AutoCloner

Multiple sequence alignment - TraesCS6A01G290500

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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	TraesCS6A01G290500	chr6A	100.000	4696	0	0	1	4696	522054697	522059392	0.000000e+00	8672.0
1	TraesCS6A01G290500	chr6A	87.879	132	11	4	4104	4230	522036400	522036531	2.930000e-32	150.0
2	TraesCS6A01G290500	chr6A	88.119	101	11	1	4456	4556	522036721	522036820	8.250000e-23	119.0
3	TraesCS6A01G290500	chr6A	82.883	111	10	5	3978	4087	522036219	522036321	1.800000e-14	91.6
4	TraesCS6A01G290500	chr6D	91.098	3707	263	23	1032	4696	380569474	380573155	0.000000e+00	4955.0
5	TraesCS6A01G290500	chr6D	86.538	156	17	4	4455	4607	380595456	380595610	8.080000e-38	169.0
6	TraesCS6A01G290500	chr6D	78.855	227	18	14	4456	4667	380563702	380563913	4.930000e-25	126.0
7	TraesCS6A01G290500	chr6D	83.784	111	9	5	3978	4087	380563202	380563304	3.870000e-16	97.1
8	TraesCS6A01G290500	chr6B	93.988	2761	145	5	1514	4264	567849647	567852396	0.000000e+00	4159.0
9	TraesCS6A01G290500	chr6B	84.621	2653	390	13	1034	3678	5767371	5770013	0.000000e+00	2623.0
10	TraesCS6A01G290500	chr6B	91.714	1050	62	16	1	1032	21015434	21014392	0.000000e+00	1434.0
11	TraesCS6A01G290500	chr6B	74.989	2319	529	37	1155	3448	47299409	47297117	0.000000e+00	1022.0
12	TraesCS6A01G290500	chr6B	88.451	381	17	3	4342	4696	567852392	567852771	7.220000e-118	435.0
13	TraesCS6A01G290500	chr6B	86.885	122	15	1	4110	4230	567823595	567823716	8.200000e-28	135.0
14	TraesCS6A01G290500	chr6B	88.393	112	10	3	4456	4567	567823905	567824013	1.060000e-26	132.0
15	TraesCS6A01G290500	chr3B	98.749	1039	12	1	1	1038	344310308	344309270	0.000000e+00	1845.0
16	TraesCS6A01G290500	chr3B	93.511	262	12	4	771	1032	7305910	7305654	7.370000e-103	385.0
17	TraesCS6A01G290500	chr2B	98.356	1034	15	2	1	1032	673229933	673228900	0.000000e+00	1814.0
18	TraesCS6A01G290500	chr2B	93.296	1059	47	16	1	1041	759271403	759272455	0.000000e+00	1541.0
19	TraesCS6A01G290500	chr2B	90.840	1048	72	16	1	1032	19870136	19869097	0.000000e+00	1382.0
20	TraesCS6A01G290500	chr2B	75.833	1920	420	38	1766	3665	714494122	714496017	0.000000e+00	935.0
21	TraesCS6A01G290500	chr2B	77.821	1560	307	27	2113	3658	788842304	788840770	0.000000e+00	928.0
22	TraesCS6A01G290500	chr1A	96.303	1055	16	10	1	1032	324860014	324861068	0.000000e+00	1711.0
23	TraesCS6A01G290500	chr1B	95.511	1047	29	7	1	1032	673919080	673918037	0.000000e+00	1657.0
24	TraesCS6A01G290500	chr1B	86.604	1060	108	19	1	1032	661049626	661050679	0.000000e+00	1140.0
25	TraesCS6A01G290500	chr7B	92.830	1046	53	14	4	1032	665498561	665497521	0.000000e+00	1496.0
26	TraesCS6A01G290500	chr2D	75.911	1922	389	56	1766	3665	590065106	590066975	0.000000e+00	917.0
27	TraesCS6A01G290500	chr2D	81.078	946	166	13	2238	3178	646490173	646491110	0.000000e+00	743.0
28	TraesCS6A01G290500	chr5A	77.002	874	166	25	2819	3675	688247102	688246247	7.120000e-128	468.0
29	TraesCS6A01G290500	chr5B	79.627	643	127	4	2530	3170	694007445	694006805	4.280000e-125	459.0
30	TraesCS6A01G290500	chr3A	82.540	189	31	2	2230	2417	44607486	44607673	1.050000e-36	165.0
31	TraesCS6A01G290500	chr3D	80.423	189	35	2	2230	2417	32208265	32208452	4.900000e-30	143.0

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	TraesCS6A01G290500	chr6A	522054697	522059392	4695	False	8672	8672	100.0000	1	4696	1	chr6A.!!$F1	4695
1	TraesCS6A01G290500	chr6D	380569474	380573155	3681	False	4955	4955	91.0980	1032	4696	1	chr6D.!!$F1	3664
2	TraesCS6A01G290500	chr6B	5767371	5770013	2642	False	2623	2623	84.6210	1034	3678	1	chr6B.!!$F1	2644
3	TraesCS6A01G290500	chr6B	567849647	567852771	3124	False	2297	4159	91.2195	1514	4696	2	chr6B.!!$F3	3182
4	TraesCS6A01G290500	chr6B	21014392	21015434	1042	True	1434	1434	91.7140	1	1032	1	chr6B.!!$R1	1031
5	TraesCS6A01G290500	chr6B	47297117	47299409	2292	True	1022	1022	74.9890	1155	3448	1	chr6B.!!$R2	2293
6	TraesCS6A01G290500	chr3B	344309270	344310308	1038	True	1845	1845	98.7490	1	1038	1	chr3B.!!$R2	1037
7	TraesCS6A01G290500	chr2B	673228900	673229933	1033	True	1814	1814	98.3560	1	1032	1	chr2B.!!$R2	1031
8	TraesCS6A01G290500	chr2B	759271403	759272455	1052	False	1541	1541	93.2960	1	1041	1	chr2B.!!$F2	1040
9	TraesCS6A01G290500	chr2B	19869097	19870136	1039	True	1382	1382	90.8400	1	1032	1	chr2B.!!$R1	1031
10	TraesCS6A01G290500	chr2B	714494122	714496017	1895	False	935	935	75.8330	1766	3665	1	chr2B.!!$F1	1899
11	TraesCS6A01G290500	chr2B	788840770	788842304	1534	True	928	928	77.8210	2113	3658	1	chr2B.!!$R3	1545
12	TraesCS6A01G290500	chr1A	324860014	324861068	1054	False	1711	1711	96.3030	1	1032	1	chr1A.!!$F1	1031
13	TraesCS6A01G290500	chr1B	673918037	673919080	1043	True	1657	1657	95.5110	1	1032	1	chr1B.!!$R1	1031
14	TraesCS6A01G290500	chr1B	661049626	661050679	1053	False	1140	1140	86.6040	1	1032	1	chr1B.!!$F1	1031
15	TraesCS6A01G290500	chr7B	665497521	665498561	1040	True	1496	1496	92.8300	4	1032	1	chr7B.!!$R1	1028
16	TraesCS6A01G290500	chr2D	590065106	590066975	1869	False	917	917	75.9110	1766	3665	1	chr2D.!!$F1	1899
17	TraesCS6A01G290500	chr2D	646490173	646491110	937	False	743	743	81.0780	2238	3178	1	chr2D.!!$F2	940
18	TraesCS6A01G290500	chr5A	688246247	688247102	855	True	468	468	77.0020	2819	3675	1	chr5A.!!$R1	856
19	TraesCS6A01G290500	chr5B	694006805	694007445	640	True	459	459	79.6270	2530	3170	1	chr5B.!!$R1	640

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
135	136	1.227674	GCACCTATCCCGCTGAAGG	60.228	63.158	0.00	0.00	35.14	3.46	F
1072	1135	0.323360	TAGCCTCCCCATGTTGCAAC	60.323	55.000	22.83	22.83	0.00	4.17	F
1144	1207	0.179062	ATCGTCCCAGCATCTTCAGC	60.179	55.000	0.00	0.00	0.00	4.26	F
1375	1439	0.310854	GACTTGGTTGCACCTTTCGG	59.689	55.000	6.83	0.00	39.58	4.30	F
2971	3035	0.248621	GGACATTATGCTTGGCGTGC	60.249	55.000	0.00	0.00	0.00	5.34	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1142	1205	0.250295	TGCAGCAACGGAAAGTAGCT	60.250	50.000	0.00	0.00	35.63	3.32	R
1915	1979	1.064758	GGTGAGGTTGTCCATGGCATA	60.065	52.381	6.96	0.00	35.89	3.14	R
2971	3035	1.134280	CAGGTACTCCATTGCCTCTGG	60.134	57.143	0.00	0.00	34.60	3.86	R
3267	3356	1.419012	TCCCATGAATGCTAGCTCTGG	59.581	52.381	17.23	13.95	0.00	3.86	R
4640	4779	0.392998	AGGTTATCAGCAACAGCCGG	60.393	55.000	0.00	0.00	0.00	6.13	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
67	68	4.196626	TCACCACTAAATCCTTGTACGG	57.803	45.455	0.00	0.00	0.00	4.02
135	136	1.227674	GCACCTATCCCGCTGAAGG	60.228	63.158	0.00	0.00	35.14	3.46
1018	1081	4.463050	TTAATGGAAAGGGGTTGTGAGT	57.537	40.909	0.00	0.00	0.00	3.41
1041	1104	5.817784	TCCGGTTGGAAAAATATACCAGAA	58.182	37.500	0.00	0.00	42.85	3.02
1072	1135	0.323360	TAGCCTCCCCATGTTGCAAC	60.323	55.000	22.83	22.83	0.00	4.17
1073	1136	1.907807	GCCTCCCCATGTTGCAACA	60.908	57.895	32.78	32.78	44.06	3.33
1087	1150	7.434307	CCATGTTGCAACAATTTGATCTCTATC	59.566	37.037	34.06	0.45	43.03	2.08
1128	1191	1.321805	TTCCATTGGGCCTTGCATCG	61.322	55.000	4.53	0.00	0.00	3.84
1130	1193	1.434696	CATTGGGCCTTGCATCGTC	59.565	57.895	4.53	0.00	0.00	4.20
1137	1200	1.452651	CCTTGCATCGTCCCAGCAT	60.453	57.895	0.00	0.00	38.19	3.79
1142	1205	0.462581	GCATCGTCCCAGCATCTTCA	60.463	55.000	0.00	0.00	0.00	3.02
1144	1207	0.179062	ATCGTCCCAGCATCTTCAGC	60.179	55.000	0.00	0.00	0.00	4.26
1145	1208	1.220206	CGTCCCAGCATCTTCAGCT	59.780	57.895	0.00	0.00	44.62	4.24
1150	1213	2.573462	TCCCAGCATCTTCAGCTACTTT	59.427	45.455	0.00	0.00	41.14	2.66
1151	1214	2.941720	CCCAGCATCTTCAGCTACTTTC	59.058	50.000	0.00	0.00	41.14	2.62
1153	1216	2.606725	CAGCATCTTCAGCTACTTTCCG	59.393	50.000	0.00	0.00	41.14	4.30
1185	1248	1.750778	CTATTTGTGGATGTGGTGCCC	59.249	52.381	0.00	0.00	0.00	5.36
1186	1249	1.250154	ATTTGTGGATGTGGTGCCCG	61.250	55.000	0.00	0.00	0.00	6.13
1187	1250	2.632602	TTTGTGGATGTGGTGCCCGT	62.633	55.000	0.00	0.00	0.00	5.28
1215	1278	2.928116	GGCTAAGCTACCACAACTTACG	59.072	50.000	0.00	0.00	0.00	3.18
1216	1279	2.347755	GCTAAGCTACCACAACTTACGC	59.652	50.000	0.00	0.00	0.00	4.42
1232	1295	4.161565	ACTTACGCTGATTTCTATGGGTGA	59.838	41.667	0.00	0.00	0.00	4.02
1257	1320	2.421739	CTAGTTGGCCCGATCCCG	59.578	66.667	0.00	0.00	0.00	5.14
1286	1350	3.438216	TGGAAATCTCACCATGCTCAA	57.562	42.857	0.00	0.00	0.00	3.02
1288	1352	3.245016	TGGAAATCTCACCATGCTCAACT	60.245	43.478	0.00	0.00	0.00	3.16
1302	1366	2.670414	GCTCAACTTCCTTGACATCTCG	59.330	50.000	0.00	0.00	33.65	4.04
1312	1376	3.056821	CCTTGACATCTCGTACTCCAACA	60.057	47.826	0.00	0.00	0.00	3.33
1356	1420	3.475566	TTGGGAGAACTGAGACAACTG	57.524	47.619	0.00	0.00	0.00	3.16
1363	1427	3.452627	AGAACTGAGACAACTGACTTGGT	59.547	43.478	0.00	0.00	33.66	3.67
1375	1439	0.310854	GACTTGGTTGCACCTTTCGG	59.689	55.000	6.83	0.00	39.58	4.30
1394	1458	3.576982	TCGGACAATCAACTAACAGGTCT	59.423	43.478	0.00	0.00	0.00	3.85
1398	1462	6.571731	CGGACAATCAACTAACAGGTCTCTTA	60.572	42.308	0.00	0.00	0.00	2.10
1448	1512	6.824305	AATGTCTGTCTTAAGTTTGGGATG	57.176	37.500	1.63	0.00	0.00	3.51
1454	1518	4.941263	TGTCTTAAGTTTGGGATGGAATCG	59.059	41.667	1.63	0.00	46.86	3.34
1481	1545	0.320160	GGACCAGTACCGTCAACACC	60.320	60.000	11.61	0.00	31.55	4.16
1564	1628	2.086251	TTTCTTGGCCAGCCTTTGCG	62.086	55.000	5.11	0.00	44.33	4.85
1660	1724	4.128643	CCTCTCGACTAACCTGGTAGTAG	58.871	52.174	0.00	1.49	34.40	2.57
1729	1793	7.221067	CACTATCAAATCTTAGTGGTCTTCGTC	59.779	40.741	2.83	0.00	40.94	4.20
1813	1877	0.820226	TCTCCAGGCACTTGATCTCG	59.180	55.000	0.00	0.00	34.60	4.04
1915	1979	6.898171	ATATGTTATCTGGCTCCATACCAT	57.102	37.500	0.00	0.00	36.36	3.55
1925	1989	2.025981	GCTCCATACCATATGCCATGGA	60.026	50.000	24.23	24.23	43.60	3.41
1945	2009	3.003480	GACAACCTCACCATGTTAGAGC	58.997	50.000	0.00	0.00	0.00	4.09
1995	2059	4.870426	TCTTCGACAATACCATCAAGCTTC	59.130	41.667	0.00	0.00	0.00	3.86
2064	2128	4.895668	AACCGGTACATTACCTTCTGAA	57.104	40.909	8.00	0.00	46.81	3.02
2094	2158	5.682869	CATATGCAAAGTATGGACGTGATG	58.317	41.667	0.00	0.00	29.34	3.07
2117	2181	5.425539	TGGATCTTTCTAGTAACCTCTTGGG	59.574	44.000	0.00	0.00	41.89	4.12
2139	2203	3.440522	GTGGTAGCCTTCCAAGTTCATTC	59.559	47.826	0.00	0.00	36.68	2.67
2183	2247	8.842358	TTAACCTACCTAAATCTTTCACACAG	57.158	34.615	0.00	0.00	0.00	3.66
2894	2958	4.464008	CTTCAGTACATGCCCAATGGTAT	58.536	43.478	0.00	0.00	40.94	2.73
2971	3035	0.248621	GGACATTATGCTTGGCGTGC	60.249	55.000	0.00	0.00	0.00	5.34
3192	3269	7.979537	GGTATGTACTTGTTATGATCACACAGA	59.020	37.037	0.00	0.00	0.00	3.41
3525	3626	2.430694	TCATCGTCGTCATCCTCCATTT	59.569	45.455	0.00	0.00	0.00	2.32
3558	3659	6.148811	TGGAAACTTTCTTGTGTCGATATTCC	59.851	38.462	1.57	0.00	33.70	3.01
3641	3742	5.506649	GGTCGTGAGGCTCAAAAACATTAAA	60.507	40.000	20.62	0.00	34.89	1.52
3735	3836	8.344831	TGCATCTATGTAGTGCATAATTTTCAC	58.655	33.333	2.42	0.00	43.30	3.18
3745	3846	7.147976	AGTGCATAATTTTCACTTTTCCACTC	58.852	34.615	0.00	0.00	37.78	3.51
3944	4055	8.258708	TCATCCAATAATGCAATGATTTGTGAA	58.741	29.630	0.00	0.00	35.17	3.18
4042	4153	1.266718	TCGAAAGTTGACATGCCTTGC	59.733	47.619	0.00	0.00	0.00	4.01
4075	4186	4.887748	TGGCTTATGCTCTGCTATAGAAC	58.112	43.478	3.21	0.00	39.59	3.01
4087	4198	2.032620	CTATAGAACGGGGCAGTGAGT	58.967	52.381	0.00	0.00	0.00	3.41
4088	4199	0.537188	ATAGAACGGGGCAGTGAGTG	59.463	55.000	0.00	0.00	0.00	3.51
4148	4259	9.988350	CACATAGGTACACATGAGTAAAAATTC	57.012	33.333	4.46	0.00	0.00	2.17
4211	4322	3.821033	GCCTGTTGTGATTTACTTCCTGT	59.179	43.478	0.00	0.00	0.00	4.00
4272	4383	1.808411	TCTTCAGTTTAAGCTGCCGG	58.192	50.000	13.99	0.00	36.49	6.13
4273	4384	0.169009	CTTCAGTTTAAGCTGCCGGC	59.831	55.000	22.73	22.73	42.19	6.13
4298	4409	6.270815	GTCGTTACTATGTGGCTTGAATCTA	58.729	40.000	0.00	0.00	0.00	1.98
4365	4478	6.473758	GTTTAGATCCCTAGACCTTTGTGTT	58.526	40.000	0.00	0.00	0.00	3.32
4369	4482	4.612264	TCCCTAGACCTTTGTGTTACAC	57.388	45.455	8.76	8.76	34.56	2.90
4370	4483	3.968649	TCCCTAGACCTTTGTGTTACACA	59.031	43.478	14.73	14.73	43.02	3.72
4390	4503	0.380378	TGTGGAGCGTCAACAAAAGC	59.620	50.000	0.00	0.00	0.00	3.51
4393	4506	1.452145	GGAGCGTCAACAAAAGCCCA	61.452	55.000	0.00	0.00	0.00	5.36
4412	4525	3.002656	CCCATGCGTTGTCTATGATGTTC	59.997	47.826	0.00	0.00	0.00	3.18
4414	4527	2.267426	TGCGTTGTCTATGATGTTCCG	58.733	47.619	0.00	0.00	0.00	4.30
4417	4530	2.029244	CGTTGTCTATGATGTTCCGCAC	59.971	50.000	0.00	0.00	0.00	5.34
4451	4564	3.006247	CAGTAAGAAGCTTTCAGAGGGC	58.994	50.000	0.00	0.00	0.00	5.19
4561	4700	1.066430	CCCATTCGGAACTTCCTTCGA	60.066	52.381	6.25	0.00	33.30	3.71
4582	4721	7.095695	TCGAAATTTTGAAGTCTTTTCTGGT	57.904	32.000	5.60	0.00	0.00	4.00
4603	4742	4.158384	GTTGATGTTTATGCTTCACACCG	58.842	43.478	0.00	0.00	0.00	4.94
4623	4762	2.623416	CGTTTCTCCCCTCTTTTGCTTT	59.377	45.455	0.00	0.00	0.00	3.51
4630	4769	4.482990	TCCCCTCTTTTGCTTTGAGATTT	58.517	39.130	0.00	0.00	0.00	2.17
4640	4779	4.801891	TGCTTTGAGATTTCTGCATGTTC	58.198	39.130	0.00	0.00	0.00	3.18

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
67	68	0.322008	CAGGTTTCTCTCCAGCCACC	60.322	60.000	0.00	0.00	0.00	4.61
135	136	4.948847	AGTTGCCAAAGGAAAATCTTGAC	58.051	39.130	0.00	0.00	0.00	3.18
285	286	3.365265	CAGCGTCCCCCAAACTGC	61.365	66.667	0.00	0.00	0.00	4.40
1018	1081	5.438698	TCTGGTATATTTTTCCAACCGGA	57.561	39.130	9.46	0.00	42.05	5.14
1041	1104	3.527665	TGGGGAGGCTAAAGCTTCTATTT	59.472	43.478	13.03	0.00	45.19	1.40
1056	1119	1.269012	ATTGTTGCAACATGGGGAGG	58.731	50.000	31.48	0.00	38.95	4.30
1087	1150	4.829064	TTTGACCCTCGAATTTGTTCTG	57.171	40.909	0.00	0.00	0.00	3.02
1128	1191	1.484240	AGTAGCTGAAGATGCTGGGAC	59.516	52.381	0.00	0.00	41.32	4.46
1130	1193	2.706339	AAGTAGCTGAAGATGCTGGG	57.294	50.000	0.00	0.00	41.32	4.45
1137	1200	2.037251	AGCAACGGAAAGTAGCTGAAGA	59.963	45.455	0.00	0.00	33.67	2.87
1142	1205	0.250295	TGCAGCAACGGAAAGTAGCT	60.250	50.000	0.00	0.00	35.63	3.32
1144	1207	3.189287	AGATTTGCAGCAACGGAAAGTAG	59.811	43.478	7.54	0.00	29.26	2.57
1145	1208	3.146066	AGATTTGCAGCAACGGAAAGTA	58.854	40.909	7.54	0.00	29.26	2.24
1150	1213	4.095410	CAAATAGATTTGCAGCAACGGA	57.905	40.909	7.54	0.00	40.42	4.69
1208	1271	4.876107	CACCCATAGAAATCAGCGTAAGTT	59.124	41.667	0.00	0.00	41.68	2.66
1215	1278	4.498682	GCATTGTCACCCATAGAAATCAGC	60.499	45.833	0.00	0.00	0.00	4.26
1216	1279	4.037208	GGCATTGTCACCCATAGAAATCAG	59.963	45.833	0.00	0.00	0.00	2.90
1257	1320	1.200948	GTGAGATTTCCAAGCACAGGC	59.799	52.381	0.00	0.00	41.61	4.85
1286	1350	3.444388	GGAGTACGAGATGTCAAGGAAGT	59.556	47.826	0.00	0.00	0.00	3.01
1288	1352	3.427573	TGGAGTACGAGATGTCAAGGAA	58.572	45.455	0.00	0.00	0.00	3.36
1375	1439	6.590677	GGTAAGAGACCTGTTAGTTGATTGTC	59.409	42.308	0.00	0.00	45.89	3.18
1418	1482	9.533253	CCAAACTTAAGACAGACATTTTTGAAT	57.467	29.630	10.09	0.00	0.00	2.57
1419	1483	7.978975	CCCAAACTTAAGACAGACATTTTTGAA	59.021	33.333	10.09	0.00	0.00	2.69
1432	1496	4.335594	CCGATTCCATCCCAAACTTAAGAC	59.664	45.833	10.09	0.00	0.00	3.01
1438	1502	0.625849	AGCCGATTCCATCCCAAACT	59.374	50.000	0.00	0.00	0.00	2.66
1448	1512	1.153349	GGTCCAGTCAGCCGATTCC	60.153	63.158	0.00	0.00	0.00	3.01
1454	1518	1.597461	GGTACTGGTCCAGTCAGCC	59.403	63.158	28.07	22.38	41.21	4.85
1481	1545	4.080863	ACACTAGAGGCCTGTTATTTCCAG	60.081	45.833	12.00	0.00	0.00	3.86
1500	1564	9.072375	TGATTCTCTCGAATATCAAGATACACT	57.928	33.333	0.00	0.00	39.89	3.55
1564	1628	2.607038	GGGTTTGAAGTTGCCGACAATC	60.607	50.000	0.00	0.00	38.27	2.67
1632	1696	2.097142	CAGGTTAGTCGAGAGGTTACCG	59.903	54.545	0.00	0.00	0.00	4.02
1660	1724	7.120789	CCAAATGGTTATTCTTTGCTTCAAC	57.879	36.000	0.00	0.00	0.00	3.18
1693	1757	9.965902	ACTAAGATTTGATAGTGTTTCTGGAAT	57.034	29.630	0.00	0.00	31.35	3.01
1729	1793	5.452078	TGGTTGTTGGAAAAGCTTATCAG	57.548	39.130	0.00	0.00	0.00	2.90
1813	1877	2.101415	GGCCAACCATTCTATTTCCAGC	59.899	50.000	0.00	0.00	35.26	4.85
1886	1950	3.997021	GGAGCCAGATAACATATTGTCCG	59.003	47.826	0.00	0.00	0.00	4.79
1915	1979	1.064758	GGTGAGGTTGTCCATGGCATA	60.065	52.381	6.96	0.00	35.89	3.14
1925	1989	2.371841	TGCTCTAACATGGTGAGGTTGT	59.628	45.455	10.82	0.00	0.00	3.32
1995	2059	9.449719	AGTTGGATAAGGTTACTGTGATAAAAG	57.550	33.333	0.00	0.00	0.00	2.27
2089	2153	7.354751	AGAGGTTACTAGAAAGATCCATCAC	57.645	40.000	0.00	0.00	0.00	3.06
2090	2154	7.147655	CCAAGAGGTTACTAGAAAGATCCATCA	60.148	40.741	0.00	0.00	0.00	3.07
2094	2158	5.919755	CCCAAGAGGTTACTAGAAAGATCC	58.080	45.833	0.00	0.00	0.00	3.36
2117	2181	2.561478	TGAACTTGGAAGGCTACCAC	57.439	50.000	0.00	0.00	37.13	4.16
2139	2203	1.750193	ATAACATGGCAACCTGTCCG	58.250	50.000	0.00	0.00	45.33	4.79
2280	2344	5.267587	AGGTAGGTGAAGTTAACGAGGTAT	58.732	41.667	0.00	0.00	0.00	2.73
2682	2746	5.352846	GCCTTTGAAAACTTTGCCAAAACTA	59.647	36.000	0.00	0.00	0.00	2.24
2894	2958	1.140652	TGTGCAAGTGTGTCTCCATGA	59.859	47.619	0.00	0.00	0.00	3.07
2971	3035	1.134280	CAGGTACTCCATTGCCTCTGG	60.134	57.143	0.00	0.00	34.60	3.86
3267	3356	1.419012	TCCCATGAATGCTAGCTCTGG	59.581	52.381	17.23	13.95	0.00	3.86
3525	3626	3.960102	ACAAGAAAGTTTCCATTGCAGGA	59.040	39.130	12.05	0.00	35.41	3.86
3558	3659	1.135257	CGAACACTCTAGACCCAGCTG	60.135	57.143	6.78	6.78	0.00	4.24
3641	3742	4.400567	GCCATGAAAGCAGAGTAATCCTTT	59.599	41.667	0.00	0.00	0.00	3.11
3771	3881	2.749621	CCTCTTTCCACAGGTGTATTGC	59.250	50.000	0.00	0.00	0.00	3.56
3781	3891	3.831323	TGCAGAAAATCCTCTTTCCACA	58.169	40.909	0.00	0.00	36.18	4.17
3896	4007	9.901724	GATGAATCTTTACAAGTACACATTACG	57.098	33.333	0.00	0.00	0.00	3.18
3970	4081	7.121974	ACTCAAGATGAAAACACACTATTCG	57.878	36.000	0.00	0.00	0.00	3.34
4023	4134	1.689959	GCAAGGCATGTCAACTTTCG	58.310	50.000	0.00	0.00	0.00	3.46
4042	4153	2.742053	AGCATAAGCCAACACAACTACG	59.258	45.455	0.00	0.00	43.56	3.51
4087	4198	5.670485	AGTGAATAACTGAATATCCGTGCA	58.330	37.500	0.00	0.00	37.88	4.57
4148	4259	3.535561	ACGGTTCCTGATTGATGCTAAG	58.464	45.455	0.00	0.00	0.00	2.18
4184	4295	2.554032	AGTAAATCACAACAGGCAGTGC	59.446	45.455	6.55	6.55	35.76	4.40
4211	4322	6.358974	TGAATGATGAACTCTCTTGTGGTA	57.641	37.500	0.00	0.00	0.00	3.25
4272	4383	1.323534	CAAGCCACATAGTAACGACGC	59.676	52.381	0.00	0.00	0.00	5.19
4273	4384	2.871133	TCAAGCCACATAGTAACGACG	58.129	47.619	0.00	0.00	0.00	5.12
4298	4409	7.341445	TCACTACCAGTTTTAGTGCAAATTT	57.659	32.000	4.89	0.00	44.18	1.82
4365	4478	1.069358	TGTTGACGCTCCACATGTGTA	59.931	47.619	23.79	8.12	0.00	2.90
4369	4482	2.653890	CTTTTGTTGACGCTCCACATG	58.346	47.619	0.00	0.00	0.00	3.21
4370	4483	1.001378	GCTTTTGTTGACGCTCCACAT	60.001	47.619	0.00	0.00	0.00	3.21
4390	4503	2.564771	ACATCATAGACAACGCATGGG	58.435	47.619	8.44	8.44	0.00	4.00
4393	4506	2.866156	CGGAACATCATAGACAACGCAT	59.134	45.455	0.00	0.00	0.00	4.73
4412	4525	2.162208	ACTGCAGAAATAACATGTGCGG	59.838	45.455	23.35	4.17	44.52	5.69
4414	4527	6.182039	TCTTACTGCAGAAATAACATGTGC	57.818	37.500	23.35	0.00	34.62	4.57
4417	4530	7.081526	AGCTTCTTACTGCAGAAATAACATG	57.918	36.000	23.35	0.56	32.24	3.21
4540	4679	1.066430	CGAAGGAAGTTCCGAATGGGA	60.066	52.381	16.31	0.00	42.75	4.37
4561	4700	9.101655	CATCAACCAGAAAAGACTTCAAAATTT	57.898	29.630	0.00	0.00	0.00	1.82
4582	4721	3.818210	ACGGTGTGAAGCATAAACATCAA	59.182	39.130	0.00	0.00	0.00	2.57
4603	4742	3.636764	TCAAAGCAAAAGAGGGGAGAAAC	59.363	43.478	0.00	0.00	0.00	2.78
4623	4762	2.358957	CCGGAACATGCAGAAATCTCA	58.641	47.619	0.00	0.00	0.00	3.27
4630	4769	1.073025	AACAGCCGGAACATGCAGA	59.927	52.632	5.05	0.00	0.00	4.26
4640	4779	0.392998	AGGTTATCAGCAACAGCCGG	60.393	55.000	0.00	0.00	0.00	6.13

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.