AutoCloner

Multiple sequence alignment - TraesCS6D01G244400

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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	TraesCS6D01G244400	chr6D	100.000	6402	0	0	1	6402	346704531	346698130	0.000000e+00	11823.0
1	TraesCS6D01G244400	chr6D	96.038	732	28	1	2538	3268	131986018	131986749	0.000000e+00	1190.0
2	TraesCS6D01G244400	chr6D	94.251	661	22	5	1	651	455485315	455484661	0.000000e+00	996.0
3	TraesCS6D01G244400	chr6D	79.084	808	103	36	1221	2010	346838763	346838004	4.460000e-136	496.0
4	TraesCS6D01G244400	chr6D	90.343	321	26	3	2218	2536	346837932	346837615	3.570000e-112	416.0
5	TraesCS6D01G244400	chr6D	92.208	231	15	2	3270	3498	466653700	466653471	2.230000e-84	324.0
6	TraesCS6D01G244400	chr6D	91.064	235	21	0	2303	2537	466653927	466653693	1.040000e-82	318.0
7	TraesCS6D01G244400	chr6D	96.000	100	4	0	646	745	455473066	455472967	5.140000e-36	163.0
8	TraesCS6D01G244400	chr6D	81.548	168	26	5	4234	4399	346836532	346836368	4.030000e-27	134.0
9	TraesCS6D01G244400	chr6B	91.572	2385	116	37	4052	6402	534513876	534516209	0.000000e+00	3212.0
10	TraesCS6D01G244400	chr6B	90.536	951	58	10	857	1799	534510149	534511075	0.000000e+00	1229.0
11	TraesCS6D01G244400	chr6B	87.791	688	53	21	1857	2537	534511071	534511734	0.000000e+00	776.0
12	TraesCS6D01G244400	chr6B	79.412	612	82	31	1223	1823	534228221	534228799	6.020000e-105	392.0
13	TraesCS6D01G244400	chr6B	94.760	229	11	1	3270	3498	711882564	711882337	7.890000e-94	355.0
14	TraesCS6D01G244400	chr6B	88.889	243	19	1	2303	2537	711882799	711882557	6.280000e-75	292.0
15	TraesCS6D01G244400	chr6B	86.232	276	12	10	3694	3969	534513543	534513792	6.320000e-70	276.0
16	TraesCS6D01G244400	chr6B	90.909	165	14	1	3343	3506	534512298	534512462	3.000000e-53	220.0
17	TraesCS6D01G244400	chr6B	94.667	75	1	1	3270	3344	534511727	534511798	5.250000e-21	113.0
18	TraesCS6D01G244400	chr6B	83.019	106	6	8	744	839	534508567	534508670	1.140000e-12	86.1
19	TraesCS6D01G244400	chr6A	93.283	1444	54	14	4975	6402	496840004	496841420	0.000000e+00	2089.0
20	TraesCS6D01G244400	chr6A	89.771	1398	81	17	759	2109	496829981	496831363	0.000000e+00	1733.0
21	TraesCS6D01G244400	chr6A	86.177	1049	65	39	3662	4645	496832669	496833702	0.000000e+00	1061.0
22	TraesCS6D01G244400	chr6A	92.814	334	24	0	2204	2537	496831505	496831838	9.650000e-133	484.0
23	TraesCS6D01G244400	chr6A	77.576	883	120	51	1223	2082	496573015	496573842	4.520000e-126	462.0
24	TraesCS6D01G244400	chr6A	89.124	331	33	2	2206	2536	496573832	496574159	5.970000e-110	409.0
25	TraesCS6D01G244400	chr6A	74.646	777	119	43	3655	4399	496574997	496575727	8.180000e-69	272.0
26	TraesCS6D01G244400	chr6A	89.000	200	16	4	3349	3544	496832267	496832464	6.410000e-60	243.0
27	TraesCS6D01G244400	chr6A	88.824	170	12	4	4779	4942	496839836	496840004	1.090000e-47	202.0
28	TraesCS6D01G244400	chr6A	96.296	54	2	0	4664	4717	496839571	496839624	8.840000e-14	89.8
29	TraesCS6D01G244400	chr3D	96.900	742	21	2	4	744	418841065	418840325	0.000000e+00	1242.0
30	TraesCS6D01G244400	chr3D	94.301	193	9	2	1	191	131237554	131237362	1.750000e-75	294.0
31	TraesCS6D01G244400	chr3D	94.118	68	2	1	2129	2194	386736158	386736091	1.140000e-17	102.0
32	TraesCS6D01G244400	chr2A	96.311	732	26	1	2538	3268	651596571	651597302	0.000000e+00	1201.0
33	TraesCS6D01G244400	chr2A	95.082	732	35	1	2538	3268	699572435	699571704	0.000000e+00	1151.0
34	TraesCS6D01G244400	chr2A	94.573	737	36	3	2535	3268	174779110	174779845	0.000000e+00	1136.0
35	TraesCS6D01G244400	chr1B	95.771	733	29	2	2538	3268	596157212	596157944	0.000000e+00	1181.0
36	TraesCS6D01G244400	chr1B	94.694	735	38	1	2535	3268	515444461	515445195	0.000000e+00	1140.0
37	TraesCS6D01G244400	chr1B	91.045	67	4	2	2129	2194	647172251	647172186	8.840000e-14	89.8
38	TraesCS6D01G244400	chr5A	95.510	735	28	3	2538	3268	275088099	275087366	0.000000e+00	1170.0
39	TraesCS6D01G244400	chr5A	91.534	756	56	4	1	749	670094473	670095227	0.000000e+00	1035.0
40	TraesCS6D01G244400	chr7A	94.723	739	36	2	2533	3268	393484790	393484052	0.000000e+00	1146.0
41	TraesCS6D01G244400	chr3A	94.687	734	35	4	2538	3270	385153555	385154285	0.000000e+00	1136.0
42	TraesCS6D01G244400	chr2D	96.302	649	23	1	98	745	607138636	607137988	0.000000e+00	1064.0
43	TraesCS6D01G244400	chr2D	91.408	419	29	3	333	744	207070053	207070471	9.310000e-158	568.0
44	TraesCS6D01G244400	chr2D	90.909	418	32	2	333	744	337431941	337431524	2.020000e-154	556.0
45	TraesCS6D01G244400	chr2D	88.544	419	41	3	333	746	588172602	588172186	9.580000e-138	501.0
46	TraesCS6D01G244400	chr2D	93.085	188	12	1	189	376	588172707	588172521	2.270000e-69	274.0
47	TraesCS6D01G244400	chr2D	89.894	188	19	0	189	376	337432047	337431860	6.410000e-60	243.0
48	TraesCS6D01G244400	chr2D	100.000	34	0	0	4811	4844	131171002	131170969	5.360000e-06	63.9
49	TraesCS6D01G244400	chr7D	91.449	421	27	4	333	745	191550172	191550591	2.590000e-158	569.0
50	TraesCS6D01G244400	chr7D	92.708	192	13	1	1	191	26755417	26755226	6.320000e-70	276.0
51	TraesCS6D01G244400	chr7D	92.308	65	2	2	2129	2193	489109229	489109290	8.840000e-14	89.8
52	TraesCS6D01G244400	chr5D	88.278	418	43	2	333	745	398505332	398504916	4.460000e-136	496.0
53	TraesCS6D01G244400	chr5D	94.211	190	9	2	1	188	310032154	310032343	8.120000e-74	289.0
54	TraesCS6D01G244400	chr5D	93.617	188	11	1	189	376	398505437	398505251	4.890000e-71	279.0
55	TraesCS6D01G244400	chr5D	95.161	62	1	2	2129	2189	106810488	106810548	5.280000e-16	97.1
56	TraesCS6D01G244400	chr1D	93.782	193	10	2	1	191	98920957	98920765	8.120000e-74	289.0
57	TraesCS6D01G244400	chr1D	93.782	193	10	2	1	191	361846795	361846603	8.120000e-74	289.0
58	TraesCS6D01G244400	chr1D	93.782	193	9	3	1	191	355501328	355501137	2.920000e-73	287.0
59	TraesCS6D01G244400	chr1D	93.651	63	2	2	2129	2189	53456970	53456908	6.830000e-15	93.5
60	TraesCS6D01G244400	chr1D	89.855	69	4	3	2123	2189	22588277	22588344	1.140000e-12	86.1
61	TraesCS6D01G244400	chr4B	100.000	51	0	0	1957	2007	620943437	620943487	1.900000e-15	95.3
62	TraesCS6D01G244400	chr5B	93.651	63	2	2	2129	2189	711994135	711994073	6.830000e-15	93.5
63	TraesCS6D01G244400	chr3B	93.750	64	1	2	2129	2189	49145699	49145636	6.830000e-15	93.5
64	TraesCS6D01G244400	chr3B	93.651	63	2	1	2129	2189	242163034	242162972	6.830000e-15	93.5

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	TraesCS6D01G244400	chr6D	346698130	346704531	6401	True	11823.000000	11823	100.000000	1	6402	1	chr6D.!!$R1	6401
1	TraesCS6D01G244400	chr6D	131986018	131986749	731	False	1190.000000	1190	96.038000	2538	3268	1	chr6D.!!$F1	730
2	TraesCS6D01G244400	chr6D	455484661	455485315	654	True	996.000000	996	94.251000	1	651	1	chr6D.!!$R3	650
3	TraesCS6D01G244400	chr6D	346836368	346838763	2395	True	348.666667	496	83.658333	1221	4399	3	chr6D.!!$R4	3178
4	TraesCS6D01G244400	chr6B	534508567	534516209	7642	False	844.585714	3212	89.246571	744	6402	7	chr6B.!!$F2	5658
5	TraesCS6D01G244400	chr6B	534228221	534228799	578	False	392.000000	392	79.412000	1223	1823	1	chr6B.!!$F1	600
6	TraesCS6D01G244400	chr6A	496829981	496833702	3721	False	880.250000	1733	89.440500	759	4645	4	chr6A.!!$F2	3886
7	TraesCS6D01G244400	chr6A	496839571	496841420	1849	False	793.600000	2089	92.801000	4664	6402	3	chr6A.!!$F3	1738
8	TraesCS6D01G244400	chr6A	496573015	496575727	2712	False	381.000000	462	80.448667	1223	4399	3	chr6A.!!$F1	3176
9	TraesCS6D01G244400	chr3D	418840325	418841065	740	True	1242.000000	1242	96.900000	4	744	1	chr3D.!!$R3	740
10	TraesCS6D01G244400	chr2A	651596571	651597302	731	False	1201.000000	1201	96.311000	2538	3268	1	chr2A.!!$F2	730
11	TraesCS6D01G244400	chr2A	699571704	699572435	731	True	1151.000000	1151	95.082000	2538	3268	1	chr2A.!!$R1	730
12	TraesCS6D01G244400	chr2A	174779110	174779845	735	False	1136.000000	1136	94.573000	2535	3268	1	chr2A.!!$F1	733
13	TraesCS6D01G244400	chr1B	596157212	596157944	732	False	1181.000000	1181	95.771000	2538	3268	1	chr1B.!!$F2	730
14	TraesCS6D01G244400	chr1B	515444461	515445195	734	False	1140.000000	1140	94.694000	2535	3268	1	chr1B.!!$F1	733
15	TraesCS6D01G244400	chr5A	275087366	275088099	733	True	1170.000000	1170	95.510000	2538	3268	1	chr5A.!!$R1	730
16	TraesCS6D01G244400	chr5A	670094473	670095227	754	False	1035.000000	1035	91.534000	1	749	1	chr5A.!!$F1	748
17	TraesCS6D01G244400	chr7A	393484052	393484790	738	True	1146.000000	1146	94.723000	2533	3268	1	chr7A.!!$R1	735
18	TraesCS6D01G244400	chr3A	385153555	385154285	730	False	1136.000000	1136	94.687000	2538	3270	1	chr3A.!!$F1	732
19	TraesCS6D01G244400	chr2D	607137988	607138636	648	True	1064.000000	1064	96.302000	98	745	1	chr2D.!!$R2	647
20	TraesCS6D01G244400	chr2D	337431524	337432047	523	True	399.500000	556	90.401500	189	744	2	chr2D.!!$R3	555
21	TraesCS6D01G244400	chr2D	588172186	588172707	521	True	387.500000	501	90.814500	189	746	2	chr2D.!!$R4	557
22	TraesCS6D01G244400	chr5D	398504916	398505437	521	True	387.500000	496	90.947500	189	745	2	chr5D.!!$R1	556

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
963	2471	0.034059	ACTGCACAAGAGGAACGGAG	59.966	55.0	0.00	0.00	4.63	F
1998	3580	0.036010	AAGTTGATCCTGTGAGCCCG	60.036	55.0	0.00	0.00	6.13	F
2164	3747	0.602106	ATCGATTGATGCAGAGGCCG	60.602	55.0	0.00	40.13	6.13	F
3240	4907	0.466963	AGAACCGAACCGTTTCACCT	59.533	50.0	0.00	0.00	4.00	F
3790	7241	0.179094	CCGCAGGCGTGGTAAGATAA	60.179	55.0	13.07	46.14	1.75	F
4131	7638	0.249120	CGACATAACCCAGTGCTCCA	59.751	55.0	0.00	0.00	3.86	F
4956	8696	0.250124	CAAGCACAACACCCGGTAGA	60.250	55.0	0.00	0.00	2.59	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Hairpin	End Stability	Orientation
2145	3728	0.602106	CGGCCTCTGCATCAATCGAT	60.602	55.0	0.00	40.13	3.59	R
2997	4664	0.304705	CTTTGATCCGCGTACATGCC	59.695	55.0	4.92	0.00	4.40	R
3722	7173	0.321298	TTCTTTGCCGAGCCCTGTAC	60.321	55.0	0.00	0.00	2.90	R
4916	8656	0.037697	TGTCTACGGTCACACATGCC	60.038	55.0	0.00	0.00	4.40	R
5136	8883	0.102844	CAGCAGTTGTTTGGTGGTGG	59.897	55.0	0.00	41.58	4.61	R
5295	9044	0.181114	TTGGATCTGGAGGAATGCCG	59.819	55.0	0.00	39.96	5.69	R
5911	9673	0.335019	AAGGGATGCCTTGGGGTAAC	59.665	55.0	18.95	34.45	2.50	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
68	70	2.261671	GCGTCGTGGTGGAGATGT	59.738	61.111	0.00	0.00	0.00	3.06
247	250	1.208052	CTTGATCCAGAGCGAGGGAAA	59.792	52.381	0.00	0.00	36.62	3.13
433	437	1.689582	GGTGGGGAGGGATCTTCGT	60.690	63.158	0.00	0.00	0.00	3.85
508	522	1.292061	GAGCGCTCTAGAAGACTCGA	58.708	55.000	29.88	0.00	0.00	4.04
627	650	3.006247	GCAGAGGGTGTTTTTGCAAAAA	58.994	40.909	28.85	28.85	35.67	1.94
678	701	1.577328	GCCATACATTGCCGATCGGG	61.577	60.000	33.98	20.13	39.58	5.14
690	713	1.448540	GATCGGGCGGCATAGATGG	60.449	63.158	12.47	0.00	0.00	3.51
735	758	5.123186	CACCACCAACTCGCATTTTTATAGA	59.877	40.000	0.00	0.00	0.00	1.98
766	789	7.949434	AGATTAGATTTTTACTCGACGGGTAT	58.051	34.615	8.70	0.00	0.00	2.73
767	790	9.071276	AGATTAGATTTTTACTCGACGGGTATA	57.929	33.333	8.70	0.50	0.00	1.47
795	822	0.251787	GGATACCCATTGCCATCCCC	60.252	60.000	0.00	0.00	32.38	4.81
796	823	0.779997	GATACCCATTGCCATCCCCT	59.220	55.000	0.00	0.00	0.00	4.79
797	824	1.147817	GATACCCATTGCCATCCCCTT	59.852	52.381	0.00	0.00	0.00	3.95
895	2394	1.094073	CATTGGGAAGCTCGAGGCAG	61.094	60.000	15.58	0.00	44.79	4.85
956	2464	0.976641	TGTCCCTACTGCACAAGAGG	59.023	55.000	0.00	0.00	0.00	3.69
957	2465	1.267121	GTCCCTACTGCACAAGAGGA	58.733	55.000	0.95	0.21	0.00	3.71
958	2466	1.623811	GTCCCTACTGCACAAGAGGAA	59.376	52.381	0.95	0.00	0.00	3.36
959	2467	1.623811	TCCCTACTGCACAAGAGGAAC	59.376	52.381	0.95	0.00	0.00	3.62
960	2468	1.673033	CCCTACTGCACAAGAGGAACG	60.673	57.143	0.95	0.00	0.00	3.95
961	2469	1.673033	CCTACTGCACAAGAGGAACGG	60.673	57.143	0.00	0.00	0.00	4.44
962	2470	1.272490	CTACTGCACAAGAGGAACGGA	59.728	52.381	0.00	0.00	0.00	4.69
963	2471	0.034059	ACTGCACAAGAGGAACGGAG	59.966	55.000	0.00	0.00	0.00	4.63
964	2472	0.318441	CTGCACAAGAGGAACGGAGA	59.682	55.000	0.00	0.00	0.00	3.71
965	2473	0.318441	TGCACAAGAGGAACGGAGAG	59.682	55.000	0.00	0.00	0.00	3.20
1089	2597	3.537874	CCGGCCTCCCTCTTACCG	61.538	72.222	0.00	0.00	43.44	4.02
1199	2715	2.676822	TTCCTCCTCACGCTCGCT	60.677	61.111	0.00	0.00	0.00	4.93
1200	2716	2.606155	CTTCCTCCTCACGCTCGCTC	62.606	65.000	0.00	0.00	0.00	5.03
1201	2717	4.200283	CCTCCTCACGCTCGCTCC	62.200	72.222	0.00	0.00	0.00	4.70
1202	2718	3.137459	CTCCTCACGCTCGCTCCT	61.137	66.667	0.00	0.00	0.00	3.69
1407	2947	0.888619	TCAGTTGTCCTAGCCTGACG	59.111	55.000	0.00	0.00	35.46	4.35
1408	2948	0.603569	CAGTTGTCCTAGCCTGACGT	59.396	55.000	0.00	0.00	35.46	4.34
1548	3088	1.068402	TCAAATTCACTCGTCGCCGTA	60.068	47.619	0.00	0.00	35.01	4.02
1555	3098	2.126618	TCGTCGCCGTAGCACTTG	60.127	61.111	0.00	0.00	39.83	3.16
1574	3117	5.352293	CACTTGCTACAGAATTCAGTGCATA	59.648	40.000	20.22	13.71	0.00	3.14
1755	3319	1.202770	ACAACCCTGGTACACTTCAGC	60.203	52.381	0.00	0.00	0.00	4.26
1823	3391	2.289945	CCAGGTTTCTAGCAGCAGTTCT	60.290	50.000	0.00	0.00	0.00	3.01
1827	3396	4.081917	AGGTTTCTAGCAGCAGTTCTAGTC	60.082	45.833	0.00	0.00	35.13	2.59
1838	3407	1.827969	AGTTCTAGTCTGCGATTGCCT	59.172	47.619	1.50	0.00	41.78	4.75
1839	3408	3.024547	AGTTCTAGTCTGCGATTGCCTA	58.975	45.455	1.50	0.00	41.78	3.93
1840	3409	3.067461	AGTTCTAGTCTGCGATTGCCTAG	59.933	47.826	1.50	6.44	41.78	3.02
1841	3410	1.957177	TCTAGTCTGCGATTGCCTAGG	59.043	52.381	3.67	3.67	41.78	3.02
1842	3411	1.683917	CTAGTCTGCGATTGCCTAGGT	59.316	52.381	11.31	0.00	41.78	3.08
1843	3412	0.905357	AGTCTGCGATTGCCTAGGTT	59.095	50.000	11.31	0.00	41.78	3.50
1844	3413	1.134670	AGTCTGCGATTGCCTAGGTTC	60.135	52.381	11.31	4.63	41.78	3.62
1845	3414	0.901827	TCTGCGATTGCCTAGGTTCA	59.098	50.000	11.31	0.00	41.78	3.18
1846	3415	1.277842	TCTGCGATTGCCTAGGTTCAA	59.722	47.619	11.31	7.48	41.78	2.69
1847	3416	2.092968	TCTGCGATTGCCTAGGTTCAAT	60.093	45.455	11.31	12.21	41.78	2.57
1849	3418	4.067896	CTGCGATTGCCTAGGTTCAATAT	58.932	43.478	11.31	0.00	41.78	1.28
1852	3421	4.319766	GCGATTGCCTAGGTTCAATATGTG	60.320	45.833	11.31	5.10	33.49	3.21
1853	3422	4.319766	CGATTGCCTAGGTTCAATATGTGC	60.320	45.833	11.31	0.08	33.49	4.57
1854	3423	3.931907	TGCCTAGGTTCAATATGTGCT	57.068	42.857	11.31	0.00	0.00	4.40
1906	3488	2.857152	TGAGTGCGCAATTTGTCAAAAC	59.143	40.909	14.00	0.00	0.00	2.43
1998	3580	0.036010	AAGTTGATCCTGTGAGCCCG	60.036	55.000	0.00	0.00	0.00	6.13
2109	3692	1.302431	TTGGGTGTGTGCATCCTCG	60.302	57.895	0.00	0.00	46.06	4.63
2123	3706	2.281539	TCCTCGGTGTCACTACTTGA	57.718	50.000	2.35	0.00	0.00	3.02
2129	3712	5.929992	CCTCGGTGTCACTACTTGATTTTTA	59.070	40.000	2.35	0.00	36.32	1.52
2130	3713	6.425721	CCTCGGTGTCACTACTTGATTTTTAA	59.574	38.462	2.35	0.00	36.32	1.52
2131	3714	7.041644	CCTCGGTGTCACTACTTGATTTTTAAA	60.042	37.037	2.35	0.00	36.32	1.52
2132	3715	7.857569	TCGGTGTCACTACTTGATTTTTAAAG	58.142	34.615	2.35	0.00	36.32	1.85
2133	3716	7.711772	TCGGTGTCACTACTTGATTTTTAAAGA	59.288	33.333	2.35	0.00	36.32	2.52
2135	3718	9.612620	GGTGTCACTACTTGATTTTTAAAGATG	57.387	33.333	2.35	0.00	36.32	2.90
2137	3720	9.349713	TGTCACTACTTGATTTTTAAAGATGGT	57.650	29.630	0.00	0.00	36.32	3.55
2140	3723	9.965824	CACTACTTGATTTTTAAAGATGGTTGT	57.034	29.630	0.00	0.00	0.00	3.32
2144	3727	9.423061	ACTTGATTTTTAAAGATGGTTGTATGC	57.577	29.630	0.00	0.00	0.00	3.14
2145	3728	9.421806	CTTGATTTTTAAAGATGGTTGTATGCA	57.578	29.630	0.00	0.00	0.00	3.96
2146	3729	9.941325	TTGATTTTTAAAGATGGTTGTATGCAT	57.059	25.926	3.79	3.79	0.00	3.96
2147	3730	9.585099	TGATTTTTAAAGATGGTTGTATGCATC	57.415	29.630	0.19	0.00	0.00	3.91
2148	3731	8.633075	ATTTTTAAAGATGGTTGTATGCATCG	57.367	30.769	0.19	0.00	0.00	3.84
2152	3735	5.428496	AAGATGGTTGTATGCATCGATTG	57.572	39.130	0.19	0.00	0.00	2.67
2153	3736	4.707105	AGATGGTTGTATGCATCGATTGA	58.293	39.130	0.19	0.00	0.00	2.57
2163	3746	0.873054	CATCGATTGATGCAGAGGCC	59.127	55.000	10.05	0.00	45.06	5.19
2164	3747	0.602106	ATCGATTGATGCAGAGGCCG	60.602	55.000	0.00	0.00	40.13	6.13
2174	3757	1.583495	GCAGAGGCCGGGTGTTTAAC	61.583	60.000	2.18	0.00	0.00	2.01
2231	3881	8.984891	TTTTAAATATGGACAGAGCACAAATG	57.015	30.769	0.00	0.00	0.00	2.32
2363	4021	4.868450	TGTTCCTAACAACGAAACTGTG	57.132	40.909	0.00	0.00	38.72	3.66
2370	4028	2.542907	AACGAAACTGTGGCAGGCG	61.543	57.895	0.00	4.42	35.51	5.52
2458	4116	1.142185	CGATACTGCACTGCGACAGG	61.142	60.000	10.80	2.65	38.25	4.00
2581	4240	6.523840	ACTTAAACCGTACTTGAACCATACA	58.476	36.000	0.00	0.00	0.00	2.29
2822	4486	4.081420	AGTGCATCTACAACAGTTAGGGAG	60.081	45.833	0.00	0.00	0.00	4.30
2959	4626	5.579384	CAAACACATTCGATTTGCATGTT	57.421	34.783	0.00	0.00	0.00	2.71
2978	4645	6.573289	GCATGTTGTGTTTCCCCATAATACAA	60.573	38.462	0.00	0.00	35.25	2.41
2997	4664	4.587306	ACAAAATTACATAGTGCATCGCG	58.413	39.130	0.00	0.00	0.00	5.87
3063	4730	4.441913	GCTTATTGCACATAACCAATGCCT	60.442	41.667	0.00	0.00	39.39	4.75
3093	4760	5.397109	CCGGTTTGGACCCATAGTTTATAGT	60.397	44.000	0.00	0.00	43.42	2.12
3240	4907	0.466963	AGAACCGAACCGTTTCACCT	59.533	50.000	0.00	0.00	0.00	4.00
3273	4941	2.519013	ACCATTCTCAGGTTTGAAGGC	58.481	47.619	0.00	0.00	35.33	4.35
3278	4946	3.131709	TCTCAGGTTTGAAGGCAGAAG	57.868	47.619	0.00	0.00	31.69	2.85
3321	4989	7.759489	TCTGTTTTTGCCACTTTGTAGATAT	57.241	32.000	0.00	0.00	0.00	1.63
3322	4990	8.177119	TCTGTTTTTGCCACTTTGTAGATATT	57.823	30.769	0.00	0.00	0.00	1.28
3323	4991	9.290988	TCTGTTTTTGCCACTTTGTAGATATTA	57.709	29.630	0.00	0.00	0.00	0.98
3463	5800	1.000385	CCACGCTGAGGCATTTTTCAA	60.000	47.619	0.00	0.00	38.60	2.69
3474	5811	7.092079	TGAGGCATTTTTCAATGATGTAGTTG	58.908	34.615	0.00	0.00	42.35	3.16
3499	5836	3.186409	ACACATGTATGCACGTTTGACTC	59.814	43.478	0.00	0.00	0.00	3.36
3500	5837	2.742053	ACATGTATGCACGTTTGACTCC	59.258	45.455	0.00	0.00	0.00	3.85
3511	5848	2.297597	CGTTTGACTCCTCTCTTCACCT	59.702	50.000	0.00	0.00	0.00	4.00
3512	5849	3.658709	GTTTGACTCCTCTCTTCACCTG	58.341	50.000	0.00	0.00	0.00	4.00
3514	5851	3.464720	TGACTCCTCTCTTCACCTGAT	57.535	47.619	0.00	0.00	0.00	2.90
3515	5852	3.784178	TGACTCCTCTCTTCACCTGATT	58.216	45.455	0.00	0.00	0.00	2.57
3550	6866	8.922931	ATATAACAAACTGTGGCATGATATGA	57.077	30.769	0.00	0.00	0.00	2.15
3553	6869	6.534475	ACAAACTGTGGCATGATATGAAAT	57.466	33.333	0.00	0.00	0.00	2.17
3556	6872	7.546667	ACAAACTGTGGCATGATATGAAATTTC	59.453	33.333	11.41	11.41	0.00	2.17
3563	6879	5.916883	GGCATGATATGAAATTTCCGAGTTG	59.083	40.000	15.48	7.53	0.00	3.16
3645	7009	6.530913	AGTATACGTATCATTTTGCAGCAG	57.469	37.500	12.24	0.00	0.00	4.24
3646	7010	2.549633	ACGTATCATTTTGCAGCAGC	57.450	45.000	0.00	0.00	42.57	5.25
3660	7024	1.529438	CAGCAGCAGCAACAAAAATGG	59.471	47.619	3.17	0.00	45.49	3.16
3672	7039	4.001618	ACAAAAATGGTTTGCGCCTATT	57.998	36.364	4.18	0.00	32.93	1.73
3723	7174	3.281341	CATTGTGTGCAAATACCGTGT	57.719	42.857	0.00	0.00	38.21	4.49
3724	7175	4.411993	CATTGTGTGCAAATACCGTGTA	57.588	40.909	0.00	0.00	38.21	2.90
3725	7176	3.881780	TTGTGTGCAAATACCGTGTAC	57.118	42.857	0.00	0.00	32.80	2.90
3742	7193	0.321298	TACAGGGCTCGGCAAAGAAC	60.321	55.000	0.00	0.00	0.00	3.01
3772	7223	1.363807	GTGCACTTCCAAGTTGCCC	59.636	57.895	10.32	0.00	37.08	5.36
3789	7240	1.440060	CCGCAGGCGTGGTAAGATA	59.560	57.895	13.07	0.00	46.14	1.98
3790	7241	0.179094	CCGCAGGCGTGGTAAGATAA	60.179	55.000	13.07	0.00	46.14	1.75
3791	7242	1.540363	CCGCAGGCGTGGTAAGATAAT	60.540	52.381	13.07	0.00	46.14	1.28
3792	7243	2.288579	CCGCAGGCGTGGTAAGATAATA	60.289	50.000	13.07	0.00	46.14	0.98
3793	7244	2.729882	CGCAGGCGTGGTAAGATAATAC	59.270	50.000	8.72	0.00	34.35	1.89
3794	7245	3.552273	CGCAGGCGTGGTAAGATAATACT	60.552	47.826	8.72	0.00	34.35	2.12
3843	7294	3.004210	CACATCTAGAGATCAGACCACGG	59.996	52.174	0.00	0.00	31.21	4.94
3974	7426	1.691976	TGGCAGGTTATCATCCGGTAG	59.308	52.381	0.00	0.00	0.00	3.18
3978	7430	4.505039	GGCAGGTTATCATCCGGTAGAAAT	60.505	45.833	0.00	0.00	0.00	2.17
3979	7431	4.691216	GCAGGTTATCATCCGGTAGAAATC	59.309	45.833	0.00	0.00	0.00	2.17
3980	7432	5.511545	GCAGGTTATCATCCGGTAGAAATCT	60.512	44.000	0.00	1.83	0.00	2.40
3992	7476	3.860536	GGTAGAAATCTCGCTTGACACTC	59.139	47.826	0.00	0.00	0.00	3.51
4094	7601	1.152567	AGAGGGCTCCGATCCTGAG	60.153	63.158	3.13	3.13	32.74	3.35
4101	7608	2.069465	CTCCGATCCTGAGTGGCGAG	62.069	65.000	0.00	0.00	35.26	5.03
4131	7638	0.249120	CGACATAACCCAGTGCTCCA	59.751	55.000	0.00	0.00	0.00	3.86
4197	7706	1.466856	TGGTCGGTCAGCTATACGTT	58.533	50.000	0.00	0.00	0.00	3.99
4198	7707	2.642427	TGGTCGGTCAGCTATACGTTA	58.358	47.619	0.00	0.00	0.00	3.18
4199	7708	2.355756	TGGTCGGTCAGCTATACGTTAC	59.644	50.000	0.00	0.00	0.00	2.50
4213	7752	2.627945	ACGTTACGTATACTCACCGGA	58.372	47.619	9.46	0.00	38.73	5.14
4406	7947	3.323775	AGTAAACCACCCTCTTCCTTCA	58.676	45.455	0.00	0.00	0.00	3.02
4410	7951	2.192263	ACCACCCTCTTCCTTCATCTC	58.808	52.381	0.00	0.00	0.00	2.75
4417	7958	2.303549	CTTCCTTCATCTCGCGCCCT	62.304	60.000	0.00	0.00	0.00	5.19
4431	7972	1.877443	GCGCCCTTTAGTTGAGTTTCA	59.123	47.619	0.00	0.00	0.00	2.69
4521	8074	1.061546	GGTTGGGGACTGGTTCTACA	58.938	55.000	0.00	0.00	0.00	2.74
4596	8149	3.153369	ACACTAATTGATGCACCACCA	57.847	42.857	0.00	0.00	0.00	4.17
4597	8150	2.819608	ACACTAATTGATGCACCACCAC	59.180	45.455	0.00	0.00	0.00	4.16
4598	8151	2.164219	CACTAATTGATGCACCACCACC	59.836	50.000	0.00	0.00	0.00	4.61
4761	8323	1.401552	CCGATGTTCCATTGCGATGTT	59.598	47.619	13.01	0.00	0.00	2.71
4764	8326	2.987413	TGTTCCATTGCGATGTTGTC	57.013	45.000	13.01	1.77	0.00	3.18
4779	8341	7.148623	TGCGATGTTGTCAAATTTATGTACGTA	60.149	33.333	0.00	0.00	0.00	3.57
4786	8348	8.428186	TGTCAAATTTATGTACGTATTCCCTC	57.572	34.615	0.00	0.00	0.00	4.30
4787	8349	7.496591	TGTCAAATTTATGTACGTATTCCCTCC	59.503	37.037	0.00	0.00	0.00	4.30
4788	8350	7.496591	GTCAAATTTATGTACGTATTCCCTCCA	59.503	37.037	0.00	0.00	0.00	3.86
4808	8543	8.102676	CCCTCCATTCCAAATTTGAACTAAAAT	58.897	33.333	19.86	6.44	0.00	1.82
4821	8556	6.438259	TGAACTAAAATCAACCACGACAAA	57.562	33.333	0.00	0.00	0.00	2.83
4873	8612	1.158484	TCCGCTGTACTCGAGATCCG	61.158	60.000	21.68	13.12	40.25	4.18
4916	8656	1.616994	GGTTCATCTCCCCCAAACCAG	60.617	57.143	0.00	0.00	39.33	4.00
4942	8682	0.319555	GTGACCGTAGACAGCAAGCA	60.320	55.000	0.00	0.00	0.00	3.91
4956	8696	0.250124	CAAGCACAACACCCGGTAGA	60.250	55.000	0.00	0.00	0.00	2.59
4958	8698	1.670083	GCACAACACCCGGTAGACC	60.670	63.158	0.00	0.00	0.00	3.85
4959	8699	1.749665	CACAACACCCGGTAGACCA	59.250	57.895	0.00	0.00	35.14	4.02
5029	8770	2.801996	CACCAATGCAGCGCAACG	60.802	61.111	11.47	0.00	43.62	4.10
5080	8821	1.665161	GCAGCACAACTTCTCACATGC	60.665	52.381	0.00	0.00	0.00	4.06
5135	8882	5.106078	ACCGTTAAAGAAACTGAAGCAACAA	60.106	36.000	0.00	0.00	35.81	2.83
5136	8883	5.229260	CCGTTAAAGAAACTGAAGCAACAAC	59.771	40.000	0.00	0.00	35.81	3.32
5137	8884	5.229260	CGTTAAAGAAACTGAAGCAACAACC	59.771	40.000	0.00	0.00	35.81	3.77
5147	8894	0.534873	AGCAACAACCACCACCAAAC	59.465	50.000	0.00	0.00	0.00	2.93
5316	9065	1.478288	GGCATTCCTCCAGATCCAAGG	60.478	57.143	0.00	0.00	0.00	3.61
5326	9075	0.842635	AGATCCAAGGCAAGGGCTAG	59.157	55.000	0.00	0.00	37.50	3.42
5341	9090	2.040178	GGCTAGAAGATCCTCCCGAAA	58.960	52.381	0.00	0.00	0.00	3.46
5350	9099	3.389656	AGATCCTCCCGAAATCCTTTCTC	59.610	47.826	0.00	0.00	37.52	2.87
5383	9132	3.297620	AGCCCGCTTGTTGCAAGG	61.298	61.111	0.00	0.00	43.06	3.61
5486	9235	1.880027	CTTTCTCCGGTTCCCAAACAG	59.120	52.381	0.00	0.00	37.10	3.16
5502	9253	5.188359	CCCAAACAGATCATGGAAGGAAAAT	59.812	40.000	8.04	0.00	36.27	1.82
5503	9254	6.380846	CCCAAACAGATCATGGAAGGAAAATA	59.619	38.462	8.04	0.00	36.27	1.40
5567	9318	5.911178	AGAGGACCCAATTATAGGTTGATCA	59.089	40.000	0.00	0.00	36.17	2.92
5582	9333	6.316694	GGTTGATCAACAGACCCTCAGTCA	62.317	50.000	33.42	0.00	42.87	3.41
5824	9585	5.363939	AGCATTATTACAGAACTCCTGCTC	58.636	41.667	0.00	0.00	46.81	4.26
5868	9629	4.885022	AGCCATGGCAATGTCAACAACAT	61.885	43.478	37.18	9.60	43.98	2.71
5911	9673	6.228273	AGTGTACAACAGTGAAATCATTCG	57.772	37.500	0.00	0.00	38.46	3.34
6029	9791	0.031721	CGGGCGTATAGAGGTGGAAC	59.968	60.000	0.00	0.00	0.00	3.62
6042	9804	3.941483	GAGGTGGAACTCATATGGTTGTG	59.059	47.826	12.50	0.00	37.44	3.33
6243	10005	1.483827	CAGGAGCAGTAGCATCCAGAA	59.516	52.381	0.00	0.00	45.49	3.02

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
68	70	3.736100	CGCAGCACAATCGCCCAA	61.736	61.111	0.00	0.00	0.00	4.12
154	156	1.192146	CCCCTTTGTCCGTCTCCTCA	61.192	60.000	0.00	0.00	0.00	3.86
165	167	3.330720	CTCCTCCGCCCCCTTTGT	61.331	66.667	0.00	0.00	0.00	2.83
247	250	1.760086	CCTCCACTGCCTCTCGGAT	60.760	63.158	0.00	0.00	0.00	4.18
260	263	3.062466	CGTCACCGCTCTCCTCCA	61.062	66.667	0.00	0.00	0.00	3.86
291	294	1.395826	GCCCATAGACAGAGCTCCGT	61.396	60.000	10.93	6.10	0.00	4.69
433	437	2.091541	GACAGCCGGATTTGAATTGGA	58.908	47.619	5.05	0.00	0.00	3.53
627	650	1.271379	CAAGCCATGTGTCACTTGCAT	59.729	47.619	12.30	1.83	33.77	3.96
636	659	1.552337	AGATCGAGACAAGCCATGTGT	59.448	47.619	0.00	0.00	44.12	3.72
735	758	9.719279	CGTCGAGTAAAAATCTAATCTCTACTT	57.281	33.333	0.00	0.00	0.00	2.24
746	769	7.281040	TCATATACCCGTCGAGTAAAAATCT	57.719	36.000	0.00	0.00	0.00	2.40
747	770	6.585322	CCTCATATACCCGTCGAGTAAAAATC	59.415	42.308	0.00	0.00	0.00	2.17
748	771	6.266103	TCCTCATATACCCGTCGAGTAAAAAT	59.734	38.462	0.00	0.00	0.00	1.82
749	772	5.593909	TCCTCATATACCCGTCGAGTAAAAA	59.406	40.000	0.00	0.00	0.00	1.94
750	773	5.132502	TCCTCATATACCCGTCGAGTAAAA	58.867	41.667	0.00	0.00	0.00	1.52
751	774	4.717877	TCCTCATATACCCGTCGAGTAAA	58.282	43.478	0.00	0.00	0.00	2.01
752	775	4.356405	TCCTCATATACCCGTCGAGTAA	57.644	45.455	0.00	0.00	0.00	2.24
753	776	4.356405	TTCCTCATATACCCGTCGAGTA	57.644	45.455	0.00	0.00	0.00	2.59
754	777	2.945080	TCCTCATATACCCGTCGAGT	57.055	50.000	0.00	0.00	0.00	4.18
755	778	3.119459	CCATTCCTCATATACCCGTCGAG	60.119	52.174	0.00	0.00	0.00	4.04
756	779	2.823747	CCATTCCTCATATACCCGTCGA	59.176	50.000	0.00	0.00	0.00	4.20
757	780	2.823747	TCCATTCCTCATATACCCGTCG	59.176	50.000	0.00	0.00	0.00	5.12
795	822	4.870363	ACGTTTGTTTTCCATGGATGAAG	58.130	39.130	17.06	4.80	0.00	3.02
796	823	4.927978	ACGTTTGTTTTCCATGGATGAA	57.072	36.364	17.06	11.04	0.00	2.57
797	824	4.457603	CCTACGTTTGTTTTCCATGGATGA	59.542	41.667	17.06	4.60	0.00	2.92
866	2365	1.712977	CTTCCCAATGCGAGCTGCTC	61.713	60.000	19.53	19.53	46.63	4.26
895	2394	3.470567	CGGAACAGACGTCGCTGC	61.471	66.667	10.46	3.04	39.51	5.25
956	2464	1.321074	ACGGGATGGTCTCTCCGTTC	61.321	60.000	0.00	0.00	43.82	3.95
957	2465	1.305046	ACGGGATGGTCTCTCCGTT	60.305	57.895	0.00	0.00	43.82	4.44
958	2466	2.052690	CACGGGATGGTCTCTCCGT	61.053	63.158	0.00	0.00	45.76	4.69
959	2467	2.786495	CCACGGGATGGTCTCTCCG	61.786	68.421	0.00	0.00	44.46	4.63
960	2468	3.221222	CCACGGGATGGTCTCTCC	58.779	66.667	0.00	0.00	44.46	3.71
1047	2555	0.540365	ACCTGGTGGAAAGCATGGTG	60.540	55.000	0.00	0.00	37.04	4.17
1089	2597	2.044946	GGACTGGACCATGGTGGC	60.045	66.667	25.52	10.52	42.67	5.01
1126	2636	1.739035	CGTACATATATGCCCGGCCAG	60.739	57.143	12.79	0.00	0.00	4.85
1158	2674	2.301738	GGTGGAGGGTCAGGGAAGG	61.302	68.421	0.00	0.00	0.00	3.46
1290	2810	4.867599	GATGGTCGTCGTCCCCGC	62.868	72.222	6.05	0.00	0.00	6.13
1391	2931	0.317479	ACACGTCAGGCTAGGACAAC	59.683	55.000	5.90	0.00	34.97	3.32
1407	2947	3.665323	GCACGATTCACAAGATCACACAC	60.665	47.826	0.00	0.00	0.00	3.82
1408	2948	2.480037	GCACGATTCACAAGATCACACA	59.520	45.455	0.00	0.00	0.00	3.72
1555	3098	4.191544	TGGTATGCACTGAATTCTGTAGC	58.808	43.478	16.53	19.62	0.00	3.58
1574	3117	3.882888	TCGAGCTCAACATTTTTCTTGGT	59.117	39.130	15.40	0.00	0.00	3.67
1699	3263	1.089920	CAAGATCCCGGTGAAAGCAG	58.910	55.000	0.00	0.00	0.00	4.24
1755	3319	1.379044	GGATGGCCAGGTGGTGAAG	60.379	63.158	13.05	0.00	37.57	3.02
1802	3367	2.079925	GAACTGCTGCTAGAAACCTGG	58.920	52.381	0.00	0.00	0.00	4.45
1823	3391	1.776662	ACCTAGGCAATCGCAGACTA	58.223	50.000	9.30	0.00	42.51	2.59
1827	3396	1.737838	TTGAACCTAGGCAATCGCAG	58.262	50.000	9.30	0.00	41.24	5.18
1830	3399	4.319766	GCACATATTGAACCTAGGCAATCG	60.320	45.833	15.51	11.64	36.27	3.34
1833	3402	4.235079	AGCACATATTGAACCTAGGCAA	57.765	40.909	9.30	6.48	0.00	4.52
1864	3443	5.688823	TCATTATTGAGCGCATAAATTCCG	58.311	37.500	11.47	0.00	0.00	4.30
1906	3488	6.109359	CCTTATTCCAGTTGTAGAAGTCTGG	58.891	44.000	3.53	3.53	46.00	3.86
2090	3672	1.577328	CGAGGATGCACACACCCAAC	61.577	60.000	0.00	0.00	0.00	3.77
2109	3692	9.612620	CATCTTTAAAAATCAAGTAGTGACACC	57.387	33.333	0.84	0.00	39.72	4.16
2123	3706	8.465999	TCGATGCATACAACCATCTTTAAAAAT	58.534	29.630	0.00	0.00	36.55	1.82
2129	3712	5.589855	TCAATCGATGCATACAACCATCTTT	59.410	36.000	0.00	0.00	36.55	2.52
2130	3713	5.125356	TCAATCGATGCATACAACCATCTT	58.875	37.500	0.00	0.00	36.55	2.40
2131	3714	4.707105	TCAATCGATGCATACAACCATCT	58.293	39.130	0.00	0.00	36.55	2.90
2132	3715	5.388111	CATCAATCGATGCATACAACCATC	58.612	41.667	0.00	0.00	42.54	3.51
2133	3716	5.366829	CATCAATCGATGCATACAACCAT	57.633	39.130	0.00	0.00	42.54	3.55
2145	3728	0.602106	CGGCCTCTGCATCAATCGAT	60.602	55.000	0.00	0.00	40.13	3.59
2146	3729	1.227350	CGGCCTCTGCATCAATCGA	60.227	57.895	0.00	0.00	40.13	3.59
2147	3730	2.249535	CCGGCCTCTGCATCAATCG	61.250	63.158	0.00	0.00	40.13	3.34
2148	3731	1.895707	CCCGGCCTCTGCATCAATC	60.896	63.158	0.00	0.00	40.13	2.67
2152	3735	3.628646	AACACCCGGCCTCTGCATC	62.629	63.158	0.00	0.00	40.13	3.91
2153	3736	1.847798	TAAACACCCGGCCTCTGCAT	61.848	55.000	0.00	0.00	40.13	3.96
2231	3881	1.132643	CCTCGCACCTCTGTAGTGTAC	59.867	57.143	0.00	0.00	37.56	2.90
2345	4003	2.215196	GCCACAGTTTCGTTGTTAGGA	58.785	47.619	0.00	0.00	0.00	2.94
2346	4004	1.944024	TGCCACAGTTTCGTTGTTAGG	59.056	47.619	0.00	0.00	0.00	2.69
2350	4008	1.724582	GCCTGCCACAGTTTCGTTGT	61.725	55.000	0.00	0.00	0.00	3.32
2363	4021	1.448119	GGAGGAAATTAGCGCCTGCC	61.448	60.000	2.29	0.00	44.31	4.85
2370	4028	5.016831	TCCTTGGAAAAGGAGGAAATTAGC	58.983	41.667	3.04	0.00	43.68	3.09
2458	4116	1.093159	CTGGCAGGAGCTGATGAAAC	58.907	55.000	6.61	0.00	41.70	2.78
2566	4225	5.865552	ACATGTACGTGTATGGTTCAAGTAC	59.134	40.000	19.15	12.49	44.53	2.73
2581	4240	6.032956	TGGTTTTGAGAGATACATGTACGT	57.967	37.500	7.96	0.00	0.00	3.57
2723	4382	3.874392	ACATTGAAGCAAACCCATAGC	57.126	42.857	0.00	0.00	0.00	2.97
2817	4481	3.260884	TCTCAACGATAACTTTGCTCCCT	59.739	43.478	0.00	0.00	0.00	4.20
2822	4486	4.565564	ACCGTATCTCAACGATAACTTTGC	59.434	41.667	0.00	0.00	45.68	3.68
2978	4645	2.032030	GCCGCGATGCACTATGTAATTT	60.032	45.455	8.23	0.00	0.00	1.82
2997	4664	0.304705	CTTTGATCCGCGTACATGCC	59.695	55.000	4.92	0.00	0.00	4.40
3093	4760	7.878644	GGGCTTAAACAATTGGGTTATTAACAA	59.121	33.333	10.83	0.00	0.00	2.83
3105	4772	6.463360	AGTTGGTTATGGGCTTAAACAATTG	58.537	36.000	3.24	3.24	40.02	2.32
3347	5680	2.734079	CAACGCACTTTCTTCTCTCTCC	59.266	50.000	0.00	0.00	0.00	3.71
3463	5800	6.678655	GCATACATGTGTTGCAACTACATCAT	60.679	38.462	28.97	23.85	34.53	2.45
3474	5811	2.330231	AACGTGCATACATGTGTTGC	57.670	45.000	21.99	21.99	45.43	4.17
3499	5836	9.083422	TCTACATAATAATCAGGTGAAGAGAGG	57.917	37.037	0.00	0.00	0.00	3.69
3526	5865	8.744568	TTCATATCATGCCACAGTTTGTTATA	57.255	30.769	0.00	0.00	0.00	0.98
3532	5871	7.043565	GGAAATTTCATATCATGCCACAGTTT	58.956	34.615	19.49	0.00	0.00	2.66
3537	5876	5.009010	ACTCGGAAATTTCATATCATGCCAC	59.991	40.000	19.49	0.00	0.00	5.01
3563	6879	1.000496	ACTCCGTTCAAGTTCGAGTCC	60.000	52.381	0.00	0.00	0.00	3.85
3572	6888	7.827819	TTCTTATATTGTCACTCCGTTCAAG	57.172	36.000	0.00	0.00	0.00	3.02
3623	6986	5.140177	GCTGCTGCAAAATGATACGTATAC	58.860	41.667	8.34	3.25	39.41	1.47
3624	6987	5.342806	GCTGCTGCAAAATGATACGTATA	57.657	39.130	8.34	0.00	39.41	1.47
3627	6990	2.549633	GCTGCTGCAAAATGATACGT	57.450	45.000	11.11	0.00	39.41	3.57
3640	7003	1.529438	CCATTTTTGTTGCTGCTGCTG	59.471	47.619	17.00	0.77	40.48	4.41
3645	7009	2.718663	GCAAACCATTTTTGTTGCTGC	58.281	42.857	0.00	0.00	0.00	5.25
3646	7010	2.850254	GCGCAAACCATTTTTGTTGCTG	60.850	45.455	0.30	1.46	33.41	4.41
3649	7013	1.939255	AGGCGCAAACCATTTTTGTTG	59.061	42.857	10.83	0.00	0.00	3.33
3652	7016	5.355467	AAAATAGGCGCAAACCATTTTTG	57.645	34.783	10.83	0.00	31.86	2.44
3672	7039	7.010738	CAGGTACAAGAAGAGACAACGTAAAAA	59.989	37.037	0.00	0.00	0.00	1.94
3676	7043	4.823442	TCAGGTACAAGAAGAGACAACGTA	59.177	41.667	0.00	0.00	0.00	3.57
3677	7044	3.635373	TCAGGTACAAGAAGAGACAACGT	59.365	43.478	0.00	0.00	0.00	3.99
3678	7045	4.238761	TCAGGTACAAGAAGAGACAACG	57.761	45.455	0.00	0.00	0.00	4.10
3679	7046	4.859798	CGATCAGGTACAAGAAGAGACAAC	59.140	45.833	0.00	0.00	0.00	3.32
3681	7048	3.119459	GCGATCAGGTACAAGAAGAGACA	60.119	47.826	0.00	0.00	0.00	3.41
3682	7049	3.119459	TGCGATCAGGTACAAGAAGAGAC	60.119	47.826	0.00	0.00	0.00	3.36
3684	7051	3.510388	TGCGATCAGGTACAAGAAGAG	57.490	47.619	0.00	0.00	0.00	2.85
3722	7173	0.321298	TTCTTTGCCGAGCCCTGTAC	60.321	55.000	0.00	0.00	0.00	2.90
3723	7174	0.321298	GTTCTTTGCCGAGCCCTGTA	60.321	55.000	0.00	0.00	0.00	2.74
3724	7175	1.600916	GTTCTTTGCCGAGCCCTGT	60.601	57.895	0.00	0.00	0.00	4.00
3725	7176	0.890996	AAGTTCTTTGCCGAGCCCTG	60.891	55.000	0.00	0.00	0.00	4.45
3742	7193	2.673368	GGAAGTGCACGAAGATGGTAAG	59.327	50.000	12.01	0.00	0.00	2.34
3772	7223	1.865865	ATTATCTTACCACGCCTGCG	58.134	50.000	10.40	10.40	46.03	5.18
3789	7240	7.228706	GTGGTAGCCATTGCAAGTATTAGTATT	59.771	37.037	4.94	0.00	41.13	1.89
3790	7241	6.710744	GTGGTAGCCATTGCAAGTATTAGTAT	59.289	38.462	4.94	0.00	41.13	2.12
3791	7242	6.053005	GTGGTAGCCATTGCAAGTATTAGTA	58.947	40.000	4.94	0.00	41.13	1.82
3792	7243	4.881850	GTGGTAGCCATTGCAAGTATTAGT	59.118	41.667	4.94	0.00	41.13	2.24
3793	7244	4.881273	TGTGGTAGCCATTGCAAGTATTAG	59.119	41.667	4.94	0.00	41.13	1.73
3794	7245	4.849518	TGTGGTAGCCATTGCAAGTATTA	58.150	39.130	4.94	0.00	41.13	0.98
3843	7294	2.869801	GCAACTTGTTTTTGTAAGGGGC	59.130	45.455	0.00	0.00	0.00	5.80
3974	7426	1.059835	GCGAGTGTCAAGCGAGATTTC	59.940	52.381	0.00	0.00	0.00	2.17
3992	7476	2.787249	CCTTGCTTGATGGACGCG	59.213	61.111	3.53	3.53	0.00	6.01
3995	7495	1.820519	TGAATGCCTTGCTTGATGGAC	59.179	47.619	0.00	0.00	0.00	4.02
4045	7552	3.564027	GCCGTACCTGCATGCGAC	61.564	66.667	14.09	7.44	0.00	5.19
4076	7583	1.152567	CTCAGGATCGGAGCCCTCT	60.153	63.158	9.01	0.00	0.00	3.69
4101	7608	1.090052	GTTATGTCGTCCCTGCAGCC	61.090	60.000	8.66	0.00	0.00	4.85
4131	7638	2.569134	GGTCTCGAGCTGCTTCGT	59.431	61.111	7.81	0.00	41.22	3.85
4197	7706	2.866156	CGTTCTCCGGTGAGTATACGTA	59.134	50.000	16.44	0.00	39.75	3.57
4198	7707	1.667724	CGTTCTCCGGTGAGTATACGT	59.332	52.381	16.44	0.00	39.75	3.57
4199	7708	1.596464	GCGTTCTCCGGTGAGTATACG	60.596	57.143	19.10	19.10	39.75	3.06
4213	7752	2.590575	CCAACCACCGTGCGTTCT	60.591	61.111	0.00	0.00	0.00	3.01
4284	7823	4.247380	CAGCCCTCTGGATCCGGC	62.247	72.222	16.48	17.34	41.96	6.13
4379	7918	2.258109	AGAGGGTGGTTTACTCTGTCC	58.742	52.381	0.00	0.00	41.28	4.02
4406	7947	0.535335	TCAACTAAAGGGCGCGAGAT	59.465	50.000	12.10	0.00	0.00	2.75
4410	7951	0.872388	AAACTCAACTAAAGGGCGCG	59.128	50.000	0.00	0.00	0.00	6.86
4417	7958	5.997746	CAGGACAGGATGAAACTCAACTAAA	59.002	40.000	0.00	0.00	39.69	1.85
4431	7972	1.140312	AACACACACCAGGACAGGAT	58.860	50.000	0.00	0.00	0.00	3.24
4535	8088	2.283529	GGGGCAGTCCGTCTTCTGA	61.284	63.158	0.00	0.00	36.01	3.27
4761	8323	7.496591	GGAGGGAATACGTACATAAATTTGACA	59.503	37.037	0.00	0.00	0.00	3.58
4764	8326	7.795482	TGGAGGGAATACGTACATAAATTTG	57.205	36.000	0.00	0.00	0.00	2.32
4779	8341	5.786975	AGTTCAAATTTGGAATGGAGGGAAT	59.213	36.000	17.90	0.00	0.00	3.01
4788	8350	9.844257	TGGTTGATTTTAGTTCAAATTTGGAAT	57.156	25.926	17.90	11.48	35.03	3.01
4808	8543	6.183360	TGTTCCAAAATATTTGTCGTGGTTGA	60.183	34.615	13.75	2.93	0.00	3.18
4812	8547	6.007936	TCTGTTCCAAAATATTTGTCGTGG	57.992	37.500	9.50	9.50	0.00	4.94
4855	8594	1.280142	CGGATCTCGAGTACAGCGG	59.720	63.158	13.13	0.00	42.43	5.52
4873	8612	1.133356	AGCTGGGGATAAATTCAGGGC	60.133	52.381	0.00	0.00	0.00	5.19
4916	8656	0.037697	TGTCTACGGTCACACATGCC	60.038	55.000	0.00	0.00	0.00	4.40
4942	8682	0.470456	TCTGGTCTACCGGGTGTTGT	60.470	55.000	10.66	0.00	42.72	3.32
5135	8882	0.324275	AGCAGTTGTTTGGTGGTGGT	60.324	50.000	0.00	0.00	0.00	4.16
5136	8883	0.102844	CAGCAGTTGTTTGGTGGTGG	59.897	55.000	0.00	0.00	41.58	4.61
5137	8884	3.646650	CAGCAGTTGTTTGGTGGTG	57.353	52.632	0.00	0.00	41.58	4.17
5147	8894	6.835914	GCATAGGCTATAATTACAGCAGTTG	58.164	40.000	17.14	11.18	39.63	3.16
5183	8931	3.054655	ACTGTTGTCCTGTTGTGGTACTT	60.055	43.478	0.00	0.00	0.00	2.24
5295	9044	0.181114	TTGGATCTGGAGGAATGCCG	59.819	55.000	0.00	0.00	39.96	5.69
5316	9065	1.071542	GGAGGATCTTCTAGCCCTTGC	59.928	57.143	4.68	0.00	32.30	4.01
5326	9075	3.847671	AAGGATTTCGGGAGGATCTTC	57.152	47.619	0.00	0.00	33.73	2.87
5383	9132	2.435059	GGAAGCGCTGGTCACTCC	60.435	66.667	12.58	9.66	0.00	3.85
5530	9281	3.246203	TGGGTCCTCTTATCCTACAACCA	60.246	47.826	0.00	0.00	0.00	3.67
5567	9318	3.177228	AGCTATTGACTGAGGGTCTGTT	58.823	45.455	0.00	0.00	44.74	3.16
5582	9333	8.213679	ACCTTGTATGACAATGTATGAGCTATT	58.786	33.333	0.00	0.00	37.48	1.73
5840	9601	6.067350	TGTTGACATTGCCATGGCTATTATA	58.933	36.000	35.53	18.46	39.54	0.98
5892	9654	6.148150	GGGTAACGAATGATTTCACTGTTGTA	59.852	38.462	0.00	0.00	37.60	2.41
5911	9673	0.335019	AAGGGATGCCTTGGGGTAAC	59.665	55.000	18.95	0.00	34.45	2.50
6029	9791	0.659427	CAGCGGCACAACCATATGAG	59.341	55.000	3.65	0.00	39.03	2.90
6042	9804	1.212751	GGACAACCATTTCAGCGGC	59.787	57.895	0.00	0.00	35.97	6.53
6349	10114	4.119862	CACTAGTTCATGGGACGTATTGG	58.880	47.826	0.00	0.00	0.00	3.16
6353	10118	2.094390	GTGCACTAGTTCATGGGACGTA	60.094	50.000	10.32	0.00	0.00	3.57
6355	10120	1.337728	TGTGCACTAGTTCATGGGACG	60.338	52.381	19.41	0.00	0.00	4.79

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.