AutoCloner

Multiple sequence alignment - TraesCS4D01G198900

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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	TraesCS4D01G198900	chr4D	100.000	4173	0	0	1	4173	345432862	345428690	0.000000e+00	7707
1	TraesCS4D01G198900	chr4D	90.216	603	49	3	63	664	223879209	223879802	0.000000e+00	778
2	TraesCS4D01G198900	chr4A	94.017	2390	84	22	1791	4158	120140986	120143338	0.000000e+00	3567
3	TraesCS4D01G198900	chr4A	91.419	1142	62	13	665	1775	120139794	120140930	0.000000e+00	1533
4	TraesCS4D01G198900	chr4B	94.552	1854	52	10	2219	4050	427070406	427068580	0.000000e+00	2819
5	TraesCS4D01G198900	chr4B	88.992	972	56	25	665	1596	427073090	427072130	0.000000e+00	1155
6	TraesCS4D01G198900	chr4B	96.441	562	16	2	1664	2224	427071049	427070491	0.000000e+00	924
7	TraesCS4D01G198900	chr4B	93.671	79	3	2	1589	1665	427071965	427071887	2.640000e-22	117
8	TraesCS4D01G198900	chr3D	93.514	663	42	1	3	664	71973699	71974361	0.000000e+00	985
9	TraesCS4D01G198900	chr6D	92.632	665	30	8	1	664	377542424	377541778	0.000000e+00	939
10	TraesCS4D01G198900	chr7B	91.811	635	43	7	2847	3473	486675988	486675355	0.000000e+00	876
11	TraesCS4D01G198900	chr5B	91.866	627	45	5	2853	3473	237114367	237113741	0.000000e+00	870
12	TraesCS4D01G198900	chr2B	91.892	629	42	8	2853	3473	51991109	51990482	0.000000e+00	870
13	TraesCS4D01G198900	chr1A	91.733	629	41	9	2853	3473	453782631	453783256	0.000000e+00	863
14	TraesCS4D01G198900	chr5A	91.415	629	45	8	2853	3473	603010077	603009450	0.000000e+00	854
15	TraesCS4D01G198900	chr5A	89.139	488	37	2	1	487	469071154	469071626	9.990000e-166	593
16	TraesCS4D01G198900	chr3B	91.181	635	38	8	2853	3470	188239526	188240159	0.000000e+00	846
17	TraesCS4D01G198900	chr6A	89.387	669	56	3	1	664	601670150	601669492	0.000000e+00	828
18	TraesCS4D01G198900	chr6A	92.197	487	37	1	1	486	24835936	24835450	0.000000e+00	688
19	TraesCS4D01G198900	chr1B	88.889	630	41	14	2853	3473	216531527	216530918	0.000000e+00	749
20	TraesCS4D01G198900	chr7D	87.302	630	45	12	2853	3473	70124354	70124957	0.000000e+00	688
21	TraesCS4D01G198900	chr7A	92.324	482	36	1	7	487	200063464	200063945	0.000000e+00	684
22	TraesCS4D01G198900	chr6B	91.803	488	38	2	1	487	227837691	227838177	0.000000e+00	678
23	TraesCS4D01G198900	chr6B	90.349	487	47	0	1	487	578656959	578657445	1.270000e-179	640
24	TraesCS4D01G198900	chr2A	91.811	403	32	1	86	487	51544657	51544255	1.010000e-155	560
25	TraesCS4D01G198900	chr5D	87.677	495	30	6	1	487	95957338	95957809	7.890000e-152	547

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	TraesCS4D01G198900	chr4D	345428690	345432862	4172	True	7707.00	7707	100.000	1	4173	1	chr4D.!!$R1	4172
1	TraesCS4D01G198900	chr4D	223879209	223879802	593	False	778.00	778	90.216	63	664	1	chr4D.!!$F1	601
2	TraesCS4D01G198900	chr4A	120139794	120143338	3544	False	2550.00	3567	92.718	665	4158	2	chr4A.!!$F1	3493
3	TraesCS4D01G198900	chr4B	427068580	427073090	4510	True	1253.75	2819	93.414	665	4050	4	chr4B.!!$R1	3385
4	TraesCS4D01G198900	chr3D	71973699	71974361	662	False	985.00	985	93.514	3	664	1	chr3D.!!$F1	661
5	TraesCS4D01G198900	chr6D	377541778	377542424	646	True	939.00	939	92.632	1	664	1	chr6D.!!$R1	663
6	TraesCS4D01G198900	chr7B	486675355	486675988	633	True	876.00	876	91.811	2847	3473	1	chr7B.!!$R1	626
7	TraesCS4D01G198900	chr5B	237113741	237114367	626	True	870.00	870	91.866	2853	3473	1	chr5B.!!$R1	620
8	TraesCS4D01G198900	chr2B	51990482	51991109	627	True	870.00	870	91.892	2853	3473	1	chr2B.!!$R1	620
9	TraesCS4D01G198900	chr1A	453782631	453783256	625	False	863.00	863	91.733	2853	3473	1	chr1A.!!$F1	620
10	TraesCS4D01G198900	chr5A	603009450	603010077	627	True	854.00	854	91.415	2853	3473	1	chr5A.!!$R1	620
11	TraesCS4D01G198900	chr3B	188239526	188240159	633	False	846.00	846	91.181	2853	3470	1	chr3B.!!$F1	617
12	TraesCS4D01G198900	chr6A	601669492	601670150	658	True	828.00	828	89.387	1	664	1	chr6A.!!$R2	663
13	TraesCS4D01G198900	chr1B	216530918	216531527	609	True	749.00	749	88.889	2853	3473	1	chr1B.!!$R1	620
14	TraesCS4D01G198900	chr7D	70124354	70124957	603	False	688.00	688	87.302	2853	3473	1	chr7D.!!$F1	620

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
131	132	0.944386	GGAAGCAAGACAACGAGCAA	59.056	50.000	0.00	0.00	0.00	3.91	F
196	197	1.443872	GCCGAACAGTCGTCGTCAT	60.444	57.895	0.00	0.00	46.21	3.06	F
491	499	1.684983	GGCGTGGTTATCAGCCTACTA	59.315	52.381	0.00	0.00	45.67	1.82	F
528	541	2.136298	TGGCTGTCCTGAAACAACAA	57.864	45.000	0.00	0.00	0.00	2.83	F
1456	1521	2.287608	GCTTCCTTTGTTCCAACCGAAG	60.288	50.000	7.41	7.41	0.00	3.79	F
1463	1528	0.240945	GTTCCAACCGAAGTGCATGG	59.759	55.000	0.00	0.00	0.00	3.66	F
1471	1536	1.609061	CCGAAGTGCATGGTCTGTTCT	60.609	52.381	0.00	0.00	0.00	3.01	F
2304	3514	1.680314	CTGCCCTTTCCCTGGAAGC	60.680	63.158	0.00	0.61	35.38	3.86	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1444	1509	0.240945	CCATGCACTTCGGTTGGAAC	59.759	55.000	0.00	0.00	0.00	3.62	R
1447	1512	0.606401	AGACCATGCACTTCGGTTGG	60.606	55.000	0.00	0.00	31.63	3.77	R
1457	1522	1.948834	CACACAAGAACAGACCATGCA	59.051	47.619	0.00	0.00	0.00	3.96	R
1459	1524	1.948834	TGCACACAAGAACAGACCATG	59.051	47.619	0.00	0.00	0.00	3.66	R
2592	3806	2.098934	ACATGCTCTGAGATCGACTGAC	59.901	50.000	9.28	0.00	0.00	3.51	R
2630	3844	2.360475	GTGGCTTGGGAGTCTGCC	60.360	66.667	2.82	2.82	45.10	4.85	R
2971	4200	3.644884	TTCGGTGAGAACTCTGAGAAC	57.355	47.619	12.44	4.83	33.14	3.01	R
3593	4849	4.175962	TCTTGGGTTCCCTCAGATTACTT	58.824	43.478	9.43	0.00	0.00	2.24	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
131	132	0.944386	GGAAGCAAGACAACGAGCAA	59.056	50.000	0.00	0.00	0.00	3.91
196	197	1.443872	GCCGAACAGTCGTCGTCAT	60.444	57.895	0.00	0.00	46.21	3.06
420	427	5.220381	GTTTCGCTCGTGATAAGGATATCA	58.780	41.667	4.83	0.00	44.38	2.15
491	499	1.684983	GGCGTGGTTATCAGCCTACTA	59.315	52.381	0.00	0.00	45.67	1.82
497	510	5.243283	CGTGGTTATCAGCCTACTATTACCT	59.757	44.000	0.00	0.00	0.00	3.08
528	541	2.136298	TGGCTGTCCTGAAACAACAA	57.864	45.000	0.00	0.00	0.00	2.83
588	601	2.333938	ACGTTGTCGACCGTCTGG	59.666	61.111	14.12	0.00	40.62	3.86
681	694	3.110293	TCCGGAAGAAATAGTGGAGGA	57.890	47.619	0.00	0.00	0.00	3.71
690	703	7.066404	GGAAGAAATAGTGGAGGAGTCAAAATC	59.934	40.741	0.00	0.00	0.00	2.17
910	937	3.710722	CAGCCACGCCTCCTCCTT	61.711	66.667	0.00	0.00	0.00	3.36
948	985	4.643733	CGATTAGCAGAGAGGCCG	57.356	61.111	0.00	0.00	0.00	6.13
1025	1064	2.767960	GGATACTACTGGTTTCCGGGAA	59.232	50.000	5.09	5.09	36.59	3.97
1206	1246	4.980590	TGCCGCTGTTGATTACTTAATTG	58.019	39.130	0.00	0.00	0.00	2.32
1208	1255	4.351192	CCGCTGTTGATTACTTAATTGCC	58.649	43.478	0.00	0.00	0.00	4.52
1218	1265	6.426937	TGATTACTTAATTGCCGATTAGCTCC	59.573	38.462	0.00	0.00	32.06	4.70
1259	1310	4.979815	TGTTGTGTTGTAGTGATAGTGTCG	59.020	41.667	0.00	0.00	0.00	4.35
1294	1345	5.599999	ATCATAGTATTAGCCCGATCACC	57.400	43.478	0.00	0.00	0.00	4.02
1320	1371	6.680625	GCATCTGAAATTCAAGATGCTGATGT	60.681	38.462	30.43	5.02	44.72	3.06
1336	1394	4.433022	GCTGATGTTCACTTTACTCGTTCG	60.433	45.833	0.00	0.00	0.00	3.95
1384	1442	4.214971	ACAGATTGCAGAACAGTGTGAATC	59.785	41.667	0.00	0.85	33.49	2.52
1456	1521	2.287608	GCTTCCTTTGTTCCAACCGAAG	60.288	50.000	7.41	7.41	0.00	3.79
1457	1522	2.721425	TCCTTTGTTCCAACCGAAGT	57.279	45.000	0.00	0.00	0.00	3.01
1459	1524	1.269051	CCTTTGTTCCAACCGAAGTGC	60.269	52.381	0.00	0.00	0.00	4.40
1460	1525	1.403679	CTTTGTTCCAACCGAAGTGCA	59.596	47.619	0.00	0.00	0.00	4.57
1463	1528	0.240945	GTTCCAACCGAAGTGCATGG	59.759	55.000	0.00	0.00	0.00	3.66
1471	1536	1.609061	CCGAAGTGCATGGTCTGTTCT	60.609	52.381	0.00	0.00	0.00	3.01
1482	1547	2.017049	GGTCTGTTCTTGTGTGCACTT	58.983	47.619	19.41	0.00	0.00	3.16
1527	1592	2.143925	GCATCTACAATAAGGACCGGC	58.856	52.381	0.00	0.00	0.00	6.13
1528	1593	2.484770	GCATCTACAATAAGGACCGGCA	60.485	50.000	0.00	0.00	0.00	5.69
1531	1596	4.497291	TCTACAATAAGGACCGGCATTT	57.503	40.909	0.00	0.00	0.00	2.32
1543	1608	4.475944	GACCGGCATTTATATTGTCATGC	58.524	43.478	0.00	0.00	41.17	4.06
1793	2913	7.425577	ACGTGTTAGTTCCTTTTTACATACC	57.574	36.000	0.00	0.00	0.00	2.73
1994	3114	9.498176	GAGTTAGATTAAAAAGGTCCTGTTACA	57.502	33.333	0.00	0.00	0.00	2.41
2044	3164	1.755179	ATGTGCACCTTGTGATAGGC	58.245	50.000	15.69	0.00	38.99	3.93
2148	3268	8.861086	CAGTAACCTATGACATCCTACTGTTAT	58.139	37.037	13.14	0.00	33.33	1.89
2304	3514	1.680314	CTGCCCTTTCCCTGGAAGC	60.680	63.158	0.00	0.61	35.38	3.86
2403	3617	4.404507	AAAATCGACGAAACATCCAGTG	57.595	40.909	0.00	0.00	0.00	3.66
2476	3690	9.803507	ATTACCCTTATTGTAAAGCTATTACCC	57.196	33.333	12.99	0.00	32.37	3.69
2477	3691	7.461633	ACCCTTATTGTAAAGCTATTACCCT	57.538	36.000	12.99	6.16	0.00	4.34
2478	3692	7.879558	ACCCTTATTGTAAAGCTATTACCCTT	58.120	34.615	12.99	0.00	0.00	3.95
2479	3693	9.006405	ACCCTTATTGTAAAGCTATTACCCTTA	57.994	33.333	12.99	0.00	0.00	2.69
2592	3806	7.481642	ACTTTGTTGACGTATGATCCTAGTAG	58.518	38.462	0.00	0.00	0.00	2.57
2841	4068	5.697633	GTGAAAACATCCACATTTGATTGCT	59.302	36.000	0.00	0.00	33.72	3.91
3246	4475	8.997621	TGGAAGTCTGTATTGTACATTTAGTC	57.002	34.615	0.00	0.00	38.15	2.59
3408	4649	7.361457	TGAAATACTGGGTCACCTAGAATAG	57.639	40.000	15.44	0.00	38.80	1.73
3454	4703	4.424061	TGCTCCTGATGTGAATTTTTCG	57.576	40.909	0.00	0.00	0.00	3.46
3513	4762	5.692204	GTGTGACCAACGGATCATCTAATAG	59.308	44.000	0.00	0.00	0.00	1.73
3519	4768	7.434492	ACCAACGGATCATCTAATAGTAGTTG	58.566	38.462	2.52	2.52	36.13	3.16
3520	4769	7.069578	ACCAACGGATCATCTAATAGTAGTTGT	59.930	37.037	7.85	0.00	35.03	3.32
3521	4770	8.573885	CCAACGGATCATCTAATAGTAGTTGTA	58.426	37.037	7.85	0.00	35.03	2.41
3522	4771	9.613957	CAACGGATCATCTAATAGTAGTTGTAG	57.386	37.037	7.85	2.63	33.00	2.74
3523	4772	8.338072	ACGGATCATCTAATAGTAGTTGTAGG	57.662	38.462	7.85	1.27	31.51	3.18
3524	4773	8.162085	ACGGATCATCTAATAGTAGTTGTAGGA	58.838	37.037	7.85	0.00	31.51	2.94
3593	4849	0.325602	TGGACATGTGCAGAGCATCA	59.674	50.000	16.89	0.00	41.91	3.07
3779	5039	1.812571	CTTTGCCGCTTACATTGGAGT	59.187	47.619	0.00	0.00	0.00	3.85
3941	5202	4.012374	TCAGACAAAGGCATTTCCATCTC	58.988	43.478	0.00	0.00	37.29	2.75
4038	5299	4.148348	GGCGATGCTAGTCTACAATTAACG	59.852	45.833	0.00	0.00	0.00	3.18
4040	5301	4.143803	CGATGCTAGTCTACAATTAACGCG	60.144	45.833	3.53	3.53	0.00	6.01
4050	5311	7.281549	AGTCTACAATTAACGCGGGAAAATTAT	59.718	33.333	12.47	2.53	0.00	1.28
4057	5318	3.551846	ACGCGGGAAAATTATCATTCCT	58.448	40.909	12.47	0.00	43.75	3.36
4065	5326	7.148086	CGGGAAAATTATCATTCCTCAAGACAA	60.148	37.037	6.60	0.00	43.75	3.18
4158	5420	9.880157	AATATTCAGAAATGCTGCTTACATTTT	57.120	25.926	11.61	1.86	45.33	1.82
4159	5421	7.591006	ATTCAGAAATGCTGCTTACATTTTG	57.409	32.000	11.61	11.33	45.33	2.44
4160	5422	6.088016	TCAGAAATGCTGCTTACATTTTGT	57.912	33.333	11.61	3.19	45.33	2.83
4161	5423	6.514947	TCAGAAATGCTGCTTACATTTTGTT	58.485	32.000	11.61	2.20	45.33	2.83
4162	5424	6.421501	TCAGAAATGCTGCTTACATTTTGTTG	59.578	34.615	11.61	10.74	45.33	3.33
4163	5425	6.421501	CAGAAATGCTGCTTACATTTTGTTGA	59.578	34.615	11.61	0.00	45.33	3.18
4164	5426	6.643770	AGAAATGCTGCTTACATTTTGTTGAG	59.356	34.615	11.61	0.00	45.33	3.02
4165	5427	4.241590	TGCTGCTTACATTTTGTTGAGG	57.758	40.909	0.00	0.00	0.00	3.86
4166	5428	3.888323	TGCTGCTTACATTTTGTTGAGGA	59.112	39.130	0.00	0.00	0.00	3.71
4167	5429	4.523943	TGCTGCTTACATTTTGTTGAGGAT	59.476	37.500	0.00	0.00	0.00	3.24
4168	5430	5.709631	TGCTGCTTACATTTTGTTGAGGATA	59.290	36.000	0.00	0.00	0.00	2.59
4169	5431	6.377996	TGCTGCTTACATTTTGTTGAGGATAT	59.622	34.615	0.00	0.00	0.00	1.63
4170	5432	7.555914	TGCTGCTTACATTTTGTTGAGGATATA	59.444	33.333	0.00	0.00	0.00	0.86
4171	5433	8.072567	GCTGCTTACATTTTGTTGAGGATATAG	58.927	37.037	0.00	0.00	0.00	1.31
4172	5434	7.930217	TGCTTACATTTTGTTGAGGATATAGC	58.070	34.615	0.00	0.00	0.00	2.97

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
91	92	2.543802	CGATCCAGCTAGTCGGCGA	61.544	63.158	4.99	4.99	37.29	5.54
97	98	1.739338	CTTCCGGCGATCCAGCTAGT	61.739	60.000	9.30	0.00	37.29	2.57
196	197	0.612174	AGCTCGTCCAGGCTTGTCTA	60.612	55.000	0.00	0.00	34.96	2.59
252	259	4.077184	CGGCTAACCCCTGCGTCA	62.077	66.667	0.00	0.00	0.00	4.35
437	445	3.183793	TCAGCTATTGACACGCATCAT	57.816	42.857	0.00	0.00	0.00	2.45
491	499	3.203040	AGCCATTCCTGCAACTAGGTAAT	59.797	43.478	0.00	0.00	38.99	1.89
497	510	1.340017	GGACAGCCATTCCTGCAACTA	60.340	52.381	0.00	0.00	36.29	2.24
528	541	2.887152	GTCCATTTTCCTGCAACTCACT	59.113	45.455	0.00	0.00	0.00	3.41
588	601	0.433492	CCGTTCGATCGTGTGTTGAC	59.567	55.000	15.94	3.37	0.00	3.18
642	655	4.320870	CGGAAAAAGCTTACCTTCTACCA	58.679	43.478	0.00	0.00	31.99	3.25
681	694	4.405358	TGCAAAGGTTTCTGGATTTTGACT	59.595	37.500	0.00	0.00	32.05	3.41
947	984	3.573491	GGATTCTTTCCCCGCGCG	61.573	66.667	25.67	25.67	38.75	6.86
948	985	1.715862	GAAGGATTCTTTCCCCGCGC	61.716	60.000	0.00	0.00	46.81	6.86
1025	1064	3.890674	GCCGTCGAGCCAAGAATT	58.109	55.556	0.00	0.00	0.00	2.17
1218	1265	0.732880	CAACCGTGAGACTAGTGGCG	60.733	60.000	0.00	0.00	0.00	5.69
1259	1310	8.581578	GCTAATACTATGATATTCTAGAGGGGC	58.418	40.741	0.00	0.00	0.00	5.80
1320	1371	3.713858	TGTCCGAACGAGTAAAGTGAA	57.286	42.857	0.00	0.00	0.00	3.18
1336	1394	3.462021	GTCCAGTAAGCAGATCATGTCC	58.538	50.000	0.00	0.00	0.00	4.02
1444	1509	0.240945	CCATGCACTTCGGTTGGAAC	59.759	55.000	0.00	0.00	0.00	3.62
1447	1512	0.606401	AGACCATGCACTTCGGTTGG	60.606	55.000	0.00	0.00	31.63	3.77
1456	1521	1.949525	ACACAAGAACAGACCATGCAC	59.050	47.619	0.00	0.00	0.00	4.57
1457	1522	1.948834	CACACAAGAACAGACCATGCA	59.051	47.619	0.00	0.00	0.00	3.96
1459	1524	1.948834	TGCACACAAGAACAGACCATG	59.051	47.619	0.00	0.00	0.00	3.66
1460	1525	1.949525	GTGCACACAAGAACAGACCAT	59.050	47.619	13.17	0.00	0.00	3.55
1463	1528	2.792542	GCAAGTGCACACAAGAACAGAC	60.793	50.000	21.04	0.00	41.59	3.51
1527	1592	9.970395	AACACTAATGGCATGACAATATAAATG	57.030	29.630	4.70	0.40	0.00	2.32
1543	1608	6.145338	ACGACCTGTATAGAACACTAATGG	57.855	41.667	0.00	0.00	33.45	3.16
1819	2939	8.895932	AAGAAACTAACATTTCGTTCATATGC	57.104	30.769	0.00	0.00	42.37	3.14
2044	3164	5.792741	TCTTCCTTTGGTGCCAAATTAATG	58.207	37.500	15.75	5.16	43.78	1.90
2403	3617	8.078596	ACTCTTCAATTTTGTCAATCTAGTTGC	58.921	33.333	0.00	0.00	37.74	4.17
2462	3676	7.660617	GGAGTTCCATAAGGGTAATAGCTTTAC	59.339	40.741	0.00	0.68	38.11	2.01
2463	3677	7.348801	TGGAGTTCCATAAGGGTAATAGCTTTA	59.651	37.037	0.00	0.00	42.01	1.85
2464	3678	6.159751	TGGAGTTCCATAAGGGTAATAGCTTT	59.840	38.462	0.00	0.00	42.01	3.51
2465	3679	5.670361	TGGAGTTCCATAAGGGTAATAGCTT	59.330	40.000	0.00	0.00	42.01	3.74
2466	3680	5.224441	TGGAGTTCCATAAGGGTAATAGCT	58.776	41.667	0.00	0.00	42.01	3.32
2467	3681	5.071923	ACTGGAGTTCCATAAGGGTAATAGC	59.928	44.000	0.48	0.00	46.46	2.97
2468	3682	6.749036	ACTGGAGTTCCATAAGGGTAATAG	57.251	41.667	0.48	0.00	46.46	1.73
2469	3683	7.133133	GAACTGGAGTTCCATAAGGGTAATA	57.867	40.000	8.14	0.00	46.42	0.98
2470	3684	6.002653	GAACTGGAGTTCCATAAGGGTAAT	57.997	41.667	8.14	0.00	46.42	1.89
2471	3685	5.431179	GAACTGGAGTTCCATAAGGGTAA	57.569	43.478	8.14	0.00	46.42	2.85
2577	3791	5.228665	TCGACTGACTACTAGGATCATACG	58.771	45.833	0.00	4.28	0.00	3.06
2592	3806	2.098934	ACATGCTCTGAGATCGACTGAC	59.901	50.000	9.28	0.00	0.00	3.51
2630	3844	2.360475	GTGGCTTGGGAGTCTGCC	60.360	66.667	2.82	2.82	45.10	4.85
2971	4200	3.644884	TTCGGTGAGAACTCTGAGAAC	57.355	47.619	12.44	4.83	33.14	3.01
3384	4625	6.901300	ACTATTCTAGGTGACCCAGTATTTCA	59.099	38.462	0.00	0.00	0.00	2.69
3408	4649	9.043079	CATAATCATGGATGCTGATCAGTATAC	57.957	37.037	24.81	24.81	35.27	1.47
3412	4656	4.700692	GCATAATCATGGATGCTGATCAGT	59.299	41.667	23.38	4.98	44.15	3.41
3454	4703	8.108551	TGAAGTTACTAGGAAGTGAGAACTAC	57.891	38.462	0.00	0.00	33.07	2.73
3520	4769	9.032624	GCTACCCATCACTAAATAATACTCCTA	57.967	37.037	0.00	0.00	0.00	2.94
3521	4770	7.735321	AGCTACCCATCACTAAATAATACTCCT	59.265	37.037	0.00	0.00	0.00	3.69
3522	4771	7.908453	AGCTACCCATCACTAAATAATACTCC	58.092	38.462	0.00	0.00	0.00	3.85
3523	4772	9.209175	CAAGCTACCCATCACTAAATAATACTC	57.791	37.037	0.00	0.00	0.00	2.59
3524	4773	8.714906	ACAAGCTACCCATCACTAAATAATACT	58.285	33.333	0.00	0.00	0.00	2.12
3593	4849	4.175962	TCTTGGGTTCCCTCAGATTACTT	58.824	43.478	9.43	0.00	0.00	2.24
3779	5039	5.912892	TGTAGACACACTCTGTTTTGATGA	58.087	37.500	0.00	0.00	31.03	2.92
3941	5202	4.916183	AGAAGTCCAATTTTCAGAGGGAG	58.084	43.478	0.00	0.00	0.00	4.30
4038	5299	5.299279	TCTTGAGGAATGATAATTTTCCCGC	59.701	40.000	3.47	0.00	41.99	6.13
4040	5301	7.645058	TGTCTTGAGGAATGATAATTTTCCC	57.355	36.000	3.47	0.00	41.99	3.97
4071	5332	7.725844	ACCAATTGTAGAAACTCTGGAGATTTT	59.274	33.333	4.43	0.00	30.96	1.82
4076	5337	6.884280	AAACCAATTGTAGAAACTCTGGAG	57.116	37.500	4.43	0.00	0.00	3.86
4142	5404	5.010922	TCCTCAACAAAATGTAAGCAGCATT	59.989	36.000	0.00	0.00	38.09	3.56

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.