AutoCloner

Multiple sequence alignment - TraesCS5D01G439000

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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	TraesCS5D01G439000	chr5D	100.000	3357	0	0	1	3357	492594361	492591005	0.000000e+00	6200.0
1	TraesCS5D01G439000	chr5D	84.018	1802	217	31	905	2652	492569143	492567359	0.000000e+00	1666.0
2	TraesCS5D01G439000	chr5D	83.901	1702	217	33	902	2570	238177553	238179230	0.000000e+00	1572.0
3	TraesCS5D01G439000	chr5D	92.385	893	52	13	16	900	522116364	522115480	0.000000e+00	1258.0
4	TraesCS5D01G439000	chr5D	91.741	896	59	11	16	900	129715420	129716311	0.000000e+00	1230.0
5	TraesCS5D01G439000	chr5D	93.505	739	24	11	164	901	67771640	67772355	0.000000e+00	1077.0
6	TraesCS5D01G439000	chr5D	93.362	693	23	8	208	900	67765337	67766006	0.000000e+00	1003.0
7	TraesCS5D01G439000	chr5D	77.049	1037	183	41	947	1948	492609707	492608691	2.280000e-151	545.0
8	TraesCS5D01G439000	chr5B	94.335	2277	85	17	901	3163	607845348	607847594	0.000000e+00	3450.0
9	TraesCS5D01G439000	chr5B	90.489	2271	143	29	901	3163	607839077	607841282	0.000000e+00	2929.0
10	TraesCS5D01G439000	chr5B	84.009	1776	218	31	902	2630	607866803	607868559	0.000000e+00	1646.0
11	TraesCS5D01G439000	chr5B	84.375	1568	202	35	902	2441	267301467	267299915	0.000000e+00	1498.0
12	TraesCS5D01G439000	chr5B	81.365	381	59	10	1991	2366	562792179	562791806	1.960000e-77	300.0
13	TraesCS5D01G439000	chr5B	87.500	104	13	0	1505	1608	10348311	10348414	1.640000e-23	121.0
14	TraesCS5D01G439000	chr5B	79.429	175	22	11	2723	2890	618195855	618195688	9.850000e-21	111.0
15	TraesCS5D01G439000	chr5A	92.534	2143	120	24	901	3032	615298173	615300286	0.000000e+00	3035.0
16	TraesCS5D01G439000	chr5A	95.354	1679	64	8	901	2570	615309225	615310898	0.000000e+00	2656.0
17	TraesCS5D01G439000	chr5A	83.871	1674	227	27	902	2543	316513981	316512319	0.000000e+00	1555.0
18	TraesCS5D01G439000	chr5A	83.883	1061	142	16	905	1945	615305264	615306315	0.000000e+00	985.0
19	TraesCS5D01G439000	chr5A	81.842	380	59	8	1991	2366	577929470	577929097	9.040000e-81	311.0
20	TraesCS5D01G439000	chr5A	83.381	349	30	10	2307	2629	615306796	615307142	7.040000e-77	298.0
21	TraesCS5D01G439000	chr5A	97.248	109	3	0	3031	3139	615300391	615300499	5.720000e-43	185.0
22	TraesCS5D01G439000	chr7D	96.930	912	10	2	1	900	138009449	138010354	0.000000e+00	1513.0
23	TraesCS5D01G439000	chr7D	93.900	918	30	4	7	900	136844014	136843099	0.000000e+00	1362.0
24	TraesCS5D01G439000	chr7D	93.736	894	32	8	7	900	328936460	328935591	0.000000e+00	1319.0
25	TraesCS5D01G439000	chr7D	90.642	919	61	11	17	915	530934888	530935801	0.000000e+00	1197.0
26	TraesCS5D01G439000	chr6D	91.676	925	35	12	16	900	79527458	79526536	0.000000e+00	1243.0
27	TraesCS5D01G439000	chr6D	95.960	693	27	1	208	900	345686856	345687547	0.000000e+00	1123.0
28	TraesCS5D01G439000	chr4D	90.829	905	49	17	16	900	385565010	385565900	0.000000e+00	1181.0
29	TraesCS5D01G439000	chr1D	90.403	917	47	16	22	901	154306393	154305481	0.000000e+00	1168.0
30	TraesCS5D01G439000	chr2D	92.680	724	29	12	198	900	416263519	416264239	0.000000e+00	1022.0
31	TraesCS5D01G439000	chr3D	92.785	693	25	9	208	900	281371437	281370770	0.000000e+00	979.0
32	TraesCS5D01G439000	chr4A	95.082	61	3	0	1550	1610	717952178	717952238	2.760000e-16	97.1

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	TraesCS5D01G439000	chr5D	492591005	492594361	3356	True	6200	6200	100.000000	1	3357	1	chr5D.!!$R2	3356
1	TraesCS5D01G439000	chr5D	492567359	492569143	1784	True	1666	1666	84.018000	905	2652	1	chr5D.!!$R1	1747
2	TraesCS5D01G439000	chr5D	238177553	238179230	1677	False	1572	1572	83.901000	902	2570	1	chr5D.!!$F4	1668
3	TraesCS5D01G439000	chr5D	522115480	522116364	884	True	1258	1258	92.385000	16	900	1	chr5D.!!$R4	884
4	TraesCS5D01G439000	chr5D	129715420	129716311	891	False	1230	1230	91.741000	16	900	1	chr5D.!!$F3	884
5	TraesCS5D01G439000	chr5D	67771640	67772355	715	False	1077	1077	93.505000	164	901	1	chr5D.!!$F2	737
6	TraesCS5D01G439000	chr5D	67765337	67766006	669	False	1003	1003	93.362000	208	900	1	chr5D.!!$F1	692
7	TraesCS5D01G439000	chr5D	492608691	492609707	1016	True	545	545	77.049000	947	1948	1	chr5D.!!$R3	1001
8	TraesCS5D01G439000	chr5B	607845348	607847594	2246	False	3450	3450	94.335000	901	3163	1	chr5B.!!$F3	2262
9	TraesCS5D01G439000	chr5B	607839077	607841282	2205	False	2929	2929	90.489000	901	3163	1	chr5B.!!$F2	2262
10	TraesCS5D01G439000	chr5B	607866803	607868559	1756	False	1646	1646	84.009000	902	2630	1	chr5B.!!$F4	1728
11	TraesCS5D01G439000	chr5B	267299915	267301467	1552	True	1498	1498	84.375000	902	2441	1	chr5B.!!$R1	1539
12	TraesCS5D01G439000	chr5A	615298173	615300499	2326	False	1610	3035	94.891000	901	3139	2	chr5A.!!$F1	2238
13	TraesCS5D01G439000	chr5A	316512319	316513981	1662	True	1555	1555	83.871000	902	2543	1	chr5A.!!$R1	1641
14	TraesCS5D01G439000	chr5A	615305264	615310898	5634	False	1313	2656	87.539333	901	2629	3	chr5A.!!$F2	1728
15	TraesCS5D01G439000	chr7D	138009449	138010354	905	False	1513	1513	96.930000	1	900	1	chr7D.!!$F1	899
16	TraesCS5D01G439000	chr7D	136843099	136844014	915	True	1362	1362	93.900000	7	900	1	chr7D.!!$R1	893
17	TraesCS5D01G439000	chr7D	328935591	328936460	869	True	1319	1319	93.736000	7	900	1	chr7D.!!$R2	893
18	TraesCS5D01G439000	chr7D	530934888	530935801	913	False	1197	1197	90.642000	17	915	1	chr7D.!!$F2	898
19	TraesCS5D01G439000	chr6D	79526536	79527458	922	True	1243	1243	91.676000	16	900	1	chr6D.!!$R1	884
20	TraesCS5D01G439000	chr6D	345686856	345687547	691	False	1123	1123	95.960000	208	900	1	chr6D.!!$F1	692
21	TraesCS5D01G439000	chr4D	385565010	385565900	890	False	1181	1181	90.829000	16	900	1	chr4D.!!$F1	884
22	TraesCS5D01G439000	chr1D	154305481	154306393	912	True	1168	1168	90.403000	22	901	1	chr1D.!!$R1	879
23	TraesCS5D01G439000	chr2D	416263519	416264239	720	False	1022	1022	92.680000	198	900	1	chr2D.!!$F1	702
24	TraesCS5D01G439000	chr3D	281370770	281371437	667	True	979	979	92.785000	208	900	1	chr3D.!!$R1	692

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	Self end TH	Hairpin	End Stability	Orientation
969	1165	0.830444	TGGTAGTCCAACGGCTGACT	60.83	55.0	0.0	7.88	43.85	3.41	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2546	6761	1.379443	CCACACCATGAGCAGCCAT	60.379	57.895	0.0	0.0	0.0	4.4	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
20	21	1.065418	CAGGATTTAAGCCGGGTCAGT	60.065	52.381	6.62	0.00	0.00	3.41
177	181	8.185505	TGTTGTTTTACAGGATCAGTTTAACAC	58.814	33.333	0.00	10.06	0.00	3.32
389	439	2.047844	CCCGGCAGACACAGTCAG	60.048	66.667	0.00	0.00	34.60	3.51
953	1148	1.339055	CCGTCAATGACTGGATGTGGT	60.339	52.381	15.66	0.00	31.51	4.16
969	1165	0.830444	TGGTAGTCCAACGGCTGACT	60.830	55.000	0.00	7.88	43.85	3.41
1021	1217	0.314818	GCGACGCTATGTTAAACGGC	60.315	55.000	13.73	0.00	0.00	5.68
1043	1239	3.976701	ATGCGTTCCTTCTGCCCCG	62.977	63.158	0.00	0.00	0.00	5.73
1056	1252	2.569354	GCCCCGCACCAATGTTCAA	61.569	57.895	0.00	0.00	0.00	2.69
1069	1265	4.454161	CCAATGTTCAACAACGGTCTATCA	59.546	41.667	0.00	0.00	34.95	2.15
2068	6256	3.068732	GTGCTGCAGGATCACTAGATGTA	59.931	47.826	17.12	0.00	33.72	2.29
2382	6573	1.593196	GTAGAAGTGTTGCTGTGCCA	58.407	50.000	0.00	0.00	0.00	4.92
2450	6645	6.720112	AATGATTATGTTATGCTGGCTTGT	57.280	33.333	0.00	0.00	0.00	3.16
2451	6646	5.503662	TGATTATGTTATGCTGGCTTGTG	57.496	39.130	0.00	0.00	0.00	3.33
2484	6684	5.811399	ACATGTGTTTGTATTGGGTATCG	57.189	39.130	0.00	0.00	0.00	2.92
2546	6761	4.851843	AGCTGTTGAGATGATTGATTCCA	58.148	39.130	0.00	0.00	0.00	3.53
2578	6801	1.686052	GGTGTGGCTTGAAATCACCAA	59.314	47.619	7.61	0.00	45.22	3.67
2607	6832	9.285770	GTACGCCTAAAAGATATTTTTCCTTTG	57.714	33.333	2.97	0.00	31.30	2.77
2753	6980	7.861872	CCAAAAGCAAATGAACCCTTTTTATTG	59.138	33.333	0.00	0.00	35.88	1.90
3154	7491	5.139435	TCCTGGATATGCTTCGTATTCTG	57.861	43.478	0.00	0.00	0.00	3.02
3163	7500	4.460263	TGCTTCGTATTCTGCCCAATATT	58.540	39.130	0.00	0.00	0.00	1.28
3164	7501	4.887071	TGCTTCGTATTCTGCCCAATATTT	59.113	37.500	0.00	0.00	0.00	1.40
3165	7502	5.359576	TGCTTCGTATTCTGCCCAATATTTT	59.640	36.000	0.00	0.00	0.00	1.82
3166	7503	6.127479	TGCTTCGTATTCTGCCCAATATTTTT	60.127	34.615	0.00	0.00	0.00	1.94
3186	7523	5.549742	TTTTTGAGACATTTCTGCCCAAT	57.450	34.783	0.00	0.00	29.47	3.16
3187	7524	6.662865	TTTTTGAGACATTTCTGCCCAATA	57.337	33.333	0.00	0.00	29.47	1.90
3188	7525	6.855763	TTTTGAGACATTTCTGCCCAATAT	57.144	33.333	0.00	0.00	29.47	1.28
3189	7526	7.953005	TTTTGAGACATTTCTGCCCAATATA	57.047	32.000	0.00	0.00	29.47	0.86
3190	7527	7.953005	TTTGAGACATTTCTGCCCAATATAA	57.047	32.000	0.00	0.00	29.47	0.98
3191	7528	8.537728	TTTGAGACATTTCTGCCCAATATAAT	57.462	30.769	0.00	0.00	29.47	1.28
3192	7529	8.537728	TTGAGACATTTCTGCCCAATATAATT	57.462	30.769	0.00	0.00	29.47	1.40
3193	7530	7.944061	TGAGACATTTCTGCCCAATATAATTG	58.056	34.615	0.00	0.00	29.47	2.32
3194	7531	7.779326	TGAGACATTTCTGCCCAATATAATTGA	59.221	33.333	1.23	0.00	29.47	2.57
3195	7532	7.945134	AGACATTTCTGCCCAATATAATTGAC	58.055	34.615	1.23	0.00	0.00	3.18
3196	7533	7.560991	AGACATTTCTGCCCAATATAATTGACA	59.439	33.333	1.23	0.00	0.00	3.58
3197	7534	8.253867	ACATTTCTGCCCAATATAATTGACAT	57.746	30.769	1.23	0.00	0.00	3.06
3198	7535	9.365906	ACATTTCTGCCCAATATAATTGACATA	57.634	29.630	1.23	0.00	0.00	2.29
3202	7539	9.812347	TTCTGCCCAATATAATTGACATAATCT	57.188	29.630	1.23	0.00	0.00	2.40
3203	7540	9.453572	TCTGCCCAATATAATTGACATAATCTC	57.546	33.333	1.23	0.00	0.00	2.75
3204	7541	8.579850	TGCCCAATATAATTGACATAATCTCC	57.420	34.615	1.23	0.00	0.00	3.71
3205	7542	7.615365	TGCCCAATATAATTGACATAATCTCCC	59.385	37.037	1.23	0.00	0.00	4.30
3206	7543	7.615365	GCCCAATATAATTGACATAATCTCCCA	59.385	37.037	1.23	0.00	0.00	4.37
3207	7544	9.532494	CCCAATATAATTGACATAATCTCCCAA	57.468	33.333	1.23	0.00	0.00	4.12
3218	7555	9.967451	TGACATAATCTCCCAACTTATAAAACA	57.033	29.630	0.00	0.00	0.00	2.83
3224	7561	9.927668	AATCTCCCAACTTATAAAACATTTGTG	57.072	29.630	0.00	0.00	0.00	3.33
3225	7562	8.472007	TCTCCCAACTTATAAAACATTTGTGT	57.528	30.769	0.00	0.00	0.00	3.72
3226	7563	8.356657	TCTCCCAACTTATAAAACATTTGTGTG	58.643	33.333	0.00	0.00	0.00	3.82
3227	7564	8.012957	TCCCAACTTATAAAACATTTGTGTGT	57.987	30.769	0.00	0.00	0.00	3.72
3228	7565	7.923344	TCCCAACTTATAAAACATTTGTGTGTG	59.077	33.333	0.00	0.00	31.49	3.82
3229	7566	7.307101	CCCAACTTATAAAACATTTGTGTGTGC	60.307	37.037	0.00	0.00	31.49	4.57
3230	7567	6.984740	ACTTATAAAACATTTGTGTGTGCG	57.015	33.333	0.00	0.00	31.49	5.34
3231	7568	6.500041	ACTTATAAAACATTTGTGTGTGCGT	58.500	32.000	0.00	0.00	31.49	5.24
3232	7569	6.416455	ACTTATAAAACATTTGTGTGTGCGTG	59.584	34.615	0.00	0.00	31.49	5.34
3233	7570	2.645730	AAACATTTGTGTGTGCGTGT	57.354	40.000	0.00	0.00	31.49	4.49
3234	7571	2.645730	AACATTTGTGTGTGCGTGTT	57.354	40.000	0.00	0.00	31.49	3.32
3235	7572	2.645730	ACATTTGTGTGTGCGTGTTT	57.354	40.000	0.00	0.00	0.00	2.83
3236	7573	2.953020	ACATTTGTGTGTGCGTGTTTT	58.047	38.095	0.00	0.00	0.00	2.43
3237	7574	3.321497	ACATTTGTGTGTGCGTGTTTTT	58.679	36.364	0.00	0.00	0.00	1.94
3263	7600	2.772568	TTGAGGAAATTGTGTGTGCG	57.227	45.000	0.00	0.00	0.00	5.34
3264	7601	1.674359	TGAGGAAATTGTGTGTGCGT	58.326	45.000	0.00	0.00	0.00	5.24
3265	7602	1.333308	TGAGGAAATTGTGTGTGCGTG	59.667	47.619	0.00	0.00	0.00	5.34
3266	7603	1.333619	GAGGAAATTGTGTGTGCGTGT	59.666	47.619	0.00	0.00	0.00	4.49
3267	7604	1.065401	AGGAAATTGTGTGTGCGTGTG	59.935	47.619	0.00	0.00	0.00	3.82
3268	7605	1.202245	GGAAATTGTGTGTGCGTGTGT	60.202	47.619	0.00	0.00	0.00	3.72
3269	7606	1.845568	GAAATTGTGTGTGCGTGTGTG	59.154	47.619	0.00	0.00	0.00	3.82
3270	7607	0.808125	AATTGTGTGTGCGTGTGTGT	59.192	45.000	0.00	0.00	0.00	3.72
3271	7608	0.098552	ATTGTGTGTGCGTGTGTGTG	59.901	50.000	0.00	0.00	0.00	3.82
3272	7609	1.231296	TTGTGTGTGCGTGTGTGTGT	61.231	50.000	0.00	0.00	0.00	3.72
3273	7610	1.231296	TGTGTGTGCGTGTGTGTGTT	61.231	50.000	0.00	0.00	0.00	3.32
3274	7611	0.520412	GTGTGTGCGTGTGTGTGTTC	60.520	55.000	0.00	0.00	0.00	3.18
3275	7612	1.296577	GTGTGCGTGTGTGTGTTCG	60.297	57.895	0.00	0.00	0.00	3.95
3276	7613	1.738464	TGTGCGTGTGTGTGTTCGT	60.738	52.632	0.00	0.00	0.00	3.85
3277	7614	1.296577	GTGCGTGTGTGTGTTCGTG	60.297	57.895	0.00	0.00	0.00	4.35
3278	7615	2.323105	GCGTGTGTGTGTTCGTGG	59.677	61.111	0.00	0.00	0.00	4.94
3279	7616	2.323105	CGTGTGTGTGTTCGTGGC	59.677	61.111	0.00	0.00	0.00	5.01
3280	7617	2.171079	CGTGTGTGTGTTCGTGGCT	61.171	57.895	0.00	0.00	0.00	4.75
3281	7618	1.701545	CGTGTGTGTGTTCGTGGCTT	61.702	55.000	0.00	0.00	0.00	4.35
3282	7619	0.027586	GTGTGTGTGTTCGTGGCTTC	59.972	55.000	0.00	0.00	0.00	3.86
3283	7620	0.391793	TGTGTGTGTTCGTGGCTTCA	60.392	50.000	0.00	0.00	0.00	3.02
3284	7621	0.027586	GTGTGTGTTCGTGGCTTCAC	59.972	55.000	0.00	0.00	38.00	3.18
3292	7629	3.102097	GTGGCTTCACGCTATGCC	58.898	61.111	7.37	7.37	45.10	4.40
3293	7630	2.124736	TGGCTTCACGCTATGCCC	60.125	61.111	10.76	0.00	44.32	5.36
3294	7631	3.272334	GGCTTCACGCTATGCCCG	61.272	66.667	3.79	0.00	39.49	6.13
3295	7632	2.511600	GCTTCACGCTATGCCCGT	60.512	61.111	0.00	0.00	39.91	5.28
3296	7633	2.106683	GCTTCACGCTATGCCCGTT	61.107	57.895	0.00	0.00	36.69	4.44
3297	7634	1.715585	CTTCACGCTATGCCCGTTG	59.284	57.895	0.00	0.00	36.69	4.10
3298	7635	2.309764	CTTCACGCTATGCCCGTTGC	62.310	60.000	0.00	0.00	36.69	4.17
3302	7639	3.573491	GCTATGCCCGTTGCGACC	61.573	66.667	0.00	0.00	45.60	4.79
3303	7640	2.895372	CTATGCCCGTTGCGACCC	60.895	66.667	0.00	0.00	45.60	4.46
3304	7641	3.673956	CTATGCCCGTTGCGACCCA	62.674	63.158	0.00	0.00	45.60	4.51
3305	7642	2.940890	CTATGCCCGTTGCGACCCAT	62.941	60.000	0.00	2.01	45.60	4.00
3306	7643	2.933878	TATGCCCGTTGCGACCCATC	62.934	60.000	0.00	0.00	45.60	3.51
3308	7645	2.819595	CCCGTTGCGACCCATCAG	60.820	66.667	0.00	0.00	0.00	2.90
3309	7646	2.264480	CCGTTGCGACCCATCAGA	59.736	61.111	0.00	0.00	0.00	3.27
3310	7647	1.811266	CCGTTGCGACCCATCAGAG	60.811	63.158	0.00	0.00	0.00	3.35
3311	7648	1.215382	CGTTGCGACCCATCAGAGA	59.785	57.895	0.00	0.00	0.00	3.10
3312	7649	0.803768	CGTTGCGACCCATCAGAGAG	60.804	60.000	0.00	0.00	0.00	3.20
3313	7650	1.086634	GTTGCGACCCATCAGAGAGC	61.087	60.000	0.00	0.00	0.00	4.09
3314	7651	1.543944	TTGCGACCCATCAGAGAGCA	61.544	55.000	0.00	0.00	0.00	4.26
3315	7652	1.227205	GCGACCCATCAGAGAGCAG	60.227	63.158	0.00	0.00	0.00	4.24
3316	7653	1.227205	CGACCCATCAGAGAGCAGC	60.227	63.158	0.00	0.00	0.00	5.25
3317	7654	1.227205	GACCCATCAGAGAGCAGCG	60.227	63.158	0.00	0.00	0.00	5.18
3318	7655	1.954362	GACCCATCAGAGAGCAGCGT	61.954	60.000	0.00	0.00	0.00	5.07
3319	7656	0.684479	ACCCATCAGAGAGCAGCGTA	60.684	55.000	0.00	0.00	0.00	4.42
3320	7657	0.031857	CCCATCAGAGAGCAGCGTAG	59.968	60.000	0.00	0.00	0.00	3.51
3321	7658	0.031857	CCATCAGAGAGCAGCGTAGG	59.968	60.000	0.00	0.00	0.00	3.18
3322	7659	0.597118	CATCAGAGAGCAGCGTAGGC	60.597	60.000	0.00	0.00	40.37	3.93
3339	7676	4.537433	CTCAGGCCTGCTACCGCC	62.537	72.222	28.91	0.00	46.09	6.13
3346	7683	4.845580	CTGCTACCGCCCAGGCAG	62.846	72.222	9.78	0.00	46.52	4.85
3355	7692	3.644606	CCCAGGCAGGCAGTCAGT	61.645	66.667	0.00	0.00	35.39	3.41
3356	7693	2.046507	CCAGGCAGGCAGTCAGTC	60.047	66.667	0.00	0.00	0.00	3.51

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
389	439	1.375523	CTGTGTCTGCCGGGTTACC	60.376	63.158	2.18	0.00	0.00	2.85
953	1148	1.180029	GGTAGTCAGCCGTTGGACTA	58.820	55.000	0.00	0.00	42.30	2.59
969	1165	1.624312	TCATAACGTTGCAGGTGGGTA	59.376	47.619	11.99	0.00	0.00	3.69
1021	1217	0.449388	GGCAGAAGGAACGCATTCAG	59.551	55.000	0.00	0.00	37.28	3.02
1043	1239	1.202359	ACCGTTGTTGAACATTGGTGC	60.202	47.619	17.71	0.00	35.49	5.01
1056	1252	3.258372	TCAGCTTCTTGATAGACCGTTGT	59.742	43.478	0.00	0.00	0.00	3.32
2223	6411	2.354072	CGAGCTCCCGATCTTCGC	60.354	66.667	8.47	0.00	38.82	4.70
2382	6573	2.100989	CCTACAGAACGGAAGGCTACT	58.899	52.381	0.00	0.00	0.00	2.57
2450	6645	6.757897	ACAAACACATGTTCTTCTTTCTCA	57.242	33.333	0.00	0.00	37.25	3.27
2451	6646	9.173939	CAATACAAACACATGTTCTTCTTTCTC	57.826	33.333	0.00	0.00	37.25	2.87
2484	6684	3.602390	TCGAGCAAAAGTAAAGCACAC	57.398	42.857	0.00	0.00	0.00	3.82
2546	6761	1.379443	CCACACCATGAGCAGCCAT	60.379	57.895	0.00	0.00	0.00	4.40
2578	6801	9.185680	AGGAAAAATATCTTTTAGGCGTACAAT	57.814	29.630	0.00	0.00	33.44	2.71
2753	6980	6.948589	ACCTCTATTTTCAGGGTTCTAGAAC	58.051	40.000	24.73	24.73	40.45	3.01
3164	7501	5.549742	ATTGGGCAGAAATGTCTCAAAAA	57.450	34.783	0.00	0.00	28.78	1.94
3165	7502	6.855763	ATATTGGGCAGAAATGTCTCAAAA	57.144	33.333	0.00	0.00	28.78	2.44
3166	7503	7.953005	TTATATTGGGCAGAAATGTCTCAAA	57.047	32.000	0.00	0.00	28.78	2.69
3167	7504	8.415553	CAATTATATTGGGCAGAAATGTCTCAA	58.584	33.333	0.00	0.00	28.78	3.02
3168	7505	7.779326	TCAATTATATTGGGCAGAAATGTCTCA	59.221	33.333	0.00	0.00	28.78	3.27
3169	7506	8.078596	GTCAATTATATTGGGCAGAAATGTCTC	58.921	37.037	0.00	0.00	28.78	3.36
3170	7507	7.560991	TGTCAATTATATTGGGCAGAAATGTCT	59.439	33.333	0.00	0.00	32.85	3.41
3171	7508	7.715657	TGTCAATTATATTGGGCAGAAATGTC	58.284	34.615	0.00	0.00	0.00	3.06
3172	7509	7.658525	TGTCAATTATATTGGGCAGAAATGT	57.341	32.000	0.00	0.00	0.00	2.71
3176	7513	9.812347	AGATTATGTCAATTATATTGGGCAGAA	57.188	29.630	0.00	0.00	0.00	3.02
3177	7514	9.453572	GAGATTATGTCAATTATATTGGGCAGA	57.546	33.333	0.00	0.00	0.00	4.26
3178	7515	8.680903	GGAGATTATGTCAATTATATTGGGCAG	58.319	37.037	0.00	0.00	0.00	4.85
3179	7516	7.615365	GGGAGATTATGTCAATTATATTGGGCA	59.385	37.037	0.00	0.00	0.00	5.36
3180	7517	7.615365	TGGGAGATTATGTCAATTATATTGGGC	59.385	37.037	0.00	0.00	0.00	5.36
3181	7518	9.532494	TTGGGAGATTATGTCAATTATATTGGG	57.468	33.333	0.00	0.00	0.00	4.12
3192	7529	9.967451	TGTTTTATAAGTTGGGAGATTATGTCA	57.033	29.630	0.00	0.00	0.00	3.58
3198	7535	9.927668	CACAAATGTTTTATAAGTTGGGAGATT	57.072	29.630	0.00	0.00	0.00	2.40
3199	7536	9.088987	ACACAAATGTTTTATAAGTTGGGAGAT	57.911	29.630	0.00	0.00	34.46	2.75
3200	7537	8.356657	CACACAAATGTTTTATAAGTTGGGAGA	58.643	33.333	0.00	0.00	36.72	3.71
3201	7538	8.141268	ACACACAAATGTTTTATAAGTTGGGAG	58.859	33.333	0.00	0.00	36.72	4.30
3202	7539	7.923344	CACACACAAATGTTTTATAAGTTGGGA	59.077	33.333	0.00	0.00	36.72	4.37
3203	7540	7.307101	GCACACACAAATGTTTTATAAGTTGGG	60.307	37.037	0.00	0.00	36.72	4.12
3204	7541	7.563270	GCACACACAAATGTTTTATAAGTTGG	58.437	34.615	0.00	0.00	36.72	3.77
3205	7542	7.043722	ACGCACACACAAATGTTTTATAAGTTG	60.044	33.333	0.00	0.00	36.72	3.16
3206	7543	6.975772	ACGCACACACAAATGTTTTATAAGTT	59.024	30.769	0.00	0.00	36.72	2.66
3207	7544	6.416455	CACGCACACACAAATGTTTTATAAGT	59.584	34.615	0.00	0.00	36.72	2.24
3208	7545	6.416455	ACACGCACACACAAATGTTTTATAAG	59.584	34.615	0.00	0.00	36.72	1.73
3209	7546	6.266323	ACACGCACACACAAATGTTTTATAA	58.734	32.000	0.00	0.00	36.72	0.98
3210	7547	5.822278	ACACGCACACACAAATGTTTTATA	58.178	33.333	0.00	0.00	36.72	0.98
3211	7548	4.677584	ACACGCACACACAAATGTTTTAT	58.322	34.783	0.00	0.00	36.72	1.40
3212	7549	4.098055	ACACGCACACACAAATGTTTTA	57.902	36.364	0.00	0.00	36.72	1.52
3213	7550	2.953020	ACACGCACACACAAATGTTTT	58.047	38.095	0.00	0.00	36.72	2.43
3214	7551	2.645730	ACACGCACACACAAATGTTT	57.354	40.000	0.00	0.00	36.72	2.83
3215	7552	2.645730	AACACGCACACACAAATGTT	57.354	40.000	0.00	0.00	36.72	2.71
3216	7553	2.645730	AAACACGCACACACAAATGT	57.354	40.000	0.00	0.00	40.80	2.71
3217	7554	3.987807	AAAAACACGCACACACAAATG	57.012	38.095	0.00	0.00	0.00	2.32
3241	7578	3.862267	CGCACACACAATTTCCTCAAAAA	59.138	39.130	0.00	0.00	0.00	1.94
3242	7579	3.119316	ACGCACACACAATTTCCTCAAAA	60.119	39.130	0.00	0.00	0.00	2.44
3243	7580	2.425312	ACGCACACACAATTTCCTCAAA	59.575	40.909	0.00	0.00	0.00	2.69
3244	7581	2.020720	ACGCACACACAATTTCCTCAA	58.979	42.857	0.00	0.00	0.00	3.02
3245	7582	1.333308	CACGCACACACAATTTCCTCA	59.667	47.619	0.00	0.00	0.00	3.86
3246	7583	1.333619	ACACGCACACACAATTTCCTC	59.666	47.619	0.00	0.00	0.00	3.71
3247	7584	1.065401	CACACGCACACACAATTTCCT	59.935	47.619	0.00	0.00	0.00	3.36
3248	7585	1.202245	ACACACGCACACACAATTTCC	60.202	47.619	0.00	0.00	0.00	3.13
3249	7586	1.845568	CACACACGCACACACAATTTC	59.154	47.619	0.00	0.00	0.00	2.17
3250	7587	1.201181	ACACACACGCACACACAATTT	59.799	42.857	0.00	0.00	0.00	1.82
3251	7588	0.808125	ACACACACGCACACACAATT	59.192	45.000	0.00	0.00	0.00	2.32
3252	7589	0.098552	CACACACACGCACACACAAT	59.901	50.000	0.00	0.00	0.00	2.71
3253	7590	1.231296	ACACACACACGCACACACAA	61.231	50.000	0.00	0.00	0.00	3.33
3254	7591	1.231296	AACACACACACGCACACACA	61.231	50.000	0.00	0.00	0.00	3.72
3255	7592	0.520412	GAACACACACACGCACACAC	60.520	55.000	0.00	0.00	0.00	3.82
3256	7593	1.791024	GAACACACACACGCACACA	59.209	52.632	0.00	0.00	0.00	3.72
3257	7594	1.296577	CGAACACACACACGCACAC	60.297	57.895	0.00	0.00	0.00	3.82
3258	7595	1.738464	ACGAACACACACACGCACA	60.738	52.632	0.00	0.00	0.00	4.57
3259	7596	1.296577	CACGAACACACACACGCAC	60.297	57.895	0.00	0.00	0.00	5.34
3260	7597	2.456948	CCACGAACACACACACGCA	61.457	57.895	0.00	0.00	0.00	5.24
3261	7598	2.323105	CCACGAACACACACACGC	59.677	61.111	0.00	0.00	0.00	5.34
3262	7599	1.701545	AAGCCACGAACACACACACG	61.702	55.000	0.00	0.00	0.00	4.49
3263	7600	0.027586	GAAGCCACGAACACACACAC	59.972	55.000	0.00	0.00	0.00	3.82
3264	7601	0.391793	TGAAGCCACGAACACACACA	60.392	50.000	0.00	0.00	0.00	3.72
3265	7602	0.027586	GTGAAGCCACGAACACACAC	59.972	55.000	0.00	0.00	33.10	3.82
3266	7603	2.389386	GTGAAGCCACGAACACACA	58.611	52.632	0.00	0.00	33.10	3.72
3279	7616	1.715585	CAACGGGCATAGCGTGAAG	59.284	57.895	0.00	0.00	0.00	3.02
3280	7617	2.395360	GCAACGGGCATAGCGTGAA	61.395	57.895	0.00	0.00	43.97	3.18
3281	7618	2.817834	GCAACGGGCATAGCGTGA	60.818	61.111	0.00	0.00	43.97	4.35
3282	7619	4.222589	CGCAACGGGCATAGCGTG	62.223	66.667	0.00	0.00	45.17	5.34
3285	7622	3.573491	GGTCGCAACGGGCATAGC	61.573	66.667	2.26	0.00	45.17	2.97
3286	7623	2.895372	GGGTCGCAACGGGCATAG	60.895	66.667	2.26	0.00	45.17	2.23
3287	7624	2.933878	GATGGGTCGCAACGGGCATA	62.934	60.000	0.00	0.00	45.17	3.14
3288	7625	4.424711	ATGGGTCGCAACGGGCAT	62.425	61.111	0.00	0.00	45.17	4.40
3291	7628	2.819595	CTGATGGGTCGCAACGGG	60.820	66.667	0.00	0.00	0.00	5.28
3292	7629	1.811266	CTCTGATGGGTCGCAACGG	60.811	63.158	0.00	0.00	0.00	4.44
3293	7630	0.803768	CTCTCTGATGGGTCGCAACG	60.804	60.000	0.00	0.00	0.00	4.10
3294	7631	1.086634	GCTCTCTGATGGGTCGCAAC	61.087	60.000	0.00	0.00	0.00	4.17
3295	7632	1.219124	GCTCTCTGATGGGTCGCAA	59.781	57.895	0.00	0.00	0.00	4.85
3296	7633	1.953231	CTGCTCTCTGATGGGTCGCA	61.953	60.000	0.00	0.00	0.00	5.10
3297	7634	1.227205	CTGCTCTCTGATGGGTCGC	60.227	63.158	0.00	0.00	0.00	5.19
3298	7635	1.227205	GCTGCTCTCTGATGGGTCG	60.227	63.158	0.00	0.00	0.00	4.79
3299	7636	1.227205	CGCTGCTCTCTGATGGGTC	60.227	63.158	0.00	0.00	0.00	4.46
3300	7637	0.684479	TACGCTGCTCTCTGATGGGT	60.684	55.000	0.00	0.00	0.00	4.51
3301	7638	0.031857	CTACGCTGCTCTCTGATGGG	59.968	60.000	0.00	0.00	0.00	4.00
3302	7639	0.031857	CCTACGCTGCTCTCTGATGG	59.968	60.000	0.00	0.00	0.00	3.51
3303	7640	0.597118	GCCTACGCTGCTCTCTGATG	60.597	60.000	0.00	0.00	0.00	3.07
3304	7641	0.754957	AGCCTACGCTGCTCTCTGAT	60.755	55.000	0.00	0.00	46.19	2.90
3305	7642	1.379176	AGCCTACGCTGCTCTCTGA	60.379	57.895	0.00	0.00	46.19	3.27
3306	7643	3.205395	AGCCTACGCTGCTCTCTG	58.795	61.111	0.00	0.00	46.19	3.35
3322	7659	4.537433	GGCGGTAGCAGGCCTGAG	62.537	72.222	37.21	20.31	45.93	3.35
3338	7675	3.618780	GACTGACTGCCTGCCTGGG	62.619	68.421	0.00	0.00	36.00	4.45
3339	7676	2.046507	GACTGACTGCCTGCCTGG	60.047	66.667	0.00	0.00	39.35	4.45

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.