AutoCloner

Multiple sequence alignment - TraesCS5A01G067700

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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	TraesCS5A01G067700	chr5A	100.000	3693	0	0	1	3693	75047960	75051652	0.000000e+00	6820.0
1	TraesCS5A01G067700	chr5B	90.069	2769	192	32	1	2744	88735444	88738154	0.000000e+00	3513.0
2	TraesCS5A01G067700	chr5B	93.779	1286	51	10	680	1954	88779691	88780958	0.000000e+00	1905.0
3	TraesCS5A01G067700	chr5B	86.298	1788	147	37	224	1963	88704096	88705833	0.000000e+00	1855.0
4	TraesCS5A01G067700	chr5B	96.359	769	21	2	1956	2724	88781177	88781938	0.000000e+00	1258.0
5	TraesCS5A01G067700	chr5B	90.482	767	49	9	1990	2753	88705820	88706565	0.000000e+00	990.0
6	TraesCS5A01G067700	chr5B	90.413	605	56	2	2744	3347	701692062	701691459	0.000000e+00	795.0
7	TraesCS5A01G067700	chr5B	90.609	575	42	9	1	573	88778637	88779201	0.000000e+00	752.0
8	TraesCS5A01G067700	chr5B	78.561	695	138	10	2739	3430	191141850	191141164	7.280000e-122	448.0
9	TraesCS5A01G067700	chr5B	77.637	474	84	16	2092	2559	85180632	85181089	6.080000e-68	268.0
10	TraesCS5A01G067700	chrUn	93.779	1286	51	10	680	1954	227383814	227382547	0.000000e+00	1905.0
11	TraesCS5A01G067700	chrUn	90.609	575	42	9	1	573	227384868	227384304	0.000000e+00	752.0
12	TraesCS5A01G067700	chr5D	90.933	1147	87	6	1601	2744	79105720	79106852	0.000000e+00	1526.0
13	TraesCS5A01G067700	chr5D	82.477	1421	126	53	227	1608	79104239	79105575	0.000000e+00	1131.0
14	TraesCS5A01G067700	chr5D	95.658	691	24	1	1969	2659	79140022	79140706	0.000000e+00	1105.0
15	TraesCS5A01G067700	chr5D	87.875	800	50	16	594	1388	79137519	79138276	0.000000e+00	896.0
16	TraesCS5A01G067700	chr5D	90.261	575	43	10	1	573	79136721	79137284	0.000000e+00	739.0
17	TraesCS5A01G067700	chr5D	76.543	486	92	16	2092	2571	76754332	76753863	2.850000e-61	246.0
18	TraesCS5A01G067700	chr5D	96.154	78	2	1	2667	2744	79149610	79149686	3.870000e-25	126.0
19	TraesCS5A01G067700	chr7D	93.803	952	55	2	2743	3693	488802274	488801326	0.000000e+00	1428.0
20	TraesCS5A01G067700	chr7D	92.706	850	61	1	2845	3693	59879325	59878476	0.000000e+00	1225.0
21	TraesCS5A01G067700	chr2D	90.556	953	88	2	2742	3693	559216864	559217815	0.000000e+00	1260.0
22	TraesCS5A01G067700	chr2D	93.147	788	53	1	2907	3693	612757468	612756681	0.000000e+00	1155.0
23	TraesCS5A01G067700	chr4D	90.042	954	92	2	2743	3693	130448237	130449190	0.000000e+00	1232.0
24	TraesCS5A01G067700	chr6B	91.001	889	79	1	2806	3693	56072611	56073499	0.000000e+00	1197.0
25	TraesCS5A01G067700	chr6B	87.342	79	7	3	2746	2823	56072418	56072494	1.830000e-13	87.9
26	TraesCS5A01G067700	chr4B	89.357	949	97	2	2746	3693	67057549	67058494	0.000000e+00	1190.0
27	TraesCS5A01G067700	chr6D	90.888	878	79	1	2817	3693	144026774	144027651	0.000000e+00	1177.0
28	TraesCS5A01G067700	chr7B	89.850	867	83	4	2830	3693	463630252	463629388	0.000000e+00	1109.0
29	TraesCS5A01G067700	chr1A	89.015	883	71	11	894	1770	475709321	475710183	0.000000e+00	1070.0
30	TraesCS5A01G067700	chr1A	89.168	757	52	12	1990	2744	475710317	475711045	0.000000e+00	917.0
31	TraesCS5A01G067700	chr1A	89.406	623	45	7	2132	2753	475616056	475616658	0.000000e+00	765.0
32	TraesCS5A01G067700	chr1A	90.411	146	14	0	1818	1963	475710185	475710330	3.760000e-45	193.0
33	TraesCS5A01G067700	chr7A	83.120	468	72	6	2744	3208	204684966	204684503	1.590000e-113	420.0
34	TraesCS5A01G067700	chr2A	86.170	282	37	2	2744	3025	65240966	65241245	1.670000e-78	303.0
35	TraesCS5A01G067700	chr2B	86.441	59	2	5	217	273	362143195	362143249	3.980000e-05	60.2

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	TraesCS5A01G067700	chr5A	75047960	75051652	3692	False	6820.000000	6820	100.000000	1	3693	1	chr5A.!!$F1	3692
1	TraesCS5A01G067700	chr5B	88735444	88738154	2710	False	3513.000000	3513	90.069000	1	2744	1	chr5B.!!$F2	2743
2	TraesCS5A01G067700	chr5B	88704096	88706565	2469	False	1422.500000	1855	88.390000	224	2753	2	chr5B.!!$F3	2529
3	TraesCS5A01G067700	chr5B	88778637	88781938	3301	False	1305.000000	1905	93.582333	1	2724	3	chr5B.!!$F4	2723
4	TraesCS5A01G067700	chr5B	701691459	701692062	603	True	795.000000	795	90.413000	2744	3347	1	chr5B.!!$R2	603
5	TraesCS5A01G067700	chr5B	191141164	191141850	686	True	448.000000	448	78.561000	2739	3430	1	chr5B.!!$R1	691
6	TraesCS5A01G067700	chrUn	227382547	227384868	2321	True	1328.500000	1905	92.194000	1	1954	2	chrUn.!!$R1	1953
7	TraesCS5A01G067700	chr5D	79104239	79106852	2613	False	1328.500000	1526	86.705000	227	2744	2	chr5D.!!$F2	2517
8	TraesCS5A01G067700	chr5D	79136721	79140706	3985	False	913.333333	1105	91.264667	1	2659	3	chr5D.!!$F3	2658
9	TraesCS5A01G067700	chr7D	488801326	488802274	948	True	1428.000000	1428	93.803000	2743	3693	1	chr7D.!!$R2	950
10	TraesCS5A01G067700	chr7D	59878476	59879325	849	True	1225.000000	1225	92.706000	2845	3693	1	chr7D.!!$R1	848
11	TraesCS5A01G067700	chr2D	559216864	559217815	951	False	1260.000000	1260	90.556000	2742	3693	1	chr2D.!!$F1	951
12	TraesCS5A01G067700	chr2D	612756681	612757468	787	True	1155.000000	1155	93.147000	2907	3693	1	chr2D.!!$R1	786
13	TraesCS5A01G067700	chr4D	130448237	130449190	953	False	1232.000000	1232	90.042000	2743	3693	1	chr4D.!!$F1	950
14	TraesCS5A01G067700	chr6B	56072418	56073499	1081	False	642.450000	1197	89.171500	2746	3693	2	chr6B.!!$F1	947
15	TraesCS5A01G067700	chr4B	67057549	67058494	945	False	1190.000000	1190	89.357000	2746	3693	1	chr4B.!!$F1	947
16	TraesCS5A01G067700	chr6D	144026774	144027651	877	False	1177.000000	1177	90.888000	2817	3693	1	chr6D.!!$F1	876
17	TraesCS5A01G067700	chr7B	463629388	463630252	864	True	1109.000000	1109	89.850000	2830	3693	1	chr7B.!!$R1	863
18	TraesCS5A01G067700	chr1A	475616056	475616658	602	False	765.000000	765	89.406000	2132	2753	1	chr1A.!!$F1	621
19	TraesCS5A01G067700	chr1A	475709321	475711045	1724	False	726.666667	1070	89.531333	894	2744	3	chr1A.!!$F2	1850

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
656	1097	0.251474	ACTAGTCTGGCGGTGTGGTA	60.251	55.0	0.0	0.0	0.0	3.25	F
1063	1598	0.248843	CGAGGAAGAGGAAAGCAGCT	59.751	55.0	0.0	0.0	0.0	4.24	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2490	4420	0.173708	GCCAAGAAGTCCTCGTCGAT	59.826	55.0	0.0	0.0	0.0	3.59	R
3011	5078	0.097325	TGGAACGAACGCAACACAAC	59.903	50.0	0.0	0.0	0.0	3.32	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
57	58	4.092237	GCATATGCGCCGTATTTGTATGTA	59.908	41.667	12.82	0.00	0.00	2.29
93	94	3.003275	ACTTCAATGTGTACCGCAAGTTG	59.997	43.478	0.00	0.00	0.00	3.16
97	98	4.757657	TCAATGTGTACCGCAAGTTGTAAT	59.242	37.500	4.48	0.00	0.00	1.89
104	105	7.440556	TGTGTACCGCAAGTTGTAATAGTAAAA	59.559	33.333	4.48	0.00	0.00	1.52
130	131	0.388659	TTTGCGCCAAGTTCAAGCAT	59.611	45.000	4.18	0.00	37.68	3.79
131	132	1.242989	TTGCGCCAAGTTCAAGCATA	58.757	45.000	4.18	0.00	37.68	3.14
261	262	8.723311	CCAATGTTAATGAAAATGACAAGCAAT	58.277	29.630	0.00	0.00	0.00	3.56
318	320	2.355010	AGGGATTCTTGGTATGCAGC	57.645	50.000	0.00	0.00	0.00	5.25
319	321	0.947244	GGGATTCTTGGTATGCAGCG	59.053	55.000	0.00	0.00	0.00	5.18
320	322	0.947244	GGATTCTTGGTATGCAGCGG	59.053	55.000	0.00	0.00	0.00	5.52
325	327	1.002746	TTGGTATGCAGCGGCTTCA	60.003	52.632	10.92	4.50	41.91	3.02
338	340	1.068333	CGGCTTCACTTTGGTTGATGG	60.068	52.381	0.00	0.00	0.00	3.51
454	469	4.335416	TCAAAAGAAGCACTAATGGAGGG	58.665	43.478	0.00	0.00	0.00	4.30
526	543	5.001237	TGTGTCAAAACTCTCGTCTACAA	57.999	39.130	0.00	0.00	0.00	2.41
581	630	1.610554	GGCCAGAATGTTGCCAGCAT	61.611	55.000	0.00	0.00	42.19	3.79
608	1049	5.448225	CGCTCACTAAACGTATGTCCTCTTA	60.448	44.000	0.00	0.00	0.00	2.10
634	1075	3.939939	TCAGCCGCTGCAGTCCAA	61.940	61.111	15.98	0.00	41.13	3.53
635	1076	3.429141	CAGCCGCTGCAGTCCAAG	61.429	66.667	16.64	0.96	41.13	3.61
636	1077	3.946201	AGCCGCTGCAGTCCAAGT	61.946	61.111	16.64	0.00	41.13	3.16
637	1078	2.047274	GCCGCTGCAGTCCAAGTA	60.047	61.111	16.64	0.00	37.47	2.24
638	1079	2.391389	GCCGCTGCAGTCCAAGTAC	61.391	63.158	16.64	0.00	37.47	2.73
639	1080	1.293498	CCGCTGCAGTCCAAGTACT	59.707	57.895	16.64	0.00	0.00	2.73
656	1097	0.251474	ACTAGTCTGGCGGTGTGGTA	60.251	55.000	0.00	0.00	0.00	3.25
675	1116	4.081862	TGGTAACGGAGAATGAAGACGAAT	60.082	41.667	0.00	0.00	42.51	3.34
676	1117	4.267928	GGTAACGGAGAATGAAGACGAATG	59.732	45.833	0.00	0.00	0.00	2.67
754	1250	2.409570	GTGGAGAATTAGGGTAGGCCT	58.590	52.381	11.78	11.78	34.45	5.19
794	1290	7.093992	GGAATGAGATTTTATAGGACCGAGAG	58.906	42.308	0.00	0.00	0.00	3.20
849	1345	0.320374	CCGTCCAACCAGCTAGACAA	59.680	55.000	0.00	0.00	0.00	3.18
878	1374	6.303903	ACAGTTTCCTATTTATACGGTGGT	57.696	37.500	0.00	0.00	0.00	4.16
879	1375	6.714278	ACAGTTTCCTATTTATACGGTGGTT	58.286	36.000	0.00	0.00	0.00	3.67
880	1376	6.820152	ACAGTTTCCTATTTATACGGTGGTTC	59.180	38.462	0.00	0.00	0.00	3.62
881	1377	6.259387	CAGTTTCCTATTTATACGGTGGTTCC	59.741	42.308	0.00	0.00	0.00	3.62
882	1378	4.961438	TCCTATTTATACGGTGGTTCCC	57.039	45.455	0.00	0.00	0.00	3.97
883	1379	4.559726	TCCTATTTATACGGTGGTTCCCT	58.440	43.478	0.00	0.00	0.00	4.20
884	1380	4.590222	TCCTATTTATACGGTGGTTCCCTC	59.410	45.833	0.00	0.00	0.00	4.30
885	1381	3.851458	ATTTATACGGTGGTTCCCTCC	57.149	47.619	0.00	0.00	34.16	4.30
890	1386	3.400188	GGTGGTTCCCTCCGTCAT	58.600	61.111	0.00	0.00	0.00	3.06
891	1387	1.221021	GGTGGTTCCCTCCGTCATC	59.779	63.158	0.00	0.00	0.00	2.92
892	1388	1.153628	GTGGTTCCCTCCGTCATCG	60.154	63.158	0.00	0.00	0.00	3.84
905	1425	0.385974	GTCATCGCAAACCAGCACAC	60.386	55.000	0.00	0.00	0.00	3.82
906	1426	1.440850	CATCGCAAACCAGCACACG	60.441	57.895	0.00	0.00	0.00	4.49
907	1427	2.616330	ATCGCAAACCAGCACACGG	61.616	57.895	0.00	0.00	0.00	4.94
909	1429	2.331451	GCAAACCAGCACACGGAC	59.669	61.111	0.00	0.00	0.00	4.79
910	1430	2.477176	GCAAACCAGCACACGGACA	61.477	57.895	0.00	0.00	0.00	4.02
955	1486	4.742201	TGCTTCGGCGGCTCTGAC	62.742	66.667	7.21	0.00	45.37	3.51
1063	1598	0.248843	CGAGGAAGAGGAAAGCAGCT	59.751	55.000	0.00	0.00	0.00	4.24
1151	1692	2.582436	GAGGCGGATCGGGTGAAA	59.418	61.111	2.13	0.00	0.00	2.69
1154	1695	0.463833	AGGCGGATCGGGTGAAAATC	60.464	55.000	2.13	0.00	0.00	2.17
1210	1751	3.418047	TGCGATCCTCGGTGAGATAATA	58.582	45.455	0.00	0.00	40.84	0.98
1309	1850	1.215647	GAACCTCGACTGCCGTCAT	59.784	57.895	9.06	0.00	40.23	3.06
1457	2004	0.760945	CTGTCTCCTATCCCCCGCTT	60.761	60.000	0.00	0.00	0.00	4.68
1622	3332	3.491652	GGCTTCAGCGGCTCGAAC	61.492	66.667	0.00	3.56	43.26	3.95
1772	3482	5.468746	AGAAGCGTTACAGTCAGCAATTTTA	59.531	36.000	0.00	0.00	0.00	1.52
1831	3544	0.250338	GTGCCCCTTGTCTCGAAAGT	60.250	55.000	0.00	0.00	0.00	2.66
1874	3587	2.627945	GGGATTTGCGTGTATCAGTGA	58.372	47.619	0.00	0.00	0.00	3.41
1976	3906	5.191722	ACTCCAGCCTTAATCATTCTTACCA	59.808	40.000	0.00	0.00	0.00	3.25
2112	4042	2.223782	GCACAATCAAGTGTTTGGCTCA	60.224	45.455	6.96	0.00	41.52	4.26
2113	4043	3.737663	GCACAATCAAGTGTTTGGCTCAA	60.738	43.478	6.96	0.00	41.52	3.02
2215	4145	6.375455	AGGTGATGATTAATTGTTCACTGACC	59.625	38.462	18.13	8.40	37.45	4.02
2390	4320	6.072728	TCCGTCTGAAAATTATGGTGTTGAAG	60.073	38.462	0.00	0.00	0.00	3.02
2560	4490	1.303561	GGGCTTCACATGGTGCTCA	60.304	57.895	0.00	0.00	32.98	4.26
2638	4568	8.740123	TGAGTGGTAGTTTTGAAAATACTTCA	57.260	30.769	12.13	10.79	38.91	3.02
2661	4591	5.304686	TGTTTGGTCCAGTGAGAAGTTAT	57.695	39.130	0.00	0.00	0.00	1.89
2724	4654	6.554334	ACAACGATTAGCTATTGTGTTTGT	57.446	33.333	9.17	5.29	34.08	2.83
2725	4655	6.370593	ACAACGATTAGCTATTGTGTTTGTG	58.629	36.000	9.17	0.50	34.08	3.33
2791	4722	4.082026	GCAGCTTTTCATTGATACTTGGGT	60.082	41.667	0.00	0.00	0.00	4.51
2792	4723	5.567423	GCAGCTTTTCATTGATACTTGGGTT	60.567	40.000	0.00	0.00	0.00	4.11
2793	4724	6.458210	CAGCTTTTCATTGATACTTGGGTTT	58.542	36.000	0.00	0.00	0.00	3.27
2888	4955	5.194432	CCTGTAGTGAGCTTTCCTAGTCTA	58.806	45.833	0.00	0.00	0.00	2.59
3011	5078	4.552767	GCGATGGTTGGTTTCTGAATATCG	60.553	45.833	0.00	0.00	38.23	2.92
3015	5082	5.067273	TGGTTGGTTTCTGAATATCGTTGT	58.933	37.500	0.00	0.00	0.00	3.32
3052	5119	1.227823	CGACCACCAAACCAGCTGA	60.228	57.895	17.39	0.00	0.00	4.26
3066	5133	3.175240	CTGAACGAGTGCGCTCCG	61.175	66.667	21.21	17.49	42.48	4.63
3086	5153	2.543445	CGTGGCTTCTTTGTTGATGCAA	60.543	45.455	0.00	0.00	38.40	4.08
3125	5192	0.036010	CTCGATCCAAAGCACCAGGT	60.036	55.000	0.00	0.00	0.00	4.00
3126	5193	0.400213	TCGATCCAAAGCACCAGGTT	59.600	50.000	0.00	0.00	36.96	3.50
3130	5197	2.270352	TCCAAAGCACCAGGTTAGTG	57.730	50.000	0.00	0.00	38.30	2.74
3184	5251	2.092374	GCAGCGAGCAATGATGTCA	58.908	52.632	0.00	0.00	44.79	3.58
3241	5308	0.811616	GGTGCACGACATCCTCCATC	60.812	60.000	11.45	0.00	0.00	3.51
3291	5358	2.607750	AGGCCAGCCTTTCCTCGA	60.608	61.111	5.04	0.00	45.70	4.04
3459	5527	3.276846	ACGCCGTTTGCTGTCCAC	61.277	61.111	0.00	0.00	38.05	4.02
3465	5533	1.238439	CGTTTGCTGTCCACTTCCAT	58.762	50.000	0.00	0.00	0.00	3.41
3468	5536	0.961019	TTGCTGTCCACTTCCATTGC	59.039	50.000	0.00	0.00	0.00	3.56
3534	5602	3.500343	CCACAGTTTCAGGAATTCCCTT	58.500	45.455	21.22	0.00	44.85	3.95
3537	5605	4.342092	CACAGTTTCAGGAATTCCCTTGTT	59.658	41.667	21.22	0.00	44.85	2.83
3600	5668	1.165907	TGTTCTCCAAGGCTTGTGCG	61.166	55.000	24.57	10.70	40.82	5.34
3638	5706	1.535860	GGTGCAATGCTGAAACAACGT	60.536	47.619	6.82	0.00	0.00	3.99
3677	5745	2.156098	GTTGATGCCCTTAAACCACGA	58.844	47.619	0.00	0.00	0.00	4.35

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
9	10	1.591158	CGCAGACGTTAACTGTGTTGT	59.409	47.619	3.71	0.00	39.88	3.32
37	38	5.177881	CCTTTACATACAAATACGGCGCATA	59.822	40.000	10.83	0.32	0.00	3.14
57	58	7.781056	ACACATTGAAGTGATACAAAACCTTT	58.219	30.769	0.57	0.00	42.05	3.11
93	94	6.356190	GGCGCAAACGATCATTTTACTATTAC	59.644	38.462	10.83	0.00	43.93	1.89
97	98	3.685272	TGGCGCAAACGATCATTTTACTA	59.315	39.130	10.83	0.00	43.93	1.82
104	105	0.881118	AACTTGGCGCAAACGATCAT	59.119	45.000	10.83	0.00	43.93	2.45
130	131	3.193267	ACACGAGTAAATTACACCGGCTA	59.807	43.478	17.29	0.00	33.45	3.93
131	132	2.028748	ACACGAGTAAATTACACCGGCT	60.029	45.455	17.29	0.00	33.45	5.52
221	222	9.354673	TCATTAACATTGGAAAAGAGAGAGTTT	57.645	29.630	0.00	0.00	0.00	2.66
261	262	5.336150	TGTTTTCCAAGAAGCAACAATCA	57.664	34.783	0.00	0.00	0.00	2.57
318	320	1.068333	CCATCAACCAAAGTGAAGCCG	60.068	52.381	0.00	0.00	0.00	5.52
319	321	1.963515	ACCATCAACCAAAGTGAAGCC	59.036	47.619	0.00	0.00	0.00	4.35
320	322	2.887152	AGACCATCAACCAAAGTGAAGC	59.113	45.455	0.00	0.00	0.00	3.86
338	340	9.003658	TCCAGTTCAAGAAATTAAGATGAAGAC	57.996	33.333	0.00	0.00	31.24	3.01
446	460	2.605299	GGCATGGCTCCCTCCATT	59.395	61.111	12.86	0.00	44.04	3.16
526	543	1.725066	CGTGGACAACCGCAACTTT	59.275	52.632	0.00	0.00	46.01	2.66
581	630	3.495193	GACATACGTTTAGTGAGCGACA	58.505	45.455	0.00	0.00	35.76	4.35
630	1071	1.272313	ACCGCCAGACTAGTACTTGGA	60.272	52.381	19.49	0.00	0.00	3.53
631	1072	1.135083	CACCGCCAGACTAGTACTTGG	60.135	57.143	0.00	13.57	0.00	3.61
634	1075	1.174783	CACACCGCCAGACTAGTACT	58.825	55.000	0.00	0.00	0.00	2.73
635	1076	0.172803	CCACACCGCCAGACTAGTAC	59.827	60.000	0.00	0.00	0.00	2.73
636	1077	0.251474	ACCACACCGCCAGACTAGTA	60.251	55.000	0.00	0.00	0.00	1.82
637	1078	0.251474	TACCACACCGCCAGACTAGT	60.251	55.000	0.00	0.00	0.00	2.57
638	1079	0.892755	TTACCACACCGCCAGACTAG	59.107	55.000	0.00	0.00	0.00	2.57
639	1080	0.604578	GTTACCACACCGCCAGACTA	59.395	55.000	0.00	0.00	0.00	2.59
656	1097	3.056107	TCCATTCGTCTTCATTCTCCGTT	60.056	43.478	0.00	0.00	0.00	4.44
675	1116	2.574450	GTTCCGTTACAAAACCCTCCA	58.426	47.619	0.00	0.00	31.46	3.86
676	1117	1.532437	CGTTCCGTTACAAAACCCTCC	59.468	52.381	0.00	0.00	31.46	4.30
849	1345	6.927381	CCGTATAAATAGGAAACTGTCGGATT	59.073	38.462	0.00	0.00	43.88	3.01
878	1374	0.672401	GTTTGCGATGACGGAGGGAA	60.672	55.000	0.00	0.00	41.35	3.97
879	1375	1.079405	GTTTGCGATGACGGAGGGA	60.079	57.895	0.00	0.00	41.35	4.20
880	1376	2.106683	GGTTTGCGATGACGGAGGG	61.107	63.158	0.00	0.00	41.35	4.30
881	1377	1.361668	CTGGTTTGCGATGACGGAGG	61.362	60.000	0.00	0.00	41.35	4.30
882	1378	1.970917	GCTGGTTTGCGATGACGGAG	61.971	60.000	0.00	0.00	41.35	4.63
883	1379	2.032634	GCTGGTTTGCGATGACGGA	61.033	57.895	0.00	0.00	40.15	4.69
884	1380	2.324330	TGCTGGTTTGCGATGACGG	61.324	57.895	0.00	0.00	40.15	4.79
885	1381	1.154413	GTGCTGGTTTGCGATGACG	60.154	57.895	0.00	0.00	42.93	4.35
886	1382	0.385974	GTGTGCTGGTTTGCGATGAC	60.386	55.000	0.00	0.00	35.36	3.06
887	1383	1.840630	CGTGTGCTGGTTTGCGATGA	61.841	55.000	0.00	0.00	35.36	2.92
888	1384	1.440850	CGTGTGCTGGTTTGCGATG	60.441	57.895	0.00	0.00	35.36	3.84
889	1385	2.616330	CCGTGTGCTGGTTTGCGAT	61.616	57.895	0.00	0.00	35.36	4.58
890	1386	3.276091	CCGTGTGCTGGTTTGCGA	61.276	61.111	0.00	0.00	35.36	5.10
891	1387	3.276091	TCCGTGTGCTGGTTTGCG	61.276	61.111	0.00	0.00	35.36	4.85
892	1388	2.331451	GTCCGTGTGCTGGTTTGC	59.669	61.111	0.00	0.00	0.00	3.68
905	1425	2.608261	GGAGAGAGTGTTTCTGTGTCCG	60.608	54.545	0.00	0.00	39.38	4.79
906	1426	2.289133	GGGAGAGAGTGTTTCTGTGTCC	60.289	54.545	0.71	0.71	45.21	4.02
907	1427	2.289133	GGGGAGAGAGTGTTTCTGTGTC	60.289	54.545	0.00	0.00	35.87	3.67
909	1429	1.694150	TGGGGAGAGAGTGTTTCTGTG	59.306	52.381	0.00	0.00	35.87	3.66
910	1430	1.974236	CTGGGGAGAGAGTGTTTCTGT	59.026	52.381	0.00	0.00	35.87	3.41
955	1486	1.630148	GGTGGAAGAACACGAGATCG	58.370	55.000	0.00	0.00	42.23	3.69
1147	1688	2.930040	GTCGAGATCTTGCCGATTTTCA	59.070	45.455	8.09	0.00	34.71	2.69
1151	1692	0.249073	CGGTCGAGATCTTGCCGATT	60.249	55.000	28.02	0.00	44.57	3.34
1154	1695	2.956964	GCGGTCGAGATCTTGCCG	60.957	66.667	27.81	27.81	44.60	5.69
1210	1751	1.308216	CTTGGTGGGGAGGAGGGAT	60.308	63.158	0.00	0.00	0.00	3.85
1283	1824	3.692406	GTCGAGGTTCAGGGGCGT	61.692	66.667	0.00	0.00	0.00	5.68
1447	1994	2.757124	CCTAGCCAAAGCGGGGGAT	61.757	63.158	0.00	0.00	46.67	3.85
1457	2004	3.941081	CTCCTCGAGCCTAGCCAA	58.059	61.111	6.99	0.00	0.00	4.52
1622	3332	2.031314	CCGTGATGCTGCTATGAACAAG	59.969	50.000	0.00	0.00	0.00	3.16
1831	3544	5.257262	CGGTCCTGATCTAGATGGAATAGA	58.743	45.833	10.74	0.00	33.93	1.98
1874	3587	2.094182	TCTCAAACTTAGGCGCGAAGAT	60.094	45.455	23.02	11.64	0.00	2.40
1963	3893	9.829507	CTAGAAGTCTCAATGGTAAGAATGATT	57.170	33.333	0.00	0.00	0.00	2.57
1964	3894	8.986991	ACTAGAAGTCTCAATGGTAAGAATGAT	58.013	33.333	0.00	0.00	0.00	2.45
1976	3906	7.147637	GGGATGGAAGTTACTAGAAGTCTCAAT	60.148	40.741	0.00	0.00	0.00	2.57
2112	4042	5.010282	CCAAACTAAGAGTGGGCATAGTTT	58.990	41.667	4.43	4.43	44.90	2.66
2113	4043	4.288626	TCCAAACTAAGAGTGGGCATAGTT	59.711	41.667	0.00	0.00	39.57	2.24
2115	4045	4.487714	TCCAAACTAAGAGTGGGCATAG	57.512	45.455	0.00	0.00	32.95	2.23
2215	4145	3.733684	GCCGCCAAACACAAGGTATTATG	60.734	47.826	0.00	0.00	0.00	1.90
2390	4320	4.879545	TCTGGTTTTCTGCCGGAATAATAC	59.120	41.667	5.05	0.00	38.36	1.89
2490	4420	0.173708	GCCAAGAAGTCCTCGTCGAT	59.826	55.000	0.00	0.00	0.00	3.59
2491	4421	1.176619	TGCCAAGAAGTCCTCGTCGA	61.177	55.000	0.00	0.00	0.00	4.20
2492	4422	0.319555	TTGCCAAGAAGTCCTCGTCG	60.320	55.000	0.00	0.00	0.00	5.12
2493	4423	1.878953	TTTGCCAAGAAGTCCTCGTC	58.121	50.000	0.00	0.00	0.00	4.20
2494	4424	1.947456	GTTTTGCCAAGAAGTCCTCGT	59.053	47.619	0.00	0.00	0.00	4.18
2495	4425	1.946768	TGTTTTGCCAAGAAGTCCTCG	59.053	47.619	0.00	0.00	0.00	4.63
2560	4490	2.032030	CGTTCCGCAGTGAAATGAAACT	60.032	45.455	0.00	0.00	0.00	2.66
2638	4568	3.864789	ACTTCTCACTGGACCAAACAT	57.135	42.857	0.00	0.00	0.00	2.71
2695	4625	5.121611	CACAATAGCTAATCGTTGTTGGACA	59.878	40.000	7.55	0.00	32.87	4.02
2888	4955	3.309296	TCCTCAACAGACCAAGAGAACT	58.691	45.455	0.00	0.00	0.00	3.01
3011	5078	0.097325	TGGAACGAACGCAACACAAC	59.903	50.000	0.00	0.00	0.00	3.32
3015	5082	1.656594	CGATATGGAACGAACGCAACA	59.343	47.619	0.00	0.00	0.00	3.33
3066	5133	2.798976	TGCATCAACAAAGAAGCCAC	57.201	45.000	0.00	0.00	31.61	5.01
3086	5153	3.825014	GAGCAGTCCAATGGCATCATTAT	59.175	43.478	0.00	0.00	41.29	1.28
3125	5192	1.131303	CCCTCCACCACCACCACTAA	61.131	60.000	0.00	0.00	0.00	2.24
3126	5193	1.537889	CCCTCCACCACCACCACTA	60.538	63.158	0.00	0.00	0.00	2.74
3130	5197	4.035102	GCTCCCTCCACCACCACC	62.035	72.222	0.00	0.00	0.00	4.61
3241	5308	1.233285	GCTCTCTATGCAATGGGCCG	61.233	60.000	0.00	0.00	43.89	6.13
3291	5358	1.537990	GCAACACGGCCAATGTTCTTT	60.538	47.619	17.44	0.00	38.22	2.52
3459	5527	0.933097	CCGATCGAGTGCAATGGAAG	59.067	55.000	18.66	0.70	0.00	3.46
3465	5533	1.888436	AAGAGCCCGATCGAGTGCAA	61.888	55.000	18.66	0.00	0.00	4.08
3468	5536	0.803768	CACAAGAGCCCGATCGAGTG	60.804	60.000	18.66	9.21	0.00	3.51
3506	5574	0.326264	CCTGAAACTGTGGGAGGGAG	59.674	60.000	0.00	0.00	0.00	4.30
3508	5576	0.771127	TTCCTGAAACTGTGGGAGGG	59.229	55.000	0.00	0.00	0.00	4.30

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.