AutoCloner

Multiple sequence alignment - TraesCS3D01G002100

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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	TraesCS3D01G002100	chr3D	100.000	3665	0	0	1	3665	950006	953670	0.000000e+00	6769.0
1	TraesCS3D01G002100	chr3D	82.578	574	70	13	1735	2303	974592	974044	2.560000e-131	479.0
2	TraesCS3D01G002100	chr3D	89.677	155	15	1	1	154	27679771	27679925	2.890000e-46	196.0
3	TraesCS3D01G002100	chr3D	89.677	155	15	1	1	154	475125272	475125426	2.890000e-46	196.0
4	TraesCS3D01G002100	chr3D	73.746	339	59	20	3272	3590	112062962	112063290	5.010000e-19	106.0
5	TraesCS3D01G002100	chrUn	94.893	2095	79	13	629	2697	34166834	34164742	0.000000e+00	3251.0
6	TraesCS3D01G002100	chrUn	96.546	579	18	1	3089	3665	34164064	34163486	0.000000e+00	957.0
7	TraesCS3D01G002100	chrUn	92.259	633	46	3	1	631	34167625	34166994	0.000000e+00	894.0
8	TraesCS3D01G002100	chrUn	97.312	372	7	3	2706	3075	34164480	34164110	2.400000e-176	628.0
9	TraesCS3D01G002100	chrUn	85.596	604	73	6	1953	2555	34420626	34421216	4.020000e-174	621.0
10	TraesCS3D01G002100	chr3A	90.650	2385	146	29	1086	3434	8317315	8314972	0.000000e+00	3097.0
11	TraesCS3D01G002100	chr3A	81.002	579	76	13	1735	2303	8233138	8232584	2.620000e-116	429.0
12	TraesCS3D01G002100	chr3A	86.769	325	43	0	1128	1452	8576384	8576708	2.690000e-96	363.0
13	TraesCS3D01G002100	chr3A	86.503	163	21	1	453	614	56967481	56967319	1.050000e-40	178.0
14	TraesCS3D01G002100	chr3A	82.051	156	24	3	453	607	147525075	147525227	2.970000e-26	130.0
15	TraesCS3D01G002100	chr3A	83.969	131	20	1	489	618	175242759	175242889	1.380000e-24	124.0
16	TraesCS3D01G002100	chr3A	81.081	111	13	4	864	966	8261895	8261785	8.440000e-12	82.4
17	TraesCS3D01G002100	chr5D	91.613	155	12	1	1	154	284900514	284900360	2.870000e-51	213.0
18	TraesCS3D01G002100	chr6D	90.968	155	13	1	1	154	55080330	55080484	1.330000e-49	207.0
19	TraesCS3D01G002100	chr2D	90.968	155	13	1	1	154	25657389	25657543	1.330000e-49	207.0
20	TraesCS3D01G002100	chr2D	90.260	154	14	1	1	153	403382992	403382839	2.230000e-47	200.0
21	TraesCS3D01G002100	chr2D	89.032	155	16	1	1	154	557668046	557667892	1.340000e-44	191.0
22	TraesCS3D01G002100	chr2D	77.895	190	31	10	2886	3071	537332176	537332358	1.390000e-19	108.0
23	TraesCS3D01G002100	chr1D	89.032	155	16	1	1	154	332075150	332075304	1.340000e-44	191.0
24	TraesCS3D01G002100	chr1D	88.679	53	6	0	2252	2304	154795395	154795447	8.500000e-07	65.8
25	TraesCS3D01G002100	chr7B	85.965	171	18	5	450	616	328508390	328508558	1.050000e-40	178.0
26	TraesCS3D01G002100	chr7B	92.453	53	4	0	2252	2304	161779495	161779547	3.920000e-10	76.8
27	TraesCS3D01G002100	chr7B	100.000	32	0	0	412	443	354290195	354290164	3.950000e-05	60.2
28	TraesCS3D01G002100	chr5B	85.976	164	22	1	453	615	616732014	616731851	1.350000e-39	174.0
29	TraesCS3D01G002100	chr6B	89.394	132	12	2	203	333	31173812	31173942	8.140000e-37	165.0
30	TraesCS3D01G002100	chr6B	83.125	160	24	3	458	615	149466342	149466184	3.820000e-30	143.0
31	TraesCS3D01G002100	chr6B	88.043	92	9	2	244	333	31131180	31131271	1.390000e-19	108.0
32	TraesCS3D01G002100	chr2B	88.722	133	14	1	204	335	691186035	691186167	1.050000e-35	161.0
33	TraesCS3D01G002100	chr2B	77.536	138	25	5	3272	3407	798778702	798778835	1.090000e-10	78.7
34	TraesCS3D01G002100	chr2B	100.000	32	0	0	413	444	223094435	223094404	3.950000e-05	60.2
35	TraesCS3D01G002100	chr7A	84.756	164	20	3	453	615	727900101	727899942	3.790000e-35	159.0
36	TraesCS3D01G002100	chr7A	86.567	134	16	2	203	334	663361234	663361367	2.950000e-31	147.0
37	TraesCS3D01G002100	chr7A	75.000	336	51	21	3272	3588	631299611	631299932	1.380000e-24	124.0
38	TraesCS3D01G002100	chr7A	90.566	53	5	0	2252	2304	206913670	206913722	1.830000e-08	71.3
39	TraesCS3D01G002100	chr4D	87.786	131	15	1	206	335	77292141	77292011	6.340000e-33	152.0
40	TraesCS3D01G002100	chr4D	85.000	140	14	2	203	335	333873365	333873226	6.380000e-28	135.0
41	TraesCS3D01G002100	chr4D	100.000	32	0	0	412	443	286389768	286389737	3.950000e-05	60.2
42	TraesCS3D01G002100	chr2A	83.537	164	24	3	453	615	609730370	609730531	2.280000e-32	150.0
43	TraesCS3D01G002100	chr2A	74.515	412	63	28	3272	3661	31571075	31570684	1.370000e-29	141.0
44	TraesCS3D01G002100	chr3B	85.385	130	17	2	205	333	813260090	813259962	2.300000e-27	134.0
45	TraesCS3D01G002100	chr7D	86.207	116	13	3	221	335	614375093	614374980	4.970000e-24	122.0
46	TraesCS3D01G002100	chr7D	84.932	73	10	1	339	410	503687722	503687650	5.080000e-09	73.1
47	TraesCS3D01G002100	chr6A	81.119	143	26	1	453	594	516223449	516223307	2.990000e-21	113.0

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	TraesCS3D01G002100	chr3D	950006	953670	3664	False	6769.0	6769	100.0000	1	3665	1	chr3D.!!$F1	3664
1	TraesCS3D01G002100	chr3D	974044	974592	548	True	479.0	479	82.5780	1735	2303	1	chr3D.!!$R1	568
2	TraesCS3D01G002100	chrUn	34163486	34167625	4139	True	1432.5	3251	95.2525	1	3665	4	chrUn.!!$R1	3664
3	TraesCS3D01G002100	chrUn	34420626	34421216	590	False	621.0	621	85.5960	1953	2555	1	chrUn.!!$F1	602
4	TraesCS3D01G002100	chr3A	8314972	8317315	2343	True	3097.0	3097	90.6500	1086	3434	1	chr3A.!!$R3	2348
5	TraesCS3D01G002100	chr3A	8232584	8233138	554	True	429.0	429	81.0020	1735	2303	1	chr3A.!!$R1	568

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
879	1059	0.023732	CTCGCAACGTCGTGCTTATG	59.976	55.0	10.30	4.39	42.62	1.90	F
1208	1394	0.389166	CCAGAACAGGCTCGAGTGTC	60.389	60.0	15.13	4.43	0.00	3.67	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1790	1982	1.153369	CCATGAACGCGTCCTCCAT	60.153	57.895	14.44	11.24	0.00	3.41	R
3163	3678	1.144913	TCCAAAGGTGTTGGAGGAAGG	59.855	52.381	3.67	0.00	43.17	3.46	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
52	53	4.745751	CCGTCGGCCTTGCGGTAA	62.746	66.667	17.70	0.00	40.53	2.85
155	156	2.224621	GGTCCCATCATCGTCCAATCAT	60.225	50.000	0.00	0.00	0.00	2.45
163	164	0.541392	TCGTCCAATCATGAGTGGGG	59.459	55.000	34.92	27.35	45.85	4.96
179	180	1.971695	GGGTGCCACTACCTGCAAC	60.972	63.158	0.00	0.00	44.44	4.17
214	215	0.907704	ACGGAACTGCCACCCATCTA	60.908	55.000	0.00	0.00	35.94	1.98
224	225	0.248907	CACCCATCTACACGTAGCCG	60.249	60.000	0.00	0.00	40.83	5.52
245	246	2.293318	ACCCTCGCTGAATGGAGCA	61.293	57.895	0.00	0.00	39.07	4.26
492	493	0.673644	GATTGGTCCCACTCCACACG	60.674	60.000	0.00	0.00	34.45	4.49
503	504	3.393800	CACTCCACACGAAGTTTGATCT	58.606	45.455	0.00	0.00	41.30	2.75
504	505	3.809832	CACTCCACACGAAGTTTGATCTT	59.190	43.478	0.00	0.00	41.30	2.40
505	506	4.058817	ACTCCACACGAAGTTTGATCTTC	58.941	43.478	0.00	0.00	41.30	2.87
506	507	4.058124	CTCCACACGAAGTTTGATCTTCA	58.942	43.478	0.00	0.00	41.30	3.02
508	509	5.063204	TCCACACGAAGTTTGATCTTCAAT	58.937	37.500	0.00	0.00	41.30	2.57
509	510	6.227522	TCCACACGAAGTTTGATCTTCAATA	58.772	36.000	0.00	0.00	41.30	1.90
512	513	8.023128	CCACACGAAGTTTGATCTTCAATAAAT	58.977	33.333	0.00	0.00	41.30	1.40
513	514	8.843733	CACACGAAGTTTGATCTTCAATAAATG	58.156	33.333	0.00	0.00	41.30	2.32
516	517	6.974622	CGAAGTTTGATCTTCAATAAATGGGG	59.025	38.462	7.13	0.00	42.53	4.96
517	518	7.148086	CGAAGTTTGATCTTCAATAAATGGGGA	60.148	37.037	7.13	0.00	42.53	4.81
518	519	8.434589	AAGTTTGATCTTCAATAAATGGGGAA	57.565	30.769	0.00	0.00	36.11	3.97
549	550	7.362056	CCCTGTGTATCACTTGTCAATTTTAGG	60.362	40.741	1.72	0.00	35.11	2.69
563	565	6.007703	TCAATTTTAGGATTGAACTCGGGTT	58.992	36.000	0.00	0.00	41.65	4.11
568	570	3.939066	AGGATTGAACTCGGGTTGTTAG	58.061	45.455	4.77	0.00	35.58	2.34
569	571	3.581332	AGGATTGAACTCGGGTTGTTAGA	59.419	43.478	4.77	0.00	35.58	2.10
586	588	1.081906	GACTGCACAACCACATGCG	60.082	57.895	0.00	0.00	45.13	4.73
590	592	2.302230	GCACAACCACATGCGCAAC	61.302	57.895	17.11	0.00	30.97	4.17
593	595	1.661197	CAACCACATGCGCAACCAC	60.661	57.895	17.11	0.00	0.00	4.16
594	596	1.827789	AACCACATGCGCAACCACT	60.828	52.632	17.11	0.00	0.00	4.00
651	816	5.835113	ACATGTTCCCAGTATGTTTATGC	57.165	39.130	0.00	0.00	31.38	3.14
673	838	3.935203	CGACTTGTCATGCCAGTAATCTT	59.065	43.478	1.59	0.00	0.00	2.40
695	860	7.661040	TCTTGTGATGATGCTAATCTCGATTA	58.339	34.615	0.00	0.00	33.61	1.75
751	916	7.254727	GCTGGATCAGAAGTTCTTTGCTTATAG	60.255	40.741	1.56	0.00	32.44	1.31
752	917	7.624549	TGGATCAGAAGTTCTTTGCTTATAGT	58.375	34.615	1.56	0.00	0.00	2.12
814	990	5.357032	AGAAGAAGAAACATTCAAACCGTGT	59.643	36.000	0.00	0.00	0.00	4.49
836	1012	0.661020	CAAACCGTTGAAACCGCTCT	59.339	50.000	0.00	0.00	36.83	4.09
879	1059	0.023732	CTCGCAACGTCGTGCTTATG	59.976	55.000	10.30	4.39	42.62	1.90
912	1092	1.827969	GGGGATGGATCGTAGGATGAG	59.172	57.143	1.92	0.00	31.51	2.90
944	1124	3.147595	CTCCTCGGGTCATCGCCA	61.148	66.667	0.00	0.00	0.00	5.69
968	1151	2.283173	TGCAGAGAGGGAGCGACA	60.283	61.111	0.00	0.00	0.00	4.35
996	1179	2.030562	ACAAACACCTCGAGGGCG	59.969	61.111	34.04	25.87	40.27	6.13
1062	1248	2.742053	GGAACGTACCACTCGTAGTACA	59.258	50.000	0.38	0.00	40.69	2.90
1063	1249	3.181516	GGAACGTACCACTCGTAGTACAG	60.182	52.174	0.38	0.17	40.69	2.74
1064	1250	1.734465	ACGTACCACTCGTAGTACAGC	59.266	52.381	0.38	0.00	39.03	4.40
1070	1256	1.132643	CACTCGTAGTACAGCAGGACC	59.867	57.143	0.38	0.00	0.00	4.46
1072	1258	1.402259	CTCGTAGTACAGCAGGACCAG	59.598	57.143	0.38	0.00	0.00	4.00
1078	1264	0.969149	TACAGCAGGACCAGAGTGTG	59.031	55.000	0.00	0.00	0.00	3.82
1079	1265	1.670406	CAGCAGGACCAGAGTGTGC	60.670	63.158	0.00	0.00	34.20	4.57
1178	1364	2.140138	ATGATCATCCGGGCGGTGA	61.140	57.895	1.18	1.61	36.47	4.02
1208	1394	0.389166	CCAGAACAGGCTCGAGTGTC	60.389	60.000	15.13	4.43	0.00	3.67
1470	1656	4.488136	CAGCTACATGGCCCGGCA	62.488	66.667	12.58	0.00	0.00	5.69
1508	1694	0.545646	TCATCCCAATCACATCGGCA	59.454	50.000	0.00	0.00	0.00	5.69
1509	1695	0.664761	CATCCCAATCACATCGGCAC	59.335	55.000	0.00	0.00	0.00	5.01
1573	1762	1.834856	CTGGCTCCCTGCAGACTCAA	61.835	60.000	17.39	0.00	45.15	3.02
1614	1806	1.000717	GCAGGTAAGCTCGATCTCCTC	60.001	57.143	0.00	0.00	0.00	3.71
1989	2190	1.228337	TGACGACGTCCTGGGAGAA	60.228	57.895	24.33	0.77	0.00	2.87
2630	2850	1.136803	GCGACAGTACCGAACGTTTTC	60.137	52.381	0.46	0.00	0.00	2.29
2651	2871	4.261801	TCTTTCACCTCCCATCGATTTTC	58.738	43.478	0.00	0.00	0.00	2.29
2890	3371	2.801111	TGTACAATGCGTGCGTTTTCTA	59.199	40.909	0.00	0.00	31.89	2.10
2937	3418	6.182627	TCTTGCATATTCACCACTCATCTTT	58.817	36.000	0.00	0.00	0.00	2.52
3080	3563	1.200483	GATGCGACATGACACTACCG	58.800	55.000	0.00	0.00	0.00	4.02
3081	3564	0.806102	ATGCGACATGACACTACCGC	60.806	55.000	0.00	0.00	42.52	5.68
3163	3678	4.510340	GTGATAATGGTATTGTCGTGTCCC	59.490	45.833	0.00	0.00	0.00	4.46
3192	3709	1.949465	ACACCTTTGGACGAGAACAC	58.051	50.000	0.00	0.00	0.00	3.32
3245	3762	5.708697	TCCACCAATGCATGATAATCATCTC	59.291	40.000	0.00	0.00	34.28	2.75
3360	3881	7.093201	ACAATTAAATGGCTCTTTCCATCATGT	60.093	33.333	0.00	0.00	45.64	3.21
3458	3980	6.486253	AAGATCACAACACATCACATGTAC	57.514	37.500	0.00	0.00	42.70	2.90
3481	4003	5.518487	ACGTCCTGCAAAAACAAGTTAAATG	59.482	36.000	0.00	0.00	0.00	2.32
3490	4012	8.435430	GCAAAAACAAGTTAAATGCCTCTAATC	58.565	33.333	6.36	0.00	0.00	1.75
3524	4046	1.264749	ATCGTGGCTGCTAGGGTTGA	61.265	55.000	5.88	0.00	0.00	3.18
3526	4048	1.741770	GTGGCTGCTAGGGTTGACG	60.742	63.158	0.00	0.00	0.00	4.35
3546	4068	1.198408	GTTGCAAACCGTTAGCTACCC	59.802	52.381	0.00	0.00	42.21	3.69
3626	4150	7.905604	ACACGAGACATAATGAAAAATCTCA	57.094	32.000	0.00	0.00	33.66	3.27

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
3	4	1.735198	CATGGCGCTGCAAAGGTTG	60.735	57.895	7.64	0.00	0.00	3.77
52	53	1.207329	GAGGAGGAGCGGTGTTACATT	59.793	52.381	0.00	0.00	0.00	2.71
126	127	1.517242	GATGATGGGACCTTCGATGC	58.483	55.000	0.00	0.00	0.00	3.91
163	164	0.310854	GTTGTTGCAGGTAGTGGCAC	59.689	55.000	10.29	10.29	40.23	5.01
196	197	0.462047	GTAGATGGGTGGCAGTTCCG	60.462	60.000	0.00	0.00	37.80	4.30
224	225	2.825836	CCATTCAGCGAGGGTGGC	60.826	66.667	0.00	0.00	0.00	5.01
233	234	1.303561	TGGTGGTGCTCCATTCAGC	60.304	57.895	11.31	0.00	46.20	4.26
245	246	4.887190	GGGTGTTGCGGTGGTGGT	62.887	66.667	0.00	0.00	0.00	4.16
320	321	1.220749	GAATGCGGCAGTCAGGGTA	59.779	57.895	23.86	0.00	0.00	3.69
391	392	2.701006	CCGCTACGTCGGCAAATG	59.299	61.111	2.46	0.00	43.18	2.32
480	481	0.944386	CAAACTTCGTGTGGAGTGGG	59.056	55.000	0.00	0.00	0.00	4.61
492	493	8.066612	TCCCCATTTATTGAAGATCAAACTTC	57.933	34.615	0.00	0.00	40.12	3.01
516	517	4.583073	ACAAGTGATACACAGGGGTTTTTC	59.417	41.667	4.75	0.00	36.74	2.29
517	518	4.542697	ACAAGTGATACACAGGGGTTTTT	58.457	39.130	4.75	0.00	36.74	1.94
518	519	4.142038	GACAAGTGATACACAGGGGTTTT	58.858	43.478	4.75	0.00	36.74	2.43
527	528	9.559958	CAATCCTAAAATTGACAAGTGATACAC	57.440	33.333	0.00	0.00	38.64	2.90
549	550	4.389077	CAGTCTAACAACCCGAGTTCAATC	59.611	45.833	0.00	0.00	32.45	2.67
563	565	2.700722	TGTGGTTGTGCAGTCTAACA	57.299	45.000	0.00	0.00	0.00	2.41
568	570	1.081906	CGCATGTGGTTGTGCAGTC	60.082	57.895	0.00	0.00	41.32	3.51
569	571	3.033184	CGCATGTGGTTGTGCAGT	58.967	55.556	0.00	0.00	41.32	4.40
580	582	2.620112	GCTCAGTGGTTGCGCATGT	61.620	57.895	12.75	0.00	37.46	3.21
586	588	2.970974	GCCTTCGCTCAGTGGTTGC	61.971	63.158	0.00	0.00	0.00	4.17
599	601	2.415776	GCATATGCAGAGAGAGCCTTC	58.584	52.381	22.84	0.00	41.59	3.46
620	622	8.150827	ACATACTGGGAACATGTAGCATATAT	57.849	34.615	0.00	0.00	41.51	0.86
636	800	3.938963	ACAAGTCGCATAAACATACTGGG	59.061	43.478	0.00	0.00	0.00	4.45
651	816	3.525537	AGATTACTGGCATGACAAGTCG	58.474	45.455	1.11	0.00	0.00	4.18
722	887	4.022503	GCAAAGAACTTCTGATCCAGCTTT	60.023	41.667	0.00	0.00	0.00	3.51
725	890	3.080319	AGCAAAGAACTTCTGATCCAGC	58.920	45.455	0.00	0.00	0.00	4.85
814	990	1.433879	CGGTTTCAACGGTTTGGCA	59.566	52.632	0.00	0.00	33.06	4.92
836	1012	6.932400	AGACTTCATATAAAACGACAACCACA	59.068	34.615	0.00	0.00	0.00	4.17
845	1021	5.181084	CGTTGCGAGACTTCATATAAAACG	58.819	41.667	0.00	0.00	0.00	3.60
879	1059	3.698263	ATCCCCTCTCGACCCACCC	62.698	68.421	0.00	0.00	0.00	4.61
912	1092	2.221981	CGAGGAGTTGTCAAAGTCAAGC	59.778	50.000	0.00	0.00	37.46	4.01
944	1124	2.164865	CTCCCTCTCTGCAGCGTGTT	62.165	60.000	9.47	0.00	0.00	3.32
968	1151	3.222603	GAGGTGTTTGTGGAAATGGTCT	58.777	45.455	0.00	0.00	0.00	3.85
996	1179	2.289565	AGGTAGCCTTTTTATCAGCGC	58.710	47.619	0.00	0.00	0.00	5.92
1017	1200	5.923114	CCGTACTATAGCTACAAGTAGACGA	59.077	44.000	22.73	4.93	35.21	4.20
1050	1236	1.132643	GGTCCTGCTGTACTACGAGTG	59.867	57.143	0.00	0.00	0.00	3.51
1062	1248	2.746359	GCACACTCTGGTCCTGCT	59.254	61.111	0.00	0.00	0.00	4.24
1063	1249	2.359230	GGCACACTCTGGTCCTGC	60.359	66.667	0.00	0.00	0.00	4.85
1064	1250	3.150949	TGGCACACTCTGGTCCTG	58.849	61.111	0.00	0.00	0.00	3.86
1178	1364	2.397413	CTGTTCTGGTGGGCCGTCTT	62.397	60.000	0.00	0.00	37.67	3.01
1186	1372	1.079543	CTCGAGCCTGTTCTGGTGG	60.080	63.158	0.00	0.00	0.00	4.61
1223	1409	2.726274	GTCGACCGTGGACACACT	59.274	61.111	3.51	0.00	45.50	3.55
1356	1542	0.537188	GGATCCGAAGAACTGGCTGA	59.463	55.000	0.00	0.00	0.00	4.26
1393	1579	6.713762	ATCCTGTTGTTGACTTGATTGAAA	57.286	33.333	0.00	0.00	0.00	2.69
1426	1612	2.362397	GCTGAGGTTGAGGATGACGATA	59.638	50.000	0.00	0.00	0.00	2.92
1470	1656	3.963129	TGAAGGACTTGGTTGAAGTGTT	58.037	40.909	0.00	0.00	45.48	3.32
1508	1694	0.673644	GCTATTGTGGCAGTCGGTGT	60.674	55.000	0.00	0.00	0.00	4.16
1509	1695	1.369091	GGCTATTGTGGCAGTCGGTG	61.369	60.000	0.00	0.00	0.00	4.94
1573	1762	3.460672	CTGCGACACCACCACCAGT	62.461	63.158	0.00	0.00	0.00	4.00
1614	1806	4.929707	GCGCCCTGGGGTTATCGG	62.930	72.222	16.03	0.00	37.65	4.18
1645	1837	3.434319	CTGGTCGCCGCTGCAATT	61.434	61.111	0.00	0.00	37.32	2.32
1790	1982	1.153369	CCATGAACGCGTCCTCCAT	60.153	57.895	14.44	11.24	0.00	3.41
2182	2386	4.131088	GTGCCGACGACCTCCTCC	62.131	72.222	0.00	0.00	0.00	4.30
2417	2621	4.056125	CGCCTCCAGCTGACGTGA	62.056	66.667	17.39	2.35	40.39	4.35
2595	2815	2.285083	TGTCGCGGAGAATTAAATGGG	58.715	47.619	6.13	0.00	0.00	4.00
2630	2850	4.095483	CAGAAAATCGATGGGAGGTGAAAG	59.905	45.833	0.00	0.00	0.00	2.62
2703	2929	4.816385	CGCCTCTCCAACATGTATACAAAT	59.184	41.667	10.14	0.00	0.00	2.32
2890	3371	8.217188	AGAGGCTTTCTATGATGGATTATTCT	57.783	34.615	0.00	0.00	33.23	2.40
2943	3424	8.870075	AGACTTTTAAGATTACAGAAAGGCAT	57.130	30.769	3.20	0.00	37.71	4.40
2944	3425	7.390718	GGAGACTTTTAAGATTACAGAAAGGCA	59.609	37.037	3.20	0.00	37.71	4.75
2945	3426	7.608376	AGGAGACTTTTAAGATTACAGAAAGGC	59.392	37.037	0.00	0.00	37.44	4.35
2951	3432	8.848474	TTTGGAGGAGACTTTTAAGATTACAG	57.152	34.615	0.00	0.00	44.43	2.74
3146	3661	1.580059	AGGGGACACGACAATACCAT	58.420	50.000	0.00	0.00	0.00	3.55
3163	3678	1.144913	TCCAAAGGTGTTGGAGGAAGG	59.855	52.381	3.67	0.00	43.17	3.46
3192	3709	6.878923	TGATGTTATGTTGTAGGTGAAGAAGG	59.121	38.462	0.00	0.00	0.00	3.46
3245	3762	9.289303	GTTATAGTTGTAATTGCAAAGACATGG	57.711	33.333	10.72	0.00	0.00	3.66
3360	3881	7.936496	ACATGTCATGTGTTTTATGGTATGA	57.064	32.000	17.74	0.00	43.01	2.15
3411	3933	4.083643	CGTCATGGGAATGAGATTGTATGC	60.084	45.833	0.00	0.00	0.00	3.14
3458	3980	5.556194	GCATTTAACTTGTTTTTGCAGGACG	60.556	40.000	0.00	0.00	0.00	4.79
3508	4030	1.741770	CGTCAACCCTAGCAGCCAC	60.742	63.158	0.00	0.00	0.00	5.01
3511	4033	1.912371	GCAACGTCAACCCTAGCAGC	61.912	60.000	0.00	0.00	0.00	5.25
3524	4046	1.528161	GTAGCTAACGGTTTGCAACGT	59.472	47.619	24.82	9.09	46.48	3.99
3526	4048	1.198408	GGGTAGCTAACGGTTTGCAAC	59.802	52.381	24.82	15.01	0.00	4.17
3626	4150	1.074889	ACGAAGTTTGGTATGGGGCTT	59.925	47.619	0.00	0.00	37.78	4.35

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.