AutoCloner

Multiple sequence alignment - TraesCS3A01G069400

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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	TraesCS3A01G069400	chr3A	100.000	4593	0	0	1	4593	41654161	41649569	0.000000e+00	8482.0
1	TraesCS3A01G069400	chr3A	97.685	216	4	1	3963	4177	41645156	41644941	2.020000e-98	370.0
2	TraesCS3A01G069400	chr3D	96.939	3398	67	12	1	3389	30088923	30085554	0.000000e+00	5664.0
3	TraesCS3A01G069400	chr3D	97.549	612	14	1	3352	3962	30085555	30084944	0.000000e+00	1046.0
4	TraesCS3A01G069400	chr3D	82.645	363	49	9	2267	2618	608203284	608202925	4.460000e-80	309.0
5	TraesCS3A01G069400	chr3D	80.930	215	36	4	2453	2664	95953356	95953144	1.020000e-36	165.0
6	TraesCS3A01G069400	chr7A	96.835	632	18	2	3963	4593	54947193	54947823	0.000000e+00	1055.0
7	TraesCS3A01G069400	chr7A	83.208	399	43	9	2283	2657	11356278	11355880	1.220000e-90	344.0
8	TraesCS3A01G069400	chr7A	96.190	210	6	2	3963	4171	54960955	54961163	4.400000e-90	342.0
9	TraesCS3A01G069400	chr7A	78.095	420	69	16	2263	2661	674736708	674737125	1.280000e-60	244.0
10	TraesCS3A01G069400	chr7A	78.043	419	70	16	2263	2661	674751443	674751859	1.280000e-60	244.0
11	TraesCS3A01G069400	chr7A	95.833	48	2	0	361	408	553237182	553237135	1.370000e-10	78.7
12	TraesCS3A01G069400	chr4A	93.981	648	24	7	3960	4593	30355843	30356489	0.000000e+00	966.0
13	TraesCS3A01G069400	chr4A	82.597	362	49	14	2309	2661	633052170	633052526	1.610000e-79	307.0
14	TraesCS3A01G069400	chr4A	87.892	223	12	7	3963	4171	30361227	30361448	9.870000e-62	248.0
15	TraesCS3A01G069400	chr4A	81.435	237	33	7	2267	2494	671600631	671600397	2.820000e-42	183.0
16	TraesCS3A01G069400	chr4A	96.364	55	1	1	1097	1150	734874293	734874239	6.330000e-14	89.8
17	TraesCS3A01G069400	chr4A	96.364	55	1	1	1097	1150	736112588	736112534	6.330000e-14	89.8
18	TraesCS3A01G069400	chr3B	93.199	647	27	7	3961	4593	572261253	572260610	0.000000e+00	935.0
19	TraesCS3A01G069400	chr3B	91.553	438	32	1	4156	4593	556423009	556423441	2.360000e-167	599.0
20	TraesCS3A01G069400	chr3B	86.547	223	15	7	3963	4171	572256193	572255972	9.940000e-57	231.0
21	TraesCS3A01G069400	chr7B	95.423	568	23	3	4027	4593	696257005	696257570	0.000000e+00	902.0
22	TraesCS3A01G069400	chr7B	91.950	646	36	8	3962	4593	47596067	47596710	0.000000e+00	891.0
23	TraesCS3A01G069400	chr7B	86.996	223	14	10	3963	4171	696270590	696270811	2.140000e-58	237.0
24	TraesCS3A01G069400	chr7B	86.161	224	15	8	3963	4172	47601144	47601365	1.290000e-55	228.0
25	TraesCS3A01G069400	chr7B	94.643	56	1	2	1107	1162	165100268	165100215	8.190000e-13	86.1
26	TraesCS3A01G069400	chr1B	93.519	432	28	0	4162	4593	474664353	474663922	1.080000e-180	643.0
27	TraesCS3A01G069400	chr2A	92.361	432	33	0	4162	4593	395894273	395893842	2.350000e-172	616.0
28	TraesCS3A01G069400	chr4B	92.891	422	30	0	4172	4593	638831159	638831580	8.450000e-172	614.0
29	TraesCS3A01G069400	chr4B	94.231	52	3	0	359	410	89928343	89928394	3.810000e-11	80.5
30	TraesCS3A01G069400	chr4B	91.489	47	4	0	254	300	656133941	656133895	1.070000e-06	65.8
31	TraesCS3A01G069400	chr4B	89.362	47	5	0	2380	2426	665417779	665417733	4.960000e-05	60.2
32	TraesCS3A01G069400	chr5B	82.482	411	50	17	2267	2664	123767931	123767530	1.580000e-89	340.0
33	TraesCS3A01G069400	chr5B	93.443	61	4	0	3962	4022	590567758	590567818	1.760000e-14	91.6
34	TraesCS3A01G069400	chr5A	81.351	370	56	10	2264	2626	555595516	555595153	5.810000e-74	289.0
35	TraesCS3A01G069400	chr5A	98.077	52	0	1	1099	1150	601437150	601437100	6.330000e-14	89.8
36	TraesCS3A01G069400	chr5A	95.918	49	2	0	360	408	320566000	320565952	3.810000e-11	80.5
37	TraesCS3A01G069400	chr5A	94.000	50	3	0	359	408	749942	749893	4.930000e-10	76.8
38	TraesCS3A01G069400	chr5D	80.863	371	54	13	2264	2626	439979436	439979075	4.530000e-70	276.0
39	TraesCS3A01G069400	chr6A	79.598	348	50	13	2281	2618	403322970	403323306	3.570000e-56	230.0
40	TraesCS3A01G069400	chr6A	98.077	52	1	0	1099	1150	581742973	581742922	1.760000e-14	91.6
41	TraesCS3A01G069400	chr7D	76.750	400	63	15	2267	2661	51452263	51452637	3.630000e-46	196.0
42	TraesCS3A01G069400	chr7D	78.205	234	31	8	2267	2491	476009948	476010170	1.040000e-26	132.0
43	TraesCS3A01G069400	chr7D	83.544	79	10	2	334	409	615768964	615768886	2.290000e-08	71.3
44	TraesCS3A01G069400	chr6D	98.148	54	0	1	1098	1150	382611184	382611131	4.890000e-15	93.5
45	TraesCS3A01G069400	chr6D	89.552	67	4	3	1085	1148	30079493	30079427	1.060000e-11	82.4
46	TraesCS3A01G069400	chr2B	91.429	70	3	2	342	408	433113472	433113403	4.890000e-15	93.5
47	TraesCS3A01G069400	chr2B	82.278	79	11	1	333	408	9827821	9827899	1.070000e-06	65.8
48	TraesCS3A01G069400	chr4D	94.643	56	2	1	1096	1150	447129610	447129555	8.190000e-13	86.1
49	TraesCS3A01G069400	chr1D	96.000	50	2	0	359	408	387891084	387891035	1.060000e-11	82.4

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	TraesCS3A01G069400	chr3A	41649569	41654161	4592	True	8482	8482	100.000	1	4593	1	chr3A.!!$R2	4592
1	TraesCS3A01G069400	chr3D	30084944	30088923	3979	True	3355	5664	97.244	1	3962	2	chr3D.!!$R3	3961
2	TraesCS3A01G069400	chr7A	54947193	54947823	630	False	1055	1055	96.835	3963	4593	1	chr7A.!!$F1	630
3	TraesCS3A01G069400	chr4A	30355843	30356489	646	False	966	966	93.981	3960	4593	1	chr4A.!!$F1	633
4	TraesCS3A01G069400	chr3B	572260610	572261253	643	True	935	935	93.199	3961	4593	1	chr3B.!!$R2	632
5	TraesCS3A01G069400	chr7B	696257005	696257570	565	False	902	902	95.423	4027	4593	1	chr7B.!!$F3	566
6	TraesCS3A01G069400	chr7B	47596067	47596710	643	False	891	891	91.950	3962	4593	1	chr7B.!!$F1	631

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
262	263	0.098728	GACACCGGGCATGAAATTCG	59.901	55.0	6.32	0.00	3.34	F
275	276	0.101399	AAATTCGCCGTGTTTGCACA	59.899	45.0	0.00	45.50	4.57	F
1445	1449	0.039978	AGCAGAGTTCGAGTCACACG	60.040	55.0	0.00	0.00	4.49	F
3063	3072	0.247655	CGTCCATACGCAACATGCAC	60.248	55.0	2.99	45.36	4.57	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Hairpin	End Stability	Orientation
1299	1303	1.625616	AGAGCGATGTACGTTTTCCG	58.374	50.000	0.00	44.60	4.30	R
1513	1519	2.455032	GAGTCACATCCTCGTCATTCG	58.545	52.381	0.00	41.41	3.34	R
3392	3437	0.034089	GATGGGGGAGAAGTTGGGTG	60.034	60.000	0.00	0.00	4.61	R
4046	4105	1.002134	CGGTTGGCAATCTCCACCT	60.002	57.895	9.12	35.50	4.00	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
86	87	5.752098	AATGTACTCGCAAGTAACGTAAC	57.248	39.130	0.00	0.00	39.66	2.50
184	185	3.769536	CGAATTCCCAATAACAACAGGC	58.230	45.455	0.00	0.00	0.00	4.85
192	193	3.242284	CCAATAACAACAGGCGTATCACG	60.242	47.826	0.00	0.00	45.88	4.35
224	225	1.656818	AACTTGCGCTTGCGCCATAT	61.657	50.000	32.10	16.35	43.34	1.78
236	237	5.569059	GCTTGCGCCATATATAACAATCAAC	59.431	40.000	4.18	0.00	0.00	3.18
262	263	0.098728	GACACCGGGCATGAAATTCG	59.901	55.000	6.32	0.00	0.00	3.34
275	276	0.101399	AAATTCGCCGTGTTTGCACA	59.899	45.000	0.00	0.00	45.50	4.57
282	283	1.071568	GCCGTGTTTGCACAAATTTCG	60.072	47.619	0.00	5.18	45.50	3.46
286	287	3.182967	GTGTTTGCACAAATTTCGTCCA	58.817	40.909	0.00	0.00	44.64	4.02
291	292	3.388308	TGCACAAATTTCGTCCAATTGG	58.612	40.909	19.08	19.08	0.00	3.16
326	327	9.289303	GTAATTAAATGTATGCAAACAGTCTGG	57.711	33.333	4.53	0.00	31.70	3.86
365	366	2.741985	TGCATCTGTGGCGAACGG	60.742	61.111	0.00	0.00	36.38	4.44
559	560	3.845259	TACGCATGGCCGTCTCCC	61.845	66.667	0.00	0.00	42.20	4.30
562	563	4.241555	GCATGGCCGTCTCCCGAT	62.242	66.667	0.00	0.00	39.56	4.18
563	564	2.280389	CATGGCCGTCTCCCGATG	60.280	66.667	0.00	0.00	39.56	3.84
564	565	4.241555	ATGGCCGTCTCCCGATGC	62.242	66.667	0.00	0.00	39.56	3.91
576	577	0.758734	CCCGATGCCTTGGACTATCA	59.241	55.000	0.00	0.00	0.00	2.15
578	579	2.224621	CCCGATGCCTTGGACTATCAAT	60.225	50.000	0.00	0.00	0.00	2.57
579	580	3.007940	CCCGATGCCTTGGACTATCAATA	59.992	47.826	0.00	0.00	0.00	1.90
580	581	3.997021	CCGATGCCTTGGACTATCAATAC	59.003	47.826	0.00	0.00	0.00	1.89
581	582	4.262635	CCGATGCCTTGGACTATCAATACT	60.263	45.833	0.00	0.00	0.00	2.12
582	583	5.047306	CCGATGCCTTGGACTATCAATACTA	60.047	44.000	0.00	0.00	0.00	1.82
583	584	5.864474	CGATGCCTTGGACTATCAATACTAC	59.136	44.000	0.00	0.00	0.00	2.73
585	586	4.347000	TGCCTTGGACTATCAATACTACCC	59.653	45.833	0.00	0.00	0.00	3.69
587	588	5.013183	GCCTTGGACTATCAATACTACCCAT	59.987	44.000	0.00	0.00	0.00	4.00
588	589	6.212791	GCCTTGGACTATCAATACTACCCATA	59.787	42.308	0.00	0.00	0.00	2.74
589	590	7.579723	GCCTTGGACTATCAATACTACCCATAG	60.580	44.444	0.00	0.00	34.25	2.23
590	591	7.093289	CCTTGGACTATCAATACTACCCATAGG	60.093	44.444	0.00	0.00	40.04	2.57
753	757	0.240945	CTTTGCCTAAAGGTGCACCG	59.759	55.000	29.68	16.36	39.67	4.94
858	862	7.666623	TCTAAGCATCATATAACCATCGTTCA	58.333	34.615	0.00	0.00	33.17	3.18
1063	1067	1.265635	CAAATCGAGCAACACGGGAAA	59.734	47.619	0.00	0.00	0.00	3.13
1117	1121	5.316987	AGGAAAATGTTTGTACTCCCTCTG	58.683	41.667	0.00	0.00	0.00	3.35
1237	1241	4.054780	AGTGTCTTGCTCAACTTTCGTA	57.945	40.909	0.00	0.00	0.00	3.43
1238	1242	3.802685	AGTGTCTTGCTCAACTTTCGTAC	59.197	43.478	0.00	0.00	0.00	3.67
1239	1243	2.792674	TGTCTTGCTCAACTTTCGTACG	59.207	45.455	9.53	9.53	0.00	3.67
1240	1244	2.793232	GTCTTGCTCAACTTTCGTACGT	59.207	45.455	16.05	0.00	0.00	3.57
1241	1245	3.244579	GTCTTGCTCAACTTTCGTACGTT	59.755	43.478	16.05	0.00	0.00	3.99
1242	1246	4.442073	GTCTTGCTCAACTTTCGTACGTTA	59.558	41.667	16.05	1.72	0.00	3.18
1243	1247	4.442073	TCTTGCTCAACTTTCGTACGTTAC	59.558	41.667	16.05	0.00	0.00	2.50
1244	1248	3.968649	TGCTCAACTTTCGTACGTTACT	58.031	40.909	16.05	0.00	0.00	2.24
1299	1303	8.939929	TGCTGCATAATATCTATTTGAAGTAGC	58.060	33.333	0.00	0.00	0.00	3.58
1437	1441	2.046864	CCTCCCGAGCAGAGTTCGA	61.047	63.158	4.84	0.00	40.36	3.71
1440	1444	1.137825	CCCGAGCAGAGTTCGAGTC	59.862	63.158	4.84	0.00	40.36	3.36
1445	1449	0.039978	AGCAGAGTTCGAGTCACACG	60.040	55.000	0.00	0.00	0.00	4.49
1478	1484	9.005318	TCCTTCATTAATTACTGGGTATGGTTA	57.995	33.333	3.27	0.00	0.00	2.85
1513	1519	3.870633	ACCTGATGAGTTTACTCCGTC	57.129	47.619	7.39	6.47	42.20	4.79
1533	1539	2.097629	TCGAATGACGAGGATGTGACTC	59.902	50.000	0.00	0.00	46.45	3.36
1680	1686	7.716799	AATATAGTGAGCCATTCCACAAAAA	57.283	32.000	0.00	0.00	35.84	1.94
1744	1750	8.833231	AGATTGTTCATAAAGATATACCCGTG	57.167	34.615	0.00	0.00	0.00	4.94
1816	1822	3.278574	CTTCGCTGTGAAATTGGGGATA	58.721	45.455	5.06	0.00	35.79	2.59
1860	1866	3.502211	GCGGAGAAAATCTGGAAAACTGA	59.498	43.478	0.00	0.00	34.56	3.41
1987	1993	6.783708	TGTAAACTTCTGTTGACCCAAAAT	57.216	33.333	0.00	0.00	36.85	1.82
2223	2229	3.437049	GTGGTCCATAGCTTTGTGACTTC	59.563	47.826	18.09	11.54	0.00	3.01
2331	2337	5.580297	CCCACGCAATAAAACATAGCAAAAT	59.420	36.000	0.00	0.00	0.00	1.82
2408	2414	6.325919	CTTGCAAAGTTAGGTGGTCAAATA	57.674	37.500	0.00	0.00	39.70	1.40
2465	2473	5.455056	AAATTACCCAAAATGTACGTGCA	57.545	34.783	9.28	9.28	0.00	4.57
2519	2527	1.134280	AGAGCTCCCGGATGTCATTTG	60.134	52.381	10.93	0.00	0.00	2.32
2646	2654	2.046892	CACCGAGCTGGGGTTCAG	60.047	66.667	19.90	0.00	44.64	3.02
2836	2845	2.286365	TCGAAAATCCACCTTTGCCT	57.714	45.000	0.00	0.00	0.00	4.75
2874	2883	5.010282	AGTAAGCCATTCCACCAAAAGTAG	58.990	41.667	0.00	0.00	0.00	2.57
3018	3027	7.114388	GCTAAGTGTTGCACCTTGTTTTTATAC	59.886	37.037	0.00	0.00	34.49	1.47
3019	3028	6.709018	AGTGTTGCACCTTGTTTTTATACT	57.291	33.333	0.00	0.00	34.49	2.12
3020	3029	7.811117	AGTGTTGCACCTTGTTTTTATACTA	57.189	32.000	0.00	0.00	34.49	1.82
3021	3030	8.404107	AGTGTTGCACCTTGTTTTTATACTAT	57.596	30.769	0.00	0.00	34.49	2.12
3022	3031	9.509956	AGTGTTGCACCTTGTTTTTATACTATA	57.490	29.630	0.00	0.00	34.49	1.31
3063	3072	0.247655	CGTCCATACGCAACATGCAC	60.248	55.000	2.99	0.00	45.36	4.57
3081	3090	2.290367	GCACATTATATCCAACTGCGCA	59.710	45.455	10.98	10.98	0.00	6.09
3183	3192	1.080435	AGCATCTGTCATGTCGTGCG	61.080	55.000	0.00	0.00	37.63	5.34
3221	3230	1.315257	CGTTTGGGGATCTTGGCAGG	61.315	60.000	0.00	0.00	0.00	4.85
3268	3277	6.513180	TCTACTCACGACTCAAAATTGAAGT	58.487	36.000	0.00	0.18	36.64	3.01
3275	3284	9.214957	TCACGACTCAAAATTGAAGTGTATTAT	57.785	29.630	17.59	0.00	37.86	1.28
3408	3454	2.160853	ACCACCCAACTTCTCCCCC	61.161	63.158	0.00	0.00	0.00	5.40
3445	3491	5.677319	AACATATATATGTCCCGACCCAG	57.323	43.478	25.01	0.00	45.55	4.45
3502	3548	1.302511	GAACGACTGTGGCACCCAT	60.303	57.895	16.26	0.00	35.28	4.00
3587	3633	0.391130	CGAATCGCTGGACCCAAAGA	60.391	55.000	0.00	0.00	0.00	2.52
3735	3781	9.655769	CTTTATCATTTTATCGTGTGGATTCAG	57.344	33.333	0.00	0.00	36.55	3.02
3879	3925	5.751028	TGTTTTTACTAATGTGCTTTGTGGC	59.249	36.000	0.00	0.00	0.00	5.01
3892	3938	5.048713	GTGCTTTGTGGCTCTTACTAACAAT	60.049	40.000	0.00	0.00	31.34	2.71
4046	4105	4.905456	ACAATCGAGGGGATTACAGGATTA	59.095	41.667	0.00	0.00	43.52	1.75
4261	4323	3.645884	CTTTTGTGAACCCATCTGCAAG	58.354	45.455	0.00	0.00	0.00	4.01
4262	4324	0.961019	TTGTGAACCCATCTGCAAGC	59.039	50.000	0.00	0.00	0.00	4.01
4484	4546	5.032327	AGATGATCTCAGCTGTTGCATTA	57.968	39.130	14.67	0.00	41.59	1.90
4514	4576	4.739195	CTTTGTACTCTGCCTCAGTACTC	58.261	47.826	14.60	0.00	44.54	2.59
4519	4581	0.037734	TCTGCCTCAGTACTCGACCA	59.962	55.000	0.00	0.00	32.61	4.02

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
86	87	5.913137	TGCCTGGAACTTATAATTTGTGG	57.087	39.130	0.00	0.00	0.00	4.17
184	185	4.680171	TCTGGTCTATATGCGTGATACG	57.320	45.455	0.00	0.00	45.88	3.06
192	193	2.221981	GCGCAAGTTCTGGTCTATATGC	59.778	50.000	0.30	0.00	41.68	3.14
224	225	4.696402	GTGTCCCGTTGGTTGATTGTTATA	59.304	41.667	0.00	0.00	0.00	0.98
252	253	1.386412	GCAAACACGGCGAATTTCATG	59.614	47.619	16.62	0.95	0.00	3.07
275	276	8.147704	ACTTTATGAACCAATTGGACGAAATTT	58.852	29.630	31.22	12.60	38.94	1.82
317	318	0.546122	TCCAACACTGCCAGACTGTT	59.454	50.000	0.00	0.00	0.00	3.16
319	320	1.224069	CGTCCAACACTGCCAGACTG	61.224	60.000	0.00	0.00	0.00	3.51
320	321	1.069765	CGTCCAACACTGCCAGACT	59.930	57.895	0.00	0.00	0.00	3.24
321	322	1.961277	CCGTCCAACACTGCCAGAC	60.961	63.158	0.00	0.00	0.00	3.51
322	323	2.425592	CCGTCCAACACTGCCAGA	59.574	61.111	0.00	0.00	0.00	3.86
323	324	3.357079	GCCGTCCAACACTGCCAG	61.357	66.667	0.00	0.00	0.00	4.85
346	347	2.743752	CGTTCGCCACAGATGCAGG	61.744	63.158	0.00	0.00	0.00	4.85
347	348	2.743752	CCGTTCGCCACAGATGCAG	61.744	63.158	0.00	0.00	0.00	4.41
348	349	2.520465	ATCCGTTCGCCACAGATGCA	62.520	55.000	0.00	0.00	0.00	3.96
349	350	1.815421	ATCCGTTCGCCACAGATGC	60.815	57.895	0.00	0.00	0.00	3.91
350	351	2.009108	CATCCGTTCGCCACAGATG	58.991	57.895	0.00	0.00	34.61	2.90
351	352	1.815421	GCATCCGTTCGCCACAGAT	60.815	57.895	0.00	0.00	0.00	2.90
352	353	2.434185	GCATCCGTTCGCCACAGA	60.434	61.111	0.00	0.00	0.00	3.41
353	354	3.853330	CGCATCCGTTCGCCACAG	61.853	66.667	0.00	0.00	0.00	3.66
365	366	0.248621	CGCAAATTTCCTCCCGCATC	60.249	55.000	0.00	0.00	0.00	3.91
559	560	4.887748	AGTATTGATAGTCCAAGGCATCG	58.112	43.478	0.00	0.00	0.00	3.84
560	561	6.166982	GGTAGTATTGATAGTCCAAGGCATC	58.833	44.000	0.00	0.00	0.00	3.91
561	562	5.013183	GGGTAGTATTGATAGTCCAAGGCAT	59.987	44.000	0.00	0.00	0.00	4.40
562	563	4.347000	GGGTAGTATTGATAGTCCAAGGCA	59.653	45.833	0.00	0.00	0.00	4.75
563	564	4.347000	TGGGTAGTATTGATAGTCCAAGGC	59.653	45.833	0.00	0.00	0.00	4.35
564	565	6.688073	ATGGGTAGTATTGATAGTCCAAGG	57.312	41.667	0.00	0.00	0.00	3.61
565	566	7.579723	GCCTATGGGTAGTATTGATAGTCCAAG	60.580	44.444	0.00	0.00	34.45	3.61
566	567	6.212791	GCCTATGGGTAGTATTGATAGTCCAA	59.787	42.308	0.00	0.00	34.45	3.53
581	582	0.830648	GTGAGCACTGCCTATGGGTA	59.169	55.000	0.00	0.00	34.45	3.69
582	583	1.604378	GTGAGCACTGCCTATGGGT	59.396	57.895	0.00	0.00	34.45	4.51
583	584	1.522355	CGTGAGCACTGCCTATGGG	60.522	63.158	0.00	0.00	0.00	4.00
585	586	1.202452	TCATCGTGAGCACTGCCTATG	60.202	52.381	0.00	0.00	0.00	2.23
587	588	0.457443	CTCATCGTGAGCACTGCCTA	59.543	55.000	0.00	0.00	37.72	3.93
588	589	1.217511	CTCATCGTGAGCACTGCCT	59.782	57.895	0.00	0.00	37.72	4.75
589	590	0.390340	TTCTCATCGTGAGCACTGCC	60.390	55.000	9.34	0.00	43.95	4.85
590	591	0.718343	GTTCTCATCGTGAGCACTGC	59.282	55.000	9.34	0.00	43.95	4.40
751	755	8.459521	TTTCTAACAACATAAATTCATTGCGG	57.540	30.769	0.00	0.00	0.00	5.69
789	793	5.419542	GGATTCACCTTTAGCCAATTTTCC	58.580	41.667	0.00	0.00	35.41	3.13
1063	1067	6.996282	CCGGATATGAATTACTTACCTTTGGT	59.004	38.462	0.00	0.00	40.16	3.67
1237	1241	8.851541	TTCATGAAATTTAACCCTAGTAACGT	57.148	30.769	5.45	0.00	0.00	3.99
1238	1242	9.931210	GATTCATGAAATTTAACCCTAGTAACG	57.069	33.333	13.09	0.00	0.00	3.18
1242	1246	8.416329	GCATGATTCATGAAATTTAACCCTAGT	58.584	33.333	26.94	0.00	43.81	2.57
1243	1247	8.415553	TGCATGATTCATGAAATTTAACCCTAG	58.584	33.333	26.94	0.00	43.81	3.02
1244	1248	8.303780	TGCATGATTCATGAAATTTAACCCTA	57.696	30.769	26.94	0.00	43.81	3.53
1299	1303	1.625616	AGAGCGATGTACGTTTTCCG	58.374	50.000	0.00	0.00	44.60	4.30
1513	1519	2.455032	GAGTCACATCCTCGTCATTCG	58.545	52.381	0.00	0.00	41.41	3.34
1533	1539	4.619760	TGTTGCTTCGTCTTCAGTATTACG	59.380	41.667	0.00	0.00	36.71	3.18
1540	1546	2.866156	TCTGTTGTTGCTTCGTCTTCAG	59.134	45.455	0.00	0.00	0.00	3.02
1621	1627	7.687941	ATAGCTTTGCAACAGTACTATGTTT	57.312	32.000	0.00	0.00	41.41	2.83
1744	1750	3.187227	AGTGCAACATGAGACGATTTGAC	59.813	43.478	0.00	0.00	41.43	3.18
1816	1822	5.564651	CGCTCAACCACATCCAAAAATTAGT	60.565	40.000	0.00	0.00	0.00	2.24
2029	2035	9.054922	TGGAAAAACAAATGAAAATCTGAATCC	57.945	29.630	0.00	0.00	0.00	3.01
2042	2048	8.663911	ACAACACTAACAATGGAAAAACAAATG	58.336	29.630	0.00	0.00	0.00	2.32
2115	2121	3.197265	GCAAAACAAGCAACATGGACTT	58.803	40.909	0.00	0.00	0.00	3.01
2223	2229	2.607635	CGACAATTTCGTATGACCCCAG	59.392	50.000	0.00	0.00	43.24	4.45
2257	2263	4.988540	TGTAGAACAACCACTTCATCGAAG	59.011	41.667	2.22	2.22	44.37	3.79
2408	2414	1.751924	GTACAGAGCTCCTCGGATGTT	59.248	52.381	10.93	0.00	35.36	2.71
2460	2468	1.910819	GTTGTGTTCAAACAGTGCACG	59.089	47.619	12.01	9.15	40.05	5.34
2465	2473	8.825667	AAAATTACAAGTTGTGTTCAAACAGT	57.174	26.923	18.90	0.00	41.98	3.55
2519	2527	2.559440	TGGTTGCAAAATTTGGTGCTC	58.441	42.857	14.29	8.47	41.48	4.26
2612	2620	2.668212	GCAGCCACGCTACACCAA	60.668	61.111	0.00	0.00	36.40	3.67
2613	2621	3.934962	TGCAGCCACGCTACACCA	61.935	61.111	0.00	0.00	36.40	4.17
2646	2654	3.323751	TCAAGTAGGGAAAGTAACGGC	57.676	47.619	0.00	0.00	0.00	5.68
2836	2845	9.547753	GAATGGCTTACTATTACTTGATCAAGA	57.452	33.333	36.15	19.12	40.79	3.02
2874	2883	4.563976	CCATGCGAATTTCAGAATGTTTCC	59.436	41.667	0.00	0.00	37.40	3.13
2924	2933	6.865333	AGCGATCTCTTCGATTGTCCAAAAC	61.865	44.000	0.00	0.00	45.90	2.43
3054	3063	5.688621	GCAGTTGGATATAATGTGCATGTTG	59.311	40.000	0.00	0.00	0.00	3.33
3102	3111	6.796785	ATCAATCCCCTTTAGGATGTTTTG	57.203	37.500	0.00	0.00	46.31	2.44
3103	3112	9.506042	AAATATCAATCCCCTTTAGGATGTTTT	57.494	29.630	0.00	0.00	46.31	2.43
3392	3437	0.034089	GATGGGGGAGAAGTTGGGTG	60.034	60.000	0.00	0.00	0.00	4.61
3445	3491	3.589988	AGAAACGACATGTCAGGATCAC	58.410	45.455	24.93	9.34	0.00	3.06
3502	3548	4.216687	CCCAAGCACTTTACGTGGAAATTA	59.783	41.667	0.00	0.00	43.97	1.40
3519	3565	2.180017	CGCTGATGTTGCCCAAGC	59.820	61.111	0.00	0.00	40.48	4.01
3587	3633	3.671716	ACTTCGGCGATTCCTTTTAGTT	58.328	40.909	11.76	0.00	0.00	2.24
3649	3695	2.823196	TGTGAACAGAGCAACGTTTG	57.177	45.000	0.00	0.00	0.00	2.93
3653	3699	1.526887	ACGAATGTGAACAGAGCAACG	59.473	47.619	0.00	0.00	0.00	4.10
3719	3765	4.693566	GTCAAACCTGAATCCACACGATAA	59.306	41.667	0.00	0.00	31.88	1.75
3847	3893	6.320164	AGCACATTAGTAAAAACAGAACCACA	59.680	34.615	0.00	0.00	0.00	4.17
3879	3925	8.740906	TGTAGGTCTTCTCATTGTTAGTAAGAG	58.259	37.037	0.00	0.00	0.00	2.85
3892	3938	3.834813	AGTGCAGATTGTAGGTCTTCTCA	59.165	43.478	0.00	0.00	0.00	3.27
4012	4058	5.793817	TCCCCTCGATTGTGTCAATATATG	58.206	41.667	0.00	0.00	0.00	1.78
4046	4105	1.002134	CGGTTGGCAATCTCCACCT	60.002	57.895	9.12	0.00	35.50	4.00
4128	4188	7.673641	CCTCAAATATAGGAGATAGAGGCAT	57.326	40.000	5.38	0.00	36.08	4.40
4261	4323	7.098074	AGATTCATTCCTTCAAAAGATCAGC	57.902	36.000	0.00	0.00	0.00	4.26
4514	4576	1.069703	CAAGCAACAGTGTCATGGTCG	60.070	52.381	0.00	0.00	0.00	4.79
4519	4581	2.579873	AGAAGCAAGCAACAGTGTCAT	58.420	42.857	0.00	0.00	0.00	3.06

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.