AutoCloner

Multiple sequence alignment - TraesCS3D01G000500

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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	TraesCS3D01G000500	chr3D	100.000	3256	0	0	1	3256	392910	389655	0.000000e+00	6013.0
1	TraesCS3D01G000500	chr3D	83.310	713	98	12	1574	2277	357095	356395	3.540000e-179	638.0
2	TraesCS3D01G000500	chr3D	85.830	247	31	3	1092	1338	357470	357228	3.220000e-65	259.0
3	TraesCS3D01G000500	chr3B	91.945	2545	142	32	1	2542	6116559	6119043	0.000000e+00	3506.0
4	TraesCS3D01G000500	chr3B	92.656	1457	83	8	1	1454	5803986	5802551	0.000000e+00	2076.0
5	TraesCS3D01G000500	chr3B	82.566	304	37	8	2603	2891	6119041	6119343	1.500000e-63	254.0
6	TraesCS3D01G000500	chr3B	89.340	197	21	0	1092	1288	6126335	6126531	6.980000e-62	248.0
7	TraesCS3D01G000500	chr3B	87.805	164	20	0	1092	1255	6144900	6145063	3.320000e-45	193.0
8	TraesCS3D01G000500	chr3A	89.318	1863	130	22	1451	3256	9111355	9113205	0.000000e+00	2274.0
9	TraesCS3D01G000500	chr3A	90.872	1457	75	28	1	1452	9109278	9110681	0.000000e+00	1901.0
10	TraesCS3D01G000500	chr3A	93.936	1039	54	8	21	1054	9127992	9129026	0.000000e+00	1561.0
11	TraesCS3D01G000500	chr3A	82.016	734	101	13	1565	2279	9185920	9186641	2.160000e-166	595.0
12	TraesCS3D01G000500	chr3A	88.715	319	21	2	2944	3248	9114238	9114555	3.070000e-100	375.0
13	TraesCS3D01G000500	chr3A	85.933	327	19	9	1252	1570	9129071	9129378	1.130000e-84	324.0
14	TraesCS3D01G000500	chr3A	89.899	198	18	2	1577	1773	711203432	711203628	1.500000e-63	254.0
15	TraesCS3D01G000500	chr3A	86.179	123	14	3	2924	3045	705960885	705961005	2.640000e-26	130.0
16	TraesCS3D01G000500	chr3A	90.411	73	7	0	1084	1156	9129029	9129101	2.670000e-16	97.1
17	TraesCS3D01G000500	chr4B	91.584	202	17	0	1575	1776	659520584	659520785	2.470000e-71	279.0
18	TraesCS3D01G000500	chr4D	91.542	201	17	0	1576	1776	508432412	508432212	8.900000e-71	278.0
19	TraesCS3D01G000500	chr4D	86.154	65	4	3	2891	2955	499451372	499451313	7.540000e-07	65.8
20	TraesCS3D01G000500	chr5A	91.000	200	18	0	1577	1776	693674498	693674299	1.490000e-68	270.0
21	TraesCS3D01G000500	chr5A	89.268	205	15	3	1571	1775	85164865	85164668	1.940000e-62	250.0
22	TraesCS3D01G000500	chr1D	91.525	118	6	3	1175	1290	300326527	300326412	3.360000e-35	159.0
23	TraesCS3D01G000500	chr1A	91.379	116	6	3	1175	1288	374690360	374690247	4.350000e-34	156.0
24	TraesCS3D01G000500	chr1A	85.938	128	13	5	2920	3045	386825283	386825407	7.330000e-27	132.0
25	TraesCS3D01G000500	chr1B	90.517	116	9	2	1175	1289	405525785	405525671	5.630000e-33	152.0
26	TraesCS3D01G000500	chr1B	89.130	46	4	1	1346	1390	588635167	588635122	4.540000e-04	56.5
27	TraesCS3D01G000500	chr5D	87.302	126	12	4	2920	3043	72694439	72694562	1.220000e-29	141.0
28	TraesCS3D01G000500	chr5D	85.039	127	16	3	2920	3045	26424999	26425123	3.410000e-25	126.0
29	TraesCS3D01G000500	chr5D	78.756	193	27	8	2894	3082	521155042	521155224	2.050000e-22	117.0
30	TraesCS3D01G000500	chr7D	85.714	126	14	4	2920	3043	99929813	99929936	2.640000e-26	130.0
31	TraesCS3D01G000500	chr7D	86.179	123	14	3	2924	3045	277734411	277734291	2.640000e-26	130.0
32	TraesCS3D01G000500	chr2D	86.957	115	12	3	2930	3043	557090785	557090897	3.410000e-25	126.0
33	TraesCS3D01G000500	chr6B	90.000	60	3	3	2896	2954	589135260	589135317	1.250000e-09	75.0

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	TraesCS3D01G000500	chr3D	389655	392910	3255	True	6013.000000	6013	100.000000	1	3256	1	chr3D.!!$R1	3255
1	TraesCS3D01G000500	chr3D	356395	357470	1075	True	448.500000	638	84.570000	1092	2277	2	chr3D.!!$R2	1185
2	TraesCS3D01G000500	chr3B	5802551	5803986	1435	True	2076.000000	2076	92.656000	1	1454	1	chr3B.!!$R1	1453
3	TraesCS3D01G000500	chr3B	6116559	6119343	2784	False	1880.000000	3506	87.255500	1	2891	2	chr3B.!!$F3	2890
4	TraesCS3D01G000500	chr3A	9109278	9114555	5277	False	1516.666667	2274	89.635000	1	3256	3	chr3A.!!$F4	3255
5	TraesCS3D01G000500	chr3A	9127992	9129378	1386	False	660.700000	1561	90.093333	21	1570	3	chr3A.!!$F5	1549
6	TraesCS3D01G000500	chr3A	9185920	9186641	721	False	595.000000	595	82.016000	1565	2279	1	chr3A.!!$F1	714

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
467	474	0.322456	TTCCACAGAAATGAGGGCCG	60.322	55.0	0.0	0.0	0.0	6.13	F
1056	1082	0.323816	TCCTCTGCATCCTCGTCACT	60.324	55.0	0.0	0.0	0.0	3.41	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2052	2814	1.561542	CCCTGTTGGAGCCATCTTACT	59.438	52.381	0.0	0.0	35.39	2.24	R
2679	3466	0.179145	ATCTTGTTCGCCGGTACTCG	60.179	55.000	1.9	0.0	38.88	4.18	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
332	339	7.862675	AGTTGATCTATTGGCCTAACTAAACT	58.137	34.615	3.32	1.96	0.00	2.66
338	345	3.334583	TGGCCTAACTAAACTGAGCAG	57.665	47.619	3.32	0.00	0.00	4.24
373	380	5.644636	ACACCTCAACTTTTTCGAACAACTA	59.355	36.000	0.00	0.00	0.00	2.24
448	455	7.434307	CCTAAACATCTTGATAATCGTACGTGT	59.566	37.037	16.05	5.09	0.00	4.49
467	474	0.322456	TTCCACAGAAATGAGGGCCG	60.322	55.000	0.00	0.00	0.00	6.13
567	574	2.141517	GACGATCTTGGCCATCATCAG	58.858	52.381	19.56	9.62	0.00	2.90
593	600	1.893801	CGTCCCACTTACTCCTCTGTT	59.106	52.381	0.00	0.00	0.00	3.16
661	668	2.028385	AGTTGGAAAACGAGGTAGCGAT	60.028	45.455	0.00	0.00	34.83	4.58
1054	1062	1.035923	GATCCTCTGCATCCTCGTCA	58.964	55.000	0.00	0.00	0.00	4.35
1056	1082	0.323816	TCCTCTGCATCCTCGTCACT	60.324	55.000	0.00	0.00	0.00	3.41
1068	1094	1.078214	CGTCACTCATGCCCATGGT	60.078	57.895	11.73	3.17	39.24	3.55
1324	1354	9.909644	CACCTTACGCTATCATTAGTTTACTAT	57.090	33.333	0.00	0.00	0.00	2.12
1436	1466	2.472029	AGATTGGAGGGAGTACCACTG	58.528	52.381	0.00	0.00	43.89	3.66
1437	1467	1.486726	GATTGGAGGGAGTACCACTGG	59.513	57.143	0.00	0.00	43.89	4.00
1561	2277	3.481453	TGTTTATGTGCAGCCTGTAACA	58.519	40.909	5.09	5.09	0.00	2.41
1598	2341	3.932710	TGCAGATAAGGTGCTTAAAGTCG	59.067	43.478	0.00	0.00	41.78	4.18
1790	2541	1.593265	GTACCACACCCACCTACCG	59.407	63.158	0.00	0.00	0.00	4.02
1818	2569	2.371179	CCAGTCAGCATCATACCCATCT	59.629	50.000	0.00	0.00	0.00	2.90
1819	2570	3.556633	CCAGTCAGCATCATACCCATCTC	60.557	52.174	0.00	0.00	0.00	2.75
1994	2747	1.595311	TGGCAATCCTGGTGGAGTAT	58.405	50.000	0.00	0.00	46.91	2.12
2052	2814	3.982372	GAGTCGCGACCGAATGGCA	62.982	63.158	34.08	0.00	46.34	4.92
2186	2948	2.022129	GTCCGGCAAGACACTCGTG	61.022	63.158	0.00	0.00	36.73	4.35
2313	3091	4.336280	GAAGCAATGAAAAGGGGAGTACT	58.664	43.478	0.00	0.00	0.00	2.73
2323	3101	5.584551	AAAGGGGAGTACTCTGATTTGTT	57.415	39.130	21.88	5.55	0.00	2.83
2324	3102	4.828072	AGGGGAGTACTCTGATTTGTTC	57.172	45.455	21.88	2.38	0.00	3.18
2378	3156	1.399744	TATGTAGCAGGCTGGGACGG	61.400	60.000	17.64	0.00	38.10	4.79
2401	3179	1.167851	CTGTGATGTCCGGTTGCATT	58.832	50.000	0.00	0.00	0.00	3.56
2402	3180	0.880441	TGTGATGTCCGGTTGCATTG	59.120	50.000	0.00	0.00	0.00	2.82
2403	3181	0.456653	GTGATGTCCGGTTGCATTGC	60.457	55.000	0.00	0.46	0.00	3.56
2404	3182	0.892814	TGATGTCCGGTTGCATTGCA	60.893	50.000	7.38	7.38	36.47	4.08
2405	3183	0.457035	GATGTCCGGTTGCATTGCAT	59.543	50.000	12.95	0.00	38.76	3.96
2421	3199	2.125147	ATGTGTGCCCGTCCATCG	60.125	61.111	0.00	0.00	39.52	3.84
2423	3201	1.609635	ATGTGTGCCCGTCCATCGTA	61.610	55.000	0.00	0.00	37.94	3.43
2424	3202	1.143183	GTGTGCCCGTCCATCGTAT	59.857	57.895	0.00	0.00	37.94	3.06
2425	3203	0.386476	GTGTGCCCGTCCATCGTATA	59.614	55.000	0.00	0.00	37.94	1.47
2426	3204	1.112950	TGTGCCCGTCCATCGTATAA	58.887	50.000	0.00	0.00	37.94	0.98
2429	3207	2.735134	GTGCCCGTCCATCGTATAATTC	59.265	50.000	0.00	0.00	37.94	2.17
2430	3208	2.365941	TGCCCGTCCATCGTATAATTCA	59.634	45.455	0.00	0.00	37.94	2.57
2431	3209	3.007506	TGCCCGTCCATCGTATAATTCAT	59.992	43.478	0.00	0.00	37.94	2.57
2432	3210	3.370978	GCCCGTCCATCGTATAATTCATG	59.629	47.826	0.00	0.00	37.94	3.07
2433	3211	4.566004	CCCGTCCATCGTATAATTCATGT	58.434	43.478	0.00	0.00	37.94	3.21
2434	3212	4.388773	CCCGTCCATCGTATAATTCATGTG	59.611	45.833	0.00	0.00	37.94	3.21
2435	3213	4.143115	CCGTCCATCGTATAATTCATGTGC	60.143	45.833	0.00	0.00	37.94	4.57
2436	3214	4.686091	CGTCCATCGTATAATTCATGTGCT	59.314	41.667	0.00	0.00	34.52	4.40
2437	3215	5.177511	CGTCCATCGTATAATTCATGTGCTT	59.822	40.000	0.00	0.00	34.52	3.91
2548	3334	1.142465	GATCTGCACCACATGATCCCT	59.858	52.381	0.00	0.00	31.80	4.20
2549	3335	0.253894	TCTGCACCACATGATCCCTG	59.746	55.000	0.00	0.00	0.00	4.45
2588	3374	6.094464	GCTTTTTCTACGGGGAAGCTTTATTA	59.906	38.462	0.00	0.00	39.56	0.98
2594	3380	2.101917	CGGGGAAGCTTTATTAGGACGA	59.898	50.000	0.00	0.00	0.00	4.20
2634	3420	2.670934	CAGCTTTGCCGAGTGCCT	60.671	61.111	0.00	0.00	40.16	4.75
2638	3424	0.673644	GCTTTGCCGAGTGCCTAGAA	60.674	55.000	0.00	0.00	40.16	2.10
2650	3436	3.817647	AGTGCCTAGAAAACTCTGCAAAG	59.182	43.478	0.00	0.00	0.00	2.77
2652	3438	3.149981	GCCTAGAAAACTCTGCAAAGGT	58.850	45.455	0.00	0.00	0.00	3.50
2673	3460	2.542178	TCGGAAACAACTCGACAATGTG	59.458	45.455	0.00	0.00	0.00	3.21
2676	3463	4.668289	GGAAACAACTCGACAATGTGTTT	58.332	39.130	0.00	0.02	0.00	2.83
2679	3466	2.223479	ACAACTCGACAATGTGTTTGCC	60.223	45.455	0.00	0.00	39.03	4.52
2680	3467	0.586319	ACTCGACAATGTGTTTGCCG	59.414	50.000	0.00	0.00	41.88	5.69
2681	3468	0.865111	CTCGACAATGTGTTTGCCGA	59.135	50.000	0.00	0.00	46.06	5.54
2682	3469	0.865111	TCGACAATGTGTTTGCCGAG	59.135	50.000	0.00	0.00	43.88	4.63
2684	3471	1.795872	CGACAATGTGTTTGCCGAGTA	59.204	47.619	0.00	0.00	43.00	2.59
2686	3473	1.877443	ACAATGTGTTTGCCGAGTACC	59.123	47.619	0.00	0.00	39.03	3.34
2698	3490	0.179145	CGAGTACCGGCGAACAAGAT	60.179	55.000	9.30	0.00	33.91	2.40
2701	3493	1.274167	AGTACCGGCGAACAAGATTCA	59.726	47.619	9.30	0.00	0.00	2.57
2706	3498	0.449388	GGCGAACAAGATTCAGCCAG	59.551	55.000	13.78	0.00	43.65	4.85
2713	3505	2.107204	ACAAGATTCAGCCAGGAACACT	59.893	45.455	0.00	0.00	0.00	3.55
2715	3507	1.280421	AGATTCAGCCAGGAACACTCC	59.720	52.381	0.00	0.00	42.81	3.85
2757	3550	3.798202	AGTGCTTATCATCGGAAACTCC	58.202	45.455	0.00	0.00	0.00	3.85
2863	3664	0.592637	CACCGCATCAACTTTGCTGA	59.407	50.000	0.00	0.00	37.96	4.26
2871	3672	0.825010	CAACTTTGCTGAGTGCCCCT	60.825	55.000	0.00	0.00	42.00	4.79
2948	3754	6.272558	GGAGTTCCCCACCTGAATATATTACT	59.727	42.308	0.00	0.00	0.00	2.24
2957	3763	9.265901	CCACCTGAATATATTACTCAAAGTCTG	57.734	37.037	0.00	0.00	0.00	3.51
2958	3764	8.768955	CACCTGAATATATTACTCAAAGTCTGC	58.231	37.037	0.00	0.00	0.00	4.26
2976	3782	1.635663	GCCGACGCAGCAAAGTACAT	61.636	55.000	0.00	0.00	34.03	2.29
3010	3816	1.374758	GGTGGAACGTGCAGAGAGG	60.375	63.158	0.00	0.00	38.12	3.69
3014	3820	0.173708	GGAACGTGCAGAGAGGTAGG	59.826	60.000	0.00	0.00	0.00	3.18
3017	3823	0.889306	ACGTGCAGAGAGGTAGGAAC	59.111	55.000	0.00	0.00	0.00	3.62
3023	3829	1.115467	AGAGAGGTAGGAACGCCATG	58.885	55.000	0.00	0.00	36.29	3.66
3030	3836	2.541556	GTAGGAACGCCATGAGAAGAC	58.458	52.381	0.00	0.00	36.29	3.01
3031	3837	0.108615	AGGAACGCCATGAGAAGACG	60.109	55.000	0.00	0.00	36.29	4.18
3038	3844	1.186200	CCATGAGAAGACGTCCTCCA	58.814	55.000	13.01	9.61	0.00	3.86
3068	3874	6.040278	ACTCGTCTTCATGATATGATGTGACT	59.960	38.462	19.25	7.13	39.39	3.41
3087	3907	7.863722	TGTGACTAGAGATCTAAGTCTAAGGT	58.136	38.462	26.34	9.16	32.67	3.50
3133	3953	3.605634	ACCTAAATAACATGTCGCTGCA	58.394	40.909	0.00	0.00	0.00	4.41
3150	3970	1.153005	CAGGCAGCCCAGATCTTCC	60.153	63.158	8.22	0.00	0.00	3.46
3153	3973	0.822532	GGCAGCCCAGATCTTCCATG	60.823	60.000	0.00	0.00	0.00	3.66
3155	3975	1.814634	GCAGCCCAGATCTTCCATGAG	60.815	57.143	0.00	0.00	0.00	2.90
3223	4043	0.603569	AGAGTAGCGTCCCACAACTG	59.396	55.000	0.00	0.00	0.00	3.16
3234	4054	1.810151	CCCACAACTGGTTTATGTCCG	59.190	52.381	0.00	0.00	35.46	4.79
3238	4058	2.151202	CAACTGGTTTATGTCCGCAGT	58.849	47.619	0.00	0.00	0.00	4.40
3250	4070	0.522626	TCCGCAGTCGACGAACAATA	59.477	50.000	10.46	0.00	38.10	1.90

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
39	40	4.886247	TTTTTCGTGGTGTTGGACTTAG	57.114	40.909	0.00	0.00	0.00	2.18
229	234	7.432148	AGGGAAAAATTGTAAAGAGTTTGGT	57.568	32.000	0.00	0.00	0.00	3.67
270	276	5.512942	TTTAGGGTTGATCAATGTCTCCA	57.487	39.130	12.12	0.00	0.00	3.86
332	339	2.618241	GGTGTGTGTGATTTTCTGCTCA	59.382	45.455	0.00	0.00	0.00	4.26
338	345	4.900635	AGTTGAGGTGTGTGTGATTTTC	57.099	40.909	0.00	0.00	0.00	2.29
448	455	0.322456	CGGCCCTCATTTCTGTGGAA	60.322	55.000	0.00	0.00	38.11	3.53
467	474	2.872858	ACTTCTGACTTCGGCAAGTTTC	59.127	45.455	4.29	0.00	43.37	2.78
501	508	2.174363	TGGTGTCTGAGCATTGACAG	57.826	50.000	6.04	0.00	42.84	3.51
506	513	3.939740	ATACCATGGTGTCTGAGCATT	57.060	42.857	28.17	0.00	40.98	3.56
567	574	0.108756	GAGTAAGTGGGACGGCTGAC	60.109	60.000	0.00	0.00	0.00	3.51
593	600	3.304123	CGTCGTTTAAAGTGGCAATTGGA	60.304	43.478	7.72	0.00	0.00	3.53
707	715	3.089284	GTGGGCTAAACTGGCTTGTTAT	58.911	45.455	0.00	0.00	0.00	1.89
1026	1034	0.976590	TGCAGAGGATCAGAGCAGCT	60.977	55.000	0.00	0.00	35.35	4.24
1054	1062	0.625316	TAGCAACCATGGGCATGAGT	59.375	50.000	18.09	5.95	41.20	3.41
1056	1082	0.747644	CGTAGCAACCATGGGCATGA	60.748	55.000	18.09	0.00	41.20	3.07
1248	1274	2.626780	GCCCTTGCCGTCCTTGAAC	61.627	63.158	0.00	0.00	0.00	3.18
1324	1354	5.943416	AGTAACATAATTGCTTGCAGGTGTA	59.057	36.000	0.00	0.00	0.00	2.90
1492	2197	4.352887	TGAATGCATGCACGTGAATAATG	58.647	39.130	25.37	16.63	0.00	1.90
1539	2244	3.501828	TGTTACAGGCTGCACATAAACAG	59.498	43.478	15.89	0.00	36.96	3.16
1561	2277	1.958323	TGCATTTGCAGTGCACGAT	59.042	47.368	19.58	12.29	46.76	3.73
1643	2386	3.022406	GACCGGGTAGTAGTTCATGTCT	58.978	50.000	6.32	0.00	0.00	3.41
1751	2494	4.910195	ACCTCTTGAACTGCATGTTGATA	58.090	39.130	6.31	0.00	39.30	2.15
1812	2563	6.573289	CGATCTCAATAAGGTAAGGAGATGGG	60.573	46.154	7.14	0.00	43.36	4.00
1818	2569	5.241949	GCTCTCGATCTCAATAAGGTAAGGA	59.758	44.000	0.00	0.00	0.00	3.36
1819	2570	5.242838	AGCTCTCGATCTCAATAAGGTAAGG	59.757	44.000	0.00	0.00	0.00	2.69
2052	2814	1.561542	CCCTGTTGGAGCCATCTTACT	59.438	52.381	0.00	0.00	35.39	2.24
2138	2900	3.864686	CGCAACGAGAATGGCCCG	61.865	66.667	0.00	0.00	0.00	6.13
2186	2948	2.124695	GGGATGACCTGTTCGGCC	60.125	66.667	0.00	0.00	35.61	6.13
2295	3073	5.165961	TCAGAGTACTCCCCTTTTCATTG	57.834	43.478	19.38	7.13	0.00	2.82
2373	3151	4.760047	ACATCACAGGCGCCGTCC	62.760	66.667	23.20	0.00	0.00	4.79
2378	3156	4.760047	ACCGGACATCACAGGCGC	62.760	66.667	9.46	0.00	0.00	6.53
2403	3181	2.463620	CGATGGACGGGCACACATG	61.464	63.158	0.00	0.00	38.46	3.21
2404	3182	2.125147	CGATGGACGGGCACACAT	60.125	61.111	0.00	0.00	38.46	3.21
2492	3278	7.119992	TGTCTAATGCACAACCGTAAATGTATT	59.880	33.333	0.00	0.00	32.97	1.89
2565	3351	6.600427	CCTAATAAAGCTTCCCCGTAGAAAAA	59.400	38.462	0.00	0.00	0.00	1.94
2569	3355	4.343239	GTCCTAATAAAGCTTCCCCGTAGA	59.657	45.833	0.00	0.00	0.00	2.59
2588	3374	3.181475	CCAGTAATGTGCTATGTCGTCCT	60.181	47.826	0.00	0.00	0.00	3.85
2594	3380	3.265737	TGGTTCCCAGTAATGTGCTATGT	59.734	43.478	0.00	0.00	0.00	2.29
2634	3420	3.070446	TCCGACCTTTGCAGAGTTTTCTA	59.930	43.478	3.25	0.00	30.73	2.10
2638	3424	2.341846	TTCCGACCTTTGCAGAGTTT	57.658	45.000	3.25	0.00	0.00	2.66
2652	3438	2.542178	CACATTGTCGAGTTGTTTCCGA	59.458	45.455	0.00	0.00	0.00	4.55
2679	3466	0.179145	ATCTTGTTCGCCGGTACTCG	60.179	55.000	1.90	0.00	38.88	4.18
2680	3467	1.925185	GAATCTTGTTCGCCGGTACTC	59.075	52.381	1.90	0.00	0.00	2.59
2681	3468	1.274167	TGAATCTTGTTCGCCGGTACT	59.726	47.619	1.90	0.00	0.00	2.73
2682	3469	1.659098	CTGAATCTTGTTCGCCGGTAC	59.341	52.381	1.90	0.00	0.00	3.34
2684	3471	1.298859	GCTGAATCTTGTTCGCCGGT	61.299	55.000	1.90	0.00	0.00	5.28
2686	3473	1.298157	TGGCTGAATCTTGTTCGCCG	61.298	55.000	14.21	0.00	39.32	6.46
2698	3490	1.371183	CGGAGTGTTCCTGGCTGAA	59.629	57.895	0.00	0.00	41.67	3.02
2701	3493	0.608640	CTAACGGAGTGTTCCTGGCT	59.391	55.000	0.00	0.00	45.00	4.75
2713	3505	3.656559	GGCAAAGTAACTCACTAACGGA	58.343	45.455	0.00	0.00	36.04	4.69
2715	3507	3.311106	TCGGCAAAGTAACTCACTAACG	58.689	45.455	0.00	0.00	36.04	3.18
2717	3509	4.304110	CACTCGGCAAAGTAACTCACTAA	58.696	43.478	0.00	0.00	36.04	2.24
2720	3512	1.194772	GCACTCGGCAAAGTAACTCAC	59.805	52.381	0.00	0.00	43.97	3.51
2871	3672	1.674359	ACAATGTTGAACACGAGCCA	58.326	45.000	0.00	0.00	0.00	4.75
2914	3715	3.658422	GGGAACTCCACCCACCCC	61.658	72.222	0.00	0.00	46.05	4.95
2933	3739	7.934120	GGCAGACTTTGAGTAATATATTCAGGT	59.066	37.037	0.00	0.00	0.00	4.00
2938	3744	6.641314	CGTCGGCAGACTTTGAGTAATATATT	59.359	38.462	15.11	2.97	44.93	1.28
2948	3754	2.419620	TGCGTCGGCAGACTTTGA	59.580	55.556	15.11	0.00	46.21	2.69
2957	3763	1.635663	ATGTACTTTGCTGCGTCGGC	61.636	55.000	4.02	4.02	40.52	5.54
2958	3764	1.635844	TATGTACTTTGCTGCGTCGG	58.364	50.000	0.00	0.00	0.00	4.79
2976	3782	4.637387	TCCACCGTTCCCTTGTAATTTA	57.363	40.909	0.00	0.00	0.00	1.40
3010	3816	2.541556	GTCTTCTCATGGCGTTCCTAC	58.458	52.381	0.00	0.00	0.00	3.18
3014	3820	0.992802	GACGTCTTCTCATGGCGTTC	59.007	55.000	8.70	0.00	35.86	3.95
3017	3823	0.526524	GAGGACGTCTTCTCATGGCG	60.527	60.000	19.51	0.00	0.00	5.69
3023	3829	1.819288	TGACATGGAGGACGTCTTCTC	59.181	52.381	24.68	18.14	0.00	2.87
3030	3836	0.179161	GACGAGTGACATGGAGGACG	60.179	60.000	0.00	0.00	0.00	4.79
3031	3837	1.178276	AGACGAGTGACATGGAGGAC	58.822	55.000	0.00	0.00	0.00	3.85
3038	3844	6.396829	TCATATCATGAAGACGAGTGACAT	57.603	37.500	0.00	0.00	36.11	3.06
3081	3901	9.226606	TGACCAACATTCTGTAATAAACCTTAG	57.773	33.333	0.00	0.00	0.00	2.18
3111	3931	4.760878	TGCAGCGACATGTTATTTAGGTA	58.239	39.130	0.00	0.00	0.00	3.08
3133	3953	0.992431	ATGGAAGATCTGGGCTGCCT	60.992	55.000	19.68	0.00	31.83	4.75
3141	3961	5.049167	GCTTACACTCTCATGGAAGATCTG	58.951	45.833	0.00	0.00	42.38	2.90
3150	3970	4.993584	ACTTGTTCTGCTTACACTCTCATG	59.006	41.667	0.00	0.00	0.00	3.07
3153	3973	3.743396	CCACTTGTTCTGCTTACACTCTC	59.257	47.826	0.00	0.00	0.00	3.20
3155	3975	2.224314	GCCACTTGTTCTGCTTACACTC	59.776	50.000	0.00	0.00	0.00	3.51
3223	4043	0.997196	GTCGACTGCGGACATAAACC	59.003	55.000	8.70	0.00	38.28	3.27
3234	4054	0.997196	GGGTATTGTTCGTCGACTGC	59.003	55.000	14.70	4.04	0.00	4.40

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.