AutoCloner

Multiple sequence alignment - TraesCS1B01G071100

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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	TraesCS1B01G071100	chr1B	100.000	2278	0	0	995	3272	56016955	56019232	0.000000e+00	4207.0
1	TraesCS1B01G071100	chr1B	97.780	1216	23	3	995	2209	55998303	55999515	0.000000e+00	2093.0
2	TraesCS1B01G071100	chr1B	97.059	1224	24	4	995	2209	55977036	55978256	0.000000e+00	2050.0
3	TraesCS1B01G071100	chr1B	92.180	1202	93	1	1008	2209	56140945	56139745	0.000000e+00	1698.0
4	TraesCS1B01G071100	chr1B	100.000	694	0	0	1	694	56015961	56016654	0.000000e+00	1282.0
5	TraesCS1B01G071100	chr1B	96.408	696	18	5	1	694	55976207	55976897	0.000000e+00	1140.0
6	TraesCS1B01G071100	chr1B	87.743	873	101	6	995	1864	55964151	55965020	0.000000e+00	1014.0
7	TraesCS1B01G071100	chr1B	88.889	576	49	8	2702	3269	56138985	56138417	0.000000e+00	695.0
8	TraesCS1B01G071100	chr1B	95.929	393	14	2	303	694	55997571	55997962	1.280000e-178	636.0
9	TraesCS1B01G071100	chr1B	85.890	489	55	8	217	694	56141746	56141261	2.910000e-140	508.0
10	TraesCS1B01G071100	chr1B	91.204	216	17	2	3055	3268	55978746	55978961	3.190000e-75	292.0
11	TraesCS1B01G071100	chr1B	91.244	217	15	4	3055	3268	56000005	56000220	3.190000e-75	292.0
12	TraesCS1B01G071100	chr1B	90.306	196	15	2	423	614	55944841	55945036	1.510000e-63	254.0
13	TraesCS1B01G071100	chr1B	80.435	322	38	10	2318	2614	56139694	56139373	4.250000e-54	222.0
14	TraesCS1B01G071100	chr1A	88.369	1625	134	25	1015	2619	35536206	35537795	0.000000e+00	1903.0
15	TraesCS1B01G071100	chr1A	86.707	1640	183	21	998	2622	35578649	35577030	0.000000e+00	1788.0
16	TraesCS1B01G071100	chr1A	85.384	1642	191	28	995	2619	35485995	35487604	0.000000e+00	1657.0
17	TraesCS1B01G071100	chr1A	86.416	1487	160	25	1145	2614	35525789	35527250	0.000000e+00	1589.0
18	TraesCS1B01G071100	chr1A	88.754	578	50	8	2702	3271	35576649	35576079	0.000000e+00	693.0
19	TraesCS1B01G071100	chr1A	89.006	473	42	6	217	679	35514565	35515037	7.870000e-161	577.0
20	TraesCS1B01G071100	chr1A	87.935	489	47	9	217	694	35579252	35578765	1.700000e-157	566.0
21	TraesCS1B01G071100	chr1A	89.767	430	34	6	217	636	35535471	35535900	2.870000e-150	542.0
22	TraesCS1B01G071100	chr1A	89.598	423	26	10	224	634	35485052	35485468	3.740000e-144	521.0
23	TraesCS1B01G071100	chr1A	73.900	1364	290	45	1010	2327	31032438	31031095	1.360000e-133	486.0
24	TraesCS1B01G071100	chr1A	89.182	379	32	3	2622	2991	35537921	35538299	6.390000e-127	464.0
25	TraesCS1B01G071100	chr1A	89.606	279	12	5	2996	3269	35538457	35538723	4.040000e-89	339.0
26	TraesCS1B01G071100	chr1A	90.000	220	17	5	3055	3271	35527367	35527584	2.490000e-71	279.0
27	TraesCS1B01G071100	chr1A	88.688	221	19	5	3055	3271	35487717	35487935	6.960000e-67	265.0
28	TraesCS1B01G071100	chr1A	82.114	123	13	7	2328	2444	25314823	25314704	2.690000e-16	97.1
29	TraesCS1B01G071100	chr1A	92.453	53	4	0	86	138	35513786	35513838	3.500000e-10	76.8
30	TraesCS1B01G071100	chr1D	87.775	1636	160	28	998	2614	36315606	36317220	0.000000e+00	1877.0
31	TraesCS1B01G071100	chr1D	86.520	816	75	26	1824	2623	36362365	36361569	0.000000e+00	865.0
32	TraesCS1B01G071100	chr1D	88.320	488	43	9	217	694	36363757	36363274	1.020000e-159	573.0
33	TraesCS1B01G071100	chr1D	89.619	289	21	7	312	591	36314955	36315243	3.100000e-95	359.0
34	TraesCS1B01G071100	chr1D	88.018	217	23	3	3057	3271	36317339	36317554	1.510000e-63	254.0
35	TraesCS1B01G071100	chr1D	90.244	123	10	2	86	208	36314452	36314572	3.380000e-35	159.0
36	TraesCS1B01G071100	chr1D	91.837	49	3	1	638	685	36315257	36315305	2.110000e-07	67.6
37	TraesCS1B01G071100	chrUn	81.250	128	15	7	2322	2443	332331	332455	9.670000e-16	95.3
38	TraesCS1B01G071100	chrUn	81.967	122	13	7	2328	2443	319352129	319352011	9.670000e-16	95.3
39	TraesCS1B01G071100	chr4D	94.340	53	3	0	86	138	336663895	336663947	7.520000e-12	82.4
40	TraesCS1B01G071100	chr4B	93.478	46	3	0	86	131	414865548	414865593	5.860000e-08	69.4

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	TraesCS1B01G071100	chr1B	56015961	56019232	3271	False	2744.500000	4207	100.000000	1	3272	2	chr1B.!!$F5	3271
1	TraesCS1B01G071100	chr1B	55976207	55978961	2754	False	1160.666667	2050	94.890333	1	3268	3	chr1B.!!$F3	3267
2	TraesCS1B01G071100	chr1B	55964151	55965020	869	False	1014.000000	1014	87.743000	995	1864	1	chr1B.!!$F2	869
3	TraesCS1B01G071100	chr1B	55997571	56000220	2649	False	1007.000000	2093	94.984333	303	3268	3	chr1B.!!$F4	2965
4	TraesCS1B01G071100	chr1B	56138417	56141746	3329	True	780.750000	1698	86.848500	217	3269	4	chr1B.!!$R1	3052
5	TraesCS1B01G071100	chr1A	35576079	35579252	3173	True	1015.666667	1788	87.798667	217	3271	3	chr1A.!!$R3	3054
6	TraesCS1B01G071100	chr1A	35525789	35527584	1795	False	934.000000	1589	88.208000	1145	3271	2	chr1A.!!$F3	2126
7	TraesCS1B01G071100	chr1A	35485052	35487935	2883	False	814.333333	1657	87.890000	224	3271	3	chr1A.!!$F1	3047
8	TraesCS1B01G071100	chr1A	35535471	35538723	3252	False	812.000000	1903	89.231000	217	3269	4	chr1A.!!$F4	3052
9	TraesCS1B01G071100	chr1A	31031095	31032438	1343	True	486.000000	486	73.900000	1010	2327	1	chr1A.!!$R2	1317
10	TraesCS1B01G071100	chr1A	35513786	35515037	1251	False	326.900000	577	90.729500	86	679	2	chr1A.!!$F2	593
11	TraesCS1B01G071100	chr1D	36361569	36363757	2188	True	719.000000	865	87.420000	217	2623	2	chr1D.!!$R1	2406
12	TraesCS1B01G071100	chr1D	36314452	36317554	3102	False	543.320000	1877	89.498600	86	3271	5	chr1D.!!$F1	3185

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
636	1309	0.669318	AATGGAGCGTACACACACGG	60.669	55.0	0.0	0.0	42.18	4.94	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2534	3570	0.038343	CCACAAGGGGCGACAAATTG	60.038	55.0	0.0	0.0	0.0	2.32	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
89	90	6.546034	CCTAACCTTCCATGTTGGTTTATAGG	59.454	42.308	15.98	13.44	43.07	2.57
148	149	6.757897	TTGAAATATGCCTCGTGATTCTTT	57.242	33.333	0.00	0.00	0.00	2.52
149	150	7.857734	TTGAAATATGCCTCGTGATTCTTTA	57.142	32.000	0.00	0.00	0.00	1.85
624	1297	6.548993	AGGGAAAATTCATAGAGAAATGGAGC	59.451	38.462	0.00	0.00	40.22	4.70
636	1309	0.669318	AATGGAGCGTACACACACGG	60.669	55.000	0.00	0.00	42.18	4.94
1058	1942	3.576078	ATCTCAGATCTCGTCCTCACT	57.424	47.619	0.00	0.00	0.00	3.41
2203	3181	0.865769	GCACTAGTGGTGGTTCGTTG	59.134	55.000	23.95	0.00	45.44	4.10
2209	3187	0.736053	GTGGTGGTTCGTTGCTTTGA	59.264	50.000	0.00	0.00	0.00	2.69
2280	3290	3.003897	GTCCTCGATGCTCCAGTTAGTAG	59.996	52.174	0.00	0.00	0.00	2.57
2281	3291	2.952978	CCTCGATGCTCCAGTTAGTAGT	59.047	50.000	0.00	0.00	0.00	2.73
2282	3292	4.135306	CCTCGATGCTCCAGTTAGTAGTA	58.865	47.826	0.00	0.00	0.00	1.82
2283	3293	4.023878	CCTCGATGCTCCAGTTAGTAGTAC	60.024	50.000	0.00	0.00	0.00	2.73
2284	3294	3.558829	TCGATGCTCCAGTTAGTAGTACG	59.441	47.826	0.00	0.00	0.00	3.67
2285	3295	3.311871	CGATGCTCCAGTTAGTAGTACGT	59.688	47.826	0.00	0.00	0.00	3.57
2286	3296	4.201891	CGATGCTCCAGTTAGTAGTACGTT	60.202	45.833	0.00	0.00	0.00	3.99
2287	3297	4.691860	TGCTCCAGTTAGTAGTACGTTC	57.308	45.455	0.00	0.00	0.00	3.95
2288	3298	3.125829	TGCTCCAGTTAGTAGTACGTTCG	59.874	47.826	0.00	0.00	0.00	3.95
2289	3299	3.126000	GCTCCAGTTAGTAGTACGTTCGT	59.874	47.826	0.00	2.91	0.00	3.85
2290	3300	4.378874	GCTCCAGTTAGTAGTACGTTCGTT	60.379	45.833	2.62	0.00	0.00	3.85
2291	3301	5.034554	TCCAGTTAGTAGTACGTTCGTTG	57.965	43.478	2.62	0.00	0.00	4.10
2292	3302	4.754618	TCCAGTTAGTAGTACGTTCGTTGA	59.245	41.667	2.62	0.00	0.00	3.18
2293	3303	5.412594	TCCAGTTAGTAGTACGTTCGTTGAT	59.587	40.000	2.62	0.00	0.00	2.57
2294	3304	5.510674	CCAGTTAGTAGTACGTTCGTTGATG	59.489	44.000	2.62	0.00	0.00	3.07
2295	3305	6.082338	CAGTTAGTAGTACGTTCGTTGATGT	58.918	40.000	2.62	0.00	0.00	3.06
2296	3306	6.248001	CAGTTAGTAGTACGTTCGTTGATGTC	59.752	42.308	2.62	0.00	0.00	3.06
2297	3307	6.148480	AGTTAGTAGTACGTTCGTTGATGTCT	59.852	38.462	2.62	0.00	0.00	3.41
2298	3308	7.331934	AGTTAGTAGTACGTTCGTTGATGTCTA	59.668	37.037	2.62	0.00	0.00	2.59
2299	3309	6.674694	AGTAGTACGTTCGTTGATGTCTAT	57.325	37.500	2.62	0.00	0.00	1.98
2300	3310	6.713520	AGTAGTACGTTCGTTGATGTCTATC	58.286	40.000	2.62	0.00	0.00	2.08
2301	3311	4.918037	AGTACGTTCGTTGATGTCTATCC	58.082	43.478	2.62	0.00	32.09	2.59
2302	3312	3.160777	ACGTTCGTTGATGTCTATCCC	57.839	47.619	0.00	0.00	32.09	3.85
2303	3313	2.159142	ACGTTCGTTGATGTCTATCCCC	60.159	50.000	0.00	0.00	32.09	4.81
2304	3314	2.100916	CGTTCGTTGATGTCTATCCCCT	59.899	50.000	0.00	0.00	32.09	4.79
2305	3315	3.317149	CGTTCGTTGATGTCTATCCCCTA	59.683	47.826	0.00	0.00	32.09	3.53
2306	3316	4.022242	CGTTCGTTGATGTCTATCCCCTAT	60.022	45.833	0.00	0.00	32.09	2.57
2307	3317	5.509163	CGTTCGTTGATGTCTATCCCCTATT	60.509	44.000	0.00	0.00	32.09	1.73
2308	3318	5.468540	TCGTTGATGTCTATCCCCTATTG	57.531	43.478	0.00	0.00	32.09	1.90
2309	3319	3.997021	CGTTGATGTCTATCCCCTATTGC	59.003	47.826	0.00	0.00	32.09	3.56
2310	3320	4.503123	CGTTGATGTCTATCCCCTATTGCA	60.503	45.833	0.00	0.00	32.09	4.08
2311	3321	5.376625	GTTGATGTCTATCCCCTATTGCAA	58.623	41.667	0.00	0.00	32.09	4.08
2312	3322	5.848286	TGATGTCTATCCCCTATTGCAAT	57.152	39.130	17.56	17.56	32.09	3.56
2313	3323	5.809001	TGATGTCTATCCCCTATTGCAATC	58.191	41.667	16.86	0.00	32.09	2.67
2316	3326	7.237471	TGATGTCTATCCCCTATTGCAATCTTA	59.763	37.037	16.86	0.00	32.09	2.10
2358	3380	3.795688	TCCATCCCTATTGCAATCTCC	57.204	47.619	16.86	0.00	0.00	3.71
2364	3386	1.869767	CCTATTGCAATCTCCGTGCTC	59.130	52.381	16.86	0.00	42.69	4.26
2365	3387	1.869767	CTATTGCAATCTCCGTGCTCC	59.130	52.381	16.86	0.00	42.69	4.70
2366	3388	0.035152	ATTGCAATCTCCGTGCTCCA	60.035	50.000	5.99	0.00	42.69	3.86
2367	3389	0.674581	TTGCAATCTCCGTGCTCCAG	60.675	55.000	0.00	0.00	42.69	3.86
2368	3390	1.078848	GCAATCTCCGTGCTCCAGT	60.079	57.895	0.00	0.00	39.00	4.00
2372	3394	1.853963	ATCTCCGTGCTCCAGTTAGT	58.146	50.000	0.00	0.00	0.00	2.24
2373	3395	2.502142	TCTCCGTGCTCCAGTTAGTA	57.498	50.000	0.00	0.00	0.00	1.82
2385	3420	5.064071	GCTCCAGTTAGTATGTTTCTTGCTC	59.936	44.000	0.00	0.00	0.00	4.26
2434	3470	2.376228	TAACTGCTGTGGCGAGTGCA	62.376	55.000	0.00	0.00	45.35	4.57
2499	3535	4.417506	CGAACCAAAAGGTTTCGAAAACT	58.582	39.130	22.63	22.63	37.60	2.66
2543	3579	1.274798	GGGTGTTGCGCAATTTGTCG	61.275	55.000	27.79	8.29	0.00	4.35
2549	3597	2.961768	CGCAATTTGTCGCCCCTT	59.038	55.556	0.00	0.00	0.00	3.95
2614	3663	9.376075	GAATGACATACATATATCTGAACCCTG	57.624	37.037	0.00	0.00	38.38	4.45
2617	3666	6.091555	ACATACATATATCTGAACCCTGGGT	58.908	40.000	14.05	14.05	37.65	4.51
2618	3667	4.982241	ACATATATCTGAACCCTGGGTG	57.018	45.455	21.38	7.31	35.34	4.61
2619	3668	4.566837	ACATATATCTGAACCCTGGGTGA	58.433	43.478	21.38	13.20	35.34	4.02
2620	3669	5.165652	ACATATATCTGAACCCTGGGTGAT	58.834	41.667	21.38	19.37	35.34	3.06
2624	3814	0.987294	CTGAACCCTGGGTGATCTGT	59.013	55.000	21.38	1.21	35.34	3.41
2639	3829	3.623060	TGATCTGTTGAGCCGCTTATTTC	59.377	43.478	0.00	0.00	0.00	2.17
2676	3866	9.967346	TTAAACAAATTTGGTTCGTATCAATGA	57.033	25.926	24.23	0.75	39.21	2.57
2742	4101	5.864418	AATCCATCAATGATCTTGGTTGG	57.136	39.130	6.72	6.72	0.00	3.77
2768	4127	1.169661	AGCCGTCCGATTTTGCAACA	61.170	50.000	0.00	0.00	0.00	3.33
2808	4167	6.989155	AGATCATACCGATAACCCTAACAA	57.011	37.500	0.00	0.00	33.17	2.83
2829	4188	5.128171	ACAACGCATCTACCTTAGTTATGGA	59.872	40.000	0.00	0.00	0.00	3.41
2858	4217	6.584185	ACATTGACATGCATGCATATGTAT	57.416	33.333	31.39	21.18	39.77	2.29
2902	4262	6.607198	ACTCTTCATATTGTTTGGGGGTTATG	59.393	38.462	0.00	0.00	0.00	1.90
2904	4264	6.379703	TCTTCATATTGTTTGGGGGTTATGTG	59.620	38.462	0.00	0.00	0.00	3.21
2952	4312	6.900186	TCCTTTCCTATAAATGCCATTTGGAA	59.100	34.615	12.86	13.26	37.39	3.53
2994	4354	2.691409	TTCGTTGGATTAGCCTCCTG	57.309	50.000	0.00	0.00	36.20	3.86
3063	4576	2.174210	ACCCTCATCAACATGGGATCAG	59.826	50.000	3.70	0.00	42.11	2.90
3069	4582	2.308722	AACATGGGATCAGGCGGGT	61.309	57.895	0.00	0.00	0.00	5.28
3213	4733	6.988580	TGATCATCTCAAGTCATGTATTGTCC	59.011	38.462	10.87	0.00	0.00	4.02
3222	4742	8.081633	TCAAGTCATGTATTGTCCATTTGAAAC	58.918	33.333	10.87	0.00	0.00	2.78

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
48	49	2.365941	GTTAGGTGGAGAGGAGCATACC	59.634	54.545	0.00	0.00	0.00	2.73
89	90	3.545633	GAATTCTTTGCACACTCGTCAC	58.454	45.455	0.00	0.00	0.00	3.67
148	149	2.903784	AGATGGCCGCTAACACCATATA	59.096	45.455	0.00	0.00	44.20	0.86
149	150	1.699634	AGATGGCCGCTAACACCATAT	59.300	47.619	0.00	0.00	44.20	1.78
510	1177	5.379187	AGTGCATACCATGAAATGCTGATA	58.621	37.500	23.90	8.85	46.87	2.15
545	1213	6.465084	ACTAATGTTTCAGTGTACCTTCCTC	58.535	40.000	0.00	0.00	0.00	3.71
624	1297	0.031043	TGGACTTCCGTGTGTGTACG	59.969	55.000	0.00	0.00	43.35	3.67
636	1309	3.907894	TTGCCGTTTTATGTGGACTTC	57.092	42.857	0.00	0.00	0.00	3.01
1058	1942	1.915489	AGAGGGGTATGTTGTGATGCA	59.085	47.619	0.00	0.00	0.00	3.96
1236	2131	1.197721	CGACGTTGTAACTACCTCCGT	59.802	52.381	0.00	0.00	0.00	4.69
1357	2255	3.716195	TGTCCGGGGTGATGGCTG	61.716	66.667	0.00	0.00	0.00	4.85
1470	2368	2.233305	ACCTCAGGGTACTTGTCGAT	57.767	50.000	0.00	0.00	45.32	3.59
1707	2605	4.530857	GCGGCTATGCGGGAGTGT	62.531	66.667	0.00	0.00	0.00	3.55
2203	3181	6.080648	TCCAATTGCTGATGATATCAAAGC	57.919	37.500	25.85	25.85	39.11	3.51
2209	3187	4.758674	CGTCCTTCCAATTGCTGATGATAT	59.241	41.667	0.00	0.00	0.00	1.63
2280	3290	4.040376	GGGATAGACATCAACGAACGTAC	58.960	47.826	0.00	0.00	32.32	3.67
2281	3291	3.067180	GGGGATAGACATCAACGAACGTA	59.933	47.826	0.00	0.00	32.32	3.57
2282	3292	2.159142	GGGGATAGACATCAACGAACGT	60.159	50.000	0.00	0.00	32.32	3.99
2283	3293	2.100916	AGGGGATAGACATCAACGAACG	59.899	50.000	0.00	0.00	32.32	3.95
2284	3294	3.821421	AGGGGATAGACATCAACGAAC	57.179	47.619	0.00	0.00	32.32	3.95
2285	3295	5.741964	GCAATAGGGGATAGACATCAACGAA	60.742	44.000	0.00	0.00	32.32	3.85
2286	3296	4.262463	GCAATAGGGGATAGACATCAACGA	60.262	45.833	0.00	0.00	32.32	3.85
2287	3297	3.997021	GCAATAGGGGATAGACATCAACG	59.003	47.826	0.00	0.00	32.32	4.10
2288	3298	4.973168	TGCAATAGGGGATAGACATCAAC	58.027	43.478	0.00	0.00	32.32	3.18
2289	3299	5.645056	TTGCAATAGGGGATAGACATCAA	57.355	39.130	0.00	0.00	32.32	2.57
2290	3300	5.549228	AGATTGCAATAGGGGATAGACATCA	59.451	40.000	12.97	0.00	32.32	3.07
2291	3301	6.059787	AGATTGCAATAGGGGATAGACATC	57.940	41.667	12.97	0.00	0.00	3.06
2292	3302	6.460103	AAGATTGCAATAGGGGATAGACAT	57.540	37.500	12.97	0.00	0.00	3.06
2293	3303	5.912149	AAGATTGCAATAGGGGATAGACA	57.088	39.130	12.97	0.00	0.00	3.41
2294	3304	7.148171	GCATTAAGATTGCAATAGGGGATAGAC	60.148	40.741	12.97	0.00	39.90	2.59
2295	3305	6.886459	GCATTAAGATTGCAATAGGGGATAGA	59.114	38.462	12.97	0.00	39.90	1.98
2296	3306	6.888632	AGCATTAAGATTGCAATAGGGGATAG	59.111	38.462	12.97	0.24	42.62	2.08
2297	3307	6.793478	AGCATTAAGATTGCAATAGGGGATA	58.207	36.000	12.97	0.00	42.62	2.59
2298	3308	5.648247	AGCATTAAGATTGCAATAGGGGAT	58.352	37.500	12.97	0.68	42.62	3.85
2299	3309	5.065613	AGCATTAAGATTGCAATAGGGGA	57.934	39.130	12.97	0.00	42.62	4.81
2300	3310	6.006449	ACTAGCATTAAGATTGCAATAGGGG	58.994	40.000	12.97	1.63	42.62	4.79
2301	3311	7.661437	TGTACTAGCATTAAGATTGCAATAGGG	59.339	37.037	12.97	0.56	42.62	3.53
2302	3312	8.607441	TGTACTAGCATTAAGATTGCAATAGG	57.393	34.615	12.97	0.00	42.62	2.57
2305	3315	8.285394	CGAATGTACTAGCATTAAGATTGCAAT	58.715	33.333	12.83	12.83	42.62	3.56
2306	3316	7.279981	ACGAATGTACTAGCATTAAGATTGCAA	59.720	33.333	0.00	0.00	42.62	4.08
2307	3317	6.761242	ACGAATGTACTAGCATTAAGATTGCA	59.239	34.615	2.59	0.00	42.62	4.08
2308	3318	7.178712	ACGAATGTACTAGCATTAAGATTGC	57.821	36.000	0.00	0.00	38.98	3.56
2311	3321	9.811995	TGTTAACGAATGTACTAGCATTAAGAT	57.188	29.630	0.26	0.00	38.98	2.40
2312	3322	9.811995	ATGTTAACGAATGTACTAGCATTAAGA	57.188	29.630	0.26	0.00	38.98	2.10
2316	3326	7.045416	TGGATGTTAACGAATGTACTAGCATT	58.955	34.615	0.26	0.00	41.28	3.56
2358	3380	4.495422	AGAAACATACTAACTGGAGCACG	58.505	43.478	0.00	0.00	0.00	5.34
2364	3386	6.876257	AGAAGAGCAAGAAACATACTAACTGG	59.124	38.462	0.00	0.00	0.00	4.00
2365	3387	7.897575	AGAAGAGCAAGAAACATACTAACTG	57.102	36.000	0.00	0.00	0.00	3.16
2366	3388	8.910351	AAAGAAGAGCAAGAAACATACTAACT	57.090	30.769	0.00	0.00	0.00	2.24
2367	3389	8.994170	AGAAAGAAGAGCAAGAAACATACTAAC	58.006	33.333	0.00	0.00	0.00	2.34
2368	3390	9.209175	GAGAAAGAAGAGCAAGAAACATACTAA	57.791	33.333	0.00	0.00	0.00	2.24
2372	3394	8.807118	TCTAGAGAAAGAAGAGCAAGAAACATA	58.193	33.333	0.00	0.00	0.00	2.29
2373	3395	7.675062	TCTAGAGAAAGAAGAGCAAGAAACAT	58.325	34.615	0.00	0.00	0.00	2.71
2434	3470	6.040616	AGCTATATTGCGACCAAGTAGTACTT	59.959	38.462	9.85	9.85	37.14	2.24
2452	3488	1.475034	CCACACGCCAACCAGCTATAT	60.475	52.381	0.00	0.00	0.00	0.86
2534	3570	0.038343	CCACAAGGGGCGACAAATTG	60.038	55.000	0.00	0.00	0.00	2.32
2549	3597	1.369692	CTGACACGCTAACCCCACA	59.630	57.895	0.00	0.00	0.00	4.17
2614	3663	2.109126	GCGGCTCAACAGATCACCC	61.109	63.158	0.00	0.00	0.00	4.61
2617	3666	2.988010	ATAAGCGGCTCAACAGATCA	57.012	45.000	1.45	0.00	0.00	2.92
2618	3667	3.873952	AGAAATAAGCGGCTCAACAGATC	59.126	43.478	1.45	0.00	0.00	2.75
2619	3668	3.878778	AGAAATAAGCGGCTCAACAGAT	58.121	40.909	1.45	0.00	0.00	2.90
2620	3669	3.334583	AGAAATAAGCGGCTCAACAGA	57.665	42.857	1.45	0.00	0.00	3.41
2624	3814	3.605634	TGCTAAGAAATAAGCGGCTCAA	58.394	40.909	1.45	0.00	41.77	3.02
2683	3873	2.031420	CCATCTATTTCACAGCATGGCG	60.031	50.000	0.00	0.00	43.62	5.69
2684	3874	2.954318	ACCATCTATTTCACAGCATGGC	59.046	45.455	0.00	0.00	43.62	4.40
2689	3884	6.855836	TCAATCAAACCATCTATTTCACAGC	58.144	36.000	0.00	0.00	0.00	4.40
2721	4076	4.875389	ACCAACCAAGATCATTGATGGAT	58.125	39.130	21.81	0.00	36.75	3.41
2742	4101	0.745468	AAATCGGACGGCTAGGAGAC	59.255	55.000	0.00	0.00	0.00	3.36
2808	4167	5.598769	GTTCCATAACTAAGGTAGATGCGT	58.401	41.667	0.00	0.00	32.54	5.24
2829	4188	2.330286	CATGCATGTCAATGTTGCGTT	58.670	42.857	18.91	0.00	39.23	4.84
2883	4242	5.186797	ACACACATAACCCCCAAACAATATG	59.813	40.000	0.00	0.00	0.00	1.78
2902	4262	7.807977	AACCATATGGATTAGAATCACACAC	57.192	36.000	28.77	0.00	37.15	3.82
2904	4264	7.721399	AGGAAACCATATGGATTAGAATCACAC	59.279	37.037	28.77	7.18	37.15	3.82
2952	4312	0.105760	TGGTGGCACCATTCCTTTGT	60.106	50.000	34.67	0.00	44.79	2.83
3083	4596	1.153881	GGAACAGTCGCTCGGGTAC	60.154	63.158	0.00	0.00	0.00	3.34
3113	4631	7.599998	GCAAAACATAGGATTGTCACAAAAGAT	59.400	33.333	0.00	0.00	0.00	2.40
3128	4646	4.039124	AGGTTTGGAAGTGCAAAACATAGG	59.961	41.667	14.63	0.00	35.88	2.57
3234	4754	5.393027	GGTCGAGTTGCATGGAAATTTGTAT	60.393	40.000	0.00	0.00	0.00	2.29
3235	4755	4.083003	GGTCGAGTTGCATGGAAATTTGTA	60.083	41.667	0.00	0.00	0.00	2.41

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.