AutoCloner

Multiple sequence alignment - TraesCS7A01G030300

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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	TraesCS7A01G030300	chr7A	100.000	2348	0	0	1	2348	12284493	12282146	0.000000e+00	4337.0
1	TraesCS7A01G030300	chr7A	89.272	1044	72	14	616	1626	12198777	12197741	0.000000e+00	1271.0
2	TraesCS7A01G030300	chr7A	92.628	312	20	2	997	1308	12202299	12201991	1.660000e-121	446.0
3	TraesCS7A01G030300	chr7A	87.391	230	29	0	1011	1240	32528915	32529144	4.980000e-67	265.0
4	TraesCS7A01G030300	chr7A	85.306	245	32	4	998	1240	19816654	19816896	1.390000e-62	250.0
5	TraesCS7A01G030300	chr7D	89.757	742	51	16	816	1550	12549584	12548861	0.000000e+00	926.0
6	TraesCS7A01G030300	chr7D	82.430	996	93	32	616	1549	12547289	12546314	0.000000e+00	795.0
7	TraesCS7A01G030300	chr7D	86.685	368	41	2	1	367	21032460	21032820	3.630000e-108	401.0
8	TraesCS7A01G030300	chr7D	81.616	495	66	13	1	489	368569190	368569665	1.020000e-103	387.0
9	TraesCS7A01G030300	chr4A	82.120	1085	104	49	616	1637	725581060	725582117	0.000000e+00	846.0
10	TraesCS7A01G030300	chr4A	86.314	738	68	24	1635	2347	681106800	681107529	0.000000e+00	773.0
11	TraesCS7A01G030300	chr4A	81.081	740	100	26	1640	2348	2765372	2766102	2.640000e-154	555.0
12	TraesCS7A01G030300	chr4A	81.633	490	63	14	1068	1550	725571830	725572299	4.740000e-102	381.0
13	TraesCS7A01G030300	chr4A	96.552	58	2	0	997	1054	725571780	725571837	1.920000e-16	97.1
14	TraesCS7A01G030300	chr1B	86.301	730	70	20	1640	2347	161579399	161580120	0.000000e+00	767.0
15	TraesCS7A01G030300	chr1B	81.714	525	78	11	1	522	660942855	660943364	2.790000e-114	422.0
16	TraesCS7A01G030300	chr6B	84.690	725	88	17	1640	2348	142164943	142164226	0.000000e+00	702.0
17	TraesCS7A01G030300	chrUn	80.159	756	113	21	1625	2348	75808049	75808799	4.440000e-147	531.0
18	TraesCS7A01G030300	chrUn	80.268	745	108	24	1638	2348	331686235	331685496	2.070000e-145	525.0
19	TraesCS7A01G030300	chrUn	80.079	758	110	23	1625	2348	333766782	333767532	2.070000e-145	525.0
20	TraesCS7A01G030300	chrUn	82.798	529	65	16	1841	2348	344492530	344492007	1.280000e-122	449.0
21	TraesCS7A01G030300	chr5D	83.219	584	64	15	1	573	498648475	498649035	2.690000e-139	505.0
22	TraesCS7A01G030300	chr5D	81.229	586	89	12	1	578	344448132	344447560	9.890000e-124	453.0
23	TraesCS7A01G030300	chr5D	85.124	363	51	2	1	360	354383626	354383264	3.690000e-98	368.0
24	TraesCS7A01G030300	chr1A	80.837	621	73	22	1714	2298	41407422	41406812	1.660000e-121	446.0
25	TraesCS7A01G030300	chr3B	81.955	532	67	17	1	524	229308319	229308829	7.760000e-115	424.0
26	TraesCS7A01G030300	chr2D	79.730	592	82	20	1	578	553735909	553735342	6.080000e-106	394.0
27	TraesCS7A01G030300	chr2D	81.184	473	70	13	1	462	420518918	420519382	1.720000e-96	363.0
28	TraesCS7A01G030300	chr2D	88.929	280	30	1	1	279	46330186	46329907	6.210000e-91	344.0
29	TraesCS7A01G030300	chr6A	81.316	380	66	5	4	379	183949810	183950188	1.050000e-78	303.0
30	TraesCS7A01G030300	chr6D	96.364	55	2	0	1771	1825	338906375	338906321	8.940000e-15	91.6
31	TraesCS7A01G030300	chr4D	83.721	86	11	3	1640	1723	364552403	364552487	6.960000e-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	TraesCS7A01G030300	chr7A	12282146	12284493	2347	True	4337.00	4337	100.0000	1	2348	1	chr7A.!!$R1	2347
1	TraesCS7A01G030300	chr7A	12197741	12202299	4558	True	858.50	1271	90.9500	616	1626	2	chr7A.!!$R2	1010
2	TraesCS7A01G030300	chr7D	12546314	12549584	3270	True	860.50	926	86.0935	616	1550	2	chr7D.!!$R1	934
3	TraesCS7A01G030300	chr4A	725581060	725582117	1057	False	846.00	846	82.1200	616	1637	1	chr4A.!!$F3	1021
4	TraesCS7A01G030300	chr4A	681106800	681107529	729	False	773.00	773	86.3140	1635	2347	1	chr4A.!!$F2	712
5	TraesCS7A01G030300	chr4A	2765372	2766102	730	False	555.00	555	81.0810	1640	2348	1	chr4A.!!$F1	708
6	TraesCS7A01G030300	chr4A	725571780	725572299	519	False	239.05	381	89.0925	997	1550	2	chr4A.!!$F4	553
7	TraesCS7A01G030300	chr1B	161579399	161580120	721	False	767.00	767	86.3010	1640	2347	1	chr1B.!!$F1	707
8	TraesCS7A01G030300	chr1B	660942855	660943364	509	False	422.00	422	81.7140	1	522	1	chr1B.!!$F2	521
9	TraesCS7A01G030300	chr6B	142164226	142164943	717	True	702.00	702	84.6900	1640	2348	1	chr6B.!!$R1	708
10	TraesCS7A01G030300	chrUn	75808049	75808799	750	False	531.00	531	80.1590	1625	2348	1	chrUn.!!$F1	723
11	TraesCS7A01G030300	chrUn	331685496	331686235	739	True	525.00	525	80.2680	1638	2348	1	chrUn.!!$R1	710
12	TraesCS7A01G030300	chrUn	333766782	333767532	750	False	525.00	525	80.0790	1625	2348	1	chrUn.!!$F2	723
13	TraesCS7A01G030300	chrUn	344492007	344492530	523	True	449.00	449	82.7980	1841	2348	1	chrUn.!!$R2	507
14	TraesCS7A01G030300	chr5D	498648475	498649035	560	False	505.00	505	83.2190	1	573	1	chr5D.!!$F1	572
15	TraesCS7A01G030300	chr5D	344447560	344448132	572	True	453.00	453	81.2290	1	578	1	chr5D.!!$R1	577
16	TraesCS7A01G030300	chr1A	41406812	41407422	610	True	446.00	446	80.8370	1714	2298	1	chr1A.!!$R1	584
17	TraesCS7A01G030300	chr3B	229308319	229308829	510	False	424.00	424	81.9550	1	524	1	chr3B.!!$F1	523
18	TraesCS7A01G030300	chr2D	553735342	553735909	567	True	394.00	394	79.7300	1	578	1	chr2D.!!$R2	577

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
20	21	0.108615	CCTCGTCAAGCCGAAGATGT	60.109	55.0	0.0	0.0	36.24	3.06	F
737	4804	0.263468	GGCTAGAAGACCTCCCCTCT	59.737	60.0	0.0	0.0	0.00	3.69	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1056	5160	0.107703	CCTTGGCCTGCGTGATCTTA	60.108	55.0	3.32	0.0	0.00	2.10	R
1806	5949	0.245539	TAGGCCAACGAAAGGAGTCG	59.754	55.0	5.01	0.0	46.54	4.18	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
20	21	0.108615	CCTCGTCAAGCCGAAGATGT	60.109	55.000	0.00	0.00	36.24	3.06
115	117	0.803117	CGAGGACTACGTCAAGCTGA	59.197	55.000	0.00	0.00	33.68	4.26
124	126	1.620819	ACGTCAAGCTGAAGATGGAGT	59.379	47.619	0.00	0.00	30.40	3.85
195	197	1.194781	AGGGCAGTGTCATCGTCCTT	61.195	55.000	0.00	0.00	0.00	3.36
235	237	4.708386	TACCGCCGCCAACCAAGG	62.708	66.667	0.00	0.00	0.00	3.61
243	245	2.429930	CCAACCAAGGCTGTCCGA	59.570	61.111	0.00	0.00	37.47	4.55
259	261	2.045926	GACAAGGCGATGCAGGGT	60.046	61.111	0.00	0.00	0.00	4.34
279	281	2.590114	GGGGTGCAGTAAGGACGGT	61.590	63.158	0.00	0.00	39.86	4.83
280	282	1.259840	GGGGTGCAGTAAGGACGGTA	61.260	60.000	0.00	0.00	39.86	4.02
306	308	1.208293	GTGAAGAAGGAGAAGGCCGAT	59.792	52.381	0.00	0.00	0.00	4.18
308	310	0.543749	AAGAAGGAGAAGGCCGATGG	59.456	55.000	0.00	0.00	0.00	3.51
398	429	4.168760	GGCGCGTAGTTCTCTTTTAGTTA	58.831	43.478	8.43	0.00	0.00	2.24
513	569	7.434013	GGCTGAGTTTATTTTTCAGAAAAACGA	59.566	33.333	20.94	10.96	42.57	3.85
524	580	3.125316	CAGAAAAACGACGTCTGGGTTA	58.875	45.455	14.70	0.00	36.04	2.85
542	598	1.255882	TAGGTTTGAGTCGGCGGTTA	58.744	50.000	7.21	0.00	0.00	2.85
574	630	5.257082	TCATCCTCACGTCGATATTTTCA	57.743	39.130	0.00	0.00	0.00	2.69
578	634	1.921887	TCACGTCGATATTTTCACCGC	59.078	47.619	0.00	0.00	0.00	5.68
579	635	1.924524	CACGTCGATATTTTCACCGCT	59.075	47.619	0.00	0.00	0.00	5.52
580	636	3.110358	CACGTCGATATTTTCACCGCTA	58.890	45.455	0.00	0.00	0.00	4.26
581	637	3.734231	CACGTCGATATTTTCACCGCTAT	59.266	43.478	0.00	0.00	0.00	2.97
582	638	4.208460	CACGTCGATATTTTCACCGCTATT	59.792	41.667	0.00	0.00	0.00	1.73
583	639	4.807304	ACGTCGATATTTTCACCGCTATTT	59.193	37.500	0.00	0.00	0.00	1.40
586	642	5.174398	GTCGATATTTTCACCGCTATTTCGA	59.826	40.000	0.00	0.00	31.39	3.71
588	644	3.675467	ATTTTCACCGCTATTTCGAGC	57.325	42.857	0.00	0.00	39.20	5.03
589	645	1.365699	TTTCACCGCTATTTCGAGCC	58.634	50.000	0.00	0.00	39.43	4.70
591	647	1.887707	CACCGCTATTTCGAGCCCC	60.888	63.158	0.00	0.00	39.43	5.80
592	648	2.280865	CCGCTATTTCGAGCCCCC	60.281	66.667	0.00	0.00	39.43	5.40
593	649	2.661866	CGCTATTTCGAGCCCCCG	60.662	66.667	0.00	0.00	39.43	5.73
594	650	2.280865	GCTATTTCGAGCCCCCGG	60.281	66.667	0.00	0.00	36.38	5.73
595	651	2.426023	CTATTTCGAGCCCCCGGG	59.574	66.667	15.80	15.80	38.57	5.73
618	674	1.065701	GAACGGCTCGAGATGCTCTTA	59.934	52.381	18.75	0.00	0.00	2.10
624	680	2.230025	GCTCGAGATGCTCTTATGCCTA	59.770	50.000	18.75	0.00	0.00	3.93
640	4699	1.043116	CCTATCCCGTGCTGGAGTGA	61.043	60.000	0.00	0.00	42.00	3.41
645	4704	2.125952	CGTGCTGGAGTGATGCGA	60.126	61.111	0.00	0.00	0.00	5.10
665	4724	3.733337	GATCGCACTTGATTACCTCCAT	58.267	45.455	0.00	0.00	0.00	3.41
698	4765	2.364324	GCATGTGCATTGATTCCCTCAT	59.636	45.455	0.00	0.00	41.59	2.90
703	4770	3.316308	GTGCATTGATTCCCTCATGTACC	59.684	47.826	0.00	0.00	32.72	3.34
712	4779	5.808366	TTCCCTCATGTACCTGTGATATC	57.192	43.478	0.00	0.00	0.00	1.63
715	4782	3.261897	CCTCATGTACCTGTGATATCCCC	59.738	52.174	0.00	0.00	0.00	4.81
719	4786	1.893801	GTACCTGTGATATCCCCTCGG	59.106	57.143	0.00	0.00	0.00	4.63
727	4794	2.378886	TGATATCCCCTCGGCTAGAAGA	59.621	50.000	0.00	0.00	0.00	2.87
728	4795	2.289592	TATCCCCTCGGCTAGAAGAC	57.710	55.000	0.00	0.00	0.00	3.01
729	4796	0.470268	ATCCCCTCGGCTAGAAGACC	60.470	60.000	0.00	0.00	0.00	3.85
730	4797	1.075896	CCCCTCGGCTAGAAGACCT	60.076	63.158	0.00	0.00	0.00	3.85
731	4798	1.110518	CCCCTCGGCTAGAAGACCTC	61.111	65.000	0.00	0.00	0.00	3.85
733	4800	1.110518	CCTCGGCTAGAAGACCTCCC	61.111	65.000	0.00	0.00	0.00	4.30
734	4801	1.076192	TCGGCTAGAAGACCTCCCC	60.076	63.158	0.00	0.00	0.00	4.81
735	4802	1.075896	CGGCTAGAAGACCTCCCCT	60.076	63.158	0.00	0.00	0.00	4.79
737	4804	0.263468	GGCTAGAAGACCTCCCCTCT	59.737	60.000	0.00	0.00	0.00	3.69
738	4805	1.499870	GGCTAGAAGACCTCCCCTCTA	59.500	57.143	0.00	0.00	0.00	2.43
739	4806	2.111077	GGCTAGAAGACCTCCCCTCTAT	59.889	54.545	0.00	0.00	0.00	1.98
746	4831	0.470268	ACCTCCCCTCTATCGAAGCC	60.470	60.000	0.00	0.00	0.00	4.35
747	4832	1.528292	CCTCCCCTCTATCGAAGCCG	61.528	65.000	0.00	0.00	37.07	5.52
844	4932	2.514013	CGTTCGTCCACGCATAGCC	61.514	63.158	0.00	0.00	39.60	3.93
875	4963	4.398319	CCCCTATATAAAACACAGGCCAG	58.602	47.826	5.01	0.00	0.00	4.85
893	4983	1.532868	CAGAGGCAGTACACTTGCAAC	59.467	52.381	7.75	1.76	0.00	4.17
898	4988	1.532868	GCAGTACACTTGCAACTCCAG	59.467	52.381	0.00	0.00	0.00	3.86
900	4990	3.802329	GCAGTACACTTGCAACTCCAGTA	60.802	47.826	0.00	0.00	0.00	2.74
906	4996	3.876914	CACTTGCAACTCCAGTAACAAGA	59.123	43.478	20.47	0.00	40.56	3.02
925	5015	4.311816	AGATCCAAACAAACACAGCAAG	57.688	40.909	0.00	0.00	0.00	4.01
928	5018	0.922717	CAAACAAACACAGCAAGCCG	59.077	50.000	0.00	0.00	0.00	5.52
929	5019	0.814457	AAACAAACACAGCAAGCCGA	59.186	45.000	0.00	0.00	0.00	5.54
930	5020	0.814457	AACAAACACAGCAAGCCGAA	59.186	45.000	0.00	0.00	0.00	4.30
931	5021	0.381801	ACAAACACAGCAAGCCGAAG	59.618	50.000	0.00	0.00	0.00	3.79
936	5026	1.159285	CACAGCAAGCCGAAGAATCA	58.841	50.000	0.00	0.00	0.00	2.57
941	5031	1.399791	GCAAGCCGAAGAATCAAGAGG	59.600	52.381	0.00	0.00	0.00	3.69
942	5032	1.399791	CAAGCCGAAGAATCAAGAGGC	59.600	52.381	0.00	0.00	44.45	4.70
943	5033	2.009888	GCCGAAGAATCAAGAGGCG	58.990	57.895	0.00	0.00	34.94	5.52
950	5040	0.811616	GAATCAAGAGGCGCATCGGT	60.812	55.000	17.28	5.90	0.00	4.69
951	5041	0.811616	AATCAAGAGGCGCATCGGTC	60.812	55.000	17.28	0.51	0.00	4.79
970	5060	1.140452	TCATCAATCAGCAGGAGGAGC	59.860	52.381	0.00	0.00	0.00	4.70
973	5063	1.093159	CAATCAGCAGGAGGAGCAAC	58.907	55.000	0.00	0.00	0.00	4.17
1009	5113	0.376502	GAAGAAGAAGATGCAGGCGC	59.623	55.000	0.00	0.00	39.24	6.53
1011	5115	2.439156	AAGAAGATGCAGGCGCCC	60.439	61.111	26.15	9.73	37.32	6.13
1056	5160	2.032681	GCGGTGAAGGCCAAGACT	59.967	61.111	5.01	0.00	0.00	3.24
1626	5764	1.879380	TCCTGCCGTTTGATTCTTGTG	59.121	47.619	0.00	0.00	0.00	3.33
1659	5798	3.674997	TCGGAGCTGCTAAAAATCAGTT	58.325	40.909	0.15	0.00	33.09	3.16
1677	5816	4.112634	CAGTTGACTGAGACTTCACGAAA	58.887	43.478	5.19	0.00	46.59	3.46
1685	5824	4.550422	TGAGACTTCACGAAATCTCAGTG	58.450	43.478	15.00	0.00	41.99	3.66
1707	5846	1.369091	CGCCTCAACCTTTGGATCGG	61.369	60.000	0.00	0.00	0.00	4.18
1709	5848	1.886655	GCCTCAACCTTTGGATCGGTT	60.887	52.381	0.00	0.00	43.99	4.44
1730	5869	3.641437	TTGCTTTAAGATTTGCGCAGT	57.359	38.095	11.31	3.07	0.00	4.40
1731	5870	4.757799	TTGCTTTAAGATTTGCGCAGTA	57.242	36.364	11.31	2.97	0.00	2.74
1739	5878	1.128692	GATTTGCGCAGTACAGTGTCC	59.871	52.381	11.31	0.00	0.00	4.02
1743	5882	0.319555	GCGCAGTACAGTGTCCTTGA	60.320	55.000	0.30	0.00	0.00	3.02
1782	5922	0.868406	CGTGAGTCTGGCCTGTTTTC	59.132	55.000	3.32	4.21	0.00	2.29
1787	5929	1.215423	AGTCTGGCCTGTTTTCCTGTT	59.785	47.619	3.32	0.00	0.00	3.16
1806	5949	3.181518	TGTTCGTTTCGTTGTTTGGTCTC	60.182	43.478	0.00	0.00	0.00	3.36
1821	5964	1.669211	GGTCTCGACTCCTTTCGTTGG	60.669	57.143	0.00	0.00	40.07	3.77
1822	5965	0.038526	TCTCGACTCCTTTCGTTGGC	60.039	55.000	0.00	0.00	40.07	4.52
1823	5966	1.005394	TCGACTCCTTTCGTTGGCC	60.005	57.895	0.00	0.00	40.07	5.36
1826	5969	1.134788	CGACTCCTTTCGTTGGCCTAT	60.135	52.381	3.32	0.00	34.16	2.57
1828	5971	3.429822	CGACTCCTTTCGTTGGCCTATTA	60.430	47.826	3.32	0.00	34.16	0.98
1829	5972	4.510571	GACTCCTTTCGTTGGCCTATTAA	58.489	43.478	3.32	0.00	0.00	1.40
1830	5973	4.913784	ACTCCTTTCGTTGGCCTATTAAA	58.086	39.130	3.32	0.48	0.00	1.52
1831	5974	4.941873	ACTCCTTTCGTTGGCCTATTAAAG	59.058	41.667	3.32	10.35	0.00	1.85
1837	5997	1.099689	TTGGCCTATTAAAGCGTGGC	58.900	50.000	3.32	0.00	42.56	5.01
1838	5998	0.034960	TGGCCTATTAAAGCGTGGCA	60.035	50.000	3.32	0.00	44.85	4.92
1839	5999	0.663153	GGCCTATTAAAGCGTGGCAG	59.337	55.000	0.00	0.00	44.85	4.85
1861	6021	1.082104	CTGGTGTTCGGCGCTTTTC	60.082	57.895	7.64	0.00	0.00	2.29
1880	6048	7.057402	GCTTTTCTCGTTGTTTGCTTTTTATC	58.943	34.615	0.00	0.00	0.00	1.75
1990	6162	2.093973	GGTCCTGTCACATACACTCCTG	60.094	54.545	0.00	0.00	33.45	3.86
1994	6166	3.259374	CCTGTCACATACACTCCTGTCTT	59.741	47.826	0.00	0.00	33.45	3.01
1996	6168	3.895041	TGTCACATACACTCCTGTCTTCA	59.105	43.478	0.00	0.00	31.43	3.02
2002	6174	5.361285	ACATACACTCCTGTCTTCATACTCC	59.639	44.000	0.00	0.00	0.00	3.85
2051	6224	2.298729	GTGCAAGTGGCCATCCTTTTTA	59.701	45.455	9.72	0.00	43.89	1.52
2184	6370	9.086336	CAATTGCTTCTTTAGTCTTGTTTTTGA	57.914	29.630	0.00	0.00	0.00	2.69
2321	6525	6.879188	TTTTTAATATTTTAGCGCACCAGC	57.121	33.333	11.47	0.00	37.42	4.85

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
38	39	1.002576	TGTCGTCGTGCTCGTTCTAAA	60.003	47.619	8.17	0.00	38.33	1.85
40	41	0.800631	ATGTCGTCGTGCTCGTTCTA	59.199	50.000	8.17	0.00	38.33	2.10
115	117	1.001641	GGCACTGGCACTCCATCTT	60.002	57.895	0.00	0.00	42.51	2.40
195	197	1.838568	CGTCGTCGTCACTGTCCTCA	61.839	60.000	0.00	0.00	0.00	3.86
235	237	2.125512	ATCGCCTTGTCGGACAGC	60.126	61.111	11.14	11.18	33.16	4.40
243	245	1.221840	CTACCCTGCATCGCCTTGT	59.778	57.895	0.00	0.00	0.00	3.16
259	261	0.974010	CCGTCCTTACTGCACCCCTA	60.974	60.000	0.00	0.00	0.00	3.53
279	281	1.545841	TCTCCTTCTTCACGCTGCTA	58.454	50.000	0.00	0.00	0.00	3.49
280	282	0.681733	TTCTCCTTCTTCACGCTGCT	59.318	50.000	0.00	0.00	0.00	4.24
439	472	8.507249	AGACTAGGCGATTTTATTGATATTTGC	58.493	33.333	0.00	0.00	0.00	3.68
451	485	4.737855	TTCAGCTAGACTAGGCGATTTT	57.262	40.909	11.48	0.00	0.00	1.82
466	501	3.009723	CAAACACGACCCATATTCAGCT	58.990	45.455	0.00	0.00	0.00	4.24
513	569	2.036862	GACTCAAACCTAACCCAGACGT	59.963	50.000	0.00	0.00	0.00	4.34
524	580	0.037605	CTAACCGCCGACTCAAACCT	60.038	55.000	0.00	0.00	0.00	3.50
542	598	4.003648	GACGTGAGGATGATTGGTTTTCT	58.996	43.478	0.00	0.00	0.00	2.52
550	606	6.201044	GTGAAAATATCGACGTGAGGATGATT	59.799	38.462	0.00	0.00	0.00	2.57
552	608	5.041287	GTGAAAATATCGACGTGAGGATGA	58.959	41.667	0.00	0.00	0.00	2.92
555	611	3.732774	CGGTGAAAATATCGACGTGAGGA	60.733	47.826	0.00	0.00	0.00	3.71
558	614	1.921887	GCGGTGAAAATATCGACGTGA	59.078	47.619	0.00	0.00	33.79	4.35
574	630	2.504519	GGGGCTCGAAATAGCGGT	59.495	61.111	0.00	0.00	43.74	5.68
578	634	2.426023	CCCGGGGGCTCGAAATAG	59.574	66.667	14.71	0.00	0.00	1.73
598	654	4.005032	GAGCATCTCGAGCCGTTC	57.995	61.111	7.81	4.81	0.00	3.95
610	666	2.027745	CACGGGATAGGCATAAGAGCAT	60.028	50.000	0.00	0.00	35.83	3.79
612	668	1.941668	GCACGGGATAGGCATAAGAGC	60.942	57.143	0.00	0.00	0.00	4.09
613	669	1.620819	AGCACGGGATAGGCATAAGAG	59.379	52.381	0.00	0.00	0.00	2.85
614	670	1.344438	CAGCACGGGATAGGCATAAGA	59.656	52.381	0.00	0.00	0.00	2.10
618	674	1.762522	CTCCAGCACGGGATAGGCAT	61.763	60.000	0.00	0.00	36.09	4.40
624	680	1.524002	CATCACTCCAGCACGGGAT	59.476	57.895	0.00	0.00	36.09	3.85
645	4704	3.470709	CATGGAGGTAATCAAGTGCGAT	58.529	45.455	0.00	0.00	0.00	4.58
651	4710	3.003394	TGGTGCATGGAGGTAATCAAG	57.997	47.619	0.00	0.00	0.00	3.02
694	4761	4.163427	AGGGGATATCACAGGTACATGAG	58.837	47.826	15.54	6.57	0.00	2.90
698	4765	2.594131	CGAGGGGATATCACAGGTACA	58.406	52.381	7.40	0.00	0.00	2.90
703	4770	1.821753	CTAGCCGAGGGGATATCACAG	59.178	57.143	7.40	0.00	32.80	3.66
712	4779	1.075896	AGGTCTTCTAGCCGAGGGG	60.076	63.158	0.00	0.00	0.00	4.79
715	4782	1.110518	GGGGAGGTCTTCTAGCCGAG	61.111	65.000	0.00	0.00	0.00	4.63
719	4786	3.427573	GATAGAGGGGAGGTCTTCTAGC	58.572	54.545	0.00	0.00	0.00	3.42
737	4804	1.536072	GCATGACTCACGGCTTCGATA	60.536	52.381	0.00	0.00	37.63	2.92
738	4805	0.807667	GCATGACTCACGGCTTCGAT	60.808	55.000	0.00	0.00	37.63	3.59
739	4806	1.446099	GCATGACTCACGGCTTCGA	60.446	57.895	0.00	0.00	37.63	3.71
746	4831	1.062047	GCTGCATGCATGACTCACG	59.938	57.895	30.64	7.95	42.31	4.35
747	4832	1.310216	TGGCTGCATGCATGACTCAC	61.310	55.000	30.64	15.02	45.15	3.51
795	4883	4.874977	TTGGCGACGACGTGTGCA	62.875	61.111	19.70	6.89	41.98	4.57
823	4911	3.993376	TATGCGTGGACGAACGGGC	62.993	63.158	2.73	0.00	43.75	6.13
827	4915	2.514013	CGGCTATGCGTGGACGAAC	61.514	63.158	12.94	0.00	40.18	3.95
855	4943	5.308825	CCTCTGGCCTGTGTTTTATATAGG	58.691	45.833	3.32	0.00	0.00	2.57
856	4944	4.757149	GCCTCTGGCCTGTGTTTTATATAG	59.243	45.833	3.32	0.00	44.06	1.31
875	4963	1.801178	GAGTTGCAAGTGTACTGCCTC	59.199	52.381	12.53	1.69	0.00	4.70
883	4973	3.275617	TGTTACTGGAGTTGCAAGTGT	57.724	42.857	12.53	6.24	0.00	3.55
887	4977	4.072131	GGATCTTGTTACTGGAGTTGCAA	58.928	43.478	0.00	0.00	0.00	4.08
889	4979	3.674997	TGGATCTTGTTACTGGAGTTGC	58.325	45.455	0.00	0.00	0.00	4.17
893	4983	6.039270	TGTTTGTTTGGATCTTGTTACTGGAG	59.961	38.462	0.00	0.00	0.00	3.86
898	4988	5.458779	GCTGTGTTTGTTTGGATCTTGTTAC	59.541	40.000	0.00	0.00	0.00	2.50
900	4990	4.081752	TGCTGTGTTTGTTTGGATCTTGTT	60.082	37.500	0.00	0.00	0.00	2.83
906	4996	2.483538	GGCTTGCTGTGTTTGTTTGGAT	60.484	45.455	0.00	0.00	0.00	3.41
925	5015	2.009888	CGCCTCTTGATTCTTCGGC	58.990	57.895	0.00	0.00	0.00	5.54
928	5018	1.260033	CGATGCGCCTCTTGATTCTTC	59.740	52.381	4.18	0.00	0.00	2.87
929	5019	1.293924	CGATGCGCCTCTTGATTCTT	58.706	50.000	4.18	0.00	0.00	2.52
930	5020	0.531532	CCGATGCGCCTCTTGATTCT	60.532	55.000	4.18	0.00	0.00	2.40
931	5021	0.811616	ACCGATGCGCCTCTTGATTC	60.812	55.000	4.18	0.00	0.00	2.52
936	5026	1.227380	GATGACCGATGCGCCTCTT	60.227	57.895	4.18	0.00	0.00	2.85
941	5031	0.234106	CTGATTGATGACCGATGCGC	59.766	55.000	0.00	0.00	0.00	6.09
942	5032	0.234106	GCTGATTGATGACCGATGCG	59.766	55.000	0.00	0.00	0.00	4.73
943	5033	1.263484	CTGCTGATTGATGACCGATGC	59.737	52.381	0.00	0.00	0.00	3.91
950	5040	1.140452	GCTCCTCCTGCTGATTGATGA	59.860	52.381	0.00	0.00	0.00	2.92
951	5041	1.134189	TGCTCCTCCTGCTGATTGATG	60.134	52.381	0.00	0.00	0.00	3.07
970	5060	2.169789	CCGATCGAGCAGCTGGTTG	61.170	63.158	24.53	24.53	0.00	3.77
973	5063	4.598894	CCCCGATCGAGCAGCTGG	62.599	72.222	18.66	7.03	0.00	4.85
1009	5113	1.003696	GTCCTTCACCTTCTCCTTGGG	59.996	57.143	0.00	0.00	0.00	4.12
1011	5115	1.338200	CCGTCCTTCACCTTCTCCTTG	60.338	57.143	0.00	0.00	0.00	3.61
1056	5160	0.107703	CCTTGGCCTGCGTGATCTTA	60.108	55.000	3.32	0.00	0.00	2.10
1252	5356	2.978010	CCCGTGCTTGTGGTGGTC	60.978	66.667	0.00	0.00	0.00	4.02
1626	5764	2.541762	GCAGCTCCGATCATGTAACTTC	59.458	50.000	0.00	0.00	0.00	3.01
1659	5798	4.799678	GAGATTTCGTGAAGTCTCAGTCA	58.200	43.478	22.66	0.00	46.80	3.41
1677	5816	0.247736	GTTGAGGCGTCCACTGAGAT	59.752	55.000	3.56	0.00	0.00	2.75
1685	5824	0.322546	ATCCAAAGGTTGAGGCGTCC	60.323	55.000	3.56	0.00	0.00	4.79
1707	5846	4.209080	ACTGCGCAAATCTTAAAGCAAAAC	59.791	37.500	13.05	0.00	34.04	2.43
1709	5848	3.976169	ACTGCGCAAATCTTAAAGCAAA	58.024	36.364	13.05	0.00	34.04	3.68
1730	5869	4.641396	CCAATTGAGTCAAGGACACTGTA	58.359	43.478	11.91	0.00	34.60	2.74
1731	5870	3.480470	CCAATTGAGTCAAGGACACTGT	58.520	45.455	11.91	0.00	34.60	3.55
1739	5878	6.268566	GCTTTAATAGGCCAATTGAGTCAAG	58.731	40.000	11.91	0.00	0.00	3.02
1743	5882	4.096382	CACGCTTTAATAGGCCAATTGAGT	59.904	41.667	5.01	0.00	0.00	3.41
1782	5922	2.159490	ACCAAACAACGAAACGAACAGG	60.159	45.455	0.00	0.00	0.00	4.00
1787	5929	1.589320	CGAGACCAAACAACGAAACGA	59.411	47.619	0.00	0.00	0.00	3.85
1806	5949	0.245539	TAGGCCAACGAAAGGAGTCG	59.754	55.000	5.01	0.00	46.54	4.18
1821	5964	0.663153	CCTGCCACGCTTTAATAGGC	59.337	55.000	0.00	0.00	45.41	3.93
1822	5965	1.308998	CCCTGCCACGCTTTAATAGG	58.691	55.000	0.00	0.00	0.00	2.57
1823	5966	1.308998	CCCCTGCCACGCTTTAATAG	58.691	55.000	0.00	0.00	0.00	1.73
1826	5969	2.675075	GCCCCTGCCACGCTTTAA	60.675	61.111	0.00	0.00	0.00	1.52
1852	6012	1.120437	CAAACAACGAGAAAAGCGCC	58.880	50.000	2.29	0.00	0.00	6.53
1855	6015	4.840401	AAAAGCAAACAACGAGAAAAGC	57.160	36.364	0.00	0.00	0.00	3.51
1857	6017	7.262048	AGGATAAAAAGCAAACAACGAGAAAA	58.738	30.769	0.00	0.00	0.00	2.29
1861	6021	7.463469	AAAAGGATAAAAAGCAAACAACGAG	57.537	32.000	0.00	0.00	0.00	4.18
1996	6168	5.286221	ACACCCATACTACAAAGGGAGTAT	58.714	41.667	2.90	0.00	42.23	2.12
2002	6174	5.773176	AGGAAAAACACCCATACTACAAAGG	59.227	40.000	0.00	0.00	0.00	3.11
2156	6340	9.435688	AAAAACAAGACTAAAGAAGCAATTGTT	57.564	25.926	7.40	0.00	38.79	2.83
2220	6420	3.988379	ACTCACGTTGCACATTGAAAT	57.012	38.095	0.00	0.00	0.00	2.17
2315	6519	2.161012	CACTAGAAATGTGCAGCTGGTG	59.839	50.000	17.12	6.93	34.39	4.17
2321	6525	3.317150	TCGTGTCACTAGAAATGTGCAG	58.683	45.455	0.00	0.00	35.58	4.41

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.