AutoCloner

Multiple sequence alignment - TraesCS3D01G159400

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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	TraesCS3D01G159400	chr3D	100.000	3784	0	0	1	3784	128998507	128994724	0.000000e+00	6988.0
1	TraesCS3D01G159400	chr3D	97.133	558	11	3	1	556	147685594	147686148	0.000000e+00	937.0
2	TraesCS3D01G159400	chr3D	88.843	484	24	13	1	482	53610905	53611360	5.490000e-158	568.0
3	TraesCS3D01G159400	chr3D	95.671	231	10	0	545	775	147686173	147686403	4.620000e-99	372.0
4	TraesCS3D01G159400	chr3D	94.468	235	13	0	545	779	355615548	355615782	2.780000e-96	363.0
5	TraesCS3D01G159400	chr3D	89.362	47	4	1	1971	2016	128996452	128996406	1.470000e-04	58.4
6	TraesCS3D01G159400	chr3D	89.362	47	4	1	2056	2102	128996537	128996492	1.470000e-04	58.4
7	TraesCS3D01G159400	chr3A	94.284	1627	59	16	778	2389	141008373	141009980	0.000000e+00	2459.0
8	TraesCS3D01G159400	chr3A	90.967	941	51	11	2580	3497	141010445	141011374	0.000000e+00	1236.0
9	TraesCS3D01G159400	chr3A	95.876	194	8	0	2388	2581	141010014	141010207	7.890000e-82	315.0
10	TraesCS3D01G159400	chr3A	92.424	198	6	5	3587	3784	141040587	141040775	1.340000e-69	274.0
11	TraesCS3D01G159400	chr3B	89.091	1155	57	28	777	1920	182748261	182747165	0.000000e+00	1371.0
12	TraesCS3D01G159400	chr3B	87.918	687	62	15	2472	3147	182746542	182745866	0.000000e+00	789.0
13	TraesCS3D01G159400	chr3B	85.624	633	52	13	3175	3784	182745872	182745256	2.480000e-176	628.0
14	TraesCS3D01G159400	chr7D	91.957	746	39	11	48	777	184206698	184207438	0.000000e+00	1026.0
15	TraesCS3D01G159400	chr7D	97.674	559	6	5	1	555	40835436	40835991	0.000000e+00	953.0
16	TraesCS3D01G159400	chr7D	96.250	560	16	5	1	556	112043741	112044299	0.000000e+00	913.0
17	TraesCS3D01G159400	chr7D	93.939	561	16	5	1	556	635703160	635703707	0.000000e+00	832.0
18	TraesCS3D01G159400	chr7D	96.930	228	7	0	548	775	517100456	517100229	2.130000e-102	383.0
19	TraesCS3D01G159400	chr1D	90.488	799	36	19	1	777	87089250	87090030	0.000000e+00	1018.0
20	TraesCS3D01G159400	chr4B	96.589	557	16	3	1	556	75123240	75123794	0.000000e+00	920.0
21	TraesCS3D01G159400	chr4B	78.764	518	84	18	1368	1870	520220277	520220783	1.310000e-84	324.0
22	TraesCS3D01G159400	chr4B	80.893	403	56	15	2409	2794	520221462	520221860	7.950000e-77	298.0
23	TraesCS3D01G159400	chr4B	87.023	131	14	3	972	1100	520219623	520219752	1.100000e-30	145.0
24	TraesCS3D01G159400	chr5B	95.161	558	19	4	1	555	681336507	681335955	0.000000e+00	874.0
25	TraesCS3D01G159400	chr2D	93.570	591	19	8	1	574	603607999	603607411	0.000000e+00	863.0
26	TraesCS3D01G159400	chr6D	93.380	574	16	9	1	574	35498387	35497836	0.000000e+00	830.0
27	TraesCS3D01G159400	chr6D	96.957	230	7	0	548	777	31845217	31844988	1.650000e-103	387.0
28	TraesCS3D01G159400	chr6D	95.671	231	9	1	545	775	419629395	419629624	1.660000e-98	370.0
29	TraesCS3D01G159400	chr4D	78.209	670	112	25	1368	2015	423599174	423599831	7.620000e-107	398.0
30	TraesCS3D01G159400	chr4D	80.583	515	77	17	2409	2904	423600211	423600721	3.570000e-100	375.0
31	TraesCS3D01G159400	chr4D	95.671	231	10	0	545	775	49798015	49798245	4.620000e-99	372.0
32	TraesCS3D01G159400	chr5D	96.537	231	8	0	545	775	458756640	458756870	2.130000e-102	383.0
33	TraesCS3D01G159400	chr4A	78.559	569	104	11	1458	2016	40451438	40450878	3.590000e-95	359.0
34	TraesCS3D01G159400	chr4A	79.869	457	73	13	2447	2887	40446199	40445746	2.190000e-82	316.0
35	TraesCS3D01G159400	chr4A	87.500	120	14	1	982	1100	40452784	40452665	1.830000e-28	137.0

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	TraesCS3D01G159400	chr3D	128994724	128998507	3783	True	2368.266667	6988	92.908000	1	3784	3	chr3D.!!$R1	3783
1	TraesCS3D01G159400	chr3D	147685594	147686403	809	False	654.500000	937	96.402000	1	775	2	chr3D.!!$F3	774
2	TraesCS3D01G159400	chr3A	141008373	141011374	3001	False	1336.666667	2459	93.709000	778	3497	3	chr3A.!!$F2	2719
3	TraesCS3D01G159400	chr3B	182745256	182748261	3005	True	929.333333	1371	87.544333	777	3784	3	chr3B.!!$R1	3007
4	TraesCS3D01G159400	chr7D	184206698	184207438	740	False	1026.000000	1026	91.957000	48	777	1	chr7D.!!$F3	729
5	TraesCS3D01G159400	chr7D	40835436	40835991	555	False	953.000000	953	97.674000	1	555	1	chr7D.!!$F1	554
6	TraesCS3D01G159400	chr7D	112043741	112044299	558	False	913.000000	913	96.250000	1	556	1	chr7D.!!$F2	555
7	TraesCS3D01G159400	chr7D	635703160	635703707	547	False	832.000000	832	93.939000	1	556	1	chr7D.!!$F4	555
8	TraesCS3D01G159400	chr1D	87089250	87090030	780	False	1018.000000	1018	90.488000	1	777	1	chr1D.!!$F1	776
9	TraesCS3D01G159400	chr4B	75123240	75123794	554	False	920.000000	920	96.589000	1	556	1	chr4B.!!$F1	555
10	TraesCS3D01G159400	chr4B	520219623	520221860	2237	False	255.666667	324	82.226667	972	2794	3	chr4B.!!$F2	1822
11	TraesCS3D01G159400	chr5B	681335955	681336507	552	True	874.000000	874	95.161000	1	555	1	chr5B.!!$R1	554
12	TraesCS3D01G159400	chr2D	603607411	603607999	588	True	863.000000	863	93.570000	1	574	1	chr2D.!!$R1	573
13	TraesCS3D01G159400	chr6D	35497836	35498387	551	True	830.000000	830	93.380000	1	574	1	chr6D.!!$R2	573
14	TraesCS3D01G159400	chr4D	423599174	423600721	1547	False	386.500000	398	79.396000	1368	2904	2	chr4D.!!$F2	1536
15	TraesCS3D01G159400	chr4A	40450878	40452784	1906	True	248.000000	359	83.029500	982	2016	2	chr4A.!!$R2	1034

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
856	972	0.107654	GAATGTTGGCCTACGCTCCT	60.108	55.0	12.78	0.0	34.44	3.69	F
857	973	0.328258	AATGTTGGCCTACGCTCCTT	59.672	50.0	12.78	0.0	34.44	3.36	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2765	4579	1.067283	ACTCACATCTTCAGCTCCGTG	60.067	52.381	0.00	0.0	0.0	4.94	R
2866	4690	5.062308	GCCGAATGAAACTGTAACTACTGAG	59.938	44.000	1.28	0.0	0.0	3.35	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
423	451	1.848652	AACGAAGAAGATCGGAGGGA	58.151	50.000	1.59	0.00	46.82	4.20
741	857	3.264450	ACTGGGGTCAGATCTCGATTTTT	59.736	43.478	0.00	0.00	43.49	1.94
803	919	2.919859	GCTCCTTTCTAACCGTTACGAC	59.080	50.000	6.24	0.00	0.00	4.34
819	935	1.807573	GACGAAGCGGAAGAGGCTG	60.808	63.158	0.00	0.00	41.39	4.85
856	972	0.107654	GAATGTTGGCCTACGCTCCT	60.108	55.000	12.78	0.00	34.44	3.69
857	973	0.328258	AATGTTGGCCTACGCTCCTT	59.672	50.000	12.78	0.00	34.44	3.36
858	974	0.392998	ATGTTGGCCTACGCTCCTTG	60.393	55.000	12.78	0.00	34.44	3.61
859	975	1.003718	GTTGGCCTACGCTCCTTGT	60.004	57.895	3.32	0.00	34.44	3.16
860	976	1.019805	GTTGGCCTACGCTCCTTGTC	61.020	60.000	3.32	0.00	34.44	3.18
861	977	1.192146	TTGGCCTACGCTCCTTGTCT	61.192	55.000	3.32	0.00	34.44	3.41
862	978	1.142097	GGCCTACGCTCCTTGTCTC	59.858	63.158	0.00	0.00	34.44	3.36
863	979	1.605058	GGCCTACGCTCCTTGTCTCA	61.605	60.000	0.00	0.00	34.44	3.27
864	980	0.461961	GCCTACGCTCCTTGTCTCAT	59.538	55.000	0.00	0.00	0.00	2.90
865	981	1.537135	GCCTACGCTCCTTGTCTCATC	60.537	57.143	0.00	0.00	0.00	2.92
866	982	1.067821	CCTACGCTCCTTGTCTCATCC	59.932	57.143	0.00	0.00	0.00	3.51
867	983	0.738975	TACGCTCCTTGTCTCATCCG	59.261	55.000	0.00	0.00	0.00	4.18
868	984	1.227089	CGCTCCTTGTCTCATCCGG	60.227	63.158	0.00	0.00	0.00	5.14
1137	1312	0.530744	TTGTTCCTGGAGATCCGACG	59.469	55.000	0.00	0.00	39.43	5.12
1206	2289	2.195922	GCATGGCGAAATGTGGAATTC	58.804	47.619	0.00	0.00	0.00	2.17
1225	2314	2.175202	TCTCTTCTCTGAAGGTGAGCC	58.825	52.381	7.37	0.00	0.00	4.70
1284	2374	3.511934	AGAGCTATTCGTATGACCCCATC	59.488	47.826	0.00	0.00	34.31	3.51
1288	2378	2.589798	TTCGTATGACCCCATCGAAC	57.410	50.000	0.00	0.00	37.38	3.95
1290	2380	2.036387	TCGTATGACCCCATCGAACAT	58.964	47.619	0.00	0.00	33.11	2.71
1296	2386	2.835156	TGACCCCATCGAACATGAGTAA	59.165	45.455	0.00	0.00	0.00	2.24
1387	2482	3.449018	AGACAGTTCAGTCACAGTTGAGT	59.551	43.478	0.00	0.00	40.98	3.41
1389	2484	3.195610	ACAGTTCAGTCACAGTTGAGTCA	59.804	43.478	0.00	0.00	32.63	3.41
1544	2649	2.819608	GGAGCTTAATTGTGGCTTGACA	59.180	45.455	0.00	0.00	36.37	3.58
1549	2654	4.487948	CTTAATTGTGGCTTGACACCATG	58.512	43.478	3.97	0.00	39.95	3.66
1600	2705	8.034215	TGATAACAATTAGGTGCTTCAATTTGG	58.966	33.333	0.00	0.00	0.00	3.28
2034	3365	2.875933	CAGGTGAAGTCGCTTGGTTTAA	59.124	45.455	0.00	0.00	30.95	1.52
2052	3383	2.955342	AAGCATTTTTGCCACCCATT	57.045	40.000	0.00	0.00	34.90	3.16
2054	3385	2.781923	AGCATTTTTGCCACCCATTTC	58.218	42.857	0.00	0.00	34.90	2.17
2074	3405	7.147846	CCATTTCCTTCCATGTGCTTAAATACT	60.148	37.037	0.00	0.00	0.00	2.12
2085	3416	9.577110	CATGTGCTTAAATACTTGTGATGAATT	57.423	29.630	0.00	0.00	0.00	2.17
2213	3547	2.102252	TGACATGTTTTGTTTGAGGGGC	59.898	45.455	0.00	0.00	39.18	5.80
2378	3836	4.453478	ACCTTATAGCATGTGATGATTGCG	59.547	41.667	0.00	0.00	41.22	4.85
2403	3964	5.538813	GGAGGAGGTTTTCTTTTGGTGTATT	59.461	40.000	0.00	0.00	0.00	1.89
2526	4101	5.107989	GCGACAACGATTCATATCAATACGT	60.108	40.000	0.00	0.00	42.66	3.57
2549	4124	7.090173	CGTCACCCTTGTTATTTTTCATGAAT	58.910	34.615	9.40	0.00	0.00	2.57
2551	4126	7.872483	GTCACCCTTGTTATTTTTCATGAATGT	59.128	33.333	9.40	1.17	0.00	2.71
2574	4149	3.127030	GTGGCTGTAGTTGCTTATGTTCC	59.873	47.826	0.00	0.00	0.00	3.62
2597	4411	8.477984	TCCAAGTTATCATTTTTAAGCAATGC	57.522	30.769	0.00	0.00	32.49	3.56
2637	4451	3.997021	CCATAACGAGAGAGTTGTTTGCT	59.003	43.478	0.00	0.00	34.33	3.91
2866	4690	4.049869	GCTGCTATTAGACCTACGTTTCC	58.950	47.826	0.00	0.00	0.00	3.13
2885	4709	6.645415	CGTTTCCTCAGTAGTTACAGTTTCAT	59.355	38.462	0.00	0.00	0.00	2.57
2888	4718	6.387465	TCCTCAGTAGTTACAGTTTCATTCG	58.613	40.000	0.00	0.00	0.00	3.34
2918	4748	0.880278	TGTTTGAGCCGCAGTCTGAC	60.880	55.000	3.32	0.00	0.00	3.51
2955	4786	5.246429	ACTTGGGAGTTTGTTTTTGTTGGTA	59.754	36.000	0.00	0.00	29.87	3.25
2990	4821	4.079970	CAGATATTTGGATGGCAGATGCT	58.920	43.478	4.59	0.00	41.70	3.79
3003	4834	4.080695	TGGCAGATGCTTGATCTTTAGACT	60.081	41.667	4.59	0.00	39.64	3.24
3004	4835	4.272991	GGCAGATGCTTGATCTTTAGACTG	59.727	45.833	4.59	0.00	39.64	3.51
3020	4851	3.270877	AGACTGTTGCTTTCGTTGAAGT	58.729	40.909	0.00	0.00	0.00	3.01
3048	4879	4.154918	AGCGCAGAATTTGTTCTAAAGGAG	59.845	41.667	11.47	0.00	0.00	3.69
3064	4896	0.620556	GGAGGGAGGAATGTCTGCAA	59.379	55.000	0.00	0.00	0.00	4.08
3164	4997	6.039941	GTGCATCAGGTGAGTAACTAGAGTAT	59.960	42.308	0.00	0.00	0.00	2.12
3186	5019	1.407979	CGTAAGGGGCACTAGTCGATT	59.592	52.381	0.00	0.00	0.00	3.34
3200	5033	7.255381	GCACTAGTCGATTGGGTTCTATAAGTA	60.255	40.741	0.00	0.00	0.00	2.24
3235	5068	2.884639	GCACCTGTTATTCAGTTGGTGT	59.115	45.455	10.94	0.00	42.19	4.16
3242	5075	5.258051	TGTTATTCAGTTGGTGTTATCCCC	58.742	41.667	0.00	0.00	0.00	4.81
3266	5099	5.789521	TGAACCGTTTCAGATTCATGTCTA	58.210	37.500	0.00	0.00	36.79	2.59
3277	5110	8.340618	TCAGATTCATGTCTAAAAAGGAAAGG	57.659	34.615	0.00	0.00	0.00	3.11
3325	5172	7.430211	CCAATCAAGAATGTTGTGTTGATATCG	59.570	37.037	10.58	0.00	38.42	2.92
3387	5234	4.653801	AGAACATGTAAAAGCCTTTGGGTT	59.346	37.500	0.00	0.00	46.01	4.11
3403	5250	1.815003	GGGTTGACCTTGAAGATGCAG	59.185	52.381	0.00	0.00	35.85	4.41
3419	5266	3.042871	TGCAGCATTTGGAATTTCACC	57.957	42.857	0.00	0.00	0.00	4.02
3453	5301	2.202892	CGGCTTCTTCGGCCTACC	60.203	66.667	0.00	0.00	46.73	3.18
3503	5353	2.533942	CGACTTTGAAAAAGGCGGTTTG	59.466	45.455	18.04	0.00	44.58	2.93
3505	5355	2.498078	ACTTTGAAAAAGGCGGTTTGGA	59.502	40.909	4.86	0.00	0.00	3.53
3506	5356	2.880963	TTGAAAAAGGCGGTTTGGAG	57.119	45.000	0.00	0.00	0.00	3.86
3507	5357	0.387565	TGAAAAAGGCGGTTTGGAGC	59.612	50.000	0.00	0.00	0.00	4.70
3508	5358	0.387565	GAAAAAGGCGGTTTGGAGCA	59.612	50.000	0.00	0.00	34.54	4.26
3509	5359	0.104120	AAAAAGGCGGTTTGGAGCAC	59.896	50.000	0.00	0.00	34.54	4.40
3510	5360	1.040339	AAAAGGCGGTTTGGAGCACA	61.040	50.000	0.00	0.00	34.54	4.57
3511	5361	0.827507	AAAGGCGGTTTGGAGCACAT	60.828	50.000	0.00	0.00	34.54	3.21
3512	5362	1.526575	AAGGCGGTTTGGAGCACATG	61.527	55.000	0.00	0.00	34.54	3.21
3515	5365	1.875963	CGGTTTGGAGCACATGGAC	59.124	57.895	0.00	0.00	0.00	4.02
3532	5382	1.544246	GGACGCCACCTAAGCAAAAAT	59.456	47.619	0.00	0.00	0.00	1.82
3533	5383	2.029380	GGACGCCACCTAAGCAAAAATT	60.029	45.455	0.00	0.00	0.00	1.82
3534	5384	3.242518	GACGCCACCTAAGCAAAAATTC	58.757	45.455	0.00	0.00	0.00	2.17
3535	5385	2.890945	ACGCCACCTAAGCAAAAATTCT	59.109	40.909	0.00	0.00	0.00	2.40
3563	5413	5.114785	TGGTCAATTTTACGATGGTTGTG	57.885	39.130	0.00	0.00	0.00	3.33
3572	5422	1.541147	ACGATGGTTGTGGATTGCAAG	59.459	47.619	4.94	0.00	0.00	4.01
3580	5430	1.543642	TGGATTGCAAGGGAGGGGA	60.544	57.895	4.94	0.00	0.00	4.81
3600	5465	1.221840	GGCCGAAATGAGCTGGAGA	59.778	57.895	0.00	0.00	0.00	3.71
3633	5498	6.128063	GCATCTTCTACTCAAGTGCAGATTTT	60.128	38.462	0.00	0.00	33.85	1.82
3636	5501	6.648310	TCTTCTACTCAAGTGCAGATTTTCTG	59.352	38.462	0.08	0.08	46.90	3.02
3642	5507	2.100991	GCAGATTTTCTGGGCGCG	59.899	61.111	0.00	0.00	44.43	6.86
3668	5533	0.613260	AGGACATCAAAGCGTGGCTA	59.387	50.000	0.00	0.00	38.25	3.93
3669	5534	0.727398	GGACATCAAAGCGTGGCTAC	59.273	55.000	0.00	0.00	38.25	3.58
3700	5565	4.870123	ACACTGAAATAAAGCATTGGCA	57.130	36.364	0.00	0.00	44.61	4.92
3710	5575	7.748691	AATAAAGCATTGGCAAAACTTCAAT	57.251	28.000	15.71	10.98	44.61	2.57
3711	5576	8.845413	AATAAAGCATTGGCAAAACTTCAATA	57.155	26.923	15.71	7.79	44.61	1.90
3727	5592	2.002586	CAATAGAGTGTTGGAGTGGCG	58.997	52.381	0.00	0.00	0.00	5.69
3746	5611	3.085223	AGCTCCTTGGCTCCTTGG	58.915	61.111	0.00	0.00	38.24	3.61
3751	5616	0.401738	TCCTTGGCTCCTTGGTCTTG	59.598	55.000	0.00	0.00	0.00	3.02
3773	5638	4.225208	GTTCACAGATTTCTCTTGCTTGC	58.775	43.478	0.00	0.00	0.00	4.01

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
318	346	8.585018	CCCTCCAATAAGTTTTAATCAAACACT	58.415	33.333	0.61	0.00	46.55	3.55
423	451	1.231751	TCTCATCCCCTCCACTCCCT	61.232	60.000	0.00	0.00	0.00	4.20
684	800	3.136626	CGAGATTTGACCCTTTCCCCTAT	59.863	47.826	0.00	0.00	0.00	2.57
741	857	5.415077	TCGTGTTCTGACCCTTTTGTTAAAA	59.585	36.000	0.00	0.00	0.00	1.52
758	874	0.781787	GGCGGCAAAATTTCGTGTTC	59.218	50.000	3.07	0.00	0.00	3.18
803	919	2.510238	CCAGCCTCTTCCGCTTCG	60.510	66.667	0.00	0.00	33.17	3.79
804	920	2.124942	CCCAGCCTCTTCCGCTTC	60.125	66.667	0.00	0.00	33.17	3.86
805	921	4.416738	GCCCAGCCTCTTCCGCTT	62.417	66.667	0.00	0.00	33.17	4.68
848	964	0.738975	CGGATGAGACAAGGAGCGTA	59.261	55.000	0.00	0.00	0.00	4.42
856	972	1.002624	GCCCAACCGGATGAGACAA	60.003	57.895	14.18	0.00	0.00	3.18
857	973	0.616395	TAGCCCAACCGGATGAGACA	60.616	55.000	14.18	0.00	0.00	3.41
858	974	0.539986	TTAGCCCAACCGGATGAGAC	59.460	55.000	14.18	1.90	0.00	3.36
859	975	1.065709	GTTTAGCCCAACCGGATGAGA	60.066	52.381	14.18	0.00	0.00	3.27
860	976	1.379527	GTTTAGCCCAACCGGATGAG	58.620	55.000	14.18	0.00	0.00	2.90
861	977	0.034863	GGTTTAGCCCAACCGGATGA	60.035	55.000	14.18	0.00	37.07	2.92
862	978	2.489040	GGTTTAGCCCAACCGGATG	58.511	57.895	9.46	6.59	37.07	3.51
1137	1312	2.341760	GCTCAGTCGACACAACGAATAC	59.658	50.000	19.50	0.00	43.75	1.89
1206	2289	2.671130	GGCTCACCTTCAGAGAAGAG	57.329	55.000	8.26	0.16	35.09	2.85
1233	2322	3.365520	TCGTCAAAACCGACACATAATCG	59.634	43.478	0.00	0.00	39.33	3.34
1284	2374	8.131731	TCTAGACAGATGAATTACTCATGTTCG	58.868	37.037	0.00	0.00	45.23	3.95
1288	2378	8.081633	GTCCTCTAGACAGATGAATTACTCATG	58.918	40.741	0.00	0.00	44.04	3.07
1290	2380	7.575414	GTCCTCTAGACAGATGAATTACTCA	57.425	40.000	0.00	0.00	45.55	3.41
1400	2495	4.211125	TGATCACAACCCAACTAGCAAAA	58.789	39.130	0.00	0.00	0.00	2.44
1407	2502	1.620822	GGCTTGATCACAACCCAACT	58.379	50.000	0.00	0.00	33.36	3.16
1512	2617	7.631377	GCCACAATTAAGCTCCAAAATCATACT	60.631	37.037	0.00	0.00	0.00	2.12
1544	2649	5.733620	AATTCAAATGACTGAAGCATGGT	57.266	34.783	0.00	0.00	38.66	3.55
1549	2654	7.536622	CAGACACTAAATTCAAATGACTGAAGC	59.463	37.037	0.00	0.00	38.66	3.86
1600	2705	3.180613	GCTCTAGTCGTAAAGGAGCAAC	58.819	50.000	8.14	0.00	45.79	4.17
1887	3081	2.736721	TGCTTGACTGCGACAGATTAAC	59.263	45.455	12.77	2.00	35.18	2.01
1889	3083	2.029020	AGTGCTTGACTGCGACAGATTA	60.029	45.455	12.77	0.00	35.18	1.75
2034	3365	2.552809	GGAAATGGGTGGCAAAAATGCT	60.553	45.455	0.40	0.00	34.73	3.79
2052	3383	6.719370	ACAAGTATTTAAGCACATGGAAGGAA	59.281	34.615	0.00	0.00	0.00	3.36
2054	3385	6.150976	TCACAAGTATTTAAGCACATGGAAGG	59.849	38.462	0.00	0.00	0.00	3.46
2074	3405	6.448207	TGAGTGTGTCAAAATTCATCACAA	57.552	33.333	0.00	0.00	39.99	3.33
2085	3416	3.541996	TGAGCTCTTGAGTGTGTCAAA	57.458	42.857	16.19	0.00	44.83	2.69
2134	3465	5.066764	GCACACGGTTAACCATAATACCATT	59.933	40.000	24.14	0.00	35.14	3.16
2152	3483	4.481930	TTATTCACTCAAAAGGCACACG	57.518	40.909	0.00	0.00	0.00	4.49
2378	3836	2.628178	CACCAAAAGAAAACCTCCTCCC	59.372	50.000	0.00	0.00	0.00	4.30
2508	4082	5.010719	AGGGTGACGTATTGATATGAATCGT	59.989	40.000	10.38	10.38	34.60	3.73
2526	4101	7.871973	CACATTCATGAAAAATAACAAGGGTGA	59.128	33.333	13.09	0.00	0.00	4.02
2549	4124	2.920724	TAAGCAACTACAGCCACACA	57.079	45.000	0.00	0.00	0.00	3.72
2551	4126	3.417069	ACATAAGCAACTACAGCCACA	57.583	42.857	0.00	0.00	0.00	4.17
2574	4149	8.254178	TGGCATTGCTTAAAAATGATAACTTG	57.746	30.769	8.82	0.00	37.22	3.16
2597	4411	6.692681	CGTTATGGTTTTCTGCATAAGAATGG	59.307	38.462	0.00	0.00	44.46	3.16
2605	4419	4.832248	TCTCTCGTTATGGTTTTCTGCAT	58.168	39.130	0.00	0.00	0.00	3.96
2637	4451	2.575532	CTCAGGTGCCAAGTTTCTGAA	58.424	47.619	0.00	0.00	34.58	3.02
2765	4579	1.067283	ACTCACATCTTCAGCTCCGTG	60.067	52.381	0.00	0.00	0.00	4.94
2866	4690	5.062308	GCCGAATGAAACTGTAACTACTGAG	59.938	44.000	1.28	0.00	0.00	3.35
2885	4709	1.036707	CAAACAAAAGGAGGGCCGAA	58.963	50.000	0.00	0.00	39.96	4.30
2888	4718	0.318441	GCTCAAACAAAAGGAGGGCC	59.682	55.000	0.00	0.00	0.00	5.80
2943	4774	3.252458	AGACAGGCGATACCAACAAAAAC	59.748	43.478	0.00	0.00	43.14	2.43
2952	4783	3.875838	CTGCTAGACAGGCGATACC	57.124	57.895	0.00	0.00	43.19	2.73
2990	4821	5.758296	ACGAAAGCAACAGTCTAAAGATCAA	59.242	36.000	0.00	0.00	0.00	2.57
3003	4834	3.189495	TGACAACTTCAACGAAAGCAACA	59.811	39.130	0.00	0.00	0.00	3.33
3004	4835	3.753842	TGACAACTTCAACGAAAGCAAC	58.246	40.909	0.00	0.00	0.00	4.17
3020	4851	2.618241	AGAACAAATTCTGCGCTGACAA	59.382	40.909	17.22	3.63	43.86	3.18
3048	4879	2.206576	AACTTGCAGACATTCCTCCC	57.793	50.000	0.00	0.00	0.00	4.30
3122	4955	2.093816	TGCACTAGATGGACAGCAAGAG	60.094	50.000	0.00	0.00	0.00	2.85
3164	4997	1.033746	CGACTAGTGCCCCTTACGGA	61.034	60.000	0.00	0.00	0.00	4.69
3179	5012	7.724506	TCAGATACTTATAGAACCCAATCGACT	59.275	37.037	0.00	0.00	0.00	4.18
3180	5013	7.883217	TCAGATACTTATAGAACCCAATCGAC	58.117	38.462	0.00	0.00	0.00	4.20
3186	5019	8.603898	TCAGTTTCAGATACTTATAGAACCCA	57.396	34.615	0.00	0.00	0.00	4.51
3200	5033	2.107204	ACAGGTGCCTTCAGTTTCAGAT	59.893	45.455	0.00	0.00	0.00	2.90
3299	5146	7.430211	CGATATCAACACAACATTCTTGATTGG	59.570	37.037	3.12	0.00	35.47	3.16
3317	5164	4.867608	TGTCGATGCTGAAAACGATATCAA	59.132	37.500	3.12	0.00	37.14	2.57
3325	5172	3.433615	AGTTAGCTGTCGATGCTGAAAAC	59.566	43.478	21.07	17.36	41.32	2.43
3387	5234	2.502142	ATGCTGCATCTTCAAGGTCA	57.498	45.000	9.81	0.00	0.00	4.02
3403	5250	2.368655	AGCGGTGAAATTCCAAATGC	57.631	45.000	0.00	0.00	0.00	3.56
3419	5266	1.006832	CCGAGTATGAACCCAAAGCG	58.993	55.000	0.00	0.00	0.00	4.68
3503	5353	3.127533	GTGGCGTCCATGTGCTCC	61.128	66.667	1.90	0.00	35.28	4.70
3505	5355	1.836999	TTAGGTGGCGTCCATGTGCT	61.837	55.000	1.90	0.00	35.28	4.40
3506	5356	1.369091	CTTAGGTGGCGTCCATGTGC	61.369	60.000	1.90	0.00	35.28	4.57
3507	5357	1.369091	GCTTAGGTGGCGTCCATGTG	61.369	60.000	1.90	0.00	35.28	3.21
3508	5358	1.078426	GCTTAGGTGGCGTCCATGT	60.078	57.895	1.90	0.00	35.28	3.21
3509	5359	0.676466	TTGCTTAGGTGGCGTCCATG	60.676	55.000	1.90	0.00	35.28	3.66
3510	5360	0.037590	TTTGCTTAGGTGGCGTCCAT	59.962	50.000	1.90	0.00	35.28	3.41
3511	5361	0.179015	TTTTGCTTAGGTGGCGTCCA	60.179	50.000	1.65	0.00	0.00	4.02
3512	5362	0.955905	TTTTTGCTTAGGTGGCGTCC	59.044	50.000	0.00	0.00	0.00	4.79
3515	5365	3.575965	AGAATTTTTGCTTAGGTGGCG	57.424	42.857	0.00	0.00	0.00	5.69
3532	5382	6.078202	TCGTAAAATTGACCATGCAAAGAA	57.922	33.333	0.00	0.00	0.00	2.52
3533	5383	5.697473	TCGTAAAATTGACCATGCAAAGA	57.303	34.783	0.00	0.00	0.00	2.52
3534	5384	5.289193	CCATCGTAAAATTGACCATGCAAAG	59.711	40.000	0.00	0.00	0.00	2.77
3535	5385	5.167121	CCATCGTAAAATTGACCATGCAAA	58.833	37.500	0.00	0.00	0.00	3.68
3545	5395	5.062058	GCAATCCACAACCATCGTAAAATTG	59.938	40.000	0.00	0.00	0.00	2.32
3563	5413	1.076705	GTCCCCTCCCTTGCAATCC	60.077	63.158	0.00	0.00	0.00	3.01
3580	5430	2.436646	CCAGCTCATTTCGGCCGT	60.437	61.111	27.15	1.97	0.00	5.68
3588	5438	1.220206	CGGCAGTCTCCAGCTCATT	59.780	57.895	0.00	0.00	0.00	2.57
3589	5439	1.986757	ACGGCAGTCTCCAGCTCAT	60.987	57.895	0.00	0.00	0.00	2.90
3600	5465	0.898320	AGTAGAAGATGCACGGCAGT	59.102	50.000	0.00	0.00	43.65	4.40
3633	5498	4.697756	CTCCCAAACGCGCCCAGA	62.698	66.667	5.73	0.00	0.00	3.86
3642	5507	1.200020	CGCTTTGATGTCCTCCCAAAC	59.800	52.381	0.00	0.00	0.00	2.93
3668	5533	8.995220	TGCTTTATTTCAGTGTTAATAAGACGT	58.005	29.630	0.00	0.00	30.41	4.34
3669	5534	9.988350	ATGCTTTATTTCAGTGTTAATAAGACG	57.012	29.630	10.72	0.00	30.41	4.18
3678	5543	5.212532	TGCCAATGCTTTATTTCAGTGTT	57.787	34.783	0.00	0.00	38.71	3.32
3700	5565	6.263168	CCACTCCAACACTCTATTGAAGTTTT	59.737	38.462	0.00	0.00	0.00	2.43
3710	5575	0.541063	TCCGCCACTCCAACACTCTA	60.541	55.000	0.00	0.00	0.00	2.43
3711	5576	1.821061	CTCCGCCACTCCAACACTCT	61.821	60.000	0.00	0.00	0.00	3.24
3739	5604	3.475566	TCTGTGAACAAGACCAAGGAG	57.524	47.619	0.00	0.00	0.00	3.69
3740	5605	4.437682	AATCTGTGAACAAGACCAAGGA	57.562	40.909	0.00	0.00	0.00	3.36
3741	5606	4.823989	AGAAATCTGTGAACAAGACCAAGG	59.176	41.667	0.00	0.00	0.00	3.61
3742	5607	5.762218	AGAGAAATCTGTGAACAAGACCAAG	59.238	40.000	0.00	0.00	0.00	3.61
3743	5608	5.684704	AGAGAAATCTGTGAACAAGACCAA	58.315	37.500	0.00	0.00	0.00	3.67
3744	5609	5.296151	AGAGAAATCTGTGAACAAGACCA	57.704	39.130	0.00	0.00	0.00	4.02
3745	5610	5.561725	GCAAGAGAAATCTGTGAACAAGACC	60.562	44.000	0.00	0.00	0.00	3.85
3746	5611	5.238214	AGCAAGAGAAATCTGTGAACAAGAC	59.762	40.000	0.00	0.00	0.00	3.01
3751	5616	4.023365	AGCAAGCAAGAGAAATCTGTGAAC	60.023	41.667	0.00	0.00	0.00	3.18

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.