AutoCloner

Multiple sequence alignment - TraesCS5D01G248300

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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	TraesCS5D01G248300	chr5D	100.000	7381	0	0	1	7381	355198854	355206234	0.000000e+00	13631.0
1	TraesCS5D01G248300	chr5D	96.864	287	7	2	3456	3742	355201618	355201902	5.180000e-131	479.0
2	TraesCS5D01G248300	chr5D	96.864	287	7	2	2765	3049	355202309	355202595	5.180000e-131	479.0
3	TraesCS5D01G248300	chr5D	88.158	76	9	0	2650	2725	6435879	6435804	2.840000e-14	91.6
4	TraesCS5D01G248300	chr5A	97.801	2956	64	1	4400	7355	457435436	457438390	0.000000e+00	5097.0
5	TraesCS5D01G248300	chr5A	97.903	2003	38	3	623	2624	457431849	457433848	0.000000e+00	3463.0
6	TraesCS5D01G248300	chr5A	95.431	985	25	12	3161	4129	457434459	457435439	0.000000e+00	1552.0
7	TraesCS5D01G248300	chr5A	81.338	1854	318	24	4728	6563	705844083	705842240	0.000000e+00	1482.0
8	TraesCS5D01G248300	chr5A	96.880	641	16	4	1	639	457431042	457431680	0.000000e+00	1070.0
9	TraesCS5D01G248300	chr5A	96.907	582	13	4	2588	3164	457433843	457434424	0.000000e+00	970.0
10	TraesCS5D01G248300	chr5A	96.864	287	8	1	3456	3742	457434024	457434309	5.180000e-131	479.0
11	TraesCS5D01G248300	chr5A	96.167	287	9	2	2765	3049	457434754	457435040	1.120000e-127	468.0
12	TraesCS5D01G248300	chr5A	97.143	35	1	0	2731	2765	457434331	457434365	8.000000e-05	60.2
13	TraesCS5D01G248300	chr5B	96.825	2929	70	7	4453	7381	419998121	420001026	0.000000e+00	4872.0
14	TraesCS5D01G248300	chr5B	95.247	1620	34	16	1121	2725	419996009	419997600	0.000000e+00	2525.0
15	TraesCS5D01G248300	chr5B	95.367	626	23	4	370	992	419995387	419996009	0.000000e+00	990.0
16	TraesCS5D01G248300	chr5B	93.238	281	15	2	49	326	419995111	419995390	1.920000e-110	411.0
17	TraesCS5D01G248300	chr6A	84.041	1742	257	16	4654	6385	572136839	572138569	0.000000e+00	1657.0
18	TraesCS5D01G248300	chr6A	78.037	1202	181	52	891	2049	572134706	572135867	0.000000e+00	680.0
19	TraesCS5D01G248300	chr6A	79.264	299	48	10	1102	1389	158907243	158907538	5.840000e-46	196.0
20	TraesCS5D01G248300	chr6D	83.649	1743	259	19	4654	6385	427483487	427485214	0.000000e+00	1616.0
21	TraesCS5D01G248300	chr6D	76.798	1474	236	61	628	2049	427481030	427482449	0.000000e+00	730.0
22	TraesCS5D01G248300	chr6B	84.785	1584	226	14	4794	6370	643264124	643265699	0.000000e+00	1576.0
23	TraesCS5D01G248300	chr6B	76.087	1518	245	75	593	2049	643261900	643263360	0.000000e+00	684.0
24	TraesCS5D01G248300	chr6B	75.420	476	85	24	2144	2596	88219790	88219324	1.260000e-47	202.0
25	TraesCS5D01G248300	chr6B	77.211	294	49	14	1109	1389	212629282	212628994	9.920000e-34	156.0
26	TraesCS5D01G248300	chr4B	81.907	1846	314	15	4729	6563	625975191	625977027	0.000000e+00	1541.0
27	TraesCS5D01G248300	chr4B	81.230	1854	320	24	4728	6563	665877098	665875255	0.000000e+00	1471.0
28	TraesCS5D01G248300	chr4B	76.286	350	57	20	2218	2553	665557791	665558128	5.930000e-36	163.0
29	TraesCS5D01G248300	chr4B	82.456	114	16	3	2442	2551	625974582	625974695	6.100000e-16	97.1
30	TraesCS5D01G248300	chrUn	81.056	1932	330	31	4654	6563	108321644	108323561	0.000000e+00	1507.0
31	TraesCS5D01G248300	chr7A	78.232	611	94	17	3162	3756	663948971	663949558	9.110000e-94	355.0
32	TraesCS5D01G248300	chr1B	84.426	366	52	5	3257	3619	264350415	264350052	9.110000e-94	355.0
33	TraesCS5D01G248300	chr1B	90.278	72	7	0	3525	3596	264350042	264349971	2.190000e-15	95.3
34	TraesCS5D01G248300	chr1B	90.141	71	7	0	2655	2725	509018121	509018191	7.890000e-15	93.5
35	TraesCS5D01G248300	chr7B	78.654	520	71	17	3255	3759	633677329	633676835	7.190000e-80	309.0
36	TraesCS5D01G248300	chr1D	84.058	276	42	2	3161	3435	423601429	423601703	1.580000e-66	265.0
37	TraesCS5D01G248300	chr1A	83.883	273	40	4	3161	3431	519624289	519624559	2.640000e-64	257.0
38	TraesCS5D01G248300	chr3A	77.992	259	43	13	593	843	697370668	697370920	4.610000e-32	150.0
39	TraesCS5D01G248300	chr3D	93.939	66	4	0	2660	2725	416223590	416223525	4.710000e-17	100.0
40	TraesCS5D01G248300	chr3D	91.176	68	6	0	2658	2725	423852766	423852699	7.890000e-15	93.5
41	TraesCS5D01G248300	chr4A	90.541	74	6	1	2650	2723	575420302	575420230	6.100000e-16	97.1
42	TraesCS5D01G248300	chr2D	92.424	66	5	0	2659	2724	516912964	516913029	2.190000e-15	95.3
43	TraesCS5D01G248300	chr2A	89.041	73	8	0	2653	2725	80458343	80458271	2.840000e-14	91.6

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	TraesCS5D01G248300	chr5D	355198854	355206234	7380	False	13631.00	13631	100.00000	1	7381	1	chr5D.!!$F1	7380
1	TraesCS5D01G248300	chr5D	355201618	355202595	977	False	479.00	479	96.86400	2765	3742	2	chr5D.!!$F2	977
2	TraesCS5D01G248300	chr5A	457431042	457438390	7348	False	1644.90	5097	96.88700	1	7355	8	chr5A.!!$F1	7354
3	TraesCS5D01G248300	chr5A	705842240	705844083	1843	True	1482.00	1482	81.33800	4728	6563	1	chr5A.!!$R1	1835
4	TraesCS5D01G248300	chr5B	419995111	420001026	5915	False	2199.50	4872	95.16925	49	7381	4	chr5B.!!$F1	7332
5	TraesCS5D01G248300	chr6A	572134706	572138569	3863	False	1168.50	1657	81.03900	891	6385	2	chr6A.!!$F2	5494
6	TraesCS5D01G248300	chr6D	427481030	427485214	4184	False	1173.00	1616	80.22350	628	6385	2	chr6D.!!$F1	5757
7	TraesCS5D01G248300	chr6B	643261900	643265699	3799	False	1130.00	1576	80.43600	593	6370	2	chr6B.!!$F1	5777
8	TraesCS5D01G248300	chr4B	665875255	665877098	1843	True	1471.00	1471	81.23000	4728	6563	1	chr4B.!!$R1	1835
9	TraesCS5D01G248300	chr4B	625974582	625977027	2445	False	819.05	1541	82.18150	2442	6563	2	chr4B.!!$F2	4121
10	TraesCS5D01G248300	chrUn	108321644	108323561	1917	False	1507.00	1507	81.05600	4654	6563	1	chrUn.!!$F1	1909
11	TraesCS5D01G248300	chr7A	663948971	663949558	587	False	355.00	355	78.23200	3162	3756	1	chr7A.!!$F1	594

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
81	82	1.694696	GACCCTAGAATTGGATCGGCT	59.305	52.381	0.00	0.00	0.00	5.52	F
1020	1232	1.116308	TGTCTTGTTGTGACCGGAGA	58.884	50.000	9.46	0.00	33.83	3.71	F
1190	1409	4.406456	TGTGGCACAGTAAAATTCCTCAT	58.594	39.130	17.96	0.00	41.80	2.90	F
3783	4383	0.471780	TTCTGGAGCTCCACACTGGA	60.472	55.000	32.00	22.97	45.98	3.86	F
3857	4480	0.038744	CCCAGCAATTCCCAGTCAGT	59.961	55.000	0.00	0.00	0.00	3.41	F
4139	4762	0.971386	CCACCTGCTCAGCCAAAAAT	59.029	50.000	0.00	0.00	0.00	1.82	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1725	1968	7.230108	AGCAGAATCATATGGACAAATACCTTG	59.770	37.037	2.13	0.00	41.19	3.61	R
2761	3127	4.072131	GGTCACTCTTGTTTAGGCATTCA	58.928	43.478	0.00	0.00	0.00	2.57	R
3788	4388	0.120377	TATGGGACCTTGTGGGACCT	59.880	55.000	3.57	0.00	46.67	3.85	R
4716	5390	3.569701	AGGGAAATACAAGTGCACAACAG	59.430	43.478	21.04	7.93	0.00	3.16	R
6083	6765	4.461431	TCGCCTATCTCAACAGAAACTACA	59.539	41.667	0.00	0.00	30.24	2.74	R
6457	7147	5.850557	AACAAACATCCTTCACATCAACA	57.149	34.783	0.00	0.00	0.00	3.33	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
40	41	4.058817	GTTCCTCAGTTGTCACACCTAAG	58.941	47.826	0.00	0.00	0.00	2.18
81	82	1.694696	GACCCTAGAATTGGATCGGCT	59.305	52.381	0.00	0.00	0.00	5.52
202	203	2.886523	CTGGTCCTTGTCTGCATTTTCA	59.113	45.455	0.00	0.00	0.00	2.69
204	205	2.350772	GGTCCTTGTCTGCATTTTCACG	60.351	50.000	0.00	0.00	0.00	4.35
248	249	3.629398	GCCAAATACTCTGCTGCAATACT	59.371	43.478	3.02	0.00	0.00	2.12
257	259	5.112220	TCTGCTGCAATACTTTGTCAAAG	57.888	39.130	21.34	21.34	44.10	2.77
542	548	6.457257	CGTGCATGATCTTGTTTCATATGTCA	60.457	38.462	0.00	0.00	32.63	3.58
698	889	4.484236	TGCATTTGAGCAGTTAATTTCGG	58.516	39.130	0.00	0.00	40.11	4.30
873	1074	5.635120	GTCCCATAAATGCCCTCTTATTCT	58.365	41.667	0.00	0.00	0.00	2.40
991	1203	4.576216	ACTGATGTATACTCTTCTGGCG	57.424	45.455	4.17	0.00	0.00	5.69
1008	1220	2.076863	GGCGTTAGCTTGATGTCTTGT	58.923	47.619	0.00	0.00	44.37	3.16
1020	1232	1.116308	TGTCTTGTTGTGACCGGAGA	58.884	50.000	9.46	0.00	33.83	3.71
1190	1409	4.406456	TGTGGCACAGTAAAATTCCTCAT	58.594	39.130	17.96	0.00	41.80	2.90
1192	1411	5.048083	TGTGGCACAGTAAAATTCCTCATTC	60.048	40.000	17.96	0.00	41.80	2.67
1193	1412	5.048083	GTGGCACAGTAAAATTCCTCATTCA	60.048	40.000	13.86	0.00	41.80	2.57
1725	1968	5.073311	TGCTGGAACTACTTCTCACATAC	57.927	43.478	0.00	0.00	0.00	2.39
2148	2472	9.736414	AAGAGTTTCATATGATCATATCCAAGG	57.264	33.333	22.76	12.91	31.98	3.61
3781	4381	1.277273	TCATTCTGGAGCTCCACACTG	59.723	52.381	32.00	24.39	42.01	3.66
3783	4383	0.471780	TTCTGGAGCTCCACACTGGA	60.472	55.000	32.00	22.97	45.98	3.86
3784	4384	1.188219	TCTGGAGCTCCACACTGGAC	61.188	60.000	32.00	2.34	42.67	4.02
3785	4385	1.459348	TGGAGCTCCACACTGGACA	60.459	57.895	32.00	5.33	42.67	4.02
3786	4386	1.004440	GGAGCTCCACACTGGACAC	60.004	63.158	28.43	0.00	42.67	3.67
3787	4387	1.748403	GAGCTCCACACTGGACACA	59.252	57.895	0.87	0.00	42.67	3.72
3788	4388	0.106708	GAGCTCCACACTGGACACAA	59.893	55.000	0.87	0.00	42.67	3.33
3789	4389	0.107456	AGCTCCACACTGGACACAAG	59.893	55.000	0.00	0.00	42.67	3.16
3790	4390	0.886490	GCTCCACACTGGACACAAGG	60.886	60.000	0.00	0.00	42.67	3.61
3791	4391	0.469917	CTCCACACTGGACACAAGGT	59.530	55.000	0.00	0.00	42.67	3.50
3792	4392	0.468226	TCCACACTGGACACAAGGTC	59.532	55.000	0.00	0.00	42.67	3.85
3857	4480	0.038744	CCCAGCAATTCCCAGTCAGT	59.961	55.000	0.00	0.00	0.00	3.41
3878	4501	2.232696	TGCATCTTGAACTGTACGGCTA	59.767	45.455	0.23	0.00	0.00	3.93
3935	4558	3.623960	TGTTACGGCCATTTATGCTACAC	59.376	43.478	2.24	0.00	0.00	2.90
3972	4595	8.783833	AGTGTGTATAAATCATAGATCATGCC	57.216	34.615	0.00	0.00	34.35	4.40
3979	4602	8.701908	ATAAATCATAGATCATGCCACAAGTT	57.298	30.769	0.00	0.00	34.35	2.66
3980	4603	9.797642	ATAAATCATAGATCATGCCACAAGTTA	57.202	29.630	0.00	0.00	34.35	2.24
4063	4686	1.534729	ATGTTTTCGGAAGACCTGGC	58.465	50.000	8.71	0.00	41.84	4.85
4139	4762	0.971386	CCACCTGCTCAGCCAAAAAT	59.029	50.000	0.00	0.00	0.00	1.82
4141	4764	2.094545	CCACCTGCTCAGCCAAAAATAC	60.095	50.000	0.00	0.00	0.00	1.89
4143	4766	3.194116	CACCTGCTCAGCCAAAAATACAT	59.806	43.478	0.00	0.00	0.00	2.29
4144	4767	3.445096	ACCTGCTCAGCCAAAAATACATC	59.555	43.478	0.00	0.00	0.00	3.06
4145	4768	3.488047	CCTGCTCAGCCAAAAATACATCG	60.488	47.826	0.00	0.00	0.00	3.84
4147	4770	3.755905	TGCTCAGCCAAAAATACATCGAA	59.244	39.130	0.00	0.00	0.00	3.71
4148	4771	4.398988	TGCTCAGCCAAAAATACATCGAAT	59.601	37.500	0.00	0.00	0.00	3.34
4192	4823	4.765195	AATAGGGTGGCATGGGAATATT	57.235	40.909	0.00	0.00	0.00	1.28
4198	4829	5.025453	GGGTGGCATGGGAATATTATCATT	58.975	41.667	0.00	0.00	0.00	2.57
4199	4830	6.010828	AGGGTGGCATGGGAATATTATCATTA	60.011	38.462	0.00	0.00	0.00	1.90
4200	4831	6.667414	GGGTGGCATGGGAATATTATCATTAA	59.333	38.462	0.00	0.00	0.00	1.40
4201	4832	7.345392	GGGTGGCATGGGAATATTATCATTAAT	59.655	37.037	0.00	0.00	32.75	1.40
4202	4833	8.416329	GGTGGCATGGGAATATTATCATTAATC	58.584	37.037	0.00	0.00	30.64	1.75
4203	4834	9.193806	GTGGCATGGGAATATTATCATTAATCT	57.806	33.333	0.00	0.00	30.64	2.40
4204	4835	9.772605	TGGCATGGGAATATTATCATTAATCTT	57.227	29.630	0.00	0.00	30.64	2.40
4228	4866	2.307496	ACACCCATTTGCCTCATCAA	57.693	45.000	0.00	0.00	0.00	2.57
4243	4889	6.889177	TGCCTCATCAACCATCAGTTTTTATA	59.111	34.615	0.00	0.00	36.18	0.98
4245	4891	7.917505	GCCTCATCAACCATCAGTTTTTATAAG	59.082	37.037	0.00	0.00	36.18	1.73
4253	4899	8.189119	ACCATCAGTTTTTATAAGGAAAGCAA	57.811	30.769	0.00	0.00	0.00	3.91
4259	4905	9.643693	CAGTTTTTATAAGGAAAGCAACATGAT	57.356	29.630	0.00	0.00	0.00	2.45
4269	4915	3.708403	AGCAACATGATGAGACCAGAA	57.292	42.857	7.22	0.00	0.00	3.02
4271	4917	3.755378	AGCAACATGATGAGACCAGAAAC	59.245	43.478	7.22	0.00	0.00	2.78
4277	4923	4.687901	TGATGAGACCAGAAACTTGTGA	57.312	40.909	0.00	0.00	0.00	3.58
4281	4927	4.058124	TGAGACCAGAAACTTGTGATTCG	58.942	43.478	0.00	0.00	31.40	3.34
4282	4928	4.058817	GAGACCAGAAACTTGTGATTCGT	58.941	43.478	0.00	0.00	31.40	3.85
4290	4936	2.138320	ACTTGTGATTCGTCACTGCTG	58.862	47.619	9.64	0.00	40.97	4.41
4316	4962	5.424757	CATCCAGCACAAAATTCCATCATT	58.575	37.500	0.00	0.00	0.00	2.57
4321	4967	6.128391	CCAGCACAAAATTCCATCATTTGAAG	60.128	38.462	4.65	0.00	37.46	3.02
4323	4969	5.410439	GCACAAAATTCCATCATTTGAAGCT	59.590	36.000	4.65	0.00	37.46	3.74
4341	5005	8.574251	TTGAAGCTATAAAGTTTATTCCAGCA	57.426	30.769	22.19	11.33	0.00	4.41
4346	5010	3.942130	AAAGTTTATTCCAGCACAGCC	57.058	42.857	0.00	0.00	0.00	4.85
4347	5011	2.584835	AGTTTATTCCAGCACAGCCA	57.415	45.000	0.00	0.00	0.00	4.75
4348	5012	2.440409	AGTTTATTCCAGCACAGCCAG	58.560	47.619	0.00	0.00	0.00	4.85
4360	5026	1.467734	CACAGCCAGAAGTGCTTCATC	59.532	52.381	13.58	3.22	41.84	2.92
4366	5032	2.161808	CCAGAAGTGCTTCATCTTGCTG	59.838	50.000	13.58	2.37	41.84	4.41
4371	5037	2.038952	AGTGCTTCATCTTGCTGGTGTA	59.961	45.455	0.00	0.00	0.00	2.90
4372	5038	2.417933	GTGCTTCATCTTGCTGGTGTAG	59.582	50.000	0.00	0.00	0.00	2.74
4373	5039	2.012673	GCTTCATCTTGCTGGTGTAGG	58.987	52.381	0.00	0.00	0.00	3.18
4380	5046	2.969950	TCTTGCTGGTGTAGGTAGTTGT	59.030	45.455	0.00	0.00	0.00	3.32
4381	5047	3.389983	TCTTGCTGGTGTAGGTAGTTGTT	59.610	43.478	0.00	0.00	0.00	2.83
4392	5058	7.042254	GGTGTAGGTAGTTGTTTCAAGTGTAAG	60.042	40.741	0.78	0.00	0.00	2.34
4510	5182	6.891624	TCTCATTGATTCTTGTTCAGTTTCG	58.108	36.000	0.00	0.00	0.00	3.46
4716	5390	2.113860	TTCTGTGCCCTTGTAGATGC	57.886	50.000	0.00	0.00	0.00	3.91
5042	5724	1.202417	TGCCGCTCTCACTGTATTAGC	60.202	52.381	0.00	0.00	0.00	3.09
5132	5814	7.065443	GGTACCTTGTGGTTTGACTGTATATTC	59.935	40.741	4.06	0.00	46.05	1.75
6083	6765	1.842562	CTTGGGATCCACATGAGGACT	59.157	52.381	14.58	4.09	41.30	3.85
6457	7147	9.897744	CACAACTTCATCTATGTTAAACATTGT	57.102	29.630	0.00	0.00	39.88	2.71
6477	7169	5.185668	TGTGTTGATGTGAAGGATGTTTG	57.814	39.130	0.00	0.00	0.00	2.93
6499	7191	8.482429	GTTTGTTTCTGAGAAACATTGCATTAG	58.518	33.333	33.43	0.00	40.29	1.73
6700	7392	4.585879	TGGAAGCTATTGTTGAACCTACC	58.414	43.478	0.00	0.00	0.00	3.18
6760	7452	4.900652	AGTAGACATGATGCTCTGGAATCT	59.099	41.667	0.00	0.00	0.00	2.40
6892	7584	0.620556	GAAGCAAGTCCTGGGGATCA	59.379	55.000	0.00	0.00	32.73	2.92
6907	7599	1.202580	GGATCATCGAAGGGAGTGTGG	60.203	57.143	0.00	0.00	0.00	4.17
6962	7654	5.356882	TTGTTCTGCTTGCTGTGTATAAC	57.643	39.130	0.00	0.00	0.00	1.89
7127	7819	6.694411	GTGTTTATGATCCAAATGAGATGCAC	59.306	38.462	0.00	0.00	0.00	4.57
7161	7853	6.673154	TGCAGTATCTCTGACAATGATTTG	57.327	37.500	0.00	0.00	46.27	2.32
7373	8065	1.462283	CAGCGTGTTTCAGGATGTCTG	59.538	52.381	0.59	0.00	44.68	3.51

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
25	26	1.978580	CCCCTCTTAGGTGTGACAACT	59.021	52.381	8.72	8.72	34.83	3.16
40	41	0.253327	GGGACACACTGAATCCCCTC	59.747	60.000	9.95	0.00	45.70	4.30
81	82	0.250684	TGAAATCAGCACAGGCCGAA	60.251	50.000	0.00	0.00	42.56	4.30
202	203	3.777106	ATCCATTCATGACCTATGCGT	57.223	42.857	0.00	0.00	36.70	5.24
204	205	4.142816	GCGTAATCCATTCATGACCTATGC	60.143	45.833	0.00	0.00	36.70	3.14
257	259	9.764363	TGTGAATTCACCTATACAGATCAATAC	57.236	33.333	30.66	4.84	45.88	1.89
366	372	0.040157	GCATTCAGTTTGTGCTGCGA	60.040	50.000	0.00	0.00	36.49	5.10
445	451	8.844244	GTCCAGAATGCATCAAGTATAAGAATT	58.156	33.333	0.00	0.00	31.97	2.17
602	608	6.901357	CAGTGTAACACAAACTAAAACCGTAC	59.099	38.462	0.00	0.00	41.43	3.67
698	889	8.895932	ATTGATAAACAAAGATACTTTGCGAC	57.104	30.769	19.64	10.35	42.03	5.19
873	1074	6.928348	TCTCTGGGAACTAGAACACATTAA	57.072	37.500	0.00	0.00	0.00	1.40
991	1203	5.444122	GTCACAACAAGACATCAAGCTAAC	58.556	41.667	0.00	0.00	36.06	2.34
1725	1968	7.230108	AGCAGAATCATATGGACAAATACCTTG	59.770	37.037	2.13	0.00	41.19	3.61
2761	3127	4.072131	GGTCACTCTTGTTTAGGCATTCA	58.928	43.478	0.00	0.00	0.00	2.57
3783	4383	0.182775	GACCTTGTGGGACCTTGTGT	59.817	55.000	0.00	0.00	38.76	3.72
3784	4384	0.537371	GGACCTTGTGGGACCTTGTG	60.537	60.000	0.00	0.00	44.62	3.33
3785	4385	1.716028	GGGACCTTGTGGGACCTTGT	61.716	60.000	3.57	0.00	46.67	3.16
3786	4386	1.074951	GGGACCTTGTGGGACCTTG	59.925	63.158	3.57	0.00	46.67	3.61
3787	4387	0.776080	ATGGGACCTTGTGGGACCTT	60.776	55.000	3.57	0.00	46.67	3.50
3788	4388	0.120377	TATGGGACCTTGTGGGACCT	59.880	55.000	3.57	0.00	46.67	3.85
3789	4389	1.222567	ATATGGGACCTTGTGGGACC	58.777	55.000	0.00	0.00	46.74	4.46
3790	4390	3.009143	GGATATATGGGACCTTGTGGGAC	59.991	52.174	0.00	0.00	38.76	4.46
3791	4391	3.256704	GGATATATGGGACCTTGTGGGA	58.743	50.000	0.00	0.00	38.76	4.37
3792	4392	2.986019	TGGATATATGGGACCTTGTGGG	59.014	50.000	0.00	0.00	41.89	4.61
3793	4393	4.350816	TCTTGGATATATGGGACCTTGTGG	59.649	45.833	0.00	0.00	39.83	4.17
3851	4474	3.482156	ACAGTTCAAGATGCACTGACT	57.518	42.857	15.29	1.45	42.83	3.41
3857	4480	1.001974	AGCCGTACAGTTCAAGATGCA	59.998	47.619	0.00	0.00	0.00	3.96
4052	4675	6.360370	TCATTACATATAGCCAGGTCTTCC	57.640	41.667	0.00	0.00	0.00	3.46
4144	4767	1.398041	TCATTGCCTTGCTCGAATTCG	59.602	47.619	21.78	21.78	41.45	3.34
4145	4768	3.174375	GTTCATTGCCTTGCTCGAATTC	58.826	45.455	0.00	0.00	0.00	2.17
4147	4770	1.474077	GGTTCATTGCCTTGCTCGAAT	59.526	47.619	0.00	0.00	0.00	3.34
4148	4771	0.881118	GGTTCATTGCCTTGCTCGAA	59.119	50.000	0.00	0.00	0.00	3.71
4160	4791	3.245586	TGCCACCCTATTTCAGGTTCATT	60.246	43.478	0.00	0.00	43.80	2.57
4178	4809	9.772605	AAGATTAATGATAATATTCCCATGCCA	57.227	29.630	0.00	0.00	29.20	4.92
4198	4829	7.147391	TGAGGCAAATGGGTGTATAGAAGATTA	60.147	37.037	0.00	0.00	0.00	1.75
4199	4830	6.018433	AGGCAAATGGGTGTATAGAAGATT	57.982	37.500	0.00	0.00	0.00	2.40
4200	4831	5.132648	TGAGGCAAATGGGTGTATAGAAGAT	59.867	40.000	0.00	0.00	0.00	2.40
4201	4832	4.473196	TGAGGCAAATGGGTGTATAGAAGA	59.527	41.667	0.00	0.00	0.00	2.87
4202	4833	4.780815	TGAGGCAAATGGGTGTATAGAAG	58.219	43.478	0.00	0.00	0.00	2.85
4203	4834	4.853468	TGAGGCAAATGGGTGTATAGAA	57.147	40.909	0.00	0.00	0.00	2.10
4204	4835	4.411869	TGATGAGGCAAATGGGTGTATAGA	59.588	41.667	0.00	0.00	0.00	1.98
4205	4836	4.717877	TGATGAGGCAAATGGGTGTATAG	58.282	43.478	0.00	0.00	0.00	1.31
4206	4837	4.787135	TGATGAGGCAAATGGGTGTATA	57.213	40.909	0.00	0.00	0.00	1.47
4213	4847	2.761767	TGATGGTTGATGAGGCAAATGG	59.238	45.455	0.00	0.00	0.00	3.16
4228	4866	7.775053	TGCTTTCCTTATAAAAACTGATGGT	57.225	32.000	0.00	0.00	0.00	3.55
4243	4889	3.760684	GGTCTCATCATGTTGCTTTCCTT	59.239	43.478	0.00	0.00	0.00	3.36
4245	4891	3.084039	TGGTCTCATCATGTTGCTTTCC	58.916	45.455	0.00	0.95	0.00	3.13
4253	4899	4.758674	CACAAGTTTCTGGTCTCATCATGT	59.241	41.667	0.00	0.00	0.00	3.21
4259	4905	4.058124	CGAATCACAAGTTTCTGGTCTCA	58.942	43.478	0.00	0.00	0.00	3.27
4316	4962	8.458843	GTGCTGGAATAAACTTTATAGCTTCAA	58.541	33.333	12.75	0.00	0.00	2.69
4321	4967	6.202226	GCTGTGCTGGAATAAACTTTATAGC	58.798	40.000	7.44	7.44	0.00	2.97
4323	4969	6.184068	TGGCTGTGCTGGAATAAACTTTATA	58.816	36.000	0.00	0.00	0.00	0.98
4340	5004	1.467734	GATGAAGCACTTCTGGCTGTG	59.532	52.381	11.44	0.00	41.66	3.66
4341	5005	1.350351	AGATGAAGCACTTCTGGCTGT	59.650	47.619	11.44	0.00	41.66	4.40
4346	5010	2.161808	CCAGCAAGATGAAGCACTTCTG	59.838	50.000	11.44	3.04	40.14	3.02
4347	5011	2.224719	ACCAGCAAGATGAAGCACTTCT	60.225	45.455	11.44	0.00	40.14	2.85
4348	5012	2.095364	CACCAGCAAGATGAAGCACTTC	60.095	50.000	3.37	3.37	39.91	3.01
4360	5026	3.402628	ACAACTACCTACACCAGCAAG	57.597	47.619	0.00	0.00	0.00	4.01
4366	5032	5.121105	ACACTTGAAACAACTACCTACACC	58.879	41.667	0.00	0.00	0.00	4.16
4371	5037	7.506114	TCATCTTACACTTGAAACAACTACCT	58.494	34.615	0.00	0.00	0.00	3.08
4372	5038	7.724305	TCATCTTACACTTGAAACAACTACC	57.276	36.000	0.00	0.00	0.00	3.18
4373	5039	8.988934	TCATCATCTTACACTTGAAACAACTAC	58.011	33.333	0.00	0.00	0.00	2.73
4380	5046	7.360353	CGAAAGCTCATCATCTTACACTTGAAA	60.360	37.037	0.00	0.00	0.00	2.69
4381	5047	6.091305	CGAAAGCTCATCATCTTACACTTGAA	59.909	38.462	0.00	0.00	0.00	2.69
4392	5058	4.585364	CATGAACACGAAAGCTCATCATC	58.415	43.478	0.00	0.00	0.00	2.92
4510	5182	4.640647	AGTCACCCAAGAAACAAGAGAAAC	59.359	41.667	0.00	0.00	0.00	2.78
4716	5390	3.569701	AGGGAAATACAAGTGCACAACAG	59.430	43.478	21.04	7.93	0.00	3.16
6083	6765	4.461431	TCGCCTATCTCAACAGAAACTACA	59.539	41.667	0.00	0.00	30.24	2.74
6429	7119	8.862325	ATGTTTAACATAGATGAAGTTGTGGA	57.138	30.769	9.02	0.00	36.99	4.02
6457	7147	5.850557	AACAAACATCCTTCACATCAACA	57.149	34.783	0.00	0.00	0.00	3.33
6477	7169	7.588512	AGACTAATGCAATGTTTCTCAGAAAC	58.411	34.615	21.56	21.56	0.00	2.78
6499	7191	9.657121	GCAACAAGAAATCATATAGCTAAAGAC	57.343	33.333	0.00	0.00	0.00	3.01
6700	7392	6.391227	AAGTTTCCACTGTTGACCTAATTG	57.609	37.500	0.00	0.00	31.60	2.32
6760	7452	2.031012	CACGAACCCAGCAGCTCA	59.969	61.111	0.00	0.00	0.00	4.26
6880	7572	0.394565	CCTTCGATGATCCCCAGGAC	59.605	60.000	0.00	0.00	32.98	3.85
6892	7584	1.296715	GCACCACACTCCCTTCGAT	59.703	57.895	0.00	0.00	0.00	3.59
6907	7599	1.952296	GATGGTGATTGATCCAGGCAC	59.048	52.381	0.00	0.00	37.14	5.01
7019	7711	9.214957	CACTAGGATCAAAACAAACTATACACA	57.785	33.333	0.00	0.00	0.00	3.72
7127	7819	6.478344	GTCAGAGATACTGCATACTTCCAAAG	59.522	42.308	0.00	0.00	45.38	2.77
7161	7853	5.812127	GCAATGTGAATATGAAAAGGAACCC	59.188	40.000	0.00	0.00	0.00	4.11
7222	7914	5.537300	TCAGTAACCTAGAAGGCATCATC	57.463	43.478	0.00	0.00	39.63	2.92
7229	7921	8.239038	TGAATCAGTATCAGTAACCTAGAAGG	57.761	38.462	0.00	0.00	42.49	3.46
7355	8047	0.798776	CCAGACATCCTGAAACACGC	59.201	55.000	0.00	0.00	45.78	5.34

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.