AutoCloner

Multiple sequence alignment - TraesCS1A01G234500

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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	TraesCS1A01G234500	chr1A	100.000	2653	0	0	873	3525	409857500	409854848	0.000000e+00	4900.0
1	TraesCS1A01G234500	chr1A	100.000	589	0	0	1	589	409858372	409857784	0.000000e+00	1088.0
2	TraesCS1A01G234500	chr1A	90.990	788	61	4	2081	2861	17870921	17871705	0.000000e+00	1053.0
3	TraesCS1A01G234500	chr1A	88.760	258	24	4	180	436	514938604	514938351	9.500000e-81	311.0
4	TraesCS1A01G234500	chr1A	88.043	184	14	3	1877	2053	17869768	17869950	9.910000e-51	211.0
5	TraesCS1A01G234500	chr1A	88.608	79	7	2	1774	1851	12784209	12784286	1.040000e-15	95.3
6	TraesCS1A01G234500	chr3B	97.193	2672	56	4	873	3525	804115422	804118093	0.000000e+00	4501.0
7	TraesCS1A01G234500	chr3B	91.117	788	58	6	2081	2861	734998479	734999261	0.000000e+00	1057.0
8	TraesCS1A01G234500	chr3B	86.353	447	25	7	178	589	804114915	804115360	4.150000e-124	455.0
9	TraesCS1A01G234500	chr3B	84.028	432	43	11	179	588	189426244	189425817	3.300000e-105	392.0
10	TraesCS1A01G234500	chr3B	88.889	180	12	3	1877	2049	734997354	734997532	7.660000e-52	215.0
11	TraesCS1A01G234500	chr3A	97.302	1890	40	5	1059	2941	567999083	568000968	0.000000e+00	3197.0
12	TraesCS1A01G234500	chr3A	91.656	791	47	7	2081	2861	94161761	94162542	0.000000e+00	1077.0
13	TraesCS1A01G234500	chr3A	93.972	564	18	1	2978	3525	568000971	568001534	0.000000e+00	839.0
14	TraesCS1A01G234500	chr3A	86.806	432	33	5	180	589	567998492	567998921	8.920000e-126	460.0
15	TraesCS1A01G234500	chr3A	88.333	180	13	3	1877	2049	94145649	94145827	3.570000e-50	209.0
16	TraesCS1A01G234500	chr3D	96.404	1474	35	3	2069	3525	571464230	571465702	0.000000e+00	2412.0
17	TraesCS1A01G234500	chr3D	95.181	996	42	2	1059	2048	571453849	571454844	0.000000e+00	1568.0
18	TraesCS1A01G234500	chr3D	97.699	869	16	2	2066	2934	579496006	579495142	0.000000e+00	1491.0
19	TraesCS1A01G234500	chr3D	95.247	526	9	1	3016	3525	579495143	579494618	0.000000e+00	819.0
20	TraesCS1A01G234500	chr3D	94.241	191	9	2	2673	2861	382809856	382810046	1.240000e-74	291.0
21	TraesCS1A01G234500	chr3D	77.136	398	43	24	176	538	511940208	511939824	1.670000e-43	187.0
22	TraesCS1A01G234500	chr3D	76.709	395	43	23	181	538	532142659	532142277	1.300000e-39	174.0
23	TraesCS1A01G234500	chr3D	88.608	79	7	2	1774	1851	141455853	141455930	1.040000e-15	95.3
24	TraesCS1A01G234500	chr4D	96.145	1323	40	3	1059	2374	214994400	214995718	0.000000e+00	2150.0
25	TraesCS1A01G234500	chr4D	88.811	143	10	3	3046	3183	359683735	359683594	1.680000e-38	171.0
26	TraesCS1A01G234500	chr6B	95.455	1122	49	2	907	2027	130110699	130111819	0.000000e+00	1788.0
27	TraesCS1A01G234500	chr6B	97.627	590	13	1	2389	2978	130111822	130112410	0.000000e+00	1011.0
28	TraesCS1A01G234500	chr6B	94.095	525	15	1	3017	3525	130112407	130112931	0.000000e+00	784.0
29	TraesCS1A01G234500	chr6B	85.874	446	28	5	179	589	130109946	130110391	3.230000e-120	442.0
30	TraesCS1A01G234500	chr2B	96.556	842	28	1	873	1713	4570164	4569323	0.000000e+00	1393.0
31	TraesCS1A01G234500	chr2B	85.650	446	25	13	180	589	4571027	4570585	1.940000e-117	433.0
32	TraesCS1A01G234500	chr2B	92.053	151	11	1	3206	3355	757065177	757065027	9.910000e-51	211.0
33	TraesCS1A01G234500	chr2B	91.391	151	13	0	436	586	633308673	633308523	1.280000e-49	207.0
34	TraesCS1A01G234500	chr2B	93.814	97	5	1	2922	3017	678068870	678068966	1.020000e-30	145.0
35	TraesCS1A01G234500	chr2B	90.476	105	9	1	2922	3026	46846072	46846175	1.710000e-28	137.0
36	TraesCS1A01G234500	chr5D	91.751	788	55	5	2081	2861	539738175	539738959	0.000000e+00	1086.0
37	TraesCS1A01G234500	chr5D	88.889	180	12	3	1877	2049	539737020	539737198	7.660000e-52	215.0
38	TraesCS1A01G234500	chr5D	91.304	69	6	0	1783	1851	254356545	254356477	1.040000e-15	95.3
39	TraesCS1A01G234500	chr7B	96.070	458	17	1	1140	1596	88141425	88141882	0.000000e+00	745.0
40	TraesCS1A01G234500	chr7B	84.454	714	71	13	1059	1741	683925226	683925930	0.000000e+00	667.0
41	TraesCS1A01G234500	chr7B	83.678	435	43	13	178	588	98981004	98981434	5.520000e-103	385.0
42	TraesCS1A01G234500	chr7B	90.323	155	13	1	3198	3352	526430882	526430730	5.970000e-48	202.0
43	TraesCS1A01G234500	chr7B	93.750	96	6	0	2926	3021	66196614	66196709	1.020000e-30	145.0
44	TraesCS1A01G234500	chr7D	84.756	656	63	13	1102	1741	602913875	602914509	1.070000e-174	623.0
45	TraesCS1A01G234500	chr7D	92.697	178	13	0	3348	3525	468942749	468942572	1.260000e-64	257.0
46	TraesCS1A01G234500	chr7D	89.163	203	19	3	2586	2786	468943571	468943370	2.100000e-62	250.0
47	TraesCS1A01G234500	chr7D	91.720	157	7	1	3202	3352	36659733	36659889	2.760000e-51	213.0
48	TraesCS1A01G234500	chr4B	82.550	447	37	10	180	589	350966871	350967313	4.330000e-94	355.0
49	TraesCS1A01G234500	chr4B	96.739	92	3	0	2926	3017	187091158	187091067	1.690000e-33	154.0
50	TraesCS1A01G234500	chrUn	81.798	445	42	14	180	588	254615469	254615910	1.570000e-88	337.0
51	TraesCS1A01G234500	chrUn	81.573	445	43	9	180	588	375587025	375586584	7.290000e-87	331.0
52	TraesCS1A01G234500	chr1B	81.839	435	33	10	190	589	55530387	55530810	1.220000e-84	324.0
53	TraesCS1A01G234500	chr1D	88.085	235	22	5	275	504	479511733	479511500	1.250000e-69	274.0
54	TraesCS1A01G234500	chr5A	91.429	175	15	0	3351	3525	554993718	554993544	1.260000e-59	241.0
55	TraesCS1A01G234500	chr5A	91.429	175	15	0	3351	3525	555018192	555018018	1.260000e-59	241.0
56	TraesCS1A01G234500	chr5A	91.429	175	15	0	3351	3525	555029385	555029211	1.260000e-59	241.0
57	TraesCS1A01G234500	chr2A	92.000	150	11	1	3206	3354	418618398	418618249	3.570000e-50	209.0
58	TraesCS1A01G234500	chr5B	97.727	88	2	0	2933	3020	697972381	697972294	6.090000e-33	152.0
59	TraesCS1A01G234500	chr5B	92.929	99	6	1	2923	3020	317294229	317294327	3.670000e-30	143.0
60	TraesCS1A01G234500	chr6D	91.304	69	6	0	1783	1851	450266293	450266225	1.040000e-15	95.3

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	TraesCS1A01G234500	chr1A	409854848	409858372	3524	True	2994.000000	4900	100.000000	1	3525	2	chr1A.!!$R2	3524
1	TraesCS1A01G234500	chr1A	17869768	17871705	1937	False	632.000000	1053	89.516500	1877	2861	2	chr1A.!!$F2	984
2	TraesCS1A01G234500	chr3B	804114915	804118093	3178	False	2478.000000	4501	91.773000	178	3525	2	chr3B.!!$F2	3347
3	TraesCS1A01G234500	chr3B	734997354	734999261	1907	False	636.000000	1057	90.003000	1877	2861	2	chr3B.!!$F1	984
4	TraesCS1A01G234500	chr3A	567998492	568001534	3042	False	1498.666667	3197	92.693333	180	3525	3	chr3A.!!$F3	3345
5	TraesCS1A01G234500	chr3A	94161761	94162542	781	False	1077.000000	1077	91.656000	2081	2861	1	chr3A.!!$F2	780
6	TraesCS1A01G234500	chr3D	571464230	571465702	1472	False	2412.000000	2412	96.404000	2069	3525	1	chr3D.!!$F4	1456
7	TraesCS1A01G234500	chr3D	571453849	571454844	995	False	1568.000000	1568	95.181000	1059	2048	1	chr3D.!!$F3	989
8	TraesCS1A01G234500	chr3D	579494618	579496006	1388	True	1155.000000	1491	96.473000	2066	3525	2	chr3D.!!$R3	1459
9	TraesCS1A01G234500	chr4D	214994400	214995718	1318	False	2150.000000	2150	96.145000	1059	2374	1	chr4D.!!$F1	1315
10	TraesCS1A01G234500	chr6B	130109946	130112931	2985	False	1006.250000	1788	93.262750	179	3525	4	chr6B.!!$F1	3346
11	TraesCS1A01G234500	chr2B	4569323	4571027	1704	True	913.000000	1393	91.103000	180	1713	2	chr2B.!!$R3	1533
12	TraesCS1A01G234500	chr5D	539737020	539738959	1939	False	650.500000	1086	90.320000	1877	2861	2	chr5D.!!$F1	984
13	TraesCS1A01G234500	chr7B	683925226	683925930	704	False	667.000000	667	84.454000	1059	1741	1	chr7B.!!$F4	682
14	TraesCS1A01G234500	chr7D	602913875	602914509	634	False	623.000000	623	84.756000	1102	1741	1	chr7D.!!$F2	639
15	TraesCS1A01G234500	chr7D	468942572	468943571	999	True	253.500000	257	90.930000	2586	3525	2	chr7D.!!$R1	939

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
47	48	0.035458	AGGGGCGAAGACAGAACAAG	59.965	55.0	0.00	37.00	3.16	F
166	167	0.038618	TGACCCAGATTGTGACGTCG	60.039	55.0	11.62	31.25	5.12	F
1165	1341	0.036306	GAAACCTTCTCCCAAGCCGA	59.964	55.0	0.00	0.00	5.54	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Hairpin	End Stability	Orientation
1135	1311	1.228552	AAGGTTTCCACGCAGCCAT	60.229	52.632	0.00	0.00	4.40	R
1331	1537	1.593209	GACGCGTTGAGGTTCACCA	60.593	57.895	15.53	38.89	4.17	R
2906	4415	2.125350	GCACCGGCTCAGAAGGAG	60.125	66.667	0.00	46.93	3.69	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
19	20	2.953466	AGTACCATGAACGCACGTAT	57.047	45.000	0.00	0.00	0.00	3.06
20	21	3.241067	AGTACCATGAACGCACGTATT	57.759	42.857	0.00	0.00	0.00	1.89
21	22	2.927477	AGTACCATGAACGCACGTATTG	59.073	45.455	0.00	0.00	0.00	1.90
22	23	2.087501	ACCATGAACGCACGTATTGA	57.912	45.000	0.00	0.00	0.00	2.57
23	24	1.730064	ACCATGAACGCACGTATTGAC	59.270	47.619	0.00	0.00	0.00	3.18
24	25	1.729517	CCATGAACGCACGTATTGACA	59.270	47.619	0.00	0.00	0.00	3.58
25	26	2.473868	CCATGAACGCACGTATTGACAC	60.474	50.000	0.00	0.00	0.00	3.67
26	27	1.854227	TGAACGCACGTATTGACACA	58.146	45.000	0.00	0.00	0.00	3.72
27	28	1.523515	TGAACGCACGTATTGACACAC	59.476	47.619	0.00	0.00	0.00	3.82
28	29	1.523515	GAACGCACGTATTGACACACA	59.476	47.619	0.00	0.00	0.00	3.72
29	30	1.136690	ACGCACGTATTGACACACAG	58.863	50.000	0.00	0.00	0.00	3.66
30	31	0.438445	CGCACGTATTGACACACAGG	59.562	55.000	0.00	0.00	0.00	4.00
31	32	0.796312	GCACGTATTGACACACAGGG	59.204	55.000	0.00	0.00	0.00	4.45
32	33	1.438651	CACGTATTGACACACAGGGG	58.561	55.000	0.00	0.00	0.00	4.79
33	34	0.321298	ACGTATTGACACACAGGGGC	60.321	55.000	0.00	0.00	0.00	5.80
34	35	1.358725	CGTATTGACACACAGGGGCG	61.359	60.000	0.00	0.00	0.00	6.13
35	36	0.036765	GTATTGACACACAGGGGCGA	60.037	55.000	0.00	0.00	0.00	5.54
36	37	0.687920	TATTGACACACAGGGGCGAA	59.312	50.000	0.00	0.00	0.00	4.70
37	38	0.606401	ATTGACACACAGGGGCGAAG	60.606	55.000	0.00	0.00	0.00	3.79
38	39	1.691195	TTGACACACAGGGGCGAAGA	61.691	55.000	0.00	0.00	0.00	2.87
39	40	1.668151	GACACACAGGGGCGAAGAC	60.668	63.158	0.00	0.00	0.00	3.01
40	41	2.377628	GACACACAGGGGCGAAGACA	62.378	60.000	0.00	0.00	37.00	3.41
41	42	1.669115	CACACAGGGGCGAAGACAG	60.669	63.158	0.00	0.00	37.00	3.51
42	43	1.837051	ACACAGGGGCGAAGACAGA	60.837	57.895	0.00	0.00	37.00	3.41
43	44	1.371183	CACAGGGGCGAAGACAGAA	59.629	57.895	0.00	0.00	37.00	3.02
44	45	0.951040	CACAGGGGCGAAGACAGAAC	60.951	60.000	0.00	0.00	37.00	3.01
45	46	1.371183	CAGGGGCGAAGACAGAACA	59.629	57.895	0.00	0.00	37.00	3.18
46	47	0.250295	CAGGGGCGAAGACAGAACAA	60.250	55.000	0.00	0.00	37.00	2.83
47	48	0.035458	AGGGGCGAAGACAGAACAAG	59.965	55.000	0.00	0.00	37.00	3.16
48	49	0.955919	GGGGCGAAGACAGAACAAGG	60.956	60.000	0.00	0.00	37.00	3.61
49	50	0.955919	GGGCGAAGACAGAACAAGGG	60.956	60.000	0.00	0.00	37.00	3.95
50	51	1.578206	GGCGAAGACAGAACAAGGGC	61.578	60.000	0.00	0.00	31.66	5.19
51	52	0.884704	GCGAAGACAGAACAAGGGCA	60.885	55.000	0.00	0.00	0.00	5.36
52	53	1.813513	CGAAGACAGAACAAGGGCAT	58.186	50.000	0.00	0.00	0.00	4.40
53	54	1.466167	CGAAGACAGAACAAGGGCATG	59.534	52.381	0.00	0.00	0.00	4.06
54	55	1.200948	GAAGACAGAACAAGGGCATGC	59.799	52.381	9.90	9.90	0.00	4.06
55	56	0.610232	AGACAGAACAAGGGCATGCC	60.610	55.000	29.47	29.47	0.00	4.40
65	66	3.625099	GGCATGCCCAAAGATGCT	58.375	55.556	27.24	0.00	43.77	3.79
66	67	2.811307	GGCATGCCCAAAGATGCTA	58.189	52.632	27.24	0.00	43.77	3.49
67	68	0.386838	GGCATGCCCAAAGATGCTAC	59.613	55.000	27.24	0.00	43.77	3.58
68	69	1.105457	GCATGCCCAAAGATGCTACA	58.895	50.000	6.36	0.00	41.52	2.74
69	70	1.202336	GCATGCCCAAAGATGCTACAC	60.202	52.381	6.36	0.00	41.52	2.90
70	71	2.372264	CATGCCCAAAGATGCTACACT	58.628	47.619	0.00	0.00	0.00	3.55
71	72	3.544684	CATGCCCAAAGATGCTACACTA	58.455	45.455	0.00	0.00	0.00	2.74
72	73	2.985896	TGCCCAAAGATGCTACACTAC	58.014	47.619	0.00	0.00	0.00	2.73
73	74	2.571653	TGCCCAAAGATGCTACACTACT	59.428	45.455	0.00	0.00	0.00	2.57
74	75	3.198872	GCCCAAAGATGCTACACTACTC	58.801	50.000	0.00	0.00	0.00	2.59
75	76	3.448686	CCCAAAGATGCTACACTACTCG	58.551	50.000	0.00	0.00	0.00	4.18
76	77	3.130516	CCCAAAGATGCTACACTACTCGA	59.869	47.826	0.00	0.00	0.00	4.04
77	78	4.106197	CCAAAGATGCTACACTACTCGAC	58.894	47.826	0.00	0.00	0.00	4.20
78	79	4.106197	CAAAGATGCTACACTACTCGACC	58.894	47.826	0.00	0.00	0.00	4.79
79	80	3.284793	AGATGCTACACTACTCGACCT	57.715	47.619	0.00	0.00	0.00	3.85
80	81	4.418973	AGATGCTACACTACTCGACCTA	57.581	45.455	0.00	0.00	0.00	3.08
81	82	4.128643	AGATGCTACACTACTCGACCTAC	58.871	47.826	0.00	0.00	0.00	3.18
82	83	2.274437	TGCTACACTACTCGACCTACG	58.726	52.381	0.00	0.00	44.09	3.51
83	84	2.275318	GCTACACTACTCGACCTACGT	58.725	52.381	0.00	0.00	43.13	3.57
84	85	2.030213	GCTACACTACTCGACCTACGTG	59.970	54.545	0.00	0.00	43.13	4.49
86	87	2.498167	ACACTACTCGACCTACGTGTT	58.502	47.619	0.00	0.00	44.41	3.32
87	88	3.664107	ACACTACTCGACCTACGTGTTA	58.336	45.455	0.00	0.00	44.41	2.41
88	89	4.065088	ACACTACTCGACCTACGTGTTAA	58.935	43.478	0.00	0.00	44.41	2.01
89	90	4.083802	ACACTACTCGACCTACGTGTTAAC	60.084	45.833	0.00	0.00	44.41	2.01
90	91	4.153117	CACTACTCGACCTACGTGTTAACT	59.847	45.833	7.22	0.00	44.41	2.24
91	92	4.757149	ACTACTCGACCTACGTGTTAACTT	59.243	41.667	7.22	0.00	44.41	2.66
92	93	4.574599	ACTCGACCTACGTGTTAACTTT	57.425	40.909	7.22	0.00	44.41	2.66
93	94	5.689383	ACTCGACCTACGTGTTAACTTTA	57.311	39.130	7.22	0.00	44.41	1.85
94	95	6.259550	ACTCGACCTACGTGTTAACTTTAT	57.740	37.500	7.22	0.00	44.41	1.40
95	96	6.317857	ACTCGACCTACGTGTTAACTTTATC	58.682	40.000	7.22	0.00	44.41	1.75
96	97	5.640732	TCGACCTACGTGTTAACTTTATCC	58.359	41.667	7.22	0.00	43.13	2.59
97	98	4.800471	CGACCTACGTGTTAACTTTATCCC	59.200	45.833	7.22	0.00	37.22	3.85
98	99	5.393461	CGACCTACGTGTTAACTTTATCCCT	60.393	44.000	7.22	0.00	37.22	4.20
99	100	6.364568	ACCTACGTGTTAACTTTATCCCTT	57.635	37.500	7.22	0.00	0.00	3.95
100	101	6.168389	ACCTACGTGTTAACTTTATCCCTTG	58.832	40.000	7.22	0.00	0.00	3.61
101	102	6.014327	ACCTACGTGTTAACTTTATCCCTTGA	60.014	38.462	7.22	0.00	0.00	3.02
102	103	7.046033	CCTACGTGTTAACTTTATCCCTTGAT	58.954	38.462	7.22	0.00	34.87	2.57
103	104	7.551617	CCTACGTGTTAACTTTATCCCTTGATT	59.448	37.037	7.22	0.00	32.18	2.57
104	105	7.754851	ACGTGTTAACTTTATCCCTTGATTT	57.245	32.000	7.22	0.00	32.18	2.17
105	106	7.813645	ACGTGTTAACTTTATCCCTTGATTTC	58.186	34.615	7.22	0.00	32.18	2.17
106	107	7.446013	ACGTGTTAACTTTATCCCTTGATTTCA	59.554	33.333	7.22	0.00	32.18	2.69
107	108	7.962918	CGTGTTAACTTTATCCCTTGATTTCAG	59.037	37.037	7.22	0.00	32.18	3.02
108	109	7.755373	GTGTTAACTTTATCCCTTGATTTCAGC	59.245	37.037	7.22	0.00	32.18	4.26
109	110	7.450014	TGTTAACTTTATCCCTTGATTTCAGCA	59.550	33.333	7.22	0.00	32.18	4.41
110	111	8.470002	GTTAACTTTATCCCTTGATTTCAGCAT	58.530	33.333	0.00	0.00	32.18	3.79
111	112	6.461110	ACTTTATCCCTTGATTTCAGCATG	57.539	37.500	0.00	0.00	32.18	4.06
112	113	6.189859	ACTTTATCCCTTGATTTCAGCATGA	58.810	36.000	0.00	0.00	36.34	3.07
113	114	6.096001	ACTTTATCCCTTGATTTCAGCATGAC	59.904	38.462	0.00	0.00	37.34	3.06
114	115	5.378230	TATCCCTTGATTTCAGCATGACT	57.622	39.130	0.00	0.00	37.34	3.41
115	116	5.371526	TATCCCTTGATTTCAGCATGACTC	58.628	41.667	0.00	0.00	37.34	3.36
116	117	5.131642	TATCCCTTGATTTCAGCATGACTCT	59.868	40.000	0.00	0.00	37.34	3.24
117	118	6.687393	TATCCCTTGATTTCAGCATGACTCTC	60.687	42.308	0.00	0.00	37.34	3.20
118	119	9.000443	TATCCCTTGATTTCAGCATGACTCTCA	62.000	40.741	0.00	0.00	37.34	3.27
124	125	3.036075	TCAGCATGACTCTCACTTGTG	57.964	47.619	0.00	0.00	42.56	3.33
125	126	2.629617	TCAGCATGACTCTCACTTGTGA	59.370	45.455	0.00	3.32	42.56	3.58
126	127	3.260128	TCAGCATGACTCTCACTTGTGAT	59.740	43.478	3.79	0.00	42.56	3.06
127	128	4.001652	CAGCATGACTCTCACTTGTGATT	58.998	43.478	3.79	0.00	39.69	2.57
128	129	4.454847	CAGCATGACTCTCACTTGTGATTT	59.545	41.667	3.79	0.00	39.69	2.17
129	130	5.048921	CAGCATGACTCTCACTTGTGATTTT	60.049	40.000	3.79	0.00	39.69	1.82
130	131	6.148315	CAGCATGACTCTCACTTGTGATTTTA	59.852	38.462	3.79	0.00	39.69	1.52
131	132	6.712095	AGCATGACTCTCACTTGTGATTTTAA	59.288	34.615	3.79	0.00	0.00	1.52
132	133	6.798959	GCATGACTCTCACTTGTGATTTTAAC	59.201	38.462	3.79	0.00	0.00	2.01
133	134	6.861065	TGACTCTCACTTGTGATTTTAACC	57.139	37.500	3.79	0.00	0.00	2.85
134	135	5.763204	TGACTCTCACTTGTGATTTTAACCC	59.237	40.000	3.79	0.00	0.00	4.11
135	136	5.070685	ACTCTCACTTGTGATTTTAACCCC	58.929	41.667	3.79	0.00	0.00	4.95
136	137	4.069304	TCTCACTTGTGATTTTAACCCCG	58.931	43.478	3.79	0.00	0.00	5.73
137	138	3.818773	CTCACTTGTGATTTTAACCCCGT	59.181	43.478	3.79	0.00	0.00	5.28
138	139	3.566322	TCACTTGTGATTTTAACCCCGTG	59.434	43.478	0.00	0.00	0.00	4.94
139	140	2.295070	ACTTGTGATTTTAACCCCGTGC	59.705	45.455	0.00	0.00	0.00	5.34
140	141	1.249407	TGTGATTTTAACCCCGTGCC	58.751	50.000	0.00	0.00	0.00	5.01
141	142	1.202952	TGTGATTTTAACCCCGTGCCT	60.203	47.619	0.00	0.00	0.00	4.75
142	143	1.201414	GTGATTTTAACCCCGTGCCTG	59.799	52.381	0.00	0.00	0.00	4.85
143	144	0.815095	GATTTTAACCCCGTGCCTGG	59.185	55.000	0.00	0.00	0.00	4.45
144	145	0.113580	ATTTTAACCCCGTGCCTGGT	59.886	50.000	0.00	0.00	36.06	4.00
145	146	0.769873	TTTTAACCCCGTGCCTGGTA	59.230	50.000	0.00	0.00	33.52	3.25
146	147	0.325602	TTTAACCCCGTGCCTGGTAG	59.674	55.000	0.00	0.00	33.52	3.18
147	148	0.837260	TTAACCCCGTGCCTGGTAGT	60.837	55.000	0.00	0.00	33.52	2.73
148	149	1.546589	TAACCCCGTGCCTGGTAGTG	61.547	60.000	0.00	0.00	33.52	2.74
149	150	3.000819	CCCCGTGCCTGGTAGTGA	61.001	66.667	0.00	0.00	0.00	3.41
150	151	2.264794	CCCGTGCCTGGTAGTGAC	59.735	66.667	0.00	0.00	0.00	3.67
152	153	2.264794	CGTGCCTGGTAGTGACCC	59.735	66.667	0.00	0.00	46.32	4.46
153	154	2.579657	CGTGCCTGGTAGTGACCCA	61.580	63.158	0.00	0.00	46.32	4.51
154	155	1.296715	GTGCCTGGTAGTGACCCAG	59.703	63.158	1.39	1.39	46.32	4.45
161	162	2.615391	TGGTAGTGACCCAGATTGTGA	58.385	47.619	0.00	0.00	46.32	3.58
162	163	2.301870	TGGTAGTGACCCAGATTGTGAC	59.698	50.000	0.00	0.00	46.32	3.67
163	164	2.607187	GTAGTGACCCAGATTGTGACG	58.393	52.381	0.00	0.00	0.00	4.35
164	165	1.048601	AGTGACCCAGATTGTGACGT	58.951	50.000	0.00	0.00	0.00	4.34
165	166	1.000955	AGTGACCCAGATTGTGACGTC	59.999	52.381	9.11	9.11	0.00	4.34
166	167	0.038618	TGACCCAGATTGTGACGTCG	60.039	55.000	11.62	0.00	31.25	5.12
167	168	0.242825	GACCCAGATTGTGACGTCGA	59.757	55.000	11.62	0.00	0.00	4.20
168	169	0.677288	ACCCAGATTGTGACGTCGAA	59.323	50.000	11.62	6.68	0.00	3.71
169	170	1.069513	ACCCAGATTGTGACGTCGAAA	59.930	47.619	11.62	8.13	0.00	3.46
170	171	2.289444	ACCCAGATTGTGACGTCGAAAT	60.289	45.455	11.62	12.75	0.00	2.17
171	172	2.348666	CCCAGATTGTGACGTCGAAATC	59.651	50.000	24.70	24.70	0.00	2.17
172	173	2.348666	CCAGATTGTGACGTCGAAATCC	59.651	50.000	26.76	15.86	30.83	3.01
173	174	3.254060	CAGATTGTGACGTCGAAATCCT	58.746	45.455	26.76	17.19	30.83	3.24
174	175	3.679980	CAGATTGTGACGTCGAAATCCTT	59.320	43.478	26.76	14.78	30.83	3.36
175	176	4.152402	CAGATTGTGACGTCGAAATCCTTT	59.848	41.667	26.76	14.28	30.83	3.11
176	177	3.870723	TTGTGACGTCGAAATCCTTTG	57.129	42.857	11.62	0.00	0.00	2.77
186	187	7.713750	ACGTCGAAATCCTTTGATATCTCTAA	58.286	34.615	3.98	0.00	0.00	2.10
188	189	9.197694	CGTCGAAATCCTTTGATATCTCTAATT	57.802	33.333	3.98	0.00	0.00	1.40
238	239	2.815503	CGGGTTTTATTTTCGTCCCACT	59.184	45.455	0.00	0.00	35.08	4.00
244	245	6.072119	GGTTTTATTTTCGTCCCACTTCATCT	60.072	38.462	0.00	0.00	0.00	2.90
248	249	1.348064	TCGTCCCACTTCATCTGGTT	58.652	50.000	0.00	0.00	0.00	3.67
282	285	2.127651	TTGGTACTTCCTCCCACCTT	57.872	50.000	0.00	0.00	37.07	3.50
293	296	0.118346	TCCCACCTTCCTCTTAGCCA	59.882	55.000	0.00	0.00	0.00	4.75
306	309	4.202070	CCTCTTAGCCACGAAAAACCAAAA	60.202	41.667	0.00	0.00	0.00	2.44
378	381	1.691976	AGAACCCATCTGTCACGAACA	59.308	47.619	0.00	0.00	36.88	3.18
401	418	4.571372	AAACAAACCGGCGAAGATTAAA	57.429	36.364	9.30	0.00	0.00	1.52
508	545	3.589654	CTTCGTCCCTTCGCTGCCA	62.590	63.158	0.00	0.00	0.00	4.92
971	1146	2.203998	CCCCTCCCACACACTCCT	60.204	66.667	0.00	0.00	0.00	3.69
1057	1233	0.114560	TCTTCCTTCCTCCTGTCGGT	59.885	55.000	0.00	0.00	0.00	4.69
1075	1251	2.663196	GGGTCAGGTCCCTCAACG	59.337	66.667	0.00	0.00	43.85	4.10
1135	1311	4.966787	GGTGCAACAAGGCCCCGA	62.967	66.667	0.00	0.00	39.98	5.14
1136	1312	2.676471	GTGCAACAAGGCCCCGAT	60.676	61.111	0.00	0.00	36.32	4.18
1165	1341	0.036306	GAAACCTTCTCCCAAGCCGA	59.964	55.000	0.00	0.00	0.00	5.54
1168	1344	1.201429	ACCTTCTCCCAAGCCGATGT	61.201	55.000	0.00	0.00	0.00	3.06
1302	1493	1.299976	GAACTCGTCCCCATTGCCT	59.700	57.895	0.00	0.00	0.00	4.75
1368	1574	4.067512	TGCTCCTCGGAGGCCTCT	62.068	66.667	31.36	0.00	42.19	3.69
1810	2020	3.377933	GGCTAGAGAGGCTTGCTTC	57.622	57.895	0.00	0.00	44.83	3.86
1931	2148	3.953712	TGTTGCTTGCTACTGCTACTA	57.046	42.857	8.43	0.00	40.48	1.82
2362	3544	6.320418	CCCTCTGTAGTTTAAGGTGTTTGTTT	59.680	38.462	0.00	0.00	0.00	2.83
2598	3782	9.191995	GTATGGTTTTATCAACAGTTCTTTTGG	57.808	33.333	0.00	0.00	0.00	3.28
2780	3972	3.632145	ACAACCTCAAAAGAATTGCTCGT	59.368	39.130	0.00	0.00	0.00	4.18
3061	4570	4.624452	GGACACTGTTACCAGATACGTTTC	59.376	45.833	0.00	0.00	41.50	2.78
3382	4923	5.447818	GCAGCAATTTAGAACTAAGACGCAT	60.448	40.000	0.00	0.00	0.00	4.73

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
1	2	2.924926	TCAATACGTGCGTTCATGGTAC	59.075	45.455	1.66	0.00	33.54	3.34
3	4	1.730064	GTCAATACGTGCGTTCATGGT	59.270	47.619	1.66	0.00	33.54	3.55
4	5	1.729517	TGTCAATACGTGCGTTCATGG	59.270	47.619	1.66	0.00	33.54	3.66
6	7	2.156891	GTGTGTCAATACGTGCGTTCAT	59.843	45.455	1.66	0.00	0.00	2.57
7	8	1.523515	GTGTGTCAATACGTGCGTTCA	59.476	47.619	1.66	0.00	0.00	3.18
8	9	1.523515	TGTGTGTCAATACGTGCGTTC	59.476	47.619	1.66	0.00	0.00	3.95
9	10	1.525197	CTGTGTGTCAATACGTGCGTT	59.475	47.619	1.66	0.00	0.00	4.84
10	11	1.136690	CTGTGTGTCAATACGTGCGT	58.863	50.000	0.00	2.05	0.00	5.24
11	12	0.438445	CCTGTGTGTCAATACGTGCG	59.562	55.000	0.00	0.00	0.00	5.34
12	13	0.796312	CCCTGTGTGTCAATACGTGC	59.204	55.000	0.00	0.00	0.00	5.34
13	14	1.438651	CCCCTGTGTGTCAATACGTG	58.561	55.000	0.00	0.00	0.00	4.49
14	15	0.321298	GCCCCTGTGTGTCAATACGT	60.321	55.000	0.00	0.00	0.00	3.57
15	16	1.358725	CGCCCCTGTGTGTCAATACG	61.359	60.000	0.00	0.00	0.00	3.06
16	17	0.036765	TCGCCCCTGTGTGTCAATAC	60.037	55.000	0.00	0.00	0.00	1.89
17	18	0.687920	TTCGCCCCTGTGTGTCAATA	59.312	50.000	0.00	0.00	0.00	1.90
18	19	0.606401	CTTCGCCCCTGTGTGTCAAT	60.606	55.000	0.00	0.00	0.00	2.57
19	20	1.227823	CTTCGCCCCTGTGTGTCAA	60.228	57.895	0.00	0.00	0.00	3.18
20	21	2.137528	TCTTCGCCCCTGTGTGTCA	61.138	57.895	0.00	0.00	0.00	3.58
21	22	1.668151	GTCTTCGCCCCTGTGTGTC	60.668	63.158	0.00	0.00	0.00	3.67
22	23	2.383245	CTGTCTTCGCCCCTGTGTGT	62.383	60.000	0.00	0.00	0.00	3.72
23	24	1.669115	CTGTCTTCGCCCCTGTGTG	60.669	63.158	0.00	0.00	0.00	3.82
24	25	1.407656	TTCTGTCTTCGCCCCTGTGT	61.408	55.000	0.00	0.00	0.00	3.72
25	26	0.951040	GTTCTGTCTTCGCCCCTGTG	60.951	60.000	0.00	0.00	0.00	3.66
26	27	1.371558	GTTCTGTCTTCGCCCCTGT	59.628	57.895	0.00	0.00	0.00	4.00
27	28	0.250295	TTGTTCTGTCTTCGCCCCTG	60.250	55.000	0.00	0.00	0.00	4.45
28	29	0.035458	CTTGTTCTGTCTTCGCCCCT	59.965	55.000	0.00	0.00	0.00	4.79
29	30	0.955919	CCTTGTTCTGTCTTCGCCCC	60.956	60.000	0.00	0.00	0.00	5.80
30	31	0.955919	CCCTTGTTCTGTCTTCGCCC	60.956	60.000	0.00	0.00	0.00	6.13
31	32	1.578206	GCCCTTGTTCTGTCTTCGCC	61.578	60.000	0.00	0.00	0.00	5.54
32	33	0.884704	TGCCCTTGTTCTGTCTTCGC	60.885	55.000	0.00	0.00	0.00	4.70
33	34	1.466167	CATGCCCTTGTTCTGTCTTCG	59.534	52.381	0.00	0.00	0.00	3.79
34	35	1.200948	GCATGCCCTTGTTCTGTCTTC	59.799	52.381	6.36	0.00	0.00	2.87
35	36	1.251251	GCATGCCCTTGTTCTGTCTT	58.749	50.000	6.36	0.00	0.00	3.01
36	37	0.610232	GGCATGCCCTTGTTCTGTCT	60.610	55.000	27.24	0.00	0.00	3.41
37	38	1.885871	GGCATGCCCTTGTTCTGTC	59.114	57.895	27.24	0.00	0.00	3.51
38	39	4.102113	GGCATGCCCTTGTTCTGT	57.898	55.556	27.24	0.00	0.00	3.41
48	49	0.386838	GTAGCATCTTTGGGCATGCC	59.613	55.000	29.47	29.47	45.63	4.40
49	50	1.105457	TGTAGCATCTTTGGGCATGC	58.895	50.000	9.90	9.90	44.96	4.06
50	51	2.372264	AGTGTAGCATCTTTGGGCATG	58.628	47.619	0.00	0.00	0.00	4.06
51	52	2.814805	AGTGTAGCATCTTTGGGCAT	57.185	45.000	0.00	0.00	0.00	4.40
52	53	2.571653	AGTAGTGTAGCATCTTTGGGCA	59.428	45.455	0.00	0.00	0.00	5.36
53	54	3.198872	GAGTAGTGTAGCATCTTTGGGC	58.801	50.000	0.00	0.00	0.00	5.36
54	55	3.130516	TCGAGTAGTGTAGCATCTTTGGG	59.869	47.826	0.00	0.00	0.00	4.12
55	56	4.106197	GTCGAGTAGTGTAGCATCTTTGG	58.894	47.826	0.00	0.00	0.00	3.28
56	57	4.106197	GGTCGAGTAGTGTAGCATCTTTG	58.894	47.826	0.00	0.00	0.00	2.77
57	58	4.017808	AGGTCGAGTAGTGTAGCATCTTT	58.982	43.478	0.00	0.00	0.00	2.52
58	59	3.622630	AGGTCGAGTAGTGTAGCATCTT	58.377	45.455	0.00	0.00	0.00	2.40
59	60	3.284793	AGGTCGAGTAGTGTAGCATCT	57.715	47.619	0.00	0.00	0.00	2.90
60	61	3.059733	CGTAGGTCGAGTAGTGTAGCATC	60.060	52.174	0.00	0.00	42.86	3.91
61	62	2.871022	CGTAGGTCGAGTAGTGTAGCAT	59.129	50.000	0.00	0.00	42.86	3.79
62	63	2.274437	CGTAGGTCGAGTAGTGTAGCA	58.726	52.381	0.00	0.00	42.86	3.49
63	64	2.030213	CACGTAGGTCGAGTAGTGTAGC	59.970	54.545	0.00	0.00	42.86	3.58
64	65	3.257393	ACACGTAGGTCGAGTAGTGTAG	58.743	50.000	9.38	0.00	41.07	2.74
65	66	3.319137	ACACGTAGGTCGAGTAGTGTA	57.681	47.619	9.38	0.00	41.07	2.90
66	67	2.175878	ACACGTAGGTCGAGTAGTGT	57.824	50.000	6.34	6.34	41.07	3.55
67	68	4.153117	AGTTAACACGTAGGTCGAGTAGTG	59.847	45.833	8.61	0.00	41.91	2.74
68	69	4.319177	AGTTAACACGTAGGTCGAGTAGT	58.681	43.478	8.61	0.00	41.91	2.73
69	70	4.935885	AGTTAACACGTAGGTCGAGTAG	57.064	45.455	8.61	0.00	41.91	2.57
70	71	5.689383	AAAGTTAACACGTAGGTCGAGTA	57.311	39.130	8.61	0.00	41.91	2.59
71	72	4.574599	AAAGTTAACACGTAGGTCGAGT	57.425	40.909	8.61	0.00	44.31	4.18
72	73	5.741040	GGATAAAGTTAACACGTAGGTCGAG	59.259	44.000	8.61	0.00	42.86	4.04
73	74	5.393027	GGGATAAAGTTAACACGTAGGTCGA	60.393	44.000	8.61	0.00	42.86	4.20
74	75	4.800471	GGGATAAAGTTAACACGTAGGTCG	59.200	45.833	8.61	0.00	46.00	4.79
75	76	5.970592	AGGGATAAAGTTAACACGTAGGTC	58.029	41.667	8.61	0.00	0.00	3.85
76	77	6.014327	TCAAGGGATAAAGTTAACACGTAGGT	60.014	38.462	8.61	0.00	0.00	3.08
77	78	6.400568	TCAAGGGATAAAGTTAACACGTAGG	58.599	40.000	8.61	0.00	0.00	3.18
78	79	8.488651	AATCAAGGGATAAAGTTAACACGTAG	57.511	34.615	8.61	0.00	32.09	3.51
79	80	8.851541	AAATCAAGGGATAAAGTTAACACGTA	57.148	30.769	8.61	0.00	32.09	3.57
80	81	7.446013	TGAAATCAAGGGATAAAGTTAACACGT	59.554	33.333	8.61	0.00	32.09	4.49
81	82	7.812648	TGAAATCAAGGGATAAAGTTAACACG	58.187	34.615	8.61	0.00	32.09	4.49
82	83	7.755373	GCTGAAATCAAGGGATAAAGTTAACAC	59.245	37.037	8.61	0.00	32.09	3.32
83	84	7.450014	TGCTGAAATCAAGGGATAAAGTTAACA	59.550	33.333	8.61	0.00	32.09	2.41
84	85	7.826690	TGCTGAAATCAAGGGATAAAGTTAAC	58.173	34.615	0.00	0.00	32.09	2.01
85	86	8.469200	CATGCTGAAATCAAGGGATAAAGTTAA	58.531	33.333	0.00	0.00	32.09	2.01
86	87	7.833682	TCATGCTGAAATCAAGGGATAAAGTTA	59.166	33.333	0.00	0.00	32.09	2.24
87	88	6.664816	TCATGCTGAAATCAAGGGATAAAGTT	59.335	34.615	0.00	0.00	32.09	2.66
88	89	6.096001	GTCATGCTGAAATCAAGGGATAAAGT	59.904	38.462	0.00	0.00	32.09	2.66
89	90	6.320672	AGTCATGCTGAAATCAAGGGATAAAG	59.679	38.462	0.00	0.00	32.09	1.85
90	91	6.189859	AGTCATGCTGAAATCAAGGGATAAA	58.810	36.000	0.00	0.00	32.09	1.40
91	92	5.759059	AGTCATGCTGAAATCAAGGGATAA	58.241	37.500	0.00	0.00	32.09	1.75
92	93	5.131642	AGAGTCATGCTGAAATCAAGGGATA	59.868	40.000	0.00	0.00	32.09	2.59
93	94	4.079901	AGAGTCATGCTGAAATCAAGGGAT	60.080	41.667	0.00	0.00	34.43	3.85
94	95	3.265221	AGAGTCATGCTGAAATCAAGGGA	59.735	43.478	0.00	0.00	0.00	4.20
95	96	3.618351	AGAGTCATGCTGAAATCAAGGG	58.382	45.455	0.00	0.00	0.00	3.95
96	97	4.094590	GTGAGAGTCATGCTGAAATCAAGG	59.905	45.833	0.00	0.00	0.00	3.61
97	98	4.936411	AGTGAGAGTCATGCTGAAATCAAG	59.064	41.667	0.00	0.00	0.00	3.02
98	99	4.903054	AGTGAGAGTCATGCTGAAATCAA	58.097	39.130	0.00	0.00	0.00	2.57
99	100	4.548451	AGTGAGAGTCATGCTGAAATCA	57.452	40.909	0.00	0.00	0.00	2.57
100	101	4.694509	ACAAGTGAGAGTCATGCTGAAATC	59.305	41.667	0.00	0.00	0.00	2.17
101	102	4.454847	CACAAGTGAGAGTCATGCTGAAAT	59.545	41.667	0.00	0.00	0.00	2.17
102	103	3.811497	CACAAGTGAGAGTCATGCTGAAA	59.189	43.478	0.00	0.00	0.00	2.69
103	104	3.070015	TCACAAGTGAGAGTCATGCTGAA	59.930	43.478	0.00	0.00	34.14	3.02
104	105	2.629617	TCACAAGTGAGAGTCATGCTGA	59.370	45.455	0.00	0.00	34.14	4.26
105	106	3.036075	TCACAAGTGAGAGTCATGCTG	57.964	47.619	0.00	0.00	34.14	4.41
106	107	3.977134	ATCACAAGTGAGAGTCATGCT	57.023	42.857	8.99	0.00	43.61	3.79
107	108	5.368256	AAAATCACAAGTGAGAGTCATGC	57.632	39.130	8.99	0.00	43.61	4.06
108	109	7.301054	GGTTAAAATCACAAGTGAGAGTCATG	58.699	38.462	8.99	0.00	43.61	3.07
109	110	6.431234	GGGTTAAAATCACAAGTGAGAGTCAT	59.569	38.462	8.99	0.00	43.61	3.06
110	111	5.763204	GGGTTAAAATCACAAGTGAGAGTCA	59.237	40.000	8.99	0.00	43.61	3.41
111	112	5.181433	GGGGTTAAAATCACAAGTGAGAGTC	59.819	44.000	8.99	0.00	43.61	3.36
112	113	5.070685	GGGGTTAAAATCACAAGTGAGAGT	58.929	41.667	8.99	0.00	43.61	3.24
113	114	4.154195	CGGGGTTAAAATCACAAGTGAGAG	59.846	45.833	8.99	0.00	43.61	3.20
114	115	4.069304	CGGGGTTAAAATCACAAGTGAGA	58.931	43.478	8.99	0.00	43.61	3.27
115	116	3.818773	ACGGGGTTAAAATCACAAGTGAG	59.181	43.478	8.99	0.00	43.61	3.51
116	117	3.566322	CACGGGGTTAAAATCACAAGTGA	59.434	43.478	5.24	5.24	44.59	3.41
117	118	3.855524	GCACGGGGTTAAAATCACAAGTG	60.856	47.826	0.00	0.00	0.00	3.16
118	119	2.295070	GCACGGGGTTAAAATCACAAGT	59.705	45.455	0.00	0.00	0.00	3.16
119	120	2.352323	GGCACGGGGTTAAAATCACAAG	60.352	50.000	0.00	0.00	0.00	3.16
120	121	1.614413	GGCACGGGGTTAAAATCACAA	59.386	47.619	0.00	0.00	0.00	3.33
121	122	1.202952	AGGCACGGGGTTAAAATCACA	60.203	47.619	0.00	0.00	0.00	3.58
122	123	1.201414	CAGGCACGGGGTTAAAATCAC	59.799	52.381	0.00	0.00	0.00	3.06
123	124	1.540267	CAGGCACGGGGTTAAAATCA	58.460	50.000	0.00	0.00	0.00	2.57
124	125	0.815095	CCAGGCACGGGGTTAAAATC	59.185	55.000	0.00	0.00	40.98	2.17
125	126	2.970205	CCAGGCACGGGGTTAAAAT	58.030	52.632	0.00	0.00	40.98	1.82
126	127	4.504112	CCAGGCACGGGGTTAAAA	57.496	55.556	0.00	0.00	40.98	1.52
134	135	2.264794	GGTCACTACCAGGCACGG	59.735	66.667	0.00	0.00	45.98	4.94
142	143	2.674177	CGTCACAATCTGGGTCACTACC	60.674	54.545	0.00	0.00	45.97	3.18
143	144	2.029290	ACGTCACAATCTGGGTCACTAC	60.029	50.000	0.00	0.00	0.00	2.73
144	145	2.230508	GACGTCACAATCTGGGTCACTA	59.769	50.000	11.55	0.00	0.00	2.74
145	146	1.000955	GACGTCACAATCTGGGTCACT	59.999	52.381	11.55	0.00	0.00	3.41
146	147	1.429463	GACGTCACAATCTGGGTCAC	58.571	55.000	11.55	0.00	0.00	3.67
147	148	0.038618	CGACGTCACAATCTGGGTCA	60.039	55.000	17.16	0.00	0.00	4.02
148	149	0.242825	TCGACGTCACAATCTGGGTC	59.757	55.000	17.16	0.00	0.00	4.46
149	150	0.677288	TTCGACGTCACAATCTGGGT	59.323	50.000	17.16	0.00	0.00	4.51
150	151	1.790755	TTTCGACGTCACAATCTGGG	58.209	50.000	17.16	0.00	0.00	4.45
151	152	2.348666	GGATTTCGACGTCACAATCTGG	59.651	50.000	25.00	6.58	0.00	3.86
152	153	3.254060	AGGATTTCGACGTCACAATCTG	58.746	45.455	25.00	7.19	0.00	2.90
153	154	3.594603	AGGATTTCGACGTCACAATCT	57.405	42.857	25.00	14.61	0.00	2.40
154	155	4.151689	TCAAAGGATTTCGACGTCACAATC	59.848	41.667	20.91	20.91	35.03	2.67
155	156	4.062293	TCAAAGGATTTCGACGTCACAAT	58.938	39.130	17.16	12.35	35.03	2.71
156	157	3.459145	TCAAAGGATTTCGACGTCACAA	58.541	40.909	17.16	7.63	35.03	3.33
157	158	3.100658	TCAAAGGATTTCGACGTCACA	57.899	42.857	17.16	0.00	35.03	3.58
158	159	5.749109	AGATATCAAAGGATTTCGACGTCAC	59.251	40.000	17.16	1.04	35.03	3.67
159	160	5.902681	AGATATCAAAGGATTTCGACGTCA	58.097	37.500	17.16	0.00	35.03	4.35
160	161	6.210078	AGAGATATCAAAGGATTTCGACGTC	58.790	40.000	5.18	5.18	35.03	4.34
161	162	6.150396	AGAGATATCAAAGGATTTCGACGT	57.850	37.500	5.32	0.00	35.03	4.34
162	163	8.749841	ATTAGAGATATCAAAGGATTTCGACG	57.250	34.615	5.32	0.00	35.03	5.12
186	187	6.875972	ACCTACCAACTGAGACATTAGAAT	57.124	37.500	0.00	0.00	0.00	2.40
188	189	5.568825	GCAACCTACCAACTGAGACATTAGA	60.569	44.000	0.00	0.00	0.00	2.10
261	264	2.424793	AGGTGGGAGGAAGTACCAAAA	58.575	47.619	0.00	0.00	42.04	2.44
282	285	2.105134	TGGTTTTTCGTGGCTAAGAGGA	59.895	45.455	0.00	0.00	0.00	3.71
378	381	3.446310	AATCTTCGCCGGTTTGTTTTT	57.554	38.095	1.90	0.00	0.00	1.94
417	434	1.227853	GTGCGGGAGTTTGGTCAGT	60.228	57.895	0.00	0.00	0.00	3.41
488	525	2.657237	CAGCGAAGGGACGAAGGT	59.343	61.111	0.00	0.00	35.09	3.50
508	545	2.066999	GCGAAGGGATCTGGAGGGT	61.067	63.158	0.00	0.00	0.00	4.34
1111	1287	2.990967	CTTGTTGCACCCCGGCAT	60.991	61.111	0.00	0.00	44.48	4.40
1120	1296	2.676121	CATCGGGGCCTTGTTGCA	60.676	61.111	0.84	0.00	0.00	4.08
1135	1311	1.228552	AAGGTTTCCACGCAGCCAT	60.229	52.632	0.00	0.00	0.00	4.40
1136	1312	1.896660	GAAGGTTTCCACGCAGCCA	60.897	57.895	0.00	0.00	0.00	4.75
1165	1341	1.841302	TTCTCTGGCGCCTTCCACAT	61.841	55.000	29.70	0.00	31.74	3.21
1168	1344	2.665000	CTTCTCTGGCGCCTTCCA	59.335	61.111	29.70	5.90	34.42	3.53
1331	1537	1.593209	GACGCGTTGAGGTTCACCA	60.593	57.895	15.53	0.00	38.89	4.17
1810	2020	3.247411	TCTGACGTAGCAAACACAACATG	59.753	43.478	0.00	0.00	0.00	3.21
1931	2148	8.247562	ACTACAAAACAACACAATAACACACAT	58.752	29.630	0.00	0.00	0.00	3.21
2362	3544	6.337356	GCAGTATTTTATGGGCTGCTAAAAA	58.663	36.000	8.69	6.83	46.20	1.94
2598	3782	3.081061	TCATACCATTGTGTCAACTGCC	58.919	45.455	0.00	0.00	0.00	4.85
2780	3972	5.468746	GTCTGCTACTTGGAAACATGTTACA	59.531	40.000	12.39	11.43	45.53	2.41
2906	4415	2.125350	GCACCGGCTCAGAAGGAG	60.125	66.667	0.00	0.00	46.93	3.69
3061	4570	2.756760	CTCCACCATGGACTGAAATTGG	59.243	50.000	21.47	13.17	42.67	3.16
3190	4715	6.260936	CGGAGGGAGTATTTTCTAACGTACTA	59.739	42.308	0.00	0.00	0.00	1.82
3320	4861	8.645110	CCCTCCGTTCCTAAATATAAGTCTTTA	58.355	37.037	0.00	0.00	0.00	1.85

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.