AutoCloner

Multiple sequence alignment - TraesCS5D01G497700

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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	TraesCS5D01G497700	chr5D	100.000	2315	0	0	1	2315	527840566	527842880	0.000000e+00	4276.0
1	TraesCS5D01G497700	chr5D	93.548	124	5	1	1	121	16595230	16595107	5.080000e-42	182.0
2	TraesCS5D01G497700	chr5D	93.548	124	5	2	1	121	108110986	108110863	5.080000e-42	182.0
3	TraesCS5D01G497700	chr5B	95.466	772	20	10	539	1308	664502658	664503416	0.000000e+00	1218.0
4	TraesCS5D01G497700	chr5B	92.619	691	23	16	1287	1976	664503488	664504151	0.000000e+00	968.0
5	TraesCS5D01G497700	chr5B	91.692	662	35	11	654	1295	664474446	664475107	0.000000e+00	900.0
6	TraesCS5D01G497700	chr5B	90.732	669	35	12	654	1295	664416020	664416688	0.000000e+00	867.0
7	TraesCS5D01G497700	chr5B	90.347	404	28	5	146	547	664501556	664501950	9.480000e-144	520.0
8	TraesCS5D01G497700	chr5B	91.867	332	22	5	1276	1603	664416760	664417090	2.100000e-125	459.0
9	TraesCS5D01G497700	chr5B	92.453	318	21	3	1288	1603	664475193	664475509	3.510000e-123	451.0
10	TraesCS5D01G497700	chr5B	92.337	261	20	0	2055	2315	664504211	664504471	2.810000e-99	372.0
11	TraesCS5D01G497700	chr5B	86.192	239	33	0	2077	2315	664475621	664475859	2.280000e-65	259.0
12	TraesCS5D01G497700	chr5B	87.615	218	26	1	2077	2294	664417202	664417418	3.820000e-63	252.0
13	TraesCS5D01G497700	chr5B	79.085	153	23	9	262	409	129361416	129361564	1.890000e-16	97.1
14	TraesCS5D01G497700	chr3D	89.597	769	59	13	557	1308	2967530	2968294	0.000000e+00	957.0
15	TraesCS5D01G497700	chr3D	88.138	607	40	14	1288	1866	2968367	2968969	0.000000e+00	693.0
16	TraesCS5D01G497700	chr3D	87.243	243	19	5	2083	2315	2969142	2969382	1.360000e-67	267.0
17	TraesCS5D01G497700	chr3D	93.548	124	1	4	1	121	78374760	78374641	6.570000e-41	178.0
18	TraesCS5D01G497700	chr3D	92.453	53	4	0	357	409	32340945	32340997	2.470000e-10	76.8
19	TraesCS5D01G497700	chr5A	92.284	648	38	8	669	1308	655188326	655188969	0.000000e+00	909.0
20	TraesCS5D01G497700	chr5A	92.284	648	38	8	669	1308	655224488	655225131	0.000000e+00	909.0
21	TraesCS5D01G497700	chr5A	87.346	648	48	25	648	1284	654850748	654851372	0.000000e+00	712.0
22	TraesCS5D01G497700	chr5A	93.808	323	14	3	1288	1605	654851470	654851791	4.470000e-132	481.0
23	TraesCS5D01G497700	chr5A	92.749	331	20	3	1290	1618	655189044	655189372	2.080000e-130	475.0
24	TraesCS5D01G497700	chr5A	92.447	331	21	3	1290	1618	655225206	655225534	9.680000e-129	470.0
25	TraesCS5D01G497700	chr5A	88.922	334	36	1	1983	2315	655225970	655226303	5.950000e-111	411.0
26	TraesCS5D01G497700	chr5A	84.504	413	34	11	1621	2016	655189409	655189808	4.670000e-102	381.0
27	TraesCS5D01G497700	chr5A	84.504	413	34	11	1621	2016	655225571	655225970	4.670000e-102	381.0
28	TraesCS5D01G497700	chr5A	90.411	219	20	1	1983	2200	655189808	655190026	1.050000e-73	287.0
29	TraesCS5D01G497700	chr5A	83.594	256	32	7	153	407	216991201	216991447	4.970000e-57	231.0
30	TraesCS5D01G497700	chr5A	80.738	244	35	9	161	401	698891768	698891534	1.830000e-41	180.0
31	TraesCS5D01G497700	chr5A	91.176	102	6	3	554	655	655188172	655188270	4.010000e-28	135.0
32	TraesCS5D01G497700	chr5A	91.176	102	6	3	554	655	655224334	655224432	4.010000e-28	135.0
33	TraesCS5D01G497700	chr5A	89.873	79	5	3	554	632	654849864	654849939	5.260000e-17	99.0
34	TraesCS5D01G497700	chr3B	88.114	774	62	20	557	1308	2880013	2879248	0.000000e+00	893.0
35	TraesCS5D01G497700	chr3B	86.634	606	45	17	1288	1866	2879175	2878579	2.510000e-179	638.0
36	TraesCS5D01G497700	chr3B	84.326	319	34	10	2003	2315	2878475	2878167	4.840000e-77	298.0
37	TraesCS5D01G497700	chr7D	88.026	618	55	15	678	1287	401549939	401550545	0.000000e+00	713.0
38	TraesCS5D01G497700	chr7D	92.440	291	22	0	1288	1578	401550640	401550930	1.280000e-112	416.0
39	TraesCS5D01G497700	chr7D	94.958	119	3	2	6	121	110218440	110218558	1.410000e-42	183.0
40	TraesCS5D01G497700	chr7D	86.486	74	7	3	324	395	524866106	524866034	6.860000e-11	78.7
41	TraesCS5D01G497700	chr7A	86.230	610	54	19	704	1290	459209171	459209773	3.240000e-178	634.0
42	TraesCS5D01G497700	chrUn	94.355	124	4	1	1	121	190744833	190744710	1.090000e-43	187.0
43	TraesCS5D01G497700	chrUn	100.000	30	0	0	381	410	283527907	283527878	3.210000e-04	56.5
44	TraesCS5D01G497700	chr6D	94.355	124	4	1	1	121	465425542	465425665	1.090000e-43	187.0
45	TraesCS5D01G497700	chr6D	94.215	121	7	0	1	121	471151065	471151185	3.930000e-43	185.0
46	TraesCS5D01G497700	chr4D	93.548	124	5	1	1	121	297111348	297111471	5.080000e-42	182.0
47	TraesCS5D01G497700	chr2B	94.167	120	4	2	5	121	96262984	96262865	1.830000e-41	180.0
48	TraesCS5D01G497700	chr2B	89.412	85	8	1	325	408	17109391	17109475	3.150000e-19	106.0
49	TraesCS5D01G497700	chr2B	78.676	136	28	1	276	410	159851393	159851528	3.170000e-14	89.8
50	TraesCS5D01G497700	chr6B	84.328	134	13	3	153	285	695011213	695011087	8.680000e-25	124.0
51	TraesCS5D01G497700	chr6B	85.567	97	6	6	317	409	684786652	684786560	6.810000e-16	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	TraesCS5D01G497700	chr5D	527840566	527842880	2314	False	4276.000000	4276	100.000000	1	2315	1	chr5D.!!$F1	2314
1	TraesCS5D01G497700	chr5B	664501556	664504471	2915	False	769.500000	1218	92.692250	146	2315	4	chr5B.!!$F4	2169
2	TraesCS5D01G497700	chr5B	664474446	664475859	1413	False	536.666667	900	90.112333	654	2315	3	chr5B.!!$F3	1661
3	TraesCS5D01G497700	chr5B	664416020	664417418	1398	False	526.000000	867	90.071333	654	2294	3	chr5B.!!$F2	1640
4	TraesCS5D01G497700	chr3D	2967530	2969382	1852	False	639.000000	957	88.326000	557	2315	3	chr3D.!!$F2	1758
5	TraesCS5D01G497700	chr5A	655224334	655226303	1969	False	461.200000	909	89.866600	554	2315	5	chr5A.!!$F4	1761
6	TraesCS5D01G497700	chr5A	655188172	655190026	1854	False	437.400000	909	90.224800	554	2200	5	chr5A.!!$F3	1646
7	TraesCS5D01G497700	chr5A	654849864	654851791	1927	False	430.666667	712	90.342333	554	1605	3	chr5A.!!$F2	1051
8	TraesCS5D01G497700	chr3B	2878167	2880013	1846	True	609.666667	893	86.358000	557	2315	3	chr3B.!!$R1	1758
9	TraesCS5D01G497700	chr7D	401549939	401550930	991	False	564.500000	713	90.233000	678	1578	2	chr7D.!!$F2	900
10	TraesCS5D01G497700	chr7A	459209171	459209773	602	False	634.000000	634	86.230000	704	1290	1	chr7A.!!$F1	586

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	Self end TH	Hairpin	End Stability	Orientation
584	1301	0.031585	TCTTCCGAACACACGTCCAG	59.968	55.0	0.0	0.0	0.0	3.86	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2033	3804	0.436913	CACGCGCGTTAGATTGTTGA	59.563	50.0	35.9	0.0	0.0	3.18	R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
20	21	1.679153	GAGTCGTGGGAGAAGAGATCC	59.321	57.143	0.00	0.00	35.99	3.36
24	25	3.143338	GGGAGAAGAGATCCCGCC	58.857	66.667	0.00	0.00	46.85	6.13
25	26	2.731374	GGAGAAGAGATCCCGCCG	59.269	66.667	0.00	0.00	0.00	6.46
26	27	2.028337	GAGAAGAGATCCCGCCGC	59.972	66.667	0.00	0.00	0.00	6.53
27	28	3.507597	GAGAAGAGATCCCGCCGCC	62.508	68.421	0.00	0.00	0.00	6.13
28	29	4.951963	GAAGAGATCCCGCCGCCG	62.952	72.222	0.00	0.00	0.00	6.46
82	83	4.292178	GGCGGCGAGGAGGAGATG	62.292	72.222	12.98	0.00	0.00	2.90
83	84	3.532155	GCGGCGAGGAGGAGATGT	61.532	66.667	12.98	0.00	0.00	3.06
84	85	2.725008	CGGCGAGGAGGAGATGTC	59.275	66.667	0.00	0.00	0.00	3.06
85	86	2.121538	CGGCGAGGAGGAGATGTCA	61.122	63.158	0.00	0.00	0.00	3.58
86	87	1.739049	GGCGAGGAGGAGATGTCAG	59.261	63.158	0.00	0.00	0.00	3.51
87	88	1.739049	GCGAGGAGGAGATGTCAGG	59.261	63.158	0.00	0.00	0.00	3.86
88	89	1.743321	GCGAGGAGGAGATGTCAGGG	61.743	65.000	0.00	0.00	0.00	4.45
89	90	1.112315	CGAGGAGGAGATGTCAGGGG	61.112	65.000	0.00	0.00	0.00	4.79
90	91	0.263172	GAGGAGGAGATGTCAGGGGA	59.737	60.000	0.00	0.00	0.00	4.81
91	92	0.264359	AGGAGGAGATGTCAGGGGAG	59.736	60.000	0.00	0.00	0.00	4.30
92	93	0.762461	GGAGGAGATGTCAGGGGAGG	60.762	65.000	0.00	0.00	0.00	4.30
93	94	0.762461	GAGGAGATGTCAGGGGAGGG	60.762	65.000	0.00	0.00	0.00	4.30
94	95	1.231751	AGGAGATGTCAGGGGAGGGA	61.232	60.000	0.00	0.00	0.00	4.20
95	96	1.051556	GGAGATGTCAGGGGAGGGAC	61.052	65.000	0.00	0.00	34.63	4.46
96	97	1.381872	AGATGTCAGGGGAGGGACG	60.382	63.158	0.00	0.00	36.83	4.79
97	98	1.381327	GATGTCAGGGGAGGGACGA	60.381	63.158	0.00	0.00	36.83	4.20
98	99	1.381872	ATGTCAGGGGAGGGACGAG	60.382	63.158	0.00	0.00	36.83	4.18
99	100	2.760385	GTCAGGGGAGGGACGAGG	60.760	72.222	0.00	0.00	0.00	4.63
100	101	2.944954	TCAGGGGAGGGACGAGGA	60.945	66.667	0.00	0.00	0.00	3.71
101	102	2.760385	CAGGGGAGGGACGAGGAC	60.760	72.222	0.00	0.00	0.00	3.85
102	103	4.444081	AGGGGAGGGACGAGGACG	62.444	72.222	0.00	0.00	45.75	4.79
123	124	4.077184	CGGCGCTAGGGTTCCACA	62.077	66.667	7.64	0.00	0.00	4.17
124	125	2.436115	GGCGCTAGGGTTCCACAC	60.436	66.667	7.64	0.00	0.00	3.82
125	126	2.345991	GCGCTAGGGTTCCACACA	59.654	61.111	8.77	0.00	0.00	3.72
126	127	1.741770	GCGCTAGGGTTCCACACAG	60.742	63.158	8.77	0.00	0.00	3.66
127	128	1.079127	CGCTAGGGTTCCACACAGG	60.079	63.158	0.00	0.00	39.47	4.00
136	137	2.896278	TCCACACAGGAGGATACGG	58.104	57.895	0.00	0.00	43.07	4.02
137	138	0.686441	TCCACACAGGAGGATACGGG	60.686	60.000	0.00	0.00	43.07	5.28
138	139	0.686441	CCACACAGGAGGATACGGGA	60.686	60.000	0.00	0.00	46.39	5.14
139	140	0.460311	CACACAGGAGGATACGGGAC	59.540	60.000	0.00	0.00	46.39	4.46
156	157	2.657143	GGACGAGTCAAGAGGATACCT	58.343	52.381	5.55	0.00	36.03	3.08
169	170	1.066573	GGATACCTCGAGATGCCATGG	60.067	57.143	15.71	7.63	0.00	3.66
173	174	3.451556	CTCGAGATGCCATGGCGGT	62.452	63.158	30.87	22.26	45.51	5.68
192	193	3.660865	GGTATGGTATTGAAGGCTACCG	58.339	50.000	0.00	0.00	40.28	4.02
229	230	4.989168	CGGTAGGCTTCTCCATGTATAAAC	59.011	45.833	0.00	0.00	37.29	2.01
237	238	3.884693	TCTCCATGTATAAACGCCGTCTA	59.115	43.478	0.00	0.00	0.00	2.59
238	239	4.023450	TCTCCATGTATAAACGCCGTCTAG	60.023	45.833	0.00	0.00	0.00	2.43
239	240	3.884693	TCCATGTATAAACGCCGTCTAGA	59.115	43.478	0.00	0.00	0.00	2.43
240	241	3.979495	CCATGTATAAACGCCGTCTAGAC	59.021	47.826	13.18	13.18	0.00	2.59
241	242	4.261489	CCATGTATAAACGCCGTCTAGACT	60.261	45.833	20.34	3.41	0.00	3.24
242	243	4.542662	TGTATAAACGCCGTCTAGACTC	57.457	45.455	20.34	10.93	0.00	3.36
243	244	4.194640	TGTATAAACGCCGTCTAGACTCT	58.805	43.478	20.34	1.68	0.00	3.24
260	261	5.945155	AGACTCTAGACGTTGATCAACTTC	58.055	41.667	28.58	28.58	39.14	3.01
313	314	2.811410	ACCCTACCGTCACAGACAATA	58.189	47.619	0.00	0.00	32.09	1.90
314	315	3.167485	ACCCTACCGTCACAGACAATAA	58.833	45.455	0.00	0.00	32.09	1.40
317	318	4.142026	CCCTACCGTCACAGACAATAATGA	60.142	45.833	0.00	0.00	32.09	2.57
322	323	4.991056	CCGTCACAGACAATAATGATAGGG	59.009	45.833	0.00	0.00	32.09	3.53
342	343	3.245264	GGGAAAAGGGTCAGATCCTGAAA	60.245	47.826	1.77	0.00	42.46	2.69
343	344	4.407365	GGAAAAGGGTCAGATCCTGAAAA	58.593	43.478	1.77	0.00	42.46	2.29
344	345	4.832823	GGAAAAGGGTCAGATCCTGAAAAA	59.167	41.667	1.77	0.00	42.46	1.94
365	366	6.535963	AAAAATTTGGATGAGGTCAGATCC	57.464	37.500	0.00	0.00	38.98	3.36
388	389	5.122869	CCGGCTAAACTTTAGTAAAAGGGTC	59.877	44.000	9.77	0.00	45.39	4.46
396	397	6.788243	ACTTTAGTAAAAGGGTCAAAACACG	58.212	36.000	0.00	0.00	45.39	4.49
584	1301	0.031585	TCTTCCGAACACACGTCCAG	59.968	55.000	0.00	0.00	0.00	3.86
694	2213	4.056050	ACTGGCACACGAACTAAACTTAG	58.944	43.478	0.00	0.00	36.82	2.18
739	2264	4.093556	GCTAAACTCTCCCAAGATTCAACG	59.906	45.833	0.00	0.00	0.00	4.10
877	2406	0.239347	GCGTTTGAGAACTGCAGCAT	59.761	50.000	15.27	2.22	36.23	3.79
936	2472	7.935338	AAGAAAACAACATCATTAGCAACTG	57.065	32.000	0.00	0.00	0.00	3.16
1397	3059	1.893062	CTCGGTGAGGAGCATGTCA	59.107	57.895	0.00	0.00	0.00	3.58
1643	3347	7.976826	AGTCTAGACGAGAAATAACTACTGTG	58.023	38.462	17.07	0.00	35.37	3.66
1685	3390	3.274095	TGATTGCACCGACCATATGAA	57.726	42.857	3.65	0.00	0.00	2.57
1686	3391	3.819368	TGATTGCACCGACCATATGAAT	58.181	40.909	3.65	0.00	0.00	2.57
1770	3478	7.575414	TGCTTTTGTGTTAAGAGTGGATTAA	57.425	32.000	0.00	0.00	0.00	1.40
1907	3641	2.993899	GGACCAAATCGTGACACTACTG	59.006	50.000	3.68	0.00	0.00	2.74
1913	3647	6.367969	ACCAAATCGTGACACTACTGATAAAC	59.632	38.462	3.68	0.00	0.00	2.01
1966	3704	3.394719	TCTCATCGTCTAGTGAGGATCG	58.605	50.000	7.92	0.00	43.42	3.69
1967	3705	2.482336	CTCATCGTCTAGTGAGGATCGG	59.518	54.545	1.07	0.00	43.42	4.18
1968	3706	2.104281	TCATCGTCTAGTGAGGATCGGA	59.896	50.000	0.00	0.00	43.42	4.55
1969	3707	1.950828	TCGTCTAGTGAGGATCGGAC	58.049	55.000	0.00	0.00	38.61	4.79
1970	3708	1.208776	TCGTCTAGTGAGGATCGGACA	59.791	52.381	0.00	0.00	38.61	4.02
2025	3796	2.314246	TCGGCATGATCAGATCAGAGT	58.686	47.619	18.13	0.00	43.53	3.24
2033	3804	6.518706	GCATGATCAGATCAGAGTCTACCAAT	60.519	42.308	18.13	0.00	43.53	3.16
2051	3823	1.355971	ATCAACAATCTAACGCGCGT	58.644	45.000	32.73	32.73	0.00	6.01
2094	3888	2.295885	GCAAGGACAGGGAGAATCATG	58.704	52.381	0.00	0.00	36.25	3.07
2106	3900	5.251005	AGGGAGAATCATGATGTGCTATCAT	59.749	40.000	9.46	10.12	39.16	2.45
2116	3910	1.067416	TGCTATCATGGACGGCGAC	59.933	57.895	16.62	7.58	0.00	5.19
2167	3971	4.760047	GAGCCGCCGAGCTTGGAA	62.760	66.667	25.25	0.00	45.15	3.53
2300	4104	4.612412	AAACGACGAAGCCGGGCA	62.612	61.111	23.09	0.00	40.78	5.36

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
8	9	2.731374	CGGCGGGATCTCTTCTCC	59.269	66.667	0.00	0.00	0.00	3.71
9	10	2.028337	GCGGCGGGATCTCTTCTC	59.972	66.667	9.78	0.00	0.00	2.87
10	11	3.541713	GGCGGCGGGATCTCTTCT	61.542	66.667	9.78	0.00	0.00	2.85
11	12	4.951963	CGGCGGCGGGATCTCTTC	62.952	72.222	25.36	0.00	0.00	2.87
65	66	4.292178	CATCTCCTCCTCGCCGCC	62.292	72.222	0.00	0.00	0.00	6.13
66	67	3.492311	GACATCTCCTCCTCGCCGC	62.492	68.421	0.00	0.00	0.00	6.53
67	68	2.069465	CTGACATCTCCTCCTCGCCG	62.069	65.000	0.00	0.00	0.00	6.46
68	69	1.739049	CTGACATCTCCTCCTCGCC	59.261	63.158	0.00	0.00	0.00	5.54
69	70	1.739049	CCTGACATCTCCTCCTCGC	59.261	63.158	0.00	0.00	0.00	5.03
70	71	1.112315	CCCCTGACATCTCCTCCTCG	61.112	65.000	0.00	0.00	0.00	4.63
71	72	0.263172	TCCCCTGACATCTCCTCCTC	59.737	60.000	0.00	0.00	0.00	3.71
72	73	0.264359	CTCCCCTGACATCTCCTCCT	59.736	60.000	0.00	0.00	0.00	3.69
73	74	0.762461	CCTCCCCTGACATCTCCTCC	60.762	65.000	0.00	0.00	0.00	4.30
74	75	0.762461	CCCTCCCCTGACATCTCCTC	60.762	65.000	0.00	0.00	0.00	3.71
75	76	1.231751	TCCCTCCCCTGACATCTCCT	61.232	60.000	0.00	0.00	0.00	3.69
76	77	1.051556	GTCCCTCCCCTGACATCTCC	61.052	65.000	0.00	0.00	0.00	3.71
77	78	1.395826	CGTCCCTCCCCTGACATCTC	61.396	65.000	0.00	0.00	0.00	2.75
78	79	1.381872	CGTCCCTCCCCTGACATCT	60.382	63.158	0.00	0.00	0.00	2.90
79	80	1.381327	TCGTCCCTCCCCTGACATC	60.381	63.158	0.00	0.00	0.00	3.06
80	81	1.381872	CTCGTCCCTCCCCTGACAT	60.382	63.158	0.00	0.00	0.00	3.06
81	82	2.037367	CTCGTCCCTCCCCTGACA	59.963	66.667	0.00	0.00	0.00	3.58
82	83	2.760385	CCTCGTCCCTCCCCTGAC	60.760	72.222	0.00	0.00	0.00	3.51
83	84	2.944954	TCCTCGTCCCTCCCCTGA	60.945	66.667	0.00	0.00	0.00	3.86
84	85	2.760385	GTCCTCGTCCCTCCCCTG	60.760	72.222	0.00	0.00	0.00	4.45
85	86	4.444081	CGTCCTCGTCCCTCCCCT	62.444	72.222	0.00	0.00	0.00	4.79
106	107	4.077184	TGTGGAACCCTAGCGCCG	62.077	66.667	2.29	0.00	34.36	6.46
107	108	2.436115	GTGTGGAACCCTAGCGCC	60.436	66.667	2.29	0.00	34.36	6.53
108	109	1.741770	CTGTGTGGAACCCTAGCGC	60.742	63.158	0.00	0.00	34.36	5.92
109	110	1.079127	CCTGTGTGGAACCCTAGCG	60.079	63.158	0.00	0.00	38.35	4.26
110	111	0.250513	CTCCTGTGTGGAACCCTAGC	59.749	60.000	0.00	0.00	45.63	3.42
111	112	0.905357	CCTCCTGTGTGGAACCCTAG	59.095	60.000	0.00	0.00	45.63	3.02
112	113	0.490017	TCCTCCTGTGTGGAACCCTA	59.510	55.000	0.00	0.00	45.63	3.53
113	114	0.178861	ATCCTCCTGTGTGGAACCCT	60.179	55.000	0.00	0.00	45.63	4.34
114	115	1.209747	GTATCCTCCTGTGTGGAACCC	59.790	57.143	0.00	0.00	45.63	4.11
115	116	1.134788	CGTATCCTCCTGTGTGGAACC	60.135	57.143	0.00	0.00	45.63	3.62
116	117	1.134788	CCGTATCCTCCTGTGTGGAAC	60.135	57.143	0.00	0.00	45.63	3.62
117	118	1.191535	CCGTATCCTCCTGTGTGGAA	58.808	55.000	0.00	0.00	45.63	3.53
118	119	0.686441	CCCGTATCCTCCTGTGTGGA	60.686	60.000	0.00	0.00	43.86	4.02
119	120	0.686441	TCCCGTATCCTCCTGTGTGG	60.686	60.000	0.00	0.00	37.10	4.17
120	121	0.460311	GTCCCGTATCCTCCTGTGTG	59.540	60.000	0.00	0.00	0.00	3.82
121	122	1.035932	CGTCCCGTATCCTCCTGTGT	61.036	60.000	0.00	0.00	0.00	3.72
122	123	0.750546	TCGTCCCGTATCCTCCTGTG	60.751	60.000	0.00	0.00	0.00	3.66
123	124	0.465824	CTCGTCCCGTATCCTCCTGT	60.466	60.000	0.00	0.00	0.00	4.00
124	125	0.465824	ACTCGTCCCGTATCCTCCTG	60.466	60.000	0.00	0.00	0.00	3.86
125	126	0.179023	GACTCGTCCCGTATCCTCCT	60.179	60.000	0.00	0.00	0.00	3.69
126	127	0.465097	TGACTCGTCCCGTATCCTCC	60.465	60.000	0.00	0.00	0.00	4.30
127	128	1.334243	CTTGACTCGTCCCGTATCCTC	59.666	57.143	0.00	0.00	0.00	3.71
128	129	1.064906	TCTTGACTCGTCCCGTATCCT	60.065	52.381	0.00	0.00	0.00	3.24
129	130	1.334243	CTCTTGACTCGTCCCGTATCC	59.666	57.143	0.00	0.00	0.00	2.59
130	131	1.334243	CCTCTTGACTCGTCCCGTATC	59.666	57.143	0.00	0.00	0.00	2.24
131	132	1.064906	TCCTCTTGACTCGTCCCGTAT	60.065	52.381	0.00	0.00	0.00	3.06
132	133	0.325933	TCCTCTTGACTCGTCCCGTA	59.674	55.000	0.00	0.00	0.00	4.02
133	134	0.323542	ATCCTCTTGACTCGTCCCGT	60.324	55.000	0.00	0.00	0.00	5.28
134	135	1.334243	GTATCCTCTTGACTCGTCCCG	59.666	57.143	0.00	0.00	0.00	5.14
135	136	1.682323	GGTATCCTCTTGACTCGTCCC	59.318	57.143	0.00	0.00	0.00	4.46
136	137	2.619646	GAGGTATCCTCTTGACTCGTCC	59.380	54.545	8.38	0.00	46.41	4.79
137	138	3.974871	GAGGTATCCTCTTGACTCGTC	57.025	52.381	8.38	0.00	46.41	4.20
147	148	1.621992	TGGCATCTCGAGGTATCCTC	58.378	55.000	13.56	5.79	46.44	3.71
148	149	1.898472	CATGGCATCTCGAGGTATCCT	59.102	52.381	13.56	0.00	36.03	3.24
149	150	1.066573	CCATGGCATCTCGAGGTATCC	60.067	57.143	13.56	10.74	0.00	2.59
150	151	1.674221	GCCATGGCATCTCGAGGTATC	60.674	57.143	32.08	1.35	41.49	2.24
151	152	0.322975	GCCATGGCATCTCGAGGTAT	59.677	55.000	32.08	0.00	41.49	2.73
156	157	1.471829	ATACCGCCATGGCATCTCGA	61.472	55.000	34.93	14.57	43.94	4.04
158	159	0.957395	CCATACCGCCATGGCATCTC	60.957	60.000	34.93	6.90	43.94	2.75
169	170	2.256117	AGCCTTCAATACCATACCGC	57.744	50.000	0.00	0.00	0.00	5.68
173	174	3.396260	GCGGTAGCCTTCAATACCATA	57.604	47.619	2.61	0.00	41.35	2.74
237	238	5.945155	GAAGTTGATCAACGTCTAGAGTCT	58.055	41.667	33.62	13.60	45.50	3.24
250	251	5.592104	TCAATAGCGGTAGAAGTTGATCA	57.408	39.130	0.00	0.00	0.00	2.92
260	261	1.995484	CGCCATGATCAATAGCGGTAG	59.005	52.381	22.47	5.91	42.93	3.18
313	314	5.163045	GGATCTGACCCTTTTCCCTATCATT	60.163	44.000	0.00	0.00	0.00	2.57
314	315	4.352298	GGATCTGACCCTTTTCCCTATCAT	59.648	45.833	0.00	0.00	0.00	2.45
317	318	3.718956	CAGGATCTGACCCTTTTCCCTAT	59.281	47.826	0.00	0.00	32.44	2.57
342	343	5.126061	CGGATCTGACCTCATCCAAATTTTT	59.874	40.000	0.00	0.00	38.92	1.94
343	344	4.641989	CGGATCTGACCTCATCCAAATTTT	59.358	41.667	0.00	0.00	38.92	1.82
344	345	4.202441	CGGATCTGACCTCATCCAAATTT	58.798	43.478	0.00	0.00	38.92	1.82
345	346	3.434167	CCGGATCTGACCTCATCCAAATT	60.434	47.826	2.08	0.00	38.92	1.82
346	347	2.105477	CCGGATCTGACCTCATCCAAAT	59.895	50.000	2.08	0.00	38.92	2.32
350	351	1.118356	AGCCGGATCTGACCTCATCC	61.118	60.000	5.05	0.00	36.01	3.51
352	353	2.088104	TTAGCCGGATCTGACCTCAT	57.912	50.000	5.05	0.00	0.00	2.90
353	354	1.480954	GTTTAGCCGGATCTGACCTCA	59.519	52.381	5.05	0.00	0.00	3.86
354	355	1.757699	AGTTTAGCCGGATCTGACCTC	59.242	52.381	5.05	0.00	0.00	3.85
355	356	1.867363	AGTTTAGCCGGATCTGACCT	58.133	50.000	5.05	1.53	0.00	3.85
361	362	6.037940	CCCTTTTACTAAAGTTTAGCCGGATC	59.962	42.308	20.31	0.00	39.29	3.36
365	366	5.702209	TGACCCTTTTACTAAAGTTTAGCCG	59.298	40.000	20.31	6.45	39.29	5.52
388	389	1.870402	GGGGCCAATTTTCGTGTTTTG	59.130	47.619	4.39	0.00	0.00	2.44
439	441	3.495193	CTGTGAATGCTGTCAAAATCCG	58.505	45.455	0.00	0.00	0.00	4.18
584	1301	8.445493	CAAAAATTTATCAGAACCTTGAATGCC	58.555	33.333	0.00	0.00	0.00	4.40
694	2213	9.520515	TTAGCTCCATTTTTATTAGGGATGATC	57.479	33.333	0.00	0.00	0.00	2.92
877	2406	1.992277	GAGGCCAAGCTGAGGGAGA	60.992	63.158	5.01	0.00	0.00	3.71
936	2472	6.441093	TCAATTCCATTATGACTTGTGAGC	57.559	37.500	0.00	0.00	0.00	4.26
1353	3015	1.186200	CTCAACCTCGACCTCATCCA	58.814	55.000	0.00	0.00	0.00	3.41
1588	3257	5.065859	CACCCTTGTCGCATATGAAATTGTA	59.934	40.000	6.97	0.00	0.00	2.41
1589	3258	4.016444	ACCCTTGTCGCATATGAAATTGT	58.984	39.130	6.97	0.00	0.00	2.71
1590	3259	4.142403	ACACCCTTGTCGCATATGAAATTG	60.142	41.667	6.97	0.00	0.00	2.32
1592	3261	3.378112	CACACCCTTGTCGCATATGAAAT	59.622	43.478	6.97	0.00	31.66	2.17
1593	3262	2.746904	CACACCCTTGTCGCATATGAAA	59.253	45.455	6.97	0.00	31.66	2.69
1770	3478	8.051535	AGTCATTGATCAGTCCAAATCTAACAT	58.948	33.333	0.00	0.00	0.00	2.71
1883	3607	1.420138	AGTGTCACGATTTGGTCCCTT	59.580	47.619	0.00	0.00	0.00	3.95
1886	3610	2.993899	CAGTAGTGTCACGATTTGGTCC	59.006	50.000	0.00	0.00	0.00	4.46
1907	3641	8.391106	ACTTACGATTGCTGATTCTTGTTTATC	58.609	33.333	0.00	0.00	0.00	1.75
1913	3647	5.784750	TGACTTACGATTGCTGATTCTTG	57.215	39.130	0.00	0.00	0.00	3.02
2025	3796	4.565166	CGCGTTAGATTGTTGATTGGTAGA	59.435	41.667	0.00	0.00	0.00	2.59
2033	3804	0.436913	CACGCGCGTTAGATTGTTGA	59.563	50.000	35.90	0.00	0.00	3.18
2094	3888	1.151668	GCCGTCCATGATAGCACATC	58.848	55.000	0.00	0.00	0.00	3.06
2106	3900	2.058001	ATGGATCAGTCGCCGTCCA	61.058	57.895	0.00	0.00	44.22	4.02
2116	3910	0.940126	GCAAGGTACGCATGGATCAG	59.060	55.000	0.00	0.00	0.00	2.90
2167	3971	2.970324	AACGTCGCATGTGCCGTT	60.970	55.556	21.02	21.02	41.55	4.44
2257	4061	2.736719	CGGTGAGATGCTGATCGACTTT	60.737	50.000	0.00	0.00	33.34	2.66

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.