AutoCloner

Multiple sequence alignment - TraesCS1D01G058000

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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	TraesCS1D01G058000	chr1D	100.000	3221	0	0	1	3221	38260345	38257125	0.000000e+00	5949.0
1	TraesCS1D01G058000	chr1D	87.770	2919	288	31	282	3166	37965172	37962289	0.000000e+00	3349.0
2	TraesCS1D01G058000	chr1D	85.964	2750	348	25	491	3219	38584193	38581461	0.000000e+00	2905.0
3	TraesCS1D01G058000	chr1D	86.611	2644	306	26	496	3126	38368172	38365564	0.000000e+00	2878.0
4	TraesCS1D01G058000	chr1D	84.466	2620	370	21	629	3219	36624655	36622044	0.000000e+00	2549.0
5	TraesCS1D01G058000	chr1D	84.294	2636	385	21	541	3159	37423710	37426333	0.000000e+00	2547.0
6	TraesCS1D01G058000	chr1B	95.538	2981	98	20	266	3221	57792053	57789083	0.000000e+00	4735.0
7	TraesCS1D01G058000	chr1B	87.570	2687	304	18	456	3126	58328886	58326214	0.000000e+00	3085.0
8	TraesCS1D01G058000	chr1B	84.589	2654	368	25	586	3218	56501884	56499251	0.000000e+00	2597.0
9	TraesCS1D01G058000	chr1B	84.606	2527	375	12	666	3188	57130238	57132754	0.000000e+00	2499.0
10	TraesCS1D01G058000	chr1B	95.455	110	4	1	72	180	57792168	57792059	1.190000e-39	174.0
11	TraesCS1D01G058000	chr1B	91.379	58	5	0	177	234	354429259	354429316	2.660000e-11	80.5
12	TraesCS1D01G058000	chr1B	91.379	58	5	0	177	234	415063693	415063750	2.660000e-11	80.5
13	TraesCS1D01G058000	chr1B	91.379	58	5	0	177	234	445651409	445651352	2.660000e-11	80.5
14	TraesCS1D01G058000	chr1B	91.379	58	5	0	177	234	448458133	448458076	2.660000e-11	80.5
15	TraesCS1D01G058000	chr1B	85.185	54	4	4	29	80	4339111	4339162	6.000000e-03	52.8
16	TraesCS1D01G058000	chr1A	84.971	2595	364	13	609	3188	36613124	36615707	0.000000e+00	2608.0
17	TraesCS1D01G058000	chr1A	100.000	28	0	0	51	78	500842982	500843009	6.000000e-03	52.8
18	TraesCS1D01G058000	chr7B	92.857	56	4	0	177	232	190243279	190243334	7.410000e-12	82.4
19	TraesCS1D01G058000	chr7B	91.379	58	5	0	177	234	536717244	536717301	2.660000e-11	80.5
20	TraesCS1D01G058000	chr6B	91.379	58	5	0	177	234	448974420	448974363	2.660000e-11	80.5
21	TraesCS1D01G058000	chr6B	87.302	63	7	1	172	234	413489575	413489514	1.600000e-08	71.3
22	TraesCS1D01G058000	chr6B	100.000	28	0	0	1	28	618924707	618924680	6.000000e-03	52.8
23	TraesCS1D01G058000	chr3B	91.379	58	5	0	177	234	322364183	322364240	2.660000e-11	80.5
24	TraesCS1D01G058000	chr3D	90.566	53	4	1	21	73	11431755	11431704	5.770000e-08	69.4
25	TraesCS1D01G058000	chr2A	85.714	63	3	6	23	82	606237622	606237563	9.650000e-06	62.1
26	TraesCS1D01G058000	chr7A	84.127	63	4	6	23	82	623742153	623742094	4.490000e-04	56.5
27	TraesCS1D01G058000	chr6A	84.746	59	6	3	22	79	542237360	542237416	4.490000e-04	56.5
28	TraesCS1D01G058000	chr5A	100.000	28	0	0	50	77	439190405	439190378	6.000000e-03	52.8
29	TraesCS1D01G058000	chr2B	100.000	28	0	0	1	28	268195842	268195815	6.000000e-03	52.8
30	TraesCS1D01G058000	chr2B	100.000	28	0	0	1	28	268205088	268205061	6.000000e-03	52.8

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	TraesCS1D01G058000	chr1D	38257125	38260345	3220	True	5949.0	5949	100.0000	1	3221	1	chr1D.!!$R3	3220
1	TraesCS1D01G058000	chr1D	37962289	37965172	2883	True	3349.0	3349	87.7700	282	3166	1	chr1D.!!$R2	2884
2	TraesCS1D01G058000	chr1D	38581461	38584193	2732	True	2905.0	2905	85.9640	491	3219	1	chr1D.!!$R5	2728
3	TraesCS1D01G058000	chr1D	38365564	38368172	2608	True	2878.0	2878	86.6110	496	3126	1	chr1D.!!$R4	2630
4	TraesCS1D01G058000	chr1D	36622044	36624655	2611	True	2549.0	2549	84.4660	629	3219	1	chr1D.!!$R1	2590
5	TraesCS1D01G058000	chr1D	37423710	37426333	2623	False	2547.0	2547	84.2940	541	3159	1	chr1D.!!$F1	2618
6	TraesCS1D01G058000	chr1B	58326214	58328886	2672	True	3085.0	3085	87.5700	456	3126	1	chr1B.!!$R2	2670
7	TraesCS1D01G058000	chr1B	56499251	56501884	2633	True	2597.0	2597	84.5890	586	3218	1	chr1B.!!$R1	2632
8	TraesCS1D01G058000	chr1B	57130238	57132754	2516	False	2499.0	2499	84.6060	666	3188	1	chr1B.!!$F2	2522
9	TraesCS1D01G058000	chr1B	57789083	57792168	3085	True	2454.5	4735	95.4965	72	3221	2	chr1B.!!$R5	3149
10	TraesCS1D01G058000	chr1A	36613124	36615707	2583	False	2608.0	2608	84.9710	609	3188	1	chr1A.!!$F1	2579

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
784	908	0.320771	GAACGCTCAGCCCTGAAGAA	60.321	55.000	0.00	0.00	39.39	2.52	F
958	1088	1.827789	TGCACAGAAAAAGCCGGCT	60.828	52.632	27.08	27.08	0.00	5.52	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2192	2324	2.036958	TCTTGTGCATCCATAACCCG	57.963	50.0	0.0	0.0	0.0	5.28	R
2633	2765	7.517614	TCATTGCAACTAATTTCTGGTACAA	57.482	32.0	0.0	0.0	38.7	2.41	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
22	23	5.688348	CAAGTATTTTCGGACGAAGAGAG	57.312	43.478	7.25	0.00	35.38	3.20
23	24	5.162075	CAAGTATTTTCGGACGAAGAGAGT	58.838	41.667	7.25	1.04	35.38	3.24
24	25	6.320171	CAAGTATTTTCGGACGAAGAGAGTA	58.680	40.000	7.25	0.00	35.38	2.59
25	26	5.878133	AGTATTTTCGGACGAAGAGAGTAC	58.122	41.667	7.25	5.07	35.38	2.73
26	27	4.778534	ATTTTCGGACGAAGAGAGTACA	57.221	40.909	7.25	0.00	35.38	2.90
27	28	4.572985	TTTTCGGACGAAGAGAGTACAA	57.427	40.909	7.25	0.00	35.38	2.41
28	29	4.572985	TTTCGGACGAAGAGAGTACAAA	57.427	40.909	7.25	0.00	35.38	2.83
29	30	3.826236	TCGGACGAAGAGAGTACAAAG	57.174	47.619	0.00	0.00	0.00	2.77
30	31	3.144506	TCGGACGAAGAGAGTACAAAGT	58.855	45.455	0.00	0.00	0.00	2.66
31	32	3.567164	TCGGACGAAGAGAGTACAAAGTT	59.433	43.478	0.00	0.00	0.00	2.66
32	33	4.756642	TCGGACGAAGAGAGTACAAAGTTA	59.243	41.667	0.00	0.00	0.00	2.24
33	34	5.087397	CGGACGAAGAGAGTACAAAGTTAG	58.913	45.833	0.00	0.00	0.00	2.34
34	35	5.334724	CGGACGAAGAGAGTACAAAGTTAGT	60.335	44.000	0.00	0.00	0.00	2.24
35	36	6.128445	CGGACGAAGAGAGTACAAAGTTAGTA	60.128	42.308	0.00	0.00	0.00	1.82
36	37	7.413877	CGGACGAAGAGAGTACAAAGTTAGTAT	60.414	40.741	0.00	0.00	0.00	2.12
37	38	8.887717	GGACGAAGAGAGTACAAAGTTAGTATA	58.112	37.037	0.00	0.00	0.00	1.47
65	66	9.753674	AATTGAGTCTAATTATTTTGGGACAGA	57.246	29.630	0.00	0.00	42.39	3.41
66	67	8.792830	TTGAGTCTAATTATTTTGGGACAGAG	57.207	34.615	0.00	0.00	42.39	3.35
67	68	7.338710	TGAGTCTAATTATTTTGGGACAGAGG	58.661	38.462	0.00	0.00	42.39	3.69
68	69	6.663734	AGTCTAATTATTTTGGGACAGAGGG	58.336	40.000	3.88	0.00	42.39	4.30
69	70	6.447084	AGTCTAATTATTTTGGGACAGAGGGA	59.553	38.462	3.88	0.00	42.39	4.20
70	71	6.768381	GTCTAATTATTTTGGGACAGAGGGAG	59.232	42.308	0.00	0.00	42.39	4.30
103	104	2.383855	CACAAGAACCAAACCCAAGGA	58.616	47.619	0.00	0.00	0.00	3.36
151	152	3.311966	GAGACTTGCACCAAAATCAAGC	58.688	45.455	0.00	0.00	40.45	4.01
176	178	8.731275	CCTATTGTAGGTTGTCATGTTAATCA	57.269	34.615	0.00	0.00	41.18	2.57
191	193	6.320434	TGTTAATCACATGTATTCCCTCCA	57.680	37.500	0.00	0.00	0.00	3.86
192	194	6.910191	TGTTAATCACATGTATTCCCTCCAT	58.090	36.000	0.00	0.00	0.00	3.41
193	195	6.998074	TGTTAATCACATGTATTCCCTCCATC	59.002	38.462	0.00	0.00	0.00	3.51
194	196	4.647564	ATCACATGTATTCCCTCCATCC	57.352	45.455	0.00	0.00	0.00	3.51
195	197	2.711009	TCACATGTATTCCCTCCATCCC	59.289	50.000	0.00	0.00	0.00	3.85
196	198	2.442878	CACATGTATTCCCTCCATCCCA	59.557	50.000	0.00	0.00	0.00	4.37
197	199	3.117550	CACATGTATTCCCTCCATCCCAA	60.118	47.826	0.00	0.00	0.00	4.12
198	200	3.531397	ACATGTATTCCCTCCATCCCAAA	59.469	43.478	0.00	0.00	0.00	3.28
199	201	4.016666	ACATGTATTCCCTCCATCCCAAAA	60.017	41.667	0.00	0.00	0.00	2.44
200	202	4.898014	TGTATTCCCTCCATCCCAAAAT	57.102	40.909	0.00	0.00	0.00	1.82
201	203	6.125919	ACATGTATTCCCTCCATCCCAAAATA	60.126	38.462	0.00	0.00	0.00	1.40
202	204	6.348478	TGTATTCCCTCCATCCCAAAATAA	57.652	37.500	0.00	0.00	0.00	1.40
203	205	6.133356	TGTATTCCCTCCATCCCAAAATAAC	58.867	40.000	0.00	0.00	0.00	1.89
204	206	4.965283	TTCCCTCCATCCCAAAATAACT	57.035	40.909	0.00	0.00	0.00	2.24
205	207	4.249638	TCCCTCCATCCCAAAATAACTG	57.750	45.455	0.00	0.00	0.00	3.16
206	208	3.596046	TCCCTCCATCCCAAAATAACTGT	59.404	43.478	0.00	0.00	0.00	3.55
207	209	3.954258	CCCTCCATCCCAAAATAACTGTC	59.046	47.826	0.00	0.00	0.00	3.51
208	210	4.325344	CCCTCCATCCCAAAATAACTGTCT	60.325	45.833	0.00	0.00	0.00	3.41
209	211	5.264395	CCTCCATCCCAAAATAACTGTCTT	58.736	41.667	0.00	0.00	0.00	3.01
210	212	6.423182	CCTCCATCCCAAAATAACTGTCTTA	58.577	40.000	0.00	0.00	0.00	2.10
211	213	6.889722	CCTCCATCCCAAAATAACTGTCTTAA	59.110	38.462	0.00	0.00	0.00	1.85
212	214	7.396055	CCTCCATCCCAAAATAACTGTCTTAAA	59.604	37.037	0.00	0.00	0.00	1.52
213	215	8.117813	TCCATCCCAAAATAACTGTCTTAAAC	57.882	34.615	0.00	0.00	0.00	2.01
214	216	7.947890	TCCATCCCAAAATAACTGTCTTAAACT	59.052	33.333	0.00	0.00	0.00	2.66
215	217	8.585018	CCATCCCAAAATAACTGTCTTAAACTT	58.415	33.333	0.00	0.00	0.00	2.66
254	256	7.495055	ACTAGGTTTAGGATAACGTATTGTGG	58.505	38.462	0.00	0.00	30.64	4.17
255	257	5.677567	AGGTTTAGGATAACGTATTGTGGG	58.322	41.667	0.00	0.00	0.00	4.61
256	258	5.426185	AGGTTTAGGATAACGTATTGTGGGA	59.574	40.000	0.00	0.00	0.00	4.37
257	259	5.525012	GGTTTAGGATAACGTATTGTGGGAC	59.475	44.000	0.00	0.00	0.00	4.46
258	260	3.447918	AGGATAACGTATTGTGGGACG	57.552	47.619	0.00	0.00	44.57	4.79
259	261	2.101917	AGGATAACGTATTGTGGGACGG	59.898	50.000	0.00	0.00	43.32	4.79
260	262	1.862827	GATAACGTATTGTGGGACGGC	59.137	52.381	0.00	0.00	43.32	5.68
261	263	0.458197	TAACGTATTGTGGGACGGCG	60.458	55.000	4.80	4.80	43.32	6.46
262	264	2.888534	CGTATTGTGGGACGGCGG	60.889	66.667	13.24	0.00	35.43	6.13
263	265	2.512974	GTATTGTGGGACGGCGGG	60.513	66.667	13.24	0.00	0.00	6.13
264	266	2.684294	TATTGTGGGACGGCGGGA	60.684	61.111	13.24	0.00	0.00	5.14
371	375	4.995124	ACAAGTATCGCACTCGTTCTATT	58.005	39.130	0.00	0.00	36.04	1.73
374	378	7.031372	ACAAGTATCGCACTCGTTCTATTAAA	58.969	34.615	0.00	0.00	36.04	1.52
452	512	0.787787	GCGTACGAACACATTGCAGA	59.212	50.000	21.65	0.00	0.00	4.26
453	513	1.201812	GCGTACGAACACATTGCAGAG	60.202	52.381	21.65	0.00	0.00	3.35
454	514	1.201812	CGTACGAACACATTGCAGAGC	60.202	52.381	10.44	0.00	0.00	4.09
783	907	1.293498	GAACGCTCAGCCCTGAAGA	59.707	57.895	0.00	0.00	39.39	2.87
784	908	0.320771	GAACGCTCAGCCCTGAAGAA	60.321	55.000	0.00	0.00	39.39	2.52
949	1079	2.109739	AACCGCGTGTGCACAGAAA	61.110	52.632	22.40	0.00	42.97	2.52
958	1088	1.827789	TGCACAGAAAAAGCCGGCT	60.828	52.632	27.08	27.08	0.00	5.52
998	1128	2.189521	CCACACCTACGGCATCCC	59.810	66.667	0.00	0.00	0.00	3.85
1135	1265	3.000041	CTCTGCTATGCCAAACGTACAA	59.000	45.455	0.00	0.00	0.00	2.41
1425	1556	3.181475	CCAATGTGGTCACGTATAGCTCT	60.181	47.826	0.00	0.00	31.35	4.09
2081	2213	3.168035	TCAGGGGTTTTGTATGCATGT	57.832	42.857	10.16	0.00	0.00	3.21
2082	2214	4.308526	TCAGGGGTTTTGTATGCATGTA	57.691	40.909	10.16	0.00	0.00	2.29
2151	2283	2.649531	TTCCTCGTCCCAACATTGTT	57.350	45.000	0.00	0.00	0.00	2.83
2152	2284	2.649531	TCCTCGTCCCAACATTGTTT	57.350	45.000	0.00	0.00	0.00	2.83
2633	2765	0.528017	TGCAGAAGAAGCGATCGACT	59.472	50.000	21.57	12.79	33.85	4.18

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
0	1	5.162075	ACTCTCTTCGTCCGAAAATACTTG	58.838	41.667	3.52	0.00	33.34	3.16
1	2	5.388408	ACTCTCTTCGTCCGAAAATACTT	57.612	39.130	3.52	0.00	33.34	2.24
2	3	5.413833	TGTACTCTCTTCGTCCGAAAATACT	59.586	40.000	3.52	0.00	33.34	2.12
3	4	5.634896	TGTACTCTCTTCGTCCGAAAATAC	58.365	41.667	3.52	3.41	33.34	1.89
4	5	5.885230	TGTACTCTCTTCGTCCGAAAATA	57.115	39.130	3.52	0.00	33.34	1.40
5	6	4.778534	TGTACTCTCTTCGTCCGAAAAT	57.221	40.909	3.52	0.00	33.34	1.82
6	7	4.572985	TTGTACTCTCTTCGTCCGAAAA	57.427	40.909	3.52	0.00	33.34	2.29
7	8	4.037208	ACTTTGTACTCTCTTCGTCCGAAA	59.963	41.667	3.52	0.00	33.34	3.46
8	9	3.567164	ACTTTGTACTCTCTTCGTCCGAA	59.433	43.478	1.81	1.81	0.00	4.30
9	10	3.144506	ACTTTGTACTCTCTTCGTCCGA	58.855	45.455	0.00	0.00	0.00	4.55
10	11	3.555917	ACTTTGTACTCTCTTCGTCCG	57.444	47.619	0.00	0.00	0.00	4.79
11	12	6.011476	ACTAACTTTGTACTCTCTTCGTCC	57.989	41.667	0.00	0.00	0.00	4.79
39	40	9.753674	TCTGTCCCAAAATAATTAGACTCAATT	57.246	29.630	0.00	0.00	32.91	2.32
40	41	9.401058	CTCTGTCCCAAAATAATTAGACTCAAT	57.599	33.333	0.00	0.00	0.00	2.57
41	42	7.829211	CCTCTGTCCCAAAATAATTAGACTCAA	59.171	37.037	0.00	0.00	0.00	3.02
42	43	7.338710	CCTCTGTCCCAAAATAATTAGACTCA	58.661	38.462	0.00	0.00	0.00	3.41
43	44	6.768381	CCCTCTGTCCCAAAATAATTAGACTC	59.232	42.308	0.00	0.00	0.00	3.36
44	45	6.447084	TCCCTCTGTCCCAAAATAATTAGACT	59.553	38.462	0.00	0.00	0.00	3.24
45	46	6.659824	TCCCTCTGTCCCAAAATAATTAGAC	58.340	40.000	0.00	0.00	0.00	2.59
46	47	6.447084	ACTCCCTCTGTCCCAAAATAATTAGA	59.553	38.462	0.00	0.00	0.00	2.10
47	48	6.663734	ACTCCCTCTGTCCCAAAATAATTAG	58.336	40.000	0.00	0.00	0.00	1.73
48	49	6.652205	ACTCCCTCTGTCCCAAAATAATTA	57.348	37.500	0.00	0.00	0.00	1.40
49	50	5.536497	ACTCCCTCTGTCCCAAAATAATT	57.464	39.130	0.00	0.00	0.00	1.40
50	51	5.731678	ACTACTCCCTCTGTCCCAAAATAAT	59.268	40.000	0.00	0.00	0.00	1.28
51	52	5.098663	ACTACTCCCTCTGTCCCAAAATAA	58.901	41.667	0.00	0.00	0.00	1.40
52	53	4.695606	ACTACTCCCTCTGTCCCAAAATA	58.304	43.478	0.00	0.00	0.00	1.40
53	54	3.532102	ACTACTCCCTCTGTCCCAAAAT	58.468	45.455	0.00	0.00	0.00	1.82
54	55	2.986050	ACTACTCCCTCTGTCCCAAAA	58.014	47.619	0.00	0.00	0.00	2.44
55	56	2.715763	ACTACTCCCTCTGTCCCAAA	57.284	50.000	0.00	0.00	0.00	3.28
56	57	3.532232	AGATACTACTCCCTCTGTCCCAA	59.468	47.826	0.00	0.00	0.00	4.12
57	58	3.132056	AGATACTACTCCCTCTGTCCCA	58.868	50.000	0.00	0.00	0.00	4.37
58	59	3.887916	AGATACTACTCCCTCTGTCCC	57.112	52.381	0.00	0.00	0.00	4.46
59	60	5.947566	GGAATAGATACTACTCCCTCTGTCC	59.052	48.000	0.00	0.00	0.00	4.02
60	61	6.431852	GTGGAATAGATACTACTCCCTCTGTC	59.568	46.154	4.27	0.00	0.00	3.51
61	62	6.126156	TGTGGAATAGATACTACTCCCTCTGT	60.126	42.308	4.27	0.00	0.00	3.41
62	63	6.307776	TGTGGAATAGATACTACTCCCTCTG	58.692	44.000	4.27	0.00	0.00	3.35
63	64	6.532119	TGTGGAATAGATACTACTCCCTCT	57.468	41.667	4.27	0.00	0.00	3.69
64	65	7.005296	TCTTGTGGAATAGATACTACTCCCTC	58.995	42.308	4.27	0.00	0.00	4.30
65	66	6.923670	TCTTGTGGAATAGATACTACTCCCT	58.076	40.000	4.27	0.00	0.00	4.20
66	67	7.435305	GTTCTTGTGGAATAGATACTACTCCC	58.565	42.308	4.27	0.00	36.24	4.30
67	68	7.069578	TGGTTCTTGTGGAATAGATACTACTCC	59.930	40.741	0.00	0.00	36.24	3.85
68	69	8.008513	TGGTTCTTGTGGAATAGATACTACTC	57.991	38.462	0.00	0.00	36.24	2.59
69	70	7.973048	TGGTTCTTGTGGAATAGATACTACT	57.027	36.000	0.00	0.00	36.24	2.57
70	71	8.880750	GTTTGGTTCTTGTGGAATAGATACTAC	58.119	37.037	0.00	0.00	36.24	2.73
170	172	6.467194	GGGATGGAGGGAATACATGTGATTAA	60.467	42.308	9.11	0.00	30.07	1.40
176	178	2.787956	TGGGATGGAGGGAATACATGT	58.212	47.619	2.69	2.69	30.07	3.21
180	182	6.265422	CAGTTATTTTGGGATGGAGGGAATAC	59.735	42.308	0.00	0.00	0.00	1.89
181	183	6.068498	ACAGTTATTTTGGGATGGAGGGAATA	60.068	38.462	0.00	0.00	0.00	1.75
182	184	5.211201	CAGTTATTTTGGGATGGAGGGAAT	58.789	41.667	0.00	0.00	0.00	3.01
183	185	4.045334	ACAGTTATTTTGGGATGGAGGGAA	59.955	41.667	0.00	0.00	0.00	3.97
185	187	3.954258	GACAGTTATTTTGGGATGGAGGG	59.046	47.826	0.00	0.00	0.00	4.30
186	188	4.860022	AGACAGTTATTTTGGGATGGAGG	58.140	43.478	0.00	0.00	0.00	4.30
187	189	7.938140	TTAAGACAGTTATTTTGGGATGGAG	57.062	36.000	0.00	0.00	0.00	3.86
188	190	7.947890	AGTTTAAGACAGTTATTTTGGGATGGA	59.052	33.333	0.00	0.00	0.00	3.41
189	191	8.122472	AGTTTAAGACAGTTATTTTGGGATGG	57.878	34.615	0.00	0.00	0.00	3.51
228	230	8.632679	CCACAATACGTTATCCTAAACCTAGTA	58.367	37.037	0.00	0.00	0.00	1.82
229	231	7.418254	CCCACAATACGTTATCCTAAACCTAGT	60.418	40.741	0.00	0.00	0.00	2.57
230	232	6.927381	CCCACAATACGTTATCCTAAACCTAG	59.073	42.308	0.00	0.00	0.00	3.02
231	233	6.610830	TCCCACAATACGTTATCCTAAACCTA	59.389	38.462	0.00	0.00	0.00	3.08
232	234	5.426185	TCCCACAATACGTTATCCTAAACCT	59.574	40.000	0.00	0.00	0.00	3.50
233	235	5.525012	GTCCCACAATACGTTATCCTAAACC	59.475	44.000	0.00	0.00	0.00	3.27
234	236	5.232838	CGTCCCACAATACGTTATCCTAAAC	59.767	44.000	0.00	0.00	34.48	2.01
235	237	5.350633	CGTCCCACAATACGTTATCCTAAA	58.649	41.667	0.00	0.00	34.48	1.85
236	238	4.202141	CCGTCCCACAATACGTTATCCTAA	60.202	45.833	0.00	0.00	37.40	2.69
237	239	3.318839	CCGTCCCACAATACGTTATCCTA	59.681	47.826	0.00	0.00	37.40	2.94
238	240	2.101917	CCGTCCCACAATACGTTATCCT	59.898	50.000	0.00	0.00	37.40	3.24
239	241	2.476821	CCGTCCCACAATACGTTATCC	58.523	52.381	0.00	0.00	37.40	2.59
240	242	1.862827	GCCGTCCCACAATACGTTATC	59.137	52.381	0.00	0.00	37.40	1.75
241	243	1.803625	CGCCGTCCCACAATACGTTAT	60.804	52.381	0.00	0.00	37.40	1.89
242	244	0.458197	CGCCGTCCCACAATACGTTA	60.458	55.000	0.00	0.00	37.40	3.18
243	245	1.738830	CGCCGTCCCACAATACGTT	60.739	57.895	0.00	0.00	37.40	3.99
244	246	2.125832	CGCCGTCCCACAATACGT	60.126	61.111	0.00	0.00	37.40	3.57
245	247	2.888534	CCGCCGTCCCACAATACG	60.889	66.667	0.00	0.00	38.80	3.06
246	248	2.512974	CCCGCCGTCCCACAATAC	60.513	66.667	0.00	0.00	0.00	1.89
247	249	2.684294	TCCCGCCGTCCCACAATA	60.684	61.111	0.00	0.00	0.00	1.90
248	250	4.096003	CTCCCGCCGTCCCACAAT	62.096	66.667	0.00	0.00	0.00	2.71
250	252	3.968837	ATACTCCCGCCGTCCCACA	62.969	63.158	0.00	0.00	0.00	4.17
251	253	3.148031	GATACTCCCGCCGTCCCAC	62.148	68.421	0.00	0.00	0.00	4.61
252	254	2.836360	GATACTCCCGCCGTCCCA	60.836	66.667	0.00	0.00	0.00	4.37
253	255	2.428925	TTGATACTCCCGCCGTCCC	61.429	63.158	0.00	0.00	0.00	4.46
254	256	1.227176	GTTGATACTCCCGCCGTCC	60.227	63.158	0.00	0.00	0.00	4.79
255	257	0.108520	TTGTTGATACTCCCGCCGTC	60.109	55.000	0.00	0.00	0.00	4.79
256	258	0.322322	TTTGTTGATACTCCCGCCGT	59.678	50.000	0.00	0.00	0.00	5.68
257	259	1.444836	TTTTGTTGATACTCCCGCCG	58.555	50.000	0.00	0.00	0.00	6.46
258	260	4.082463	TCAAATTTTGTTGATACTCCCGCC	60.082	41.667	8.89	0.00	32.56	6.13
259	261	5.054390	TCAAATTTTGTTGATACTCCCGC	57.946	39.130	8.89	0.00	32.56	6.13
461	521	4.865761	GGACATCGGCGTGCGCTA	62.866	66.667	16.21	5.66	41.60	4.26
590	669	0.966370	GTGGAGGAGTAGTGCGGACT	60.966	60.000	15.78	15.78	36.07	3.85
783	907	0.738389	CGAACAGGTGGTGTGCTTTT	59.262	50.000	0.00	0.00	40.26	2.27
784	908	0.107410	TCGAACAGGTGGTGTGCTTT	60.107	50.000	0.00	0.00	40.26	3.51
971	1101	1.819288	CGTAGGTGTGGACTGTGAGAT	59.181	52.381	0.00	0.00	0.00	2.75
998	1128	2.693762	CGGCAGCAACAGTCCATGG	61.694	63.158	4.97	4.97	0.00	3.66
1135	1265	2.686915	GCAGCAAGTTGATAGCCTCATT	59.313	45.455	7.16	0.00	32.72	2.57
2067	2199	9.632807	TTAACCAAATCTACATGCATACAAAAC	57.367	29.630	0.00	0.00	0.00	2.43
2192	2324	2.036958	TCTTGTGCATCCATAACCCG	57.963	50.000	0.00	0.00	0.00	5.28
2633	2765	7.517614	TCATTGCAACTAATTTCTGGTACAA	57.482	32.000	0.00	0.00	38.70	2.41

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.