AutoCloner

Multiple sequence alignment - TraesCS2D01G459800

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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	TraesCS2D01G459800	chr2D	100.000	3169	0	0	1	3169	566657759	566654591	0.000000e+00	5853.0
1	TraesCS2D01G459800	chr2D	86.538	1144	124	20	59	1178	566481859	566480722	0.000000e+00	1232.0
2	TraesCS2D01G459800	chr2D	86.264	1143	126	23	59	1178	566455537	566454403	0.000000e+00	1212.0
3	TraesCS2D01G459800	chr2D	86.079	1135	121	20	56	1178	558374105	558375214	0.000000e+00	1186.0
4	TraesCS2D01G459800	chr2D	91.097	629	38	6	1521	2147	566302461	566301849	0.000000e+00	835.0
5	TraesCS2D01G459800	chr2D	84.068	885	86	24	1365	2221	566262558	566261701	0.000000e+00	802.0
6	TraesCS2D01G459800	chr2D	81.935	930	126	22	1233	2147	566454399	566453497	0.000000e+00	749.0
7	TraesCS2D01G459800	chr2D	85.202	669	82	6	1479	2147	558376129	558376780	0.000000e+00	671.0
8	TraesCS2D01G459800	chr2D	87.119	427	40	11	890	1304	566263075	566262652	1.330000e-128	470.0
9	TraesCS2D01G459800	chr2D	84.173	417	38	12	1140	1532	566302935	566302523	2.310000e-101	379.0
10	TraesCS2D01G459800	chr2D	82.940	381	42	9	2679	3050	566300833	566300467	3.940000e-84	322.0
11	TraesCS2D01G459800	chr2D	88.596	114	6	3	2586	2697	544849964	544850072	7.130000e-27	132.0
12	TraesCS2D01G459800	chr2D	86.842	76	10	0	209	284	566263666	566263591	5.630000e-13	86.1
13	TraesCS2D01G459800	chr2A	90.353	2633	160	35	1	2589	706531610	706529028	0.000000e+00	3369.0
14	TraesCS2D01G459800	chr2A	82.890	1391	146	48	890	2221	706489585	706488228	0.000000e+00	1166.0
15	TraesCS2D01G459800	chr2A	85.976	984	77	22	1142	2098	706510969	706510020	0.000000e+00	996.0
16	TraesCS2D01G459800	chr2A	90.909	506	35	2	2675	3169	706529030	706528525	0.000000e+00	669.0
17	TraesCS2D01G459800	chr2A	81.391	489	61	22	2679	3152	706509089	706508616	3.860000e-99	372.0
18	TraesCS2D01G459800	chr2A	95.652	92	3	1	2587	2678	96243041	96243131	2.550000e-31	147.0
19	TraesCS2D01G459800	chr2A	90.196	51	4	1	730	779	2732296	2732246	7.340000e-07	65.8
20	TraesCS2D01G459800	chr2A	100.000	29	0	0	1	29	142184679	142184707	2.000000e-03	54.7
21	TraesCS2D01G459800	chr2B	91.922	1597	92	20	1	1574	679728943	679730525	0.000000e+00	2200.0
22	TraesCS2D01G459800	chr2B	93.222	1431	68	16	784	2196	679696201	679697620	0.000000e+00	2078.0
23	TraesCS2D01G459800	chr2B	83.652	1358	162	36	890	2214	679031542	679030212	0.000000e+00	1223.0
24	TraesCS2D01G459800	chr2B	87.694	1032	79	19	1139	2147	679071596	679070590	0.000000e+00	1158.0
25	TraesCS2D01G459800	chr2B	92.346	797	55	4	1	792	679693984	679694779	0.000000e+00	1129.0
26	TraesCS2D01G459800	chr2B	84.662	1154	135	27	59	1178	679306323	679305178	0.000000e+00	1112.0
27	TraesCS2D01G459800	chr2B	95.411	632	27	2	1567	2196	679743782	679744413	0.000000e+00	1005.0
28	TraesCS2D01G459800	chr2B	93.018	444	21	1	2736	3169	679745772	679746215	9.580000e-180	640.0
29	TraesCS2D01G459800	chr2B	92.342	444	24	1	2736	3169	679698853	679699296	9.650000e-175	623.0
30	TraesCS2D01G459800	chr2B	83.573	487	57	10	2692	3169	679069091	679068619	4.850000e-118	435.0
31	TraesCS2D01G459800	chr2B	92.823	209	11	3	2182	2387	679745080	679745287	1.850000e-77	300.0
32	TraesCS2D01G459800	chr2B	92.381	210	10	5	2182	2387	679698287	679698494	8.600000e-76	294.0
33	TraesCS2D01G459800	chr2B	92.929	99	1	3	2584	2681	21211481	21211574	4.260000e-29	139.0
34	TraesCS2D01G459800	chr7A	75.332	377	64	17	2681	3051	664212660	664213013	1.520000e-33	154.0
35	TraesCS2D01G459800	chr7A	96.703	91	2	1	2588	2677	590778463	590778373	1.970000e-32	150.0
36	TraesCS2D01G459800	chr7A	95.556	90	4	0	2588	2677	211639976	211639887	9.160000e-31	145.0
37	TraesCS2D01G459800	chr1D	95.652	92	2	1	2588	2677	354500693	354500784	2.550000e-31	147.0
38	TraesCS2D01G459800	chr5A	94.624	93	5	0	2585	2677	214954368	214954460	9.160000e-31	145.0
39	TraesCS2D01G459800	chr7B	92.784	97	6	1	2588	2684	708468959	708469054	4.260000e-29	139.0
40	TraesCS2D01G459800	chr7B	88.636	44	5	0	742	785	522138958	522139001	2.000000e-03	54.7
41	TraesCS2D01G459800	chr4B	91.262	103	3	2	2585	2687	104337327	104337423	5.510000e-28	135.0
42	TraesCS2D01G459800	chr5D	84.270	89	13	1	598	686	73802208	73802295	5.630000e-13	86.1
43	TraesCS2D01G459800	chr5D	100.000	30	0	0	1	30	455823379	455823350	4.420000e-04	56.5
44	TraesCS2D01G459800	chr5B	81.000	100	17	2	590	689	78705048	78704951	9.420000e-11	78.7

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	TraesCS2D01G459800	chr2D	566654591	566657759	3168	True	5853.000000	5853	100.000000	1	3169	1	chr2D.!!$R2	3168
1	TraesCS2D01G459800	chr2D	566480722	566481859	1137	True	1232.000000	1232	86.538000	59	1178	1	chr2D.!!$R1	1119
2	TraesCS2D01G459800	chr2D	566453497	566455537	2040	True	980.500000	1212	84.099500	59	2147	2	chr2D.!!$R5	2088
3	TraesCS2D01G459800	chr2D	558374105	558376780	2675	False	928.500000	1186	85.640500	56	2147	2	chr2D.!!$F2	2091
4	TraesCS2D01G459800	chr2D	566300467	566302935	2468	True	512.000000	835	86.070000	1140	3050	3	chr2D.!!$R4	1910
5	TraesCS2D01G459800	chr2D	566261701	566263666	1965	True	452.700000	802	86.009667	209	2221	3	chr2D.!!$R3	2012
6	TraesCS2D01G459800	chr2A	706528525	706531610	3085	True	2019.000000	3369	90.631000	1	3169	2	chr2A.!!$R4	3168
7	TraesCS2D01G459800	chr2A	706488228	706489585	1357	True	1166.000000	1166	82.890000	890	2221	1	chr2A.!!$R2	1331
8	TraesCS2D01G459800	chr2A	706508616	706510969	2353	True	684.000000	996	83.683500	1142	3152	2	chr2A.!!$R3	2010
9	TraesCS2D01G459800	chr2B	679728943	679730525	1582	False	2200.000000	2200	91.922000	1	1574	1	chr2B.!!$F2	1573
10	TraesCS2D01G459800	chr2B	679030212	679031542	1330	True	1223.000000	1223	83.652000	890	2214	1	chr2B.!!$R1	1324
11	TraesCS2D01G459800	chr2B	679305178	679306323	1145	True	1112.000000	1112	84.662000	59	1178	1	chr2B.!!$R2	1119
12	TraesCS2D01G459800	chr2B	679693984	679699296	5312	False	1031.000000	2078	92.572750	1	3169	4	chr2B.!!$F3	3168
13	TraesCS2D01G459800	chr2B	679068619	679071596	2977	True	796.500000	1158	85.633500	1139	3169	2	chr2B.!!$R3	2030
14	TraesCS2D01G459800	chr2B	679743782	679746215	2433	False	648.333333	1005	93.750667	1567	3169	3	chr2B.!!$F4	1602

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
517	620	1.203063	GGCCCAAGGGTTCTTCTTCTT	60.203	52.381	7.05	0.0	37.65	2.52	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2359	6432	1.306141	AAGCCGAGGTGGATCTCCA	60.306	57.895	0.0	0.0	45.3	3.86	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	8.463930	TTTAGGTTCAATTCCCATATTGCTAG	57.536	34.615	0.00	0.00	35.86	3.42
57	58	5.376625	TCAATTCCCATATTGCTAGTCCAC	58.623	41.667	0.00	0.00	35.86	4.02
141	145	9.261035	ACATGGGGTATTATCTCTAGTATTCAG	57.739	37.037	0.00	0.00	0.00	3.02
226	231	9.559958	AATCAAAGTTTATTTTGCACTAGATCG	57.440	29.630	0.00	0.00	37.83	3.69
259	264	9.566432	ACTCCAGAATCAATTAGACATTAATCC	57.434	33.333	0.00	0.00	0.00	3.01
478	581	3.702330	TCGATCGATGCACTTAAATCGT	58.298	40.909	15.15	1.19	44.63	3.73
493	596	8.124823	CACTTAAATCGTGCATGATATTTCAGT	58.875	33.333	21.49	16.29	34.73	3.41
517	620	1.203063	GGCCCAAGGGTTCTTCTTCTT	60.203	52.381	7.05	0.00	37.65	2.52
519	622	2.965831	GCCCAAGGGTTCTTCTTCTTTT	59.034	45.455	7.05	0.00	37.65	2.27
532	635	9.803315	GTTCTTCTTCTTTTGTTTAAATCCAGT	57.197	29.630	0.00	0.00	0.00	4.00
663	772	5.503927	ACTATGTTCTTGTGAAGATGGCAT	58.496	37.500	0.00	0.00	37.75	4.40
1004	2565	1.138459	CACGCAACTGCCAAACACA	59.862	52.632	0.00	0.00	37.91	3.72
1005	2566	1.138671	ACGCAACTGCCAAACACAC	59.861	52.632	0.00	0.00	37.91	3.82
1304	2893	1.197430	CCTGCTGGTGAGTCTCCCTT	61.197	60.000	8.74	0.00	0.00	3.95
1329	2938	0.739112	CTGCTCCTCTGTTCTTCCGC	60.739	60.000	0.00	0.00	0.00	5.54
1342	2957	4.879545	TGTTCTTCCGCTCTTTAGTTGTTT	59.120	37.500	0.00	0.00	0.00	2.83
1343	2958	5.007332	TGTTCTTCCGCTCTTTAGTTGTTTC	59.993	40.000	0.00	0.00	0.00	2.78
1344	2959	4.957296	TCTTCCGCTCTTTAGTTGTTTCT	58.043	39.130	0.00	0.00	0.00	2.52
1345	2960	5.365619	TCTTCCGCTCTTTAGTTGTTTCTT	58.634	37.500	0.00	0.00	0.00	2.52
1393	3038	3.547468	GCGCATGTTTGGTGCTTAATTAG	59.453	43.478	0.30	0.00	40.37	1.73
1427	3072	4.753107	TGTGGTTTCTGTCCGAGATAAAAC	59.247	41.667	0.00	0.00	0.00	2.43
1532	3824	8.095792	ACAGCATGATGATCAAAATTTTGGTTA	58.904	29.630	26.45	19.00	39.69	2.85
2099	4487	1.134530	CGATGAGACCGAGTGAACGC	61.135	60.000	0.00	0.00	0.00	4.84
2122	4517	6.456853	CGCGAAAAGATGATAGACAATTGGAA	60.457	38.462	10.83	0.00	0.00	3.53
2248	5805	4.861102	AAGGCCAAAAGATGAAAGACAG	57.139	40.909	5.01	0.00	0.00	3.51
2252	5809	4.381292	GGCCAAAAGATGAAAGACAGATGG	60.381	45.833	0.00	0.00	0.00	3.51
2297	6276	3.940209	TCAAGTCATCAATTGGTTGGC	57.060	42.857	5.42	5.74	35.99	4.52
2394	6467	4.731853	TGGCCATGAGGTCCCCGA	62.732	66.667	0.00	0.00	39.40	5.14
2417	6492	1.028330	TGCGTACCTACTCCGGTGAG	61.028	60.000	11.17	0.00	44.62	3.51
2546	6968	6.497259	AGAAACTTCACACACCTAGGAATCTA	59.503	38.462	17.98	0.00	0.00	1.98
2573	6995	4.439253	AGACTTTTTAGCTTGTGGAGGT	57.561	40.909	0.00	0.00	39.87	3.85
2576	6998	3.883489	ACTTTTTAGCTTGTGGAGGTCAC	59.117	43.478	0.00	0.00	46.23	3.67
2587	7009	1.202758	TGGAGGTCACAAAAGCGATGT	60.203	47.619	0.00	0.00	0.00	3.06
2588	7010	2.037902	TGGAGGTCACAAAAGCGATGTA	59.962	45.455	0.00	0.00	0.00	2.29
2589	7011	2.415512	GGAGGTCACAAAAGCGATGTAC	59.584	50.000	0.00	0.00	0.00	2.90
2590	7012	3.326747	GAGGTCACAAAAGCGATGTACT	58.673	45.455	0.00	0.00	0.00	2.73
2591	7013	3.326747	AGGTCACAAAAGCGATGTACTC	58.673	45.455	0.00	0.00	0.00	2.59
2592	7014	2.415512	GGTCACAAAAGCGATGTACTCC	59.584	50.000	0.00	0.00	0.00	3.85
2593	7015	2.415512	GTCACAAAAGCGATGTACTCCC	59.584	50.000	0.00	0.00	0.00	4.30
2594	7016	2.301870	TCACAAAAGCGATGTACTCCCT	59.698	45.455	0.00	0.00	0.00	4.20
2595	7017	2.673368	CACAAAAGCGATGTACTCCCTC	59.327	50.000	0.00	0.00	0.00	4.30
2596	7018	2.280628	CAAAAGCGATGTACTCCCTCC	58.719	52.381	0.00	0.00	0.00	4.30
2597	7019	0.460311	AAAGCGATGTACTCCCTCCG	59.540	55.000	0.00	0.00	0.00	4.63
2598	7020	0.683504	AAGCGATGTACTCCCTCCGT	60.684	55.000	0.00	0.00	0.00	4.69
2599	7021	1.102222	AGCGATGTACTCCCTCCGTC	61.102	60.000	0.00	0.00	0.00	4.79
2600	7022	2.031360	CGATGTACTCCCTCCGTCC	58.969	63.158	0.00	0.00	0.00	4.79
2601	7023	1.453762	CGATGTACTCCCTCCGTCCC	61.454	65.000	0.00	0.00	0.00	4.46
2602	7024	0.396695	GATGTACTCCCTCCGTCCCA	60.397	60.000	0.00	0.00	0.00	4.37
2603	7025	0.264955	ATGTACTCCCTCCGTCCCAT	59.735	55.000	0.00	0.00	0.00	4.00
2604	7026	0.928505	TGTACTCCCTCCGTCCCATA	59.071	55.000	0.00	0.00	0.00	2.74
2605	7027	1.288633	TGTACTCCCTCCGTCCCATAA	59.711	52.381	0.00	0.00	0.00	1.90
2606	7028	2.090943	TGTACTCCCTCCGTCCCATAAT	60.091	50.000	0.00	0.00	0.00	1.28
2607	7029	3.140707	TGTACTCCCTCCGTCCCATAATA	59.859	47.826	0.00	0.00	0.00	0.98
2608	7030	3.562108	ACTCCCTCCGTCCCATAATAT	57.438	47.619	0.00	0.00	0.00	1.28
2609	7031	4.687262	ACTCCCTCCGTCCCATAATATA	57.313	45.455	0.00	0.00	0.00	0.86
2610	7032	5.019657	ACTCCCTCCGTCCCATAATATAA	57.980	43.478	0.00	0.00	0.00	0.98
2611	7033	5.024118	ACTCCCTCCGTCCCATAATATAAG	58.976	45.833	0.00	0.00	0.00	1.73
2612	7034	5.222484	ACTCCCTCCGTCCCATAATATAAGA	60.222	44.000	0.00	0.00	0.00	2.10
2613	7035	5.269991	TCCCTCCGTCCCATAATATAAGAG	58.730	45.833	0.00	0.00	0.00	2.85
2614	7036	4.141914	CCCTCCGTCCCATAATATAAGAGC	60.142	50.000	0.00	0.00	0.00	4.09
2615	7037	4.440250	CCTCCGTCCCATAATATAAGAGCG	60.440	50.000	0.00	0.00	0.00	5.03
2616	7038	4.084287	TCCGTCCCATAATATAAGAGCGT	58.916	43.478	0.00	0.00	0.00	5.07
2617	7039	4.525487	TCCGTCCCATAATATAAGAGCGTT	59.475	41.667	0.00	0.00	0.00	4.84
2618	7040	5.011329	TCCGTCCCATAATATAAGAGCGTTT	59.989	40.000	0.00	0.00	0.00	3.60
2619	7041	5.699458	CCGTCCCATAATATAAGAGCGTTTT	59.301	40.000	0.00	0.00	0.00	2.43
2620	7042	6.204108	CCGTCCCATAATATAAGAGCGTTTTT	59.796	38.462	0.00	0.00	0.00	1.94
2621	7043	7.069569	CGTCCCATAATATAAGAGCGTTTTTG	58.930	38.462	0.00	0.00	0.00	2.44
2622	7044	7.042321	CGTCCCATAATATAAGAGCGTTTTTGA	60.042	37.037	0.00	0.00	0.00	2.69
2623	7045	8.068380	GTCCCATAATATAAGAGCGTTTTTGAC	58.932	37.037	0.00	0.00	0.00	3.18
2624	7046	7.771361	TCCCATAATATAAGAGCGTTTTTGACA	59.229	33.333	0.00	0.00	0.00	3.58
2625	7047	7.855904	CCCATAATATAAGAGCGTTTTTGACAC	59.144	37.037	0.00	0.00	0.00	3.67
2626	7048	8.612619	CCATAATATAAGAGCGTTTTTGACACT	58.387	33.333	0.00	0.00	0.00	3.55
2629	7051	8.542497	AATATAAGAGCGTTTTTGACACTACA	57.458	30.769	0.00	0.00	0.00	2.74
2630	7052	4.531659	AAGAGCGTTTTTGACACTACAC	57.468	40.909	0.00	0.00	0.00	2.90
2631	7053	3.793559	AGAGCGTTTTTGACACTACACT	58.206	40.909	0.00	0.00	0.00	3.55
2632	7054	4.940463	AGAGCGTTTTTGACACTACACTA	58.060	39.130	0.00	0.00	0.00	2.74
2633	7055	4.743644	AGAGCGTTTTTGACACTACACTAC	59.256	41.667	0.00	0.00	0.00	2.73
2634	7056	4.435425	AGCGTTTTTGACACTACACTACA	58.565	39.130	0.00	0.00	0.00	2.74
2635	7057	4.269363	AGCGTTTTTGACACTACACTACAC	59.731	41.667	0.00	0.00	0.00	2.90
2636	7058	4.269363	GCGTTTTTGACACTACACTACACT	59.731	41.667	0.00	0.00	0.00	3.55
2637	7059	5.459762	GCGTTTTTGACACTACACTACACTA	59.540	40.000	0.00	0.00	0.00	2.74
2638	7060	6.345565	GCGTTTTTGACACTACACTACACTAG	60.346	42.308	0.00	0.00	0.00	2.57
2639	7061	6.694411	CGTTTTTGACACTACACTACACTAGT	59.306	38.462	0.00	0.00	40.28	2.57
2668	7090	8.446599	AAAAACACTCTTATATTATGGGACGG	57.553	34.615	0.00	0.00	0.00	4.79
2669	7091	6.989155	AACACTCTTATATTATGGGACGGA	57.011	37.500	0.00	0.00	0.00	4.69
2670	7092	6.591750	ACACTCTTATATTATGGGACGGAG	57.408	41.667	0.00	0.00	0.00	4.63
2671	7093	5.480772	ACACTCTTATATTATGGGACGGAGG	59.519	44.000	0.00	0.00	0.00	4.30
2672	7094	5.024118	ACTCTTATATTATGGGACGGAGGG	58.976	45.833	0.00	0.00	0.00	4.30
2673	7095	5.222484	ACTCTTATATTATGGGACGGAGGGA	60.222	44.000	0.00	0.00	0.00	4.20
2674	7096	5.269991	TCTTATATTATGGGACGGAGGGAG	58.730	45.833	0.00	0.00	0.00	4.30
2769	7861	2.030893	CGCAGAGAGGATTTGTTTGCAA	60.031	45.455	0.00	0.00	0.00	4.08
2809	7901	9.016623	GTTGGTCTTGTCAAGTTTTATGTAAAC	57.983	33.333	12.30	0.00	45.26	2.01
2896	7988	3.250762	CGAGAAGCAAGTCCAAATCAACA	59.749	43.478	0.00	0.00	0.00	3.33
2916	8008	0.813184	AGATGCAAGCCCAAATCGTG	59.187	50.000	0.00	0.00	0.00	4.35
3050	8152	6.595716	GCACTGATGATGTTCTTACTTTAGGT	59.404	38.462	0.00	0.00	0.00	3.08
3123	8226	3.286353	TGCTTGACCAAGTTTGATGTCA	58.714	40.909	10.96	0.00	40.45	3.58

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
32	33	5.827797	TGGACTAGCAATATGGGAATTGAAC	59.172	40.000	0.91	0.00	38.84	3.18
98	99	1.393603	TGTGTTGTTGCGGGAATGAA	58.606	45.000	0.00	0.00	0.00	2.57
99	100	1.269174	CATGTGTTGTTGCGGGAATGA	59.731	47.619	0.00	0.00	0.00	2.57
141	145	4.498009	CCCTTACGGACATCATCATTTTGC	60.498	45.833	0.00	0.00	0.00	3.68
220	225	9.961264	ATTGATTCTGGAGTACTATACGATCTA	57.039	33.333	0.00	0.00	0.00	1.98
384	479	9.878599	CACTAAATTCATTACCATATTCGGTTC	57.121	33.333	0.00	0.00	40.67	3.62
478	581	1.948834	CCGCCACTGAAATATCATGCA	59.051	47.619	0.00	0.00	34.37	3.96
517	620	8.006298	ACATGAACAGACTGGATTTAAACAAA	57.994	30.769	7.51	0.00	0.00	2.83
519	622	8.684386	TTACATGAACAGACTGGATTTAAACA	57.316	30.769	7.51	0.00	0.00	2.83
532	635	4.122046	CTCATCCGCATTACATGAACAGA	58.878	43.478	0.00	0.00	0.00	3.41
585	692	9.290988	TGCTTAAAAATCTAACATTCACTGGTA	57.709	29.630	0.00	0.00	0.00	3.25
1004	2565	1.075896	GAGGAGAGATCGGTGGGGT	60.076	63.158	0.00	0.00	0.00	4.95
1005	2566	0.825840	GAGAGGAGAGATCGGTGGGG	60.826	65.000	0.00	0.00	0.00	4.96
1135	2719	2.421739	CTACCATTCCCCGCCTCG	59.578	66.667	0.00	0.00	0.00	4.63
1304	2893	3.098774	AGAACAGAGGAGCAGATCTGA	57.901	47.619	27.04	0.00	44.68	3.27
1329	2938	5.293569	ACCACACGAAGAAACAACTAAAGAG	59.706	40.000	0.00	0.00	0.00	2.85
1342	2957	2.937799	GGTGTAACAAACCACACGAAGA	59.062	45.455	0.00	0.00	44.80	2.87
1343	2958	2.940410	AGGTGTAACAAACCACACGAAG	59.060	45.455	0.00	0.00	44.80	3.79
1344	2959	2.678836	CAGGTGTAACAAACCACACGAA	59.321	45.455	0.00	0.00	44.80	3.85
1345	2960	2.281517	CAGGTGTAACAAACCACACGA	58.718	47.619	0.00	0.00	44.80	4.35
1393	3038	2.743871	GAAACCACACGAGCGCGAAC	62.744	60.000	19.05	0.64	41.64	3.95
1427	3072	7.272948	GCAAAGTACGTATATAATTCTCCGGAG	59.727	40.741	26.32	26.32	0.00	4.63
1532	3824	5.157940	ACTCTGTAATCTCAGTGCAACAT	57.842	39.130	0.00	0.00	41.43	2.71
1822	4210	2.182030	GACGCCAACGAGGAGGAG	59.818	66.667	2.86	0.00	42.23	3.69
2099	4487	9.793252	AAATTCCAATTGTCTATCATCTTTTCG	57.207	29.630	4.43	0.00	0.00	3.46
2134	4530	6.484364	AATGACTGGACAAAACTTTTCCAT	57.516	33.333	0.00	0.00	38.75	3.41
2147	4543	7.964604	AGAAGTAACAAACTAATGACTGGAC	57.035	36.000	0.00	0.00	37.50	4.02
2275	5834	4.618927	CGCCAACCAATTGATGACTTGAAT	60.619	41.667	7.12	0.00	38.15	2.57
2297	6276	4.840005	GGGGCTCCTTCCGCTTCG	62.840	72.222	0.00	0.00	36.28	3.79
2359	6432	1.306141	AAGCCGAGGTGGATCTCCA	60.306	57.895	0.00	0.00	45.30	3.86
2387	6460	2.125793	GTACGCAAGGTCGGGGAC	60.126	66.667	0.00	0.00	46.39	4.46
2394	6467	1.318158	CCGGAGTAGGTACGCAAGGT	61.318	60.000	0.00	0.00	46.39	3.50
2495	6587	1.372128	CAAGGCGCAAAGAAGCACC	60.372	57.895	10.83	0.00	36.98	5.01
2546	6968	7.346751	TCCACAAGCTAAAAAGTCTTGATTT	57.653	32.000	8.03	0.00	39.48	2.17
2567	6989	1.202758	ACATCGCTTTTGTGACCTCCA	60.203	47.619	0.00	0.00	42.23	3.86
2573	6995	2.695359	GGGAGTACATCGCTTTTGTGA	58.305	47.619	0.00	0.00	43.70	3.58
2587	7009	4.687262	ATATTATGGGACGGAGGGAGTA	57.313	45.455	0.00	0.00	0.00	2.59
2588	7010	3.562108	ATATTATGGGACGGAGGGAGT	57.438	47.619	0.00	0.00	0.00	3.85
2589	7011	5.269991	TCTTATATTATGGGACGGAGGGAG	58.730	45.833	0.00	0.00	0.00	4.30
2590	7012	5.269991	CTCTTATATTATGGGACGGAGGGA	58.730	45.833	0.00	0.00	0.00	4.20
2591	7013	4.141914	GCTCTTATATTATGGGACGGAGGG	60.142	50.000	0.00	0.00	0.00	4.30
2592	7014	4.440250	CGCTCTTATATTATGGGACGGAGG	60.440	50.000	0.00	0.00	0.00	4.30
2593	7015	4.158025	ACGCTCTTATATTATGGGACGGAG	59.842	45.833	0.00	0.00	0.00	4.63
2594	7016	4.084287	ACGCTCTTATATTATGGGACGGA	58.916	43.478	0.00	0.00	0.00	4.69
2595	7017	4.451629	ACGCTCTTATATTATGGGACGG	57.548	45.455	0.00	0.00	0.00	4.79
2596	7018	6.780706	AAAACGCTCTTATATTATGGGACG	57.219	37.500	0.00	0.00	0.00	4.79
2597	7019	8.068380	GTCAAAAACGCTCTTATATTATGGGAC	58.932	37.037	0.00	0.00	0.00	4.46
2598	7020	7.771361	TGTCAAAAACGCTCTTATATTATGGGA	59.229	33.333	0.00	0.00	0.00	4.37
2599	7021	7.855904	GTGTCAAAAACGCTCTTATATTATGGG	59.144	37.037	0.00	0.00	35.42	4.00
2600	7022	8.612619	AGTGTCAAAAACGCTCTTATATTATGG	58.387	33.333	0.00	0.00	45.69	2.74
2603	7025	9.642327	TGTAGTGTCAAAAACGCTCTTATATTA	57.358	29.630	0.00	0.00	45.69	0.98
2604	7026	8.440833	GTGTAGTGTCAAAAACGCTCTTATATT	58.559	33.333	0.00	0.00	45.69	1.28
2605	7027	7.817962	AGTGTAGTGTCAAAAACGCTCTTATAT	59.182	33.333	0.00	0.00	45.69	0.86
2606	7028	7.149973	AGTGTAGTGTCAAAAACGCTCTTATA	58.850	34.615	0.00	0.00	45.69	0.98
2607	7029	5.989777	AGTGTAGTGTCAAAAACGCTCTTAT	59.010	36.000	0.00	0.00	45.69	1.73
2608	7030	5.353938	AGTGTAGTGTCAAAAACGCTCTTA	58.646	37.500	0.00	0.00	45.69	2.10
2609	7031	4.189231	AGTGTAGTGTCAAAAACGCTCTT	58.811	39.130	0.00	0.00	45.69	2.85
2610	7032	3.793559	AGTGTAGTGTCAAAAACGCTCT	58.206	40.909	0.00	0.00	45.69	4.09
2611	7033	4.505191	TGTAGTGTAGTGTCAAAAACGCTC	59.495	41.667	0.00	0.00	45.69	5.03
2613	7035	4.269363	AGTGTAGTGTAGTGTCAAAAACGC	59.731	41.667	0.00	0.00	38.74	4.84
2614	7036	5.961395	AGTGTAGTGTAGTGTCAAAAACG	57.039	39.130	0.00	0.00	0.00	3.60
2615	7037	7.998753	ACTAGTGTAGTGTAGTGTCAAAAAC	57.001	36.000	0.00	0.00	37.69	2.43
2643	7065	8.269317	TCCGTCCCATAATATAAGAGTGTTTTT	58.731	33.333	0.00	0.00	0.00	1.94
2644	7066	7.798071	TCCGTCCCATAATATAAGAGTGTTTT	58.202	34.615	0.00	0.00	0.00	2.43
2645	7067	7.369551	TCCGTCCCATAATATAAGAGTGTTT	57.630	36.000	0.00	0.00	0.00	2.83
2646	7068	6.014499	CCTCCGTCCCATAATATAAGAGTGTT	60.014	42.308	0.00	0.00	0.00	3.32
2647	7069	5.480772	CCTCCGTCCCATAATATAAGAGTGT	59.519	44.000	0.00	0.00	0.00	3.55
2648	7070	5.105310	CCCTCCGTCCCATAATATAAGAGTG	60.105	48.000	0.00	0.00	0.00	3.51
2649	7071	5.024118	CCCTCCGTCCCATAATATAAGAGT	58.976	45.833	0.00	0.00	0.00	3.24
2650	7072	5.269991	TCCCTCCGTCCCATAATATAAGAG	58.730	45.833	0.00	0.00	0.00	2.85
2651	7073	5.222484	ACTCCCTCCGTCCCATAATATAAGA	60.222	44.000	0.00	0.00	0.00	2.10
2652	7074	5.024118	ACTCCCTCCGTCCCATAATATAAG	58.976	45.833	0.00	0.00	0.00	1.73
2653	7075	5.019657	ACTCCCTCCGTCCCATAATATAA	57.980	43.478	0.00	0.00	0.00	0.98
2654	7076	4.687262	ACTCCCTCCGTCCCATAATATA	57.313	45.455	0.00	0.00	0.00	0.86
2655	7077	3.562108	ACTCCCTCCGTCCCATAATAT	57.438	47.619	0.00	0.00	0.00	1.28
2656	7078	4.687262	ATACTCCCTCCGTCCCATAATA	57.313	45.455	0.00	0.00	0.00	0.98
2657	7079	3.562108	ATACTCCCTCCGTCCCATAAT	57.438	47.619	0.00	0.00	0.00	1.28
2658	7080	4.202749	ACATATACTCCCTCCGTCCCATAA	60.203	45.833	0.00	0.00	0.00	1.90
2659	7081	3.335786	ACATATACTCCCTCCGTCCCATA	59.664	47.826	0.00	0.00	0.00	2.74
2660	7082	2.111972	ACATATACTCCCTCCGTCCCAT	59.888	50.000	0.00	0.00	0.00	4.00
2661	7083	1.502039	ACATATACTCCCTCCGTCCCA	59.498	52.381	0.00	0.00	0.00	4.37
2662	7084	2.305858	ACATATACTCCCTCCGTCCC	57.694	55.000	0.00	0.00	0.00	4.46
2663	7085	5.948162	TGTTATACATATACTCCCTCCGTCC	59.052	44.000	0.00	0.00	0.00	4.79
2664	7086	6.432162	TGTGTTATACATATACTCCCTCCGTC	59.568	42.308	0.00	0.00	33.42	4.79
2665	7087	6.309357	TGTGTTATACATATACTCCCTCCGT	58.691	40.000	0.00	0.00	33.42	4.69
2666	7088	6.829229	TGTGTTATACATATACTCCCTCCG	57.171	41.667	0.00	0.00	33.42	4.63
2667	7089	9.654663	GATTTGTGTTATACATATACTCCCTCC	57.345	37.037	0.00	0.00	39.48	4.30
2668	7090	9.654663	GGATTTGTGTTATACATATACTCCCTC	57.345	37.037	0.00	0.00	39.48	4.30
2669	7091	9.393786	AGGATTTGTGTTATACATATACTCCCT	57.606	33.333	0.00	0.00	37.33	4.20
2769	7861	5.129815	ACAAGACCAACCCATATATACGTGT	59.870	40.000	0.00	0.00	0.00	4.49
2809	7901	8.833231	ATCGACAATAGTAGGTTATCATTTGG	57.167	34.615	0.00	0.00	0.00	3.28
2820	7912	7.658167	TCTCTCTCAGTAATCGACAATAGTAGG	59.342	40.741	0.00	0.00	0.00	3.18
2827	7919	7.104290	TCTACTTCTCTCTCAGTAATCGACAA	58.896	38.462	0.00	0.00	0.00	3.18
2896	7988	1.203052	CACGATTTGGGCTTGCATCTT	59.797	47.619	0.00	0.00	0.00	2.40
2916	8008	3.817647	TCTTTCTTTGAGCTTGCTTCTCC	59.182	43.478	0.00	0.00	0.00	3.71
2986	8088	7.823745	AAAGAATTGTTACTGTTGATCCAGT	57.176	32.000	9.24	9.24	46.94	4.00
3019	8121	4.217836	AGAACATCATCAGTGCAGTGAT	57.782	40.909	27.82	27.82	37.68	3.06
3050	8152	1.878088	AGTTAACTCAGCTCGTCGTCA	59.122	47.619	1.12	0.00	0.00	4.35
3123	8226	9.193133	CAGCGCTTACTATATTAACACTACATT	57.807	33.333	7.50	0.00	0.00	2.71
3146	8253	5.686159	ATAGCATAATTGAACAGCTCAGC	57.314	39.130	0.00	0.00	36.80	4.26

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.