AutoCloner

Multiple sequence alignment - TraesCS5A01G350100

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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	TraesCS5A01G350100	chr5A	100.000	5613	0	0	1	5613	552753389	552747777	0.000000e+00	10366.0
1	TraesCS5A01G350100	chr5A	88.707	2196	157	36	1959	4105	552674759	552676912	0.000000e+00	2597.0
2	TraesCS5A01G350100	chr5A	88.559	708	69	6	1209	1907	552674055	552674759	0.000000e+00	848.0
3	TraesCS5A01G350100	chr5A	77.443	1361	193	66	1210	2525	533830403	533831694	0.000000e+00	708.0
4	TraesCS5A01G350100	chr5A	89.184	564	48	7	4192	4755	552677268	552677818	0.000000e+00	691.0
5	TraesCS5A01G350100	chr5A	79.887	885	108	37	1057	1905	552650650	552651500	8.100000e-163	584.0
6	TraesCS5A01G350100	chr5A	82.344	657	97	14	3236	3883	533834456	533835102	2.290000e-153	553.0
7	TraesCS5A01G350100	chr5A	81.358	692	99	9	3243	3934	552630942	552630281	2.300000e-148	536.0
8	TraesCS5A01G350100	chr5A	77.059	340	45	13	1057	1382	533832010	533832330	1.250000e-36	165.0
9	TraesCS5A01G350100	chr5D	96.054	5145	104	22	1	5093	437812258	437807161	0.000000e+00	8285.0
10	TraesCS5A01G350100	chr5D	87.376	1410	82	31	2752	4119	437695565	437696920	0.000000e+00	1530.0
11	TraesCS5A01G350100	chr5D	88.616	773	55	15	1959	2728	437694733	437695475	0.000000e+00	909.0
12	TraesCS5A01G350100	chr5D	88.844	735	68	7	1185	1907	437694001	437694733	0.000000e+00	891.0
13	TraesCS5A01G350100	chr5D	77.471	1558	232	65	1209	2711	437642089	437643582	0.000000e+00	822.0
14	TraesCS5A01G350100	chr5D	78.374	1341	201	49	1057	2377	420188765	420190036	0.000000e+00	787.0
15	TraesCS5A01G350100	chr5D	89.539	564	47	6	4192	4755	437697262	437697813	0.000000e+00	704.0
16	TraesCS5A01G350100	chr5D	77.320	1358	199	63	1210	2525	420187164	420188454	0.000000e+00	701.0
17	TraesCS5A01G350100	chr5D	76.343	1378	213	61	1057	2377	437565949	437564628	7.930000e-178	634.0
18	TraesCS5A01G350100	chr5D	93.868	424	9	2	5196	5613	437807111	437806699	1.720000e-174	623.0
19	TraesCS5A01G350100	chr5D	81.617	767	118	17	1967	2714	437566701	437565939	1.030000e-171	614.0
20	TraesCS5A01G350100	chr5D	82.470	656	98	13	3236	3883	420191364	420192010	4.910000e-155	558.0
21	TraesCS5A01G350100	chr5D	78.261	299	52	8	1564	1851	370089158	370089454	4.470000e-41	180.0
22	TraesCS5A01G350100	chr5D	84.746	177	17	2	3935	4102	437616826	437616651	9.670000e-38	169.0
23	TraesCS5A01G350100	chr5D	98.077	52	1	0	5122	5173	437807163	437807112	2.150000e-14	91.6
24	TraesCS5A01G350100	chr5B	96.071	3792	84	20	860	4633	531640458	531644202	0.000000e+00	6117.0
25	TraesCS5A01G350100	chr5B	96.049	3189	84	15	39	3204	531708673	531705504	0.000000e+00	5153.0
26	TraesCS5A01G350100	chr5B	92.256	891	46	8	3235	4116	531705507	531704631	0.000000e+00	1242.0
27	TraesCS5A01G350100	chr5B	89.362	564	48	6	4192	4755	531704341	531703790	0.000000e+00	699.0
28	TraesCS5A01G350100	chr5B	96.667	420	12	1	5196	5613	531644827	531645246	0.000000e+00	697.0
29	TraesCS5A01G350100	chr5B	76.419	1374	222	55	1057	2377	439268938	439270262	0.000000e+00	649.0
30	TraesCS5A01G350100	chr5B	81.700	694	110	9	3243	3934	531621387	531620709	3.800000e-156	562.0
31	TraesCS5A01G350100	chr5B	89.277	401	8	10	4573	4963	531644203	531644578	2.370000e-128	470.0
32	TraesCS5A01G350100	chr5B	95.909	220	9	0	2	221	16161302	16161083	1.920000e-94	357.0
33	TraesCS5A01G350100	chr5B	92.273	220	7	2	2	221	250487000	250487209	2.540000e-78	303.0
34	TraesCS5A01G350100	chr5B	84.836	244	21	7	1192	1420	531639734	531639976	1.220000e-56	231.0
35	TraesCS5A01G350100	chr5B	97.170	106	3	0	5042	5147	531644720	531644825	4.470000e-41	180.0
36	TraesCS5A01G350100	chr5B	85.799	169	15	1	3935	4094	531620671	531620503	2.690000e-38	171.0
37	TraesCS5A01G350100	chr5B	100.000	44	0	0	4962	5005	531644682	531644725	1.300000e-11	82.4
38	TraesCS5A01G350100	chr6B	77.512	1423	203	69	1209	2572	608152462	608153826	0.000000e+00	747.0
39	TraesCS5A01G350100	chr6B	81.472	761	117	17	1967	2708	608188420	608187665	2.240000e-168	603.0
40	TraesCS5A01G350100	chr6B	81.120	768	120	18	1967	2714	607136311	607135549	4.840000e-165	592.0
41	TraesCS5A01G350100	chr6B	76.480	1267	189	69	1065	2275	608187660	608186447	6.260000e-164	588.0
42	TraesCS5A01G350100	chr6B	79.143	887	139	23	3243	4094	608366961	608366086	6.310000e-159	571.0
43	TraesCS5A01G350100	chr6B	81.700	694	110	10	3243	3934	607132877	607132199	3.800000e-156	562.0
44	TraesCS5A01G350100	chr6B	85.799	169	15	1	3935	4094	607132161	607131993	2.690000e-38	171.0
45	TraesCS5A01G350100	chr4B	95.909	220	9	0	2	221	632313153	632312934	1.920000e-94	357.0
46	TraesCS5A01G350100	chr4B	94.091	220	13	0	2	221	213360077	213360296	9.010000e-88	335.0
47	TraesCS5A01G350100	chr2B	95.349	215	10	0	7	221	710589486	710589272	5.380000e-90	342.0
48	TraesCS5A01G350100	chr2B	92.273	220	7	2	2	221	222792213	222792004	2.540000e-78	303.0
49	TraesCS5A01G350100	chrUn	91.818	220	8	2	2	221	328845421	328845630	1.180000e-76	298.0
50	TraesCS5A01G350100	chr1B	91.710	193	6	2	29	221	601564170	601563988	5.580000e-65	259.0
51	TraesCS5A01G350100	chr1B	90.374	187	8	2	2	188	54766884	54767060	2.610000e-58	237.0
52	TraesCS5A01G350100	chr1B	90.374	187	8	2	2	188	54771789	54771965	2.610000e-58	237.0
53	TraesCS5A01G350100	chr3D	85.268	224	31	2	300	522	442162463	442162685	4.370000e-56	230.0

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	TraesCS5A01G350100	chr5A	552747777	552753389	5612	True	10366.000000	10366	100.000000	1	5613	1	chr5A.!!$R2	5612
1	TraesCS5A01G350100	chr5A	552674055	552677818	3763	False	1378.666667	2597	88.816667	1209	4755	3	chr5A.!!$F3	3546
2	TraesCS5A01G350100	chr5A	552650650	552651500	850	False	584.000000	584	79.887000	1057	1905	1	chr5A.!!$F1	848
3	TraesCS5A01G350100	chr5A	552630281	552630942	661	True	536.000000	536	81.358000	3243	3934	1	chr5A.!!$R1	691
4	TraesCS5A01G350100	chr5A	533830403	533835102	4699	False	475.333333	708	78.948667	1057	3883	3	chr5A.!!$F2	2826
5	TraesCS5A01G350100	chr5D	437806699	437812258	5559	True	2999.866667	8285	95.999667	1	5613	3	chr5D.!!$R3	5612
6	TraesCS5A01G350100	chr5D	437694001	437697813	3812	False	1008.500000	1530	88.593750	1185	4755	4	chr5D.!!$F4	3570
7	TraesCS5A01G350100	chr5D	437642089	437643582	1493	False	822.000000	822	77.471000	1209	2711	1	chr5D.!!$F2	1502
8	TraesCS5A01G350100	chr5D	420187164	420192010	4846	False	682.000000	787	79.388000	1057	3883	3	chr5D.!!$F3	2826
9	TraesCS5A01G350100	chr5D	437564628	437566701	2073	True	624.000000	634	78.980000	1057	2714	2	chr5D.!!$R2	1657
10	TraesCS5A01G350100	chr5B	531703790	531708673	4883	True	2364.666667	5153	92.555667	39	4755	3	chr5B.!!$R3	4716
11	TraesCS5A01G350100	chr5B	531639734	531645246	5512	False	1296.233333	6117	94.003500	860	5613	6	chr5B.!!$F3	4753
12	TraesCS5A01G350100	chr5B	439268938	439270262	1324	False	649.000000	649	76.419000	1057	2377	1	chr5B.!!$F2	1320
13	TraesCS5A01G350100	chr5B	531620503	531621387	884	True	366.500000	562	83.749500	3243	4094	2	chr5B.!!$R2	851
14	TraesCS5A01G350100	chr6B	608152462	608153826	1364	False	747.000000	747	77.512000	1209	2572	1	chr6B.!!$F1	1363
15	TraesCS5A01G350100	chr6B	608186447	608188420	1973	True	595.500000	603	78.976000	1065	2708	2	chr6B.!!$R3	1643
16	TraesCS5A01G350100	chr6B	608366086	608366961	875	True	571.000000	571	79.143000	3243	4094	1	chr6B.!!$R1	851
17	TraesCS5A01G350100	chr6B	607131993	607136311	4318	True	441.666667	592	82.873000	1967	4094	3	chr6B.!!$R2	2127

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
861	876	3.276091	CGCACAACTCCAACGCCA	61.276	61.111	0.00	0.00	0.00	5.69	F
1420	1482	0.652592	GCATCGAAACCTCATGTCCG	59.347	55.000	0.00	0.00	0.00	4.79	F
1698	1802	1.009675	CTGTATTTGATGCCGCGCC	60.010	57.895	0.00	0.00	0.00	6.53	F
1775	1879	1.135575	GGCGCAATTTCAGTTCAGGAG	60.136	52.381	10.83	0.00	0.00	3.69	F
2649	6432	1.159285	TCTACATTGTGCTGCAGTGC	58.841	50.000	16.64	8.58	38.23	4.40	F
4056	8738	1.837439	TGCCGAGGGATGTTATTCACT	59.163	47.619	0.00	0.00	30.03	3.41	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1775	1879	0.526211	CCGCTTCTGGCCCTTAAAAC	59.474	55.000	0.00	0.00	37.74	2.43	R
3060	6944	3.719268	ATGATAGTTGCAAGGTCCACA	57.281	42.857	0.00	0.00	0.00	4.17	R
3525	8145	4.749976	TGGAAAGGGAAAACGAAAAACAG	58.250	39.130	0.00	0.00	0.00	3.16	R
3529	8149	6.324254	TCCTAAATGGAAAGGGAAAACGAAAA	59.676	34.615	0.00	0.00	42.94	2.29	R
4187	9148	0.262285	ACCTGCCCTAGTCCTAGTCC	59.738	60.000	0.96	0.00	0.00	3.85	R
5109	10247	0.097674	AATGAAGCAATCGCAGCGAC	59.902	50.000	22.28	7.84	39.18	5.19	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
53	54	6.640499	TCACAAATAAATGTTGTTGCTAGCAC	59.360	34.615	19.17	13.28	37.09	4.40
221	222	9.803315	CTTGTACACTACATCAGCTTAATTAGA	57.197	33.333	0.00	0.00	38.68	2.10
226	227	8.322091	ACACTACATCAGCTTAATTAGAAACCT	58.678	33.333	0.00	0.00	0.00	3.50
258	272	5.934402	AGTAGACAATTGTTCCTCCGTAT	57.066	39.130	13.36	0.00	0.00	3.06
463	477	8.098286	TCTTTCTGAATTAACTCCAATTCGGTA	58.902	33.333	14.04	5.39	45.48	4.02
584	598	5.751243	TTGCCTCTGTTTACTCTTTCAAC	57.249	39.130	0.00	0.00	0.00	3.18
861	876	3.276091	CGCACAACTCCAACGCCA	61.276	61.111	0.00	0.00	0.00	5.69
1062	1077	2.097466	ACAACGTCCTTGCAAGAAAGTG	59.903	45.455	28.05	18.75	32.41	3.16
1420	1482	0.652592	GCATCGAAACCTCATGTCCG	59.347	55.000	0.00	0.00	0.00	4.79
1698	1802	1.009675	CTGTATTTGATGCCGCGCC	60.010	57.895	0.00	0.00	0.00	6.53
1775	1879	1.135575	GGCGCAATTTCAGTTCAGGAG	60.136	52.381	10.83	0.00	0.00	3.69
1788	1892	2.820197	GTTCAGGAGTTTTAAGGGCCAG	59.180	50.000	6.18	0.00	0.00	4.85
1826	1930	2.100087	GCCTCTCTAAGCGCTCTAACTT	59.900	50.000	12.06	0.00	0.00	2.66
1840	1944	5.613360	CGCTCTAACTTGTGAGACAATGTTG	60.613	44.000	0.00	0.00	37.48	3.33
1855	1959	1.913778	TGTTGAGCACATGCCAGATT	58.086	45.000	0.00	0.00	43.38	2.40
1870	1978	3.620966	GCCAGATTAACAAGGTGAGCTCT	60.621	47.826	16.19	0.00	0.00	4.09
1908	2020	8.564574	TGAAACAAATATCTGTCTGTTGGTAAC	58.435	33.333	0.00	0.00	32.50	2.50
1909	2021	8.691661	AAACAAATATCTGTCTGTTGGTAACT	57.308	30.769	0.00	0.00	32.50	2.24
1912	2024	7.174946	ACAAATATCTGTCTGTTGGTAACTTGG	59.825	37.037	0.00	0.00	37.61	3.61
1913	2025	4.706842	ATCTGTCTGTTGGTAACTTGGT	57.293	40.909	0.00	0.00	37.61	3.67
1961	2088	6.609237	ATCATTGTATGCACTGACACATAC	57.391	37.500	6.00	6.26	45.73	2.39
1997	4015	6.489361	AGACATGATGAATAGCATTTTCCCTC	59.511	38.462	0.00	0.00	37.34	4.30
2064	4082	5.189539	CCCCCTTGTTGATTTTGATGGTAAT	59.810	40.000	0.00	0.00	0.00	1.89
2147	4165	4.619160	GCACATTCTTCAATTCTTGGGGTC	60.619	45.833	0.00	0.00	0.00	4.46
2247	5852	6.188407	TCTTACTGCATCCTGTACTACTTCT	58.812	40.000	0.00	0.00	0.00	2.85
2281	5890	7.995463	TTTTATTTGAGTTTGTGTGTAAGGC	57.005	32.000	0.00	0.00	0.00	4.35
2340	5953	5.793457	GTCGATGAGTTTATTCCCAAAAACG	59.207	40.000	0.00	0.00	39.90	3.60
2352	5966	1.324383	CAAAAACGGCCCCACTAGTT	58.676	50.000	0.00	0.00	0.00	2.24
2353	5967	1.684450	CAAAAACGGCCCCACTAGTTT	59.316	47.619	0.00	0.00	38.30	2.66
2649	6432	1.159285	TCTACATTGTGCTGCAGTGC	58.841	50.000	16.64	8.58	38.23	4.40
2930	6810	2.863809	ACCAATCGAAGGTTTCAGCTT	58.136	42.857	7.07	0.00	38.85	3.74
3077	6986	3.832527	ACTTTGTGGACCTTGCAACTAT	58.167	40.909	0.00	0.00	0.00	2.12
3208	7741	8.996271	AGATTCATTTTCTTGAAGCAAATTTCC	58.004	29.630	0.06	0.00	42.89	3.13
3320	7936	7.990886	TGGTTCTGTTGTAGTCATTACTTTTCT	59.009	33.333	0.00	0.00	37.15	2.52
3516	8136	5.476945	CCTGAGGGTTGTTACTGCTATTTTT	59.523	40.000	0.00	0.00	0.00	1.94
3864	8498	5.875910	CCACGTGTAAAATCACCAAGGTATA	59.124	40.000	15.65	0.00	35.18	1.47
3865	8499	6.540914	CCACGTGTAAAATCACCAAGGTATAT	59.459	38.462	15.65	0.00	35.18	0.86
4056	8738	1.837439	TGCCGAGGGATGTTATTCACT	59.163	47.619	0.00	0.00	30.03	3.41
4134	8818	7.588497	ATTTTCTGGCAAAATATCTACTCCC	57.412	36.000	0.00	0.00	0.00	4.30
4189	9150	8.514330	AAAAGAAATTGTGTGTACTTGTAGGA	57.486	30.769	0.00	0.00	0.00	2.94
4190	9151	7.492352	AAGAAATTGTGTGTACTTGTAGGAC	57.508	36.000	0.00	0.00	0.00	3.85
4271	9232	6.911250	ACTCATCATGATACCATACCGTAA	57.089	37.500	8.15	0.00	0.00	3.18
4525	9487	0.249120	CTCATGACAGGTGGCCGTTA	59.751	55.000	0.00	0.00	0.00	3.18
4662	9685	0.388659	TGTTCATGTTGGTTGGCTGC	59.611	50.000	0.00	0.00	0.00	5.25
4672	9695	4.680237	TTGGCTGCCTGACGTCCG	62.680	66.667	21.03	6.54	0.00	4.79
4831	9854	6.387465	TGGAAGAAAGTTGACACTATCTACG	58.613	40.000	0.00	0.00	38.03	3.51
4840	9863	7.426410	AGTTGACACTATCTACGAACCATATG	58.574	38.462	0.00	0.00	38.03	1.78
5077	10215	8.153411	CGAACATTTATTTCAAAGTTAAAGCGG	58.847	33.333	0.00	0.00	0.00	5.52
5173	10311	0.316196	CGCTATTTGCCGCTACAAGC	60.316	55.000	0.00	0.00	38.78	4.01
5183	10321	2.229965	GCTACAAGCGGCAGATAGC	58.770	57.895	1.45	8.12	44.65	2.97
5192	10330	2.190578	GCAGATAGCAACGCCCCT	59.809	61.111	0.00	0.00	44.79	4.79
5193	10331	1.452108	GCAGATAGCAACGCCCCTT	60.452	57.895	0.00	0.00	44.79	3.95
5194	10332	0.179056	GCAGATAGCAACGCCCCTTA	60.179	55.000	0.00	0.00	44.79	2.69
5327	10471	1.982073	GCAAGCCCGGAACAGAATCG	61.982	60.000	0.73	0.00	0.00	3.34
5476	10620	2.202676	GCGCGTCTCCTCCTTCAG	60.203	66.667	8.43	0.00	0.00	3.02
5573	10719	0.325671	CAGCTTCCTCCTCCCACCTA	60.326	60.000	0.00	0.00	0.00	3.08
5574	10720	0.644937	AGCTTCCTCCTCCCACCTAT	59.355	55.000	0.00	0.00	0.00	2.57
5586	10732	1.586422	CCACCTATGCATTCCGTCTG	58.414	55.000	3.54	0.00	0.00	3.51

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
84	85	5.127491	TGAACTATTTCAAAGGTGTCCGTT	58.873	37.500	0.00	0.00	38.87	4.44
86	87	5.682943	TTGAACTATTTCAAAGGTGTCCG	57.317	39.130	5.83	0.00	46.59	4.79
223	224	9.569122	AACAATTGTCTACTTATGTACAAAGGT	57.431	29.630	12.39	10.99	0.00	3.50
226	227	9.787435	AGGAACAATTGTCTACTTATGTACAAA	57.213	29.630	12.39	0.00	0.00	2.83
258	272	0.327924	CCTTATCGCCCATGCCCATA	59.672	55.000	0.00	0.00	0.00	2.74
446	460	6.827586	TTTTGCTACCGAATTGGAGTTAAT	57.172	33.333	0.00	0.00	42.00	1.40
463	477	5.972935	TGATCATCAATGCTTCATTTTGCT	58.027	33.333	0.00	0.00	31.05	3.91
562	576	5.437060	AGTTGAAAGAGTAAACAGAGGCAA	58.563	37.500	0.00	0.00	0.00	4.52
584	598	4.000988	GGTGTGGACATGTGGTAAACTAG	58.999	47.826	1.15	0.00	0.00	2.57
723	737	2.890442	GCAGCTGAGTTTGCTACTTC	57.110	50.000	20.43	0.00	38.92	3.01
861	876	6.849151	ACTAGGAAAAGGTCACCTTACAAAT	58.151	36.000	10.32	0.00	43.92	2.32
1062	1077	3.567478	ATGGACTCACTTGGCCTAATC	57.433	47.619	3.32	0.00	0.00	1.75
1238	1266	7.680730	ACACTCCTACACAATCTTGAAACTAT	58.319	34.615	0.00	0.00	0.00	2.12
1420	1482	3.674997	TGTGAGGAAACTTGTAGCATCC	58.325	45.455	0.00	0.00	44.43	3.51
1698	1802	5.179929	TGCATGTCACAATCAAGACTTACAG	59.820	40.000	0.00	0.00	35.81	2.74
1775	1879	0.526211	CCGCTTCTGGCCCTTAAAAC	59.474	55.000	0.00	0.00	37.74	2.43
1788	1892	1.410882	AGGCAAGATCTACTCCGCTTC	59.589	52.381	0.00	0.00	0.00	3.86
1826	1930	2.916640	TGTGCTCAACATTGTCTCACA	58.083	42.857	10.13	10.13	32.36	3.58
1840	1944	3.181493	CCTTGTTAATCTGGCATGTGCTC	60.181	47.826	4.84	0.00	41.70	4.26
1870	1978	9.729023	CAGATATTTGTTTCAACTGTACAACAA	57.271	29.630	4.77	4.77	37.35	2.83
1908	2020	5.931441	GCTATAAAGCCACTGATACCAAG	57.069	43.478	0.00	0.00	43.40	3.61
1961	2088	7.041508	GCTATTCATCATGTCTGAAACTAAGGG	60.042	40.741	14.43	5.08	36.30	3.95
1997	4015	6.197096	GCACAAAAGTGACAATGAAGTTACAG	59.803	38.462	0.00	0.00	31.09	2.74
2064	4082	3.565307	AGAGCAGTTCATCCCAACAAAA	58.435	40.909	0.00	0.00	0.00	2.44
2147	4165	2.768527	ACATACCTGACCATCCTGTGAG	59.231	50.000	0.00	0.00	0.00	3.51
2318	5927	5.092781	CCGTTTTTGGGAATAAACTCATCG	58.907	41.667	0.00	0.00	33.24	3.84
2649	6432	7.523293	TCATCAATCTCTTCCTTAGCTCTAG	57.477	40.000	0.00	0.00	0.00	2.43
2930	6810	4.081752	CAGCTTGGCCATGTAACCAATTAA	60.082	41.667	19.05	0.00	44.67	1.40
3060	6944	3.719268	ATGATAGTTGCAAGGTCCACA	57.281	42.857	0.00	0.00	0.00	4.17
3208	7741	5.676532	AGTTTACTCCAGATATCGTCGAG	57.323	43.478	0.00	12.48	0.00	4.04
3525	8145	4.749976	TGGAAAGGGAAAACGAAAAACAG	58.250	39.130	0.00	0.00	0.00	3.16
3528	8148	6.987404	CCTAAATGGAAAGGGAAAACGAAAAA	59.013	34.615	0.00	0.00	38.35	1.94
3529	8149	6.324254	TCCTAAATGGAAAGGGAAAACGAAAA	59.676	34.615	0.00	0.00	42.94	2.29
4056	8738	7.504238	TCCTTTATTTAAGTTCAACAAGAGGCA	59.496	33.333	0.00	0.00	31.56	4.75
4185	9146	1.781529	CCTGCCCTAGTCCTAGTCCTA	59.218	57.143	0.96	0.00	0.00	2.94
4186	9147	0.558712	CCTGCCCTAGTCCTAGTCCT	59.441	60.000	0.96	0.00	0.00	3.85
4187	9148	0.262285	ACCTGCCCTAGTCCTAGTCC	59.738	60.000	0.96	0.00	0.00	3.85
4188	9149	1.063867	TCACCTGCCCTAGTCCTAGTC	60.064	57.143	0.96	0.00	0.00	2.59
4189	9150	1.008403	TCACCTGCCCTAGTCCTAGT	58.992	55.000	0.96	0.00	0.00	2.57
4190	9151	2.390225	ATCACCTGCCCTAGTCCTAG	57.610	55.000	0.00	0.00	0.00	3.02
4307	9268	7.554118	CCACATTTCAGAGACCATACAAGTTAT	59.446	37.037	0.00	0.00	0.00	1.89
4321	9282	6.038161	TGTTGTTGAGTAACCACATTTCAGAG	59.962	38.462	0.00	0.00	37.48	3.35
4525	9487	3.640407	AGCACACATGGCTCGGGT	61.640	61.111	0.00	0.00	36.81	5.28
4662	9685	3.343788	GACTGGAGCGGACGTCAGG	62.344	68.421	18.91	9.72	0.00	3.86
4672	9695	1.312815	AGCAACACAAAGACTGGAGC	58.687	50.000	0.00	0.00	0.00	4.70
4831	9854	7.108194	TCTGCTATCATTCATCCATATGGTTC	58.892	38.462	21.28	0.00	36.34	3.62
4840	9863	4.282957	TCAGGTCTCTGCTATCATTCATCC	59.717	45.833	0.00	0.00	40.69	3.51
5109	10247	0.097674	AATGAAGCAATCGCAGCGAC	59.902	50.000	22.28	7.84	39.18	5.19
5174	10312	2.893682	AAGGGGCGTTGCTATCTGCC	62.894	60.000	0.00	0.00	46.82	4.85
5175	10313	0.179056	TAAGGGGCGTTGCTATCTGC	60.179	55.000	0.00	0.00	43.25	4.26
5176	10314	2.550830	ATAAGGGGCGTTGCTATCTG	57.449	50.000	0.00	0.00	0.00	2.90
5177	10315	3.477530	GAAATAAGGGGCGTTGCTATCT	58.522	45.455	0.00	0.00	0.00	1.98
5178	10316	2.552743	GGAAATAAGGGGCGTTGCTATC	59.447	50.000	0.00	0.00	0.00	2.08
5179	10317	2.174854	AGGAAATAAGGGGCGTTGCTAT	59.825	45.455	0.00	0.00	0.00	2.97
5180	10318	1.562475	AGGAAATAAGGGGCGTTGCTA	59.438	47.619	0.00	0.00	0.00	3.49
5181	10319	0.331616	AGGAAATAAGGGGCGTTGCT	59.668	50.000	0.00	0.00	0.00	3.91
5182	10320	0.738975	GAGGAAATAAGGGGCGTTGC	59.261	55.000	0.00	0.00	0.00	4.17
5183	10321	1.389555	GGAGGAAATAAGGGGCGTTG	58.610	55.000	0.00	0.00	0.00	4.10
5184	10322	0.257905	GGGAGGAAATAAGGGGCGTT	59.742	55.000	0.00	0.00	0.00	4.84
5185	10323	1.642513	GGGGAGGAAATAAGGGGCGT	61.643	60.000	0.00	0.00	0.00	5.68
5186	10324	1.150764	GGGGAGGAAATAAGGGGCG	59.849	63.158	0.00	0.00	0.00	6.13
5187	10325	0.634465	TTGGGGAGGAAATAAGGGGC	59.366	55.000	0.00	0.00	0.00	5.80
5188	10326	3.706389	AATTGGGGAGGAAATAAGGGG	57.294	47.619	0.00	0.00	0.00	4.79
5189	10327	3.134623	GCAAATTGGGGAGGAAATAAGGG	59.865	47.826	0.00	0.00	0.00	3.95
5190	10328	3.774216	TGCAAATTGGGGAGGAAATAAGG	59.226	43.478	0.00	0.00	0.00	2.69
5191	10329	4.677779	CGTGCAAATTGGGGAGGAAATAAG	60.678	45.833	0.00	0.00	0.00	1.73
5192	10330	3.194542	CGTGCAAATTGGGGAGGAAATAA	59.805	43.478	0.00	0.00	0.00	1.40
5193	10331	2.757868	CGTGCAAATTGGGGAGGAAATA	59.242	45.455	0.00	0.00	0.00	1.40
5194	10332	1.550072	CGTGCAAATTGGGGAGGAAAT	59.450	47.619	0.00	0.00	0.00	2.17
5573	10719	0.745845	GCCAGACAGACGGAATGCAT	60.746	55.000	0.00	0.00	0.00	3.96
5574	10720	1.375908	GCCAGACAGACGGAATGCA	60.376	57.895	0.00	0.00	0.00	3.96
5586	10732	3.453070	GAGGAGATGCCGGCCAGAC	62.453	68.421	26.77	13.01	43.43	3.51

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.