AutoCloner

Multiple sequence alignment - TraesCS2A01G468600

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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	TraesCS2A01G468600	chr2A	100.000	3522	0	0	1	3522	712540287	712536766	0.000000e+00	6505
1	TraesCS2A01G468600	chr2A	82.969	1556	206	38	1009	2528	723101463	723102995	0.000000e+00	1351
2	TraesCS2A01G468600	chr2A	85.714	406	55	2	1019	1421	723512030	723512435	3.250000e-115	425
3	TraesCS2A01G468600	chr2A	83.784	407	63	2	1017	1420	723160696	723161102	1.980000e-102	383
4	TraesCS2A01G468600	chr2A	88.785	214	19	4	676	885	69340422	69340634	1.250000e-64	257
5	TraesCS2A01G468600	chr2A	88.208	212	23	2	676	885	694469615	694469826	5.840000e-63	252
6	TraesCS2A01G468600	chr2A	77.372	274	60	2	1639	1911	723512465	723512737	1.010000e-35	161
7	TraesCS2A01G468600	chr2B	88.541	1693	142	20	898	2546	689777778	689776094	0.000000e+00	2004
8	TraesCS2A01G468600	chr2B	82.543	1117	155	27	1451	2546	712002918	712004015	0.000000e+00	946
9	TraesCS2A01G468600	chr2B	88.164	414	45	4	1009	1420	712002440	712002851	1.140000e-134	490
10	TraesCS2A01G468600	chr2B	86.085	424	56	2	1018	1438	712360212	712360635	1.490000e-123	453
11	TraesCS2A01G468600	chr2B	77.778	405	80	10	1512	1911	712360750	712361149	1.260000e-59	241
12	TraesCS2A01G468600	chr2D	90.402	1219	106	3	988	2195	573952398	573951180	0.000000e+00	1592
13	TraesCS2A01G468600	chr2D	83.180	1088	149	20	1451	2520	588499073	588500144	0.000000e+00	965
14	TraesCS2A01G468600	chr2D	87.198	414	49	4	1009	1420	588498589	588499000	5.320000e-128	468
15	TraesCS2A01G468600	chr2D	86.453	406	52	2	1019	1421	588735993	588736398	3.230000e-120	442
16	TraesCS2A01G468600	chr2D	76.790	405	84	10	1512	1911	588736527	588736926	5.920000e-53	219
17	TraesCS2A01G468600	chr2D	92.500	80	5	1	2474	2552	573951180	573951101	2.870000e-21	113
18	TraesCS2A01G468600	chr7A	96.610	944	31	1	2580	3522	543419989	543419046	0.000000e+00	1565
19	TraesCS2A01G468600	chr7A	96.081	944	36	1	2580	3522	309318452	309319395	0.000000e+00	1537
20	TraesCS2A01G468600	chr7A	93.396	212	12	2	676	885	597477835	597477624	2.640000e-81	313
21	TraesCS2A01G468600	chr6A	96.504	944	32	1	2580	3522	358245612	358244669	0.000000e+00	1559
22	TraesCS2A01G468600	chr3A	96.105	950	36	1	2574	3522	627540078	627541027	0.000000e+00	1548
23	TraesCS2A01G468600	chr3A	96.093	947	36	1	2577	3522	275249830	275250776	0.000000e+00	1543
24	TraesCS2A01G468600	chr3A	96.571	904	19	5	1	895	574853512	574852612	0.000000e+00	1487
25	TraesCS2A01G468600	chr3A	96.606	884	29	1	1	883	352717397	352718280	0.000000e+00	1465
26	TraesCS2A01G468600	chr3A	96.396	888	30	2	1	886	42307798	42306911	0.000000e+00	1461
27	TraesCS2A01G468600	chr3A	96.063	889	30	5	1	885	744566297	744567184	0.000000e+00	1443
28	TraesCS2A01G468600	chr4A	96.195	946	34	2	2578	3522	453264443	453265387	0.000000e+00	1546
29	TraesCS2A01G468600	chr4A	96.081	944	36	1	2580	3522	466404792	466405735	0.000000e+00	1537
30	TraesCS2A01G468600	chr5A	95.992	948	35	3	2577	3522	164082309	164083255	0.000000e+00	1537
31	TraesCS2A01G468600	chr5A	95.987	947	34	4	2578	3522	652012570	652011626	0.000000e+00	1535
32	TraesCS2A01G468600	chr5A	96.210	897	23	4	1	887	69983169	69984064	0.000000e+00	1458
33	TraesCS2A01G468600	chr6D	97.182	887	23	2	1	885	407821743	407820857	0.000000e+00	1498
34	TraesCS2A01G468600	chr5B	96.953	886	25	2	1	885	82039028	82039912	0.000000e+00	1485
35	TraesCS2A01G468600	chr4B	96.610	885	28	2	1	883	636702127	636703011	0.000000e+00	1467
36	TraesCS2A01G468600	chr1D	97.008	869	24	2	1	867	486367068	486366200	0.000000e+00	1459

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	TraesCS2A01G468600	chr2A	712536766	712540287	3521	True	6505.0	6505	100.0000	1	3522	1	chr2A.!!$R1	3521
1	TraesCS2A01G468600	chr2A	723101463	723102995	1532	False	1351.0	1351	82.9690	1009	2528	1	chr2A.!!$F3	1519
2	TraesCS2A01G468600	chr2A	723512030	723512737	707	False	293.0	425	81.5430	1019	1911	2	chr2A.!!$F5	892
3	TraesCS2A01G468600	chr2B	689776094	689777778	1684	True	2004.0	2004	88.5410	898	2546	1	chr2B.!!$R1	1648
4	TraesCS2A01G468600	chr2B	712002440	712004015	1575	False	718.0	946	85.3535	1009	2546	2	chr2B.!!$F1	1537
5	TraesCS2A01G468600	chr2B	712360212	712361149	937	False	347.0	453	81.9315	1018	1911	2	chr2B.!!$F2	893
6	TraesCS2A01G468600	chr2D	573951101	573952398	1297	True	852.5	1592	91.4510	988	2552	2	chr2D.!!$R1	1564
7	TraesCS2A01G468600	chr2D	588498589	588500144	1555	False	716.5	965	85.1890	1009	2520	2	chr2D.!!$F1	1511
8	TraesCS2A01G468600	chr2D	588735993	588736926	933	False	330.5	442	81.6215	1019	1911	2	chr2D.!!$F2	892
9	TraesCS2A01G468600	chr7A	543419046	543419989	943	True	1565.0	1565	96.6100	2580	3522	1	chr7A.!!$R1	942
10	TraesCS2A01G468600	chr7A	309318452	309319395	943	False	1537.0	1537	96.0810	2580	3522	1	chr7A.!!$F1	942
11	TraesCS2A01G468600	chr6A	358244669	358245612	943	True	1559.0	1559	96.5040	2580	3522	1	chr6A.!!$R1	942
12	TraesCS2A01G468600	chr3A	627540078	627541027	949	False	1548.0	1548	96.1050	2574	3522	1	chr3A.!!$F3	948
13	TraesCS2A01G468600	chr3A	275249830	275250776	946	False	1543.0	1543	96.0930	2577	3522	1	chr3A.!!$F1	945
14	TraesCS2A01G468600	chr3A	574852612	574853512	900	True	1487.0	1487	96.5710	1	895	1	chr3A.!!$R2	894
15	TraesCS2A01G468600	chr3A	352717397	352718280	883	False	1465.0	1465	96.6060	1	883	1	chr3A.!!$F2	882
16	TraesCS2A01G468600	chr3A	42306911	42307798	887	True	1461.0	1461	96.3960	1	886	1	chr3A.!!$R1	885
17	TraesCS2A01G468600	chr3A	744566297	744567184	887	False	1443.0	1443	96.0630	1	885	1	chr3A.!!$F4	884
18	TraesCS2A01G468600	chr4A	453264443	453265387	944	False	1546.0	1546	96.1950	2578	3522	1	chr4A.!!$F1	944
19	TraesCS2A01G468600	chr4A	466404792	466405735	943	False	1537.0	1537	96.0810	2580	3522	1	chr4A.!!$F2	942
20	TraesCS2A01G468600	chr5A	164082309	164083255	946	False	1537.0	1537	95.9920	2577	3522	1	chr5A.!!$F2	945
21	TraesCS2A01G468600	chr5A	652011626	652012570	944	True	1535.0	1535	95.9870	2578	3522	1	chr5A.!!$R1	944
22	TraesCS2A01G468600	chr5A	69983169	69984064	895	False	1458.0	1458	96.2100	1	887	1	chr5A.!!$F1	886
23	TraesCS2A01G468600	chr6D	407820857	407821743	886	True	1498.0	1498	97.1820	1	885	1	chr6D.!!$R1	884
24	TraesCS2A01G468600	chr5B	82039028	82039912	884	False	1485.0	1485	96.9530	1	885	1	chr5B.!!$F1	884
25	TraesCS2A01G468600	chr4B	636702127	636703011	884	False	1467.0	1467	96.6100	1	883	1	chr4B.!!$F1	882
26	TraesCS2A01G468600	chr1D	486366200	486367068	868	True	1459.0	1459	97.0080	1	867	1	chr1D.!!$R1	866

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
933	956	1.001406	GGCCATCTTTCCGAGATCGAT	59.999	52.381	0.00	43.32	3.59	F
1224	1256	0.040499	AGGCGGAGGAGAAGAAGAGT	59.960	55.000	0.00	0.00	3.24	F
1353	1385	0.108585	ACCACTGGAACTTCGTGCAT	59.891	50.000	0.71	0.00	3.96	F
2250	2366	0.179073	AAGGAGAATGACGCGGATGG	60.179	55.000	12.47	0.00	3.51	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Hairpin	End Stability	Orientation
2035	2126	0.248825	CGAGCCTCGTCAGGATTGAG	60.249	60.000	5.82	41.75	3.02	R
2210	2320	0.904649	TCCACTGCGTCATCCTCATT	59.095	50.000	0.00	0.00	2.57	R
2276	2392	1.079503	GACTCGTCAAGAACCATGGC	58.920	55.000	13.04	0.00	4.40	R
3435	3553	1.299976	GGTCCTCGCCCAATCACTT	59.700	57.895	0.00	0.00	3.16	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
114	115	1.134371	GCGTCAAGCCTAAGGGAGAAT	60.134	52.381	0.00	0.00	40.81	2.40
183	184	3.509967	TGGAGACGAAGCTTCTTATCACA	59.490	43.478	23.80	17.41	0.00	3.58
356	360	3.588842	TCCAAGAAGGACATGGATCAAGT	59.411	43.478	0.00	0.00	43.07	3.16
602	606	5.287226	GGGAAGATGATGATTTTGTGATGC	58.713	41.667	0.00	0.00	0.00	3.91
603	607	5.163488	GGGAAGATGATGATTTTGTGATGCA	60.163	40.000	0.00	0.00	0.00	3.96
787	794	5.379187	GTTGGGTTTGAGGGTTTAGTCTTA	58.621	41.667	0.00	0.00	0.00	2.10
887	910	8.174085	AGGGTTCTACTAGACATGCTCTTATAT	58.826	37.037	0.00	0.00	0.00	0.86
894	917	8.728596	ACTAGACATGCTCTTATATAAACCCT	57.271	34.615	0.00	0.00	0.00	4.34
895	918	9.824216	ACTAGACATGCTCTTATATAAACCCTA	57.176	33.333	0.00	0.00	0.00	3.53
933	956	1.001406	GGCCATCTTTCCGAGATCGAT	59.999	52.381	0.00	0.00	43.32	3.59
939	962	1.863454	CTTTCCGAGATCGATGGCTTG	59.137	52.381	0.54	0.00	43.02	4.01
942	965	1.688735	TCCGAGATCGATGGCTTGATT	59.311	47.619	0.54	0.00	43.02	2.57
951	974	3.025619	GGCTTGATTGCCGGATCG	58.974	61.111	5.05	0.00	43.74	3.69
994	1023	2.098298	CGTCATCGCCGCAAAAGG	59.902	61.111	0.00	0.00	0.00	3.11
998	1027	1.135402	GTCATCGCCGCAAAAGGAAAT	60.135	47.619	0.00	0.00	0.00	2.17
1001	1030	1.173043	TCGCCGCAAAAGGAAATGAT	58.827	45.000	0.00	0.00	0.00	2.45
1005	1034	1.550072	CCGCAAAAGGAAATGATGGGT	59.450	47.619	0.00	0.00	0.00	4.51
1007	1036	3.181487	CCGCAAAAGGAAATGATGGGTAG	60.181	47.826	0.00	0.00	0.00	3.18
1013	1045	1.152756	AAATGATGGGTAGGCCGGC	60.153	57.895	21.18	21.18	34.97	6.13
1045	1077	4.671590	TGAGCGACCTCCCGGACA	62.672	66.667	0.73	0.00	37.29	4.02
1190	1222	3.953775	CAGGGCCAACGACTGGGT	61.954	66.667	6.18	0.00	46.54	4.51
1224	1256	0.040499	AGGCGGAGGAGAAGAAGAGT	59.960	55.000	0.00	0.00	0.00	3.24
1248	1280	3.620785	GGGGCGCTCCTCGATGAT	61.621	66.667	22.28	0.00	41.67	2.45
1353	1385	0.108585	ACCACTGGAACTTCGTGCAT	59.891	50.000	0.71	0.00	0.00	3.96
1362	1394	0.249699	ACTTCGTGCATGTCGACCAA	60.250	50.000	14.12	0.00	37.05	3.67
1370	1402	1.671979	CATGTCGACCAATGGCTCAT	58.328	50.000	14.12	0.00	0.00	2.90
1375	1407	2.107366	TCGACCAATGGCTCATCTACA	58.893	47.619	0.00	0.00	0.00	2.74
1421	1456	2.202676	CCTCGACCTGCGCTTCTC	60.203	66.667	9.73	0.00	40.61	2.87
1422	1457	2.202676	CTCGACCTGCGCTTCTCC	60.203	66.667	9.73	0.00	40.61	3.71
1425	1460	2.169789	CGACCTGCGCTTCTCCATG	61.170	63.158	9.73	0.00	0.00	3.66
1538	1629	0.957888	GACAAGGCTCTTCACCTGCC	60.958	60.000	0.00	0.00	46.42	4.85
1579	1670	2.537560	CGCCTATTGCCGGCTGAAG	61.538	63.158	29.70	20.25	45.37	3.02
1753	1844	4.796231	CTCGACCAACGCCTCCGG	62.796	72.222	0.00	0.00	42.26	5.14
1766	1857	1.830408	CTCCGGAGATTCGCCCTCT	60.830	63.158	28.21	0.00	0.00	3.69
1790	1881	4.309933	CTGCTGTCACAACATGAAGTCTA	58.690	43.478	0.00	0.00	39.72	2.59
1998	2089	1.138859	CCTCCATCTGCACCATCGTAA	59.861	52.381	0.00	0.00	0.00	3.18
2006	2097	1.338674	TGCACCATCGTAAACTGGAGG	60.339	52.381	0.00	0.00	36.35	4.30
2008	2099	1.553248	CACCATCGTAAACTGGAGGGA	59.447	52.381	0.00	0.00	37.54	4.20
2019	2110	2.261729	ACTGGAGGGAAGGTTCTTCTC	58.738	52.381	7.47	3.78	0.00	2.87
2031	2122	3.463704	AGGTTCTTCTCAGGTTTCCCTTT	59.536	43.478	0.00	0.00	39.89	3.11
2033	2124	4.207955	GTTCTTCTCAGGTTTCCCTTTGT	58.792	43.478	0.00	0.00	39.89	2.83
2034	2125	4.519906	TCTTCTCAGGTTTCCCTTTGTT	57.480	40.909	0.00	0.00	39.89	2.83
2035	2126	4.461198	TCTTCTCAGGTTTCCCTTTGTTC	58.539	43.478	0.00	0.00	39.89	3.18
2036	2127	4.166144	TCTTCTCAGGTTTCCCTTTGTTCT	59.834	41.667	0.00	0.00	39.89	3.01
2037	2128	4.086706	TCTCAGGTTTCCCTTTGTTCTC	57.913	45.455	0.00	0.00	39.89	2.87
2038	2129	3.458118	TCTCAGGTTTCCCTTTGTTCTCA	59.542	43.478	0.00	0.00	39.89	3.27
2041	2132	4.827284	TCAGGTTTCCCTTTGTTCTCAATC	59.173	41.667	0.00	0.00	39.89	2.67
2048	2146	3.557054	CCCTTTGTTCTCAATCCTGACGA	60.557	47.826	0.00	0.00	33.32	4.20
2065	2163	2.970974	GAGGCTCGTGTTGCAAGGC	61.971	63.158	0.00	0.00	35.94	4.35
2068	2166	2.594303	CTCGTGTTGCAAGGCCCA	60.594	61.111	0.00	0.00	0.00	5.36
2079	2177	1.948611	GCAAGGCCCACTCGTGAATTA	60.949	52.381	0.00	0.00	0.00	1.40
2080	2178	2.432444	CAAGGCCCACTCGTGAATTAA	58.568	47.619	0.00	0.00	0.00	1.40
2082	2180	0.733150	GGCCCACTCGTGAATTAAGC	59.267	55.000	0.00	0.00	0.00	3.09
2127	2225	4.097361	GGAGCAGACCCCGAACCC	62.097	72.222	0.00	0.00	0.00	4.11
2152	2250	0.817654	TCCTGTCGCTGTACATGGAG	59.182	55.000	0.00	0.00	0.00	3.86
2196	2294	4.255510	AGAAAGATGTTACCATGGGCAT	57.744	40.909	18.09	16.55	0.00	4.40
2210	2320	1.140312	GGGCATGGACCTGGAAGATA	58.860	55.000	0.00	0.00	34.07	1.98
2224	2334	3.387699	TGGAAGATAATGAGGATGACGCA	59.612	43.478	0.00	0.00	0.00	5.24
2239	2349	1.270907	ACGCAGTGGAGAAGGAGAAT	58.729	50.000	0.00	0.00	42.51	2.40
2242	2352	2.626840	GCAGTGGAGAAGGAGAATGAC	58.373	52.381	0.00	0.00	0.00	3.06
2250	2366	0.179073	AAGGAGAATGACGCGGATGG	60.179	55.000	12.47	0.00	0.00	3.51
2286	2402	0.842635	GATGAGGAGGCCATGGTTCT	59.157	55.000	14.67	11.49	0.00	3.01
2354	2470	3.599343	GAGATCAACATGGTGCACTACA	58.401	45.455	17.98	7.60	0.00	2.74
2419	2535	2.023771	CGCGCTTGTGCTTGAGAGA	61.024	57.895	5.56	0.00	36.97	3.10
2449	2565	1.374252	CCTCGTGAAGGGGACGTTG	60.374	63.158	0.00	0.00	46.06	4.10
2452	2568	2.112297	GTGAAGGGGACGTTGGCA	59.888	61.111	0.00	0.00	36.18	4.92
2489	2605	0.593773	GAACGAGATCGAGAGCTGGC	60.594	60.000	9.58	0.00	43.02	4.85
2546	2662	6.045318	TCTCCGATGAAACAATCTCAGAATC	58.955	40.000	0.00	0.00	0.00	2.52
2549	2665	5.530171	CCGATGAAACAATCTCAGAATCCAT	59.470	40.000	0.00	0.00	0.00	3.41
2550	2666	6.427974	CGATGAAACAATCTCAGAATCCATG	58.572	40.000	0.00	0.00	0.00	3.66
2551	2667	6.037940	CGATGAAACAATCTCAGAATCCATGT	59.962	38.462	0.00	0.00	0.00	3.21
2553	2669	6.916440	TGAAACAATCTCAGAATCCATGTTG	58.084	36.000	0.00	0.00	30.64	3.33
2554	2670	4.978083	ACAATCTCAGAATCCATGTTGC	57.022	40.909	0.00	0.00	0.00	4.17
2555	2671	4.338012	ACAATCTCAGAATCCATGTTGCA	58.662	39.130	0.00	0.00	0.00	4.08
2556	2672	4.398358	ACAATCTCAGAATCCATGTTGCAG	59.602	41.667	0.00	0.00	0.00	4.41
2557	2673	3.986996	TCTCAGAATCCATGTTGCAGA	57.013	42.857	0.00	0.00	0.00	4.26
2558	2674	4.290711	TCTCAGAATCCATGTTGCAGAA	57.709	40.909	0.00	0.00	0.00	3.02
2559	2675	4.259356	TCTCAGAATCCATGTTGCAGAAG	58.741	43.478	0.00	0.00	0.00	2.85
2560	2676	4.008330	CTCAGAATCCATGTTGCAGAAGT	58.992	43.478	0.00	0.00	0.00	3.01
2561	2677	4.401022	TCAGAATCCATGTTGCAGAAGTT	58.599	39.130	0.00	0.00	0.00	2.66
2562	2678	4.456911	TCAGAATCCATGTTGCAGAAGTTC	59.543	41.667	0.00	0.00	0.00	3.01
2563	2679	4.458295	CAGAATCCATGTTGCAGAAGTTCT	59.542	41.667	0.00	0.00	0.00	3.01
2564	2680	5.048224	CAGAATCCATGTTGCAGAAGTTCTT	60.048	40.000	1.56	0.00	0.00	2.52
2565	2681	5.537674	AGAATCCATGTTGCAGAAGTTCTTT	59.462	36.000	1.56	0.00	0.00	2.52
2566	2682	5.796424	ATCCATGTTGCAGAAGTTCTTTT	57.204	34.783	1.56	0.00	0.00	2.27
2567	2683	5.186996	TCCATGTTGCAGAAGTTCTTTTC	57.813	39.130	1.56	0.00	0.00	2.29
2568	2684	3.976942	CCATGTTGCAGAAGTTCTTTTCG	59.023	43.478	1.56	0.00	32.33	3.46
2569	2685	3.065019	TGTTGCAGAAGTTCTTTTCGC	57.935	42.857	1.56	4.29	32.33	4.70
2570	2686	2.421775	TGTTGCAGAAGTTCTTTTCGCA	59.578	40.909	10.64	10.64	36.00	5.10
2571	2687	3.119673	TGTTGCAGAAGTTCTTTTCGCAA	60.120	39.130	19.11	19.11	40.57	4.85
2572	2688	3.065019	TGCAGAAGTTCTTTTCGCAAC	57.935	42.857	11.94	0.00	35.39	4.17
2573	2689	2.421775	TGCAGAAGTTCTTTTCGCAACA	59.578	40.909	11.94	0.00	35.39	3.33
2574	2690	3.066621	TGCAGAAGTTCTTTTCGCAACAT	59.933	39.130	11.94	0.00	35.39	2.71
2575	2691	3.665871	GCAGAAGTTCTTTTCGCAACATC	59.334	43.478	1.56	0.00	32.33	3.06
2699	2815	6.443849	ACAGGTAGAAGTCCCTCATTGATTTA	59.556	38.462	0.00	0.00	0.00	1.40
2806	2922	3.644823	TGACAAGAAAAGACATCGCGTA	58.355	40.909	5.77	0.00	0.00	4.42
2822	2938	1.801395	GCGTAAAGACTATGGAGCGCA	60.801	52.381	11.47	0.00	42.63	6.09
3065	3183	2.357637	CCATTGGAACACGTGTCAGTTT	59.642	45.455	23.61	5.42	39.29	2.66
3277	3395	4.832248	CCAAAGAGTGTTAGGCATCACTA	58.168	43.478	8.67	0.00	43.64	2.74
3302	3420	4.343526	AGTCTTTCTGTCTGTGTGATCTGT	59.656	41.667	0.00	0.00	0.00	3.41
3376	3494	5.682234	TTCTGAGCATCCAAGAGTCATTA	57.318	39.130	0.00	0.00	0.00	1.90
3400	3518	1.663702	CGCCGGTGAACGAAGTCTT	60.664	57.895	10.20	0.00	45.00	3.01
3453	3571	0.322546	AAAGTGATTGGGCGAGGACC	60.323	55.000	0.00	0.00	0.00	4.46
3455	3573	2.682136	TGATTGGGCGAGGACCGA	60.682	61.111	0.00	0.00	41.76	4.69

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
114	115	2.173143	TGCCTTCATCATGTGCTCCATA	59.827	45.455	0.00	0.00	30.71	2.74
183	184	4.592778	AGCTTGACCTCTTTCTTCTTCTCT	59.407	41.667	0.00	0.00	0.00	3.10
356	360	1.901159	CCTTCCACCATTGCAATTGGA	59.099	47.619	23.27	23.27	36.31	3.53
602	606	8.929827	TCATTGATGCATGGTTTAATAGTTTG	57.070	30.769	2.46	0.00	0.00	2.93
787	794	0.264657	AGGGTTGAAAAACAGGGGCT	59.735	50.000	0.00	0.00	32.77	5.19
887	910	5.221087	CCGTTTGCAAAGACTTTAGGGTTTA	60.221	40.000	13.26	0.00	0.00	2.01
889	912	3.067601	CCGTTTGCAAAGACTTTAGGGTT	59.932	43.478	13.26	0.00	0.00	4.11
890	913	2.621526	CCGTTTGCAAAGACTTTAGGGT	59.378	45.455	13.26	0.00	0.00	4.34
892	915	2.661594	GCCGTTTGCAAAGACTTTAGG	58.338	47.619	13.26	8.53	40.77	2.69
893	916	2.307049	CGCCGTTTGCAAAGACTTTAG	58.693	47.619	13.26	0.00	41.33	1.85
894	917	1.002251	CCGCCGTTTGCAAAGACTTTA	60.002	47.619	13.26	0.00	41.33	1.85
895	918	0.248866	CCGCCGTTTGCAAAGACTTT	60.249	50.000	13.26	0.00	41.33	2.66
896	919	1.358759	CCGCCGTTTGCAAAGACTT	59.641	52.632	13.26	0.00	41.33	3.01
901	924	3.565910	GATGGCCGCCGTTTGCAAA	62.566	57.895	8.05	8.05	41.33	3.68
906	929	2.340328	GGAAAGATGGCCGCCGTTT	61.340	57.895	5.36	4.76	0.00	3.60
913	936	0.389391	TCGATCTCGGAAAGATGGCC	59.611	55.000	0.00	0.00	45.06	5.36
918	941	1.403814	AGCCATCGATCTCGGAAAGA	58.596	50.000	4.50	0.00	40.29	2.52
925	948	2.965477	GCAATCAAGCCATCGATCTC	57.035	50.000	0.00	0.00	0.00	2.75
950	973	2.433145	CCATGCCGATCCGATCCG	60.433	66.667	2.69	0.00	0.00	4.18
951	974	2.738213	AAGCCATGCCGATCCGATCC	62.738	60.000	2.69	0.00	0.00	3.36
952	975	1.294659	GAAGCCATGCCGATCCGATC	61.295	60.000	0.00	0.00	0.00	3.69
979	1002	1.135431	CATTTCCTTTTGCGGCGATGA	60.135	47.619	12.98	0.00	0.00	2.92
994	1023	1.172812	GCCGGCCTACCCATCATTTC	61.173	60.000	18.11	0.00	0.00	2.17
1005	1034	4.815108	TCTCTGCTCGCCGGCCTA	62.815	66.667	23.46	8.64	0.00	3.93
1007	1036	4.959596	GATCTCTGCTCGCCGGCC	62.960	72.222	23.46	7.69	0.00	6.13
1013	1045	1.008652	CTCAGGCGATCTCTGCTCG	60.009	63.158	7.74	0.00	39.11	5.03
1124	1156	1.954146	TGGACGTTGCAGAAGACGC	60.954	57.895	8.50	2.28	42.67	5.19
1171	1203	3.953775	CCAGTCGTTGGCCCTGGT	61.954	66.667	14.98	0.00	40.87	4.00
1190	1222	1.592400	CGCCTCGTGGTAGAAGGTGA	61.592	60.000	5.26	0.00	35.27	4.02
1353	1385	0.904649	AGATGAGCCATTGGTCGACA	59.095	50.000	18.91	0.00	41.98	4.35
1362	1394	1.876837	CGCAGCATGTAGATGAGCCAT	60.877	52.381	3.61	0.00	39.31	4.40
1421	1456	1.153107	TTGCAGATCGAGGCCATGG	60.153	57.895	7.63	7.63	0.00	3.66
1422	1457	1.769098	CGTTGCAGATCGAGGCCATG	61.769	60.000	5.01	0.00	0.00	3.66
1425	1460	2.167861	GTCGTTGCAGATCGAGGCC	61.168	63.158	10.11	0.00	36.76	5.19
1521	1612	2.037136	CGGCAGGTGAAGAGCCTTG	61.037	63.158	0.00	0.00	46.14	3.61
1538	1629	1.973138	CATAGCGTCCGTATTACCCG	58.027	55.000	0.00	0.00	0.00	5.28
1766	1857	1.605232	CTTCATGTTGTGACAGCAGCA	59.395	47.619	8.34	0.00	39.58	4.41
1844	1935	1.476007	AAGGACAAGAGCGGCTCAGT	61.476	55.000	29.88	25.89	32.06	3.41
1846	1937	1.004560	CAAGGACAAGAGCGGCTCA	60.005	57.895	29.88	0.00	32.06	4.26
1998	2089	2.640332	GAGAAGAACCTTCCCTCCAGTT	59.360	50.000	3.33	0.00	0.00	3.16
2006	2097	3.413327	GGAAACCTGAGAAGAACCTTCC	58.587	50.000	3.33	0.00	0.00	3.46
2031	2122	1.066858	GCCTCGTCAGGATTGAGAACA	60.067	52.381	0.00	0.00	43.65	3.18
2033	2124	1.478510	GAGCCTCGTCAGGATTGAGAA	59.521	52.381	0.00	0.00	39.13	2.87
2034	2125	1.107114	GAGCCTCGTCAGGATTGAGA	58.893	55.000	0.00	0.00	39.13	3.27
2035	2126	0.248825	CGAGCCTCGTCAGGATTGAG	60.249	60.000	5.82	0.00	41.75	3.02
2036	2127	1.809869	CGAGCCTCGTCAGGATTGA	59.190	57.895	5.82	0.00	41.75	2.57
2037	2128	4.409342	CGAGCCTCGTCAGGATTG	57.591	61.111	5.82	0.00	39.13	2.67
2048	2146	2.980233	GCCTTGCAACACGAGCCT	60.980	61.111	0.00	0.00	0.00	4.58
2065	2163	1.737793	GTGGCTTAATTCACGAGTGGG	59.262	52.381	3.19	0.00	0.00	4.61
2068	2166	1.001633	ACGGTGGCTTAATTCACGAGT	59.998	47.619	0.00	3.63	34.93	4.18
2079	2177	4.052229	CCGAGACGACGGTGGCTT	62.052	66.667	0.00	0.00	46.70	4.35
2127	2225	2.044555	TACAGCGACAGGACCTCCG	61.045	63.158	8.14	8.14	42.08	4.63
2196	2294	4.007581	TCCTCATTATCTTCCAGGTCCA	57.992	45.455	0.00	0.00	0.00	4.02
2210	2320	0.904649	TCCACTGCGTCATCCTCATT	59.095	50.000	0.00	0.00	0.00	2.57
2224	2334	1.205893	GCGTCATTCTCCTTCTCCACT	59.794	52.381	0.00	0.00	0.00	4.00
2242	2352	3.399797	TACCGACGAACCATCCGCG	62.400	63.158	0.00	0.00	0.00	6.46
2276	2392	1.079503	GACTCGTCAAGAACCATGGC	58.920	55.000	13.04	0.00	0.00	4.40
2311	2427	3.695606	ACTCGGTGCCGCAGACAT	61.696	61.111	5.64	0.00	39.59	3.06
2354	2470	1.938657	CTCTGTGTCTCGTCGCCCAT	61.939	60.000	0.00	0.00	0.00	4.00
2419	2535	1.733041	CACGAGGACGACGCACATT	60.733	57.895	0.00	0.00	42.66	2.71
2449	2565	1.742761	TGAGCTTAGACTGCAATGCC	58.257	50.000	1.53	0.00	0.00	4.40
2452	2568	3.681897	CGTTCTTGAGCTTAGACTGCAAT	59.318	43.478	0.00	0.00	0.00	3.56
2489	2605	1.243342	TTTTCTGCATCGGCCACCAG	61.243	55.000	2.24	2.92	40.13	4.00
2527	2643	7.330900	ACATGGATTCTGAGATTGTTTCATC	57.669	36.000	0.00	0.00	0.00	2.92
2546	2662	3.976942	CGAAAAGAACTTCTGCAACATGG	59.023	43.478	0.00	0.00	0.00	3.66
2549	2665	2.421775	TGCGAAAAGAACTTCTGCAACA	59.578	40.909	0.00	0.00	34.37	3.33
2550	2666	3.065019	TGCGAAAAGAACTTCTGCAAC	57.935	42.857	0.00	0.00	34.37	4.17
2551	2667	3.119673	TGTTGCGAAAAGAACTTCTGCAA	60.120	39.130	9.21	9.21	39.82	4.08
2553	2669	3.065019	TGTTGCGAAAAGAACTTCTGC	57.935	42.857	0.00	0.00	0.00	4.26
2554	2670	4.847633	TGATGTTGCGAAAAGAACTTCTG	58.152	39.130	0.00	0.00	31.04	3.02
2555	2671	5.471456	AGATGATGTTGCGAAAAGAACTTCT	59.529	36.000	0.00	0.00	31.04	2.85
2556	2672	5.566774	CAGATGATGTTGCGAAAAGAACTTC	59.433	40.000	0.00	0.00	0.00	3.01
2557	2673	5.009010	ACAGATGATGTTGCGAAAAGAACTT	59.991	36.000	0.00	0.00	39.96	2.66
2558	2674	4.516698	ACAGATGATGTTGCGAAAAGAACT	59.483	37.500	0.00	0.00	39.96	3.01
2559	2675	4.787598	ACAGATGATGTTGCGAAAAGAAC	58.212	39.130	0.00	0.00	39.96	3.01
2560	2676	6.204688	ACTTACAGATGATGTTGCGAAAAGAA	59.795	34.615	0.00	0.00	39.96	2.52
2561	2677	5.700832	ACTTACAGATGATGTTGCGAAAAGA	59.299	36.000	0.00	0.00	39.96	2.52
2562	2678	5.791974	CACTTACAGATGATGTTGCGAAAAG	59.208	40.000	0.00	0.00	39.96	2.27
2563	2679	5.688823	CACTTACAGATGATGTTGCGAAAA	58.311	37.500	0.00	0.00	39.96	2.29
2564	2680	4.378356	GCACTTACAGATGATGTTGCGAAA	60.378	41.667	0.00	0.00	39.96	3.46
2565	2681	3.125146	GCACTTACAGATGATGTTGCGAA	59.875	43.478	0.00	0.00	39.96	4.70
2566	2682	2.672874	GCACTTACAGATGATGTTGCGA	59.327	45.455	0.00	0.00	39.96	5.10
2567	2683	2.416202	TGCACTTACAGATGATGTTGCG	59.584	45.455	0.00	0.00	43.25	4.85
2568	2684	4.334759	AGATGCACTTACAGATGATGTTGC	59.665	41.667	0.00	0.00	39.96	4.17
2569	2685	6.760298	ACTAGATGCACTTACAGATGATGTTG	59.240	38.462	0.00	0.00	39.96	3.33
2570	2686	6.760298	CACTAGATGCACTTACAGATGATGTT	59.240	38.462	0.00	0.00	39.96	2.71
2571	2687	6.279123	CACTAGATGCACTTACAGATGATGT	58.721	40.000	0.00	0.00	46.45	3.06
2572	2688	6.766452	CACTAGATGCACTTACAGATGATG	57.234	41.667	0.00	0.00	0.00	3.07
2699	2815	3.519913	GGGTCATCTCTGGTAGGAAAACT	59.480	47.826	0.00	0.00	0.00	2.66
2806	2922	3.003480	GTCTTTGCGCTCCATAGTCTTT	58.997	45.455	9.73	0.00	0.00	2.52
2822	2938	7.373778	AGAACGACAAAACAACTAAGTCTTT	57.626	32.000	0.00	0.00	0.00	2.52
3126	3244	2.042026	GTTTATGGTTGTAGGGGGTGGT	59.958	50.000	0.00	0.00	0.00	4.16
3277	3395	5.757320	CAGATCACACAGACAGAAAGACTTT	59.243	40.000	0.00	0.00	0.00	2.66
3302	3420	9.031537	TCACAATCCTCAAGTGTAATAAGTCTA	57.968	33.333	0.00	0.00	33.63	2.59
3353	3471	4.774660	ATGACTCTTGGATGCTCAGAAT	57.225	40.909	0.00	0.00	0.00	2.40
3376	3494	2.202878	CGTTCACCGGCGATCCAT	60.203	61.111	9.30	0.00	0.00	3.41
3400	3518	5.104277	TCAAGGTAGACTTCCAAACCTTCAA	60.104	40.000	3.96	0.00	46.88	2.69
3435	3553	1.299976	GGTCCTCGCCCAATCACTT	59.700	57.895	0.00	0.00	0.00	3.16

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.