AutoCloner

Multiple sequence alignment - TraesCS5D01G468700

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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	TraesCS5D01G468700	chr5D	100.000	3835	0	0	1	3835	510057065	510060899	0.000000e+00	7083.0
1	TraesCS5D01G468700	chr5D	94.057	875	33	5	31	889	564121670	564120799	0.000000e+00	1310.0
2	TraesCS5D01G468700	chr5D	93.793	870	35	4	36	889	408654430	408653564	0.000000e+00	1290.0
3	TraesCS5D01G468700	chr5B	96.928	1953	50	4	891	2834	641042342	641044293	0.000000e+00	3265.0
4	TraesCS5D01G468700	chr5B	91.781	146	10	2	2908	3053	641047100	641047243	6.500000e-48	202.0
5	TraesCS5D01G468700	chr5B	97.727	44	1	0	2849	2892	641046404	641046447	4.110000e-10	76.8
6	TraesCS5D01G468700	chr5B	100.000	30	0	0	5	34	641042321	641042350	5.350000e-04	56.5
7	TraesCS5D01G468700	chr5A	90.296	1927	98	44	1012	2892	638070016	638068133	0.000000e+00	2440.0
8	TraesCS5D01G468700	chr5A	93.478	92	6	0	891	982	638075111	638075020	1.860000e-28	137.0
9	TraesCS5D01G468700	chr4A	93.988	865	40	7	31	889	603694523	603695381	0.000000e+00	1299.0
10	TraesCS5D01G468700	chr7D	93.486	875	38	8	31	889	40735590	40736461	0.000000e+00	1282.0
11	TraesCS5D01G468700	chr7D	92.767	871	41	4	37	888	565596553	565595686	0.000000e+00	1240.0
12	TraesCS5D01G468700	chr7D	92.000	725	50	7	3109	3826	562819411	562820134	0.000000e+00	1011.0
13	TraesCS5D01G468700	chr3D	93.597	859	46	5	31	889	610158852	610158003	0.000000e+00	1273.0
14	TraesCS5D01G468700	chr3D	90.443	722	60	8	3112	3826	8513330	8512611	0.000000e+00	942.0
15	TraesCS5D01G468700	chr3D	95.082	61	3	0	829	889	373942055	373941995	3.150000e-16	97.1
16	TraesCS5D01G468700	chr1D	93.029	875	41	7	31	889	19870164	19871034	0.000000e+00	1260.0
17	TraesCS5D01G468700	chr1D	92.457	875	47	4	31	889	1447910	1447039	0.000000e+00	1232.0
18	TraesCS5D01G468700	chr1D	75.964	882	180	16	1166	2040	485554558	485555414	3.540000e-115	425.0
19	TraesCS5D01G468700	chr1D	75.578	909	183	18	1144	2043	485550865	485551743	2.760000e-111	412.0
20	TraesCS5D01G468700	chr1D	75.395	886	179	16	1164	2040	485547140	485547995	3.590000e-105	392.0
21	TraesCS5D01G468700	chr1D	81.373	306	53	3	2102	2403	485489017	485488712	2.960000e-61	246.0
22	TraesCS5D01G468700	chr1D	96.774	62	2	0	828	889	276753485	276753424	1.880000e-18	104.0
23	TraesCS5D01G468700	chr4D	92.686	875	46	8	31	889	13575020	13575892	0.000000e+00	1245.0
24	TraesCS5D01G468700	chr1A	91.008	734	57	6	3109	3835	2864796	2864065	0.000000e+00	981.0
25	TraesCS5D01G468700	chr1A	76.233	791	158	12	1259	2043	582858131	582858897	3.590000e-105	392.0
26	TraesCS5D01G468700	chr1A	79.959	489	89	8	1568	2049	582845034	582845520	6.100000e-93	351.0
27	TraesCS5D01G468700	chr1A	81.046	306	54	3	2102	2403	582694191	582693886	1.380000e-59	241.0
28	TraesCS5D01G468700	chr3B	91.010	723	58	4	3109	3825	203704806	203704085	0.000000e+00	968.0
29	TraesCS5D01G468700	chr3B	90.759	725	60	4	3109	3826	98993930	98994654	0.000000e+00	961.0
30	TraesCS5D01G468700	chr2B	90.450	733	63	5	3100	3826	374022588	374023319	0.000000e+00	959.0
31	TraesCS5D01G468700	chr2B	90.193	724	63	5	3109	3826	747814283	747813562	0.000000e+00	937.0
32	TraesCS5D01G468700	chr1B	88.661	732	73	8	3111	3835	532490409	532489681	0.000000e+00	883.0
33	TraesCS5D01G468700	chr1B	75.624	882	183	13	1166	2040	676074125	676074981	3.570000e-110	409.0
34	TraesCS5D01G468700	chr1B	75.083	907	191	15	1144	2043	676070369	676071247	1.290000e-104	390.0
35	TraesCS5D01G468700	chr1B	83.071	254	40	2	2102	2352	675790255	675790002	1.070000e-55	228.0
36	TraesCS5D01G468700	chr7B	88.736	728	68	8	3110	3826	337643440	337644164	0.000000e+00	878.0
37	TraesCS5D01G468700	chr7B	96.721	61	2	0	829	889	145061843	145061783	6.780000e-18	102.0
38	TraesCS5D01G468700	chr7B	86.076	79	10	1	829	906	32334749	32334827	2.460000e-12	84.2
39	TraesCS5D01G468700	chr2D	92.308	65	5	0	825	889	54606524	54606460	4.080000e-15	93.5

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	TraesCS5D01G468700	chr5D	510057065	510060899	3834	False	7083.000000	7083	100.000000	1	3835	1	chr5D.!!$F1	3834
1	TraesCS5D01G468700	chr5D	564120799	564121670	871	True	1310.000000	1310	94.057000	31	889	1	chr5D.!!$R2	858
2	TraesCS5D01G468700	chr5D	408653564	408654430	866	True	1290.000000	1290	93.793000	36	889	1	chr5D.!!$R1	853
3	TraesCS5D01G468700	chr5B	641042321	641047243	4922	False	900.075000	3265	96.609000	5	3053	4	chr5B.!!$F1	3048
4	TraesCS5D01G468700	chr5A	638068133	638070016	1883	True	2440.000000	2440	90.296000	1012	2892	1	chr5A.!!$R1	1880
5	TraesCS5D01G468700	chr4A	603694523	603695381	858	False	1299.000000	1299	93.988000	31	889	1	chr4A.!!$F1	858
6	TraesCS5D01G468700	chr7D	40735590	40736461	871	False	1282.000000	1282	93.486000	31	889	1	chr7D.!!$F1	858
7	TraesCS5D01G468700	chr7D	565595686	565596553	867	True	1240.000000	1240	92.767000	37	888	1	chr7D.!!$R1	851
8	TraesCS5D01G468700	chr7D	562819411	562820134	723	False	1011.000000	1011	92.000000	3109	3826	1	chr7D.!!$F2	717
9	TraesCS5D01G468700	chr3D	610158003	610158852	849	True	1273.000000	1273	93.597000	31	889	1	chr3D.!!$R3	858
10	TraesCS5D01G468700	chr3D	8512611	8513330	719	True	942.000000	942	90.443000	3112	3826	1	chr3D.!!$R1	714
11	TraesCS5D01G468700	chr1D	19870164	19871034	870	False	1260.000000	1260	93.029000	31	889	1	chr1D.!!$F1	858
12	TraesCS5D01G468700	chr1D	1447039	1447910	871	True	1232.000000	1232	92.457000	31	889	1	chr1D.!!$R1	858
13	TraesCS5D01G468700	chr1D	485547140	485555414	8274	False	409.666667	425	75.645667	1144	2043	3	chr1D.!!$F2	899
14	TraesCS5D01G468700	chr4D	13575020	13575892	872	False	1245.000000	1245	92.686000	31	889	1	chr4D.!!$F1	858
15	TraesCS5D01G468700	chr1A	2864065	2864796	731	True	981.000000	981	91.008000	3109	3835	1	chr1A.!!$R1	726
16	TraesCS5D01G468700	chr1A	582858131	582858897	766	False	392.000000	392	76.233000	1259	2043	1	chr1A.!!$F2	784
17	TraesCS5D01G468700	chr3B	203704085	203704806	721	True	968.000000	968	91.010000	3109	3825	1	chr3B.!!$R1	716
18	TraesCS5D01G468700	chr3B	98993930	98994654	724	False	961.000000	961	90.759000	3109	3826	1	chr3B.!!$F1	717
19	TraesCS5D01G468700	chr2B	374022588	374023319	731	False	959.000000	959	90.450000	3100	3826	1	chr2B.!!$F1	726
20	TraesCS5D01G468700	chr2B	747813562	747814283	721	True	937.000000	937	90.193000	3109	3826	1	chr2B.!!$R1	717
21	TraesCS5D01G468700	chr1B	532489681	532490409	728	True	883.000000	883	88.661000	3111	3835	1	chr1B.!!$R1	724
22	TraesCS5D01G468700	chr1B	676070369	676074981	4612	False	399.500000	409	75.353500	1144	2043	2	chr1B.!!$F1	899
23	TraesCS5D01G468700	chr7B	337643440	337644164	724	False	878.000000	878	88.736000	3110	3826	1	chr7B.!!$F2	716

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
889	913	0.233848	GTGTGGGCGTTAGTGTTTCG	59.766	55.0	0.00	0.0	0.00	3.46	F
1686	5484	0.548682	AGGACAGGCCTCTCACCATT	60.549	55.0	10.47	0.0	46.97	3.16	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2735	8460	4.354071	AACAAAACAAACTTTGGCATGC	57.646	36.364	9.9	9.9	40.03	4.06	R
3245	11729	0.307760	CCAGACAACGTGCCAAAGTC	59.692	55.000	0.0	0.0	0.00	3.01	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
240	243	1.140375	CGTTAGGTACCTGCGGGAC	59.860	63.158	25.33	10.22	36.25	4.46
441	444	4.069304	GGTCAAACAGTAGTTGCCATGTA	58.931	43.478	0.00	0.00	38.17	2.29
571	574	6.202954	GCCGTCTAGCAATGAATTATAGTTGT	59.797	38.462	0.00	0.00	0.00	3.32
776	782	2.203139	CTCCAACGCCCACACACA	60.203	61.111	0.00	0.00	0.00	3.72
777	783	2.515057	TCCAACGCCCACACACAC	60.515	61.111	0.00	0.00	0.00	3.82
867	891	0.674895	GCGAGTTGGAGAAGTGCCAT	60.675	55.000	0.00	0.00	34.90	4.40
889	913	0.233848	GTGTGGGCGTTAGTGTTTCG	59.766	55.000	0.00	0.00	0.00	3.46
890	914	0.881159	TGTGGGCGTTAGTGTTTCGG	60.881	55.000	0.00	0.00	0.00	4.30
891	915	1.962306	TGGGCGTTAGTGTTTCGGC	60.962	57.895	0.00	0.00	46.46	5.54
892	916	3.645286	GGCGTTAGTGTTTCGGCA	58.355	55.556	5.57	0.00	46.44	5.69
893	917	1.495951	GGCGTTAGTGTTTCGGCAG	59.504	57.895	5.57	0.00	46.44	4.85
894	918	1.226030	GGCGTTAGTGTTTCGGCAGT	61.226	55.000	5.57	0.00	46.44	4.40
895	919	0.584876	GCGTTAGTGTTTCGGCAGTT	59.415	50.000	0.00	0.00	0.00	3.16
896	920	1.003223	GCGTTAGTGTTTCGGCAGTTT	60.003	47.619	0.00	0.00	0.00	2.66
897	921	2.221517	GCGTTAGTGTTTCGGCAGTTTA	59.778	45.455	0.00	0.00	0.00	2.01
898	922	3.120442	GCGTTAGTGTTTCGGCAGTTTAT	60.120	43.478	0.00	0.00	0.00	1.40
907	931	5.046878	TGTTTCGGCAGTTTATTAGGAGAGA	60.047	40.000	0.00	0.00	0.00	3.10
910	934	5.601662	TCGGCAGTTTATTAGGAGAGATTG	58.398	41.667	0.00	0.00	0.00	2.67
1429	5221	2.050714	GCTTGGACGACGACGACA	60.051	61.111	15.32	9.64	42.66	4.35
1686	5484	0.548682	AGGACAGGCCTCTCACCATT	60.549	55.000	10.47	0.00	46.97	3.16
1750	5551	2.261671	CCTCCACCTTCGACACGG	59.738	66.667	0.00	0.00	0.00	4.94
1908	5709	4.923942	AGCCTCATCGCCGCCATG	62.924	66.667	0.00	0.00	0.00	3.66
2208	6144	1.977544	CAAGGACCGTCTCGACCCT	60.978	63.158	0.00	0.00	32.12	4.34
2430	6366	2.131183	GTGCTCCATGCTCTTATCGAC	58.869	52.381	0.00	0.00	43.37	4.20
2445	6381	7.235935	TCTTATCGACCTCCTAAAGTCAAAA	57.764	36.000	0.00	0.00	33.08	2.44
2560	6571	3.935203	GGATAATGGCGACGATGATGATT	59.065	43.478	0.00	0.00	0.00	2.57
2616	8305	3.150767	GCAGTAGGATCGAGTGGTCTAT	58.849	50.000	0.00	0.00	0.00	1.98
2624	8313	5.541868	AGGATCGAGTGGTCTATCAATGATT	59.458	40.000	0.00	0.00	28.39	2.57
2735	8460	8.231161	GCTAGCAAAAAGAAGTTTTCTACTAGG	58.769	37.037	10.63	0.00	39.61	3.02
2892	10717	8.722394	CCAGGTTTATCAGTTCTTTTCTTACTC	58.278	37.037	0.00	0.00	0.00	2.59
2894	10719	7.603024	AGGTTTATCAGTTCTTTTCTTACTCCG	59.397	37.037	0.00	0.00	0.00	4.63
2895	10720	7.601508	GGTTTATCAGTTCTTTTCTTACTCCGA	59.398	37.037	0.00	0.00	0.00	4.55
2896	10721	8.648968	GTTTATCAGTTCTTTTCTTACTCCGAG	58.351	37.037	0.00	0.00	0.00	4.63
2897	10722	6.591750	ATCAGTTCTTTTCTTACTCCGAGA	57.408	37.500	1.33	0.00	0.00	4.04
2898	10723	6.591750	TCAGTTCTTTTCTTACTCCGAGAT	57.408	37.500	1.33	0.00	0.00	2.75
2899	10724	6.994221	TCAGTTCTTTTCTTACTCCGAGATT	58.006	36.000	1.33	0.00	0.00	2.40
2900	10725	7.091443	TCAGTTCTTTTCTTACTCCGAGATTC	58.909	38.462	1.33	0.00	0.00	2.52
2901	10726	6.034044	CAGTTCTTTTCTTACTCCGAGATTCG	59.966	42.308	1.33	0.00	40.07	3.34
2902	10727	5.892160	TCTTTTCTTACTCCGAGATTCGA	57.108	39.130	1.33	0.00	43.74	3.71
2903	10728	5.881447	TCTTTTCTTACTCCGAGATTCGAG	58.119	41.667	1.33	0.00	43.74	4.04
2905	10730	6.319152	TCTTTTCTTACTCCGAGATTCGAGAT	59.681	38.462	1.33	0.00	43.74	2.75
2906	10731	6.452494	TTTCTTACTCCGAGATTCGAGATT	57.548	37.500	1.33	0.00	43.74	2.40
2907	10732	5.676532	TCTTACTCCGAGATTCGAGATTC	57.323	43.478	1.33	0.00	43.74	2.52
2908	10733	4.211584	TCTTACTCCGAGATTCGAGATTCG	59.788	45.833	1.33	7.33	43.74	3.34
2938	11400	6.188871	GGTTTTTATTTTGTGCTGGTTTTCG	58.811	36.000	0.00	0.00	0.00	3.46
2998	11460	9.809096	TGTTTAGCTTGATATTTTGTCAAACAA	57.191	25.926	0.00	0.00	35.36	2.83
3025	11487	0.179215	GCAGCGTCGAAATTCCTGTG	60.179	55.000	0.00	0.00	0.00	3.66
3051	11513	0.266152	CCTCCCACTACTCCCATCCT	59.734	60.000	0.00	0.00	0.00	3.24
3052	11514	1.710816	CTCCCACTACTCCCATCCTC	58.289	60.000	0.00	0.00	0.00	3.71
3054	11516	0.764752	CCCACTACTCCCATCCTCCC	60.765	65.000	0.00	0.00	0.00	4.30
3055	11517	0.266152	CCACTACTCCCATCCTCCCT	59.734	60.000	0.00	0.00	0.00	4.20
3057	11519	0.186386	ACTACTCCCATCCTCCCTCG	59.814	60.000	0.00	0.00	0.00	4.63
3058	11520	0.186386	CTACTCCCATCCTCCCTCGT	59.814	60.000	0.00	0.00	0.00	4.18
3059	11521	0.106167	TACTCCCATCCTCCCTCGTG	60.106	60.000	0.00	0.00	0.00	4.35
3060	11522	2.764128	TCCCATCCTCCCTCGTGC	60.764	66.667	0.00	0.00	0.00	5.34
3061	11523	3.866582	CCCATCCTCCCTCGTGCC	61.867	72.222	0.00	0.00	0.00	5.01
3062	11524	3.866582	CCATCCTCCCTCGTGCCC	61.867	72.222	0.00	0.00	0.00	5.36
3064	11526	3.083997	ATCCTCCCTCGTGCCCAC	61.084	66.667	0.00	0.00	0.00	4.61
3079	11541	4.354943	CACCCCCTCCTCCCACCT	62.355	72.222	0.00	0.00	0.00	4.00
3080	11542	3.552911	ACCCCCTCCTCCCACCTT	61.553	66.667	0.00	0.00	0.00	3.50
3082	11544	2.456840	CCCCTCCTCCCACCTTCT	59.543	66.667	0.00	0.00	0.00	2.85
3083	11545	1.229984	CCCCTCCTCCCACCTTCTT	60.230	63.158	0.00	0.00	0.00	2.52
3084	11546	0.846870	CCCCTCCTCCCACCTTCTTT	60.847	60.000	0.00	0.00	0.00	2.52
3085	11547	0.329596	CCCTCCTCCCACCTTCTTTG	59.670	60.000	0.00	0.00	0.00	2.77
3086	11548	1.068121	CCTCCTCCCACCTTCTTTGT	58.932	55.000	0.00	0.00	0.00	2.83
3087	11549	1.003696	CCTCCTCCCACCTTCTTTGTC	59.996	57.143	0.00	0.00	0.00	3.18
3091	11553	1.981495	CTCCCACCTTCTTTGTCTCCT	59.019	52.381	0.00	0.00	0.00	3.69
3094	11556	2.289945	CCCACCTTCTTTGTCTCCTCAG	60.290	54.545	0.00	0.00	0.00	3.35
3095	11557	2.289945	CCACCTTCTTTGTCTCCTCAGG	60.290	54.545	0.00	0.00	0.00	3.86
3096	11558	1.981495	ACCTTCTTTGTCTCCTCAGGG	59.019	52.381	0.00	0.00	0.00	4.45
3097	11559	2.260822	CCTTCTTTGTCTCCTCAGGGA	58.739	52.381	0.00	0.00	39.70	4.20
3098	11560	2.027653	CCTTCTTTGTCTCCTCAGGGAC	60.028	54.545	5.57	5.57	36.57	4.46
3099	11561	2.398754	TCTTTGTCTCCTCAGGGACA	57.601	50.000	10.17	10.17	40.17	4.02
3100	11562	2.689658	TCTTTGTCTCCTCAGGGACAA	58.310	47.619	18.74	18.74	46.42	3.18
3102	11564	1.056660	TTGTCTCCTCAGGGACAACC	58.943	55.000	18.74	0.00	44.28	3.77
3186	11666	2.877708	GCCTGGCTCTAGAAAAACAGCT	60.878	50.000	12.43	0.00	32.14	4.24
3200	11680	6.316140	AGAAAAACAGCTTCATATGCGACATA	59.684	34.615	0.00	0.00	35.28	2.29
3261	11745	0.865769	ATCGACTTTGGCACGTTGTC	59.134	50.000	0.00	0.00	0.00	3.18
3336	11820	4.938226	GCATGGGGTATGATTAAGAGCTAC	59.062	45.833	0.00	0.00	39.21	3.58
3392	11876	4.040755	CAGAGGAAGGGGGAGAAGAAATA	58.959	47.826	0.00	0.00	0.00	1.40
3411	11895	3.387091	AGTGTGCGCCGGACCATA	61.387	61.111	5.05	0.00	0.00	2.74
3438	11922	1.922821	GGTGGATAGTGGCCATGGT	59.077	57.895	9.72	0.00	37.81	3.55
3671	12258	1.111277	GAGAGAGAGGAGGCCAAGAC	58.889	60.000	5.01	0.00	0.00	3.01
3729	12316	3.889227	GCCATTGCAGCGTCAGTA	58.111	55.556	0.00	0.00	37.47	2.74
3763	12350	1.064314	ACAGAGAGTAGGCCGAGATGT	60.064	52.381	0.00	0.00	0.00	3.06
3785	12372	1.689959	GACGCCGAAAACGACTCTAA	58.310	50.000	0.00	0.00	0.00	2.10
3826	12543	1.054978	AGATAAGGGGAAGGGCGTCC	61.055	60.000	0.00	0.00	36.90	4.79
3828	12545	3.910784	TAAGGGGAAGGGCGTCCGT	62.911	63.158	0.00	0.00	38.72	4.69
3832	12549	3.998672	GGAAGGGCGTCCGTGTCA	61.999	66.667	0.00	0.00	38.33	3.58

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
2	3	2.098443	GCTCACGGAACAAAAGTTTGGA	59.902	45.455	8.55	0.00	42.34	3.53
98	99	2.487762	ACGTGTGGGCAATTCTAATGTG	59.512	45.455	0.00	0.00	0.00	3.21
127	129	3.806591	GTGTGGCACGAAGTAGCTA	57.193	52.632	13.77	0.00	41.61	3.32
140	142	0.534203	AGTACTTGTTGGGCGTGTGG	60.534	55.000	0.00	0.00	0.00	4.17
240	243	1.257936	CGGATGGCAACTAAATCGTCG	59.742	52.381	0.00	0.00	37.61	5.12
441	444	4.748102	CACACGTGACAACTAGGTAAACAT	59.252	41.667	25.01	0.00	0.00	2.71
571	574	4.069304	GGCAACTAGGTAAACACACATGA	58.931	43.478	0.00	0.00	0.00	3.07
801	807	4.095185	TCTTGACACGAAAACGTGGATTTT	59.905	37.500	22.77	5.35	43.44	1.82
810	816	4.831779	CGTCGTTAATCTTGACACGAAAAC	59.168	41.667	0.00	0.00	42.90	2.43
867	891	2.843401	AACACTAACGCCCACACATA	57.157	45.000	0.00	0.00	0.00	2.29
889	913	6.587273	ACTCAATCTCTCCTAATAAACTGCC	58.413	40.000	0.00	0.00	0.00	4.85
890	914	8.394121	CAAACTCAATCTCTCCTAATAAACTGC	58.606	37.037	0.00	0.00	0.00	4.40
891	915	9.442047	ACAAACTCAATCTCTCCTAATAAACTG	57.558	33.333	0.00	0.00	0.00	3.16
892	916	9.442047	CACAAACTCAATCTCTCCTAATAAACT	57.558	33.333	0.00	0.00	0.00	2.66
893	917	9.220767	ACACAAACTCAATCTCTCCTAATAAAC	57.779	33.333	0.00	0.00	0.00	2.01
894	918	9.436957	GACACAAACTCAATCTCTCCTAATAAA	57.563	33.333	0.00	0.00	0.00	1.40
895	919	7.759886	CGACACAAACTCAATCTCTCCTAATAA	59.240	37.037	0.00	0.00	0.00	1.40
896	920	7.258441	CGACACAAACTCAATCTCTCCTAATA	58.742	38.462	0.00	0.00	0.00	0.98
897	921	6.102663	CGACACAAACTCAATCTCTCCTAAT	58.897	40.000	0.00	0.00	0.00	1.73
898	922	5.470368	CGACACAAACTCAATCTCTCCTAA	58.530	41.667	0.00	0.00	0.00	2.69
907	931	3.750371	TGGAATCCGACACAAACTCAAT	58.250	40.909	0.00	0.00	0.00	2.57
910	934	2.737252	GACTGGAATCCGACACAAACTC	59.263	50.000	0.00	0.00	0.00	3.01
1053	1084	3.579586	TCGGTTTCTACTAGAAAAGGGCA	59.420	43.478	12.02	0.00	44.84	5.36
1623	5421	1.735376	CGAGGATGTGGGGGACGTAG	61.735	65.000	0.00	0.00	0.00	3.51
1686	5484	0.457166	CGGAGCCGTCGTTCATGTAA	60.457	55.000	0.00	0.00	34.35	2.41
2581	7580	6.294231	CGATCCTACTGCTAGCTTTCATCTTA	60.294	42.308	17.23	0.00	0.00	2.10
2616	8305	7.540400	CGTAGGCACACAATTTTTAATCATTGA	59.460	33.333	12.05	0.00	34.89	2.57
2624	8313	5.543714	TCTCTCGTAGGCACACAATTTTTA	58.456	37.500	0.00	0.00	0.00	1.52
2735	8460	4.354071	AACAAAACAAACTTTGGCATGC	57.646	36.364	9.90	9.90	40.03	4.06
2817	8546	8.020819	CAGTCTTCTTTTATTGAAAATACCGCA	58.979	33.333	0.00	0.00	34.08	5.69
2847	9447	9.807921	AAACCTGGATAAAATAACCGATGATAT	57.192	29.630	0.00	0.00	0.00	1.63
2883	10708	6.452494	AATCTCGAATCTCGGAGTAAGAAA	57.548	37.500	4.69	0.00	40.88	2.52
2900	10725	1.068474	AAAACCGTGCTCGAATCTCG	58.932	50.000	10.21	0.00	42.10	4.04
2901	10726	4.859629	ATAAAAACCGTGCTCGAATCTC	57.140	40.909	10.21	0.00	39.71	2.75
2902	10727	5.622770	AAATAAAAACCGTGCTCGAATCT	57.377	34.783	10.21	0.00	39.71	2.40
2903	10728	5.627780	ACAAAATAAAAACCGTGCTCGAATC	59.372	36.000	10.21	0.00	39.71	2.52
2905	10730	4.735822	CACAAAATAAAAACCGTGCTCGAA	59.264	37.500	10.21	0.00	39.71	3.71
2906	10731	4.283678	CACAAAATAAAAACCGTGCTCGA	58.716	39.130	10.21	0.00	39.71	4.04
2907	10732	3.121496	GCACAAAATAAAAACCGTGCTCG	60.121	43.478	0.14	0.14	44.77	5.03
2908	10733	4.369167	GCACAAAATAAAAACCGTGCTC	57.631	40.909	0.00	0.00	44.77	4.26
2913	11375	5.726729	AAACCAGCACAAAATAAAAACCG	57.273	34.783	0.00	0.00	0.00	4.44
2951	11413	4.082787	ACATATGAACCAGTTTTTGCGGAG	60.083	41.667	10.38	0.00	0.00	4.63
2954	11416	6.183359	GCTAAACATATGAACCAGTTTTTGCG	60.183	38.462	10.38	0.00	35.90	4.85
2998	11460	2.377628	TTTCGACGCTGCCCTCAACT	62.378	55.000	0.00	0.00	0.00	3.16
3000	11462	0.605319	AATTTCGACGCTGCCCTCAA	60.605	50.000	0.00	0.00	0.00	3.02
3004	11466	1.745489	AGGAATTTCGACGCTGCCC	60.745	57.895	0.00	0.00	0.00	5.36
3062	11524	3.891432	AAGGTGGGAGGAGGGGGTG	62.891	68.421	0.00	0.00	0.00	4.61
3064	11526	2.692741	GAAGGTGGGAGGAGGGGG	60.693	72.222	0.00	0.00	0.00	5.40
3067	11529	1.003696	GACAAAGAAGGTGGGAGGAGG	59.996	57.143	0.00	0.00	0.00	4.30
3069	11531	1.978580	GAGACAAAGAAGGTGGGAGGA	59.021	52.381	0.00	0.00	0.00	3.71
3070	11532	1.003696	GGAGACAAAGAAGGTGGGAGG	59.996	57.143	0.00	0.00	0.00	4.30
3074	11536	2.289945	CCTGAGGAGACAAAGAAGGTGG	60.290	54.545	0.00	0.00	0.00	4.61
3075	11537	2.289945	CCCTGAGGAGACAAAGAAGGTG	60.290	54.545	0.00	0.00	33.47	4.00
3076	11538	1.981495	CCCTGAGGAGACAAAGAAGGT	59.019	52.381	0.00	0.00	33.47	3.50
3079	11541	2.689658	TGTCCCTGAGGAGACAAAGAA	58.310	47.619	16.94	0.00	45.21	2.52
3080	11542	2.398754	TGTCCCTGAGGAGACAAAGA	57.601	50.000	16.94	0.00	45.21	2.52
3084	11546	2.759985	GGTTGTCCCTGAGGAGACA	58.240	57.895	15.78	15.78	45.21	3.41
3103	11565	0.529555	CAACCAAACACGCCCAAAGG	60.530	55.000	0.00	0.00	0.00	3.11
3186	11666	5.277925	CCAACTTGCATATGTCGCATATGAA	60.278	40.000	28.52	21.57	39.58	2.57
3245	11729	0.307760	CCAGACAACGTGCCAAAGTC	59.692	55.000	0.00	0.00	0.00	3.01
3261	11745	0.524862	GAGACAATGCAGGCAACCAG	59.475	55.000	0.00	0.00	37.17	4.00
3411	11895	4.227134	CTATCCACCGCAGCCGCT	62.227	66.667	0.00	0.00	35.30	5.52
3415	11899	2.897350	GCCACTATCCACCGCAGC	60.897	66.667	0.00	0.00	0.00	5.25
3501	12087	1.287815	CTAGTTCGCCACGGTGACA	59.712	57.895	10.28	0.00	34.07	3.58
3503	12089	0.319211	CAACTAGTTCGCCACGGTGA	60.319	55.000	10.28	0.00	0.00	4.02
3640	12227	2.422235	CCTCTCTCTCGTCCCACTACAT	60.422	54.545	0.00	0.00	0.00	2.29
3729	12316	1.629353	TCTCTGTCGTCCTCCTACTGT	59.371	52.381	0.00	0.00	0.00	3.55
3763	12350	3.694394	GTCGTTTTCGGCGTCGCA	61.694	61.111	20.50	0.00	44.25	5.10
3785	12372	1.324740	TTGCCCGCGTCCTACTACAT	61.325	55.000	4.92	0.00	0.00	2.29

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.