AutoCloner

Multiple sequence alignment - TraesCS3B01G577200

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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	TraesCS3B01G577200	chr3B	100.000	4962	0	0	1	4962	807290434	807285473	0.000000e+00	9164
1	TraesCS3B01G577200	chr3B	76.444	675	85	41	988	1628	816001100	816001734	1.040000e-76	298
2	TraesCS3B01G577200	chr3B	79.429	350	52	10	1955	2289	16521501	16521845	3.860000e-56	230
3	TraesCS3B01G577200	chr3B	81.905	210	33	5	1924	2130	313229634	313229427	6.600000e-39	172
4	TraesCS3B01G577200	chr3A	95.640	1835	66	10	2366	4196	729875293	729873469	0.000000e+00	2933
5	TraesCS3B01G577200	chr3A	91.839	772	52	8	4197	4961	729873425	729872658	0.000000e+00	1066
6	TraesCS3B01G577200	chr3A	94.048	672	33	4	3311	3981	729755109	729754444	0.000000e+00	1013
7	TraesCS3B01G577200	chr3A	93.958	480	20	8	1894	2370	729875813	729875340	0.000000e+00	717
8	TraesCS3B01G577200	chr3A	84.934	531	47	17	1356	1856	729876341	729875814	1.590000e-139	507
9	TraesCS3B01G577200	chr3A	88.430	363	9	13	726	1071	729877217	729876871	1.660000e-109	407
10	TraesCS3B01G577200	chr3A	88.000	350	28	5	2034	2370	729756372	729756024	7.740000e-108	401
11	TraesCS3B01G577200	chr3A	79.965	579	81	17	1373	1921	570022404	570021831	1.290000e-105	394
12	TraesCS3B01G577200	chr3D	95.916	1812	59	7	2368	4178	600125433	600123636	0.000000e+00	2922
13	TraesCS3B01G577200	chr3D	97.528	971	18	3	2447	3417	123944542	123945506	0.000000e+00	1655
14	TraesCS3B01G577200	chr3D	94.538	476	22	3	1898	2370	600125956	600125482	0.000000e+00	732
15	TraesCS3B01G577200	chr3D	84.664	639	63	20	4307	4937	71974558	71975169	5.490000e-169	604
16	TraesCS3B01G577200	chr3D	86.729	535	37	16	1351	1856	600126488	600125959	9.320000e-157	564
17	TraesCS3B01G577200	chr3D	81.037	675	47	36	714	1358	600127136	600126513	3.500000e-126	462
18	TraesCS3B01G577200	chr3D	82.353	391	31	18	988	1354	426386041	426385665	6.240000e-79	305
19	TraesCS3B01G577200	chr3D	92.727	110	6	1	3885	3994	510962176	510962069	1.850000e-34	158
20	TraesCS3B01G577200	chr4D	97.631	971	17	3	2447	3417	152578853	152577889	0.000000e+00	1661
21	TraesCS3B01G577200	chr4D	88.400	250	22	5	3953	4195	195137375	195137126	1.350000e-75	294
22	TraesCS3B01G577200	chr4D	89.956	229	19	4	3953	4178	152577888	152577661	4.860000e-75	292
23	TraesCS3B01G577200	chr4D	89.956	229	20	3	3953	4178	194366025	194365797	4.860000e-75	292
24	TraesCS3B01G577200	chr4D	84.507	284	39	4	1358	1638	294031892	294031611	4.890000e-70	276
25	TraesCS3B01G577200	chr4D	79.310	406	40	14	1474	1854	410096451	410096837	1.380000e-60	244
26	TraesCS3B01G577200	chr2D	97.631	971	17	3	2447	3417	502508743	502507779	0.000000e+00	1661
27	TraesCS3B01G577200	chr2D	79.167	408	42	13	1472	1854	291597153	291596764	4.960000e-60	243
28	TraesCS3B01G577200	chr2D	80.923	325	46	6	1955	2264	508407972	508408295	4.960000e-60	243
29	TraesCS3B01G577200	chr2D	82.511	223	25	11	4308	4527	636035822	636036033	3.050000e-42	183
30	TraesCS3B01G577200	chr2D	72.373	590	146	7	10	596	557644345	557643770	2.380000e-38	171
31	TraesCS3B01G577200	chr2D	92.727	110	6	1	3885	3994	529223744	529223851	1.850000e-34	158
32	TraesCS3B01G577200	chr5D	97.528	971	18	3	2447	3417	53119937	53118973	0.000000e+00	1655
33	TraesCS3B01G577200	chr5D	97.528	971	18	3	2447	3417	463447842	463446878	0.000000e+00	1655
34	TraesCS3B01G577200	chr5D	89.956	229	20	3	3953	4178	53118972	53118744	4.860000e-75	292
35	TraesCS3B01G577200	chr5D	85.714	259	36	1	1380	1638	123155408	123155665	6.330000e-69	272
36	TraesCS3B01G577200	chr5D	81.383	376	32	15	988	1358	481666086	481665744	6.330000e-69	272
37	TraesCS3B01G577200	chr5D	94.915	118	2	1	3605	3722	564515064	564514951	1.100000e-41	182
38	TraesCS3B01G577200	chr5D	92.727	110	6	1	3885	3994	62443291	62443184	1.850000e-34	158
39	TraesCS3B01G577200	chr6D	97.425	971	19	3	2447	3417	226231441	226232405	0.000000e+00	1650
40	TraesCS3B01G577200	chr6D	92.397	605	41	5	1	602	42938096	42938698	0.000000e+00	857
41	TraesCS3B01G577200	chr6D	89.956	229	20	3	3953	4178	226232406	226232634	4.860000e-75	292
42	TraesCS3B01G577200	chr6D	89.956	229	20	3	3953	4178	249016791	249017019	4.860000e-75	292
43	TraesCS3B01G577200	chr6D	89.956	229	20	3	3953	4178	445237522	445237294	4.860000e-75	292
44	TraesCS3B01G577200	chr6D	92.727	110	6	1	3885	3994	362896797	362896690	1.850000e-34	158
45	TraesCS3B01G577200	chr7D	97.322	971	18	4	2447	3417	91317047	91318009	0.000000e+00	1642
46	TraesCS3B01G577200	chr7D	92.231	605	42	5	1	602	69427861	69427259	0.000000e+00	852
47	TraesCS3B01G577200	chr7D	92.282	596	41	5	10	602	607104704	607104111	0.000000e+00	841
48	TraesCS3B01G577200	chr7D	83.690	374	35	13	988	1353	539123717	539123362	3.700000e-86	329
49	TraesCS3B01G577200	chr7D	92.727	110	6	1	3885	3994	59853272	59853379	1.850000e-34	158
50	TraesCS3B01G577200	chr5A	82.371	641	67	25	4307	4936	383188640	383188035	2.650000e-142	516
51	TraesCS3B01G577200	chr5A	81.013	395	37	17	988	1358	633521382	633521762	3.780000e-71	279
52	TraesCS3B01G577200	chr5A	80.563	355	47	11	1951	2289	380840131	380839783	2.290000e-63	254
53	TraesCS3B01G577200	chr7A	80.560	607	85	23	4307	4901	29705044	29704459	2.120000e-118	436
54	TraesCS3B01G577200	chr7A	80.645	372	34	16	991	1358	61448138	61447801	2.290000e-63	254
55	TraesCS3B01G577200	chr7B	76.558	947	112	49	988	1853	68916470	68917387	7.680000e-113	418
56	TraesCS3B01G577200	chr7B	85.128	195	25	3	992	1182	543521723	543521529	3.920000e-46	196
57	TraesCS3B01G577200	chr7B	85.246	122	14	4	4663	4781	561323431	561323551	6.750000e-24	122
58	TraesCS3B01G577200	chr1A	82.167	443	63	13	4371	4804	504570672	504570237	2.820000e-97	366
59	TraesCS3B01G577200	chr1D	77.793	707	79	32	988	1638	475430665	475429981	1.020000e-96	364
60	TraesCS3B01G577200	chr1D	83.333	396	27	15	988	1358	69687805	69687424	3.700000e-86	329
61	TraesCS3B01G577200	chr1D	94.915	118	2	1	3605	3722	4903087	4902974	1.100000e-41	182
62	TraesCS3B01G577200	chr1D	94.915	118	2	1	3605	3722	452101262	452101375	1.100000e-41	182
63	TraesCS3B01G577200	chr1D	92.727	110	6	1	3885	3994	8760214	8760321	1.850000e-34	158
64	TraesCS3B01G577200	chr6A	75.264	946	119	57	988	1851	97554710	97553798	1.320000e-90	344
65	TraesCS3B01G577200	chr6A	81.525	341	44	10	1958	2282	97553793	97553456	3.810000e-66	263
66	TraesCS3B01G577200	chr6A	85.567	194	24	3	990	1179	595723116	595723309	3.030000e-47	200
67	TraesCS3B01G577200	chr5B	83.540	322	41	11	4617	4935	182471548	182471860	1.750000e-74	291
68	TraesCS3B01G577200	chr4B	80.556	396	38	18	988	1358	201659888	201659507	8.190000e-68	268
69	TraesCS3B01G577200	chr1B	80.749	374	35	19	990	1358	502575552	502575893	1.770000e-64	257
70	TraesCS3B01G577200	chr6B	84.234	222	30	5	1958	2176	59501381	59501162	1.400000e-50	211

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	TraesCS3B01G577200	chr3B	807285473	807290434	4961	True	9164.0	9164	100.0000	1	4962	1	chr3B.!!$R2	4961
1	TraesCS3B01G577200	chr3B	816001100	816001734	634	False	298.0	298	76.4440	988	1628	1	chr3B.!!$F2	640
2	TraesCS3B01G577200	chr3A	729872658	729877217	4559	True	1126.0	2933	90.9602	726	4961	5	chr3A.!!$R3	4235
3	TraesCS3B01G577200	chr3A	729754444	729756372	1928	True	707.0	1013	91.0240	2034	3981	2	chr3A.!!$R2	1947
4	TraesCS3B01G577200	chr3A	570021831	570022404	573	True	394.0	394	79.9650	1373	1921	1	chr3A.!!$R1	548
5	TraesCS3B01G577200	chr3D	123944542	123945506	964	False	1655.0	1655	97.5280	2447	3417	1	chr3D.!!$F2	970
6	TraesCS3B01G577200	chr3D	600123636	600127136	3500	True	1170.0	2922	89.5550	714	4178	4	chr3D.!!$R3	3464
7	TraesCS3B01G577200	chr3D	71974558	71975169	611	False	604.0	604	84.6640	4307	4937	1	chr3D.!!$F1	630
8	TraesCS3B01G577200	chr4D	152577661	152578853	1192	True	976.5	1661	93.7935	2447	4178	2	chr4D.!!$R4	1731
9	TraesCS3B01G577200	chr2D	502507779	502508743	964	True	1661.0	1661	97.6310	2447	3417	1	chr2D.!!$R2	970
10	TraesCS3B01G577200	chr5D	463446878	463447842	964	True	1655.0	1655	97.5280	2447	3417	1	chr5D.!!$R2	970
11	TraesCS3B01G577200	chr5D	53118744	53119937	1193	True	973.5	1655	93.7420	2447	4178	2	chr5D.!!$R5	1731
12	TraesCS3B01G577200	chr6D	226231441	226232634	1193	False	971.0	1650	93.6905	2447	4178	2	chr6D.!!$F3	1731
13	TraesCS3B01G577200	chr6D	42938096	42938698	602	False	857.0	857	92.3970	1	602	1	chr6D.!!$F1	601
14	TraesCS3B01G577200	chr7D	91317047	91318009	962	False	1642.0	1642	97.3220	2447	3417	1	chr7D.!!$F2	970
15	TraesCS3B01G577200	chr7D	69427259	69427861	602	True	852.0	852	92.2310	1	602	1	chr7D.!!$R1	601
16	TraesCS3B01G577200	chr7D	607104111	607104704	593	True	841.0	841	92.2820	10	602	1	chr7D.!!$R3	592
17	TraesCS3B01G577200	chr5A	383188035	383188640	605	True	516.0	516	82.3710	4307	4936	1	chr5A.!!$R2	629
18	TraesCS3B01G577200	chr7A	29704459	29705044	585	True	436.0	436	80.5600	4307	4901	1	chr7A.!!$R1	594
19	TraesCS3B01G577200	chr7B	68916470	68917387	917	False	418.0	418	76.5580	988	1853	1	chr7B.!!$F1	865
20	TraesCS3B01G577200	chr1D	475429981	475430665	684	True	364.0	364	77.7930	988	1638	1	chr1D.!!$R3	650
21	TraesCS3B01G577200	chr6A	97553456	97554710	1254	True	303.5	344	78.3945	988	2282	2	chr6A.!!$R1	1294

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
531	533	0.105658	CCCTAGGGATCAAGGACCGA	60.106	60.0	24.99	37.50	4.69	F
655	658	0.107312	ATTTGAGCGCCTGCATCTCT	60.107	50.0	2.29	46.23	3.10	F
1101	1144	0.179084	TCTGCGCCCCTTATTCTTCG	60.179	55.0	4.18	0.00	3.79	F
1466	1804	0.251341	AGGGCAGGTTTTCAAGCGAT	60.251	50.0	0.00	0.00	4.58	F
1592	1930	0.879765	CTGCAACTGCTCCTCTTTGG	59.120	55.0	2.95	42.66	3.28	F
2477	2908	1.871080	CATCAAGGGATCCAGCGTAC	58.129	55.0	15.23	0.00	3.67	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	End Stability	Orientation
1870	2233	2.002586	CGCCAAGTAACATCAGACTGG	58.997	52.381	1.81	4.00	R
2425	2856	3.138283	TGTCTTTTCCAACTCATCCACCT	59.862	43.478	0.00	4.00	R
2794	3233	5.014544	TCATTCCCATCTGTCTCCTCTTTTT	59.985	40.000	0.00	1.94	R
3439	3880	5.583495	AGAATGAGCACGTACAGATAAGAC	58.417	41.667	0.00	3.01	R
3536	3977	2.158842	AGTTCATCATCCTGCTGCCTAC	60.159	50.000	0.00	3.18	R
3995	4437	0.245539	GAAGCAGGTACACGTAGGCA	59.754	55.000	0.00	4.75	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
32	33	1.478510	ACTGCTGTACCATCTTCTCCG	59.521	52.381	0.00	0.00	0.00	4.63
62	63	1.544825	CCACCAGGTCACCGATCTGT	61.545	60.000	3.71	0.00	38.98	3.41
117	118	1.727511	CCCCAGCGGCACATTGTATG	61.728	60.000	1.45	0.00	0.00	2.39
154	155	5.701224	TGGGACCTTCTCAAAAGTGTATTT	58.299	37.500	0.00	0.00	0.00	1.40
179	180	1.414158	TGGTTTTGGCCGGATCAAAA	58.586	45.000	23.34	23.34	40.46	2.44
197	198	6.360370	TCAAAATCCTCTACTACAAGCAGT	57.640	37.500	0.00	0.00	0.00	4.40
209	210	8.035394	TCTACTACAAGCAGTTCCTTATTGAAG	58.965	37.037	0.00	0.00	0.00	3.02
242	243	0.178891	TCTCCACTGCCTTCCTCCTT	60.179	55.000	0.00	0.00	0.00	3.36
272	273	2.291741	CTCCTGGAGCACAAACAGAAAC	59.708	50.000	11.42	0.00	34.21	2.78
289	290	3.858638	AGAAACCTATTCTCCCCCATGTT	59.141	43.478	0.00	0.00	0.00	2.71
299	300	2.307098	CTCCCCCATGTTCTTCACTTCT	59.693	50.000	0.00	0.00	0.00	2.85
301	302	3.519510	TCCCCCATGTTCTTCACTTCTAG	59.480	47.826	0.00	0.00	0.00	2.43
362	364	3.227250	CCCCCGTGTATCCAGGAC	58.773	66.667	0.00	0.00	0.00	3.85
367	369	1.475403	CCGTGTATCCAGGACTGTCT	58.525	55.000	7.85	0.00	0.00	3.41
373	375	3.701542	TGTATCCAGGACTGTCTGACATC	59.298	47.826	11.45	10.58	36.93	3.06
376	378	1.898472	CCAGGACTGTCTGACATCAGT	59.102	52.381	11.45	5.91	45.81	3.41
384	386	2.224523	TGTCTGACATCAGTTTCCCCAC	60.225	50.000	6.36	0.00	44.12	4.61
394	396	2.457323	TTTCCCCACCGCCTTCAGT	61.457	57.895	0.00	0.00	0.00	3.41
396	398	2.002018	TTCCCCACCGCCTTCAGTTT	62.002	55.000	0.00	0.00	0.00	2.66
469	471	1.153745	CTTCTCCGCTTCCGACAGG	60.154	63.158	0.00	0.00	36.29	4.00
506	508	0.179000	CCCTTCCACCTTCTCCATCG	59.821	60.000	0.00	0.00	0.00	3.84
509	511	0.537188	TTCCACCTTCTCCATCGCTC	59.463	55.000	0.00	0.00	0.00	5.03
513	515	1.144936	CCTTCTCCATCGCTCCACC	59.855	63.158	0.00	0.00	0.00	4.61
525	527	0.761802	GCTCCACCCTAGGGATCAAG	59.238	60.000	35.38	23.37	38.96	3.02
527	529	1.023719	TCCACCCTAGGGATCAAGGA	58.976	55.000	35.38	25.64	38.96	3.36
528	530	1.132500	CCACCCTAGGGATCAAGGAC	58.868	60.000	35.38	0.00	38.96	3.85
530	532	0.398664	ACCCTAGGGATCAAGGACCG	60.399	60.000	35.38	3.05	38.96	4.79
531	533	0.105658	CCCTAGGGATCAAGGACCGA	60.106	60.000	24.99	0.00	37.50	4.69
532	534	1.483307	CCCTAGGGATCAAGGACCGAT	60.483	57.143	24.99	0.00	37.50	4.18
533	535	1.896465	CCTAGGGATCAAGGACCGATC	59.104	57.143	0.00	1.71	38.86	3.69
578	581	0.834687	ACGACCAGGTGCCCTAGAAA	60.835	55.000	0.00	0.00	29.64	2.52
602	605	1.078848	GGAAGGCTGATCTGCGTGT	60.079	57.895	18.70	10.11	0.00	4.49
603	606	1.364626	GGAAGGCTGATCTGCGTGTG	61.365	60.000	18.70	0.00	0.00	3.82
604	607	1.975363	GAAGGCTGATCTGCGTGTGC	61.975	60.000	18.70	9.18	43.20	4.57
614	617	2.172419	GCGTGTGCGTGCGTTTAT	59.828	55.556	0.00	0.00	40.81	1.40
615	618	1.416820	GCGTGTGCGTGCGTTTATA	59.583	52.632	0.00	0.00	40.81	0.98
616	619	0.583083	GCGTGTGCGTGCGTTTATAG	60.583	55.000	0.00	0.00	40.81	1.31
617	620	0.986270	CGTGTGCGTGCGTTTATAGA	59.014	50.000	0.00	0.00	0.00	1.98
618	621	1.007422	CGTGTGCGTGCGTTTATAGAG	60.007	52.381	0.00	0.00	0.00	2.43
619	622	1.990563	GTGTGCGTGCGTTTATAGAGT	59.009	47.619	0.00	0.00	0.00	3.24
620	623	1.989864	TGTGCGTGCGTTTATAGAGTG	59.010	47.619	0.00	0.00	0.00	3.51
621	624	2.256174	GTGCGTGCGTTTATAGAGTGA	58.744	47.619	0.00	0.00	0.00	3.41
622	625	2.279136	GTGCGTGCGTTTATAGAGTGAG	59.721	50.000	0.00	0.00	0.00	3.51
623	626	2.094906	TGCGTGCGTTTATAGAGTGAGT	60.095	45.455	0.00	0.00	0.00	3.41
624	627	2.921754	GCGTGCGTTTATAGAGTGAGTT	59.078	45.455	0.00	0.00	0.00	3.01
625	628	3.367025	GCGTGCGTTTATAGAGTGAGTTT	59.633	43.478	0.00	0.00	0.00	2.66
626	629	4.721226	GCGTGCGTTTATAGAGTGAGTTTG	60.721	45.833	0.00	0.00	0.00	2.93
627	630	4.384846	CGTGCGTTTATAGAGTGAGTTTGT	59.615	41.667	0.00	0.00	0.00	2.83
628	631	5.609088	GTGCGTTTATAGAGTGAGTTTGTG	58.391	41.667	0.00	0.00	0.00	3.33
629	632	5.176958	GTGCGTTTATAGAGTGAGTTTGTGT	59.823	40.000	0.00	0.00	0.00	3.72
630	633	5.176774	TGCGTTTATAGAGTGAGTTTGTGTG	59.823	40.000	0.00	0.00	0.00	3.82
631	634	5.609088	CGTTTATAGAGTGAGTTTGTGTGC	58.391	41.667	0.00	0.00	0.00	4.57
632	635	5.609088	GTTTATAGAGTGAGTTTGTGTGCG	58.391	41.667	0.00	0.00	0.00	5.34
633	636	2.882927	TAGAGTGAGTTTGTGTGCGT	57.117	45.000	0.00	0.00	0.00	5.24
634	637	2.882927	AGAGTGAGTTTGTGTGCGTA	57.117	45.000	0.00	0.00	0.00	4.42
635	638	3.386768	AGAGTGAGTTTGTGTGCGTAT	57.613	42.857	0.00	0.00	0.00	3.06
636	639	4.514781	AGAGTGAGTTTGTGTGCGTATA	57.485	40.909	0.00	0.00	0.00	1.47
637	640	5.073311	AGAGTGAGTTTGTGTGCGTATAT	57.927	39.130	0.00	0.00	0.00	0.86
638	641	5.479306	AGAGTGAGTTTGTGTGCGTATATT	58.521	37.500	0.00	0.00	0.00	1.28
639	642	5.932303	AGAGTGAGTTTGTGTGCGTATATTT	59.068	36.000	0.00	0.00	0.00	1.40
640	643	5.927030	AGTGAGTTTGTGTGCGTATATTTG	58.073	37.500	0.00	0.00	0.00	2.32
641	644	5.699001	AGTGAGTTTGTGTGCGTATATTTGA	59.301	36.000	0.00	0.00	0.00	2.69
642	645	6.015504	GTGAGTTTGTGTGCGTATATTTGAG	58.984	40.000	0.00	0.00	0.00	3.02
643	646	4.969816	AGTTTGTGTGCGTATATTTGAGC	58.030	39.130	0.00	0.00	0.00	4.26
644	647	3.649870	TTGTGTGCGTATATTTGAGCG	57.350	42.857	0.00	0.00	0.00	5.03
649	652	0.110644	GCGTATATTTGAGCGCCTGC	60.111	55.000	2.29	0.00	43.52	4.85
650	653	1.217001	CGTATATTTGAGCGCCTGCA	58.783	50.000	2.29	0.00	46.23	4.41
651	654	1.800586	CGTATATTTGAGCGCCTGCAT	59.199	47.619	2.29	0.00	46.23	3.96
652	655	2.159787	CGTATATTTGAGCGCCTGCATC	60.160	50.000	2.29	0.00	46.23	3.91
653	656	2.267174	ATATTTGAGCGCCTGCATCT	57.733	45.000	2.29	0.00	46.23	2.90
654	657	1.586422	TATTTGAGCGCCTGCATCTC	58.414	50.000	2.29	0.00	46.23	2.75
655	658	0.107312	ATTTGAGCGCCTGCATCTCT	60.107	50.000	2.29	0.00	46.23	3.10
656	659	0.536724	TTTGAGCGCCTGCATCTCTA	59.463	50.000	2.29	0.00	46.23	2.43
657	660	0.536724	TTGAGCGCCTGCATCTCTAA	59.463	50.000	2.29	0.00	46.23	2.10
658	661	0.755079	TGAGCGCCTGCATCTCTAAT	59.245	50.000	2.29	0.00	46.23	1.73
659	662	1.146637	GAGCGCCTGCATCTCTAATG	58.853	55.000	2.29	0.00	46.23	1.90
660	663	0.755079	AGCGCCTGCATCTCTAATGA	59.245	50.000	2.29	0.00	46.23	2.57
661	664	1.146637	GCGCCTGCATCTCTAATGAG	58.853	55.000	0.00	0.00	42.15	2.90
662	665	1.539929	GCGCCTGCATCTCTAATGAGT	60.540	52.381	0.00	0.00	42.15	3.41
663	666	2.831333	CGCCTGCATCTCTAATGAGTT	58.169	47.619	0.00	0.00	40.98	3.01
664	667	3.201290	CGCCTGCATCTCTAATGAGTTT	58.799	45.455	0.00	0.00	40.98	2.66
665	668	3.002042	CGCCTGCATCTCTAATGAGTTTG	59.998	47.826	0.00	0.00	40.98	2.93
666	669	4.194640	GCCTGCATCTCTAATGAGTTTGA	58.805	43.478	0.00	0.00	40.98	2.69
667	670	4.637534	GCCTGCATCTCTAATGAGTTTGAA	59.362	41.667	0.00	0.00	40.98	2.69
668	671	5.124457	GCCTGCATCTCTAATGAGTTTGAAA	59.876	40.000	0.00	0.00	40.98	2.69
669	672	6.349611	GCCTGCATCTCTAATGAGTTTGAAAA	60.350	38.462	0.00	0.00	40.98	2.29
670	673	7.596494	CCTGCATCTCTAATGAGTTTGAAAAA	58.404	34.615	0.00	0.00	40.98	1.94
713	716	2.260844	CACAGGTGCAGAGAAAAGGA	57.739	50.000	0.00	0.00	0.00	3.36
714	717	2.149578	CACAGGTGCAGAGAAAAGGAG	58.850	52.381	0.00	0.00	0.00	3.69
715	718	1.771255	ACAGGTGCAGAGAAAAGGAGT	59.229	47.619	0.00	0.00	0.00	3.85
716	719	2.972713	ACAGGTGCAGAGAAAAGGAGTA	59.027	45.455	0.00	0.00	0.00	2.59
717	720	3.244249	ACAGGTGCAGAGAAAAGGAGTAC	60.244	47.826	0.00	0.00	0.00	2.73
718	721	2.972713	AGGTGCAGAGAAAAGGAGTACA	59.027	45.455	0.00	0.00	0.00	2.90
721	724	3.006967	GTGCAGAGAAAAGGAGTACAGGA	59.993	47.826	0.00	0.00	0.00	3.86
724	727	3.578716	CAGAGAAAAGGAGTACAGGACCA	59.421	47.826	0.00	0.00	0.00	4.02
735	738	1.045407	ACAGGACCAAGTCTACGCAA	58.955	50.000	0.00	0.00	32.47	4.85
756	759	2.203788	TTGGCTCTCCGTGGACCT	60.204	61.111	0.00	0.00	34.14	3.85
973	991	2.696125	GAATCCCAGCCTCCCCCA	60.696	66.667	0.00	0.00	0.00	4.96
974	992	3.023735	AATCCCAGCCTCCCCCAC	61.024	66.667	0.00	0.00	0.00	4.61
1066	1090	1.473497	GGGCTCGGTAATCCCCTCTC	61.473	65.000	0.00	0.00	34.59	3.20
1067	1091	1.660917	GCTCGGTAATCCCCTCTCG	59.339	63.158	0.00	0.00	0.00	4.04
1068	1092	1.660917	CTCGGTAATCCCCTCTCGC	59.339	63.158	0.00	0.00	0.00	5.03
1069	1093	1.807495	CTCGGTAATCCCCTCTCGCC	61.807	65.000	0.00	0.00	0.00	5.54
1070	1094	2.868986	CGGTAATCCCCTCTCGCCC	61.869	68.421	0.00	0.00	0.00	6.13
1071	1095	2.735237	GTAATCCCCTCTCGCCCG	59.265	66.667	0.00	0.00	0.00	6.13
1072	1096	3.231736	TAATCCCCTCTCGCCCGC	61.232	66.667	0.00	0.00	0.00	6.13
1101	1144	0.179084	TCTGCGCCCCTTATTCTTCG	60.179	55.000	4.18	0.00	0.00	3.79
1122	1170	5.437263	TCGTCTAGTTGCGAATTTTTGTTC	58.563	37.500	0.00	0.00	33.96	3.18
1179	1289	2.563427	GGCTGCAAACCGCTTCTC	59.437	61.111	0.50	0.00	43.06	2.87
1202	1497	8.604184	TCTCTACTCCAGTACTGTATATAAGGG	58.396	40.741	21.18	10.54	0.00	3.95
1208	1503	5.106237	CCAGTACTGTATATAAGGGCGTCTC	60.106	48.000	21.18	0.00	0.00	3.36
1209	1504	5.008980	AGTACTGTATATAAGGGCGTCTCC	58.991	45.833	0.00	0.00	0.00	3.71
1210	1505	3.840991	ACTGTATATAAGGGCGTCTCCA	58.159	45.455	0.00	0.00	36.21	3.86
1238	1533	0.529337	CTGTATGGCTGAGGCAGTCG	60.529	60.000	15.56	0.00	42.43	4.18
1288	1583	1.607628	GATTCATGATGCTGGCTGGTC	59.392	52.381	0.00	0.00	0.00	4.02
1289	1584	0.328926	TTCATGATGCTGGCTGGTCA	59.671	50.000	0.00	0.00	0.00	4.02
1291	1586	1.101635	CATGATGCTGGCTGGTCAGG	61.102	60.000	4.34	0.00	35.43	3.86
1339	1640	9.113838	AGATGATGTAATATTGGTTCTGTTGTC	57.886	33.333	0.00	0.00	0.00	3.18
1418	1756	1.503542	CTGCCGTGCTTGTGGAATC	59.496	57.895	0.00	0.00	0.00	2.52
1436	1774	3.889520	ATCGGAGTTACTTGAGGGAAC	57.110	47.619	0.00	0.00	0.00	3.62
1457	1795	2.521708	GGTGTGCAGGGCAGGTTT	60.522	61.111	0.00	0.00	40.08	3.27
1463	1801	1.005748	GCAGGGCAGGTTTTCAAGC	60.006	57.895	0.00	0.00	0.00	4.01
1465	1803	1.150536	AGGGCAGGTTTTCAAGCGA	59.849	52.632	0.00	0.00	0.00	4.93
1466	1804	0.251341	AGGGCAGGTTTTCAAGCGAT	60.251	50.000	0.00	0.00	0.00	4.58
1592	1930	0.879765	CTGCAACTGCTCCTCTTTGG	59.120	55.000	2.95	0.00	42.66	3.28
1649	2012	5.825593	AAAGATGAGTCTCCTGTGGTTTA	57.174	39.130	0.00	0.00	32.15	2.01
1655	2018	6.187727	TGAGTCTCCTGTGGTTTAAGAAAT	57.812	37.500	0.00	0.00	0.00	2.17
1659	2022	6.935208	AGTCTCCTGTGGTTTAAGAAATACAC	59.065	38.462	0.00	0.00	34.07	2.90
1678	2041	3.691118	ACACGCATTTATCTGTCATGCTT	59.309	39.130	2.18	0.00	41.06	3.91
1724	2087	7.009723	GCTCCTCTGTATTTCTTAAAACTCTCG	59.990	40.741	0.00	0.00	0.00	4.04
1758	2121	6.487668	CACAAACATATTGGATCATCAGCCTA	59.512	38.462	0.00	0.00	0.00	3.93
1796	2159	4.292186	TCTTCTTTTGGTCCTGAGGATG	57.708	45.455	3.65	0.00	32.73	3.51
1815	2178	3.402628	TGAGGACCTTTCTTTTCTCCG	57.597	47.619	0.00	0.00	0.00	4.63
1856	2219	4.232091	AGTTTGTAAGGGAGGTTCTCTCA	58.768	43.478	0.00	0.00	44.19	3.27
1857	2220	4.040584	AGTTTGTAAGGGAGGTTCTCTCAC	59.959	45.833	0.00	0.00	46.17	3.51
1890	2253	2.002586	CCAGTCTGATGTTACTTGGCG	58.997	52.381	0.00	0.00	0.00	5.69
1896	2259	6.923508	CAGTCTGATGTTACTTGGCGAATATA	59.076	38.462	0.00	0.00	0.00	0.86
1940	2305	7.336931	GGAAGAGACTGATTTTTAACCATGCTA	59.663	37.037	0.00	0.00	0.00	3.49
1950	2315	8.823220	ATTTTTAACCATGCTACCTGAATACT	57.177	30.769	0.00	0.00	0.00	2.12
2183	2562	4.650734	TCAAACTGCATGTATCTTGGTCA	58.349	39.130	0.00	0.00	0.00	4.02
2185	2564	5.355071	TCAAACTGCATGTATCTTGGTCATC	59.645	40.000	0.00	0.00	0.00	2.92
2224	2603	6.658816	TCTTCATTTTGCAGATTGGTAAGCTA	59.341	34.615	0.00	0.00	0.00	3.32
2276	2655	7.391620	AGTTTCTTCAAACACCGGAGAATATA	58.608	34.615	9.46	0.00	43.98	0.86
2282	2661	8.746052	TTCAAACACCGGAGAATATATTCATT	57.254	30.769	24.00	7.47	39.23	2.57
2300	2679	9.994432	ATATTCATTTAACAAAAGAGCTTCTCG	57.006	29.630	0.00	0.00	35.36	4.04
2363	2793	4.990426	GCAAAACAGCACCAATAGTCAATT	59.010	37.500	0.00	0.00	0.00	2.32
2477	2908	1.871080	CATCAAGGGATCCAGCGTAC	58.129	55.000	15.23	0.00	0.00	3.67
2835	3274	6.945435	TGGGAATGACATTTATGTTAGTGTGT	59.055	34.615	1.39	0.00	41.95	3.72
3122	3562	9.567848	GTACAAATATGTTGGTTAGAAACATGG	57.432	33.333	11.10	2.72	45.47	3.66
3241	3681	6.389091	TGGTGTTCTATGCATTGCTAAAAAG	58.611	36.000	3.54	0.00	0.00	2.27
3255	3696	1.975660	AAAAAGCTCTGTTACCGCCA	58.024	45.000	0.00	0.00	0.00	5.69
3328	3769	6.552350	AGCATGAGCATCCTAACCATTTTTAT	59.448	34.615	0.00	0.00	45.49	1.40
3439	3880	4.083110	ACAGCCTTTTCATGAACTGAATCG	60.083	41.667	23.33	8.06	43.30	3.34
3493	3934	4.339814	CCCTTGAGAGACCTGTATGAGTAC	59.660	50.000	0.00	0.00	0.00	2.73
3518	3959	6.237490	CGCTCTTGGTTATCGTTAACTAACTG	60.237	42.308	14.34	9.57	34.86	3.16
3594	4035	1.092345	GCGTTCAGAGGATTGGAGGC	61.092	60.000	0.00	0.00	31.10	4.70
3624	4065	5.690857	GCTTACCATACACGAAGAACTATCC	59.309	44.000	0.00	0.00	0.00	2.59
3635	4076	2.946785	AGAACTATCCGGACAGGTAGG	58.053	52.381	15.58	0.00	41.99	3.18
3652	4093	0.322975	AGGTGCTACTGACTGGCAAG	59.677	55.000	0.00	0.00	37.73	4.01
3653	4094	1.301677	GGTGCTACTGACTGGCAAGC	61.302	60.000	0.11	0.11	37.73	4.01
3654	4095	1.374631	TGCTACTGACTGGCAAGCG	60.375	57.895	2.95	0.00	35.95	4.68
3655	4096	2.744768	GCTACTGACTGGCAAGCGC	61.745	63.158	0.00	0.00	37.44	5.92
3768	4209	4.618693	GCAGAGGAAGTAACTGGAGTACAC	60.619	50.000	0.00	0.00	33.00	2.90
3966	4407	7.269084	CGTTCTAGTGTTTTTGACATAGCAATG	59.731	37.037	0.00	0.00	41.10	2.82
3995	4437	7.887381	ACTACTCGTATACCGTATAGTGTACT	58.113	38.462	0.00	0.00	37.12	2.73
3996	4438	7.810282	ACTACTCGTATACCGTATAGTGTACTG	59.190	40.741	0.00	0.00	37.12	2.74
3997	4439	5.406780	ACTCGTATACCGTATAGTGTACTGC	59.593	44.000	0.00	0.00	33.54	4.40
4014	4458	0.245539	TGCCTACGTGTACCTGCTTC	59.754	55.000	0.00	0.00	0.00	3.86
4043	4487	6.160576	AGTTGTGTTCCACATTAAGCATTT	57.839	33.333	0.00	0.00	44.16	2.32
4084	4528	6.668323	TCCACGTTTGAATGAAAAATCTCTC	58.332	36.000	0.00	0.00	0.00	3.20
4247	4735	9.745018	ATATCTATGAATCCGATGAACCAAAAT	57.255	29.630	0.00	0.00	0.00	1.82
4256	4744	5.043248	CCGATGAACCAAAATTGCTATTCC	58.957	41.667	0.00	0.00	0.00	3.01
4259	4747	5.054390	TGAACCAAAATTGCTATTCCGAC	57.946	39.130	0.00	0.00	0.00	4.79
4294	4782	9.909644	TTCTTGTAAAACTAGTCAGATAGTCAC	57.090	33.333	0.00	0.00	34.90	3.67
4302	4790	3.348119	AGTCAGATAGTCACAGCTTCGA	58.652	45.455	0.00	0.00	0.00	3.71
4385	4874	1.149627	ACAGGCGCCCAAAACTGTA	59.850	52.632	26.15	0.00	41.95	2.74
4386	4875	0.889186	ACAGGCGCCCAAAACTGTAG	60.889	55.000	26.15	2.69	41.95	2.74
4542	5037	8.722394	TGTTCCAGTTTTTAAAAATGTTTGGAC	58.278	29.630	23.85	20.36	32.25	4.02
4545	5040	8.722394	TCCAGTTTTTAAAAATGTTTGGACAAC	58.278	29.630	22.03	8.19	39.66	3.32
4937	5441	6.959671	TTCAAAACATGTTCACTTTTCCAC	57.040	33.333	12.39	0.00	0.00	4.02
4948	5452	2.095969	CACTTTTCCACGCGCTATTTGA	60.096	45.455	5.73	0.00	0.00	2.69
4950	5454	0.440758	TTTCCACGCGCTATTTGACG	59.559	50.000	5.73	0.00	0.00	4.35

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
62	63	0.044092	TGGCTGAGGACATAGGGGAA	59.956	55.000	0.00	0.00	0.00	3.97
154	155	0.693622	TCCGGCCAAAACCATAGACA	59.306	50.000	2.24	0.00	0.00	3.41
179	180	4.615513	AGGAACTGCTTGTAGTAGAGGAT	58.384	43.478	0.00	0.00	37.18	3.24
216	217	1.280421	GAAGGCAGTGGAGAATGGTCT	59.720	52.381	0.00	0.00	36.55	3.85
230	231	0.253347	AGATGGGAAGGAGGAAGGCA	60.253	55.000	0.00	0.00	0.00	4.75
259	260	4.082733	GGGAGAATAGGTTTCTGTTTGTGC	60.083	45.833	0.00	0.00	0.00	4.57
272	273	3.459598	TGAAGAACATGGGGGAGAATAGG	59.540	47.826	0.00	0.00	0.00	2.57
289	290	6.071108	CCCAATGAAGAGACTAGAAGTGAAGA	60.071	42.308	0.00	0.00	0.00	2.87
299	300	2.265367	TGGTGCCCAATGAAGAGACTA	58.735	47.619	0.00	0.00	0.00	2.59
301	302	1.815003	CTTGGTGCCCAATGAAGAGAC	59.185	52.381	7.06	0.00	43.07	3.36
358	360	3.007398	GGAAACTGATGTCAGACAGTCCT	59.993	47.826	16.41	0.00	46.59	3.85
361	363	2.039084	GGGGAAACTGATGTCAGACAGT	59.961	50.000	16.41	8.92	46.59	3.55
362	364	2.038952	TGGGGAAACTGATGTCAGACAG	59.961	50.000	16.41	3.78	46.59	3.51
367	369	0.036164	CGGTGGGGAAACTGATGTCA	59.964	55.000	0.00	0.00	0.00	3.58
373	375	1.971695	GAAGGCGGTGGGGAAACTG	60.972	63.158	0.00	0.00	0.00	3.16
376	378	2.002018	AACTGAAGGCGGTGGGGAAA	62.002	55.000	0.00	0.00	32.82	3.13
384	386	1.017387	GGATGCTAAACTGAAGGCGG	58.983	55.000	0.00	0.00	0.00	6.13
421	423	0.419459	AGGTGGGGTGGAGAAGATCT	59.581	55.000	0.00	0.00	0.00	2.75
469	471	0.659957	GGATGCTGCGGAAGATGAAC	59.340	55.000	0.00	0.00	0.00	3.18
506	508	0.761802	CTTGATCCCTAGGGTGGAGC	59.238	60.000	27.58	12.03	38.77	4.70
509	511	1.132500	GTCCTTGATCCCTAGGGTGG	58.868	60.000	27.58	20.19	36.21	4.61
513	515	1.896465	GATCGGTCCTTGATCCCTAGG	59.104	57.143	0.06	0.06	36.97	3.02
525	527	2.990066	AGAGTGAATTGGATCGGTCC	57.010	50.000	8.12	8.12	45.31	4.46
527	529	3.375699	ACCTAGAGTGAATTGGATCGGT	58.624	45.455	0.00	0.00	0.00	4.69
528	530	4.408182	AACCTAGAGTGAATTGGATCGG	57.592	45.455	0.00	0.00	0.00	4.18
530	532	5.355350	CACCAAACCTAGAGTGAATTGGATC	59.645	44.000	14.91	0.00	39.69	3.36
531	533	5.256474	CACCAAACCTAGAGTGAATTGGAT	58.744	41.667	14.91	3.54	39.69	3.41
532	534	4.506625	CCACCAAACCTAGAGTGAATTGGA	60.507	45.833	14.91	0.00	39.69	3.53
533	535	3.758554	CCACCAAACCTAGAGTGAATTGG	59.241	47.826	0.00	0.00	42.29	3.16
535	537	4.724279	ACCACCAAACCTAGAGTGAATT	57.276	40.909	0.00	0.00	31.79	2.17
536	538	4.724279	AACCACCAAACCTAGAGTGAAT	57.276	40.909	0.00	0.00	31.79	2.57
537	539	4.513406	AAACCACCAAACCTAGAGTGAA	57.487	40.909	0.00	0.00	31.79	3.18
602	605	2.094906	ACTCACTCTATAAACGCACGCA	60.095	45.455	0.00	0.00	0.00	5.24
603	606	2.527100	ACTCACTCTATAAACGCACGC	58.473	47.619	0.00	0.00	0.00	5.34
604	607	4.384846	ACAAACTCACTCTATAAACGCACG	59.615	41.667	0.00	0.00	0.00	5.34
605	608	5.176958	ACACAAACTCACTCTATAAACGCAC	59.823	40.000	0.00	0.00	0.00	5.34
606	609	5.176774	CACACAAACTCACTCTATAAACGCA	59.823	40.000	0.00	0.00	0.00	5.24
607	610	5.609088	CACACAAACTCACTCTATAAACGC	58.391	41.667	0.00	0.00	0.00	4.84
608	611	5.609088	GCACACAAACTCACTCTATAAACG	58.391	41.667	0.00	0.00	0.00	3.60
609	612	5.176958	ACGCACACAAACTCACTCTATAAAC	59.823	40.000	0.00	0.00	0.00	2.01
610	613	5.294356	ACGCACACAAACTCACTCTATAAA	58.706	37.500	0.00	0.00	0.00	1.40
611	614	4.878439	ACGCACACAAACTCACTCTATAA	58.122	39.130	0.00	0.00	0.00	0.98
612	615	4.514781	ACGCACACAAACTCACTCTATA	57.485	40.909	0.00	0.00	0.00	1.31
613	616	3.386768	ACGCACACAAACTCACTCTAT	57.613	42.857	0.00	0.00	0.00	1.98
614	617	2.882927	ACGCACACAAACTCACTCTA	57.117	45.000	0.00	0.00	0.00	2.43
615	618	2.882927	TACGCACACAAACTCACTCT	57.117	45.000	0.00	0.00	0.00	3.24
616	619	5.779806	AATATACGCACACAAACTCACTC	57.220	39.130	0.00	0.00	0.00	3.51
617	620	5.699001	TCAAATATACGCACACAAACTCACT	59.301	36.000	0.00	0.00	0.00	3.41
618	621	5.922546	TCAAATATACGCACACAAACTCAC	58.077	37.500	0.00	0.00	0.00	3.51
619	622	5.390461	GCTCAAATATACGCACACAAACTCA	60.390	40.000	0.00	0.00	0.00	3.41
620	623	5.022021	GCTCAAATATACGCACACAAACTC	58.978	41.667	0.00	0.00	0.00	3.01
621	624	4.435518	CGCTCAAATATACGCACACAAACT	60.436	41.667	0.00	0.00	0.00	2.66
622	625	3.778718	CGCTCAAATATACGCACACAAAC	59.221	43.478	0.00	0.00	0.00	2.93
623	626	3.997276	CGCTCAAATATACGCACACAAA	58.003	40.909	0.00	0.00	0.00	2.83
624	627	3.649870	CGCTCAAATATACGCACACAA	57.350	42.857	0.00	0.00	0.00	3.33
631	634	1.217001	TGCAGGCGCTCAAATATACG	58.783	50.000	7.64	0.00	39.64	3.06
632	635	3.070018	AGATGCAGGCGCTCAAATATAC	58.930	45.455	7.64	0.00	39.64	1.47
633	636	3.007290	AGAGATGCAGGCGCTCAAATATA	59.993	43.478	7.64	0.00	39.64	0.86
634	637	2.149578	GAGATGCAGGCGCTCAAATAT	58.850	47.619	7.64	0.00	39.64	1.28
635	638	1.139654	AGAGATGCAGGCGCTCAAATA	59.860	47.619	7.64	0.00	39.64	1.40
636	639	0.107312	AGAGATGCAGGCGCTCAAAT	60.107	50.000	7.64	0.00	39.64	2.32
637	640	0.536724	TAGAGATGCAGGCGCTCAAA	59.463	50.000	7.64	0.00	39.64	2.69
638	641	0.536724	TTAGAGATGCAGGCGCTCAA	59.463	50.000	7.64	0.00	39.64	3.02
639	642	0.755079	ATTAGAGATGCAGGCGCTCA	59.245	50.000	7.64	3.41	39.64	4.26
640	643	1.146637	CATTAGAGATGCAGGCGCTC	58.853	55.000	7.64	0.00	39.64	5.03
641	644	0.755079	TCATTAGAGATGCAGGCGCT	59.245	50.000	7.64	0.00	39.64	5.92
642	645	1.146637	CTCATTAGAGATGCAGGCGC	58.853	55.000	0.00	0.00	44.98	6.53
643	646	2.522836	ACTCATTAGAGATGCAGGCG	57.477	50.000	0.00	0.00	44.98	5.52
644	647	4.194640	TCAAACTCATTAGAGATGCAGGC	58.805	43.478	0.00	0.00	44.98	4.85
645	648	6.748333	TTTCAAACTCATTAGAGATGCAGG	57.252	37.500	0.00	0.00	44.98	4.85
671	674	1.066303	TGCGTGCCGATTTGAGTTTTT	59.934	42.857	0.00	0.00	0.00	1.94
672	675	0.665835	TGCGTGCCGATTTGAGTTTT	59.334	45.000	0.00	0.00	0.00	2.43
673	676	0.040425	GTGCGTGCCGATTTGAGTTT	60.040	50.000	0.00	0.00	0.00	2.66
674	677	1.574428	GTGCGTGCCGATTTGAGTT	59.426	52.632	0.00	0.00	0.00	3.01
675	678	2.667318	CGTGCGTGCCGATTTGAGT	61.667	57.895	0.00	0.00	0.00	3.41
676	679	2.096406	CGTGCGTGCCGATTTGAG	59.904	61.111	0.00	0.00	0.00	3.02
677	680	4.083600	GCGTGCGTGCCGATTTGA	62.084	61.111	6.86	0.00	0.00	2.69
678	681	4.382114	TGCGTGCGTGCCGATTTG	62.382	61.111	6.86	0.00	0.00	2.32
679	682	4.383602	GTGCGTGCGTGCCGATTT	62.384	61.111	6.86	0.00	0.00	2.17
694	697	2.149578	CTCCTTTTCTCTGCACCTGTG	58.850	52.381	0.00	0.00	0.00	3.66
695	698	1.771255	ACTCCTTTTCTCTGCACCTGT	59.229	47.619	0.00	0.00	0.00	4.00
696	699	2.557920	ACTCCTTTTCTCTGCACCTG	57.442	50.000	0.00	0.00	0.00	4.00
697	700	2.972713	TGTACTCCTTTTCTCTGCACCT	59.027	45.455	0.00	0.00	0.00	4.00
698	701	3.330267	CTGTACTCCTTTTCTCTGCACC	58.670	50.000	0.00	0.00	0.00	5.01
699	702	3.006967	TCCTGTACTCCTTTTCTCTGCAC	59.993	47.826	0.00	0.00	0.00	4.57
700	703	3.006967	GTCCTGTACTCCTTTTCTCTGCA	59.993	47.826	0.00	0.00	0.00	4.41
701	704	3.591023	GTCCTGTACTCCTTTTCTCTGC	58.409	50.000	0.00	0.00	0.00	4.26
702	705	3.578716	TGGTCCTGTACTCCTTTTCTCTG	59.421	47.826	0.00	0.00	0.00	3.35
703	706	3.858135	TGGTCCTGTACTCCTTTTCTCT	58.142	45.455	0.00	0.00	0.00	3.10
704	707	4.040584	ACTTGGTCCTGTACTCCTTTTCTC	59.959	45.833	0.00	0.00	0.00	2.87
705	708	3.974642	ACTTGGTCCTGTACTCCTTTTCT	59.025	43.478	0.00	0.00	0.00	2.52
706	709	4.040584	AGACTTGGTCCTGTACTCCTTTTC	59.959	45.833	0.00	0.00	32.18	2.29
707	710	3.974642	AGACTTGGTCCTGTACTCCTTTT	59.025	43.478	0.00	0.00	32.18	2.27
708	711	3.588569	AGACTTGGTCCTGTACTCCTTT	58.411	45.455	0.00	0.00	32.18	3.11
709	712	3.261818	AGACTTGGTCCTGTACTCCTT	57.738	47.619	0.00	0.00	32.18	3.36
710	713	3.699413	GTAGACTTGGTCCTGTACTCCT	58.301	50.000	0.00	0.00	32.18	3.69
711	714	2.422832	CGTAGACTTGGTCCTGTACTCC	59.577	54.545	0.00	0.00	32.18	3.85
712	715	2.159407	GCGTAGACTTGGTCCTGTACTC	60.159	54.545	0.00	0.00	32.18	2.59
713	716	1.817447	GCGTAGACTTGGTCCTGTACT	59.183	52.381	0.00	0.00	32.18	2.73
714	717	1.542915	TGCGTAGACTTGGTCCTGTAC	59.457	52.381	0.00	0.00	32.18	2.90
715	718	1.913778	TGCGTAGACTTGGTCCTGTA	58.086	50.000	0.00	0.00	32.18	2.74
716	719	1.045407	TTGCGTAGACTTGGTCCTGT	58.955	50.000	0.00	0.00	32.18	4.00
717	720	1.429463	GTTGCGTAGACTTGGTCCTG	58.571	55.000	0.00	0.00	32.18	3.86
718	721	0.320697	GGTTGCGTAGACTTGGTCCT	59.679	55.000	0.00	0.00	32.18	3.85
721	724	0.105408	AACGGTTGCGTAGACTTGGT	59.895	50.000	0.00	0.00	0.00	3.67
724	727	1.226030	GCCAACGGTTGCGTAGACTT	61.226	55.000	15.31	0.00	0.00	3.01
735	738	4.003788	CCACGGAGAGCCAACGGT	62.004	66.667	0.00	0.00	0.00	4.83
743	746	2.856039	TAGGCCAGGTCCACGGAGAG	62.856	65.000	5.01	0.00	0.00	3.20
846	864	0.028902	GTTGGTGTTGGTGTTCGCTC	59.971	55.000	0.00	0.00	0.00	5.03
847	865	1.711060	CGTTGGTGTTGGTGTTCGCT	61.711	55.000	0.00	0.00	0.00	4.93
848	866	1.298041	CGTTGGTGTTGGTGTTCGC	60.298	57.895	0.00	0.00	0.00	4.70
849	867	0.027063	GTCGTTGGTGTTGGTGTTCG	59.973	55.000	0.00	0.00	0.00	3.95
850	868	1.088306	TGTCGTTGGTGTTGGTGTTC	58.912	50.000	0.00	0.00	0.00	3.18
902	920	3.243334	CGAACGAACCCTACCTAGGATTC	60.243	52.174	17.98	9.64	46.63	2.52
1079	1103	1.894282	GAATAAGGGGCGCAGAGGC	60.894	63.158	10.83	0.00	45.91	4.70
1101	1144	5.709140	CGAACAAAAATTCGCAACTAGAC	57.291	39.130	0.00	0.00	44.37	2.59
1167	1277	2.028930	ACTGGAGTAGAGAAGCGGTTTG	60.029	50.000	0.00	0.00	0.00	2.93
1179	1289	6.093771	CGCCCTTATATACAGTACTGGAGTAG	59.906	46.154	26.12	13.17	34.19	2.57
1202	1497	0.171455	CAGTACTGGAGTGGAGACGC	59.829	60.000	15.49	0.00	42.66	5.19
1208	1503	2.111384	AGCCATACAGTACTGGAGTGG	58.889	52.381	26.12	26.31	34.24	4.00
1209	1504	2.760650	TCAGCCATACAGTACTGGAGTG	59.239	50.000	26.12	19.23	34.24	3.51
1210	1505	3.027412	CTCAGCCATACAGTACTGGAGT	58.973	50.000	26.12	8.69	34.24	3.85
1238	1533	2.108970	AGTACTACCTACCAAGCTGGC	58.891	52.381	0.00	0.00	42.67	4.85
1323	1618	5.123227	CCCATACGACAACAGAACCAATAT	58.877	41.667	0.00	0.00	0.00	1.28
1339	1640	4.077300	AGCATGCATATATCCCCATACG	57.923	45.455	21.98	0.00	0.00	3.06
1376	1714	6.151144	AGGTGTGCAGAGTTTAAATTGGATAC	59.849	38.462	0.00	1.44	0.00	2.24
1418	1756	3.326747	CTTGTTCCCTCAAGTAACTCCG	58.673	50.000	0.00	0.00	39.66	4.63
1436	1774	2.987547	CTGCCCTGCACACCCTTG	60.988	66.667	0.00	0.00	33.79	3.61
1440	1778	2.087462	GAAAACCTGCCCTGCACACC	62.087	60.000	0.00	0.00	33.79	4.16
1457	1795	5.393124	CAAACTAGCAATCAATCGCTTGAA	58.607	37.500	5.70	0.00	44.29	2.69
1463	1801	6.111768	AGTAAGCAAACTAGCAATCAATCG	57.888	37.500	0.00	0.00	36.85	3.34
1592	1930	6.595716	CAGTCTAATGGCCTTATAATACCAGC	59.404	42.308	3.32	0.00	35.20	4.85
1649	2012	7.609760	TGACAGATAAATGCGTGTATTTCTT	57.390	32.000	0.00	0.00	32.79	2.52
1655	2018	4.794248	GCATGACAGATAAATGCGTGTA	57.206	40.909	0.00	0.00	37.55	2.90
1678	2041	5.476945	GGAGCTTTATCCTCAGGAAAAACAA	59.523	40.000	0.00	0.00	34.34	2.83
1724	2087	8.190122	TGATCCAATATGTTTGTGAAACTATGC	58.810	33.333	0.00	0.00	41.90	3.14
1796	2159	2.077627	GCGGAGAAAAGAAAGGTCCTC	58.922	52.381	0.00	0.00	0.00	3.71
1815	2178	3.431415	ACTCCCATTCTTTTAACCCAGC	58.569	45.455	0.00	0.00	0.00	4.85
1856	2219	3.641436	TCAGACTGGTGTTCACATACAGT	59.359	43.478	15.86	15.86	44.11	3.55
1857	2220	4.257267	TCAGACTGGTGTTCACATACAG	57.743	45.455	1.81	11.10	38.67	2.74
1870	2233	2.002586	CGCCAAGTAACATCAGACTGG	58.997	52.381	1.81	0.00	0.00	4.00
1940	2305	5.896678	AGAGCTCTGTATCAAGTATTCAGGT	59.103	40.000	17.42	0.00	0.00	4.00
1977	2342	7.095183	AGAGGCCATGGATTATCAGATAAAA	57.905	36.000	18.40	0.00	0.00	1.52
2224	2603	3.594603	CACCGATGGAAAGTAGTCTGT	57.405	47.619	0.00	0.00	0.00	3.41
2276	2655	6.803807	GCGAGAAGCTCTTTTGTTAAATGAAT	59.196	34.615	0.00	0.00	44.04	2.57
2380	2810	5.945784	TCAGCCCAGAATAAATATATGGCAC	59.054	40.000	8.62	0.00	40.08	5.01
2409	2839	7.601856	TCATCCACCTTAAACATAAGCAAAAG	58.398	34.615	0.00	0.00	0.00	2.27
2425	2856	3.138283	TGTCTTTTCCAACTCATCCACCT	59.862	43.478	0.00	0.00	0.00	4.00
2477	2908	5.655488	AGTTCAACTTCATCGAGTCCATAG	58.345	41.667	0.00	0.00	0.00	2.23
2794	3233	5.014544	TCATTCCCATCTGTCTCCTCTTTTT	59.985	40.000	0.00	0.00	0.00	1.94
2835	3274	8.353684	TCACTTTGCCAATCGTAAAGATAAAAA	58.646	29.630	7.21	0.00	44.44	1.94
3439	3880	5.583495	AGAATGAGCACGTACAGATAAGAC	58.417	41.667	0.00	0.00	0.00	3.01
3493	3934	5.803967	AGTTAGTTAACGATAACCAAGAGCG	59.196	40.000	11.51	0.00	41.98	5.03
3533	3974	2.239402	TCATCATCCTGCTGCCTACAAA	59.761	45.455	0.00	0.00	0.00	2.83
3536	3977	2.158842	AGTTCATCATCCTGCTGCCTAC	60.159	50.000	0.00	0.00	0.00	3.18
3594	4035	1.677576	TCGTGTATGGTAAGCCCTACG	59.322	52.381	0.00	0.00	38.30	3.51
3624	4065	0.456221	CAGTAGCACCTACCTGTCCG	59.544	60.000	0.00	0.00	37.65	4.79
3635	4076	1.630244	CGCTTGCCAGTCAGTAGCAC	61.630	60.000	0.00	0.00	35.96	4.40
3652	4093	4.821589	ACCTAGAAGCCTGCGCGC	62.822	66.667	27.26	27.26	41.18	6.86
3653	4094	2.125512	AACCTAGAAGCCTGCGCG	60.126	61.111	0.00	0.00	41.18	6.86
3654	4095	2.754995	GCAACCTAGAAGCCTGCGC	61.755	63.158	0.00	0.00	0.00	6.09
3655	4096	1.078848	AGCAACCTAGAAGCCTGCG	60.079	57.895	0.00	0.00	38.07	5.18
3768	4209	3.058914	CCTTTCCTGTGAAAACAGTAGCG	60.059	47.826	5.24	0.00	39.88	4.26
3982	4424	2.874701	ACGTAGGCAGTACACTATACGG	59.125	50.000	18.52	6.94	36.87	4.02
3984	4426	4.889832	ACACGTAGGCAGTACACTATAC	57.110	45.455	0.00	0.00	0.00	1.47
3995	4437	0.245539	GAAGCAGGTACACGTAGGCA	59.754	55.000	0.00	0.00	0.00	4.75
3996	4438	0.459759	GGAAGCAGGTACACGTAGGC	60.460	60.000	0.00	0.00	0.00	3.93
3997	4439	1.135083	CAGGAAGCAGGTACACGTAGG	60.135	57.143	0.00	0.00	0.00	3.18
4043	4487	1.302192	GAACACAGCCGCCAGGTTA	60.302	57.895	0.00	0.00	40.50	2.85
4120	4565	9.555727	TTTATCGCCTCTAAGTAATGCTAAATT	57.444	29.630	0.00	0.00	0.00	1.82
4131	4576	7.553334	TGTCAATACTTTTATCGCCTCTAAGT	58.447	34.615	0.00	0.00	33.89	2.24
4139	4584	5.353123	TCCCAACTGTCAATACTTTTATCGC	59.647	40.000	0.00	0.00	0.00	4.58
4145	4590	6.976934	ATGTTTCCCAACTGTCAATACTTT	57.023	33.333	0.00	0.00	33.58	2.66
4208	4696	8.578151	GGATTCATAGATATATTCGAGGTACCC	58.422	40.741	8.74	0.00	0.00	3.69
4234	4722	4.734854	CGGAATAGCAATTTTGGTTCATCG	59.265	41.667	0.00	0.00	39.88	3.84
4247	4735	3.853831	TCTTACACGTCGGAATAGCAA	57.146	42.857	0.00	0.00	0.00	3.91
4256	4744	7.101993	AGTTTTACAAGAATCTTACACGTCG	57.898	36.000	0.00	0.00	0.00	5.12
4259	4747	9.188588	TGACTAGTTTTACAAGAATCTTACACG	57.811	33.333	0.00	0.00	0.00	4.49
4292	4780	1.150827	TGAGCATGTTCGAAGCTGTG	58.849	50.000	14.37	5.13	39.02	3.66
4294	4782	2.004733	TCATGAGCATGTTCGAAGCTG	58.995	47.619	14.37	8.56	39.02	4.24
4302	4790	4.325028	TTTGCAGTTTCATGAGCATGTT	57.675	36.364	8.05	0.00	39.72	2.71
4385	4874	2.396747	GAAAAACGAAACGGGCCGCT	62.397	55.000	28.71	12.24	0.00	5.52
4386	4875	2.012414	GAAAAACGAAACGGGCCGC	61.012	57.895	28.71	9.18	0.00	6.53
4542	5037	9.918630	AAATCAGAAGGACAAAAATAGATGTTG	57.081	29.630	0.00	0.00	0.00	3.33
4769	5272	5.285651	TGTGACCGATTTTTGAAAATGGAC	58.714	37.500	17.04	13.50	38.64	4.02

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.