AutoCloner

Multiple sequence alignment - TraesCS5A01G108500

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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	TraesCS5A01G108500	chr5A	100.000	5069	0	0	431	5499	194455623	194450555	0.000000e+00	9361.0
1	TraesCS5A01G108500	chr5A	100.000	96	0	0	1	96	194456053	194455958	1.570000e-40	178.0
2	TraesCS5A01G108500	chr5B	96.472	4734	129	14	632	5355	185218510	185223215	0.000000e+00	7782.0
3	TraesCS5A01G108500	chr5B	92.199	141	7	2	489	629	185218293	185218429	4.350000e-46	196.0
4	TraesCS5A01G108500	chr5B	98.947	95	1	0	1	95	185217665	185217759	2.630000e-38	171.0
5	TraesCS5A01G108500	chr5B	91.209	91	7	1	5351	5441	185223387	185223476	7.480000e-24	122.0
6	TraesCS5A01G108500	chr5D	97.307	4531	102	11	431	4956	173591112	173586597	0.000000e+00	7673.0
7	TraesCS5A01G108500	chr5D	97.163	141	4	0	5085	5225	173584919	173584779	7.120000e-59	239.0
8	TraesCS5A01G108500	chr5D	93.846	130	4	1	5228	5357	173584661	173584536	5.620000e-45	193.0
9	TraesCS5A01G108500	chr5D	100.000	96	0	0	1	96	173591678	173591583	1.570000e-40	178.0
10	TraesCS5A01G108500	chrUn	82.138	1478	190	44	1899	3344	42443336	42441901	0.000000e+00	1199.0
11	TraesCS5A01G108500	chrUn	82.877	1279	166	33	634	1883	42444575	42443321	0.000000e+00	1099.0
12	TraesCS5A01G108500	chrUn	82.799	1279	167	33	634	1883	327871882	327870628	0.000000e+00	1094.0
13	TraesCS5A01G108500	chrUn	81.086	1179	147	32	3374	4503	42441841	42440690	0.000000e+00	872.0
14	TraesCS5A01G108500	chrUn	82.212	1040	133	30	1899	2924	327870643	327869642	0.000000e+00	848.0
15	TraesCS5A01G108500	chr3D	82.974	1251	158	29	647	1874	606858713	606859931	0.000000e+00	1079.0
16	TraesCS5A01G108500	chr3D	82.043	1175	142	31	3374	4503	606861405	606862555	0.000000e+00	937.0
17	TraesCS5A01G108500	chr3D	84.386	839	104	17	1900	2725	606859926	606860750	0.000000e+00	798.0
18	TraesCS5A01G108500	chr3D	82.545	613	72	21	2752	3344	606860748	606861345	1.770000e-139	507.0
19	TraesCS5A01G108500	chr3D	92.593	108	5	2	4974	5079	61194673	61194779	9.540000e-33	152.0
20	TraesCS5A01G108500	chr3D	94.915	59	3	0	5441	5499	103161982	103161924	5.870000e-15	93.5
21	TraesCS5A01G108500	chr3A	84.536	1067	130	21	839	1883	739118085	739119138	0.000000e+00	1024.0
22	TraesCS5A01G108500	chr3A	81.350	1185	136	34	3374	4503	739120626	739121780	0.000000e+00	885.0
23	TraesCS5A01G108500	chr3A	82.265	936	120	28	1900	2828	739119124	739120020	0.000000e+00	767.0
24	TraesCS5A01G108500	chr3A	81.786	571	65	21	2790	3344	739120019	739120566	5.060000e-120	442.0
25	TraesCS5A01G108500	chr1B	93.939	99	4	1	4973	5069	572529358	572529456	1.230000e-31	148.0
26	TraesCS5A01G108500	chr4D	90.826	109	7	2	4973	5078	375135019	375134911	5.740000e-30	143.0
27	TraesCS5A01G108500	chr4D	93.220	59	4	0	5441	5499	178776667	178776609	2.730000e-13	87.9
28	TraesCS5A01G108500	chr1D	91.509	106	6	2	4973	5075	490538213	490538108	5.740000e-30	143.0
29	TraesCS5A01G108500	chr1D	93.548	62	4	0	5438	5499	128914110	128914171	5.870000e-15	93.5
30	TraesCS5A01G108500	chr1D	93.548	62	4	0	5438	5499	129092123	129092184	5.870000e-15	93.5
31	TraesCS5A01G108500	chr1D	94.915	59	3	0	5441	5499	147064528	147064470	5.870000e-15	93.5
32	TraesCS5A01G108500	chr2B	90.654	107	8	1	4972	5076	63293189	63293083	2.070000e-29	141.0
33	TraesCS5A01G108500	chr2B	87.931	116	12	1	4972	5085	719528562	719528677	9.610000e-28	135.0
34	TraesCS5A01G108500	chr2D	89.286	112	10	1	4973	5082	235244398	235244287	7.430000e-29	139.0
35	TraesCS5A01G108500	chr2D	91.935	62	5	0	5438	5499	383694183	383694244	2.730000e-13	87.9
36	TraesCS5A01G108500	chr2A	89.720	107	9	2	4971	5076	78840673	78840568	9.610000e-28	135.0
37	TraesCS5A01G108500	chr6A	92.188	64	3	2	5438	5499	219240749	219240812	7.590000e-14	89.8
38	TraesCS5A01G108500	chr4B	93.333	60	4	0	5440	5499	365968192	365968251	7.590000e-14	89.8
39	TraesCS5A01G108500	chr6D	88.571	70	7	1	5431	5499	241661000	241661069	3.530000e-12	84.2

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	TraesCS5A01G108500	chr5A	194450555	194456053	5498	True	4769.500000	9361	100.000000	1	5499	2	chr5A.!!$R1	5498
1	TraesCS5A01G108500	chr5B	185217665	185223476	5811	False	2067.750000	7782	94.706750	1	5441	4	chr5B.!!$F1	5440
2	TraesCS5A01G108500	chr5D	173584536	173591678	7142	True	2070.750000	7673	97.079000	1	5357	4	chr5D.!!$R1	5356
3	TraesCS5A01G108500	chrUn	42440690	42444575	3885	True	1056.666667	1199	82.033667	634	4503	3	chrUn.!!$R1	3869
4	TraesCS5A01G108500	chrUn	327869642	327871882	2240	True	971.000000	1094	82.505500	634	2924	2	chrUn.!!$R2	2290
5	TraesCS5A01G108500	chr3D	606858713	606862555	3842	False	830.250000	1079	82.987000	647	4503	4	chr3D.!!$F2	3856
6	TraesCS5A01G108500	chr3A	739118085	739121780	3695	False	779.500000	1024	82.484250	839	4503	4	chr3A.!!$F1	3664

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
455	592	3.749665	TGGAGATTTTGTTTGCCCAAG	57.250	42.857	0.0	0.0	0.00	3.61	F
1161	1398	0.319555	CGACAGCGAAAGGGAAGACA	60.320	55.000	0.0	0.0	40.82	3.41	F
1681	1926	1.070134	TCTTTCACGGAAGGACCACAG	59.930	52.381	0.0	0.0	38.90	3.66	F
2115	2366	1.539157	TGGCAATCCGCAAATGTGTA	58.461	45.000	0.0	0.0	45.17	2.90	F
3147	3464	4.005650	TGAAGCTCTATCTTTGCAGGTTG	58.994	43.478	0.0	0.0	0.00	3.77	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1829	2079	0.254462	TGACCAGACAACCAGCAACA	59.746	50.000	0.0	0.0	0.00	3.33	R
2679	2944	2.037251	GAGTTGAGCTTGGACAGGTGTA	59.963	50.000	0.0	0.0	31.44	2.90	R
3377	3730	2.030893	TGGCAGCAGAAAGAATCAAACG	60.031	45.455	0.0	0.0	0.00	3.60	R
3771	4124	2.884639	TCAAGGAAAGGCTTGTTAGTGC	59.115	45.455	0.0	0.0	32.83	4.40	R
4597	5003	1.082756	CGGACAAACAACAGCTCGC	60.083	57.895	0.0	0.0	0.00	5.03	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
455	592	3.749665	TGGAGATTTTGTTTGCCCAAG	57.250	42.857	0.00	0.00	0.00	3.61
490	631	7.148672	CGATCTGTCAAAATATAGATGCAGGAC	60.149	40.741	0.00	0.00	30.49	3.85
494	635	5.753438	GTCAAAATATAGATGCAGGACGTGA	59.247	40.000	0.00	0.00	0.00	4.35
516	657	6.736853	GTGACATTACATTTTCTTCTACGTGC	59.263	38.462	0.00	0.00	0.00	5.34
615	756	9.598517	TGCAAAAGAAAAAGAACATTATCAGTT	57.401	25.926	0.00	0.00	0.00	3.16
782	1004	8.281212	ACTAATCGGTTGCTTCTATGATTTTT	57.719	30.769	0.00	0.00	0.00	1.94
783	1005	9.391006	ACTAATCGGTTGCTTCTATGATTTTTA	57.609	29.630	0.00	0.00	0.00	1.52
844	1067	6.123651	TCCTCTCAGTAGACTGGATAAACTC	58.876	44.000	9.73	0.00	43.91	3.01
948	1185	5.997746	TGCTACTTCTTGCTATCTTGTTTGT	59.002	36.000	0.00	0.00	0.00	2.83
974	1211	4.219944	AGTGCATGAATCCATAATGCCATC	59.780	41.667	0.00	0.00	44.86	3.51
1023	1260	4.536765	TGGCTTCAAGAAAGGATATTCCC	58.463	43.478	0.00	0.00	37.19	3.97
1122	1359	4.404098	CACCCCGCACTGGTACCC	62.404	72.222	10.07	0.00	33.84	3.69
1161	1398	0.319555	CGACAGCGAAAGGGAAGACA	60.320	55.000	0.00	0.00	40.82	3.41
1412	1651	8.951243	ACTAAATGAAGAGCTATTTCCTTTGTC	58.049	33.333	16.85	0.00	0.00	3.18
1418	1657	4.043435	AGAGCTATTTCCTTTGTCCCAGTT	59.957	41.667	0.00	0.00	0.00	3.16
1630	1875	4.154195	GGTCGTTGTTGCAGAATACTGAAT	59.846	41.667	0.00	0.00	46.03	2.57
1668	1913	4.925646	GGTTTTCATGAGGCATTCTTTCAC	59.074	41.667	0.00	0.00	0.00	3.18
1674	1919	1.740025	GAGGCATTCTTTCACGGAAGG	59.260	52.381	0.00	0.00	0.00	3.46
1676	1921	1.468914	GGCATTCTTTCACGGAAGGAC	59.531	52.381	0.00	0.00	27.67	3.85
1681	1926	1.070134	TCTTTCACGGAAGGACCACAG	59.930	52.381	0.00	0.00	38.90	3.66
1977	2228	9.030301	GTAAATGTTTTGTGCACTACTCATTTT	57.970	29.630	28.33	18.89	36.28	1.82
1981	2232	6.529829	TGTTTTGTGCACTACTCATTTTTGAC	59.470	34.615	19.41	0.00	0.00	3.18
2105	2356	4.898829	TGACAAAGATAATGGCAATCCG	57.101	40.909	0.00	0.00	31.44	4.18
2115	2366	1.539157	TGGCAATCCGCAAATGTGTA	58.461	45.000	0.00	0.00	45.17	2.90
2210	2464	5.048154	GGAGAGTTTCTACTGTTTAGACGGT	60.048	44.000	3.06	3.06	46.81	4.83
2631	2896	6.778069	TGGATGTGTGTTTTTATGGAAGGTAA	59.222	34.615	0.00	0.00	0.00	2.85
2668	2933	6.227298	TCATTTCACAGAGAGGAATAGACC	57.773	41.667	0.00	0.00	0.00	3.85
3147	3464	4.005650	TGAAGCTCTATCTTTGCAGGTTG	58.994	43.478	0.00	0.00	0.00	3.77
3547	3900	4.134563	GACCAGGTACTTGTTTCATGTGT	58.865	43.478	4.10	0.00	33.14	3.72
3771	4124	6.539649	TTCCAATACGAAGTTTCTGTTCAG	57.460	37.500	0.00	0.00	37.78	3.02
4131	4488	9.733556	TCTATACACCATGTGAACAAGTATTTT	57.266	29.630	0.49	0.00	36.96	1.82
4252	4612	1.398692	GAACTTCAGGGCAACACCAA	58.601	50.000	0.00	0.00	42.05	3.67
4288	4651	5.751243	AATGCCATACGTGAAAAGTATCC	57.249	39.130	0.00	0.00	39.50	2.59
4585	4991	0.755686	CCCCTCTGATCTAGGTGTGC	59.244	60.000	12.10	0.00	31.70	4.57
4597	5003	1.961277	GGTGTGCTGTGTTCTCCGG	60.961	63.158	0.00	0.00	0.00	5.14
4749	5155	7.780271	TGATCCTATCTGTATAATATCTGCCGT	59.220	37.037	0.00	0.00	0.00	5.68
4905	5311	5.051816	TGTAAATGTAGCCTATGTTACGCC	58.948	41.667	0.00	0.00	31.38	5.68
4975	7003	5.409826	GCCAGTAGGTAGCTTTATGCAATAG	59.590	44.000	0.00	0.00	40.02	1.73
4983	7011	3.718956	AGCTTTATGCAATAGTCCCTCCT	59.281	43.478	0.00	0.00	45.94	3.69
4997	7027	4.017126	GTCCCTCCTTCCCAAAATAAGTG	58.983	47.826	0.00	0.00	0.00	3.16
5010	7040	9.059260	TCCCAAAATAAGTGTCAACTTTAGTAC	57.941	33.333	0.00	0.00	44.47	2.73
5057	7087	6.635030	AACTTGAGACACTTATTTTGGGAC	57.365	37.500	0.00	0.00	0.00	4.46
5063	7093	2.290705	ACACTTATTTTGGGACGGAGGG	60.291	50.000	0.00	0.00	0.00	4.30
5075	7105	3.258622	GGGACGGAGGGAGTATGATTTAG	59.741	52.174	0.00	0.00	0.00	1.85
5155	7185	2.978156	TGAGAAGGAAGGTGGCAATT	57.022	45.000	0.00	0.00	0.00	2.32
5225	7255	7.666804	TGATTGTGACATAAGGGATATTGGATG	59.333	37.037	0.00	0.00	0.00	3.51
5248	7393	3.806949	TGGGTCTCTTTTACTTGGCAT	57.193	42.857	0.00	0.00	0.00	4.40
5263	7408	9.747898	TTTACTTGGCATAGAGGAAAAATAAGA	57.252	29.630	0.00	0.00	0.00	2.10
5264	7409	7.872113	ACTTGGCATAGAGGAAAAATAAGAG	57.128	36.000	0.00	0.00	0.00	2.85
5349	7494	6.268847	AGCCTTAGAGAACCTGGAGTATAATG	59.731	42.308	0.00	0.00	0.00	1.90
5362	7682	4.382147	GGAGTATAATGATTCGGAGGCTCC	60.382	50.000	24.06	24.06	33.17	4.70
5380	7700	3.462021	CTCCGAGAGATGAAATGTTCCC	58.538	50.000	0.00	0.00	0.00	3.97
5382	7702	2.159099	CCGAGAGATGAAATGTTCCCGA	60.159	50.000	0.00	0.00	0.00	5.14
5421	7741	0.404426	GGACAAGGTAAGGGCTGGTT	59.596	55.000	0.00	0.00	0.00	3.67
5442	7762	8.803397	TGGTTCTACAGCGATATGTATATACT	57.197	34.615	13.89	2.84	35.21	2.12
5443	7763	9.895138	TGGTTCTACAGCGATATGTATATACTA	57.105	33.333	13.89	4.82	35.21	1.82
5462	7782	9.929180	ATATACTAATAAGGTACATGTGCAGTG	57.071	33.333	16.11	0.00	0.00	3.66
5463	7783	4.876107	ACTAATAAGGTACATGTGCAGTGC	59.124	41.667	16.11	8.58	0.00	4.40
5464	7784	2.849294	TAAGGTACATGTGCAGTGCA	57.151	45.000	15.37	15.37	35.60	4.57
5473	7793	2.030862	TGCAGTGCACGCATGAGA	59.969	55.556	25.28	8.77	33.55	3.27
5474	7794	1.376295	TGCAGTGCACGCATGAGAT	60.376	52.632	25.28	0.00	33.55	2.75
5475	7795	0.956902	TGCAGTGCACGCATGAGATT	60.957	50.000	25.28	0.00	33.55	2.40
5476	7796	0.169672	GCAGTGCACGCATGAGATTT	59.830	50.000	22.75	0.00	0.00	2.17
5477	7797	1.891178	CAGTGCACGCATGAGATTTG	58.109	50.000	12.01	0.00	0.00	2.32
5478	7798	0.806868	AGTGCACGCATGAGATTTGG	59.193	50.000	12.01	0.00	0.00	3.28
5479	7799	0.799534	GTGCACGCATGAGATTTGGC	60.800	55.000	0.00	0.00	0.00	4.52
5480	7800	1.242665	TGCACGCATGAGATTTGGCA	61.243	50.000	2.50	2.24	0.00	4.92
5481	7801	0.109179	GCACGCATGAGATTTGGCAA	60.109	50.000	2.50	0.00	0.00	4.52
5482	7802	1.621107	CACGCATGAGATTTGGCAAC	58.379	50.000	2.50	0.00	0.00	4.17
5483	7803	0.527565	ACGCATGAGATTTGGCAACC	59.472	50.000	2.50	0.00	0.00	3.77
5484	7804	0.527113	CGCATGAGATTTGGCAACCA	59.473	50.000	0.00	0.00	0.00	3.67
5485	7805	1.067706	CGCATGAGATTTGGCAACCAA	60.068	47.619	0.00	0.00	42.29	3.67
5486	7806	2.340337	GCATGAGATTTGGCAACCAAC	58.660	47.619	0.00	0.00	43.82	3.77
5487	7807	2.028748	GCATGAGATTTGGCAACCAACT	60.029	45.455	0.00	0.00	43.82	3.16
5488	7808	3.555586	GCATGAGATTTGGCAACCAACTT	60.556	43.478	0.00	0.00	43.82	2.66
5489	7809	4.321899	GCATGAGATTTGGCAACCAACTTA	60.322	41.667	0.00	0.00	43.82	2.24
5490	7810	5.625197	GCATGAGATTTGGCAACCAACTTAT	60.625	40.000	0.00	0.00	43.82	1.73
5491	7811	5.389859	TGAGATTTGGCAACCAACTTATG	57.610	39.130	0.00	0.00	43.82	1.90
5492	7812	5.076182	TGAGATTTGGCAACCAACTTATGA	58.924	37.500	0.00	0.00	43.82	2.15
5493	7813	5.538053	TGAGATTTGGCAACCAACTTATGAA	59.462	36.000	0.00	0.00	43.82	2.57
5494	7814	6.211184	TGAGATTTGGCAACCAACTTATGAAT	59.789	34.615	0.00	0.00	43.82	2.57
5495	7815	7.395772	TGAGATTTGGCAACCAACTTATGAATA	59.604	33.333	0.00	0.00	43.82	1.75
5496	7816	8.133024	AGATTTGGCAACCAACTTATGAATAA	57.867	30.769	0.00	0.00	43.82	1.40
5497	7817	8.592809	AGATTTGGCAACCAACTTATGAATAAA	58.407	29.630	0.00	0.00	43.82	1.40
5498	7818	9.382275	GATTTGGCAACCAACTTATGAATAAAT	57.618	29.630	0.00	0.00	43.82	1.40

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
490	631	6.948228	CACGTAGAAGAAAATGTAATGTCACG	59.052	38.462	0.00	0.00	0.00	4.35
494	635	6.092259	GGAGCACGTAGAAGAAAATGTAATGT	59.908	38.462	0.00	0.00	0.00	2.71
516	657	3.996150	AGTCTTGCACAAAACATGGAG	57.004	42.857	0.00	0.00	0.00	3.86
711	931	9.743057	TTCAACAAATTACTTTCTGGTATTGTG	57.257	29.630	0.00	0.00	30.32	3.33
782	1004	9.261035	AGAGAAACAGTAAATTCCTCAGATCTA	57.739	33.333	0.00	0.00	0.00	1.98
783	1005	8.144862	AGAGAAACAGTAAATTCCTCAGATCT	57.855	34.615	0.00	0.00	0.00	2.75
974	1211	4.082125	AGCCTGACTGGGTTAAAATGAAG	58.918	43.478	0.00	0.00	45.67	3.02
1023	1260	1.133025	CCTTGGCAAGCAATAAGGACG	59.867	52.381	21.77	0.10	41.71	4.79
1056	1293	0.504384	CAACTTGAGCTCGTGTGACG	59.496	55.000	9.64	0.00	44.19	4.35
1122	1359	3.062909	TCGGTTTTTGTTCAGTTCTCACG	59.937	43.478	0.00	0.00	0.00	4.35
1161	1398	1.203001	TCATCCAAAGCTCCCCGTTTT	60.203	47.619	0.00	0.00	0.00	2.43
1381	1620	9.692325	AGGAAATAGCTCTTCATTTAGTTGAAT	57.308	29.630	9.90	0.00	35.20	2.57
1382	1621	9.520515	AAGGAAATAGCTCTTCATTTAGTTGAA	57.479	29.630	9.90	0.00	34.55	2.69
1396	1635	3.956744	ACTGGGACAAAGGAAATAGCTC	58.043	45.455	0.00	0.00	38.70	4.09
1412	1651	4.366684	GGGTGGGCCTCAACTGGG	62.367	72.222	4.53	0.00	32.53	4.45
1418	1657	2.525592	CCTTTTGGGTGGGCCTCA	59.474	61.111	4.53	0.00	35.46	3.86
1630	1875	1.518367	AAACCACTCTCCCTGTTCCA	58.482	50.000	0.00	0.00	0.00	3.53
1668	1913	1.776662	TATCTCCTGTGGTCCTTCCG	58.223	55.000	0.00	0.00	39.52	4.30
1674	1919	7.308435	CAGTTTCAAATTTATCTCCTGTGGTC	58.692	38.462	0.00	0.00	0.00	4.02
1676	1921	6.071728	AGCAGTTTCAAATTTATCTCCTGTGG	60.072	38.462	0.00	0.00	0.00	4.17
1681	1926	8.730680	TGAGTTAGCAGTTTCAAATTTATCTCC	58.269	33.333	0.00	0.00	0.00	3.71
1829	2079	0.254462	TGACCAGACAACCAGCAACA	59.746	50.000	0.00	0.00	0.00	3.33
2105	2356	4.741676	GCAGCATAGGAAATACACATTTGC	59.258	41.667	0.00	0.00	41.42	3.68
2115	2366	7.102346	GTGTATATCTCTGCAGCATAGGAAAT	58.898	38.462	9.47	2.79	0.00	2.17
2505	2762	4.433186	TGCTCAATCGTAAAAACATGGG	57.567	40.909	0.00	0.00	0.00	4.00
2596	2859	2.309613	ACACACATCCACATGCAACTT	58.690	42.857	0.00	0.00	32.57	2.66
2631	2896	3.760684	GTGAAATGAATGGGCAGAGTTCT	59.239	43.478	0.00	0.00	0.00	3.01
2678	2943	2.438021	AGTTGAGCTTGGACAGGTGTAA	59.562	45.455	0.00	0.00	31.44	2.41
2679	2944	2.037251	GAGTTGAGCTTGGACAGGTGTA	59.963	50.000	0.00	0.00	31.44	2.90
3044	3354	4.164030	ACAAAAGAAAATGCAGGTTTCCCT	59.836	37.500	17.64	6.91	44.02	4.20
3147	3464	4.695455	TGGCACAAGTTTATACTCTTCAGC	59.305	41.667	0.00	0.00	31.99	4.26
3377	3730	2.030893	TGGCAGCAGAAAGAATCAAACG	60.031	45.455	0.00	0.00	0.00	3.60
3771	4124	2.884639	TCAAGGAAAGGCTTGTTAGTGC	59.115	45.455	0.00	0.00	32.83	4.40
4030	4387	3.582647	TGTCCATCTGGCAAGAAAGACTA	59.417	43.478	19.35	8.01	38.46	2.59
4252	4612	1.152756	GCATTAAGGGGGCATCGGT	60.153	57.895	0.00	0.00	0.00	4.69
4288	4651	3.573598	TGATTGCATACCTTTTTGTGCG	58.426	40.909	0.00	0.00	40.34	5.34
4384	4777	6.636447	CACATTCAAACTGCAACGAGAAATAA	59.364	34.615	0.00	0.00	0.00	1.40
4585	4991	2.811317	GCTCGCCGGAGAACACAG	60.811	66.667	9.83	0.00	43.27	3.66
4597	5003	1.082756	CGGACAAACAACAGCTCGC	60.083	57.895	0.00	0.00	0.00	5.03
4749	5155	6.542852	GCAAATCTACGTTAAATCAAGCAGA	58.457	36.000	0.00	0.00	0.00	4.26
4905	5311	7.750903	ACAAAGAAAAGAAAACTCTTCTGTTCG	59.249	33.333	10.36	2.27	43.91	3.95
4975	7003	4.017126	CACTTATTTTGGGAAGGAGGGAC	58.983	47.826	0.00	0.00	0.00	4.46
4983	7011	8.528044	ACTAAAGTTGACACTTATTTTGGGAA	57.472	30.769	0.00	0.00	42.89	3.97
5032	7062	7.041644	CGTCCCAAAATAAGTGTCTCAAGTTTA	60.042	37.037	0.00	0.00	0.00	2.01
5057	7087	6.651975	AGTTACTAAATCATACTCCCTCCG	57.348	41.667	0.00	0.00	0.00	4.63
5075	7105	4.430908	CCACGGGAGAGTTTCATAGTTAC	58.569	47.826	0.00	0.00	0.00	2.50
5136	7166	2.108075	TGAATTGCCACCTTCCTTCTCA	59.892	45.455	0.00	0.00	0.00	3.27
5155	7185	2.672874	GCATGTACTGTTGCGATCTTGA	59.327	45.455	0.00	0.00	0.00	3.02
5225	7255	4.585879	TGCCAAGTAAAAGAGACCCATAC	58.414	43.478	0.00	0.00	0.00	2.39
5248	7393	9.403583	GTCTCTCTCTCTCTTATTTTTCCTCTA	57.596	37.037	0.00	0.00	0.00	2.43
5261	7406	2.569853	TCGGTCAAGTCTCTCTCTCTCT	59.430	50.000	0.00	0.00	0.00	3.10
5262	7407	2.936498	CTCGGTCAAGTCTCTCTCTCTC	59.064	54.545	0.00	0.00	0.00	3.20
5263	7408	2.355716	CCTCGGTCAAGTCTCTCTCTCT	60.356	54.545	0.00	0.00	0.00	3.10
5264	7409	2.014128	CCTCGGTCAAGTCTCTCTCTC	58.986	57.143	0.00	0.00	0.00	3.20
5362	7682	3.165058	TCGGGAACATTTCATCTCTCG	57.835	47.619	0.00	0.00	0.00	4.04
5380	7700	1.339235	CGCTGCTTGCACCATTTTCG	61.339	55.000	0.00	0.00	43.06	3.46
5382	7702	0.598158	CACGCTGCTTGCACCATTTT	60.598	50.000	0.00	0.00	43.06	1.82
5436	7756	9.929180	CACTGCACATGTACCTTATTAGTATAT	57.071	33.333	0.00	0.00	0.00	0.86
5441	7761	4.875536	TGCACTGCACATGTACCTTATTAG	59.124	41.667	0.00	0.00	31.71	1.73
5442	7762	4.837972	TGCACTGCACATGTACCTTATTA	58.162	39.130	0.00	0.00	31.71	0.98
5443	7763	3.684908	TGCACTGCACATGTACCTTATT	58.315	40.909	0.00	0.00	31.71	1.40
5444	7764	3.348647	TGCACTGCACATGTACCTTAT	57.651	42.857	0.00	0.00	31.71	1.73
5445	7765	2.849294	TGCACTGCACATGTACCTTA	57.151	45.000	0.00	0.00	31.71	2.69
5446	7766	3.723772	TGCACTGCACATGTACCTT	57.276	47.368	0.00	0.00	31.71	3.50
5457	7777	0.169672	AAATCTCATGCGTGCACTGC	59.830	50.000	21.49	21.49	0.00	4.40
5458	7778	1.466866	CCAAATCTCATGCGTGCACTG	60.467	52.381	16.19	9.73	0.00	3.66
5459	7779	0.806868	CCAAATCTCATGCGTGCACT	59.193	50.000	16.19	0.00	0.00	4.40
5460	7780	0.799534	GCCAAATCTCATGCGTGCAC	60.800	55.000	6.82	6.82	0.00	4.57
5461	7781	1.242665	TGCCAAATCTCATGCGTGCA	61.243	50.000	0.00	0.00	0.00	4.57
5462	7782	0.109179	TTGCCAAATCTCATGCGTGC	60.109	50.000	0.00	0.00	0.00	5.34
5463	7783	1.621107	GTTGCCAAATCTCATGCGTG	58.379	50.000	0.00	0.00	0.00	5.34
5464	7784	0.527565	GGTTGCCAAATCTCATGCGT	59.472	50.000	0.00	0.00	0.00	5.24
5465	7785	0.527113	TGGTTGCCAAATCTCATGCG	59.473	50.000	0.00	0.00	0.00	4.73
5466	7786	2.028748	AGTTGGTTGCCAAATCTCATGC	60.029	45.455	1.79	0.00	45.73	4.06
5467	7787	3.947910	AGTTGGTTGCCAAATCTCATG	57.052	42.857	1.79	0.00	45.73	3.07
5468	7788	5.716228	TCATAAGTTGGTTGCCAAATCTCAT	59.284	36.000	1.79	0.00	45.73	2.90
5469	7789	5.076182	TCATAAGTTGGTTGCCAAATCTCA	58.924	37.500	1.79	0.00	45.73	3.27
5470	7790	5.643379	TCATAAGTTGGTTGCCAAATCTC	57.357	39.130	1.79	0.00	45.73	2.75
5471	7791	6.610075	ATTCATAAGTTGGTTGCCAAATCT	57.390	33.333	1.79	0.00	45.73	2.40
5472	7792	8.770438	TTTATTCATAAGTTGGTTGCCAAATC	57.230	30.769	1.79	0.00	45.73	2.17

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.