AutoCloner

Multiple sequence alignment - TraesCS7A01G124400

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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	TraesCS7A01G124400	chr7A	100.000	3966	0	0	1	3966	80141890	80145855	0.000000e+00	7324.0
1	TraesCS7A01G124400	chr7A	88.896	1531	147	15	1476	2991	126756607	126755085	0.000000e+00	1864.0
2	TraesCS7A01G124400	chr7A	91.084	886	63	6	1435	2306	80429408	80428525	0.000000e+00	1184.0
3	TraesCS7A01G124400	chr7A	90.856	689	53	6	2299	2983	80428164	80427482	0.000000e+00	915.0
4	TraesCS7A01G124400	chr7A	83.333	780	91	20	2216	2991	126750168	126749424	0.000000e+00	684.0
5	TraesCS7A01G124400	chr7A	96.429	364	13	0	3603	3966	249026692	249027055	5.670000e-168	601.0
6	TraesCS7A01G124400	chr7A	98.154	325	4	2	3642	3966	511928967	511928645	2.070000e-157	566.0
7	TraesCS7A01G124400	chr7A	83.891	329	37	4	891	1219	80429839	80429527	2.320000e-77	300.0
8	TraesCS7A01G124400	chr7A	87.591	137	10	4	168	304	46775822	46775693	6.860000e-33	152.0
9	TraesCS7A01G124400	chr7A	83.784	148	16	4	1061	1201	126756858	126756712	2.490000e-27	134.0
10	TraesCS7A01G124400	chr7B	91.505	2166	109	38	1268	3389	22462926	22465060	0.000000e+00	2911.0
11	TraesCS7A01G124400	chr7B	89.791	1528	133	14	1477	2991	85310158	85308641	0.000000e+00	1936.0
12	TraesCS7A01G124400	chr7B	87.739	1256	95	33	1	1222	22461704	22462934	0.000000e+00	1411.0
13	TraesCS7A01G124400	chr7B	86.358	777	73	17	1	761	22511068	22511827	0.000000e+00	817.0
14	TraesCS7A01G124400	chr7B	77.470	253	40	12	68	303	284147449	284147701	6.910000e-28	135.0
15	TraesCS7A01G124400	chr7D	93.585	1746	76	15	1266	2988	75956588	75954856	0.000000e+00	2571.0
16	TraesCS7A01G124400	chr7D	89.300	1542	152	9	1455	2988	124034243	124035779	0.000000e+00	1921.0
17	TraesCS7A01G124400	chr7D	86.196	1217	86	35	47	1224	75957751	75956578	0.000000e+00	1242.0
18	TraesCS7A01G124400	chr7D	89.630	405	25	8	2997	3389	75954785	75954386	2.130000e-137	499.0
19	TraesCS7A01G124400	chr7D	94.606	241	10	1	3393	3630	600766370	600766610	1.740000e-98	370.0
20	TraesCS7A01G124400	chr7D	85.294	136	15	5	3233	3365	227286370	227286237	6.910000e-28	135.0
21	TraesCS7A01G124400	chr7D	76.587	252	42	12	68	302	339117069	339117320	5.380000e-24	122.0
22	TraesCS7A01G124400	chr7D	87.037	108	11	2	3672	3778	188456413	188456308	6.960000e-23	119.0
23	TraesCS7A01G124400	chr3D	91.409	582	43	2	3392	3966	307107483	307106902	0.000000e+00	791.0
24	TraesCS7A01G124400	chr3D	93.952	248	10	5	3384	3626	261739674	261739921	1.740000e-98	370.0
25	TraesCS7A01G124400	chr3D	79.134	254	40	7	67	308	523208198	523207946	3.170000e-36	163.0
26	TraesCS7A01G124400	chr3D	77.165	254	40	8	68	303	422738090	422738343	8.940000e-27	132.0
27	TraesCS7A01G124400	chr3D	87.500	112	10	3	3672	3782	381953559	381953667	4.160000e-25	126.0
28	TraesCS7A01G124400	chr5A	93.382	544	18	16	3424	3966	364349238	364348712	0.000000e+00	789.0
29	TraesCS7A01G124400	chr5A	90.507	611	24	9	3378	3966	503387612	503387014	0.000000e+00	776.0
30	TraesCS7A01G124400	chr5A	86.861	137	11	7	3233	3365	293396136	293396269	3.190000e-31	147.0
31	TraesCS7A01G124400	chr5D	94.488	254	11	1	3392	3642	386727735	386727988	4.810000e-104	388.0
32	TraesCS7A01G124400	chr5D	94.332	247	10	2	3380	3622	10790711	10790957	3.740000e-100	375.0
33	TraesCS7A01G124400	chr5D	75.299	251	41	10	72	302	366750381	366750132	2.520000e-17	100.0
34	TraesCS7A01G124400	chr5D	84.314	102	16	0	201	302	412116666	412116767	2.520000e-17	100.0
35	TraesCS7A01G124400	chr6D	93.103	261	10	5	3383	3636	406004716	406004975	3.740000e-100	375.0
36	TraesCS7A01G124400	chr6D	92.969	256	11	5	3377	3627	409841508	409841761	2.250000e-97	366.0
37	TraesCS7A01G124400	chr6D	85.612	139	14	6	3231	3365	24318997	24318861	1.490000e-29	141.0
38	TraesCS7A01G124400	chr6D	81.915	94	17	0	209	302	437919540	437919633	3.290000e-11	80.5
39	TraesCS7A01G124400	chr6D	86.567	67	7	2	248	313	425887861	425887796	5.500000e-09	73.1
40	TraesCS7A01G124400	chr6D	75.472	159	31	6	2598	2752	410072038	410071884	1.980000e-08	71.3
41	TraesCS7A01G124400	chr1B	91.418	268	16	5	3381	3642	623385335	623385069	1.050000e-95	361.0
42	TraesCS7A01G124400	chr3B	91.188	261	15	6	3382	3638	712339573	712339317	8.160000e-92	348.0
43	TraesCS7A01G124400	chr4A	83.648	159	24	2	3233	3389	556840526	556840368	8.880000e-32	148.0
44	TraesCS7A01G124400	chr4A	86.239	109	14	1	196	303	24916122	24916014	2.500000e-22	117.0
45	TraesCS7A01G124400	chr4A	76.349	241	41	9	68	306	147569854	147570080	9.010000e-22	115.0
46	TraesCS7A01G124400	chr4A	83.908	87	14	0	220	306	175753257	175753343	2.540000e-12	84.2
47	TraesCS7A01G124400	chr3A	77.953	254	38	8	68	303	566132495	566132242	4.130000e-30	143.0
48	TraesCS7A01G124400	chr3A	80.899	178	25	8	1755	1926	10291194	10291368	8.940000e-27	132.0
49	TraesCS7A01G124400	chr3A	85.938	64	7	2	3863	3925	698053778	698053716	2.560000e-07	67.6
50	TraesCS7A01G124400	chr5B	82.822	163	23	5	3231	3389	647452450	647452289	1.490000e-29	141.0
51	TraesCS7A01G124400	chr5B	85.294	136	16	4	3233	3365	473881831	473881965	1.920000e-28	137.0
52	TraesCS7A01G124400	chr5B	81.988	161	25	4	3232	3389	647510908	647510749	2.490000e-27	134.0
53	TraesCS7A01G124400	chr5B	100.000	31	0	0	250	280	289162767	289162797	1.540000e-04	58.4
54	TraesCS7A01G124400	chr5B	94.595	37	0	2	254	290	248398407	248398373	5.540000e-04	56.5
55	TraesCS7A01G124400	chr6B	78.866	194	37	4	2502	2693	616868550	616868741	1.160000e-25	128.0
56	TraesCS7A01G124400	chr6B	81.538	130	17	4	3654	3778	409633167	409633294	2.520000e-17	100.0
57	TraesCS7A01G124400	chr4D	81.761	159	23	5	1755	1910	127928638	127928793	1.160000e-25	128.0
58	TraesCS7A01G124400	chr2B	76.860	242	38	8	79	303	798385523	798385763	1.940000e-23	121.0
59	TraesCS7A01G124400	chr2B	88.889	99	8	2	3672	3769	569119659	569119755	6.960000e-23	119.0
60	TraesCS7A01G124400	chr6A	75.472	159	31	6	2598	2752	555362268	555362114	1.980000e-08	71.3
61	TraesCS7A01G124400	chr6A	76.923	117	22	5	406	521	74348738	74348850	1.190000e-05	62.1

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	TraesCS7A01G124400	chr7A	80141890	80145855	3965	False	7324.000000	7324	100.000000	1	3966	1	chr7A.!!$F1	3965
1	TraesCS7A01G124400	chr7A	126755085	126756858	1773	True	999.000000	1864	86.340000	1061	2991	2	chr7A.!!$R5	1930
2	TraesCS7A01G124400	chr7A	80427482	80429839	2357	True	799.666667	1184	88.610333	891	2983	3	chr7A.!!$R4	2092
3	TraesCS7A01G124400	chr7A	126749424	126750168	744	True	684.000000	684	83.333000	2216	2991	1	chr7A.!!$R2	775
4	TraesCS7A01G124400	chr7B	22461704	22465060	3356	False	2161.000000	2911	89.622000	1	3389	2	chr7B.!!$F3	3388
5	TraesCS7A01G124400	chr7B	85308641	85310158	1517	True	1936.000000	1936	89.791000	1477	2991	1	chr7B.!!$R1	1514
6	TraesCS7A01G124400	chr7B	22511068	22511827	759	False	817.000000	817	86.358000	1	761	1	chr7B.!!$F1	760
7	TraesCS7A01G124400	chr7D	124034243	124035779	1536	False	1921.000000	1921	89.300000	1455	2988	1	chr7D.!!$F1	1533
8	TraesCS7A01G124400	chr7D	75954386	75957751	3365	True	1437.333333	2571	89.803667	47	3389	3	chr7D.!!$R3	3342
9	TraesCS7A01G124400	chr3D	307106902	307107483	581	True	791.000000	791	91.409000	3392	3966	1	chr3D.!!$R1	574
10	TraesCS7A01G124400	chr5A	364348712	364349238	526	True	789.000000	789	93.382000	3424	3966	1	chr5A.!!$R1	542
11	TraesCS7A01G124400	chr5A	503387014	503387612	598	True	776.000000	776	90.507000	3378	3966	1	chr5A.!!$R2	588

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
764	794	0.110486	TGGTTCCAAGCCTCCAAGTC	59.890	55.0	3.01	F
765	795	0.609406	GGTTCCAAGCCTCCAAGTCC	60.609	60.0	3.85	F
766	796	0.110486	GTTCCAAGCCTCCAAGTCCA	59.890	55.0	4.02	F
767	797	0.850100	TTCCAAGCCTCCAAGTCCAA	59.150	50.0	3.53	F
1349	1436	0.965363	GCCGATCCCCACAACACAAT	60.965	55.0	2.71	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Hairpin	End Stability	Orientation
2554	3064	1.132199	CCGCGTGCTCGTAGTAAGTG	61.132	60.000	4.92	39.49	3.16	R
2586	3096	2.080336	CTGGAACACCCCCACCATGT	62.080	60.000	0.00	0.00	3.21	R
2642	3152	2.972505	CGCCTTCTGGTTGTGCGT	60.973	61.111	0.00	40.33	5.24	R
2899	3409	2.329267	ACATCCTCACACTCCTTGACA	58.671	47.619	0.00	0.00	3.58	R
3229	3827	2.525368	GGGCCAATAAACAAGGACAGT	58.475	47.619	4.39	29.65	3.55	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
88	89	9.436957	CTTGCATCTATACCCGTATAAAAAGAT	57.563	33.333	0.00	0.00	0.00	2.40
98	99	6.722590	ACCCGTATAAAAAGATTCAAAAGGGT	59.277	34.615	0.00	0.00	40.67	4.34
400	416	3.044059	GCTTCGCATGCACCCAGTC	62.044	63.158	19.57	0.69	0.00	3.51
415	431	3.332485	ACCCAGTCTAATTAGCCACCAAA	59.668	43.478	7.67	0.00	0.00	3.28
433	449	3.548014	CCAAAATCGTCACAACACAGTCC	60.548	47.826	0.00	0.00	0.00	3.85
466	488	3.508793	AGCCAAAGACAATCTTCACATGG	59.491	43.478	0.00	3.59	35.27	3.66
482	504	3.006110	CACATGGCACCACTCTTCAAATT	59.994	43.478	0.00	0.00	0.00	1.82
495	517	7.260603	CACTCTTCAAATTATGTTTCATCCCC	58.739	38.462	0.00	0.00	0.00	4.81
564	586	5.862924	ATTCAACAATGACTCTAACGGTG	57.137	39.130	0.00	0.00	34.61	4.94
577	599	7.491372	TGACTCTAACGGTGTTGATTTGATATC	59.509	37.037	0.00	0.00	0.00	1.63
696	726	0.179059	TGTGCGAAGAGTTGCCTTCA	60.179	50.000	0.00	0.00	41.89	3.02
697	727	1.160137	GTGCGAAGAGTTGCCTTCAT	58.840	50.000	0.00	0.00	41.89	2.57
698	728	2.289382	TGTGCGAAGAGTTGCCTTCATA	60.289	45.455	0.00	0.00	41.89	2.15
699	729	2.939103	GTGCGAAGAGTTGCCTTCATAT	59.061	45.455	0.00	0.00	41.89	1.78
711	741	3.517500	TGCCTTCATATATATCGTGCCCA	59.482	43.478	0.00	0.00	0.00	5.36
729	759	1.265905	CCAGTAGTCCCAAAAACACGC	59.734	52.381	0.00	0.00	0.00	5.34
761	791	1.228552	GCTGGTTCCAAGCCTCCAA	60.229	57.895	0.00	0.00	0.00	3.53
762	792	1.246737	GCTGGTTCCAAGCCTCCAAG	61.247	60.000	0.00	0.00	0.00	3.61
763	793	0.111253	CTGGTTCCAAGCCTCCAAGT	59.889	55.000	0.00	0.00	0.00	3.16
764	794	0.110486	TGGTTCCAAGCCTCCAAGTC	59.890	55.000	0.00	0.00	0.00	3.01
765	795	0.609406	GGTTCCAAGCCTCCAAGTCC	60.609	60.000	0.00	0.00	0.00	3.85
766	796	0.110486	GTTCCAAGCCTCCAAGTCCA	59.890	55.000	0.00	0.00	0.00	4.02
767	797	0.850100	TTCCAAGCCTCCAAGTCCAA	59.150	50.000	0.00	0.00	0.00	3.53
803	833	1.819632	CATGCTGGCTCGGTTACCC	60.820	63.158	0.00	0.00	0.00	3.69
922	955	4.644954	CTTACGGATCTTGTTAAAACCGC	58.355	43.478	0.00	0.00	43.36	5.68
945	978	3.659089	CTTTCGTGGCCCGATCGGT	62.659	63.158	31.22	0.00	46.75	4.69
957	990	2.603892	CCCGATCGGTTGACGTATACTG	60.604	54.545	31.22	8.52	44.69	2.74
985	1027	2.435805	TGGTTGTGCTAGGGAGATGATC	59.564	50.000	0.00	0.00	0.00	2.92
986	1028	2.435805	GGTTGTGCTAGGGAGATGATCA	59.564	50.000	0.00	0.00	0.00	2.92
987	1029	3.118261	GGTTGTGCTAGGGAGATGATCAA	60.118	47.826	0.00	0.00	0.00	2.57
988	1030	4.125703	GTTGTGCTAGGGAGATGATCAAG	58.874	47.826	0.00	0.00	0.00	3.02
989	1031	2.702478	TGTGCTAGGGAGATGATCAAGG	59.298	50.000	0.00	0.00	0.00	3.61
990	1032	2.968574	GTGCTAGGGAGATGATCAAGGA	59.031	50.000	0.00	0.00	0.00	3.36
991	1033	3.006752	GTGCTAGGGAGATGATCAAGGAG	59.993	52.174	0.00	0.00	0.00	3.69
992	1034	3.116977	TGCTAGGGAGATGATCAAGGAGA	60.117	47.826	0.00	0.00	0.00	3.71
1224	1308	2.528564	ACAAGCAAGCTCTCTCTCTCT	58.471	47.619	0.00	0.00	0.00	3.10
1225	1309	2.493278	ACAAGCAAGCTCTCTCTCTCTC	59.507	50.000	0.00	0.00	0.00	3.20
1227	1311	2.648059	AGCAAGCTCTCTCTCTCTCTC	58.352	52.381	0.00	0.00	0.00	3.20
1230	1314	3.683847	GCAAGCTCTCTCTCTCTCTCTCT	60.684	52.174	0.00	0.00	0.00	3.10
1231	1315	4.125703	CAAGCTCTCTCTCTCTCTCTCTC	58.874	52.174	0.00	0.00	0.00	3.20
1233	1317	3.640967	AGCTCTCTCTCTCTCTCTCTCTC	59.359	52.174	0.00	0.00	0.00	3.20
1234	1318	3.640967	GCTCTCTCTCTCTCTCTCTCTCT	59.359	52.174	0.00	0.00	0.00	3.10
1235	1319	4.261994	GCTCTCTCTCTCTCTCTCTCTCTC	60.262	54.167	0.00	0.00	0.00	3.20
1236	1320	5.136068	TCTCTCTCTCTCTCTCTCTCTCT	57.864	47.826	0.00	0.00	0.00	3.10
1237	1321	5.136828	TCTCTCTCTCTCTCTCTCTCTCTC	58.863	50.000	0.00	0.00	0.00	3.20
1238	1322	5.103728	TCTCTCTCTCTCTCTCTCTCTCTCT	60.104	48.000	0.00	0.00	0.00	3.10
1239	1323	5.136828	TCTCTCTCTCTCTCTCTCTCTCTC	58.863	50.000	0.00	0.00	0.00	3.20
1240	1324	5.103728	TCTCTCTCTCTCTCTCTCTCTCTCT	60.104	48.000	0.00	0.00	0.00	3.10
1241	1325	5.136828	TCTCTCTCTCTCTCTCTCTCTCTC	58.863	50.000	0.00	0.00	0.00	3.20
1242	1326	5.103728	TCTCTCTCTCTCTCTCTCTCTCTCT	60.104	48.000	0.00	0.00	0.00	3.10
1243	1327	5.136828	TCTCTCTCTCTCTCTCTCTCTCTC	58.863	50.000	0.00	0.00	0.00	3.20
1244	1328	5.103728	TCTCTCTCTCTCTCTCTCTCTCTCT	60.104	48.000	0.00	0.00	0.00	3.10
1245	1329	5.136828	TCTCTCTCTCTCTCTCTCTCTCTC	58.863	50.000	0.00	0.00	0.00	3.20
1246	1330	5.103728	TCTCTCTCTCTCTCTCTCTCTCTCT	60.104	48.000	0.00	0.00	0.00	3.10
1247	1331	5.136828	TCTCTCTCTCTCTCTCTCTCTCTC	58.863	50.000	0.00	0.00	0.00	3.20
1248	1332	5.103728	TCTCTCTCTCTCTCTCTCTCTCTCT	60.104	48.000	0.00	0.00	0.00	3.10
1249	1333	5.136828	TCTCTCTCTCTCTCTCTCTCTCTC	58.863	50.000	0.00	0.00	0.00	3.20
1250	1334	5.103728	TCTCTCTCTCTCTCTCTCTCTCTCT	60.104	48.000	0.00	0.00	0.00	3.10
1251	1335	5.136828	TCTCTCTCTCTCTCTCTCTCTCTC	58.863	50.000	0.00	0.00	0.00	3.20
1252	1336	5.103728	TCTCTCTCTCTCTCTCTCTCTCTCT	60.104	48.000	0.00	0.00	0.00	3.10
1253	1337	5.136828	TCTCTCTCTCTCTCTCTCTCTCTC	58.863	50.000	0.00	0.00	0.00	3.20
1254	1338	5.103728	TCTCTCTCTCTCTCTCTCTCTCTCT	60.104	48.000	0.00	0.00	0.00	3.10
1255	1339	5.136828	TCTCTCTCTCTCTCTCTCTCTCTC	58.863	50.000	0.00	0.00	0.00	3.20
1256	1340	5.103728	TCTCTCTCTCTCTCTCTCTCTCTCT	60.104	48.000	0.00	0.00	0.00	3.10
1257	1341	5.136828	TCTCTCTCTCTCTCTCTCTCTCTC	58.863	50.000	0.00	0.00	0.00	3.20
1258	1342	5.103728	TCTCTCTCTCTCTCTCTCTCTCTCT	60.104	48.000	0.00	0.00	0.00	3.10
1259	1343	5.136828	TCTCTCTCTCTCTCTCTCTCTCTC	58.863	50.000	0.00	0.00	0.00	3.20
1260	1344	5.103728	TCTCTCTCTCTCTCTCTCTCTCTCT	60.104	48.000	0.00	0.00	0.00	3.10
1261	1345	5.136828	TCTCTCTCTCTCTCTCTCTCTCTC	58.863	50.000	0.00	0.00	0.00	3.20
1262	1346	5.103728	TCTCTCTCTCTCTCTCTCTCTCTCT	60.104	48.000	0.00	0.00	0.00	3.10
1263	1347	5.136828	TCTCTCTCTCTCTCTCTCTCTCTC	58.863	50.000	0.00	0.00	0.00	3.20
1264	1348	5.103728	TCTCTCTCTCTCTCTCTCTCTCTCT	60.104	48.000	0.00	0.00	0.00	3.10
1265	1349	5.136828	TCTCTCTCTCTCTCTCTCTCTCTC	58.863	50.000	0.00	0.00	0.00	3.20
1266	1350	5.103728	TCTCTCTCTCTCTCTCTCTCTCTCT	60.104	48.000	0.00	0.00	0.00	3.10
1267	1351	5.136828	TCTCTCTCTCTCTCTCTCTCTCTC	58.863	50.000	0.00	0.00	0.00	3.20
1268	1352	5.103728	TCTCTCTCTCTCTCTCTCTCTCTCT	60.104	48.000	0.00	0.00	0.00	3.10
1269	1353	5.136828	TCTCTCTCTCTCTCTCTCTCTCTC	58.863	50.000	0.00	0.00	0.00	3.20
1270	1354	5.103728	TCTCTCTCTCTCTCTCTCTCTCTCT	60.104	48.000	0.00	0.00	0.00	3.10
1271	1355	5.136828	TCTCTCTCTCTCTCTCTCTCTCTC	58.863	50.000	0.00	0.00	0.00	3.20
1272	1356	5.103728	TCTCTCTCTCTCTCTCTCTCTCTCT	60.104	48.000	0.00	0.00	0.00	3.10
1279	1363	2.430694	TCTCTCTCTCTCTCTCTCGTGG	59.569	54.545	0.00	0.00	0.00	4.94
1293	1377	3.123050	TCTCGTGGTCGATTTGCATATG	58.877	45.455	0.00	0.00	45.21	1.78
1313	1397	2.559231	TGTGTACTCACGATTAGGTGCA	59.441	45.455	0.00	0.00	46.49	4.57
1349	1436	0.965363	GCCGATCCCCACAACACAAT	60.965	55.000	0.00	0.00	0.00	2.71
1350	1437	1.680555	GCCGATCCCCACAACACAATA	60.681	52.381	0.00	0.00	0.00	1.90
1351	1438	2.014128	CCGATCCCCACAACACAATAC	58.986	52.381	0.00	0.00	0.00	1.89
1352	1439	2.616765	CCGATCCCCACAACACAATACA	60.617	50.000	0.00	0.00	0.00	2.29
1353	1440	3.078097	CGATCCCCACAACACAATACAA	58.922	45.455	0.00	0.00	0.00	2.41
1361	1448	4.023279	CCACAACACAATACAAGCTTGCTA	60.023	41.667	26.27	16.93	0.00	3.49
1411	1498	6.849811	GCACATGAACGAAATCTAATCATCTG	59.150	38.462	0.00	0.00	0.00	2.90
1414	1501	8.986847	ACATGAACGAAATCTAATCATCTGATC	58.013	33.333	0.00	0.00	32.75	2.92
1415	1502	9.205719	CATGAACGAAATCTAATCATCTGATCT	57.794	33.333	0.00	0.00	32.75	2.75
1416	1503	8.809159	TGAACGAAATCTAATCATCTGATCTC	57.191	34.615	0.00	0.00	32.75	2.75
1422	1509	8.760103	AAATCTAATCATCTGATCTCGTGATG	57.240	34.615	4.41	9.03	38.97	3.07
1428	1519	1.943340	TCTGATCTCGTGATGGTCTCG	59.057	52.381	4.41	0.00	35.02	4.04
1432	1523	1.675552	TCTCGTGATGGTCTCGCATA	58.324	50.000	0.00	0.00	33.88	3.14
1444	1535	7.488792	TGATGGTCTCGCATAAATCAAATTTTG	59.511	33.333	2.59	2.59	33.82	2.44
1708	1824	4.060038	CCGTACGCCAGGTCCGTT	62.060	66.667	10.49	0.00	39.88	4.44
2202	2327	1.696832	GACATGGCCGAGTTCGAAGC	61.697	60.000	0.00	0.00	43.02	3.86
2340	2835	2.364317	CCAGGCGGAGGAGAGGAA	60.364	66.667	0.00	0.00	0.00	3.36
2416	2911	1.145598	CCAGATCATGGCGTGCTCT	59.854	57.895	7.23	7.23	43.83	4.09
2481	2991	2.573869	GAGCAGCAGTAGCCACGA	59.426	61.111	0.00	0.00	43.56	4.35
2510	3020	0.972471	CTCCAAACCCAAGGCCATCC	60.972	60.000	5.01	0.00	0.00	3.51
2642	3152	2.769621	AGATCATGGGGCAGCGGA	60.770	61.111	0.00	0.00	0.00	5.54
2899	3409	2.430610	GGAGGAGCTGTCTCGCCAT	61.431	63.158	0.00	0.00	40.26	4.40
3000	3583	3.505835	AACCCGAGTTGGCAGAAAA	57.494	47.368	0.00	0.00	33.97	2.29
3041	3624	9.749490	GTTTTTGTAGTGATTTCGATCGATTTA	57.251	29.630	20.18	8.07	0.00	1.40
3107	3701	1.006086	CACAACAGTTGCAGTCGACA	58.994	50.000	19.50	0.00	0.00	4.35
3112	3706	1.599071	ACAGTTGCAGTCGACACATTG	59.401	47.619	19.50	17.00	0.00	2.82
3193	3791	3.971245	TTTGGGCAAGTCACTTTTTGT	57.029	38.095	0.00	0.00	0.00	2.83
3210	3808	9.377383	CACTTTTTGTTTTTACATACTACTCCG	57.623	33.333	0.00	0.00	0.00	4.63
3211	3809	8.562052	ACTTTTTGTTTTTACATACTACTCCGG	58.438	33.333	0.00	0.00	0.00	5.14
3229	3827	9.458727	CTACTCCGGGTTCTAATAGTAATATCA	57.541	37.037	0.00	0.00	0.00	2.15
3251	3850	1.431243	TGTCCTTGTTTATTGGCCCCT	59.569	47.619	0.00	0.00	0.00	4.79
3268	3867	3.004944	GCCCCTTTCGTATTTGTGTCAAA	59.995	43.478	0.00	0.00	0.00	2.69
3273	3872	6.145371	CCCTTTCGTATTTGTGTCAAATTTGG	59.855	38.462	17.90	0.12	0.00	3.28
3276	3875	6.378710	TCGTATTTGTGTCAAATTTGGACA	57.621	33.333	17.90	16.66	42.62	4.02
3471	4073	2.963599	TTTCGGCTTCTTTTACCCCT	57.036	45.000	0.00	0.00	0.00	4.79
3587	4212	2.266279	CCCCCTTGTCAGGTTTCTCTA	58.734	52.381	0.00	0.00	38.79	2.43
3628	4261	5.103728	TCTCTCTCTCTCTCTCTCTCTCTCT	60.104	48.000	0.00	0.00	0.00	3.10
3630	4263	5.103728	TCTCTCTCTCTCTCTCTCTCTCTCT	60.104	48.000	0.00	0.00	0.00	3.10
3632	4265	5.103728	TCTCTCTCTCTCTCTCTCTCTCTCT	60.104	48.000	0.00	0.00	0.00	3.10
3634	4267	5.103728	TCTCTCTCTCTCTCTCTCTCTCTCT	60.104	48.000	0.00	0.00	0.00	3.10
3636	4269	5.103728	TCTCTCTCTCTCTCTCTCTCTCTCT	60.104	48.000	0.00	0.00	0.00	3.10
3637	4270	5.136828	TCTCTCTCTCTCTCTCTCTCTCTC	58.863	50.000	0.00	0.00	0.00	3.20
3638	4271	5.103728	TCTCTCTCTCTCTCTCTCTCTCTCT	60.104	48.000	0.00	0.00	0.00	3.10
3639	4272	5.136828	TCTCTCTCTCTCTCTCTCTCTCTC	58.863	50.000	0.00	0.00	0.00	3.20
3640	4273	5.103728	TCTCTCTCTCTCTCTCTCTCTCTCT	60.104	48.000	0.00	0.00	0.00	3.10
3873	4506	0.257905	TCGGCCTACTGCTCCTAAGA	59.742	55.000	0.00	0.00	40.92	2.10
3879	4512	4.202409	GGCCTACTGCTCCTAAGATTTCAT	60.202	45.833	0.00	0.00	40.92	2.57

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
44	45	4.010349	GCAAGCCTAGTTAATTGTCTGGT	58.990	43.478	0.00	0.00	0.00	4.00
45	46	4.009675	TGCAAGCCTAGTTAATTGTCTGG	58.990	43.478	0.00	0.00	0.00	3.86
88	89	7.848128	AGATTAGTTCGATCTACCCTTTTGAA	58.152	34.615	2.65	0.00	32.27	2.69
98	99	3.483421	TGGCCGAGATTAGTTCGATCTA	58.517	45.455	0.00	0.00	40.36	1.98
356	372	9.685005	CGACAGATTATAGACGGTTTTAAAAAG	57.315	33.333	1.31	2.85	0.00	2.27
400	416	5.123186	TGTGACGATTTTGGTGGCTAATTAG	59.877	40.000	8.20	8.20	0.00	1.73
415	431	2.210116	GTGGACTGTGTTGTGACGATT	58.790	47.619	0.00	0.00	0.00	3.34
443	459	4.701651	CCATGTGAAGATTGTCTTTGGCTA	59.298	41.667	0.00	0.00	36.73	3.93
450	466	2.224843	TGGTGCCATGTGAAGATTGTCT	60.225	45.455	0.00	0.00	0.00	3.41
466	488	6.446318	TGAAACATAATTTGAAGAGTGGTGC	58.554	36.000	0.00	0.00	0.00	5.01
482	504	3.916359	TTGCTACGGGGATGAAACATA	57.084	42.857	0.00	0.00	0.00	2.29
495	517	1.295792	AATACCCGTGCATTGCTACG	58.704	50.000	19.72	19.72	39.83	3.51
549	571	5.995282	TCAAATCAACACCGTTAGAGTCATT	59.005	36.000	0.00	0.00	0.00	2.57
560	582	6.562270	GCTTCTACGATATCAAATCAACACCG	60.562	42.308	3.12	0.00	0.00	4.94
614	639	6.280855	AGTCAAACTTTGTAAACTTTGGCT	57.719	33.333	9.34	9.34	34.25	4.75
696	726	4.894114	GGGACTACTGGGCACGATATATAT	59.106	45.833	0.00	0.00	0.00	0.86
697	727	4.264038	TGGGACTACTGGGCACGATATATA	60.264	45.833	0.00	0.00	0.00	0.86
698	728	3.097614	GGGACTACTGGGCACGATATAT	58.902	50.000	0.00	0.00	0.00	0.86
699	729	2.158430	TGGGACTACTGGGCACGATATA	60.158	50.000	0.00	0.00	0.00	0.86
711	741	1.223187	CGCGTGTTTTTGGGACTACT	58.777	50.000	0.00	0.00	0.00	2.57
761	791	2.338984	GAGCGTCGTGGTTGGACT	59.661	61.111	0.00	0.00	32.24	3.85
762	792	2.737376	GGAGCGTCGTGGTTGGAC	60.737	66.667	0.00	0.00	0.00	4.02
763	793	3.998672	GGGAGCGTCGTGGTTGGA	61.999	66.667	0.00	0.00	0.00	3.53
764	794	4.308458	TGGGAGCGTCGTGGTTGG	62.308	66.667	0.00	0.00	0.00	3.77
765	795	3.041940	GTGGGAGCGTCGTGGTTG	61.042	66.667	0.00	0.00	0.00	3.77
766	796	4.657824	CGTGGGAGCGTCGTGGTT	62.658	66.667	0.00	0.00	0.00	3.67
803	833	4.029809	GGGGTTGACCTCACCCGG	62.030	72.222	0.00	0.00	44.46	5.73
809	839	2.034221	GCAGGTGGGGTTGACCTC	59.966	66.667	0.00	0.00	42.25	3.85
810	840	2.776526	TGCAGGTGGGGTTGACCT	60.777	61.111	0.00	0.00	45.23	3.85
889	919	0.389391	ATCCGTAAGCTCGTCATGGG	59.611	55.000	0.00	0.00	0.00	4.00
937	970	2.647337	CAGTATACGTCAACCGATCGG	58.353	52.381	32.20	32.20	40.70	4.18
957	990	1.006832	CCTAGCACAACCACATACGC	58.993	55.000	0.00	0.00	0.00	4.42
985	1027	2.354259	GCTCATGTCCTTGTCTCCTTG	58.646	52.381	0.00	0.00	0.00	3.61
986	1028	1.066573	CGCTCATGTCCTTGTCTCCTT	60.067	52.381	0.00	0.00	0.00	3.36
987	1029	0.534412	CGCTCATGTCCTTGTCTCCT	59.466	55.000	0.00	0.00	0.00	3.69
988	1030	0.460987	CCGCTCATGTCCTTGTCTCC	60.461	60.000	0.00	0.00	0.00	3.71
989	1031	1.086634	GCCGCTCATGTCCTTGTCTC	61.087	60.000	0.00	0.00	0.00	3.36
990	1032	1.078848	GCCGCTCATGTCCTTGTCT	60.079	57.895	0.00	0.00	0.00	3.41
991	1033	0.955428	TTGCCGCTCATGTCCTTGTC	60.955	55.000	0.00	0.00	0.00	3.18
992	1034	1.073025	TTGCCGCTCATGTCCTTGT	59.927	52.632	0.00	0.00	0.00	3.16
1224	1308	5.103728	AGAGAGAGAGAGAGAGAGAGAGAGA	60.104	48.000	0.00	0.00	0.00	3.10
1225	1309	5.139727	AGAGAGAGAGAGAGAGAGAGAGAG	58.860	50.000	0.00	0.00	0.00	3.20
1227	1311	5.139727	AGAGAGAGAGAGAGAGAGAGAGAG	58.860	50.000	0.00	0.00	0.00	3.20
1230	1314	5.103728	AGAGAGAGAGAGAGAGAGAGAGAGA	60.104	48.000	0.00	0.00	0.00	3.10
1231	1315	5.139727	AGAGAGAGAGAGAGAGAGAGAGAG	58.860	50.000	0.00	0.00	0.00	3.20
1233	1317	5.139727	AGAGAGAGAGAGAGAGAGAGAGAG	58.860	50.000	0.00	0.00	0.00	3.20
1234	1318	5.103728	AGAGAGAGAGAGAGAGAGAGAGAGA	60.104	48.000	0.00	0.00	0.00	3.10
1235	1319	5.139727	AGAGAGAGAGAGAGAGAGAGAGAG	58.860	50.000	0.00	0.00	0.00	3.20
1236	1320	5.103728	AGAGAGAGAGAGAGAGAGAGAGAGA	60.104	48.000	0.00	0.00	0.00	3.10
1237	1321	5.139727	AGAGAGAGAGAGAGAGAGAGAGAG	58.860	50.000	0.00	0.00	0.00	3.20
1238	1322	5.103728	AGAGAGAGAGAGAGAGAGAGAGAGA	60.104	48.000	0.00	0.00	0.00	3.10
1239	1323	5.139727	AGAGAGAGAGAGAGAGAGAGAGAG	58.860	50.000	0.00	0.00	0.00	3.20
1240	1324	5.103728	AGAGAGAGAGAGAGAGAGAGAGAGA	60.104	48.000	0.00	0.00	0.00	3.10
1241	1325	5.139727	AGAGAGAGAGAGAGAGAGAGAGAG	58.860	50.000	0.00	0.00	0.00	3.20
1242	1326	5.103728	AGAGAGAGAGAGAGAGAGAGAGAGA	60.104	48.000	0.00	0.00	0.00	3.10
1243	1327	5.139727	AGAGAGAGAGAGAGAGAGAGAGAG	58.860	50.000	0.00	0.00	0.00	3.20
1244	1328	5.103728	AGAGAGAGAGAGAGAGAGAGAGAGA	60.104	48.000	0.00	0.00	0.00	3.10
1245	1329	5.139727	AGAGAGAGAGAGAGAGAGAGAGAG	58.860	50.000	0.00	0.00	0.00	3.20
1246	1330	5.103728	AGAGAGAGAGAGAGAGAGAGAGAGA	60.104	48.000	0.00	0.00	0.00	3.10
1247	1331	5.139727	AGAGAGAGAGAGAGAGAGAGAGAG	58.860	50.000	0.00	0.00	0.00	3.20
1248	1332	5.103728	AGAGAGAGAGAGAGAGAGAGAGAGA	60.104	48.000	0.00	0.00	0.00	3.10
1249	1333	5.139727	AGAGAGAGAGAGAGAGAGAGAGAG	58.860	50.000	0.00	0.00	0.00	3.20
1250	1334	5.103728	AGAGAGAGAGAGAGAGAGAGAGAGA	60.104	48.000	0.00	0.00	0.00	3.10
1251	1335	5.139727	AGAGAGAGAGAGAGAGAGAGAGAG	58.860	50.000	0.00	0.00	0.00	3.20
1252	1336	5.136068	AGAGAGAGAGAGAGAGAGAGAGA	57.864	47.826	0.00	0.00	0.00	3.10
1253	1337	4.023279	CGAGAGAGAGAGAGAGAGAGAGAG	60.023	54.167	0.00	0.00	0.00	3.20
1254	1338	3.885901	CGAGAGAGAGAGAGAGAGAGAGA	59.114	52.174	0.00	0.00	0.00	3.10
1255	1339	3.634448	ACGAGAGAGAGAGAGAGAGAGAG	59.366	52.174	0.00	0.00	0.00	3.20
1256	1340	3.381590	CACGAGAGAGAGAGAGAGAGAGA	59.618	52.174	0.00	0.00	0.00	3.10
1257	1341	3.491619	CCACGAGAGAGAGAGAGAGAGAG	60.492	56.522	0.00	0.00	0.00	3.20
1258	1342	2.430694	CCACGAGAGAGAGAGAGAGAGA	59.569	54.545	0.00	0.00	0.00	3.10
1259	1343	2.168521	ACCACGAGAGAGAGAGAGAGAG	59.831	54.545	0.00	0.00	0.00	3.20
1260	1344	2.167693	GACCACGAGAGAGAGAGAGAGA	59.832	54.545	0.00	0.00	0.00	3.10
1261	1345	2.550978	GACCACGAGAGAGAGAGAGAG	58.449	57.143	0.00	0.00	0.00	3.20
1262	1346	1.134936	CGACCACGAGAGAGAGAGAGA	60.135	57.143	0.00	0.00	42.66	3.10
1263	1347	1.134936	TCGACCACGAGAGAGAGAGAG	60.135	57.143	0.00	0.00	43.81	3.20
1264	1348	0.896226	TCGACCACGAGAGAGAGAGA	59.104	55.000	0.00	0.00	43.81	3.10
1265	1349	3.444751	TCGACCACGAGAGAGAGAG	57.555	57.895	0.00	0.00	43.81	3.20
1279	1363	5.554510	CGTGAGTACACATATGCAAATCGAC	60.555	44.000	1.58	0.00	46.20	4.20
1293	1377	3.226346	TGCACCTAATCGTGAGTACAC	57.774	47.619	0.00	0.00	42.88	2.90
1313	1397	0.668535	GGCAAAGCTGGACGACTTTT	59.331	50.000	0.00	0.00	33.92	2.27
1353	1440	3.008835	TGGATCAAGCATTAGCAAGCT	57.991	42.857	0.00	0.00	45.49	3.74
1361	1448	3.183801	ACCCCAAATTGGATCAAGCATT	58.816	40.909	14.62	0.00	40.96	3.56
1372	1459	0.691904	ATGTGCCCAACCCCAAATTG	59.308	50.000	0.00	0.00	0.00	2.32
1411	1498	0.382158	TGCGAGACCATCACGAGATC	59.618	55.000	0.00	0.00	32.24	2.75
1414	1501	2.492019	TTATGCGAGACCATCACGAG	57.508	50.000	0.00	0.00	32.24	4.18
1415	1502	2.951457	TTTATGCGAGACCATCACGA	57.049	45.000	0.00	0.00	32.24	4.35
1416	1503	3.123050	TGATTTATGCGAGACCATCACG	58.877	45.455	0.00	0.00	33.67	4.35
1422	1509	6.099341	ACCAAAATTTGATTTATGCGAGACC	58.901	36.000	7.37	0.00	0.00	3.85
1428	1519	9.276397	GCAATGTTACCAAAATTTGATTTATGC	57.724	29.630	7.37	5.44	0.00	3.14
1432	1523	8.901793	ACTTGCAATGTTACCAAAATTTGATTT	58.098	25.926	7.37	0.00	0.00	2.17
1444	1535	3.810373	CACGAGAACTTGCAATGTTACC	58.190	45.455	0.00	2.08	34.00	2.85
1573	1685	4.162690	GGGGACTGGTAGCGGCTG	62.163	72.222	13.86	0.00	0.00	4.85
1626	1742	2.360475	GCTTCCACAGGAGGTGCC	60.360	66.667	0.00	0.00	46.50	5.01
2202	2327	2.570582	GAACAGCCTCCGGAGCTCAG	62.571	65.000	26.87	17.57	38.95	3.35
2340	2835	2.725312	ATCCTGATCTGCACGCCGT	61.725	57.895	0.00	0.00	0.00	5.68
2461	2971	3.385384	TGGCTACTGCTGCTCGCT	61.385	61.111	0.00	0.00	40.11	4.93
2498	3008	1.228063	CGATCAGGATGGCCTTGGG	60.228	63.158	3.32	0.00	43.90	4.12
2510	3020	3.135382	CTTGCAGCGACGCGATCAG	62.135	63.158	15.93	5.99	33.35	2.90
2554	3064	1.132199	CCGCGTGCTCGTAGTAAGTG	61.132	60.000	4.92	0.00	39.49	3.16
2557	3067	2.202518	GCCGCGTGCTCGTAGTAA	60.203	61.111	4.92	0.00	39.49	2.24
2586	3096	2.080336	CTGGAACACCCCCACCATGT	62.080	60.000	0.00	0.00	0.00	3.21
2642	3152	2.972505	CGCCTTCTGGTTGTGCGT	60.973	61.111	0.00	0.00	40.33	5.24
2899	3409	2.329267	ACATCCTCACACTCCTTGACA	58.671	47.619	0.00	0.00	0.00	3.58
2991	3512	5.275067	AGCTACAACAAAATTTTCTGCCA	57.725	34.783	0.00	0.00	0.00	4.92
3000	3583	9.730420	CACTACAAAAACTAGCTACAACAAAAT	57.270	29.630	0.00	0.00	0.00	1.82
3192	3790	6.401394	AGAACCCGGAGTAGTATGTAAAAAC	58.599	40.000	0.73	0.00	0.00	2.43
3193	3791	6.610075	AGAACCCGGAGTAGTATGTAAAAA	57.390	37.500	0.73	0.00	0.00	1.94
3210	3808	9.091220	AGGACAGTGATATTACTATTAGAACCC	57.909	37.037	0.00	0.00	0.00	4.11
3229	3827	2.525368	GGGCCAATAAACAAGGACAGT	58.475	47.619	4.39	0.00	29.65	3.55
3251	3850	7.258441	TGTCCAAATTTGACACAAATACGAAA	58.742	30.769	19.86	0.00	0.00	3.46
3471	4073	4.720649	TGTCCGGTTTGATTTTGTTTGA	57.279	36.364	0.00	0.00	0.00	2.69
3587	4212	5.714863	AGAGAGAGAGAGAGAGAGAGAGAT	58.285	45.833	0.00	0.00	0.00	2.75
3628	4261	1.087202	GCGTGCGAGAGAGAGAGAGA	61.087	60.000	0.00	0.00	0.00	3.10
3630	4263	2.109739	GGCGTGCGAGAGAGAGAGA	61.110	63.158	0.00	0.00	0.00	3.10
3632	4265	3.134792	GGGCGTGCGAGAGAGAGA	61.135	66.667	0.00	0.00	0.00	3.10
3873	4506	0.539986	ACACGTAGGCCCGATGAAAT	59.460	50.000	8.49	0.00	0.00	2.17

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.