AutoCloner

Multiple sequence alignment - TraesCS2A01G239100

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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	TraesCS2A01G239100	chr2A	100.000	2834	0	0	1	2834	327178580	327181413	0.000000e+00	5234
1	TraesCS2A01G239100	chr2A	93.939	132	6	2	2703	2832	84244082	84243951	6.190000e-47	198
2	TraesCS2A01G239100	chr2A	81.752	137	12	8	2137	2271	327180671	327180796	4.990000e-18	102
3	TraesCS2A01G239100	chr2A	81.752	137	12	8	2092	2217	327180716	327180850	4.990000e-18	102
4	TraesCS2A01G239100	chr2B	93.489	2012	85	21	1	1975	348089434	348087432	0.000000e+00	2948
5	TraesCS2A01G239100	chr2B	90.794	315	24	4	2214	2526	24204813	24205124	1.570000e-112	416
6	TraesCS2A01G239100	chr2B	90.123	162	16	0	1976	2137	583387115	583386954	7.950000e-51	211
7	TraesCS2A01G239100	chr2B	86.082	194	18	4	2647	2832	24205335	24205527	1.720000e-47	200
8	TraesCS2A01G239100	chr2B	84.694	196	19	5	2647	2832	671038039	671037845	4.820000e-43	185
9	TraesCS2A01G239100	chr2B	92.800	125	9	0	1975	2099	24204076	24204200	6.240000e-42	182
10	TraesCS2A01G239100	chr2B	83.146	178	14	4	1976	2137	671038719	671038542	6.330000e-32	148
11	TraesCS2A01G239100	chr2D	96.346	1259	30	6	727	1975	289159594	289160846	0.000000e+00	2056
12	TraesCS2A01G239100	chr2D	97.684	734	14	3	1	734	289157974	289158704	0.000000e+00	1258
13	TraesCS2A01G239100	chr7A	94.483	435	24	0	2214	2648	616227202	616227636	0.000000e+00	671
14	TraesCS2A01G239100	chr7A	93.514	185	11	1	2649	2832	616227687	616227871	1.000000e-69	274
15	TraesCS2A01G239100	chr7A	94.444	162	9	0	1976	2137	616227058	616227219	1.690000e-62	250
16	TraesCS2A01G239100	chr4D	93.968	315	17	1	2214	2526	7046450	7046764	2.550000e-130	475
17	TraesCS2A01G239100	chr4D	91.351	185	9	2	2649	2832	7046976	7047154	2.180000e-61	246
18	TraesCS2A01G239100	chr3A	93.016	315	20	1	2214	2526	730326646	730326332	2.570000e-125	459
19	TraesCS2A01G239100	chr3A	90.735	313	24	4	2216	2526	39707668	39707359	2.030000e-111	412
20	TraesCS2A01G239100	chr3A	86.486	185	17	2	2649	2832	730326137	730325960	2.230000e-46	196
21	TraesCS2A01G239100	chr3A	92.800	125	9	0	1975	2099	39708410	39708286	6.240000e-42	182
22	TraesCS2A01G239100	chr3A	89.683	126	10	3	2525	2648	730326295	730326171	1.050000e-34	158
23	TraesCS2A01G239100	chr3D	92.698	315	15	3	2214	2526	91690673	91690365	5.570000e-122	448
24	TraesCS2A01G239100	chr3D	88.649	185	14	2	2649	2832	91690153	91689975	4.750000e-53	219
25	TraesCS2A01G239100	chr3D	91.270	126	8	3	2525	2648	91690328	91690204	4.860000e-38	169
26	TraesCS2A01G239100	chr1A	93.537	294	19	0	2233	2526	549507739	549507446	3.350000e-119	438
27	TraesCS2A01G239100	chr1A	93.210	162	11	0	1976	2137	549507908	549507747	3.650000e-59	239
28	TraesCS2A01G239100	chr3B	89.841	315	27	4	2214	2526	459088510	459088821	1.580000e-107	399
29	TraesCS2A01G239100	chr3B	93.252	163	11	0	1975	2137	27201445	27201283	1.010000e-59	241
30	TraesCS2A01G239100	chr3B	86.154	195	17	7	2647	2832	27200781	27200588	4.790000e-48	202
31	TraesCS2A01G239100	chr3B	90.260	154	15	0	1984	2137	459088374	459088527	4.790000e-48	202
32	TraesCS2A01G239100	chr1B	89.776	313	26	5	2216	2526	264013625	264013317	2.050000e-106	396
33	TraesCS2A01G239100	chr1B	92.453	159	12	0	1979	2137	264013768	264013610	7.900000e-56	228
34	TraesCS2A01G239100	chr1B	86.387	191	17	4	2650	2832	264013103	264012914	1.720000e-47	200
35	TraesCS2A01G239100	chr6D	85.549	173	23	2	2647	2817	1410353	1410181	2.240000e-41	180

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	TraesCS2A01G239100	chr2A	327178580	327181413	2833	False	1812.666667	5234	87.834667	1	2834	3	chr2A.!!$F1	2833
1	TraesCS2A01G239100	chr2B	348087432	348089434	2002	True	2948.000000	2948	93.489000	1	1975	1	chr2B.!!$R1	1974
2	TraesCS2A01G239100	chr2B	24204076	24205527	1451	False	266.000000	416	89.892000	1975	2832	3	chr2B.!!$F1	857
3	TraesCS2A01G239100	chr2D	289157974	289160846	2872	False	1657.000000	2056	97.015000	1	1975	2	chr2D.!!$F1	1974
4	TraesCS2A01G239100	chr7A	616227058	616227871	813	False	398.333333	671	94.147000	1976	2832	3	chr7A.!!$F1	856
5	TraesCS2A01G239100	chr4D	7046450	7047154	704	False	360.500000	475	92.659500	2214	2832	2	chr4D.!!$F1	618
6	TraesCS2A01G239100	chr3A	39707359	39708410	1051	True	297.000000	412	91.767500	1975	2526	2	chr3A.!!$R1	551
7	TraesCS2A01G239100	chr3A	730325960	730326646	686	True	271.000000	459	89.728333	2214	2832	3	chr3A.!!$R2	618
8	TraesCS2A01G239100	chr3D	91689975	91690673	698	True	278.666667	448	90.872333	2214	2832	3	chr3D.!!$R1	618
9	TraesCS2A01G239100	chr3B	27200588	27201445	857	True	221.500000	241	89.703000	1975	2832	2	chr3B.!!$R1	857
10	TraesCS2A01G239100	chr1B	264012914	264013768	854	True	274.666667	396	89.538667	1979	2832	3	chr1B.!!$R1	853

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
239	242	0.250295	TCGAACAGCACAAAGGGGAG	60.250	55.0	0.0	0.0	0.0	4.30	F
930	1858	1.412079	TGCCTTGTGCTTTCATGGTT	58.588	45.0	0.0	0.0	42.0	3.67	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1087	2021	0.250727	ACAGCACGGGTAACAAGCAT	60.251	50.0	0.0	0.0	39.74	3.79	R
2416	3908	0.179250	CAACGACGCCGATGAACTTG	60.179	55.0	0.0	0.0	40.41	3.16	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
125	126	2.188817	AGTTTAGAGGAGGCGGTTGAT	58.811	47.619	0.00	0.00	0.00	2.57
239	242	0.250295	TCGAACAGCACAAAGGGGAG	60.250	55.000	0.00	0.00	0.00	4.30
268	271	7.805071	GGTGATTCGATGGATAATGATCAAAAC	59.195	37.037	0.00	0.00	33.27	2.43
438	453	3.428589	GGATTTGTTGCTTCATCCAGCTC	60.429	47.826	0.00	0.00	40.79	4.09
678	693	6.936968	AAGTCCAATCTAGTTTCTAGTGGT	57.063	37.500	10.88	0.00	0.00	4.16
839	1762	5.918608	TGCCATAGTCAGGAAAGTCTATTC	58.081	41.667	0.00	0.00	0.00	1.75
848	1771	4.578105	CAGGAAAGTCTATTCATTCCCTGC	59.422	45.833	0.00	0.00	41.83	4.85
930	1858	1.412079	TGCCTTGTGCTTTCATGGTT	58.588	45.000	0.00	0.00	42.00	3.67
985	1913	4.535781	TGAACCAGGATCACATATTTGGG	58.464	43.478	0.00	0.00	0.00	4.12
986	1914	2.949447	ACCAGGATCACATATTTGGGC	58.051	47.619	0.00	0.00	0.00	5.36
1278	2212	0.179137	TCTTCGGTAGCAGCATGACG	60.179	55.000	0.00	0.00	39.69	4.35
1670	2607	9.201127	CAACAAGATATGATCGATAATCACACT	57.799	33.333	0.00	0.00	47.00	3.55
1700	2637	1.276705	TGCTTGCTATTCGTGGTGGTA	59.723	47.619	0.00	0.00	0.00	3.25
1993	2931	8.523915	TTGGGACGAGTAAACTACATCTATAA	57.476	34.615	0.00	0.00	0.00	0.98
2037	2975	6.263617	GGGTTCACTTTGGTCACTGTATTTAA	59.736	38.462	0.00	0.00	0.00	1.52
2038	2976	7.039993	GGGTTCACTTTGGTCACTGTATTTAAT	60.040	37.037	0.00	0.00	0.00	1.40
2092	3030	1.544691	ACGTGTCACTCTATGGTCACC	59.455	52.381	0.65	0.00	33.25	4.02
2099	3037	2.099263	CACTCTATGGTCACCAGTACCG	59.901	54.545	1.19	0.00	40.08	4.02
2100	3038	2.291411	ACTCTATGGTCACCAGTACCGT	60.291	50.000	1.19	0.00	40.08	4.83
2101	3039	3.054139	ACTCTATGGTCACCAGTACCGTA	60.054	47.826	1.19	0.00	40.08	4.02
2102	3040	4.142790	CTCTATGGTCACCAGTACCGTAT	58.857	47.826	1.19	0.00	40.08	3.06
2103	3041	4.139786	TCTATGGTCACCAGTACCGTATC	58.860	47.826	1.19	0.00	40.08	2.24
2105	3043	1.006281	TGGTCACCAGTACCGTATCCT	59.994	52.381	0.00	0.00	40.08	3.24
2106	3044	2.105766	GGTCACCAGTACCGTATCCTT	58.894	52.381	0.00	0.00	0.00	3.36
2108	3046	3.518590	GTCACCAGTACCGTATCCTTTG	58.481	50.000	0.00	0.00	0.00	2.77
2110	3048	4.158394	GTCACCAGTACCGTATCCTTTGTA	59.842	45.833	0.00	0.00	0.00	2.41
2111	3049	4.957954	TCACCAGTACCGTATCCTTTGTAT	59.042	41.667	0.00	0.00	0.00	2.29
2112	3050	5.422970	TCACCAGTACCGTATCCTTTGTATT	59.577	40.000	0.00	0.00	0.00	1.89
2113	3051	6.070653	TCACCAGTACCGTATCCTTTGTATTT	60.071	38.462	0.00	0.00	0.00	1.40
2114	3052	6.596497	CACCAGTACCGTATCCTTTGTATTTT	59.404	38.462	0.00	0.00	0.00	1.82
2115	3053	6.596497	ACCAGTACCGTATCCTTTGTATTTTG	59.404	38.462	0.00	0.00	0.00	2.44
2116	3054	6.457799	CCAGTACCGTATCCTTTGTATTTTGC	60.458	42.308	0.00	0.00	0.00	3.68
2118	3056	5.560966	ACCGTATCCTTTGTATTTTGCTG	57.439	39.130	0.00	0.00	0.00	4.41
2119	3057	5.250200	ACCGTATCCTTTGTATTTTGCTGA	58.750	37.500	0.00	0.00	0.00	4.26
2120	3058	5.123344	ACCGTATCCTTTGTATTTTGCTGAC	59.877	40.000	0.00	0.00	0.00	3.51
2121	3059	5.255596	CGTATCCTTTGTATTTTGCTGACG	58.744	41.667	0.00	0.00	0.00	4.35
2122	3060	5.163893	CGTATCCTTTGTATTTTGCTGACGT	60.164	40.000	0.00	0.00	0.00	4.34
2124	3062	3.252215	TCCTTTGTATTTTGCTGACGTGG	59.748	43.478	0.00	0.00	0.00	4.94
2127	3065	1.950216	TGTATTTTGCTGACGTGGCAA	59.050	42.857	17.85	17.85	46.12	4.52
2132	3070	1.890876	TTGCTGACGTGGCAAATACT	58.109	45.000	19.00	0.00	45.05	2.12
2133	3071	1.438651	TGCTGACGTGGCAAATACTC	58.561	50.000	9.89	0.00	36.71	2.59
2134	3072	0.727398	GCTGACGTGGCAAATACTCC	59.273	55.000	0.00	0.00	0.00	3.85
2135	3073	1.676014	GCTGACGTGGCAAATACTCCT	60.676	52.381	0.00	0.00	0.00	3.69
2136	3074	2.271800	CTGACGTGGCAAATACTCCTC	58.728	52.381	0.00	0.00	0.00	3.71
2179	3667	1.001974	TGCTGACGTGGCAAATACTCT	59.998	47.619	9.89	0.00	36.71	3.24
2180	3668	2.076863	GCTGACGTGGCAAATACTCTT	58.923	47.619	0.00	0.00	0.00	2.85
2181	3669	2.094417	GCTGACGTGGCAAATACTCTTC	59.906	50.000	0.00	0.00	0.00	2.87
2182	3670	3.325870	CTGACGTGGCAAATACTCTTCA	58.674	45.455	0.00	0.00	0.00	3.02
2183	3671	3.064207	TGACGTGGCAAATACTCTTCAC	58.936	45.455	0.00	0.00	0.00	3.18
2184	3672	3.244078	TGACGTGGCAAATACTCTTCACT	60.244	43.478	0.00	0.00	0.00	3.41
2185	3673	3.326747	ACGTGGCAAATACTCTTCACTC	58.673	45.455	0.00	0.00	0.00	3.51
2186	3674	3.006967	ACGTGGCAAATACTCTTCACTCT	59.993	43.478	0.00	0.00	0.00	3.24
2187	3675	3.614616	CGTGGCAAATACTCTTCACTCTC	59.385	47.826	0.00	0.00	0.00	3.20
2188	3676	4.619394	CGTGGCAAATACTCTTCACTCTCT	60.619	45.833	0.00	0.00	0.00	3.10
2189	3677	5.393135	CGTGGCAAATACTCTTCACTCTCTA	60.393	44.000	0.00	0.00	0.00	2.43
2190	3678	5.808030	GTGGCAAATACTCTTCACTCTCTAC	59.192	44.000	0.00	0.00	0.00	2.59
2191	3679	5.717178	TGGCAAATACTCTTCACTCTCTACT	59.283	40.000	0.00	0.00	0.00	2.57
2192	3680	6.039616	GGCAAATACTCTTCACTCTCTACTG	58.960	44.000	0.00	0.00	0.00	2.74
2193	3681	5.518487	GCAAATACTCTTCACTCTCTACTGC	59.482	44.000	0.00	0.00	0.00	4.40
2194	3682	5.845391	AATACTCTTCACTCTCTACTGCC	57.155	43.478	0.00	0.00	0.00	4.85
2195	3683	3.162147	ACTCTTCACTCTCTACTGCCA	57.838	47.619	0.00	0.00	0.00	4.92
2196	3684	2.823154	ACTCTTCACTCTCTACTGCCAC	59.177	50.000	0.00	0.00	0.00	5.01
2197	3685	3.088532	CTCTTCACTCTCTACTGCCACT	58.911	50.000	0.00	0.00	0.00	4.00
2198	3686	3.085533	TCTTCACTCTCTACTGCCACTC	58.914	50.000	0.00	0.00	0.00	3.51
2199	3687	2.889170	TCACTCTCTACTGCCACTCT	57.111	50.000	0.00	0.00	0.00	3.24
2200	3688	4.019231	TCTTCACTCTCTACTGCCACTCTA	60.019	45.833	0.00	0.00	0.00	2.43
2201	3689	4.302559	TCACTCTCTACTGCCACTCTAA	57.697	45.455	0.00	0.00	0.00	2.10
2202	3690	4.663334	TCACTCTCTACTGCCACTCTAAA	58.337	43.478	0.00	0.00	0.00	1.85
2203	3691	5.077564	TCACTCTCTACTGCCACTCTAAAA	58.922	41.667	0.00	0.00	0.00	1.52
2204	3692	5.717178	TCACTCTCTACTGCCACTCTAAAAT	59.283	40.000	0.00	0.00	0.00	1.82
2205	3693	6.211584	TCACTCTCTACTGCCACTCTAAAATT	59.788	38.462	0.00	0.00	0.00	1.82
2206	3694	6.533367	CACTCTCTACTGCCACTCTAAAATTC	59.467	42.308	0.00	0.00	0.00	2.17
2207	3695	6.439058	ACTCTCTACTGCCACTCTAAAATTCT	59.561	38.462	0.00	0.00	0.00	2.40
2208	3696	6.634805	TCTCTACTGCCACTCTAAAATTCTG	58.365	40.000	0.00	0.00	0.00	3.02
2209	3697	6.211584	TCTCTACTGCCACTCTAAAATTCTGT	59.788	38.462	0.00	0.00	0.00	3.41
2210	3698	6.398918	TCTACTGCCACTCTAAAATTCTGTC	58.601	40.000	0.00	0.00	0.00	3.51
2211	3699	3.997021	ACTGCCACTCTAAAATTCTGTCG	59.003	43.478	0.00	0.00	0.00	4.35
2212	3700	4.245660	CTGCCACTCTAAAATTCTGTCGA	58.754	43.478	0.00	0.00	0.00	4.20
2231	3719	2.695359	GAACGTGGCAAATACTCCTCA	58.305	47.619	0.00	0.00	0.00	3.86
2239	3731	5.069781	GTGGCAAATACTCCTCACTCTCTAT	59.930	44.000	0.00	0.00	0.00	1.98
2363	3855	2.657237	CTCCCGAAGCCTCGTGTT	59.343	61.111	3.69	0.00	43.87	3.32
2398	3890	2.678336	GCTAACTTGAATCCCCAACTCG	59.322	50.000	0.00	0.00	0.00	4.18
2513	4007	4.448395	CCATGTTTGCGATTTTGTCAACAT	59.552	37.500	0.00	0.00	0.00	2.71
2569	4102	0.974383	TTCTTTCCCACCTCTCGTCC	59.026	55.000	0.00	0.00	0.00	4.79
2573	4106	3.775654	CCCACCTCTCGTCCAGCC	61.776	72.222	0.00	0.00	0.00	4.85
2614	4148	2.897271	TACTCCCGGTTGGTGTACTA	57.103	50.000	0.00	0.00	41.11	1.82
2619	4153	0.457337	CCGGTTGGTGTACTAGTCGC	60.457	60.000	0.00	0.00	0.00	5.19
2622	4156	1.206371	GGTTGGTGTACTAGTCGCCAT	59.794	52.381	20.87	0.00	43.55	4.40
2693	4292	1.065764	CTGCTCGCGTATGGCTACA	59.934	57.895	5.77	0.00	40.44	2.74
2696	4295	1.734137	CTCGCGTATGGCTACACCT	59.266	57.895	5.77	0.00	40.44	4.00
2697	4296	0.949397	CTCGCGTATGGCTACACCTA	59.051	55.000	5.77	0.00	40.44	3.08
2712	4311	2.027192	ACACCTAGCGGAACATCATGTT	60.027	45.455	1.52	1.52	44.37	2.71
2731	4331	1.961277	CGCCTGTTCTTTCTGCCGT	60.961	57.895	0.00	0.00	0.00	5.68
2823	4430	0.609131	CGGGGAAATGCACAGAGGTT	60.609	55.000	0.00	0.00	0.00	3.50
2832	4439	3.650950	ACAGAGGTTGCCCCGCAT	61.651	61.111	0.00	0.00	38.76	4.73
2833	4440	3.136123	CAGAGGTTGCCCCGCATG	61.136	66.667	0.00	0.00	38.76	4.06

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
239	242	4.318332	TCATTATCCATCGAATCACCTGC	58.682	43.478	0.00	0.00	0.00	4.85
268	271	0.661552	CAGAGGCCTCAATGCATTCG	59.338	55.000	33.90	5.77	0.00	3.34
330	344	2.103373	CTGACCTTCGAGGATCTTCCA	58.897	52.381	7.76	0.00	39.61	3.53
438	453	2.359975	GGGTCAAGGAAGGCACGG	60.360	66.667	0.00	0.00	0.00	4.94
678	693	6.617538	ACTACACCCTATTAGCACATAGGTA	58.382	40.000	16.31	5.61	43.22	3.08
781	1703	9.965902	ACATTCAGATTAGATTTTTCTAGGTGT	57.034	29.630	0.00	0.00	0.00	4.16
839	1762	4.946157	AGTTCATAAGTCAAGCAGGGAATG	59.054	41.667	0.00	0.00	0.00	2.67
886	1814	2.364842	ATGACGGCCCTGCTCTCT	60.365	61.111	0.00	0.00	0.00	3.10
930	1858	5.408604	GCTAAACTGCTAAAGAACTACTGCA	59.591	40.000	0.00	0.00	0.00	4.41
1087	2021	0.250727	ACAGCACGGGTAACAAGCAT	60.251	50.000	0.00	0.00	39.74	3.79
1098	2032	2.058057	GCAAAAATACCAACAGCACGG	58.942	47.619	0.00	0.00	0.00	4.94
1278	2212	2.859806	GCACTTGGAGCACATGTTGTTC	60.860	50.000	0.00	0.00	35.49	3.18
1658	2595	5.572211	CAAATGAACCCAGTGTGATTATCG	58.428	41.667	0.00	0.00	0.00	2.92
1670	2607	3.119531	CGAATAGCAAGCAAATGAACCCA	60.120	43.478	0.00	0.00	0.00	4.51
1700	2637	3.947910	TCAAGTAAAGACGAATCCGGT	57.052	42.857	0.00	0.00	40.78	5.28
1838	2775	9.394477	GAAACGAACAGCTAAAACAATAGAATT	57.606	29.630	0.00	0.00	0.00	2.17
1993	2931	4.897051	ACCCTAGGATCAAGTTCAGGTAT	58.103	43.478	11.48	0.00	0.00	2.73
2037	2975	4.632688	CGGTGACCGTATTTTGACCTTTAT	59.367	41.667	17.28	0.00	42.73	1.40
2038	2976	3.995705	CGGTGACCGTATTTTGACCTTTA	59.004	43.478	17.28	0.00	42.73	1.85
2092	3030	6.315393	AGCAAAATACAAAGGATACGGTACTG	59.685	38.462	0.00	0.00	46.39	2.74
2099	3037	6.021596	CACGTCAGCAAAATACAAAGGATAC	58.978	40.000	0.00	0.00	0.00	2.24
2100	3038	5.123186	CCACGTCAGCAAAATACAAAGGATA	59.877	40.000	0.00	0.00	0.00	2.59
2101	3039	4.082787	CCACGTCAGCAAAATACAAAGGAT	60.083	41.667	0.00	0.00	0.00	3.24
2102	3040	3.252215	CCACGTCAGCAAAATACAAAGGA	59.748	43.478	0.00	0.00	0.00	3.36
2103	3041	3.564511	CCACGTCAGCAAAATACAAAGG	58.435	45.455	0.00	0.00	0.00	3.11
2105	3043	2.359214	TGCCACGTCAGCAAAATACAAA	59.641	40.909	7.31	0.00	37.28	2.83
2106	3044	1.950216	TGCCACGTCAGCAAAATACAA	59.050	42.857	7.31	0.00	37.28	2.41
2108	3046	2.697431	TTGCCACGTCAGCAAAATAC	57.303	45.000	17.73	0.00	46.71	1.89
2114	3052	1.438651	GAGTATTTGCCACGTCAGCA	58.561	50.000	5.70	5.70	38.81	4.41
2115	3053	0.727398	GGAGTATTTGCCACGTCAGC	59.273	55.000	0.04	0.04	0.00	4.26
2116	3054	2.271800	GAGGAGTATTTGCCACGTCAG	58.728	52.381	0.00	0.00	0.00	3.51
2118	3056	1.066430	TGGAGGAGTATTTGCCACGTC	60.066	52.381	0.00	0.00	0.00	4.34
2119	3057	0.981183	TGGAGGAGTATTTGCCACGT	59.019	50.000	0.00	0.00	0.00	4.49
2120	3058	1.066143	ACTGGAGGAGTATTTGCCACG	60.066	52.381	0.00	0.00	30.86	4.94
2121	3059	2.789409	ACTGGAGGAGTATTTGCCAC	57.211	50.000	0.00	0.00	30.86	5.01
2122	3060	2.504175	GGTACTGGAGGAGTATTTGCCA	59.496	50.000	0.00	0.00	39.44	4.92
2124	3062	2.167900	ACGGTACTGGAGGAGTATTTGC	59.832	50.000	6.65	0.00	39.44	3.68
2127	3065	4.106019	AGGATACGGTACTGGAGGAGTATT	59.894	45.833	6.65	0.00	39.91	1.89
2129	3067	3.051581	AGGATACGGTACTGGAGGAGTA	58.948	50.000	6.65	0.00	46.39	2.59
2130	3068	1.851653	AGGATACGGTACTGGAGGAGT	59.148	52.381	6.65	0.00	46.39	3.85
2132	3070	3.028850	CAAAGGATACGGTACTGGAGGA	58.971	50.000	6.65	0.00	46.39	3.71
2133	3071	2.764572	ACAAAGGATACGGTACTGGAGG	59.235	50.000	6.65	0.00	46.39	4.30
2134	3072	5.786264	ATACAAAGGATACGGTACTGGAG	57.214	43.478	6.65	0.00	46.39	3.86
2135	3073	6.549433	AAATACAAAGGATACGGTACTGGA	57.451	37.500	6.65	0.00	46.39	3.86
2136	3074	6.457799	GCAAAATACAAAGGATACGGTACTGG	60.458	42.308	6.65	0.00	46.39	4.00
2179	3667	3.162147	AGAGTGGCAGTAGAGAGTGAA	57.838	47.619	0.00	0.00	0.00	3.18
2180	3668	2.889170	AGAGTGGCAGTAGAGAGTGA	57.111	50.000	0.00	0.00	0.00	3.41
2181	3669	5.392767	TTTTAGAGTGGCAGTAGAGAGTG	57.607	43.478	0.00	0.00	0.00	3.51
2182	3670	6.439058	AGAATTTTAGAGTGGCAGTAGAGAGT	59.561	38.462	0.00	0.00	0.00	3.24
2183	3671	6.756074	CAGAATTTTAGAGTGGCAGTAGAGAG	59.244	42.308	0.00	0.00	0.00	3.20
2184	3672	6.211584	ACAGAATTTTAGAGTGGCAGTAGAGA	59.788	38.462	0.00	0.00	0.00	3.10
2185	3673	6.402222	ACAGAATTTTAGAGTGGCAGTAGAG	58.598	40.000	0.00	0.00	0.00	2.43
2186	3674	6.360370	ACAGAATTTTAGAGTGGCAGTAGA	57.640	37.500	0.00	0.00	0.00	2.59
2187	3675	5.289675	CGACAGAATTTTAGAGTGGCAGTAG	59.710	44.000	0.00	0.00	0.00	2.57
2188	3676	5.047590	TCGACAGAATTTTAGAGTGGCAGTA	60.048	40.000	0.00	0.00	0.00	2.74
2189	3677	3.997021	CGACAGAATTTTAGAGTGGCAGT	59.003	43.478	0.00	0.00	0.00	4.40
2190	3678	4.245660	TCGACAGAATTTTAGAGTGGCAG	58.754	43.478	0.00	0.00	0.00	4.85
2191	3679	4.265904	TCGACAGAATTTTAGAGTGGCA	57.734	40.909	0.00	0.00	0.00	4.92
2192	3680	4.434330	CGTTCGACAGAATTTTAGAGTGGC	60.434	45.833	0.00	0.00	38.80	5.01
2193	3681	4.684703	ACGTTCGACAGAATTTTAGAGTGG	59.315	41.667	0.00	0.00	38.80	4.00
2194	3682	5.388475	CCACGTTCGACAGAATTTTAGAGTG	60.388	44.000	0.00	0.00	38.80	3.51
2195	3683	4.684703	CCACGTTCGACAGAATTTTAGAGT	59.315	41.667	0.00	0.00	38.80	3.24
2196	3684	4.434330	GCCACGTTCGACAGAATTTTAGAG	60.434	45.833	0.00	0.00	38.80	2.43
2197	3685	3.430895	GCCACGTTCGACAGAATTTTAGA	59.569	43.478	0.00	0.00	38.80	2.10
2198	3686	3.185594	TGCCACGTTCGACAGAATTTTAG	59.814	43.478	0.00	0.00	38.80	1.85
2199	3687	3.132160	TGCCACGTTCGACAGAATTTTA	58.868	40.909	0.00	0.00	38.80	1.52
2200	3688	1.944024	TGCCACGTTCGACAGAATTTT	59.056	42.857	0.00	0.00	38.80	1.82
2201	3689	1.588674	TGCCACGTTCGACAGAATTT	58.411	45.000	0.00	0.00	38.80	1.82
2202	3690	1.588674	TTGCCACGTTCGACAGAATT	58.411	45.000	0.00	0.00	38.80	2.17
2203	3691	1.588674	TTTGCCACGTTCGACAGAAT	58.411	45.000	0.00	0.00	38.80	2.40
2204	3692	1.588674	ATTTGCCACGTTCGACAGAA	58.411	45.000	0.00	0.00	0.00	3.02
2205	3693	2.063266	GTATTTGCCACGTTCGACAGA	58.937	47.619	0.00	0.00	0.00	3.41
2206	3694	2.066262	AGTATTTGCCACGTTCGACAG	58.934	47.619	0.00	0.00	0.00	3.51
2207	3695	2.063266	GAGTATTTGCCACGTTCGACA	58.937	47.619	0.00	0.00	0.00	4.35
2208	3696	1.392510	GGAGTATTTGCCACGTTCGAC	59.607	52.381	0.00	0.00	0.00	4.20
2209	3697	1.274167	AGGAGTATTTGCCACGTTCGA	59.726	47.619	0.00	0.00	0.00	3.71
2210	3698	1.659098	GAGGAGTATTTGCCACGTTCG	59.341	52.381	0.00	0.00	0.00	3.95
2211	3699	2.415512	GTGAGGAGTATTTGCCACGTTC	59.584	50.000	0.00	0.00	0.00	3.95
2212	3700	2.038557	AGTGAGGAGTATTTGCCACGTT	59.961	45.455	0.00	0.00	0.00	3.99
2231	3719	3.052944	AGAGAGGAGTGGCAATAGAGAGT	60.053	47.826	0.00	0.00	0.00	3.24
2239	3731	5.221925	ACAGAATTTTAGAGAGGAGTGGCAA	60.222	40.000	0.00	0.00	0.00	4.52
2363	3855	3.610040	AGTTAGCATCGTTCATGGACA	57.390	42.857	4.68	0.00	32.37	4.02
2416	3908	0.179250	CAACGACGCCGATGAACTTG	60.179	55.000	0.00	0.00	40.41	3.16
2487	3981	3.181482	TGACAAAATCGCAAACATGGTGT	60.181	39.130	0.00	0.00	0.00	4.16
2531	4063	0.394938	ACATGTTGGACAGCCACGTA	59.605	50.000	0.00	0.00	45.94	3.57
2544	4076	3.756117	GAGAGGTGGGAAAGAACATGTT	58.244	45.455	11.78	11.78	0.00	2.71
2569	4102	1.978617	GATTGTGGGGGTGTGGCTG	60.979	63.158	0.00	0.00	0.00	4.85
2573	4106	2.282110	TGCGATTGTGGGGGTGTG	60.282	61.111	0.00	0.00	0.00	3.82
2712	4311	4.379174	GGCAGAAAGAACAGGCGA	57.621	55.556	0.00	0.00	0.00	5.54

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.