AutoCloner

Multiple sequence alignment - TraesCS2B01G317200

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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	TraesCS2B01G317200	chr2B	100.000	3224	0	0	1	3224	452913757	452910534	0.000000e+00	5954.0
1	TraesCS2B01G317200	chr2B	95.825	503	20	1	2722	3223	666053278	666052776	0.000000e+00	811.0
2	TraesCS2B01G317200	chr2B	83.956	455	38	13	1	444	195681993	195681563	1.390000e-108	403.0
3	TraesCS2B01G317200	chr2D	94.052	2337	103	15	1	2305	382129907	382127575	0.000000e+00	3513.0
4	TraesCS2B01G317200	chr2D	92.929	396	21	5	2309	2700	382127600	382127208	1.300000e-158	569.0
5	TraesCS2B01G317200	chr2D	100.000	32	0	0	2452	2483	11788739	11788708	3.470000e-05	60.2
6	TraesCS2B01G317200	chr2A	95.141	1873	49	12	469	2305	516309460	516307594	0.000000e+00	2916.0
7	TraesCS2B01G317200	chr2A	85.138	471	47	5	1	448	745404163	745403693	8.150000e-126	460.0
8	TraesCS2B01G317200	chr2A	97.238	181	5	0	2309	2489	516307619	516307439	1.120000e-79	307.0
9	TraesCS2B01G317200	chr2A	82.684	231	33	7	219	446	698066414	698066640	7.050000e-47	198.0
10	TraesCS2B01G317200	chr3B	96.367	523	17	2	2703	3224	533444541	533445062	0.000000e+00	859.0
11	TraesCS2B01G317200	chr3B	94.892	509	21	3	2718	3224	309388208	309387703	0.000000e+00	791.0
12	TraesCS2B01G317200	chr3B	78.402	338	65	8	97	431	81809718	81809386	2.520000e-51	213.0
13	TraesCS2B01G317200	chr3B	88.732	71	8	0	2553	2623	765714009	765713939	1.590000e-13	87.9
14	TraesCS2B01G317200	chr7B	96.407	501	17	1	2725	3224	498598913	498599413	0.000000e+00	824.0
15	TraesCS2B01G317200	chr7B	96.032	504	19	1	2722	3224	739380156	739379653	0.000000e+00	819.0
16	TraesCS2B01G317200	chr6B	95.951	494	19	1	2732	3224	563975021	563975514	0.000000e+00	800.0
17	TraesCS2B01G317200	chr4A	94.922	512	23	2	2716	3224	670558806	670559317	0.000000e+00	798.0
18	TraesCS2B01G317200	chr4A	90.769	65	6	0	1210	1274	689137570	689137506	1.590000e-13	87.9
19	TraesCS2B01G317200	chr4A	90.769	65	6	0	1210	1274	689190418	689190354	1.590000e-13	87.9
20	TraesCS2B01G317200	chrUn	95.050	505	23	1	2720	3222	50437473	50437977	0.000000e+00	793.0
21	TraesCS2B01G317200	chrUn	95.050	505	23	1	2720	3222	263186158	263185654	0.000000e+00	793.0
22	TraesCS2B01G317200	chrUn	92.308	65	5	0	1210	1274	90726733	90726669	3.420000e-15	93.5
23	TraesCS2B01G317200	chrUn	92.308	65	5	0	1210	1274	90939278	90939214	3.420000e-15	93.5
24	TraesCS2B01G317200	chrUn	92.308	65	5	0	1210	1274	401026603	401026539	3.420000e-15	93.5
25	TraesCS2B01G317200	chr3D	87.146	459	45	5	3	447	303791966	303792424	2.870000e-140	508.0
26	TraesCS2B01G317200	chr1D	85.000	460	42	9	1	448	383475103	383475547	2.950000e-120	442.0
27	TraesCS2B01G317200	chr6D	83.445	447	56	12	1	444	337042709	337042278	1.800000e-107	399.0
28	TraesCS2B01G317200	chr4D	84.224	393	58	4	56	446	17427918	17428308	2.350000e-101	379.0
29	TraesCS2B01G317200	chr4D	81.674	442	68	10	1	438	72394819	72394387	3.960000e-94	355.0
30	TraesCS2B01G317200	chr1A	81.222	442	72	9	12	444	564343262	564343701	2.380000e-91	346.0
31	TraesCS2B01G317200	chr1B	79.688	448	83	6	4	447	139050259	139049816	1.870000e-82	316.0
32	TraesCS2B01G317200	chr7D	79.379	451	80	8	5	446	623844099	623843653	4.040000e-79	305.0
33	TraesCS2B01G317200	chr7D	81.857	237	34	4	219	446	521730015	521730251	1.180000e-44	191.0
34	TraesCS2B01G317200	chr7D	90.769	65	6	0	1210	1274	37234889	37234825	1.590000e-13	87.9
35	TraesCS2B01G317200	chr7A	92.308	65	5	0	1210	1274	36630004	36629940	3.420000e-15	93.5
36	TraesCS2B01G317200	chr6A	82.558	86	15	0	2545	2630	382497606	382497521	3.450000e-10	76.8

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	TraesCS2B01G317200	chr2B	452910534	452913757	3223	True	5954.0	5954	100.0000	1	3224	1	chr2B.!!$R2	3223
1	TraesCS2B01G317200	chr2B	666052776	666053278	502	True	811.0	811	95.8250	2722	3223	1	chr2B.!!$R3	501
2	TraesCS2B01G317200	chr2D	382127208	382129907	2699	True	2041.0	3513	93.4905	1	2700	2	chr2D.!!$R2	2699
3	TraesCS2B01G317200	chr2A	516307439	516309460	2021	True	1611.5	2916	96.1895	469	2489	2	chr2A.!!$R2	2020
4	TraesCS2B01G317200	chr3B	533444541	533445062	521	False	859.0	859	96.3670	2703	3224	1	chr3B.!!$F1	521
5	TraesCS2B01G317200	chr3B	309387703	309388208	505	True	791.0	791	94.8920	2718	3224	1	chr3B.!!$R2	506
6	TraesCS2B01G317200	chr7B	498598913	498599413	500	False	824.0	824	96.4070	2725	3224	1	chr7B.!!$F1	499
7	TraesCS2B01G317200	chr7B	739379653	739380156	503	True	819.0	819	96.0320	2722	3224	1	chr7B.!!$R1	502
8	TraesCS2B01G317200	chr4A	670558806	670559317	511	False	798.0	798	94.9220	2716	3224	1	chr4A.!!$F1	508
9	TraesCS2B01G317200	chrUn	50437473	50437977	504	False	793.0	793	95.0500	2720	3222	1	chrUn.!!$F1	502
10	TraesCS2B01G317200	chrUn	263185654	263186158	504	True	793.0	793	95.0500	2720	3222	1	chrUn.!!$R3	502

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
155	157	0.040204	AGGATTGGGAGCAAAGGTGG	59.960	55.0	0.0	0.0	0.00	4.61	F
305	317	0.248621	GCGCCATATTTGTGCTGGAC	60.249	55.0	0.0	0.0	31.38	4.02	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1459	1490	0.808453	ACGTTGTGTTGCTAGTGCGT	60.808	50.000	0.0	0.0	43.34	5.24	R
2244	2293	1.445582	ACGACGAAATCACCGGCTC	60.446	57.895	0.0	0.0	31.81	4.70	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
50	52	2.509336	CCACGACATCACGCCTCC	60.509	66.667	0.00	0.00	36.70	4.30
53	55	2.359169	ACGACATCACGCCTCCCAT	61.359	57.895	0.00	0.00	36.70	4.00
57	59	1.620819	GACATCACGCCTCCCATAGAT	59.379	52.381	0.00	0.00	0.00	1.98
67	69	1.622811	CTCCCATAGATGAGGCAGACC	59.377	57.143	0.00	0.00	0.00	3.85
68	70	1.062198	TCCCATAGATGAGGCAGACCA	60.062	52.381	0.00	0.00	39.06	4.02
69	71	1.983691	CCCATAGATGAGGCAGACCAT	59.016	52.381	0.00	0.00	39.06	3.55
78	80	0.835941	AGGCAGACCATGTCTCCATC	59.164	55.000	12.22	0.00	41.00	3.51
81	83	0.873312	CAGACCATGTCTCCATCGCG	60.873	60.000	0.00	0.00	41.37	5.87
82	84	1.037579	AGACCATGTCTCCATCGCGA	61.038	55.000	13.09	13.09	38.71	5.87
83	85	0.179111	GACCATGTCTCCATCGCGAA	60.179	55.000	15.24	0.00	0.00	4.70
91	93	3.499737	CCATCGCGAAGGTGTGGC	61.500	66.667	21.83	0.00	0.00	5.01
108	110	2.105128	CTCGGGCTGGACGACATC	59.895	66.667	0.00	0.00	36.25	3.06
150	152	1.004745	GAGGTGAGGATTGGGAGCAAA	59.995	52.381	0.00	0.00	0.00	3.68
155	157	0.040204	AGGATTGGGAGCAAAGGTGG	59.960	55.000	0.00	0.00	0.00	4.61
197	199	3.140814	GAATGGTTGGAGGGCGGC	61.141	66.667	0.00	0.00	0.00	6.53
228	230	2.178984	AGGAAGGGTTTGGTGGATTTGA	59.821	45.455	0.00	0.00	0.00	2.69
238	240	3.940319	TGGTGGATTTGATGCAATTTGG	58.060	40.909	0.00	0.00	30.45	3.28
244	246	4.081531	GGATTTGATGCAATTTGGAGTGGA	60.082	41.667	0.00	0.00	0.00	4.02
246	248	3.159213	TGATGCAATTTGGAGTGGAGT	57.841	42.857	0.00	0.00	0.00	3.85
255	257	2.584391	GGAGTGGAGTCGGGCTGTT	61.584	63.158	0.00	0.00	0.00	3.16
288	300	2.972505	GGCACACCCATATCCGCG	60.973	66.667	0.00	0.00	0.00	6.46
298	310	2.083774	CCATATCCGCGCCATATTTGT	58.916	47.619	0.00	0.00	0.00	2.83
305	317	0.248621	GCGCCATATTTGTGCTGGAC	60.249	55.000	0.00	0.00	31.38	4.02
375	388	2.157668	CGACTGGGTCAAAAATCGTGAG	59.842	50.000	0.00	0.00	32.09	3.51
376	389	2.484264	GACTGGGTCAAAAATCGTGAGG	59.516	50.000	0.00	0.00	32.09	3.86
377	390	1.200020	CTGGGTCAAAAATCGTGAGGC	59.800	52.381	0.00	0.00	0.00	4.70
380	393	0.872388	GTCAAAAATCGTGAGGCGGT	59.128	50.000	0.00	0.00	41.72	5.68
385	398	0.892755	AAATCGTGAGGCGGTAGTGA	59.107	50.000	0.00	0.00	41.72	3.41
413	426	1.699343	CCTTCTCGGACGTTTGAGAC	58.301	55.000	17.21	0.00	40.76	3.36
430	443	4.404098	CGGGTTTGAGGGGTCCGG	62.404	72.222	0.00	0.00	37.35	5.14
453	466	5.395768	GGTTGTAGATGCTCTTAGTGACCAT	60.396	44.000	0.00	0.00	0.00	3.55
492	505	8.356657	ACCTTGAAGATAGACATCTATTCTTCG	58.643	37.037	21.02	15.27	40.81	3.79
543	556	1.703411	CCAAAGGCAAGGGTTCTTCA	58.297	50.000	0.00	0.00	0.00	3.02
571	584	5.877012	AGTTGTAGCCTGTGATATTGAACAG	59.123	40.000	7.01	7.01	42.83	3.16
620	638	1.307097	CTCTTTCTAGCTGCCATGCC	58.693	55.000	0.00	0.00	0.00	4.40
690	716	1.224069	CTCACCGGTGCTGTGTCTTG	61.224	60.000	30.25	1.91	35.25	3.02
693	719	0.814010	ACCGGTGCTGTGTCTTGTTC	60.814	55.000	6.12	0.00	0.00	3.18
717	743	1.210155	GTGTGCCTGAACCGAATGC	59.790	57.895	0.00	0.00	0.00	3.56
720	746	4.520846	GCCTGAACCGAATGCGCG	62.521	66.667	0.00	0.00	35.83	6.86
752	778	5.063880	AGGTTGTACTTACTCTGCAAAAGG	58.936	41.667	0.00	0.00	0.00	3.11
948	979	6.347725	CCAACACAGAGTAGCTTGTTATTGAC	60.348	42.308	0.00	0.00	31.34	3.18
965	996	0.528684	GACCGTGCCATCTCTACTGC	60.529	60.000	0.00	0.00	0.00	4.40
1459	1490	1.105457	GCTGGTATGCAGCAATCCAA	58.895	50.000	18.51	7.07	44.49	3.53
1461	1492	1.064505	CTGGTATGCAGCAATCCAACG	59.935	52.381	18.51	8.13	0.00	4.10
1462	1493	0.248621	GGTATGCAGCAATCCAACGC	60.249	55.000	0.00	0.00	0.00	4.84
1476	1514	1.596954	CCAACGCACTAGCAACACAAC	60.597	52.381	0.00	0.00	42.27	3.32
1478	1516	0.808453	ACGCACTAGCAACACAACGT	60.808	50.000	0.00	0.00	42.27	3.99
1753	1794	3.236816	GTCGCAGGTGTTTGATTTGATG	58.763	45.455	0.00	0.00	0.00	3.07
1824	1873	0.538057	CAGGAGCACACACCATTGGT	60.538	55.000	1.37	1.37	35.62	3.67
1968	2017	1.153289	CCAGATCCTGTTCGCCCTG	60.153	63.158	0.00	0.00	0.00	4.45
2039	2088	1.675310	CCATGAACGGCCTGCTCAA	60.675	57.895	0.00	0.00	0.00	3.02
2173	2222	3.665675	AACATCTCGCCGCTCACCC	62.666	63.158	0.00	0.00	0.00	4.61
2289	2338	4.039488	TCAAGCTCCTTGATTTGCAATGTT	59.961	37.500	0.00	0.00	44.27	2.71
2290	2339	4.612264	AGCTCCTTGATTTGCAATGTTT	57.388	36.364	0.00	0.00	35.59	2.83
2291	2340	4.563061	AGCTCCTTGATTTGCAATGTTTC	58.437	39.130	0.00	0.00	35.59	2.78
2292	2341	4.282703	AGCTCCTTGATTTGCAATGTTTCT	59.717	37.500	0.00	0.00	35.59	2.52
2293	2342	4.992951	GCTCCTTGATTTGCAATGTTTCTT	59.007	37.500	0.00	0.00	35.59	2.52
2294	2343	5.467735	GCTCCTTGATTTGCAATGTTTCTTT	59.532	36.000	0.00	0.00	35.59	2.52
2295	2344	6.347160	GCTCCTTGATTTGCAATGTTTCTTTC	60.347	38.462	0.00	0.00	35.59	2.62
2296	2345	6.580788	TCCTTGATTTGCAATGTTTCTTTCA	58.419	32.000	0.00	0.00	35.59	2.69
2297	2346	7.046652	TCCTTGATTTGCAATGTTTCTTTCAA	58.953	30.769	0.00	0.13	35.59	2.69
2298	2347	7.225145	TCCTTGATTTGCAATGTTTCTTTCAAG	59.775	33.333	0.00	8.85	38.04	3.02
2299	2348	7.011669	CCTTGATTTGCAATGTTTCTTTCAAGT	59.988	33.333	0.00	0.00	37.11	3.16
2300	2349	8.939201	TTGATTTGCAATGTTTCTTTCAAGTA	57.061	26.923	0.00	0.00	0.00	2.24
2301	2350	8.351495	TGATTTGCAATGTTTCTTTCAAGTAC	57.649	30.769	0.00	0.00	0.00	2.73
2302	2351	8.196771	TGATTTGCAATGTTTCTTTCAAGTACT	58.803	29.630	0.00	0.00	0.00	2.73
2303	2352	7.754069	TTTGCAATGTTTCTTTCAAGTACTG	57.246	32.000	0.00	0.00	0.00	2.74
2304	2353	6.449635	TGCAATGTTTCTTTCAAGTACTGT	57.550	33.333	0.00	0.00	0.00	3.55
2305	2354	6.862209	TGCAATGTTTCTTTCAAGTACTGTT	58.138	32.000	0.00	0.00	0.00	3.16
2306	2355	7.319646	TGCAATGTTTCTTTCAAGTACTGTTT	58.680	30.769	0.00	0.00	0.00	2.83
2307	2356	7.816995	TGCAATGTTTCTTTCAAGTACTGTTTT	59.183	29.630	0.00	0.00	0.00	2.43
2308	2357	8.655970	GCAATGTTTCTTTCAAGTACTGTTTTT	58.344	29.630	0.00	0.00	0.00	1.94
2401	2450	0.589223	TTGCGATCGTGTTTGTTCCC	59.411	50.000	17.81	0.00	0.00	3.97
2498	2547	1.068741	ACGAGTTGTCCCTGTCACTTC	59.931	52.381	0.00	0.00	0.00	3.01
2551	2600	9.516546	TCTACAATATATATGTCTCGTTGTCCT	57.483	33.333	0.00	0.00	32.27	3.85
2571	2620	5.175308	GTCCTCAACAAGTCGTACTCTTTTC	59.825	44.000	0.00	0.00	0.00	2.29
2572	2621	4.148348	CCTCAACAAGTCGTACTCTTTTCG	59.852	45.833	0.00	0.00	0.00	3.46
2588	2637	7.936584	ACTCTTTTCGTAATTCAAATTCCACA	58.063	30.769	0.00	0.00	0.00	4.17
2674	2727	8.527810	CCATCTGTCTTTAAGATATACTCCCTC	58.472	40.741	0.00	0.00	33.03	4.30
2691	2744	7.850935	ACTCCCTCCGTTTCTAATTATATGA	57.149	36.000	0.00	0.00	0.00	2.15
2692	2745	7.668492	ACTCCCTCCGTTTCTAATTATATGAC	58.332	38.462	0.00	0.00	0.00	3.06
2693	2746	6.684686	TCCCTCCGTTTCTAATTATATGACG	58.315	40.000	0.00	0.00	0.00	4.35
2695	2748	5.347907	CCTCCGTTTCTAATTATATGACGGC	59.652	44.000	17.79	0.00	45.82	5.68
2696	2749	4.919168	TCCGTTTCTAATTATATGACGGCG	59.081	41.667	4.80	4.80	45.82	6.46
2697	2750	4.919168	CCGTTTCTAATTATATGACGGCGA	59.081	41.667	16.62	0.00	41.47	5.54
2698	2751	5.403166	CCGTTTCTAATTATATGACGGCGAA	59.597	40.000	16.62	0.57	41.47	4.70
2699	2752	6.399669	CCGTTTCTAATTATATGACGGCGAAG	60.400	42.308	16.62	0.00	41.47	3.79
2860	2915	3.873812	GGGGGTCGCCGGATTCAT	61.874	66.667	5.05	0.00	0.00	2.57
2926	2981	1.798813	GTTCATCGTCTTTGCTTCGGT	59.201	47.619	0.00	0.00	0.00	4.69
2974	3029	8.986929	AAATATTCTTCGGATCCTTTCTTGAT	57.013	30.769	10.75	0.00	0.00	2.57
2977	3032	5.620738	TCTTCGGATCCTTTCTTGATGAT	57.379	39.130	10.75	0.00	0.00	2.45
3030	3085	3.319122	GGAAACCAGTCTGTTCAAGCAAT	59.681	43.478	0.00	0.00	0.00	3.56
3037	3092	2.229543	GTCTGTTCAAGCAATGATGGCA	59.770	45.455	0.00	0.00	38.03	4.92

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
9	10	0.884704	GACTTGCAAGGCGGAGAACA	60.885	55.000	29.18	0.00	0.00	3.18
10	11	1.869690	GACTTGCAAGGCGGAGAAC	59.130	57.895	29.18	7.26	0.00	3.01
39	41	1.620323	TCATCTATGGGAGGCGTGATG	59.380	52.381	0.00	0.00	34.40	3.07
41	43	1.332195	CTCATCTATGGGAGGCGTGA	58.668	55.000	0.00	0.00	0.00	4.35
43	45	2.751991	CCTCATCTATGGGAGGCGT	58.248	57.895	0.00	0.00	43.80	5.68
50	52	2.371179	ACATGGTCTGCCTCATCTATGG	59.629	50.000	0.00	0.00	35.27	2.74
53	55	2.961741	GAGACATGGTCTGCCTCATCTA	59.038	50.000	3.21	0.00	43.53	1.98
57	59	2.290847	GGAGACATGGTCTGCCTCA	58.709	57.895	3.21	0.00	43.53	3.86
81	83	4.021925	AGCCCGAGCCACACCTTC	62.022	66.667	0.00	0.00	41.25	3.46
82	84	4.335647	CAGCCCGAGCCACACCTT	62.336	66.667	0.00	0.00	41.25	3.50
91	93	2.105128	GATGTCGTCCAGCCCGAG	59.895	66.667	0.00	0.00	34.56	4.63
97	99	2.105128	GCCGGAGATGTCGTCCAG	59.895	66.667	5.05	0.00	33.14	3.86
197	199	2.444895	CCCTTCCTCCTCCTCCCG	60.445	72.222	0.00	0.00	0.00	5.14
228	230	2.086869	CGACTCCACTCCAAATTGCAT	58.913	47.619	0.00	0.00	0.00	3.96
238	240	1.374758	CAACAGCCCGACTCCACTC	60.375	63.158	0.00	0.00	0.00	3.51
244	246	3.637273	GGACCCAACAGCCCGACT	61.637	66.667	0.00	0.00	0.00	4.18
274	276	1.476845	TATGGCGCGGATATGGGTGT	61.477	55.000	8.83	0.00	0.00	4.16
275	277	0.107703	ATATGGCGCGGATATGGGTG	60.108	55.000	8.83	0.00	0.00	4.61
276	278	0.618458	AATATGGCGCGGATATGGGT	59.382	50.000	8.83	0.00	0.00	4.51
288	300	2.223876	CCATGTCCAGCACAAATATGGC	60.224	50.000	0.00	0.00	38.97	4.40
318	330	0.036010	CTCAAATGTCCGGGCTGACT	60.036	55.000	7.97	0.00	36.21	3.41
328	340	1.200020	CTCAAACGGCCCTCAAATGTC	59.800	52.381	0.00	0.00	0.00	3.06
329	341	1.202879	TCTCAAACGGCCCTCAAATGT	60.203	47.619	0.00	0.00	0.00	2.71
331	343	1.614317	CCTCTCAAACGGCCCTCAAAT	60.614	52.381	0.00	0.00	0.00	2.32
356	368	2.504367	CCTCACGATTTTTGACCCAGT	58.496	47.619	0.00	0.00	0.00	4.00
405	418	1.235724	CCCTCAAACCCGTCTCAAAC	58.764	55.000	0.00	0.00	0.00	2.93
413	426	4.404098	CCGGACCCCTCAAACCCG	62.404	72.222	0.00	0.00	39.85	5.28
415	428	1.602605	CAACCGGACCCCTCAAACC	60.603	63.158	9.46	0.00	0.00	3.27
477	490	3.701542	TGCCTCACGAAGAATAGATGTCT	59.298	43.478	0.00	0.00	0.00	3.41
492	505	2.618241	TGTCTTCACAAACATGCCTCAC	59.382	45.455	0.00	0.00	0.00	3.51
543	556	6.237901	TCAATATCACAGGCTACAACTGTTT	58.762	36.000	0.00	0.00	46.38	2.83
588	601	6.356757	GCTAGAAAGAGCTTAATTCACCTG	57.643	41.667	0.00	0.19	39.50	4.00
620	638	1.745890	CATGGCATGCATCCCCTTG	59.254	57.895	21.36	8.98	0.00	3.61
647	673	1.552792	GGCACCAGAAGCTCTCTAAGT	59.447	52.381	0.00	0.00	31.12	2.24
690	716	1.525619	GTTCAGGCACACGTACAGAAC	59.474	52.381	0.00	0.00	0.00	3.01
693	719	1.282248	CGGTTCAGGCACACGTACAG	61.282	60.000	0.00	0.00	0.00	2.74
717	743	1.323534	GTACAACCTATGCACTTCGCG	59.676	52.381	0.00	0.00	46.97	5.87
720	746	6.531948	CAGAGTAAGTACAACCTATGCACTTC	59.468	42.308	0.00	0.00	40.88	3.01
752	778	3.198635	TGTTCTCATCTCCTCCATTGGAC	59.801	47.826	0.00	0.00	31.94	4.02
891	919	8.777578	TGAGTTAAGAGGATTGCTTAGGTATA	57.222	34.615	0.00	0.00	0.00	1.47
948	979	1.589993	CGCAGTAGAGATGGCACGG	60.590	63.158	0.00	0.00	0.00	4.94
965	996	1.666189	TCACTAGCTCGATCACACTCG	59.334	52.381	0.00	0.00	39.99	4.18
1353	1384	2.688666	AGGGCGGCCTTGATCTCA	60.689	61.111	27.45	0.00	0.00	3.27
1459	1490	0.808453	ACGTTGTGTTGCTAGTGCGT	60.808	50.000	0.00	0.00	43.34	5.24
1461	1492	2.468532	AAACGTTGTGTTGCTAGTGC	57.531	45.000	0.00	0.00	40.84	4.40
1462	1493	3.753842	ACAAAACGTTGTGTTGCTAGTG	58.246	40.909	18.50	0.00	46.40	2.74
1476	1514	5.701029	AAGAAAACAATGCTCACAAAACG	57.299	34.783	0.00	0.00	0.00	3.60
1478	1516	7.095910	TGAGAAAGAAAACAATGCTCACAAAA	58.904	30.769	0.00	0.00	0.00	2.44
1509	1547	6.421485	AGTTCATCAAGGCAAATCAGTATCT	58.579	36.000	0.00	0.00	0.00	1.98
1510	1548	6.690194	AGTTCATCAAGGCAAATCAGTATC	57.310	37.500	0.00	0.00	0.00	2.24
1513	1551	5.796424	AAAGTTCATCAAGGCAAATCAGT	57.204	34.783	0.00	0.00	0.00	3.41
1514	1552	6.095377	GGTAAAGTTCATCAAGGCAAATCAG	58.905	40.000	0.00	0.00	0.00	2.90
1611	1652	2.035442	GGTTGTTGGAGCCGCTCTC	61.035	63.158	19.68	10.57	41.15	3.20
1612	1653	2.032681	GGTTGTTGGAGCCGCTCT	59.967	61.111	19.68	0.00	0.00	4.09
2039	2088	3.063084	GCAGGACCTCGTCGGAGT	61.063	66.667	0.00	0.00	38.70	3.85
2173	2222	3.554692	GATCTCGCCGTTGTGCCG	61.555	66.667	0.00	0.00	0.00	5.69
2244	2293	1.445582	ACGACGAAATCACCGGCTC	60.446	57.895	0.00	0.00	31.81	4.70
2313	2362	9.561069	ACACATACAGTACTTGAAAGAATCTTT	57.439	29.630	8.12	8.12	0.00	2.52
2314	2363	8.993121	CACACATACAGTACTTGAAAGAATCTT	58.007	33.333	0.00	0.00	0.00	2.40
2315	2364	8.150945	ACACACATACAGTACTTGAAAGAATCT	58.849	33.333	0.00	0.00	0.00	2.40
2316	2365	8.223769	CACACACATACAGTACTTGAAAGAATC	58.776	37.037	0.00	0.00	0.00	2.52
2317	2366	7.931407	TCACACACATACAGTACTTGAAAGAAT	59.069	33.333	0.00	0.00	0.00	2.40
2401	2450	1.677576	TCAACAAGCAGTGCAAGAAGG	59.322	47.619	19.20	2.08	0.00	3.46
2498	2547	5.814705	GTGGAACAGAGATATCCAGTTGAAG	59.185	44.000	9.07	0.00	43.59	3.02
2549	2598	4.148348	CGAAAAGAGTACGACTTGTTGAGG	59.852	45.833	8.61	0.00	0.00	3.86
2551	2600	4.675510	ACGAAAAGAGTACGACTTGTTGA	58.324	39.130	15.39	0.00	0.00	3.18
2555	2604	7.329438	TGAATTACGAAAAGAGTACGACTTG	57.671	36.000	8.61	1.43	0.00	3.16
2558	2607	9.247562	GAATTTGAATTACGAAAAGAGTACGAC	57.752	33.333	0.00	0.00	0.00	4.34
2560	2609	8.225107	TGGAATTTGAATTACGAAAAGAGTACG	58.775	33.333	0.00	0.00	31.64	3.67
2564	2613	8.970691	ATGTGGAATTTGAATTACGAAAAGAG	57.029	30.769	0.00	0.00	31.64	2.85
2633	2686	7.939784	AGACAGATGGCGTATATATTGTAGA	57.060	36.000	0.00	0.00	0.00	2.59
2647	2700	7.038658	AGGGAGTATATCTTAAAGACAGATGGC	60.039	40.741	0.00	0.00	32.94	4.40
2688	2741	0.673333	TCAATGTGCTTCGCCGTCAT	60.673	50.000	0.00	0.00	0.00	3.06
2689	2742	1.301322	TCAATGTGCTTCGCCGTCA	60.301	52.632	0.00	0.00	0.00	4.35
2690	2743	1.132640	GTCAATGTGCTTCGCCGTC	59.867	57.895	0.00	0.00	0.00	4.79
2691	2744	0.037697	TAGTCAATGTGCTTCGCCGT	60.038	50.000	0.00	0.00	0.00	5.68
2692	2745	1.258982	GATAGTCAATGTGCTTCGCCG	59.741	52.381	0.00	0.00	0.00	6.46
2693	2746	1.258982	CGATAGTCAATGTGCTTCGCC	59.741	52.381	0.00	0.00	0.00	5.54
2694	2747	2.034507	GTCGATAGTCAATGTGCTTCGC	60.035	50.000	0.00	0.00	37.40	4.70
2695	2748	2.214244	CGTCGATAGTCAATGTGCTTCG	59.786	50.000	0.00	0.00	37.40	3.79
2696	2749	3.179830	ACGTCGATAGTCAATGTGCTTC	58.820	45.455	0.00	0.00	37.40	3.86
2697	2750	3.232213	ACGTCGATAGTCAATGTGCTT	57.768	42.857	0.00	0.00	37.40	3.91
2698	2751	2.941453	ACGTCGATAGTCAATGTGCT	57.059	45.000	0.00	0.00	37.40	4.40
2699	2752	2.462927	CGTACGTCGATAGTCAATGTGC	59.537	50.000	7.22	0.00	42.86	4.57
2700	2753	3.931824	TCGTACGTCGATAGTCAATGTG	58.068	45.455	16.05	0.00	44.01	3.21
2713	2766	2.105466	AGCCTCGAGGTCGTACGTC	61.105	63.158	31.43	12.96	40.80	4.34
2860	2915	2.477375	GAGTAAAAACGATCCACACGCA	59.523	45.455	0.00	0.00	0.00	5.24
2974	3029	0.686789	CCATAGGACCGATGGCATCA	59.313	55.000	25.88	6.84	37.64	3.07
2977	3032	0.180171	CAACCATAGGACCGATGGCA	59.820	55.000	28.23	0.00	46.76	4.92

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.