AutoCloner

Multiple sequence alignment - TraesCS3B01G331800

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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	TraesCS3B01G331800	chr3B	100.000	3742	0	0	1	3742	537311186	537307445	0.000000e+00	6911
1	TraesCS3B01G331800	chr3B	98.139	591	11	0	3150	3740	537302570	537301980	0.000000e+00	1031
2	TraesCS3B01G331800	chr3A	96.904	2261	62	6	897	3152	540683192	540685449	0.000000e+00	3781
3	TraesCS3B01G331800	chr3A	86.333	439	50	6	1	435	540671461	540671893	1.570000e-128	470
4	TraesCS3B01G331800	chr3D	96.326	2259	68	4	897	3152	410973279	410971033	0.000000e+00	3698
5	TraesCS3B01G331800	chr3D	88.533	811	80	8	1	799	410981543	410980734	0.000000e+00	970
6	TraesCS3B01G331800	chr1B	97.808	593	13	0	3150	3742	678578635	678578043	0.000000e+00	1024
7	TraesCS3B01G331800	chr1B	97.470	593	15	0	3150	3742	678595104	678594512	0.000000e+00	1013
8	TraesCS3B01G331800	chr1B	97.293	591	16	0	3150	3740	630281263	630280673	0.000000e+00	1003
9	TraesCS3B01G331800	chr1B	96.812	596	16	1	3150	3742	640810533	640809938	0.000000e+00	992
10	TraesCS3B01G331800	chr1B	83.681	766	107	12	77	827	598846457	598845695	0.000000e+00	706
11	TraesCS3B01G331800	chr1B	82.496	617	87	13	84	689	540444361	540443755	4.280000e-144	521
12	TraesCS3B01G331800	chr1B	78.464	729	123	19	109	824	102671580	102670873	2.650000e-121	446
13	TraesCS3B01G331800	chr1B	79.563	641	107	16	193	829	65556324	65555704	1.600000e-118	436
14	TraesCS3B01G331800	chr1B	81.296	540	85	12	87	612	624996263	624996800	1.240000e-114	424
15	TraesCS3B01G331800	chr2B	97.470	593	15	0	3150	3742	598592489	598593081	0.000000e+00	1013
16	TraesCS3B01G331800	chr2B	97.302	593	16	0	3150	3742	598618811	598619403	0.000000e+00	1007
17	TraesCS3B01G331800	chr2B	97.302	593	16	0	3150	3742	786565567	786564975	0.000000e+00	1007
18	TraesCS3B01G331800	chr2B	83.831	402	48	9	443	828	160906879	160907279	2.120000e-97	366
19	TraesCS3B01G331800	chr4A	97.133	593	17	0	3150	3742	742526133	742526725	0.000000e+00	1002
20	TraesCS3B01G331800	chr4D	81.984	766	109	19	86	829	6922951	6923709	1.140000e-174	623
21	TraesCS3B01G331800	chr4D	81.420	479	79	10	77	549	12415844	12416318	2.110000e-102	383
22	TraesCS3B01G331800	chr5D	84.235	647	85	13	154	790	520788642	520789281	6.870000e-172	614
23	TraesCS3B01G331800	chr5D	80.395	760	129	13	89	832	497835558	497834803	9.080000e-156	560
24	TraesCS3B01G331800	chr5D	80.218	733	103	21	86	806	402948721	402948019	2.580000e-141	512
25	TraesCS3B01G331800	chr1D	83.179	648	96	7	193	829	347783045	347782400	6.970000e-162	580
26	TraesCS3B01G331800	chr1D	82.189	539	79	12	87	612	454484577	454484043	7.370000e-122	448
27	TraesCS3B01G331800	chr7A	80.901	644	110	10	194	828	573447016	573447655	2.600000e-136	496
28	TraesCS3B01G331800	chr5A	81.838	457	72	4	384	829	574944260	574944716	1.270000e-99	374
29	TraesCS3B01G331800	chr1A	81.797	423	57	13	422	829	45788764	45789181	1.670000e-88	337

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	TraesCS3B01G331800	chr3B	537307445	537311186	3741	True	6911	6911	100.000	1	3742	1	chr3B.!!$R2	3741
1	TraesCS3B01G331800	chr3B	537301980	537302570	590	True	1031	1031	98.139	3150	3740	1	chr3B.!!$R1	590
2	TraesCS3B01G331800	chr3A	540683192	540685449	2257	False	3781	3781	96.904	897	3152	1	chr3A.!!$F2	2255
3	TraesCS3B01G331800	chr3D	410971033	410973279	2246	True	3698	3698	96.326	897	3152	1	chr3D.!!$R1	2255
4	TraesCS3B01G331800	chr3D	410980734	410981543	809	True	970	970	88.533	1	799	1	chr3D.!!$R2	798
5	TraesCS3B01G331800	chr1B	678578043	678578635	592	True	1024	1024	97.808	3150	3742	1	chr1B.!!$R7	592
6	TraesCS3B01G331800	chr1B	678594512	678595104	592	True	1013	1013	97.470	3150	3742	1	chr1B.!!$R8	592
7	TraesCS3B01G331800	chr1B	630280673	630281263	590	True	1003	1003	97.293	3150	3740	1	chr1B.!!$R5	590
8	TraesCS3B01G331800	chr1B	640809938	640810533	595	True	992	992	96.812	3150	3742	1	chr1B.!!$R6	592
9	TraesCS3B01G331800	chr1B	598845695	598846457	762	True	706	706	83.681	77	827	1	chr1B.!!$R4	750
10	TraesCS3B01G331800	chr1B	540443755	540444361	606	True	521	521	82.496	84	689	1	chr1B.!!$R3	605
11	TraesCS3B01G331800	chr1B	102670873	102671580	707	True	446	446	78.464	109	824	1	chr1B.!!$R2	715
12	TraesCS3B01G331800	chr1B	65555704	65556324	620	True	436	436	79.563	193	829	1	chr1B.!!$R1	636
13	TraesCS3B01G331800	chr1B	624996263	624996800	537	False	424	424	81.296	87	612	1	chr1B.!!$F1	525
14	TraesCS3B01G331800	chr2B	598592489	598593081	592	False	1013	1013	97.470	3150	3742	1	chr2B.!!$F2	592
15	TraesCS3B01G331800	chr2B	598618811	598619403	592	False	1007	1007	97.302	3150	3742	1	chr2B.!!$F3	592
16	TraesCS3B01G331800	chr2B	786564975	786565567	592	True	1007	1007	97.302	3150	3742	1	chr2B.!!$R1	592
17	TraesCS3B01G331800	chr4A	742526133	742526725	592	False	1002	1002	97.133	3150	3742	1	chr4A.!!$F1	592
18	TraesCS3B01G331800	chr4D	6922951	6923709	758	False	623	623	81.984	86	829	1	chr4D.!!$F1	743
19	TraesCS3B01G331800	chr5D	520788642	520789281	639	False	614	614	84.235	154	790	1	chr5D.!!$F1	636
20	TraesCS3B01G331800	chr5D	497834803	497835558	755	True	560	560	80.395	89	832	1	chr5D.!!$R2	743
21	TraesCS3B01G331800	chr5D	402948019	402948721	702	True	512	512	80.218	86	806	1	chr5D.!!$R1	720
22	TraesCS3B01G331800	chr1D	347782400	347783045	645	True	580	580	83.179	193	829	1	chr1D.!!$R1	636
23	TraesCS3B01G331800	chr1D	454484043	454484577	534	True	448	448	82.189	87	612	1	chr1D.!!$R2	525
24	TraesCS3B01G331800	chr7A	573447016	573447655	639	False	496	496	80.901	194	828	1	chr7A.!!$F1	634

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
858	899	0.031585	ACAACAACTCGTAGCTCGCA	59.968	50.0	0.0	0.0	39.67	5.1	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2836	2880	0.620556	GGCAGAATTCCAGGACAGGA	59.379	55.0	0.65	0.0	35.41	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
31	33	2.214376	TGGGGTATCAAACTTGGCAG	57.786	50.000	0.00	0.00	0.00	4.85
47	49	2.754552	TGGCAGACCATTTTACTCATGC	59.245	45.455	0.00	0.00	42.67	4.06
48	50	2.754552	GGCAGACCATTTTACTCATGCA	59.245	45.455	0.00	0.00	34.17	3.96
57	59	7.444299	ACCATTTTACTCATGCATGAAGTTTT	58.556	30.769	28.39	13.57	36.18	2.43
73	75	6.791303	TGAAGTTTTGTGAAGTATTGACACC	58.209	36.000	0.00	0.00	43.27	4.16
78	80	7.174946	AGTTTTGTGAAGTATTGACACCCATAG	59.825	37.037	0.00	0.00	43.27	2.23
173	180	3.628646	GACACAATGCGGGAGGCCT	62.629	63.158	3.86	3.86	42.61	5.19
351	366	6.619801	AATTTGACTAGATTAACCGGATGC	57.380	37.500	9.46	0.00	0.00	3.91
352	367	4.746535	TTGACTAGATTAACCGGATGCA	57.253	40.909	9.46	0.00	0.00	3.96
368	383	5.218885	CGGATGCACAACAAGTTTTTCATA	58.781	37.500	0.00	0.00	0.00	2.15
400	418	0.326618	CCTCCCACACATACTCCCCT	60.327	60.000	0.00	0.00	0.00	4.79
419	437	4.996758	CCCCTTTCAATTTCATCCAACAAC	59.003	41.667	0.00	0.00	0.00	3.32
424	442	7.871973	CCTTTCAATTTCATCCAACAACATGTA	59.128	33.333	0.00	0.00	0.00	2.29
438	456	9.299963	CCAACAACATGTATACATAAATGGTTG	57.700	33.333	27.71	27.71	39.30	3.77
471	492	3.564027	GTACATCACGGCAGCGCC	61.564	66.667	2.29	9.20	46.75	6.53
507	530	3.479489	TGAGCACATCAACATTGAGTGT	58.521	40.909	17.65	11.78	44.84	3.55
549	572	8.745590	AGTTAAGCAAGAGGAAACAAAACTTAA	58.254	29.630	0.00	0.00	0.00	1.85
732	769	2.698803	ACGATTCATGCACTTGCTACA	58.301	42.857	2.33	0.00	42.66	2.74
733	770	2.674852	ACGATTCATGCACTTGCTACAG	59.325	45.455	2.33	0.00	42.66	2.74
734	771	2.931969	CGATTCATGCACTTGCTACAGA	59.068	45.455	2.33	0.00	42.66	3.41
738	775	3.743521	TCATGCACTTGCTACAGAAAGT	58.256	40.909	2.33	0.00	44.55	2.66
765	804	5.425217	TCCCTCTGCTTCTGTGTATGAAATA	59.575	40.000	0.00	0.00	0.00	1.40
801	840	0.316937	CACGCATCGCACAACAACTT	60.317	50.000	0.00	0.00	0.00	2.66
807	846	3.119849	GCATCGCACAACAACTTATCCTT	60.120	43.478	0.00	0.00	0.00	3.36
809	848	2.734606	TCGCACAACAACTTATCCTTCG	59.265	45.455	0.00	0.00	0.00	3.79
829	870	2.137692	GGGAGTAGCTCACCATCCC	58.862	63.158	0.00	0.00	42.75	3.85
832	873	1.195115	GAGTAGCTCACCATCCCACA	58.805	55.000	0.00	0.00	0.00	4.17
833	874	0.905357	AGTAGCTCACCATCCCACAC	59.095	55.000	0.00	0.00	0.00	3.82
834	875	0.613260	GTAGCTCACCATCCCACACA	59.387	55.000	0.00	0.00	0.00	3.72
835	876	1.210478	GTAGCTCACCATCCCACACAT	59.790	52.381	0.00	0.00	0.00	3.21
836	877	0.254178	AGCTCACCATCCCACACATC	59.746	55.000	0.00	0.00	0.00	3.06
837	878	0.749454	GCTCACCATCCCACACATCC	60.749	60.000	0.00	0.00	0.00	3.51
838	879	0.107017	CTCACCATCCCACACATCCC	60.107	60.000	0.00	0.00	0.00	3.85
839	880	0.844221	TCACCATCCCACACATCCCA	60.844	55.000	0.00	0.00	0.00	4.37
840	881	0.680921	CACCATCCCACACATCCCAC	60.681	60.000	0.00	0.00	0.00	4.61
841	882	1.139498	ACCATCCCACACATCCCACA	61.139	55.000	0.00	0.00	0.00	4.17
842	883	0.039472	CCATCCCACACATCCCACAA	59.961	55.000	0.00	0.00	0.00	3.33
843	884	1.176527	CATCCCACACATCCCACAAC	58.823	55.000	0.00	0.00	0.00	3.32
844	885	0.776810	ATCCCACACATCCCACAACA	59.223	50.000	0.00	0.00	0.00	3.33
845	886	0.553333	TCCCACACATCCCACAACAA	59.447	50.000	0.00	0.00	0.00	2.83
846	887	0.673437	CCCACACATCCCACAACAAC	59.327	55.000	0.00	0.00	0.00	3.32
847	888	1.691196	CCACACATCCCACAACAACT	58.309	50.000	0.00	0.00	0.00	3.16
848	889	1.608590	CCACACATCCCACAACAACTC	59.391	52.381	0.00	0.00	0.00	3.01
849	890	1.264020	CACACATCCCACAACAACTCG	59.736	52.381	0.00	0.00	0.00	4.18
850	891	1.134220	ACACATCCCACAACAACTCGT	60.134	47.619	0.00	0.00	0.00	4.18
851	892	2.103432	ACACATCCCACAACAACTCGTA	59.897	45.455	0.00	0.00	0.00	3.43
852	893	2.736721	CACATCCCACAACAACTCGTAG	59.263	50.000	0.00	0.00	0.00	3.51
853	894	1.732259	CATCCCACAACAACTCGTAGC	59.268	52.381	0.00	0.00	0.00	3.58
854	895	1.045407	TCCCACAACAACTCGTAGCT	58.955	50.000	0.00	0.00	0.00	3.32
855	896	1.000506	TCCCACAACAACTCGTAGCTC	59.999	52.381	0.00	0.00	0.00	4.09
856	897	1.060713	CCACAACAACTCGTAGCTCG	58.939	55.000	0.00	0.00	41.41	5.03
857	898	0.435008	CACAACAACTCGTAGCTCGC	59.565	55.000	0.00	0.00	39.67	5.03
858	899	0.031585	ACAACAACTCGTAGCTCGCA	59.968	50.000	0.00	0.00	39.67	5.10
859	900	1.136690	CAACAACTCGTAGCTCGCAA	58.863	50.000	0.00	0.00	39.67	4.85
860	901	1.726791	CAACAACTCGTAGCTCGCAAT	59.273	47.619	0.00	0.00	39.67	3.56
861	902	1.630148	ACAACTCGTAGCTCGCAATC	58.370	50.000	0.00	0.00	39.67	2.67
862	903	0.924090	CAACTCGTAGCTCGCAATCC	59.076	55.000	0.00	0.00	39.67	3.01
863	904	0.818296	AACTCGTAGCTCGCAATCCT	59.182	50.000	0.00	0.00	39.67	3.24
864	905	0.818296	ACTCGTAGCTCGCAATCCTT	59.182	50.000	0.00	0.00	39.67	3.36
865	906	1.202313	ACTCGTAGCTCGCAATCCTTC	60.202	52.381	0.00	0.00	39.67	3.46
866	907	0.248498	TCGTAGCTCGCAATCCTTCG	60.248	55.000	0.00	0.00	39.67	3.79
867	908	0.525668	CGTAGCTCGCAATCCTTCGT	60.526	55.000	0.00	0.00	0.00	3.85
868	909	1.268386	CGTAGCTCGCAATCCTTCGTA	60.268	52.381	0.00	0.00	0.00	3.43
869	910	2.793585	CGTAGCTCGCAATCCTTCGTAA	60.794	50.000	0.00	0.00	0.00	3.18
870	911	2.604046	AGCTCGCAATCCTTCGTAAT	57.396	45.000	0.00	0.00	0.00	1.89
871	912	2.906354	AGCTCGCAATCCTTCGTAATT	58.094	42.857	0.00	0.00	0.00	1.40
872	913	4.054780	AGCTCGCAATCCTTCGTAATTA	57.945	40.909	0.00	0.00	0.00	1.40
873	914	4.439057	AGCTCGCAATCCTTCGTAATTAA	58.561	39.130	0.00	0.00	0.00	1.40
874	915	4.873827	AGCTCGCAATCCTTCGTAATTAAA	59.126	37.500	0.00	0.00	0.00	1.52
875	916	5.353123	AGCTCGCAATCCTTCGTAATTAAAA	59.647	36.000	0.00	0.00	0.00	1.52
876	917	6.025280	GCTCGCAATCCTTCGTAATTAAAAA	58.975	36.000	0.00	0.00	0.00	1.94
893	934	2.559998	AAAAATGGCATAAGCGTCGG	57.440	45.000	0.00	0.00	43.41	4.79
894	935	1.459450	AAAATGGCATAAGCGTCGGT	58.541	45.000	0.00	0.00	43.41	4.69
895	936	0.732571	AAATGGCATAAGCGTCGGTG	59.267	50.000	0.00	0.00	43.41	4.94
918	959	0.040067	GTTGCTCAAGCGAACCCTTG	60.040	55.000	0.00	0.00	45.83	3.61
1107	1150	3.044305	GTCGTCACAGGCCACAGC	61.044	66.667	5.01	0.00	38.76	4.40
1400	1444	0.324368	ACACGCACTCCATCCTCCTA	60.324	55.000	0.00	0.00	0.00	2.94
1433	1477	2.429236	CGCTTCGTGCTGACGTCT	60.429	61.111	17.92	0.00	46.20	4.18
1460	1504	0.676466	TGCTGTATTCCAAGTGCGGG	60.676	55.000	0.00	0.00	0.00	6.13
1490	1534	2.127609	GCACGCAAGCTGTTCGAC	60.128	61.111	9.11	0.00	45.62	4.20
1491	1535	2.598632	GCACGCAAGCTGTTCGACT	61.599	57.895	9.11	0.00	45.62	4.18
1541	1585	3.632145	GGAACGCAATGATTTCTGGGTAT	59.368	43.478	0.00	0.00	37.71	2.73
1920	1964	2.194597	GGCCGCCACCCAATCATA	59.805	61.111	3.91	0.00	0.00	2.15
1929	1973	3.880490	GCCACCCAATCATATCACGTTTA	59.120	43.478	0.00	0.00	0.00	2.01
2249	2293	4.381932	CCATCCTACCATGTTTTGCTTTCC	60.382	45.833	0.00	0.00	0.00	3.13
2264	2308	9.801873	GTTTTGCTTTCCAATATTTATGCTCTA	57.198	29.630	0.00	0.00	32.49	2.43
2267	2311	8.340618	TGCTTTCCAATATTTATGCTCTATCC	57.659	34.615	0.00	0.00	0.00	2.59
2291	2335	5.537188	GGTAAAATGCACCATGTTGAGAAA	58.463	37.500	0.00	0.00	36.01	2.52
2362	2406	4.615588	GCTTGATTGAGCTAGGAGGTAT	57.384	45.455	0.00	0.00	39.57	2.73
2453	2497	6.529220	AGAACTGATTCATAGGATTAGTGCC	58.471	40.000	0.00	0.00	37.29	5.01
2532	2576	3.319405	AGAGGGTGCACTTAGATATCACG	59.681	47.826	17.98	0.00	0.00	4.35
2579	2623	0.904649	TCATGATGAGCGTTGGGAGT	59.095	50.000	0.00	0.00	0.00	3.85
2710	2754	4.806775	GCACCGTTTTCACCATTTTAAAGT	59.193	37.500	0.00	0.00	0.00	2.66
2723	2767	5.814705	CCATTTTAAAGTTGGCAAGTGTTCA	59.185	36.000	8.61	0.00	0.00	3.18
2836	2880	6.530120	TGAACAACTACATTCACATACACCT	58.470	36.000	0.00	0.00	29.89	4.00
2960	3005	7.041780	AGTCCTGATATTGCATCAAAATACGAC	60.042	37.037	0.00	0.00	0.00	4.34
2967	3012	6.435430	TTGCATCAAAATACGACTGCTTAT	57.565	33.333	0.00	0.00	0.00	1.73
2981	3026	4.384056	ACTGCTTATCTCCATCCATTTCG	58.616	43.478	0.00	0.00	0.00	3.46
3061	3106	6.316390	CCTACATATTTCTGAACTCCCAACAC	59.684	42.308	0.00	0.00	0.00	3.32
3100	3145	5.450412	GGATGCTGAAAGACAACAAAACAGA	60.450	40.000	0.00	0.00	34.07	3.41
3127	3172	2.315925	TTCTTTGCTAGCTCATCCGG	57.684	50.000	17.23	0.00	0.00	5.14
3162	3207	4.153475	GCGAGGTACATGCTAAGAAAACAA	59.847	41.667	0.00	0.00	0.00	2.83
3628	3676	2.052690	CGGACGGGATGGAGTCACT	61.053	63.158	0.00	0.00	39.01	3.41

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
27	29	2.754552	TGCATGAGTAAAATGGTCTGCC	59.245	45.455	0.00	0.00	0.00	4.85
31	33	6.199937	ACTTCATGCATGAGTAAAATGGTC	57.800	37.500	27.25	0.00	38.19	4.02
45	47	6.917477	GTCAATACTTCACAAAACTTCATGCA	59.083	34.615	0.00	0.00	0.00	3.96
47	49	7.379529	GGTGTCAATACTTCACAAAACTTCATG	59.620	37.037	0.00	0.00	34.27	3.07
48	50	7.425606	GGTGTCAATACTTCACAAAACTTCAT	58.574	34.615	0.00	0.00	34.27	2.57
57	59	5.755409	ACTATGGGTGTCAATACTTCACA	57.245	39.130	0.00	0.00	34.27	3.58
73	75	5.485353	TGGAGATGCCCTAAGAATACTATGG	59.515	44.000	0.00	0.00	34.97	2.74
78	80	4.058817	CGTTGGAGATGCCCTAAGAATAC	58.941	47.826	0.00	0.00	34.97	1.89
146	152	0.735978	CGCATTGTGTCCGCAGACTA	60.736	55.000	1.05	0.00	43.91	2.59
173	180	2.673775	TTCAGGCAAAGTTGGATGGA	57.326	45.000	0.00	0.00	0.00	3.41
183	190	4.321601	CGGGTTGAAATGTATTCAGGCAAA	60.322	41.667	0.00	0.00	0.00	3.68
184	191	3.192422	CGGGTTGAAATGTATTCAGGCAA	59.808	43.478	0.00	0.00	0.00	4.52
351	366	9.258826	TGATCCATTTATGAAAAACTTGTTGTG	57.741	29.630	0.00	0.00	0.00	3.33
368	383	0.935942	TGGGAGGGCATGATCCATTT	59.064	50.000	12.45	0.00	37.33	2.32
419	437	7.939039	AGAGACCCAACCATTTATGTATACATG	59.061	37.037	25.48	12.11	37.15	3.21
424	442	6.158695	AGACAGAGACCCAACCATTTATGTAT	59.841	38.462	0.00	0.00	0.00	2.29
438	456	1.968493	TGTACCACAAGACAGAGACCC	59.032	52.381	0.00	0.00	0.00	4.46
471	492	1.151668	GCTCATTATGTAGCCCGCAG	58.848	55.000	5.68	0.00	32.40	5.18
488	511	3.433274	CGTACACTCAATGTTGATGTGCT	59.567	43.478	17.41	11.36	43.19	4.40
507	530	7.428282	TGCTTAACTTGTTGATTGATTCGTA	57.572	32.000	0.00	0.00	0.00	3.43
572	609	1.758440	TTCGTCAGCTGGAGGCAAGT	61.758	55.000	15.13	0.00	44.79	3.16
732	769	1.905894	GAAGCAGAGGGAGGACTTTCT	59.094	52.381	0.00	0.00	0.00	2.52
733	770	1.905894	AGAAGCAGAGGGAGGACTTTC	59.094	52.381	0.00	0.00	0.00	2.62
734	771	1.627834	CAGAAGCAGAGGGAGGACTTT	59.372	52.381	0.00	0.00	0.00	2.66
738	775	0.178921	ACACAGAAGCAGAGGGAGGA	60.179	55.000	0.00	0.00	0.00	3.71
765	804	0.884704	GTGATTGGCCGTATCCGCAT	60.885	55.000	13.42	0.00	0.00	4.73
801	840	2.092049	TGAGCTACTCCCACGAAGGATA	60.092	50.000	0.00	0.00	41.22	2.59
807	846	0.324368	ATGGTGAGCTACTCCCACGA	60.324	55.000	6.87	0.00	35.08	4.35
809	848	0.466124	GGATGGTGAGCTACTCCCAC	59.534	60.000	6.87	0.00	35.08	4.61
829	870	1.264020	CGAGTTGTTGTGGGATGTGTG	59.736	52.381	0.00	0.00	0.00	3.82
832	873	2.870435	GCTACGAGTTGTTGTGGGATGT	60.870	50.000	0.00	0.00	0.00	3.06
833	874	1.732259	GCTACGAGTTGTTGTGGGATG	59.268	52.381	0.00	0.00	0.00	3.51
834	875	1.623811	AGCTACGAGTTGTTGTGGGAT	59.376	47.619	0.00	0.00	0.00	3.85
835	876	1.000506	GAGCTACGAGTTGTTGTGGGA	59.999	52.381	0.00	0.00	0.00	4.37
836	877	1.429463	GAGCTACGAGTTGTTGTGGG	58.571	55.000	0.00	0.00	0.00	4.61
837	878	1.060713	CGAGCTACGAGTTGTTGTGG	58.939	55.000	0.00	0.00	45.77	4.17
838	879	0.435008	GCGAGCTACGAGTTGTTGTG	59.565	55.000	9.32	0.00	45.77	3.33
839	880	0.031585	TGCGAGCTACGAGTTGTTGT	59.968	50.000	9.32	0.00	45.77	3.32
840	881	1.136690	TTGCGAGCTACGAGTTGTTG	58.863	50.000	9.32	0.00	45.77	3.33
841	882	1.993370	GATTGCGAGCTACGAGTTGTT	59.007	47.619	9.32	0.00	45.77	2.83
842	883	1.630148	GATTGCGAGCTACGAGTTGT	58.370	50.000	9.32	0.00	45.77	3.32
843	884	0.924090	GGATTGCGAGCTACGAGTTG	59.076	55.000	9.32	0.00	45.77	3.16
844	885	0.818296	AGGATTGCGAGCTACGAGTT	59.182	50.000	9.32	0.00	45.77	3.01
845	886	0.818296	AAGGATTGCGAGCTACGAGT	59.182	50.000	9.32	0.00	45.77	4.18
846	887	1.482278	GAAGGATTGCGAGCTACGAG	58.518	55.000	9.32	0.00	45.77	4.18
847	888	0.248498	CGAAGGATTGCGAGCTACGA	60.248	55.000	9.32	0.00	45.77	3.43
848	889	0.525668	ACGAAGGATTGCGAGCTACG	60.526	55.000	0.00	0.00	45.66	3.51
849	890	2.486951	TACGAAGGATTGCGAGCTAC	57.513	50.000	0.00	0.00	0.00	3.58
850	891	3.728076	ATTACGAAGGATTGCGAGCTA	57.272	42.857	0.00	0.00	0.00	3.32
851	892	2.604046	ATTACGAAGGATTGCGAGCT	57.396	45.000	0.00	0.00	0.00	4.09
852	893	4.789095	TTAATTACGAAGGATTGCGAGC	57.211	40.909	0.00	0.00	0.00	5.03
874	915	1.816224	ACCGACGCTTATGCCATTTTT	59.184	42.857	0.00	0.00	35.36	1.94
875	916	1.132262	CACCGACGCTTATGCCATTTT	59.868	47.619	0.00	0.00	35.36	1.82
876	917	0.732571	CACCGACGCTTATGCCATTT	59.267	50.000	0.00	0.00	35.36	2.32
877	918	1.714899	GCACCGACGCTTATGCCATT	61.715	55.000	0.00	0.00	35.36	3.16
878	919	2.180204	GCACCGACGCTTATGCCAT	61.180	57.895	0.00	0.00	35.36	4.40
879	920	2.817834	GCACCGACGCTTATGCCA	60.818	61.111	0.00	0.00	35.36	4.92
880	921	2.511600	AGCACCGACGCTTATGCC	60.512	61.111	7.67	0.00	39.99	4.40
881	922	2.703409	CAGCACCGACGCTTATGC	59.297	61.111	0.00	0.00	41.38	3.14
882	923	1.019278	AACCAGCACCGACGCTTATG	61.019	55.000	0.00	0.00	41.38	1.90
883	924	1.019278	CAACCAGCACCGACGCTTAT	61.019	55.000	0.00	0.00	41.38	1.73
884	925	1.666553	CAACCAGCACCGACGCTTA	60.667	57.895	0.00	0.00	41.38	3.09
885	926	2.972505	CAACCAGCACCGACGCTT	60.973	61.111	0.00	0.00	41.38	4.68
895	936	1.081840	GTTCGCTTGAGCAACCAGC	60.082	57.895	3.65	0.00	46.19	4.85
1087	1130	2.430921	GTGGCCTGTGACGACGAG	60.431	66.667	3.32	0.00	0.00	4.18
1090	1133	3.044305	GCTGTGGCCTGTGACGAC	61.044	66.667	3.32	0.00	0.00	4.34
1107	1150	4.888325	ATGAGGGGGAGGGAGCGG	62.888	72.222	0.00	0.00	0.00	5.52
1120	1163	1.001764	TGGCCAGCTTGGTGATGAG	60.002	57.895	0.00	0.00	40.46	2.90
1383	1427	0.757188	CCTAGGAGGATGGAGTGCGT	60.757	60.000	1.05	0.00	37.67	5.24
1400	1444	4.016706	CGGTCCGAGCCAAACCCT	62.017	66.667	4.91	0.00	0.00	4.34
1433	1477	4.756642	CACTTGGAATACAGCACAAGAAGA	59.243	41.667	9.90	0.00	42.07	2.87
1490	1534	6.401474	CCACAACACTTCTATCACGAATTGAG	60.401	42.308	0.00	0.00	37.77	3.02
1491	1535	5.408299	CCACAACACTTCTATCACGAATTGA	59.592	40.000	0.00	0.00	39.11	2.57
1541	1585	1.243342	CGGCAAGCCCATTCTGTTCA	61.243	55.000	5.34	0.00	0.00	3.18
1603	1647	1.679311	GTCATGGAGTCAGGCACCA	59.321	57.895	0.00	0.00	41.94	4.17
1920	1964	6.238211	GCAGATAGAACAGCAATAAACGTGAT	60.238	38.462	0.00	0.00	0.00	3.06
1929	1973	3.066342	GCACATGCAGATAGAACAGCAAT	59.934	43.478	0.00	0.00	40.76	3.56
1956	2000	3.381335	GACCCTCCATAACTAACCCAGA	58.619	50.000	0.00	0.00	0.00	3.86
2264	2308	2.733956	ACATGGTGCATTTTACCGGAT	58.266	42.857	9.46	0.00	41.18	4.18
2267	2311	3.190327	TCTCAACATGGTGCATTTTACCG	59.810	43.478	5.66	0.00	41.18	4.02
2291	2335	5.901853	TCTCTTGATCATGGTATTCCTCACT	59.098	40.000	8.60	0.00	34.23	3.41
2389	2433	4.013050	CTCTGTAGTCTGTGGATGAGACA	58.987	47.826	0.00	0.00	42.07	3.41
2453	2497	1.398390	GTTTCAGGAATGTAGCCAGCG	59.602	52.381	0.00	0.00	0.00	5.18
2532	2576	1.953686	TGCTACTGCCAGTTTTTCACC	59.046	47.619	1.02	0.00	38.71	4.02
2710	2754	1.955778	CCAGACATGAACACTTGCCAA	59.044	47.619	0.00	0.00	0.00	4.52
2723	2767	8.109634	AGAGTTTGTTACCAATATTCCAGACAT	58.890	33.333	0.00	0.00	0.00	3.06
2836	2880	0.620556	GGCAGAATTCCAGGACAGGA	59.379	55.000	0.65	0.00	35.41	3.86
2960	3005	4.384056	ACGAAATGGATGGAGATAAGCAG	58.616	43.478	0.00	0.00	0.00	4.24
2967	3012	3.260632	TCTGACAACGAAATGGATGGAGA	59.739	43.478	0.00	0.00	0.00	3.71
2981	3026	1.474077	GCATTGGACCCATCTGACAAC	59.526	52.381	0.00	0.00	0.00	3.32
3061	3106	4.706476	TCAGCATCCTGACCCTTTAAATTG	59.294	41.667	0.00	0.00	42.98	2.32
3100	3145	5.620738	TGAGCTAGCAAAGAATACCAGAT	57.379	39.130	18.83	0.00	0.00	2.90
3127	3172	4.111375	TGTACCTCGCTCTTCAATCTTC	57.889	45.455	0.00	0.00	0.00	2.87

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.