AutoCloner

Multiple sequence alignment - TraesCS5A01G031300

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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	TraesCS5A01G031300	chr5A	100.000	3786	0	0	1	3786	28903617	28907402	0.000000e+00	6992.0
1	TraesCS5A01G031300	chr5A	78.771	1432	232	41	1	1418	28757703	28759076	0.000000e+00	894.0
2	TraesCS5A01G031300	chr5A	83.145	795	99	19	154	943	28756492	28757256	0.000000e+00	693.0
3	TraesCS5A01G031300	chr5A	78.788	264	27	13	1933	2194	28761542	28761778	2.360000e-32	150.0
4	TraesCS5A01G031300	chr5D	89.891	1474	109	17	2319	3786	40766141	40767580	0.000000e+00	1860.0
5	TraesCS5A01G031300	chr5D	92.672	1078	66	5	861	1933	40759689	40760758	0.000000e+00	1541.0
6	TraesCS5A01G031300	chr5D	95.011	441	22	0	379	819	40759255	40759695	0.000000e+00	693.0
7	TraesCS5A01G031300	chr5D	82.850	758	66	20	1933	2671	40889284	40889996	4.150000e-174	621.0
8	TraesCS5A01G031300	chr5D	93.860	342	15	2	1	341	40758919	40759255	9.380000e-141	510.0
9	TraesCS5A01G031300	chr5D	84.698	464	50	7	1941	2402	40745819	40746263	9.650000e-121	444.0
10	TraesCS5A01G031300	chr5D	87.291	299	27	5	2631	2928	40889911	40890199	7.840000e-87	331.0
11	TraesCS5A01G031300	chr5D	88.797	241	16	3	1704	1933	40889005	40889245	6.190000e-73	285.0
12	TraesCS5A01G031300	chr5D	83.673	294	41	5	3153	3441	40783805	40784096	1.730000e-68	270.0
13	TraesCS5A01G031300	chr5D	87.611	113	12	2	2925	3036	40906775	40906886	3.070000e-26	130.0
14	TraesCS5A01G031300	chr5D	82.000	100	17	1	158	256	391294492	391294591	2.420000e-12	84.2
15	TraesCS5A01G031300	chr5B	88.994	1372	130	4	1	1371	34542901	34544252	0.000000e+00	1677.0
16	TraesCS5A01G031300	chr5B	91.667	768	48	10	1933	2688	34565986	34566749	0.000000e+00	1050.0
17	TraesCS5A01G031300	chr5B	90.148	812	62	11	1933	2736	34555280	34556081	0.000000e+00	1040.0
18	TraesCS5A01G031300	chr5B	89.843	827	44	16	2319	3142	34545011	34545800	0.000000e+00	1026.0
19	TraesCS5A01G031300	chr5B	79.102	1426	243	35	1	1410	34287004	34288390	0.000000e+00	931.0
20	TraesCS5A01G031300	chr5B	91.636	550	26	8	1395	1933	34544245	34544785	0.000000e+00	743.0
21	TraesCS5A01G031300	chr5B	85.255	746	79	12	2592	3333	34566689	34567407	0.000000e+00	739.0
22	TraesCS5A01G031300	chr5B	87.520	633	49	14	1306	1933	34554635	34555242	0.000000e+00	704.0
23	TraesCS5A01G031300	chr5B	86.106	511	57	7	2592	3102	34555982	34556478	4.300000e-149	538.0
24	TraesCS5A01G031300	chr5B	89.924	397	18	9	1538	1933	34565573	34565948	3.400000e-135	492.0
25	TraesCS5A01G031300	chr5B	88.235	289	18	8	1649	1933	34608823	34609099	7.840000e-87	331.0
26	TraesCS5A01G031300	chr5B	81.527	406	51	11	1999	2402	34486260	34486643	2.840000e-81	313.0
27	TraesCS5A01G031300	chr5B	84.407	295	20	7	1550	1831	34288739	34289020	2.240000e-67	267.0
28	TraesCS5A01G031300	chr5B	76.304	460	88	15	870	1316	615947987	615948438	3.810000e-55	226.0
29	TraesCS5A01G031300	chr5B	85.646	209	23	4	1306	1511	34565372	34565576	2.960000e-51	213.0
30	TraesCS5A01G031300	chr5B	91.724	145	10	2	1487	1629	34607433	34607577	2.310000e-47	200.0
31	TraesCS5A01G031300	chr5B	83.163	196	22	7	1934	2129	34544827	34545011	6.500000e-38	169.0
32	TraesCS5A01G031300	chr1D	76.370	584	103	25	191	769	28069094	28069647	8.010000e-72	281.0
33	TraesCS5A01G031300	chr1D	87.500	80	10	0	613	692	18918395	18918316	4.030000e-15	93.5
34	TraesCS5A01G031300	chr7B	75.591	508	105	12	950	1443	565873460	565872958	2.270000e-57	233.0
35	TraesCS5A01G031300	chr7B	82.486	177	25	4	3610	3785	721090344	721090173	2.360000e-32	150.0
36	TraesCS5A01G031300	chr6A	76.726	391	75	13	130	512	51515553	51515935	1.780000e-48	204.0
37	TraesCS5A01G031300	chr6B	77.160	324	58	14	949	1263	67326536	67326220	1.400000e-39	174.0
38	TraesCS5A01G031300	chr6B	75.573	393	71	18	264	654	96887644	96887275	1.810000e-38	171.0
39	TraesCS5A01G031300	chr7D	83.333	180	24	5	3609	3786	538606006	538605831	1.090000e-35	161.0
40	TraesCS5A01G031300	chr7D	83.529	170	24	3	3609	3777	6755559	6755725	5.060000e-34	156.0
41	TraesCS5A01G031300	chr3A	83.523	176	26	2	3612	3786	749182806	749182633	1.090000e-35	161.0
42	TraesCS5A01G031300	chr4D	85.065	154	21	1	3633	3786	385521183	385521334	5.060000e-34	156.0
43	TraesCS5A01G031300	chr4A	83.735	166	23	3	3610	3775	631023495	631023334	1.820000e-33	154.0
44	TraesCS5A01G031300	chr1A	72.890	557	107	32	576	1125	487494310	487493791	6.550000e-33	152.0
45	TraesCS5A01G031300	chr1B	82.222	180	27	4	3609	3786	668508671	668508495	2.360000e-32	150.0
46	TraesCS5A01G031300	chr1B	82.249	169	26	3	191	358	44506182	44506347	3.940000e-30	143.0
47	TraesCS5A01G031300	chr3B	82.222	180	23	5	3608	3785	775734315	775734487	3.050000e-31	147.0
48	TraesCS5A01G031300	chr2A	77.155	232	42	10	934	1160	42793851	42794076	1.430000e-24	124.0
49	TraesCS5A01G031300	chr2A	77.056	231	44	8	934	1160	43123735	43123960	1.430000e-24	124.0
50	TraesCS5A01G031300	chr2A	77.654	179	39	1	939	1117	43002903	43003080	1.440000e-19	108.0
51	TraesCS5A01G031300	chr7A	77.333	225	40	5	1049	1263	54725460	54725237	5.140000e-24	122.0
52	TraesCS5A01G031300	chr3D	74.839	310	55	14	226	527	39601110	39600816	6.640000e-23	119.0
53	TraesCS5A01G031300	chr3D	80.460	87	13	4	191	275	175122945	175122861	3.160000e-06	63.9
54	TraesCS5A01G031300	chr2B	82.051	117	17	3	576	690	35401108	35401222	3.110000e-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	TraesCS5A01G031300	chr5A	28903617	28907402	3785	False	6992.000000	6992	100.000000	1	3786	1	chr5A.!!$F1	3785
1	TraesCS5A01G031300	chr5A	28756492	28761778	5286	False	579.000000	894	80.234667	1	2194	3	chr5A.!!$F2	2193
2	TraesCS5A01G031300	chr5D	40766141	40767580	1439	False	1860.000000	1860	89.891000	2319	3786	1	chr5D.!!$F2	1467
3	TraesCS5A01G031300	chr5D	40758919	40760758	1839	False	914.666667	1541	93.847667	1	1933	3	chr5D.!!$F6	1932
4	TraesCS5A01G031300	chr5D	40889005	40890199	1194	False	412.333333	621	86.312667	1704	2928	3	chr5D.!!$F7	1224
5	TraesCS5A01G031300	chr5B	34542901	34545800	2899	False	903.750000	1677	88.409000	1	3142	4	chr5B.!!$F4	3141
6	TraesCS5A01G031300	chr5B	34554635	34556478	1843	False	760.666667	1040	87.924667	1306	3102	3	chr5B.!!$F5	1796
7	TraesCS5A01G031300	chr5B	34565372	34567407	2035	False	623.500000	1050	88.123000	1306	3333	4	chr5B.!!$F6	2027
8	TraesCS5A01G031300	chr5B	34287004	34289020	2016	False	599.000000	931	81.754500	1	1831	2	chr5B.!!$F3	1830
9	TraesCS5A01G031300	chr5B	34607433	34609099	1666	False	265.500000	331	89.979500	1487	1933	2	chr5B.!!$F7	446
10	TraesCS5A01G031300	chr1D	28069094	28069647	553	False	281.000000	281	76.370000	191	769	1	chr1D.!!$F1	578
11	TraesCS5A01G031300	chr7B	565872958	565873460	502	True	233.000000	233	75.591000	950	1443	1	chr7B.!!$R1	493

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
584	633	0.107557	AACCCGACAAAAGTCACCGT	60.108	50.0	0.00	0.0	0.0	4.83	F
2170	6280	0.036732	TCCGATAATGCATGGCCTCC	59.963	55.0	3.32	0.0	0.0	4.30	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2351	6467	0.179045	AGGTTGCACGTTCTCAAGCT	60.179	50.0	16.28	16.28	43.59	3.74	R
3721	7936	0.032952	TTCGGCACTCGCTACAGTTT	59.967	50.0	0.00	0.00	39.05	2.66	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
53	54	7.439655	GGCCAAAACTACACATGTAATTTTTGA	59.560	33.333	24.14	0.00	37.70	2.69
118	120	1.925888	GGGCATCTCCAACCCTGAT	59.074	57.895	0.00	0.00	40.75	2.90
126	128	2.573462	TCTCCAACCCTGATCCTCAAAG	59.427	50.000	0.00	0.00	0.00	2.77
177	180	3.626028	GGAACAGTCCACAACATTGAC	57.374	47.619	0.00	0.00	44.26	3.18
295	300	6.741448	AACCGAACGAAAACATTTACATTG	57.259	33.333	0.00	0.00	0.00	2.82
345	388	9.589461	AGTAGATTAAGCTAGGCTATTCTAACA	57.411	33.333	0.00	0.00	38.25	2.41
357	400	5.405873	GGCTATTCTAACATAGTCTTTCGCC	59.594	44.000	0.00	0.00	29.90	5.54
358	401	5.983720	GCTATTCTAACATAGTCTTTCGCCA	59.016	40.000	0.00	0.00	0.00	5.69
360	403	6.663944	ATTCTAACATAGTCTTTCGCCAAC	57.336	37.500	0.00	0.00	0.00	3.77
361	404	5.401531	TCTAACATAGTCTTTCGCCAACT	57.598	39.130	0.00	0.00	0.00	3.16
480	523	1.071542	GAAGAATAGCCTCTGCCTCCC	59.928	57.143	0.00	0.00	38.69	4.30
482	525	1.075226	AATAGCCTCTGCCTCCCGA	60.075	57.895	0.00	0.00	38.69	5.14
584	633	0.107557	AACCCGACAAAAGTCACCGT	60.108	50.000	0.00	0.00	0.00	4.83
603	652	2.774687	GTTTGTGTAACCCGACCAGAT	58.225	47.619	0.00	0.00	34.36	2.90
771	821	1.075374	CCCCAGTCAAATTCCTCCACA	59.925	52.381	0.00	0.00	0.00	4.17
785	835	2.420642	CTCCACAGTCACATCAACCTG	58.579	52.381	0.00	0.00	0.00	4.00
837	887	2.046988	CAGTGCCACCATCGCTCA	60.047	61.111	0.00	0.00	0.00	4.26
846	897	1.086067	ACCATCGCTCACGCAGATTG	61.086	55.000	0.00	0.00	39.84	2.67
854	905	3.814601	ACGCAGATTGGGTGGGTA	58.185	55.556	0.00	0.00	42.20	3.69
856	907	0.907704	ACGCAGATTGGGTGGGTAGA	60.908	55.000	0.00	0.00	42.20	2.59
867	918	0.674534	GTGGGTAGAGGCATAGGACG	59.325	60.000	0.00	0.00	0.00	4.79
896	947	2.822399	CTAGGACGGCCCATGGTC	59.178	66.667	1.76	0.00	37.41	4.02
975	2376	2.831770	CCAGTATCCGGCTGGCAT	59.168	61.111	12.93	4.18	45.72	4.40
998	2399	4.687215	GCCACAGAGTCGGCTGCA	62.687	66.667	0.00	0.00	45.29	4.41
1030	2431	1.000955	GTTCCTTCTTCTGCTCACCGA	59.999	52.381	0.00	0.00	0.00	4.69
1252	2664	2.481464	GGCGCGCCAATTTAACGA	59.519	55.556	43.55	0.00	35.81	3.85
1269	2681	1.663379	CGAGTGTAGGCGGATGGACA	61.663	60.000	0.00	0.00	0.00	4.02
1280	2692	2.684881	GCGGATGGACAGATGATGTTTT	59.315	45.455	0.00	0.00	44.17	2.43
1345	2759	2.610232	GCATGTGTTTCAATTCCGGCTT	60.610	45.455	0.00	0.00	0.00	4.35
1373	2787	1.291272	GTTACGTCCGTTCTGGGCT	59.709	57.895	0.00	0.00	41.63	5.19
1375	2789	1.180456	TTACGTCCGTTCTGGGCTGA	61.180	55.000	0.00	0.00	41.63	4.26
1399	2813	0.731417	AATGCAGCACTGATCGCTTC	59.269	50.000	0.00	0.00	37.72	3.86
1402	2816	1.153765	CAGCACTGATCGCTTCGGA	60.154	57.895	0.00	0.00	37.72	4.55
1419	2864	1.966451	GACAGGAAAGGGTGCGGTG	60.966	63.158	0.00	0.00	0.00	4.94
1454	3014	2.821366	GTGGGCCTGTGAGATGCG	60.821	66.667	4.53	0.00	0.00	4.73
1469	3030	4.043037	AGATGCGCCTAGTAAACTGTAC	57.957	45.455	4.18	0.00	0.00	2.90
1969	6075	5.660533	TCCCTTTTTCTTTTCCCATATGGT	58.339	37.500	20.46	0.00	34.77	3.55
1990	6096	3.792956	GTCATGGAATGCATAACTTTGCG	59.207	43.478	0.00	0.00	46.21	4.85
2054	6162	4.881273	AGCTTGATTTTTGGTTTTTGGACC	59.119	37.500	0.00	0.00	40.23	4.46
2055	6163	4.881273	GCTTGATTTTTGGTTTTTGGACCT	59.119	37.500	0.00	0.00	40.47	3.85
2056	6164	5.356751	GCTTGATTTTTGGTTTTTGGACCTT	59.643	36.000	0.00	0.00	40.47	3.50
2057	6165	6.127758	GCTTGATTTTTGGTTTTTGGACCTTT	60.128	34.615	0.00	0.00	40.47	3.11
2059	6167	7.384439	TGATTTTTGGTTTTTGGACCTTTTC	57.616	32.000	0.00	0.00	40.47	2.29
2083	6192	7.552459	TCTTTCTTTTTGAAGAACCGGAAAAT	58.448	30.769	9.46	0.00	38.41	1.82
2088	6197	7.707464	TCTTTTTGAAGAACCGGAAAATAAACC	59.293	33.333	9.46	0.00	0.00	3.27
2106	6216	5.358298	AAACCTTTTGAGCTATTCACGTC	57.642	39.130	0.00	0.00	34.94	4.34
2170	6280	0.036732	TCCGATAATGCATGGCCTCC	59.963	55.000	3.32	0.00	0.00	4.30
2204	6314	7.778470	AACGATTTGATCTTCTCTATTCACC	57.222	36.000	0.00	0.00	0.00	4.02
2294	6410	8.440833	CACAAGTTTAATTAGGAGAGGTTAACG	58.559	37.037	0.00	0.00	0.00	3.18
2351	6467	0.889186	GAAGAGCTGGAAAACCGGCA	60.889	55.000	19.91	0.00	43.87	5.69
2388	6504	2.108168	CCTACCTCTTGGGACGATGAA	58.892	52.381	0.00	0.00	38.76	2.57
2428	6545	4.319177	GTGTTTGTTCTCTCTAGGTGCAT	58.681	43.478	0.00	0.00	0.00	3.96
2437	6554	7.604164	TGTTCTCTCTAGGTGCATTTTTCTTAG	59.396	37.037	0.00	0.00	0.00	2.18
2450	6567	6.735694	GCATTTTTCTTAGCTTTGAGTGGACA	60.736	38.462	0.00	0.00	0.00	4.02
2482	6601	3.275617	TTTGGTCTGTACTGTGTGCTT	57.724	42.857	0.00	0.00	0.00	3.91
2640	6790	0.399806	AATGAGGAGGAGGAGGAGGC	60.400	60.000	0.00	0.00	0.00	4.70
2641	6791	1.303423	ATGAGGAGGAGGAGGAGGCT	61.303	60.000	0.00	0.00	0.00	4.58
2644	6794	1.760480	GGAGGAGGAGGAGGCTGAC	60.760	68.421	0.00	0.00	0.00	3.51
2645	6795	1.000993	GAGGAGGAGGAGGCTGACA	59.999	63.158	0.00	0.00	0.00	3.58
2647	6797	0.617249	AGGAGGAGGAGGCTGACAAG	60.617	60.000	0.00	0.00	0.00	3.16
2655	6805	0.616111	GAGGCTGACAAGGAGGAGGA	60.616	60.000	0.00	0.00	0.00	3.71
2656	6806	0.617249	AGGCTGACAAGGAGGAGGAG	60.617	60.000	0.00	0.00	0.00	3.69
2659	6809	1.944177	CTGACAAGGAGGAGGAGGAA	58.056	55.000	0.00	0.00	0.00	3.36
2660	6810	1.830477	CTGACAAGGAGGAGGAGGAAG	59.170	57.143	0.00	0.00	0.00	3.46
2662	6812	2.158158	TGACAAGGAGGAGGAGGAAGAA	60.158	50.000	0.00	0.00	0.00	2.52
2668	6818	2.666317	GAGGAGGAGGAAGAAGAGGAG	58.334	57.143	0.00	0.00	0.00	3.69
2719	6917	2.808543	CGGTGACAAGAAAAAGGAGGAG	59.191	50.000	0.00	0.00	0.00	3.69
2720	6918	3.149981	GGTGACAAGAAAAAGGAGGAGG	58.850	50.000	0.00	0.00	0.00	4.30
2721	6919	3.181443	GGTGACAAGAAAAAGGAGGAGGA	60.181	47.826	0.00	0.00	0.00	3.71
2722	6920	4.068599	GTGACAAGAAAAAGGAGGAGGAG	58.931	47.826	0.00	0.00	0.00	3.69
2723	6921	3.073062	TGACAAGAAAAAGGAGGAGGAGG	59.927	47.826	0.00	0.00	0.00	4.30
2724	6922	3.327439	ACAAGAAAAAGGAGGAGGAGGA	58.673	45.455	0.00	0.00	0.00	3.71
2793	6992	1.406205	GGACCTCAGCTAACTCCAAGC	60.406	57.143	0.00	0.00	40.40	4.01
2835	7034	9.455847	CTAAATGATTTGCTGGTAATAAGAAGC	57.544	33.333	0.00	0.00	36.18	3.86
2865	7064	5.296283	GCATCTTCTGGGCAGCTATATTATG	59.704	44.000	0.00	0.00	0.00	1.90
2870	7069	9.439461	TCTTCTGGGCAGCTATATTATGTATAT	57.561	33.333	0.00	0.00	33.91	0.86
2962	7161	9.990360	TGTGTATCACTATGTTTCTGTCTAAAA	57.010	29.630	1.72	0.00	35.11	1.52
3011	7210	6.715718	TGGGGACATTTTATTTGTCGAGTAAA	59.284	34.615	0.00	0.00	43.53	2.01
3020	7219	9.480538	TTTTATTTGTCGAGTAAATTATGCGTC	57.519	29.630	11.49	0.00	0.00	5.19
3047	7246	7.066284	GCACACATTCTGTCCTGAATAAACTAT	59.934	37.037	0.00	0.00	35.18	2.12
3056	7255	8.146053	TGTCCTGAATAAACTATCCAAGAGAA	57.854	34.615	0.00	0.00	0.00	2.87
3103	7309	8.766000	TGCAGAGTAAACATTCTTATTACGAA	57.234	30.769	0.00	0.00	35.28	3.85
3104	7310	9.378551	TGCAGAGTAAACATTCTTATTACGAAT	57.621	29.630	0.00	0.00	35.28	3.34
3142	7348	6.016360	CCTGTGTTCCACAAACTATTTGATCA	60.016	38.462	8.24	0.00	44.08	2.92
3143	7349	6.734137	TGTGTTCCACAAACTATTTGATCAC	58.266	36.000	8.24	9.07	41.69	3.06
3144	7350	6.319911	TGTGTTCCACAAACTATTTGATCACA	59.680	34.615	8.24	10.93	41.69	3.58
3206	7412	5.902681	ACTAGCTTTTCCTTTTTCCAACAC	58.097	37.500	0.00	0.00	0.00	3.32
3226	7432	3.933879	GGCAACCCCTTTCCATTTG	57.066	52.632	0.00	0.00	0.00	2.32
3289	7499	3.201266	TGAAAACCTGACCACCTACAACT	59.799	43.478	0.00	0.00	0.00	3.16
3316	7526	8.421784	ACAACAATAGAGTTCAGTGAAGTAGAA	58.578	33.333	13.23	2.82	0.00	2.10
3328	7539	8.871629	TCAGTGAAGTAGAAAGAACTAGAGAT	57.128	34.615	0.00	0.00	0.00	2.75
3420	7633	2.482142	CCTTGACCTTGCTATCCTCGAC	60.482	54.545	0.00	0.00	0.00	4.20
3426	7639	2.366916	CCTTGCTATCCTCGACCTCAAT	59.633	50.000	0.00	0.00	0.00	2.57
3428	7641	4.039245	CCTTGCTATCCTCGACCTCAATAA	59.961	45.833	0.00	0.00	0.00	1.40
3526	7739	3.745803	GTCTTCTCCCGCGACGGT	61.746	66.667	8.23	0.00	46.80	4.83
3597	7812	4.722700	AGCATGGACGTGGGGTGC	62.723	66.667	0.00	0.00	37.52	5.01
3598	7813	4.722700	GCATGGACGTGGGGTGCT	62.723	66.667	0.00	0.00	37.93	4.40
3602	7817	4.699522	GGACGTGGGGTGCTGGAC	62.700	72.222	0.00	0.00	33.58	4.02
3603	7818	4.699522	GACGTGGGGTGCTGGACC	62.700	72.222	10.21	10.21	45.28	4.46
3710	7925	3.131223	CCAGATCCATATACCACCTAGCG	59.869	52.174	0.00	0.00	0.00	4.26
3712	7927	4.462834	CAGATCCATATACCACCTAGCGAA	59.537	45.833	0.00	0.00	0.00	4.70
3715	7930	4.673968	TCCATATACCACCTAGCGAAGAT	58.326	43.478	0.00	0.00	0.00	2.40
3719	7934	6.071560	CCATATACCACCTAGCGAAGATTACA	60.072	42.308	0.00	0.00	0.00	2.41
3721	7936	4.546829	ACCACCTAGCGAAGATTACAAA	57.453	40.909	0.00	0.00	0.00	2.83
3727	7942	5.995897	ACCTAGCGAAGATTACAAAAACTGT	59.004	36.000	0.00	0.00	42.47	3.55
3779	7994	2.420890	CTCCCTCATCGGAGCTGC	59.579	66.667	0.00	0.00	43.01	5.25

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
6	7	8.593945	TGGCCTCTTCAAAACATAATAAAGAT	57.406	30.769	3.32	0.00	0.00	2.40
53	54	9.985730	AATTAATTCTGTGAACATGAATGTGTT	57.014	25.926	0.00	0.00	44.53	3.32
118	120	1.334160	TACAGTGTCCGCTTTGAGGA	58.666	50.000	0.00	0.00	34.99	3.71
169	171	2.746277	GCCTCCCGCGTCAATGTT	60.746	61.111	4.92	0.00	0.00	2.71
345	388	2.699954	CCACAGTTGGCGAAAGACTAT	58.300	47.619	0.00	0.00	42.42	2.12
346	389	2.163818	CCACAGTTGGCGAAAGACTA	57.836	50.000	0.00	0.00	42.42	2.59
367	410	1.838073	TTTCTCGGGGAACAGGCTCC	61.838	60.000	0.00	0.00	33.13	4.70
377	420	0.107165	GGGGAAGACATTTCTCGGGG	60.107	60.000	0.00	0.00	0.00	5.73
381	424	3.282885	GGACATGGGGAAGACATTTCTC	58.717	50.000	0.00	0.00	0.00	2.87
451	494	0.763223	GGCTATTCTTCCCCTCCCGA	60.763	60.000	0.00	0.00	0.00	5.14
480	523	0.178068	ACCATTGATCCGGTCCTTCG	59.822	55.000	0.00	0.00	0.00	3.79
482	525	1.340991	CCAACCATTGATCCGGTCCTT	60.341	52.381	0.00	0.00	33.17	3.36
584	633	2.551287	CCATCTGGTCGGGTTACACAAA	60.551	50.000	0.00	0.00	0.00	2.83
603	652	2.197324	GGAAGGCCAACACCACCA	59.803	61.111	5.01	0.00	0.00	4.17
771	821	0.392706	TCGTGCAGGTTGATGTGACT	59.607	50.000	6.26	0.00	0.00	3.41
785	835	1.537202	AGAAAGAAGGCATGTTCGTGC	59.463	47.619	8.31	8.31	44.31	5.34
837	887	0.907704	TCTACCCACCCAATCTGCGT	60.908	55.000	0.00	0.00	0.00	5.24
846	897	0.105142	TCCTATGCCTCTACCCACCC	60.105	60.000	0.00	0.00	0.00	4.61
896	947	0.319040	CGCCGGTCTAGGATGACATG	60.319	60.000	1.90	0.00	38.61	3.21
948	2349	1.225704	GGATACTGGCTGGCTTGCT	59.774	57.895	2.00	0.00	0.00	3.91
975	2376	2.659063	CCGACTCTGTGGCCCATCA	61.659	63.158	0.00	0.00	0.00	3.07
1030	2431	1.835927	GCCCTGTGAGACAGCCTCTT	61.836	60.000	0.00	0.00	44.63	2.85
1189	2601	4.409218	GCGCCACACGTCCGTCTA	62.409	66.667	0.00	0.00	46.11	2.59
1244	2656	3.454375	CATCCGCCTACACTCGTTAAAT	58.546	45.455	0.00	0.00	0.00	1.40
1250	2662	1.065928	GTCCATCCGCCTACACTCG	59.934	63.158	0.00	0.00	0.00	4.18
1252	2664	0.324368	TCTGTCCATCCGCCTACACT	60.324	55.000	0.00	0.00	0.00	3.55
1269	2681	3.002656	CGCTCCGCATTAAAACATCATCT	59.997	43.478	0.00	0.00	0.00	2.90
1280	2692	4.395080	CGTCTTCGCTCCGCATTA	57.605	55.556	0.00	0.00	0.00	1.90
1302	2714	3.515286	CGAGAGCCTCGCCCGTTA	61.515	66.667	10.89	0.00	46.75	3.18
1345	2759	1.162698	CGGACGTAACCTCTCACTGA	58.837	55.000	0.00	0.00	0.00	3.41
1373	2787	2.188062	TCAGTGCTGCATTCATGTCA	57.812	45.000	5.27	0.00	0.00	3.58
1375	2789	1.669265	CGATCAGTGCTGCATTCATGT	59.331	47.619	5.27	0.00	0.00	3.21
1399	2813	2.742372	CGCACCCTTTCCTGTCCG	60.742	66.667	0.00	0.00	0.00	4.79
1402	2816	2.113139	CACCGCACCCTTTCCTGT	59.887	61.111	0.00	0.00	0.00	4.00
1419	2864	0.190069	ACCCAAAACCCTTTCCCTCC	59.810	55.000	0.00	0.00	0.00	4.30
1454	3014	7.808856	GCATCATAGTAGTACAGTTTACTAGGC	59.191	40.741	2.52	0.00	36.22	3.93
1469	3030	5.756833	TGCAGTCTTCATTGCATCATAGTAG	59.243	40.000	0.00	0.00	44.72	2.57
1969	6075	3.734597	GCGCAAAGTTATGCATTCCATGA	60.735	43.478	3.54	0.00	46.76	3.07
2083	6192	5.410439	GGACGTGAATAGCTCAAAAGGTTTA	59.590	40.000	0.00	0.00	35.22	2.01
2088	6197	3.334691	TGGGACGTGAATAGCTCAAAAG	58.665	45.455	0.00	0.00	35.22	2.27
2106	6216	4.084013	CGTTAACTACAAAGTGAGCTTGGG	60.084	45.833	3.71	0.00	35.62	4.12
2218	6328	2.356665	TGTCTAGCAAGCCCAAACAA	57.643	45.000	0.00	0.00	0.00	2.83
2226	6336	4.566759	TGACACGATTTATGTCTAGCAAGC	59.433	41.667	6.68	0.00	45.58	4.01
2273	6387	7.279313	TGCATCGTTAACCTCTCCTAATTAAAC	59.721	37.037	0.00	0.00	0.00	2.01
2277	6393	5.353394	TGCATCGTTAACCTCTCCTAATT	57.647	39.130	0.00	0.00	0.00	1.40
2351	6467	0.179045	AGGTTGCACGTTCTCAAGCT	60.179	50.000	16.28	16.28	43.59	3.74
2388	6504	2.660552	GGCGCGCCATACGTACAT	60.661	61.111	43.55	0.00	46.11	2.29
2428	6545	6.735694	GCATGTCCACTCAAAGCTAAGAAAAA	60.736	38.462	0.00	0.00	0.00	1.94
2437	6554	0.874390	TTCGCATGTCCACTCAAAGC	59.126	50.000	0.00	0.00	0.00	3.51
2450	6567	7.094377	ACAGTACAGACCAAAATTAATTCGCAT	60.094	33.333	0.10	0.00	0.00	4.73
2640	6790	1.830477	CTTCCTCCTCCTCCTTGTCAG	59.170	57.143	0.00	0.00	0.00	3.51
2641	6791	1.433199	TCTTCCTCCTCCTCCTTGTCA	59.567	52.381	0.00	0.00	0.00	3.58
2644	6794	2.765699	CTCTTCTTCCTCCTCCTCCTTG	59.234	54.545	0.00	0.00	0.00	3.61
2645	6795	2.292851	CCTCTTCTTCCTCCTCCTCCTT	60.293	54.545	0.00	0.00	0.00	3.36
2647	6797	1.289530	TCCTCTTCTTCCTCCTCCTCC	59.710	57.143	0.00	0.00	0.00	4.30
2655	6805	1.290732	CCTCCTCCTCCTCTTCTTCCT	59.709	57.143	0.00	0.00	0.00	3.36
2656	6806	1.289530	TCCTCCTCCTCCTCTTCTTCC	59.710	57.143	0.00	0.00	0.00	3.46
2659	6809	0.933700	CCTCCTCCTCCTCCTCTTCT	59.066	60.000	0.00	0.00	0.00	2.85
2660	6810	0.930726	TCCTCCTCCTCCTCCTCTTC	59.069	60.000	0.00	0.00	0.00	2.87
2662	6812	0.998945	CCTCCTCCTCCTCCTCCTCT	60.999	65.000	0.00	0.00	0.00	3.69
2668	6818	0.105709	CCTCTTCCTCCTCCTCCTCC	60.106	65.000	0.00	0.00	0.00	4.30
2719	6917	0.378962	CGTCGTCAGTCTGATCCTCC	59.621	60.000	5.68	0.00	0.00	4.30
2720	6918	1.370609	TCGTCGTCAGTCTGATCCTC	58.629	55.000	5.68	0.00	0.00	3.71
2721	6919	1.673400	CATCGTCGTCAGTCTGATCCT	59.327	52.381	5.68	0.00	0.00	3.24
2722	6920	1.671328	TCATCGTCGTCAGTCTGATCC	59.329	52.381	5.68	0.00	0.00	3.36
2723	6921	3.295785	CATCATCGTCGTCAGTCTGATC	58.704	50.000	5.68	0.00	0.00	2.92
2724	6922	2.033927	CCATCATCGTCGTCAGTCTGAT	59.966	50.000	5.68	0.00	0.00	2.90
2793	6992	8.715191	AATCATTTAGTCTGTCTTAAGCAGAG	57.285	34.615	22.06	13.48	42.80	3.35
2812	7011	6.608808	AGGCTTCTTATTACCAGCAAATCATT	59.391	34.615	0.00	0.00	33.64	2.57
2835	7034	2.228059	CTGCCCAGAAGATGCATAAGG	58.772	52.381	0.00	0.00	33.97	2.69
2865	7064	4.189231	ACACAACAAGGCTTCGGATATAC	58.811	43.478	0.00	0.00	0.00	1.47
2870	7069	2.158871	ACTAACACAACAAGGCTTCGGA	60.159	45.455	0.00	0.00	0.00	4.55
2962	7161	8.131100	CCAAATTAGAATGTTTCACTCGCATAT	58.869	33.333	0.00	0.00	0.00	1.78
3047	7246	9.281371	CAGAGCATCATTATTAATTCTCTTGGA	57.719	33.333	0.00	0.00	37.82	3.53
3056	7255	6.444633	GCAAGTGCAGAGCATCATTATTAAT	58.555	36.000	0.00	0.00	41.91	1.40
3103	7309	4.574828	GGAACACAGGCATACATCGTAAAT	59.425	41.667	0.00	0.00	0.00	1.40
3104	7310	3.936453	GGAACACAGGCATACATCGTAAA	59.064	43.478	0.00	0.00	0.00	2.01
3106	7312	2.498078	TGGAACACAGGCATACATCGTA	59.502	45.455	0.00	0.00	0.00	3.43
3107	7313	1.277842	TGGAACACAGGCATACATCGT	59.722	47.619	0.00	0.00	0.00	3.73
3108	7314	2.022764	TGGAACACAGGCATACATCG	57.977	50.000	0.00	0.00	0.00	3.84
3142	7348	4.586001	AGCAAGTCTGTTGGAATCAAATGT	59.414	37.500	0.00	0.00	34.28	2.71
3143	7349	4.921515	CAGCAAGTCTGTTGGAATCAAATG	59.078	41.667	0.00	0.00	38.02	2.32
3144	7350	4.828939	TCAGCAAGTCTGTTGGAATCAAAT	59.171	37.500	0.00	0.00	43.32	2.32
3206	7412	1.191489	AAATGGAAAGGGGTTGCCCG	61.191	55.000	0.00	0.00	46.66	6.13
3225	7431	1.805539	CGATTCTCCGTTGAGCGCA	60.806	57.895	11.47	0.00	38.58	6.09
3226	7432	2.998667	CGATTCTCCGTTGAGCGC	59.001	61.111	0.00	0.00	38.58	5.92
3263	7471	0.185175	GGTGGTCAGGTTTTCACCCT	59.815	55.000	0.00	0.00	45.63	4.34
3289	7499	9.074576	TCTACTTCACTGAACTCTATTGTTGTA	57.925	33.333	0.00	0.00	0.00	2.41
3316	7526	7.554959	TGTGGTCCTTTTATCTCTAGTTCTT	57.445	36.000	0.00	0.00	0.00	2.52
3328	7539	3.488778	TTAGGCGTTGTGGTCCTTTTA	57.511	42.857	0.00	0.00	0.00	1.52
3362	7573	1.221840	CCTCAGGCGGTGCTGTATT	59.778	57.895	0.00	0.00	0.00	1.89
3410	7623	5.302059	TGGAACTTATTGAGGTCGAGGATAG	59.698	44.000	0.00	0.00	43.40	2.08
3420	7633	2.743183	CGCCCTCTGGAACTTATTGAGG	60.743	54.545	0.00	0.00	42.72	3.86
3426	7639	1.993391	CCCCGCCCTCTGGAACTTA	60.993	63.158	0.00	0.00	0.00	2.24
3570	7783	1.890979	GTCCATGCTCCGCCATCTG	60.891	63.158	0.00	0.00	0.00	2.90
3571	7784	2.507944	GTCCATGCTCCGCCATCT	59.492	61.111	0.00	0.00	0.00	2.90
3688	7903	3.131223	CGCTAGGTGGTATATGGATCTGG	59.869	52.174	0.00	0.00	0.00	3.86
3699	7914	5.664294	TTTGTAATCTTCGCTAGGTGGTA	57.336	39.130	0.00	0.00	0.00	3.25
3704	7919	6.481954	ACAGTTTTTGTAATCTTCGCTAGG	57.518	37.500	0.00	0.00	38.56	3.02
3710	7925	7.010023	CACTCGCTACAGTTTTTGTAATCTTC	58.990	38.462	0.00	0.00	41.57	2.87
3712	7927	5.107065	GCACTCGCTACAGTTTTTGTAATCT	60.107	40.000	0.00	0.00	41.57	2.40
3715	7930	3.249080	GGCACTCGCTACAGTTTTTGTAA	59.751	43.478	0.00	0.00	41.57	2.41
3719	7934	0.865769	CGGCACTCGCTACAGTTTTT	59.134	50.000	0.00	0.00	38.60	1.94
3721	7936	0.032952	TTCGGCACTCGCTACAGTTT	59.967	50.000	0.00	0.00	39.05	2.66

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.