	0.00	4.52
315	361	0.117340	AGGGAGGGCAAGTGTCTAGT	59.883	55.000	0.00	0.00	0.00	2.57
320	366	0.250513	GGGCAAGTGTCTAGTGAGGG	59.749	60.000	0.00	0.00	0.00	4.30
321	367	1.267121	GGCAAGTGTCTAGTGAGGGA	58.733	55.000	0.00	0.00	0.00	4.20
456	502	1.073125	CTCTCGCTCATCCTCCTCCTA	59.927	57.143	0.00	0.00	0.00	2.94
457	503	1.707989	TCTCGCTCATCCTCCTCCTAT	59.292	52.381	0.00	0.00	0.00	2.57
458	504	2.091541	CTCGCTCATCCTCCTCCTATC	58.908	57.143	0.00	0.00	0.00	2.08
471	525	2.625883	CCTCCTATCACCACCACCACTA	60.626	54.545	0.00	0.00	0.00	2.74
519	577	1.488390	ATGGCGGCTCAAATCCAATT	58.512	45.000	11.43	0.00	31.66	2.32
527	585	4.178540	GGCTCAAATCCAATTCACACATG	58.821	43.478	0.00	0.00	0.00	3.21
566	626	0.253610	GACGGAGAGACCAGAGGAGA	59.746	60.000	0.00	0.00	38.90	3.71
569	629	0.333312	GGAGAGACCAGAGGAGACCA	59.667	60.000	0.00	0.00	38.79	4.02
748	819	5.416083	CATTTAGACCTTCGGTGTCACATA	58.584	41.667	5.12	0.00	35.25	2.29
779	851	0.333312	ACCATTTCACCGGCCCAATA	59.667	50.000	0.00	0.00	0.00	1.90
871	945	0.801067	GCCGCGCCCTCGTATATAAG	60.801	60.000	0.00	0.00	38.14	1.73
900	974	2.970639	TCGCTCTCCGACCCTTTG	59.029	61.111	0.00	0.00	41.89	2.77
1009	1088	2.360350	CCGCAGCCATGGTGAGTT	60.360	61.111	14.67	0.00	32.22	3.01
1015	1094	1.004044	CAGCCATGGTGAGTTTCCTCT	59.996	52.381	14.67	0.00	38.61	3.69
1019	1098	1.065126	CATGGTGAGTTTCCTCTCCCC	60.065	57.143	8.00	0.00	46.39	4.81
1020	1099	1.192146	TGGTGAGTTTCCTCTCCCCG	61.192	60.000	8.00	0.00	46.39	5.73
1021	1100	0.903454	GGTGAGTTTCCTCTCCCCGA	60.903	60.000	0.00	0.00	42.89	5.14
1022	1101	0.246910	GTGAGTTTCCTCTCCCCGAC	59.753	60.000	0.00	0.00	38.61	4.79
1072	1152	2.779506	GATTGTCCTGGTTTCCGAACT	58.220	47.619	0.00	0.00	36.03	3.01
1092	1172	3.967987	ACTAGCCCAGATTCGGTAGATTT	59.032	43.478	0.00	0.00	34.80	2.17
1102	1182	6.313905	CAGATTCGGTAGATTTACAACAGCTT	59.686	38.462	0.00	0.00	0.00	3.74
1120	1200	1.940883	TTCGGCGCTCGGTAGAATGT	61.941	55.000	7.64	0.00	39.77	2.71
1191	1273	4.439974	GCTGTTAATCGGATGAAATTGCCA	60.440	41.667	0.00	0.00	0.00	4.92
1199	1281	2.560105	GGATGAAATTGCCATAGGAGCC	59.440	50.000	0.00	0.00	0.00	4.70
1215	1297	5.012328	AGGAGCCGTGTATTTCTCTTAAG	57.988	43.478	0.00	0.00	0.00	1.85
1219	1301	3.000022	GCCGTGTATTTCTCTTAAGTCGC	60.000	47.826	1.63	0.00	0.00	5.19
1386	1475	2.969262	ACGGATGGGTTGGTTTGAATTT	59.031	40.909	0.00	0.00	0.00	1.82
1394	1483	6.054295	TGGGTTGGTTTGAATTTTCATCTTG	58.946	36.000	0.00	0.00	37.00	3.02
1464	1559	4.546570	TGTTAGTCGAGTTGTCATCACTG	58.453	43.478	0.00	0.00	0.00	3.66
1613	2074	5.825593	TCCTGAAACCTATGGCTATAAGG	57.174	43.478	0.00	0.00	0.00	2.69
1632	2096	9.416794	CTATAAGGAATGAGTGACATGATGTAC	57.583	37.037	0.00	0.00	39.39	2.90
1660	2124	5.494341	TCCTACAGCCTATCTCTCTATGGAT	59.506	44.000	0.00	0.00	0.00	3.41
1675	2139	1.517238	TGGATTAGGGCTGGCATACA	58.483	50.000	2.88	0.00	0.00	2.29
1709	2173	5.061179	GCTAACTCAACCTGTCCTGTTTAA	58.939	41.667	0.00	0.00	0.00	1.52
1779	2248	4.081406	AGTTCAGCATAACATCTTTGGCA	58.919	39.130	4.30	0.00	0.00	4.92
1791	2260	4.699257	ACATCTTTGGCATGAGTTCTCTTC	59.301	41.667	0.00	0.00	0.00	2.87
1856	2326	2.472695	TTTGGACCCTCGTGATTCAG	57.527	50.000	0.00	0.00	0.00	3.02
1870	2340	5.088739	CGTGATTCAGTAGCAATTTTCCAC	58.911	41.667	0.00	0.00	0.00	4.02
1934	2466	9.034544	GCTATGAAGTTCTTTTTGTTTGTCATT	57.965	29.630	4.17	0.00	0.00	2.57
1941	2473	8.835439	AGTTCTTTTTGTTTGTCATTTGTTGTT	58.165	25.926	0.00	0.00	0.00	2.83
1942	2474	9.444534	GTTCTTTTTGTTTGTCATTTGTTGTTT	57.555	25.926	0.00	0.00	0.00	2.83
1967	2500	4.798882	TCCTGGTTGTTTATTCCTGTTGT	58.201	39.130	0.00	0.00	0.00	3.32
2216	2757	8.217111	TGTGGGCATATATCTTCTTTGATGTAA	58.783	33.333	0.00	0.00	0.00	2.41
2248	2789	2.169561	ACTTTGGAAATGTTGGCCGTTT	59.830	40.909	0.00	0.00	34.95	3.60
2249	2790	3.385111	ACTTTGGAAATGTTGGCCGTTTA	59.615	39.130	0.00	0.00	32.37	2.01
2251	2792	4.608948	TTGGAAATGTTGGCCGTTTATT	57.391	36.364	0.00	0.00	32.37	1.40
2253	2794	5.723672	TGGAAATGTTGGCCGTTTATTTA	57.276	34.783	0.00	0.00	32.37	1.40
2256	2797	6.160684	GGAAATGTTGGCCGTTTATTTACTT	58.839	36.000	0.00	0.00	32.37	2.24
2257	2798	6.090223	GGAAATGTTGGCCGTTTATTTACTTG	59.910	38.462	0.00	0.00	32.37	3.16
2258	2799	5.715434	ATGTTGGCCGTTTATTTACTTGT	57.285	34.783	0.00	0.00	0.00	3.16
2259	2800	5.517322	TGTTGGCCGTTTATTTACTTGTT	57.483	34.783	0.00	0.00	0.00	2.83
2260	2801	5.903810	TGTTGGCCGTTTATTTACTTGTTT	58.096	33.333	0.00	0.00	0.00	2.83
2261	2802	5.978322	TGTTGGCCGTTTATTTACTTGTTTC	59.022	36.000	0.00	0.00	0.00	2.78
2264	2805	5.299782	TGGCCGTTTATTTACTTGTTTCTGT	59.700	36.000	0.00	0.00	0.00	3.41
2266	2807	6.143278	GGCCGTTTATTTACTTGTTTCTGTTG	59.857	38.462	0.00	0.00	0.00	3.33
2293	2836	7.707624	TTGCATCTGGATGTTTATTCTTCTT	57.292	32.000	11.52	0.00	40.80	2.52
2403	2947	2.106166	CCTGCATCCCTCTTATCTGCTT	59.894	50.000	0.00	0.00	34.02	3.91
2405	2949	3.548770	TGCATCCCTCTTATCTGCTTTG	58.451	45.455	0.00	0.00	34.02	2.77
2433	2977	9.888878	CATTTCCTTGCTATATTCTGTTATGTG	57.111	33.333	0.00	0.00	0.00	3.21
2451	2995	7.710475	TGTTATGTGTATGTATCTGACACCATG	59.290	37.037	2.22	0.00	42.17	3.66
2537	3081	5.534207	ACATCTCTCTTCTAAGCTGATGG	57.466	43.478	16.21	0.00	34.38	3.51
2555	3100	6.428159	GCTGATGGTATCCTGTTATGTTTAGG	59.572	42.308	0.00	0.00	0.00	2.69
3496	4175	8.405418	GATTAAATAAATCCTAACACTCCCCC	57.595	38.462	0.00	0.00	38.47	5.40
3497	4176	7.533923	TTAAATAAATCCTAACACTCCCCCT	57.466	36.000	0.00	0.00	0.00	4.79
3498	4177	8.641498	TTAAATAAATCCTAACACTCCCCCTA	57.359	34.615	0.00	0.00	0.00	3.53
3499	4178	7.533923	AAATAAATCCTAACACTCCCCCTAA	57.466	36.000	0.00	0.00	0.00	2.69
3500	4179	7.723109	AATAAATCCTAACACTCCCCCTAAT	57.277	36.000	0.00	0.00	0.00	1.73
3501	4180	5.648330	AAATCCTAACACTCCCCCTAATC	57.352	43.478	0.00	0.00	0.00	1.75
3502	4181	3.788116	TCCTAACACTCCCCCTAATCA	57.212	47.619	0.00	0.00	0.00	2.57
3503	4182	4.083080	TCCTAACACTCCCCCTAATCAA	57.917	45.455	0.00	0.00	0.00	2.57
3504	4183	4.641868	TCCTAACACTCCCCCTAATCAAT	58.358	43.478	0.00	0.00	0.00	2.57
3505	4184	4.412199	TCCTAACACTCCCCCTAATCAATG	59.588	45.833	0.00	0.00	0.00	2.82
3506	4185	2.736670	ACACTCCCCCTAATCAATGC	57.263	50.000	0.00	0.00	0.00	3.56
3507	4186	2.208872	ACACTCCCCCTAATCAATGCT	58.791	47.619	0.00	0.00	0.00	3.79
3508	4187	2.582636	ACACTCCCCCTAATCAATGCTT	59.417	45.455	0.00	0.00	0.00	3.91
3509	4188	2.954318	CACTCCCCCTAATCAATGCTTG	59.046	50.000	0.00	0.00	0.00	4.01
3510	4189	2.582636	ACTCCCCCTAATCAATGCTTGT	59.417	45.455	0.00	0.00	0.00	3.16
3511	4190	3.011708	ACTCCCCCTAATCAATGCTTGTT	59.988	43.478	0.00	0.00	0.00	2.83
3512	4191	4.026052	CTCCCCCTAATCAATGCTTGTTT	58.974	43.478	0.00	0.00	0.00	2.83
3513	4192	3.768757	TCCCCCTAATCAATGCTTGTTTG	59.231	43.478	0.00	0.00	0.00	2.93
3514	4193	3.515104	CCCCCTAATCAATGCTTGTTTGT	59.485	43.478	0.00	0.00	0.00	2.83
3515	4194	4.497300	CCCCTAATCAATGCTTGTTTGTG	58.503	43.478	0.00	0.00	0.00	3.33
3516	4195	3.928375	CCCTAATCAATGCTTGTTTGTGC	59.072	43.478	0.00	0.00	0.00	4.57
3517	4196	4.558178	CCTAATCAATGCTTGTTTGTGCA	58.442	39.130	0.00	0.00	43.67	4.57
3518	4197	4.624024	CCTAATCAATGCTTGTTTGTGCAG	59.376	41.667	0.00	0.00	42.74	4.41
3519	4198	3.738830	ATCAATGCTTGTTTGTGCAGT	57.261	38.095	0.00	0.00	42.74	4.40
3520	4199	4.852134	ATCAATGCTTGTTTGTGCAGTA	57.148	36.364	0.00	0.00	42.74	2.74
3521	4200	4.852134	TCAATGCTTGTTTGTGCAGTAT	57.148	36.364	0.00	0.00	42.74	2.12
3522	4201	5.199024	TCAATGCTTGTTTGTGCAGTATT	57.801	34.783	0.00	0.00	42.74	1.89
3523	4202	6.324561	TCAATGCTTGTTTGTGCAGTATTA	57.675	33.333	0.00	0.00	42.74	0.98
3524	4203	6.923012	TCAATGCTTGTTTGTGCAGTATTAT	58.077	32.000	0.00	0.00	42.74	1.28
3525	4204	7.028962	TCAATGCTTGTTTGTGCAGTATTATC	58.971	34.615	0.00	0.00	42.74	1.75
3526	4205	5.956068	TGCTTGTTTGTGCAGTATTATCA	57.044	34.783	0.00	0.00	34.84	2.15
3527	4206	6.513806	TGCTTGTTTGTGCAGTATTATCAT	57.486	33.333	0.00	0.00	34.84	2.45
3528	4207	6.554419	TGCTTGTTTGTGCAGTATTATCATC	58.446	36.000	0.00	0.00	34.84	2.92
3529	4208	6.375174	TGCTTGTTTGTGCAGTATTATCATCT	59.625	34.615	0.00	0.00	34.84	2.90

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
9	10	5.730296	ACCAGAATGATTCCTATCCTACG	57.270	43.478	0.75	0.00	39.69	3.51
147	161	4.673968	ACTGTACTATTGTGAGGGTCTGA	58.326	43.478	0.00	0.00	0.00	3.27
160	174	7.549488	GCTGGTTTAGTTCATCAACTGTACTAT	59.451	37.037	0.00	0.00	43.17	2.12
205	219	2.104170	CACTTACCCTCCCTCTCTGAC	58.896	57.143	0.00	0.00	0.00	3.51
206	220	1.717077	ACACTTACCCTCCCTCTCTGA	59.283	52.381	0.00	0.00	0.00	3.27
207	221	2.104170	GACACTTACCCTCCCTCTCTG	58.896	57.143	0.00	0.00	0.00	3.35
208	222	2.004589	AGACACTTACCCTCCCTCTCT	58.995	52.381	0.00	0.00	0.00	3.10
209	223	2.535836	AGACACTTACCCTCCCTCTC	57.464	55.000	0.00	0.00	0.00	3.20
210	224	2.384029	AGAAGACACTTACCCTCCCTCT	59.616	50.000	0.00	0.00	0.00	3.69
211	225	2.498078	CAGAAGACACTTACCCTCCCTC	59.502	54.545	0.00	0.00	0.00	4.30
214	228	4.828072	ATTCAGAAGACACTTACCCTCC	57.172	45.455	0.00	0.00	0.00	4.30
216	230	7.682787	ATGATATTCAGAAGACACTTACCCT	57.317	36.000	0.00	0.00	0.00	4.34
217	231	8.738645	AAATGATATTCAGAAGACACTTACCC	57.261	34.615	0.00	0.00	0.00	3.69
221	235	9.678260	AGCTAAAATGATATTCAGAAGACACTT	57.322	29.630	0.00	0.00	0.00	3.16
224	238	9.453572	AACAGCTAAAATGATATTCAGAAGACA	57.546	29.630	0.00	0.00	0.00	3.41
226	240	8.400947	GCAACAGCTAAAATGATATTCAGAAGA	58.599	33.333	0.00	0.00	0.00	2.87
227	241	8.186163	TGCAACAGCTAAAATGATATTCAGAAG	58.814	33.333	0.00	0.00	0.00	2.85
228	242	8.054152	TGCAACAGCTAAAATGATATTCAGAA	57.946	30.769	0.00	0.00	0.00	3.02
229	243	7.628769	TGCAACAGCTAAAATGATATTCAGA	57.371	32.000	0.00	0.00	0.00	3.27
230	244	8.132995	TGATGCAACAGCTAAAATGATATTCAG	58.867	33.333	0.00	0.00	0.00	3.02
231	245	7.998580	TGATGCAACAGCTAAAATGATATTCA	58.001	30.769	0.00	0.00	0.00	2.57
232	246	9.125906	GATGATGCAACAGCTAAAATGATATTC	57.874	33.333	4.82	0.00	0.00	1.75
233	247	7.806487	CGATGATGCAACAGCTAAAATGATATT	59.194	33.333	10.59	0.00	0.00	1.28
234	248	7.173735	TCGATGATGCAACAGCTAAAATGATAT	59.826	33.333	10.59	0.00	0.00	1.63
235	249	6.482973	TCGATGATGCAACAGCTAAAATGATA	59.517	34.615	10.59	0.00	0.00	2.15
283	297	2.035632	CCCTCCCTCTCTGACATGTAC	58.964	57.143	0.00	0.00	0.00	2.90
304	350	1.827969	CCCTCCCTCACTAGACACTTG	59.172	57.143	0.00	0.00	0.00	3.16
306	352	1.006162	GTCCCTCCCTCACTAGACACT	59.994	57.143	0.00	0.00	0.00	3.55
315	361	2.450243	GTCCAGGTCCCTCCCTCA	59.550	66.667	0.00	0.00	36.75	3.86
320	366	1.677637	GGATGTCGTCCAGGTCCCTC	61.678	65.000	6.19	0.00	46.96	4.30
321	367	1.686110	GGATGTCGTCCAGGTCCCT	60.686	63.158	6.19	0.00	46.96	4.20
456	502	2.239654	CAGGAATAGTGGTGGTGGTGAT	59.760	50.000	0.00	0.00	0.00	3.06
457	503	1.628340	CAGGAATAGTGGTGGTGGTGA	59.372	52.381	0.00	0.00	0.00	4.02
458	504	1.351017	ACAGGAATAGTGGTGGTGGTG	59.649	52.381	0.00	0.00	0.00	4.17
471	525	4.104738	TCCTTTTCTTGGAGTGACAGGAAT	59.895	41.667	0.00	0.00	36.52	3.01
519	577	4.030216	TGCCTAGTAGGATTCATGTGTGA	58.970	43.478	21.02	0.00	37.67	3.58
527	585	2.891580	TCGATGGTGCCTAGTAGGATTC	59.108	50.000	21.02	8.54	37.67	2.52
537	595	2.362503	TCTCCGTCGATGGTGCCT	60.363	61.111	22.88	0.00	0.00	4.75
566	626	1.227853	GGTTGCGAGGTGAGTTGGT	60.228	57.895	0.00	0.00	0.00	3.67
569	629	1.227853	GGTGGTTGCGAGGTGAGTT	60.228	57.895	0.00	0.00	0.00	3.01
887	961	1.002087	GAAAGCTCAAAGGGTCGGAGA	59.998	52.381	0.00	0.00	0.00	3.71
1009	1088	0.631753	AGATCAGTCGGGGAGAGGAA	59.368	55.000	0.00	0.00	0.00	3.36
1015	1094	1.144503	GGTACCTAGATCAGTCGGGGA	59.855	57.143	4.06	0.00	0.00	4.81
1019	1098	1.264557	CGCAGGTACCTAGATCAGTCG	59.735	57.143	15.80	5.71	0.00	4.18
1072	1152	4.897076	TGTAAATCTACCGAATCTGGGCTA	59.103	41.667	0.00	0.00	0.00	3.93
1102	1182	1.940883	AACATTCTACCGAGCGCCGA	61.941	55.000	17.96	0.22	41.76	5.54
1191	1273	6.324254	ACTTAAGAGAAATACACGGCTCCTAT	59.676	38.462	10.09	0.00	0.00	2.57
1199	1281	4.031426	GGTGCGACTTAAGAGAAATACACG	59.969	45.833	10.09	0.00	0.00	4.49
1215	1297	2.173382	GCATCAACACGGTGCGAC	59.827	61.111	8.30	0.00	0.00	5.19
1219	1301	1.208358	CAGCAGCATCAACACGGTG	59.792	57.895	6.58	6.58	0.00	4.94
1386	1475	2.806434	CCAATGGGGTCACAAGATGAA	58.194	47.619	0.00	0.00	39.72	2.57
1421	1510	9.522804	CTAACAAGACTGGAGACTAATGTATTC	57.477	37.037	0.00	0.00	0.00	1.75
1464	1559	4.025040	TGCATATCTGGGATCAATCACC	57.975	45.455	0.00	0.00	0.00	4.02
1613	2074	4.130118	GGGGTACATCATGTCACTCATTC	58.870	47.826	0.00	0.00	34.09	2.67
1632	2096	1.431243	AGAGATAGGCTGTAGGAGGGG	59.569	57.143	0.00	0.00	0.00	4.79
1660	2124	2.889170	TGTTTGTATGCCAGCCCTAA	57.111	45.000	0.00	0.00	0.00	2.69
1675	2139	5.182001	CAGGTTGAGTTAGCTAGCAATGTTT	59.818	40.000	18.83	0.00	0.00	2.83
1709	2173	8.147244	ACAAAAGGGAGTACATTACATACTCT	57.853	34.615	10.97	0.00	45.31	3.24
1856	2326	0.172578	GGGGCGTGGAAAATTGCTAC	59.827	55.000	0.00	0.00	0.00	3.58
1870	2340	0.243636	GTGTTTGATTCCAAGGGGCG	59.756	55.000	0.00	0.00	33.23	6.13
1934	2466	9.535878	GAATAAACAACCAGGAATAAACAACAA	57.464	29.630	0.00	0.00	0.00	2.83
1941	2473	7.507616	ACAACAGGAATAAACAACCAGGAATAA	59.492	33.333	0.00	0.00	0.00	1.40
1942	2474	7.007723	ACAACAGGAATAAACAACCAGGAATA	58.992	34.615	0.00	0.00	0.00	1.75
1976	2512	5.335269	CGTTCACCTACAAAAATGCCATACA	60.335	40.000	0.00	0.00	0.00	2.29
2216	2757	7.763985	CCAACATTTCCAAAGTAACTTGAGTTT	59.236	33.333	1.20	0.00	39.31	2.66
2248	2789	7.261325	TGCAAAGCAACAGAAACAAGTAAATA	58.739	30.769	0.00	0.00	34.76	1.40
2249	2790	6.105333	TGCAAAGCAACAGAAACAAGTAAAT	58.895	32.000	0.00	0.00	34.76	1.40
2251	2792	5.065704	TGCAAAGCAACAGAAACAAGTAA	57.934	34.783	0.00	0.00	34.76	2.24
2253	2794	3.591196	TGCAAAGCAACAGAAACAAGT	57.409	38.095	0.00	0.00	34.76	3.16
2256	2797	3.491276	CCAGATGCAAAGCAACAGAAACA	60.491	43.478	0.00	0.00	43.62	2.83
2257	2798	3.054878	CCAGATGCAAAGCAACAGAAAC	58.945	45.455	0.00	0.00	43.62	2.78
2258	2799	2.957680	TCCAGATGCAAAGCAACAGAAA	59.042	40.909	0.00	0.00	43.62	2.52
2259	2800	2.585330	TCCAGATGCAAAGCAACAGAA	58.415	42.857	0.00	0.00	43.62	3.02
2260	2801	2.275134	TCCAGATGCAAAGCAACAGA	57.725	45.000	0.00	0.00	43.62	3.41
2261	2802	2.230508	ACATCCAGATGCAAAGCAACAG	59.769	45.455	7.56	0.00	43.62	3.16
2264	2805	5.664294	ATAAACATCCAGATGCAAAGCAA	57.336	34.783	7.56	0.00	43.62	3.91
2266	2807	5.899299	AGAATAAACATCCAGATGCAAAGC	58.101	37.500	7.56	0.00	42.39	3.51
2293	2836	3.259374	TGTTGTCTTGGCCTGAAACAAAA	59.741	39.130	3.32	1.95	32.17	2.44
2403	2947	5.893255	ACAGAATATAGCAAGGAAATGGCAA	59.107	36.000	0.00	0.00	0.00	4.52
2405	2949	6.396829	AACAGAATATAGCAAGGAAATGGC	57.603	37.500	0.00	0.00	0.00	4.40
2433	2977	8.668510	AAGAAATCATGGTGTCAGATACATAC	57.331	34.615	0.00	0.00	41.10	2.39
2436	2980	6.942005	ACAAAGAAATCATGGTGTCAGATACA	59.058	34.615	0.00	0.00	35.06	2.29
2451	2995	6.426937	TGCACCTCTGTAGTAACAAAGAAATC	59.573	38.462	0.00	0.00	34.49	2.17
2537	3081	8.612619	CACAACATCCTAAACATAACAGGATAC	58.387	37.037	2.17	0.00	45.44	2.24
2555	3100	1.541588	GGGAAGTTCTGGCACAACATC	59.458	52.381	8.35	5.45	38.70	3.06
3502	4181	6.923012	TGATAATACTGCACAAACAAGCATT	58.077	32.000	0.00	0.00	40.42	3.56
3503	4182	6.513806	TGATAATACTGCACAAACAAGCAT	57.486	33.333	0.00	0.00	40.42	3.79
3504	4183	5.956068	TGATAATACTGCACAAACAAGCA	57.044	34.783	0.00	0.00	39.25	3.91
3505	4184	6.789262	AGATGATAATACTGCACAAACAAGC	58.211	36.000	0.00	0.00	0.00	4.01

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.