AutoCloner

Multiple sequence alignment - TraesCS3A01G346400

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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	TraesCS3A01G346400	chr3A	100.000	3867	0	0	1	3867	595935499	595931633	0.000000e+00	7142.0
1	TraesCS3A01G346400	chr3D	92.531	3682	149	45	227	3848	453986366	453982751	0.000000e+00	5160.0
2	TraesCS3A01G346400	chr3D	90.353	1047	71	11	843	1877	1993368	1992340	0.000000e+00	1347.0
3	TraesCS3A01G346400	chr3D	91.529	968	50	10	1914	2862	1992330	1991376	0.000000e+00	1304.0
4	TraesCS3A01G346400	chr3D	95.402	87	4	0	1	87	453986571	453986485	5.210000e-29	139.0
5	TraesCS3A01G346400	chr3D	81.746	126	9	6	3370	3491	1978653	1978538	4.110000e-15	93.5
6	TraesCS3A01G346400	chr3B	90.895	3943	174	66	1	3848	596413703	596409851	0.000000e+00	5121.0
7	TraesCS3A01G346400	chr3B	86.916	963	79	26	2517	3476	737563524	737562606	0.000000e+00	1037.0
8	TraesCS3A01G346400	chr3B	83.696	644	56	17	2837	3476	688176794	688177392	2.610000e-156	562.0
9	TraesCS3A01G346400	chr3B	83.540	644	57	17	2837	3476	688161174	688161772	1.210000e-154	556.0
10	TraesCS3A01G346400	chr3B	92.179	358	28	0	2511	2868	688159038	688159395	1.240000e-139	507.0
11	TraesCS3A01G346400	chr3B	86.486	222	12	8	3641	3844	688161887	688162108	1.080000e-55	228.0
12	TraesCS3A01G346400	chr3B	83.871	248	17	12	3641	3866	737561791	737561545	8.410000e-52	215.0
13	TraesCS3A01G346400	chr3B	85.135	222	15	8	3641	3844	688177507	688177728	1.090000e-50	211.0
14	TraesCS3A01G346400	chr7A	92.367	904	47	9	881	1770	465714	464819	0.000000e+00	1267.0
15	TraesCS3A01G346400	chr7A	85.762	892	72	27	1914	2789	464735	463883	0.000000e+00	893.0
16	TraesCS3A01G346400	chr7A	88.350	103	8	1	3372	3470	463773	463671	1.890000e-23	121.0
17	TraesCS3A01G346400	chr5B	87.127	971	73	20	2511	3476	610348525	610349448	0.000000e+00	1053.0
18	TraesCS3A01G346400	chr5B	84.274	248	16	12	3641	3866	610349562	610349808	1.810000e-53	220.0
19	TraesCS3A01G346400	chr1A	80.170	1175	184	37	1003	2142	494024276	494025436	0.000000e+00	833.0
20	TraesCS3A01G346400	chr1A	83.202	381	54	7	2397	2775	494025563	494025935	1.330000e-89	340.0
21	TraesCS3A01G346400	chr1D	82.010	806	127	15	1001	1800	391277857	391277064	0.000000e+00	669.0
22	TraesCS3A01G346400	chr1B	81.943	803	133	10	1001	1800	531535314	531536107	0.000000e+00	669.0
23	TraesCS3A01G346400	chr1B	82.632	380	58	8	2397	2775	531536598	531536970	2.880000e-86	329.0
24	TraesCS3A01G346400	chr2D	92.141	369	18	4	996	1362	636085982	636085623	9.580000e-141	510.0
25	TraesCS3A01G346400	chr2D	85.542	166	4	13	824	971	636086623	636086460	5.170000e-34	156.0
26	TraesCS3A01G346400	chrUn	90.191	367	27	2	996	1362	354266468	354266825	1.630000e-128	470.0
27	TraesCS3A01G346400	chrUn	93.676	253	16	0	1110	1362	247902077	247902329	2.820000e-101	379.0

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	TraesCS3A01G346400	chr3A	595931633	595935499	3866	True	7142.000000	7142	100.000000	1	3867	1	chr3A.!!$R1	3866
1	TraesCS3A01G346400	chr3D	453982751	453986571	3820	True	2649.500000	5160	93.966500	1	3848	2	chr3D.!!$R3	3847
2	TraesCS3A01G346400	chr3D	1991376	1993368	1992	True	1325.500000	1347	90.941000	843	2862	2	chr3D.!!$R2	2019
3	TraesCS3A01G346400	chr3B	596409851	596413703	3852	True	5121.000000	5121	90.895000	1	3848	1	chr3B.!!$R1	3847
4	TraesCS3A01G346400	chr3B	737561545	737563524	1979	True	626.000000	1037	85.393500	2517	3866	2	chr3B.!!$R2	1349
5	TraesCS3A01G346400	chr3B	688159038	688162108	3070	False	430.333333	556	87.401667	2511	3844	3	chr3B.!!$F1	1333
6	TraesCS3A01G346400	chr3B	688176794	688177728	934	False	386.500000	562	84.415500	2837	3844	2	chr3B.!!$F2	1007
7	TraesCS3A01G346400	chr7A	463671	465714	2043	True	760.333333	1267	88.826333	881	3470	3	chr7A.!!$R1	2589
8	TraesCS3A01G346400	chr5B	610348525	610349808	1283	False	636.500000	1053	85.700500	2511	3866	2	chr5B.!!$F1	1355
9	TraesCS3A01G346400	chr1A	494024276	494025935	1659	False	586.500000	833	81.686000	1003	2775	2	chr1A.!!$F1	1772
10	TraesCS3A01G346400	chr1D	391277064	391277857	793	True	669.000000	669	82.010000	1001	1800	1	chr1D.!!$R1	799
11	TraesCS3A01G346400	chr1B	531535314	531536970	1656	False	499.000000	669	82.287500	1001	2775	2	chr1B.!!$F1	1774
12	TraesCS3A01G346400	chr2D	636085623	636086623	1000	True	333.000000	510	88.841500	824	1362	2	chr2D.!!$R1	538

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	Hairpin	End Stability	Orientation
26	27	0.033366	AGTGCATTTGAAAACGGGGC	59.967	50.0	0.00	0.00	5.80	F
382	415	0.302288	TCGTGTTTGGTTTCGCTTCG	59.698	50.0	0.00	0.00	3.79	F
1896	2441	0.464735	AGGAGGAGGAGATCGTCGTG	60.465	60.0	2.79	42.57	4.35	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Hairpin	End Stability	Orientation
1896	2441	1.144936	CTGTGGATTCTCCTCCGCC	59.855	63.158	1.52	43.79	6.13	R
2364	2949	1.102154	TCTGCACCACAAACCAACAG	58.898	50.000	0.00	0.00	3.16	R
3491	5908	0.039798	TCGTGCTGACTTACGGACAC	60.040	55.000	0.00	40.48	3.67	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
26	27	0.033366	AGTGCATTTGAAAACGGGGC	59.967	50.000	0.00	0.00	0.00	5.80
125	126	1.606601	TCGCCCTCCCATATCTCGG	60.607	63.158	0.00	0.00	0.00	4.63
140	141	0.669625	CTCGGACGAAACTGAACCCC	60.670	60.000	0.00	0.00	0.00	4.95
243	275	3.950397	TCAAACTAGGCAGGTATTGTGG	58.050	45.455	0.00	0.00	0.00	4.17
254	286	7.848128	AGGCAGGTATTGTGGTATATATGTAC	58.152	38.462	1.15	1.15	0.00	2.90
256	288	7.764443	GGCAGGTATTGTGGTATATATGTACTG	59.236	40.741	9.22	0.00	0.00	2.74
267	299	8.553696	TGGTATATATGTACTGTATATGCGTCG	58.446	37.037	9.22	0.00	31.73	5.12
273	305	0.667487	CTGTATATGCGTCGGGCCAG	60.667	60.000	4.39	0.00	42.61	4.85
280	312	3.702048	CGTCGGGCCAGGAAGGAA	61.702	66.667	4.39	0.00	41.22	3.36
382	415	0.302288	TCGTGTTTGGTTTCGCTTCG	59.698	50.000	0.00	0.00	0.00	3.79
408	441	1.595382	GGGACGGCCAGATTCATCG	60.595	63.158	11.00	0.00	35.15	3.84
411	444	2.203056	CGGCCAGATTCATCGCCA	60.203	61.111	2.24	0.00	0.00	5.69
420	453	2.623416	AGATTCATCGCCATGACGTCTA	59.377	45.455	17.92	3.52	38.86	2.59
421	454	3.256879	AGATTCATCGCCATGACGTCTAT	59.743	43.478	17.92	5.91	38.86	1.98
422	455	2.422276	TCATCGCCATGACGTCTATG	57.578	50.000	17.92	16.97	33.80	2.23
423	456	1.953686	TCATCGCCATGACGTCTATGA	59.046	47.619	21.82	15.24	33.80	2.15
424	457	2.030805	TCATCGCCATGACGTCTATGAG	60.031	50.000	21.82	16.68	33.80	2.90
425	458	1.675552	TCGCCATGACGTCTATGAGA	58.324	50.000	21.82	18.02	0.00	3.27
426	459	1.604278	TCGCCATGACGTCTATGAGAG	59.396	52.381	21.82	15.55	0.00	3.20
427	460	1.777101	GCCATGACGTCTATGAGAGC	58.223	55.000	21.82	15.51	0.00	4.09
443	476	1.664321	GAGCTGGCTGGCCAAATGAG	61.664	60.000	15.47	1.28	46.63	2.90
465	498	1.152030	TGAACCCTGCAGTCTCCCT	60.152	57.895	13.81	0.00	0.00	4.20
680	713	2.165234	TGAATTCTGAGTCCTGAGCTCG	59.835	50.000	9.64	3.88	35.85	5.03
682	715	1.169577	TTCTGAGTCCTGAGCTCGAC	58.830	55.000	9.64	11.24	35.85	4.20
741	776	2.436115	GCCTAACTGTGTCCGGCC	60.436	66.667	0.00	0.00	34.75	6.13
771	811	1.804372	GCTGACGGAGAAGCCACATAG	60.804	57.143	0.00	0.00	35.40	2.23
776	816	1.537776	CGGAGAAGCCACATAGCTGAG	60.538	57.143	0.00	0.00	44.11	3.35
959	1018	4.855230	ACCACCACCACCACCCCT	62.855	66.667	0.00	0.00	0.00	4.79
1292	1810	4.821589	CTTCCTCGACAGCCCCGC	62.822	72.222	0.00	0.00	0.00	6.13
1731	2249	2.358003	GTGAGCCTCAGCGTGCTT	60.358	61.111	0.00	0.00	46.67	3.91
1800	2318	0.620556	TGAACAAGATCTGGGAGGCC	59.379	55.000	1.23	0.00	0.00	5.19
1896	2441	0.464735	AGGAGGAGGAGATCGTCGTG	60.465	60.000	2.79	0.00	42.57	4.35
2167	2714	2.687425	CACCATTCTTTCCACACACACA	59.313	45.455	0.00	0.00	0.00	3.72
2186	2733	7.114388	CACACACATGCATGATTAGATTAATGC	59.886	37.037	32.75	0.00	44.49	3.56
2212	2759	1.750399	CGTCTGATTGGGCCCTTGG	60.750	63.158	25.70	8.84	0.00	3.61
2330	2895	4.059511	TCTGCTTTTGTCCATGCAATTTG	58.940	39.130	0.00	0.00	34.90	2.32
2331	2896	3.806380	TGCTTTTGTCCATGCAATTTGT	58.194	36.364	0.00	0.00	32.12	2.83
2389	2974	2.192861	TTTGTGGTGCAGAAGCGGG	61.193	57.895	0.00	0.00	46.23	6.13
2980	5379	7.920160	TGTTTTCTTCTTTTTCATGGCTTTT	57.080	28.000	0.00	0.00	0.00	2.27
2981	5380	7.973601	TGTTTTCTTCTTTTTCATGGCTTTTC	58.026	30.769	0.00	0.00	0.00	2.29
3110	5510	8.985315	ATGCATATAAAGAGTGATTGAGGAAA	57.015	30.769	0.00	0.00	0.00	3.13
3122	5522	7.150640	AGTGATTGAGGAAAAGCAGATTTTTC	58.849	34.615	0.00	0.00	41.24	2.29
3132	5532	8.654230	GAAAAGCAGATTTTTCCTTTTTCTCT	57.346	30.769	0.00	0.00	41.24	3.10
3133	5533	9.102757	GAAAAGCAGATTTTTCCTTTTTCTCTT	57.897	29.630	0.00	0.00	41.24	2.85
3134	5534	8.654230	AAAGCAGATTTTTCCTTTTTCTCTTC	57.346	30.769	0.00	0.00	0.00	2.87
3135	5535	7.352079	AGCAGATTTTTCCTTTTTCTCTTCA	57.648	32.000	0.00	0.00	0.00	3.02
3136	5536	7.785033	AGCAGATTTTTCCTTTTTCTCTTCAA	58.215	30.769	0.00	0.00	0.00	2.69
3137	5537	7.924947	AGCAGATTTTTCCTTTTTCTCTTCAAG	59.075	33.333	0.00	0.00	0.00	3.02
3138	5538	7.708322	GCAGATTTTTCCTTTTTCTCTTCAAGT	59.292	33.333	0.00	0.00	0.00	3.16
3202	5606	2.103094	GTGGCAGCATGTAGGAGTATCA	59.897	50.000	0.00	0.00	39.31	2.15
3293	5699	3.087370	GGGATGCCCTGTTTAGACTTT	57.913	47.619	0.00	0.00	41.34	2.66
3349	5760	9.701098	TTCTACTAATTGATTGTGTAGTTTCGT	57.299	29.630	13.33	0.00	33.73	3.85
3350	5761	9.135843	TCTACTAATTGATTGTGTAGTTTCGTG	57.864	33.333	13.33	0.00	33.73	4.35
3354	5765	4.330944	TGATTGTGTAGTTTCGTGAGGT	57.669	40.909	0.00	0.00	0.00	3.85
3365	5776	0.255033	TCGTGAGGTAGGCAGCTAGA	59.745	55.000	0.00	0.00	30.99	2.43
3366	5777	0.665835	CGTGAGGTAGGCAGCTAGAG	59.334	60.000	0.00	0.00	30.99	2.43
3367	5778	1.770294	GTGAGGTAGGCAGCTAGAGT	58.230	55.000	0.00	0.00	30.99	3.24
3440	5856	2.735444	CGAGCGATGGAGTGAAAGCTTA	60.735	50.000	0.00	0.00	34.85	3.09
3444	5860	3.185391	GCGATGGAGTGAAAGCTTATAGC	59.815	47.826	0.00	0.00	42.84	2.97
3462	5878	3.149005	AGCGGACCTTCCAAATTACAA	57.851	42.857	0.00	0.00	35.91	2.41
3470	5886	8.032451	CGGACCTTCCAAATTACAATAATTGTT	58.968	33.333	0.00	0.00	39.78	2.83
3491	5908	8.446489	TTGTTCATAACATTTCGCAAAGTATG	57.554	30.769	0.00	0.00	41.79	2.39
3495	5912	7.240674	TCATAACATTTCGCAAAGTATGTGTC	58.759	34.615	0.00	0.00	40.52	3.67
3503	5920	3.060363	CGCAAAGTATGTGTCCGTAAGTC	59.940	47.826	0.00	0.00	34.75	3.01
3514	5931	1.068474	CCGTAAGTCAGCACGAAAGG	58.932	55.000	0.00	0.00	40.56	3.11
3542	5959	4.008074	TCTGCGAAGATCAAGGAAAACT	57.992	40.909	0.00	0.00	0.00	2.66
3560	5977	1.066143	ACTCACCAGGCCGTATTCTTG	60.066	52.381	0.00	0.00	0.00	3.02
3565	5982	1.942657	CCAGGCCGTATTCTTGTGATG	59.057	52.381	0.00	0.00	0.00	3.07
3570	5987	5.050091	CAGGCCGTATTCTTGTGATGTTATC	60.050	44.000	0.00	0.00	0.00	1.75
3571	5988	4.814234	GGCCGTATTCTTGTGATGTTATCA	59.186	41.667	0.00	0.00	36.84	2.15
3709	6843	4.916041	TTCAGGATCTTGTCTTGACCAT	57.084	40.909	4.57	0.00	42.00	3.55
3735	6890	1.057275	TGGCACACAGTAGGGTTCCA	61.057	55.000	0.00	0.00	0.00	3.53
3736	6891	0.328258	GGCACACAGTAGGGTTCCAT	59.672	55.000	0.00	0.00	0.00	3.41
3737	6892	1.679032	GGCACACAGTAGGGTTCCATC	60.679	57.143	0.00	0.00	0.00	3.51
3738	6893	1.279271	GCACACAGTAGGGTTCCATCT	59.721	52.381	0.00	0.00	0.00	2.90
3739	6894	2.936993	GCACACAGTAGGGTTCCATCTG	60.937	54.545	0.00	0.00	34.54	2.90
3740	6895	1.279271	ACACAGTAGGGTTCCATCTGC	59.721	52.381	7.78	0.00	32.76	4.26
3741	6896	1.556911	CACAGTAGGGTTCCATCTGCT	59.443	52.381	7.78	0.00	32.76	4.24
3798	6970	2.016171	CATGCGATGCGTCCAATCA	58.984	52.632	0.00	0.00	0.00	2.57
3848	7021	4.323417	TGGCACCACTGACATTTTACTAG	58.677	43.478	0.00	0.00	26.39	2.57
3849	7022	4.202419	TGGCACCACTGACATTTTACTAGT	60.202	41.667	0.00	0.00	26.39	2.57
3850	7023	5.012251	TGGCACCACTGACATTTTACTAGTA	59.988	40.000	0.00	0.00	26.39	1.82
3853	7026	7.042335	GCACCACTGACATTTTACTAGTATCT	58.958	38.462	2.79	0.00	0.00	1.98

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
8	9	0.033366	AGCCCCGTTTTCAAATGCAC	59.967	50.000	0.00	0.00	0.00	4.57
26	27	1.730487	CCACTCGGATCGACCTCAG	59.270	63.158	0.00	0.00	36.31	3.35
103	104	3.591254	GATATGGGAGGGCGACGGC	62.591	68.421	13.84	13.84	38.90	5.68
125	126	1.509703	GAGTGGGGTTCAGTTTCGTC	58.490	55.000	0.00	0.00	0.00	4.20
164	165	5.285370	CGTATGTATGGTATGGACGAATTCG	59.715	44.000	25.64	25.64	46.33	3.34
165	166	6.089016	CACGTATGTATGGTATGGACGAATTC	59.911	42.308	0.00	0.00	33.30	2.17
166	167	5.924254	CACGTATGTATGGTATGGACGAATT	59.076	40.000	0.00	0.00	33.30	2.17
167	168	5.242171	TCACGTATGTATGGTATGGACGAAT	59.758	40.000	0.00	0.00	33.30	3.34
168	169	4.579753	TCACGTATGTATGGTATGGACGAA	59.420	41.667	0.00	0.00	33.30	3.85
169	170	4.136051	TCACGTATGTATGGTATGGACGA	58.864	43.478	0.00	0.00	33.30	4.20
170	171	4.492791	TCACGTATGTATGGTATGGACG	57.507	45.455	0.00	0.00	35.10	4.79
171	172	6.025896	CGTATCACGTATGTATGGTATGGAC	58.974	44.000	0.00	0.00	36.74	4.02
172	173	5.392272	GCGTATCACGTATGTATGGTATGGA	60.392	44.000	0.26	0.00	44.73	3.41
177	209	2.291465	ACGCGTATCACGTATGTATGGT	59.709	45.455	11.67	0.00	44.73	3.55
243	275	8.013947	CCCGACGCATATACAGTACATATATAC	58.986	40.741	8.56	4.36	0.00	1.47
254	286	0.667487	CTGGCCCGACGCATATACAG	60.667	60.000	0.00	0.00	40.31	2.74
256	288	1.374252	CCTGGCCCGACGCATATAC	60.374	63.158	0.00	0.00	40.31	1.47
258	290	2.383245	CTTCCTGGCCCGACGCATAT	62.383	60.000	0.00	0.00	40.31	1.78
267	299	1.379176	GCTTCTTCCTTCCTGGCCC	60.379	63.158	0.00	0.00	35.26	5.80
273	305	1.308783	CGGCTTGGCTTCTTCCTTCC	61.309	60.000	0.00	0.00	0.00	3.46
280	312	0.610232	AAGATTGCGGCTTGGCTTCT	60.610	50.000	0.00	0.00	0.00	2.85
399	432	1.410517	AGACGTCATGGCGATGAATCT	59.589	47.619	28.94	15.43	40.39	2.40
408	441	1.339610	AGCTCTCATAGACGTCATGGC	59.660	52.381	19.50	15.88	0.00	4.40
411	444	1.339610	GCCAGCTCTCATAGACGTCAT	59.660	52.381	19.50	6.50	0.00	3.06
420	453	3.013327	TGGCCAGCCAGCTCTCAT	61.013	61.111	7.43	0.00	41.89	2.90
443	476	1.230324	GAGACTGCAGGGTTCACAAC	58.770	55.000	19.93	0.00	0.00	3.32
484	517	0.247185	CCCGAGCTGGTTACGGTTTA	59.753	55.000	9.64	0.00	44.34	2.01
529	562	1.418097	ATGGCGGATGACCTATGGCA	61.418	55.000	0.00	0.00	39.52	4.92
628	661	1.600413	GGTTGCTTCCAAGTTTGCTCG	60.600	52.381	0.00	0.00	0.00	5.03
632	665	0.597377	GCCGGTTGCTTCCAAGTTTG	60.597	55.000	1.90	0.00	36.87	2.93
720	753	1.741770	CGGACACAGTTAGGCCAGC	60.742	63.158	5.01	0.00	0.00	4.85
721	754	1.079127	CCGGACACAGTTAGGCCAG	60.079	63.158	5.01	0.00	0.00	4.85
821	861	2.097466	GGATGGTTGTGGCTGTAAATCG	59.903	50.000	0.00	0.00	0.00	3.34
1292	1810	3.730761	GGTGCCAGCACTTGAGCG	61.731	66.667	21.19	0.00	45.52	5.03
1800	2318	1.424493	GGATCCTGTTCTCGCGCTTG	61.424	60.000	5.56	0.00	0.00	4.01
1896	2441	1.144936	CTGTGGATTCTCCTCCGCC	59.855	63.158	1.52	0.00	43.79	6.13
1911	2456	1.456705	GCCTCCGATCTCCTCCTGT	60.457	63.158	0.00	0.00	0.00	4.00
2186	2733	3.066760	GGGCCCAATCAGACGAAAATAAG	59.933	47.826	19.95	0.00	0.00	1.73
2212	2759	2.698274	GAGGGAGACTCCAAGAAGATCC	59.302	54.545	23.06	2.30	40.49	3.36
2248	2795	8.418662	AGTTACAAGTTTCCCATTTAAAAGGAC	58.581	33.333	11.05	1.77	0.00	3.85
2364	2949	1.102154	TCTGCACCACAAACCAACAG	58.898	50.000	0.00	0.00	0.00	3.16
2389	2974	2.931386	GTCCGCGATATGCTGTGC	59.069	61.111	8.23	0.00	43.27	4.57
2896	5295	6.367969	GCTTCGTGTCTCCTAAGTTAATCAAA	59.632	38.462	0.00	0.00	0.00	2.69
2980	5379	3.634448	GGGATCGATCAGTCAAGAAGAGA	59.366	47.826	25.93	0.00	0.00	3.10
2981	5380	3.382865	TGGGATCGATCAGTCAAGAAGAG	59.617	47.826	25.93	0.00	0.00	2.85
3014	5413	1.002366	CCAGCTTGATCTGTGTACGC	58.998	55.000	0.00	0.00	32.32	4.42
3110	5510	7.785033	TGAAGAGAAAAAGGAAAAATCTGCTT	58.215	30.769	0.00	0.00	0.00	3.91
3171	5575	1.001068	CATGCTGCCACCAAAACATGA	59.999	47.619	0.00	0.00	37.65	3.07
3202	5606	3.140325	ACTCATCAACATCCCAACGTT	57.860	42.857	0.00	0.00	0.00	3.99
3217	5621	4.197750	CTCCAGGTACGTACACTACTCAT	58.802	47.826	26.02	0.00	0.00	2.90
3345	5756	1.103803	CTAGCTGCCTACCTCACGAA	58.896	55.000	0.00	0.00	0.00	3.85
3346	5757	0.255033	TCTAGCTGCCTACCTCACGA	59.745	55.000	0.00	0.00	0.00	4.35
3349	5760	2.534042	AACTCTAGCTGCCTACCTCA	57.466	50.000	0.00	0.00	0.00	3.86
3350	5761	2.295070	GCTAACTCTAGCTGCCTACCTC	59.705	54.545	0.00	0.00	46.12	3.85
3365	5776	6.757237	TCTCTACACGTATAGCTAGCTAACT	58.243	40.000	27.47	15.11	31.73	2.24
3366	5777	7.418840	TTCTCTACACGTATAGCTAGCTAAC	57.581	40.000	27.47	22.36	31.73	2.34
3367	5778	8.442632	TTTTCTCTACACGTATAGCTAGCTAA	57.557	34.615	27.47	14.27	31.73	3.09
3440	5856	4.497291	TGTAATTTGGAAGGTCCGCTAT	57.503	40.909	0.00	0.00	40.17	2.97
3444	5860	7.543756	ACAATTATTGTAATTTGGAAGGTCCG	58.456	34.615	9.02	0.00	43.27	4.79
3462	5878	9.638239	ACTTTGCGAAATGTTATGAACAATTAT	57.362	25.926	0.00	0.00	45.86	1.28
3470	5886	7.139896	ACACATACTTTGCGAAATGTTATGA	57.860	32.000	0.00	0.00	30.32	2.15
3478	5894	2.485903	ACGGACACATACTTTGCGAAA	58.514	42.857	0.00	0.00	0.00	3.46
3491	5908	0.039798	TCGTGCTGACTTACGGACAC	60.040	55.000	0.00	0.00	40.48	3.67
3495	5912	1.068474	CCTTTCGTGCTGACTTACGG	58.932	55.000	0.00	0.00	40.48	4.02
3514	5931	3.063180	CCTTGATCTTCGCAGATTGACAC	59.937	47.826	0.00	0.00	40.14	3.67
3521	5938	3.997021	GAGTTTTCCTTGATCTTCGCAGA	59.003	43.478	0.00	0.00	0.00	4.26
3523	5940	3.498397	GTGAGTTTTCCTTGATCTTCGCA	59.502	43.478	0.00	0.00	0.00	5.10
3542	5959	0.981183	ACAAGAATACGGCCTGGTGA	59.019	50.000	0.00	0.00	0.00	4.02
3585	6002	8.474025	TCACCATTTTTCTACAGTTTGATTTGT	58.526	29.630	0.00	0.00	0.00	2.83
3709	6843	1.066215	CCTACTGTGTGCCATGCTACA	60.066	52.381	0.00	0.00	0.00	2.74
3735	6890	1.179814	GGGACGGGTCGATAGCAGAT	61.180	60.000	0.00	0.00	0.00	2.90
3736	6891	1.826921	GGGACGGGTCGATAGCAGA	60.827	63.158	0.00	0.00	0.00	4.26
3737	6892	1.392710	AAGGGACGGGTCGATAGCAG	61.393	60.000	0.00	0.00	0.00	4.24
3738	6893	1.380785	AAGGGACGGGTCGATAGCA	60.381	57.895	0.00	0.00	0.00	3.49
3739	6894	1.363080	GAAGGGACGGGTCGATAGC	59.637	63.158	0.00	0.00	0.00	2.97
3740	6895	1.793134	CGGAAGGGACGGGTCGATAG	61.793	65.000	0.00	0.00	0.00	2.08
3741	6896	1.825191	CGGAAGGGACGGGTCGATA	60.825	63.158	0.00	0.00	0.00	2.92
3798	6970	4.460382	CAGTTCCTGTTTATTGGTGATGCT	59.540	41.667	0.00	0.00	0.00	3.79

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.