AutoCloner

Multiple sequence alignment - TraesCS5B01G460000

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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	TraesCS5B01G460000	chr5B	100.000	2608	0	0	1	2608	635532235	635534842	0.000000e+00	4817.0
1	TraesCS5B01G460000	chr5B	100.000	1024	0	0	3026	4049	635535260	635536283	0.000000e+00	1892.0
2	TraesCS5B01G460000	chr5B	83.370	1371	157	30	1082	2402	635515157	635516506	0.000000e+00	1203.0
3	TraesCS5B01G460000	chr5B	85.332	859	126	0	1	859	588748463	588749321	0.000000e+00	889.0
4	TraesCS5B01G460000	chr5B	87.384	753	85	9	1117	1865	635510510	635511256	0.000000e+00	856.0
5	TraesCS5B01G460000	chr5B	78.802	1052	181	14	1183	2216	635346288	635347315	0.000000e+00	669.0
6	TraesCS5B01G460000	chr5B	82.178	808	101	24	1502	2270	635467270	635468073	0.000000e+00	654.0
7	TraesCS5B01G460000	chr5B	77.143	805	157	18	1557	2351	635573713	635574500	3.710000e-120	442.0
8	TraesCS5B01G460000	chr5B	90.854	164	15	0	2443	2606	635560999	635561162	1.890000e-53	220.0
9	TraesCS5B01G460000	chr5B	90.361	166	16	0	2443	2608	635516510	635516675	6.810000e-53	219.0
10	TraesCS5B01G460000	chr5B	80.292	274	29	16	3607	3866	635608146	635608408	2.490000e-42	183.0
11	TraesCS5B01G460000	chr5B	94.595	37	2	0	4011	4047	635468857	635468893	1.570000e-04	58.4
12	TraesCS5B01G460000	chr5A	95.191	1518	54	12	918	2422	632992763	632994274	0.000000e+00	2381.0
13	TraesCS5B01G460000	chr5A	83.103	1302	168	31	1085	2367	632903707	632904975	0.000000e+00	1138.0
14	TraesCS5B01G460000	chr5A	88.693	681	50	15	3028	3689	632994827	632995499	0.000000e+00	806.0
15	TraesCS5B01G460000	chr5A	82.020	812	102	22	1582	2353	632886581	632887388	0.000000e+00	651.0
16	TraesCS5B01G460000	chr5A	82.993	441	41	20	3613	4049	632995518	632995928	6.390000e-98	368.0
17	TraesCS5B01G460000	chr5A	89.850	266	25	2	1082	1346	632886079	632886343	1.390000e-89	340.0
18	TraesCS5B01G460000	chr5A	93.296	179	12	0	2430	2608	632994597	632994775	8.630000e-67	265.0
19	TraesCS5B01G460000	chr5A	89.381	113	12	0	2490	2602	632905030	632905142	4.220000e-30	143.0
20	TraesCS5B01G460000	chr5A	91.026	78	7	0	3864	3941	633017576	633017653	5.530000e-19	106.0
21	TraesCS5B01G460000	chr5D	92.084	1617	75	22	1028	2608	505428956	505430555	0.000000e+00	2228.0
22	TraesCS5B01G460000	chr5D	84.778	1327	143	31	1082	2367	505420621	505421929	0.000000e+00	1277.0
23	TraesCS5B01G460000	chr5D	91.279	860	74	1	1	859	353440593	353441452	0.000000e+00	1171.0
24	TraesCS5B01G460000	chr5D	87.003	754	88	9	1117	1866	505410035	505410782	0.000000e+00	841.0
25	TraesCS5B01G460000	chr5D	84.658	730	85	11	1564	2270	505405726	505406451	0.000000e+00	702.0
26	TraesCS5B01G460000	chr5D	79.278	859	147	16	1401	2239	505347809	505348656	4.540000e-159	571.0
27	TraesCS5B01G460000	chr5D	89.177	462	33	2	3026	3487	505430613	505431057	9.830000e-156	560.0
28	TraesCS5B01G460000	chr5D	81.260	603	76	24	1837	2411	505410792	505411385	1.720000e-123	453.0
29	TraesCS5B01G460000	chr5D	89.139	267	26	3	1082	1346	505405207	505405472	3.020000e-86	329.0
30	TraesCS5B01G460000	chr5D	86.644	292	25	3	3526	3809	505437821	505438106	1.090000e-80	311.0
31	TraesCS5B01G460000	chr5D	89.759	166	17	0	2443	2608	505421974	505422139	3.170000e-51	213.0
32	TraesCS5B01G460000	chr5D	81.273	267	26	14	3613	3866	505543204	505543459	1.150000e-45	195.0
33	TraesCS5B01G460000	chr5D	89.844	128	11	2	3814	3941	505457759	505457884	3.240000e-36	163.0
34	TraesCS5B01G460000	chr5D	97.778	45	1	0	3486	3530	505431132	505431176	1.210000e-10	78.7
35	TraesCS5B01G460000	chr5D	100.000	30	0	0	858	887	505428704	505428733	5.650000e-04	56.5
36	TraesCS5B01G460000	chr6B	95.227	859	40	1	1	859	7754573	7753716	0.000000e+00	1358.0
37	TraesCS5B01G460000	chr3D	93.481	859	56	0	1	859	536681720	536680862	0.000000e+00	1277.0
38	TraesCS5B01G460000	chr7D	92.558	860	62	2	1	859	414189791	414188933	0.000000e+00	1232.0
39	TraesCS5B01G460000	chr4A	88.824	850	95	0	10	859	597477020	597477869	0.000000e+00	1044.0
40	TraesCS5B01G460000	chr4A	88.353	850	99	0	10	859	597346640	597347489	0.000000e+00	1022.0
41	TraesCS5B01G460000	chr4A	85.851	834	118	0	26	859	743767675	743766842	0.000000e+00	887.0
42	TraesCS5B01G460000	chr2B	86.946	858	108	4	4	859	559172279	559171424	0.000000e+00	961.0

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	TraesCS5B01G460000	chr5B	635532235	635536283	4048	False	3354.500000	4817	100.000000	1	4049	2	chr5B.!!$F8	4048
1	TraesCS5B01G460000	chr5B	588748463	588749321	858	False	889.000000	889	85.332000	1	859	1	chr5B.!!$F1	858
2	TraesCS5B01G460000	chr5B	635510510	635516675	6165	False	759.333333	1203	87.038333	1082	2608	3	chr5B.!!$F7	1526
3	TraesCS5B01G460000	chr5B	635346288	635347315	1027	False	669.000000	669	78.802000	1183	2216	1	chr5B.!!$F2	1033
4	TraesCS5B01G460000	chr5B	635573713	635574500	787	False	442.000000	442	77.143000	1557	2351	1	chr5B.!!$F4	794
5	TraesCS5B01G460000	chr5B	635467270	635468893	1623	False	356.200000	654	88.386500	1502	4047	2	chr5B.!!$F6	2545
6	TraesCS5B01G460000	chr5A	632992763	632995928	3165	False	955.000000	2381	90.043250	918	4049	4	chr5A.!!$F4	3131
7	TraesCS5B01G460000	chr5A	632903707	632905142	1435	False	640.500000	1138	86.242000	1085	2602	2	chr5A.!!$F3	1517
8	TraesCS5B01G460000	chr5A	632886079	632887388	1309	False	495.500000	651	85.935000	1082	2353	2	chr5A.!!$F2	1271
9	TraesCS5B01G460000	chr5D	353440593	353441452	859	False	1171.000000	1171	91.279000	1	859	1	chr5D.!!$F1	858
10	TraesCS5B01G460000	chr5D	505420621	505422139	1518	False	745.000000	1277	87.268500	1082	2608	2	chr5D.!!$F7	1526
11	TraesCS5B01G460000	chr5D	505428704	505431176	2472	False	730.800000	2228	94.759750	858	3530	4	chr5D.!!$F8	2672
12	TraesCS5B01G460000	chr5D	505405207	505411385	6178	False	581.250000	841	85.515000	1082	2411	4	chr5D.!!$F6	1329
13	TraesCS5B01G460000	chr5D	505347809	505348656	847	False	571.000000	571	79.278000	1401	2239	1	chr5D.!!$F2	838
14	TraesCS5B01G460000	chr6B	7753716	7754573	857	True	1358.000000	1358	95.227000	1	859	1	chr6B.!!$R1	858
15	TraesCS5B01G460000	chr3D	536680862	536681720	858	True	1277.000000	1277	93.481000	1	859	1	chr3D.!!$R1	858
16	TraesCS5B01G460000	chr7D	414188933	414189791	858	True	1232.000000	1232	92.558000	1	859	1	chr7D.!!$R1	858
17	TraesCS5B01G460000	chr4A	597477020	597477869	849	False	1044.000000	1044	88.824000	10	859	1	chr4A.!!$F2	849
18	TraesCS5B01G460000	chr4A	597346640	597347489	849	False	1022.000000	1022	88.353000	10	859	1	chr4A.!!$F1	849
19	TraesCS5B01G460000	chr4A	743766842	743767675	833	True	887.000000	887	85.851000	26	859	1	chr4A.!!$R1	833
20	TraesCS5B01G460000	chr2B	559171424	559172279	855	True	961.000000	961	86.946000	4	859	1	chr2B.!!$R1	855

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
195	197	0.105039	GATCGATGGGGACTCACCAC	59.895	60.000	0.54	41.58	4.16	F
1013	1016	0.597568	CCGAACAATGCTGCTTCCAA	59.402	50.000	0.00	0.00	3.53	F
1080	1172	1.396301	ACGCTCCGTAGAGTTCGTAAG	59.604	52.381	0.00	42.59	2.34	F
1181	1273	1.515521	CGTTTCCTCGCCTTTTGCCT	61.516	55.000	0.00	36.24	4.75	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Hairpin	End Stability	Orientation
1080	1172	0.039618	TTTGGATGGGGAAGAGTGGC	59.960	55.0	0.00	0.00	5.01	R
2045	11762	0.609151	TCACCAATGCATTTGCCCAG	59.391	50.0	9.83	41.18	4.45	R
2453	12572	1.291184	TTGCTTGCTCACCGATCACG	61.291	55.0	0.00	39.43	4.35	R
3169	13301	0.317603	CACAGCAGCAACAGCTTGTC	60.318	55.0	0.00	41.14	3.18	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
76	78	2.530406	CTCCTCCCCCATAGCCCC	60.530	72.222	0.00	0.00	0.00	5.80
106	108	3.764237	TCTACCCTGAAAACTGTCCAC	57.236	47.619	0.00	0.00	0.00	4.02
121	123	3.713764	CTGTCCACCTCCCTCTTGATAAT	59.286	47.826	0.00	0.00	0.00	1.28
129	131	2.061061	CCCTCTTGATAATCCCTGCCT	58.939	52.381	0.00	0.00	0.00	4.75
195	197	0.105039	GATCGATGGGGACTCACCAC	59.895	60.000	0.54	0.00	41.58	4.16
247	249	2.161855	CTCCCACATTACAAGCAGCAA	58.838	47.619	0.00	0.00	0.00	3.91
421	424	6.018016	GTGAGCAAAATGTGGCTTATTGTTTT	60.018	34.615	0.00	0.00	41.22	2.43
460	463	3.223435	GACACGTGTCTTGGTGCGC	62.223	63.158	35.51	11.59	41.65	6.09
560	563	1.534729	GTGCCCGAGATTTCCAAGTT	58.465	50.000	0.00	0.00	0.00	2.66
887	890	2.360483	GCTCTCGAGACATGGATTCTCA	59.640	50.000	12.08	0.00	39.71	3.27
888	891	3.181482	GCTCTCGAGACATGGATTCTCAA	60.181	47.826	12.08	0.00	39.71	3.02
889	892	4.679106	GCTCTCGAGACATGGATTCTCAAA	60.679	45.833	12.08	0.21	39.71	2.69
890	893	5.405935	TCTCGAGACATGGATTCTCAAAA	57.594	39.130	12.08	0.00	39.71	2.44
891	894	5.793817	TCTCGAGACATGGATTCTCAAAAA	58.206	37.500	12.08	0.00	39.71	1.94
913	916	2.540265	AAAGCTCTCGAGGCATATGG	57.460	50.000	22.44	4.25	0.00	2.74
914	917	1.709578	AAGCTCTCGAGGCATATGGA	58.290	50.000	22.44	0.00	0.00	3.41
915	918	1.935799	AGCTCTCGAGGCATATGGAT	58.064	50.000	22.44	3.15	0.00	3.41
916	919	3.093057	AGCTCTCGAGGCATATGGATA	57.907	47.619	22.44	0.00	0.00	2.59
920	923	5.837979	AGCTCTCGAGGCATATGGATATAAT	59.162	40.000	22.44	0.81	0.00	1.28
1013	1016	0.597568	CCGAACAATGCTGCTTCCAA	59.402	50.000	0.00	0.00	0.00	3.53
1079	1171	1.442769	ACGCTCCGTAGAGTTCGTAA	58.557	50.000	0.00	0.00	42.59	3.18
1080	1172	1.396301	ACGCTCCGTAGAGTTCGTAAG	59.604	52.381	0.00	0.00	42.59	2.34
1112	1204	4.016706	CCAAACCCTCGCCTCCGT	62.017	66.667	0.00	0.00	35.54	4.69
1181	1273	1.515521	CGTTTCCTCGCCTTTTGCCT	61.516	55.000	0.00	0.00	36.24	4.75
1478	6363	2.417516	GCCCTCTTCGCTCGCATA	59.582	61.111	0.00	0.00	0.00	3.14
1821	11472	2.358615	GTGGCATCGTGGAGTGCA	60.359	61.111	0.00	0.00	43.00	4.57
1847	11498	2.563620	TGGTACACTCCGCTTGTCAATA	59.436	45.455	0.00	0.00	0.00	1.90
1849	11500	4.403113	TGGTACACTCCGCTTGTCAATATA	59.597	41.667	0.00	0.00	0.00	0.86
2015	11705	4.080863	AGGGTAATTGATCTCAAGACGCTT	60.081	41.667	15.65	2.77	41.62	4.68
2045	11762	4.646492	ACATGTGAATTTGGGATTAGGAGC	59.354	41.667	0.00	0.00	0.00	4.70
2453	12572	0.179094	TGTGTGTGTTGTCGGTCCTC	60.179	55.000	0.00	0.00	0.00	3.71
2466	12585	1.226717	GTCCTCGTGATCGGTGAGC	60.227	63.158	3.77	0.00	37.69	4.26
2477	12596	0.039256	TCGGTGAGCAAGCAAAATGC	60.039	50.000	0.00	0.00	45.46	3.56
3091	13223	6.046593	GGGACTTTGTTTAGGAAGTTTTTGG	58.953	40.000	0.00	0.00	36.31	3.28
3169	13301	7.129109	ACTATTGTTGTATGGAACTTCGTTG	57.871	36.000	0.00	0.00	0.00	4.10
3171	13303	5.412526	TTGTTGTATGGAACTTCGTTGAC	57.587	39.130	0.00	0.00	0.00	3.18
3175	13308	3.496884	TGTATGGAACTTCGTTGACAAGC	59.503	43.478	0.00	0.00	0.00	4.01
3202	13335	2.984471	CTGCTGTGCTTGCAAATTGTAG	59.016	45.455	0.00	0.00	40.13	2.74
3205	13338	3.829948	CTGTGCTTGCAAATTGTAGGAG	58.170	45.455	0.00	0.00	0.00	3.69
3248	13383	2.979813	CCGTGCTTGCAATACTTTTCAC	59.020	45.455	0.00	0.00	0.00	3.18
3322	13480	1.271543	CCAGACTTGCAGGTGGAATCA	60.272	52.381	6.05	0.00	31.04	2.57
3326	13484	2.227388	GACTTGCAGGTGGAATCAACAG	59.773	50.000	6.05	0.00	31.71	3.16
3334	13497	4.566759	CAGGTGGAATCAACAGTACATACG	59.433	45.833	0.00	0.00	31.71	3.06
3337	13500	4.570772	GTGGAATCAACAGTACATACGCAT	59.429	41.667	0.00	0.00	0.00	4.73
3356	13519	2.306341	TGAGCAGCAGCAGTTATCTC	57.694	50.000	3.17	0.00	45.49	2.75
3368	13532	7.281999	AGCAGCAGTTATCTCCTATTCTTTTTC	59.718	37.037	0.00	0.00	0.00	2.29
3369	13533	7.281999	GCAGCAGTTATCTCCTATTCTTTTTCT	59.718	37.037	0.00	0.00	0.00	2.52
3403	13567	2.115480	CCCGAGCCCGAGATAGGA	59.885	66.667	0.00	0.00	38.22	2.94
3407	13571	0.535328	CGAGCCCGAGATAGGACTCA	60.535	60.000	0.69	0.00	38.22	3.41
3467	13631	3.059166	GCGGTTTCTGAATGCACAAAAT	58.941	40.909	0.00	0.00	0.00	1.82
3530	13909	0.249699	ATCAACACGCCGTCAGTTCA	60.250	50.000	0.00	0.00	0.00	3.18
3538	13917	2.223595	ACGCCGTCAGTTCATAGATCAG	60.224	50.000	0.00	0.00	0.00	2.90
3573	13960	5.233689	CACATGTACATAGTGTCAGCATCAG	59.766	44.000	20.91	4.97	0.00	2.90
3604	13991	1.318158	GCCACTGGCCAGAAGAATGG	61.318	60.000	39.19	32.40	44.06	3.16
3611	13998	1.106285	GCCAGAAGAATGGGCGAATT	58.894	50.000	0.00	0.00	40.97	2.17
3617	14004	4.823989	CAGAAGAATGGGCGAATTATCCTT	59.176	41.667	0.00	0.00	0.00	3.36
3635	14022	1.470098	CTTGCTGTTTCATTCTCCGGG	59.530	52.381	0.00	0.00	0.00	5.73
3643	14030	2.066393	CATTCTCCGGGGAGCCAGA	61.066	63.158	3.09	0.00	41.71	3.86
3689	14076	3.119602	CCAAGCAGTTCATTGTCATCTGG	60.120	47.826	0.00	0.00	0.00	3.86
3690	14077	2.089980	AGCAGTTCATTGTCATCTGGC	58.910	47.619	0.00	0.00	0.00	4.85
3697	14171	1.068402	CATTGTCATCTGGCGTTGCAA	60.068	47.619	0.00	0.00	0.00	4.08
3709	14183	1.061799	CGTTGCAACATTGAGCGCTC	61.062	55.000	30.42	30.42	0.00	5.03
3711	14185	1.865788	TTGCAACATTGAGCGCTCCC	61.866	55.000	33.23	12.35	0.00	4.30
3712	14186	2.334946	GCAACATTGAGCGCTCCCA	61.335	57.895	33.23	20.94	0.00	4.37
3715	14189	0.674895	AACATTGAGCGCTCCCAGAC	60.675	55.000	33.23	9.91	0.00	3.51
3730	14204	0.673022	CAGACTGCAGCTTCCTCCAC	60.673	60.000	15.27	0.00	0.00	4.02
3731	14205	1.739562	GACTGCAGCTTCCTCCACG	60.740	63.158	15.27	0.00	0.00	4.94
3734	14208	3.706373	GCAGCTTCCTCCACGGGA	61.706	66.667	0.00	0.00	0.00	5.14
3741	14215	1.651737	TTCCTCCACGGGAAGATTGA	58.348	50.000	0.00	0.00	40.08	2.57
3742	14216	1.651737	TCCTCCACGGGAAGATTGAA	58.348	50.000	0.00	0.00	31.67	2.69
3743	14217	1.555075	TCCTCCACGGGAAGATTGAAG	59.445	52.381	0.00	0.00	31.67	3.02
3744	14218	1.373570	CTCCACGGGAAGATTGAAGC	58.626	55.000	0.00	0.00	0.00	3.86
3745	14219	0.690192	TCCACGGGAAGATTGAAGCA	59.310	50.000	0.00	0.00	0.00	3.91
3746	14220	1.089920	CCACGGGAAGATTGAAGCAG	58.910	55.000	0.00	0.00	0.00	4.24
3747	14221	0.449388	CACGGGAAGATTGAAGCAGC	59.551	55.000	0.00	0.00	0.00	5.25
3751	14225	1.101331	GGAAGATTGAAGCAGCTGGG	58.899	55.000	17.12	0.00	0.00	4.45
3764	14238	2.515398	CTGGGGACTGGTGTTGCA	59.485	61.111	0.00	0.00	0.00	4.08
3765	14239	1.075482	CTGGGGACTGGTGTTGCAT	59.925	57.895	0.00	0.00	0.00	3.96
3767	14241	1.074775	GGGGACTGGTGTTGCATGA	59.925	57.895	0.00	0.00	0.00	3.07
3786	14260	1.065102	GATGTAGTAGCCGTCGAAGCA	59.935	52.381	10.96	0.00	0.00	3.91
3787	14261	0.169672	TGTAGTAGCCGTCGAAGCAC	59.830	55.000	10.96	7.15	0.00	4.40
3788	14262	0.525029	GTAGTAGCCGTCGAAGCACC	60.525	60.000	10.96	1.40	0.00	5.01
3789	14263	1.660560	TAGTAGCCGTCGAAGCACCC	61.661	60.000	10.96	0.00	0.00	4.61
3790	14264	4.124351	TAGCCGTCGAAGCACCCG	62.124	66.667	10.96	0.00	0.00	5.28
3798	14272	3.712907	GAAGCACCCGGCCTGGTA	61.713	66.667	19.64	0.00	46.50	3.25
3799	14273	3.682292	GAAGCACCCGGCCTGGTAG	62.682	68.421	19.64	14.00	46.50	3.18
3800	14274	4.715130	AGCACCCGGCCTGGTAGA	62.715	66.667	19.64	0.00	46.50	2.59
3802	14276	2.267961	CACCCGGCCTGGTAGAAC	59.732	66.667	19.64	0.00	36.67	3.01
3803	14277	2.122056	ACCCGGCCTGGTAGAACT	59.878	61.111	18.60	0.00	36.67	3.01
3804	14278	1.538135	ACCCGGCCTGGTAGAACTT	60.538	57.895	18.60	0.00	36.67	2.66
3805	14279	0.252375	ACCCGGCCTGGTAGAACTTA	60.252	55.000	18.60	0.00	36.67	2.24
3806	14280	0.177373	CCCGGCCTGGTAGAACTTAC	59.823	60.000	4.74	0.00	35.15	2.34
3807	14281	0.179119	CCGGCCTGGTAGAACTTACG	60.179	60.000	0.00	0.00	0.00	3.18
3808	14282	0.529378	CGGCCTGGTAGAACTTACGT	59.471	55.000	0.00	0.00	0.00	3.57
3809	14283	1.745087	CGGCCTGGTAGAACTTACGTA	59.255	52.381	0.00	0.00	0.00	3.57
3810	14284	2.478539	CGGCCTGGTAGAACTTACGTAC	60.479	54.545	0.00	0.00	0.00	3.67
3811	14285	2.757314	GGCCTGGTAGAACTTACGTACT	59.243	50.000	0.00	0.00	0.00	2.73
3812	14286	3.181492	GGCCTGGTAGAACTTACGTACTC	60.181	52.174	0.00	0.00	0.00	2.59
3813	14287	3.181492	GCCTGGTAGAACTTACGTACTCC	60.181	52.174	0.00	0.00	0.00	3.85
3814	14288	4.012374	CCTGGTAGAACTTACGTACTCCA	58.988	47.826	0.00	0.00	0.00	3.86
3815	14289	4.142513	CCTGGTAGAACTTACGTACTCCAC	60.143	50.000	0.00	0.00	0.00	4.02
3816	14290	3.758554	TGGTAGAACTTACGTACTCCACC	59.241	47.826	0.00	2.19	0.00	4.61
3817	14291	3.758554	GGTAGAACTTACGTACTCCACCA	59.241	47.826	0.00	0.00	0.00	4.17
3818	14292	4.142513	GGTAGAACTTACGTACTCCACCAG	60.143	50.000	0.00	0.00	0.00	4.00
3819	14293	2.230750	AGAACTTACGTACTCCACCAGC	59.769	50.000	0.00	0.00	0.00	4.85
3820	14294	0.893447	ACTTACGTACTCCACCAGCC	59.107	55.000	0.00	0.00	0.00	4.85
3821	14295	0.179145	CTTACGTACTCCACCAGCCG	60.179	60.000	0.00	0.00	0.00	5.52
3866	14340	3.434319	CACATGCCCGTGCTCACC	61.434	66.667	0.00	0.00	38.71	4.02
3933	14408	5.918426	TTTGAGGCAAAGATTATGCATGA	57.082	34.783	10.16	0.00	45.60	3.07
3947	14422	1.478916	TGCATGACGGGATCGAGTTAA	59.521	47.619	0.00	0.00	40.11	2.01
3949	14424	2.128035	CATGACGGGATCGAGTTAAGC	58.872	52.381	0.00	0.00	40.11	3.09
3953	14428	1.134788	ACGGGATCGAGTTAAGCTTGG	60.135	52.381	9.86	0.00	40.11	3.61
3999	14474	3.886123	CCAATGGACTTCCTTCCGTTAT	58.114	45.455	0.00	0.00	42.11	1.89
4014	14490	9.238368	TCCTTCCGTTATTTGAACAGATTAAAT	57.762	29.630	0.00	0.00	0.00	1.40

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
76	78	6.992715	CAGTTTTCAGGGTAGATTGTATAGGG	59.007	42.308	0.00	0.00	0.00	3.53
106	108	2.039613	GCAGGGATTATCAAGAGGGAGG	59.960	54.545	0.00	0.00	0.00	4.30
121	123	2.204074	TGTGGGCTAAGGCAGGGA	60.204	61.111	0.00	0.00	40.87	4.20
146	148	3.390967	TCATCCACAAGGTGAAGTCTGAA	59.609	43.478	0.00	0.00	35.23	3.02
195	197	0.714994	CGCAATGCCATTGTTTTCGG	59.285	50.000	18.10	0.00	42.20	4.30
421	424	4.274950	GTCCGTTTTGTGATCAAGAGGAAA	59.725	41.667	0.00	0.00	35.63	3.13
460	463	0.681243	GCTAGCAAGGAGGGGTTTGG	60.681	60.000	10.63	0.00	0.00	3.28
560	563	1.402968	GTGGTATCCACGTCGAAGCTA	59.597	52.381	0.00	0.00	44.95	3.32
892	895	3.118261	TCCATATGCCTCGAGAGCTTTTT	60.118	43.478	15.71	5.47	0.00	1.94
893	896	2.435805	TCCATATGCCTCGAGAGCTTTT	59.564	45.455	15.71	6.48	0.00	2.27
894	897	2.042464	TCCATATGCCTCGAGAGCTTT	58.958	47.619	15.71	9.93	0.00	3.51
895	898	1.709578	TCCATATGCCTCGAGAGCTT	58.290	50.000	15.71	15.35	0.00	3.74
896	899	1.935799	ATCCATATGCCTCGAGAGCT	58.064	50.000	15.71	8.23	0.00	4.09
897	900	5.521906	TTATATCCATATGCCTCGAGAGC	57.478	43.478	15.71	16.01	0.00	4.09
898	901	8.954950	AAAATTATATCCATATGCCTCGAGAG	57.045	34.615	15.71	5.19	0.00	3.20
901	904	9.476202	CGATAAAATTATATCCATATGCCTCGA	57.524	33.333	0.00	0.00	0.00	4.04
902	905	8.712363	CCGATAAAATTATATCCATATGCCTCG	58.288	37.037	0.00	0.00	0.00	4.63
903	906	9.561069	ACCGATAAAATTATATCCATATGCCTC	57.439	33.333	0.00	0.00	0.00	4.70
1079	1171	0.846427	TTGGATGGGGAAGAGTGGCT	60.846	55.000	0.00	0.00	0.00	4.75
1080	1172	0.039618	TTTGGATGGGGAAGAGTGGC	59.960	55.000	0.00	0.00	0.00	5.01
1169	1261	1.672356	GAGCTCAGGCAAAAGGCGA	60.672	57.895	9.40	0.00	46.16	5.54
1181	1273	2.041115	CACCTCCTCGACGAGCTCA	61.041	63.158	19.55	4.43	0.00	4.26
1478	6363	0.112606	TGAGGTCAGAGGTCTTCCGT	59.887	55.000	0.00	0.00	39.05	4.69
1821	11472	2.218603	CAAGCGGAGTGTACCAAGTTT	58.781	47.619	0.00	0.00	0.00	2.66
1847	11498	1.128878	CGATCGATCGGCTTCTCGTAT	59.871	52.381	34.54	0.00	45.93	3.06
1849	11500	1.280142	CGATCGATCGGCTTCTCGT	59.720	57.895	34.54	0.00	45.93	4.18
2045	11762	0.609151	TCACCAATGCATTTGCCCAG	59.391	50.000	9.83	0.00	41.18	4.45
2313	12072	8.607459	CACATATGTCCTCATGTCTAAAGTTTC	58.393	37.037	5.07	0.00	33.12	2.78
2453	12572	1.291184	TTGCTTGCTCACCGATCACG	61.291	55.000	0.00	0.00	39.43	4.35
2466	12585	4.508492	TCAACTGAATGTGCATTTTGCTTG	59.492	37.500	0.00	0.80	45.31	4.01
2477	12596	1.901591	ACCAGGCTCAACTGAATGTG	58.098	50.000	0.00	0.00	40.97	3.21
2514	12633	9.890085	CATAAATGCAAGAAAATAACAACATCG	57.110	29.630	0.00	0.00	0.00	3.84
3169	13301	0.317603	CACAGCAGCAACAGCTTGTC	60.318	55.000	0.00	0.00	41.14	3.18
3171	13303	1.660575	GCACAGCAGCAACAGCTTG	60.661	57.895	0.00	0.00	41.14	4.01
3175	13308	1.660575	GCAAGCACAGCAGCAACAG	60.661	57.895	0.00	0.00	36.85	3.16
3202	13335	4.105486	GCAACAACTTCTTCAACAACTCC	58.895	43.478	0.00	0.00	0.00	3.85
3205	13338	4.562789	GGAAGCAACAACTTCTTCAACAAC	59.437	41.667	4.46	0.00	44.51	3.32
3248	13383	4.689812	CCATTCTCAAGAACACAGAGTGAG	59.310	45.833	3.88	0.00	36.80	3.51
3289	13446	5.316167	TGCAAGTCTGGTTATCTTGACAAT	58.684	37.500	8.08	0.00	40.35	2.71
3296	13453	2.026822	CCACCTGCAAGTCTGGTTATCT	60.027	50.000	0.00	0.00	43.52	1.98
3322	13480	3.190079	CTGCTCATGCGTATGTACTGTT	58.810	45.455	13.39	0.00	43.34	3.16
3326	13484	1.524355	CTGCTGCTCATGCGTATGTAC	59.476	52.381	13.39	7.37	43.34	2.90
3334	13497	1.002684	GATAACTGCTGCTGCTCATGC	60.003	52.381	17.00	1.02	40.48	4.06
3337	13500	1.134580	GGAGATAACTGCTGCTGCTCA	60.135	52.381	17.00	0.00	40.48	4.26
3368	13532	1.468914	GGGTTGCGCCTTTTCTCTAAG	59.531	52.381	4.18	0.00	37.43	2.18
3369	13533	1.530323	GGGTTGCGCCTTTTCTCTAA	58.470	50.000	4.18	0.00	37.43	2.10
3382	13546	2.701163	CTATCTCGGGCTCGGGTTGC	62.701	65.000	5.37	0.00	38.21	4.17
3403	13567	0.842467	AAGTGGGGCTAGGCTTGAGT	60.842	55.000	16.80	0.52	0.00	3.41
3407	13571	0.777446	TTCAAAGTGGGGCTAGGCTT	59.223	50.000	16.80	0.00	0.00	4.35
3467	13631	9.374711	TGTATATTAGATGTTACCAGTCCATCA	57.625	33.333	10.99	0.00	37.93	3.07
3604	13991	3.128589	TGAAACAGCAAGGATAATTCGCC	59.871	43.478	0.00	0.00	0.00	5.54
3611	13998	4.191544	CGGAGAATGAAACAGCAAGGATA	58.808	43.478	0.00	0.00	0.00	2.59
3617	14004	0.322456	CCCCGGAGAATGAAACAGCA	60.322	55.000	0.73	0.00	0.00	4.41
3689	14076	2.709999	GCGCTCAATGTTGCAACGC	61.710	57.895	23.79	18.58	36.73	4.84
3690	14077	1.061799	GAGCGCTCAATGTTGCAACG	61.062	55.000	31.91	11.66	0.00	4.10
3697	14171	1.078848	GTCTGGGAGCGCTCAATGT	60.079	57.895	36.27	0.95	0.00	2.71
3709	14183	1.078567	GAGGAAGCTGCAGTCTGGG	60.079	63.158	16.64	0.00	0.00	4.45
3711	14185	0.673022	GTGGAGGAAGCTGCAGTCTG	60.673	60.000	16.64	0.00	0.00	3.51
3712	14186	1.676384	GTGGAGGAAGCTGCAGTCT	59.324	57.895	16.64	10.20	0.00	3.24
3715	14189	2.435586	CCGTGGAGGAAGCTGCAG	60.436	66.667	10.11	10.11	45.00	4.41
3730	14204	0.731417	CAGCTGCTTCAATCTTCCCG	59.269	55.000	0.00	0.00	0.00	5.14
3731	14205	1.101331	CCAGCTGCTTCAATCTTCCC	58.899	55.000	8.66	0.00	0.00	3.97
3734	14208	0.700564	TCCCCAGCTGCTTCAATCTT	59.299	50.000	8.66	0.00	0.00	2.40
3739	14213	2.752358	CAGTCCCCAGCTGCTTCA	59.248	61.111	8.66	0.00	0.00	3.02
3740	14214	2.045536	CCAGTCCCCAGCTGCTTC	60.046	66.667	8.66	0.00	32.93	3.86
3741	14215	2.856000	ACCAGTCCCCAGCTGCTT	60.856	61.111	8.66	0.00	32.93	3.91
3742	14216	3.644606	CACCAGTCCCCAGCTGCT	61.645	66.667	8.66	0.00	32.93	4.24
3743	14217	3.497884	AACACCAGTCCCCAGCTGC	62.498	63.158	8.66	0.00	32.93	5.25
3744	14218	1.601759	CAACACCAGTCCCCAGCTG	60.602	63.158	6.78	6.78	0.00	4.24
3745	14219	2.839098	CAACACCAGTCCCCAGCT	59.161	61.111	0.00	0.00	0.00	4.24
3746	14220	2.985847	GCAACACCAGTCCCCAGC	60.986	66.667	0.00	0.00	0.00	4.85
3747	14221	1.075482	ATGCAACACCAGTCCCCAG	59.925	57.895	0.00	0.00	0.00	4.45
3751	14225	1.538047	ACATCATGCAACACCAGTCC	58.462	50.000	0.00	0.00	0.00	3.85
3759	14233	2.540101	GACGGCTACTACATCATGCAAC	59.460	50.000	0.00	0.00	0.00	4.17
3760	14234	2.798145	CGACGGCTACTACATCATGCAA	60.798	50.000	0.00	0.00	0.00	4.08
3764	14238	2.287668	GCTTCGACGGCTACTACATCAT	60.288	50.000	0.00	0.00	0.00	2.45
3765	14239	1.065102	GCTTCGACGGCTACTACATCA	59.935	52.381	0.00	0.00	0.00	3.07
3767	14241	1.100510	TGCTTCGACGGCTACTACAT	58.899	50.000	10.31	0.00	0.00	2.29
3786	14260	0.252375	TAAGTTCTACCAGGCCGGGT	60.252	55.000	30.96	30.96	45.10	5.28
3787	14261	0.177373	GTAAGTTCTACCAGGCCGGG	59.823	60.000	21.67	21.67	40.22	5.73
3788	14262	0.179119	CGTAAGTTCTACCAGGCCGG	60.179	60.000	11.48	11.48	42.50	6.13
3789	14263	3.340727	CGTAAGTTCTACCAGGCCG	57.659	57.895	0.00	0.00	0.00	6.13
3803	14277	1.597797	CCGGCTGGTGGAGTACGTAA	61.598	60.000	2.29	0.00	0.00	3.18
3804	14278	2.048023	CCGGCTGGTGGAGTACGTA	61.048	63.158	2.29	0.00	0.00	3.57
3805	14279	3.379445	CCGGCTGGTGGAGTACGT	61.379	66.667	2.29	0.00	0.00	3.57
3806	14280	4.814294	GCCGGCTGGTGGAGTACG	62.814	72.222	22.15	0.00	37.67	3.67
3807	14281	3.391382	AGCCGGCTGGTGGAGTAC	61.391	66.667	32.33	0.00	37.67	2.73
3808	14282	3.390521	CAGCCGGCTGGTGGAGTA	61.391	66.667	42.81	0.00	40.17	2.59
3810	14284	4.463879	CTCAGCCGGCTGGTGGAG	62.464	72.222	46.58	34.99	43.75	3.86
3812	14286	4.767255	GACTCAGCCGGCTGGTGG	62.767	72.222	46.58	36.83	43.75	4.61
3813	14287	4.767255	GGACTCAGCCGGCTGGTG	62.767	72.222	46.58	39.09	43.75	4.17
3815	14289	3.710722	AAGGACTCAGCCGGCTGG	61.711	66.667	46.58	38.24	43.75	4.85
3816	14290	2.435586	CAAGGACTCAGCCGGCTG	60.436	66.667	44.24	44.24	44.86	4.85
3817	14291	4.400961	GCAAGGACTCAGCCGGCT	62.401	66.667	27.08	27.08	32.61	5.52
3818	14292	4.400961	AGCAAGGACTCAGCCGGC	62.401	66.667	21.89	21.89	34.61	6.13
3819	14293	2.435586	CAGCAAGGACTCAGCCGG	60.436	66.667	0.00	0.00	0.00	6.13
3820	14294	1.004560	TTCAGCAAGGACTCAGCCG	60.005	57.895	0.00	0.00	0.00	5.52
3821	14295	0.036022	AGTTCAGCAAGGACTCAGCC	59.964	55.000	0.00	0.00	0.00	4.85
3866	14340	1.098869	TAGAGAGCAAGCCTGACGAG	58.901	55.000	0.00	0.00	0.00	4.18
3909	14384	6.255020	GTCATGCATAATCTTTGCCTCAAAAG	59.745	38.462	0.00	0.00	39.39	2.27
3922	14397	2.926200	CTCGATCCCGTCATGCATAATC	59.074	50.000	0.00	0.00	37.05	1.75
3923	14398	2.300152	ACTCGATCCCGTCATGCATAAT	59.700	45.455	0.00	0.00	37.05	1.28
3933	14408	1.134788	CCAAGCTTAACTCGATCCCGT	60.135	52.381	0.00	0.00	37.05	5.28
3949	14424	1.745489	GGTCAGCCGCTTACCCAAG	60.745	63.158	12.13	0.00	34.66	3.61
3999	14474	8.109705	TCTGCTTAGCATTTAATCTGTTCAAA	57.890	30.769	7.58	0.00	38.13	2.69
4014	14490	3.198417	TGTGATGGAGATTCTGCTTAGCA	59.802	43.478	6.76	6.76	36.92	3.49

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.