AutoCloner

Multiple sequence alignment - TraesCS3D01G093600

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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	TraesCS3D01G093600	chr3D	100.000	4564	0	0	1	4564	47652820	47657383	0.000000e+00	8429.0
1	TraesCS3D01G093600	chr3D	92.500	40	3	0	4324	4363	49547007	49546968	1.770000e-04	58.4
2	TraesCS3D01G093600	chr3D	92.500	40	2	1	4312	4351	433733930	433733892	6.380000e-04	56.5
3	TraesCS3D01G093600	chr3B	92.606	2421	111	31	1571	3943	74891138	74888738	0.000000e+00	3417.0
4	TraesCS3D01G093600	chr3B	90.175	1547	109	17	55	1566	74892736	74891198	0.000000e+00	1975.0
5	TraesCS3D01G093600	chr3B	92.000	50	3	1	737	785	736653169	736653120	8.190000e-08	69.4
6	TraesCS3D01G093600	chr3B	90.566	53	2	3	4313	4364	422508512	422508562	2.950000e-07	67.6
7	TraesCS3D01G093600	chr3B	84.615	65	9	1	713	776	788164095	788164159	3.810000e-06	63.9
8	TraesCS3D01G093600	chr3B	82.353	68	12	0	4324	4391	425728727	425728660	4.930000e-05	60.2
9	TraesCS3D01G093600	chr3A	93.362	2290	92	17	2315	4564	59807878	59810147	0.000000e+00	3332.0
10	TraesCS3D01G093600	chr3A	93.721	1529	79	11	806	2324	59806311	59807832	0.000000e+00	2276.0
11	TraesCS3D01G093600	chr3A	89.650	686	59	9	3	679	217718124	217718806	0.000000e+00	863.0
12	TraesCS3D01G093600	chr2D	90.365	685	56	6	1	679	284550127	284549447	0.000000e+00	891.0
13	TraesCS3D01G093600	chr2D	93.023	43	3	0	4309	4351	640217124	640217082	3.810000e-06	63.9
14	TraesCS3D01G093600	chr7B	89.826	688	56	11	1	679	366050253	366049571	0.000000e+00	870.0
15	TraesCS3D01G093600	chr7B	89.286	56	4	2	724	778	23412131	23412077	8.190000e-08	69.4
16	TraesCS3D01G093600	chr7B	81.579	76	6	6	4281	4351	611733962	611733890	6.380000e-04	56.5
17	TraesCS3D01G093600	chr4B	89.635	685	64	5	1	679	22841778	22842461	0.000000e+00	865.0
18	TraesCS3D01G093600	chr6B	89.650	686	59	9	3	679	684937275	684936593	0.000000e+00	863.0
19	TraesCS3D01G093600	chr5A	89.650	686	59	9	3	679	195988288	195987606	0.000000e+00	863.0
20	TraesCS3D01G093600	chr5A	89.650	686	59	9	3	679	574792079	574792761	0.000000e+00	863.0
21	TraesCS3D01G093600	chr2A	89.650	686	59	9	3	679	260846872	260846190	0.000000e+00	863.0
22	TraesCS3D01G093600	chr2A	95.349	43	2	0	4309	4351	765711380	765711338	8.190000e-08	69.4
23	TraesCS3D01G093600	chr6A	85.821	134	16	2	678	808	183377292	183377425	6.160000e-29	139.0
24	TraesCS3D01G093600	chr6D	91.489	94	7	1	714	806	140084691	140084598	1.330000e-25	128.0
25	TraesCS3D01G093600	chr6D	93.878	49	3	0	727	775	56935226	56935178	1.760000e-09	75.0
26	TraesCS3D01G093600	chr5D	81.679	131	22	2	678	806	406357830	406357960	1.740000e-19	108.0
27	TraesCS3D01G093600	chr5B	80.769	130	20	4	680	806	487252576	487252703	3.760000e-16	97.1
28	TraesCS3D01G093600	chr2B	84.375	64	7	2	4309	4370	801216003	801216065	4.930000e-05	60.2

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	TraesCS3D01G093600	chr3D	47652820	47657383	4563	False	8429	8429	100.0000	1	4564	1	chr3D.!!$F1	4563
1	TraesCS3D01G093600	chr3B	74888738	74892736	3998	True	2696	3417	91.3905	55	3943	2	chr3B.!!$R3	3888
2	TraesCS3D01G093600	chr3A	59806311	59810147	3836	False	2804	3332	93.5415	806	4564	2	chr3A.!!$F2	3758
3	TraesCS3D01G093600	chr3A	217718124	217718806	682	False	863	863	89.6500	3	679	1	chr3A.!!$F1	676
4	TraesCS3D01G093600	chr2D	284549447	284550127	680	True	891	891	90.3650	1	679	1	chr2D.!!$R1	678
5	TraesCS3D01G093600	chr7B	366049571	366050253	682	True	870	870	89.8260	1	679	1	chr7B.!!$R2	678
6	TraesCS3D01G093600	chr4B	22841778	22842461	683	False	865	865	89.6350	1	679	1	chr4B.!!$F1	678
7	TraesCS3D01G093600	chr6B	684936593	684937275	682	True	863	863	89.6500	3	679	1	chr6B.!!$R1	676
8	TraesCS3D01G093600	chr5A	195987606	195988288	682	True	863	863	89.6500	3	679	1	chr5A.!!$R1	676
9	TraesCS3D01G093600	chr5A	574792079	574792761	682	False	863	863	89.6500	3	679	1	chr5A.!!$F1	676
10	TraesCS3D01G093600	chr2A	260846190	260846872	682	True	863	863	89.6500	3	679	1	chr2A.!!$R1	676

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
35	38	0.323633	TGACCCCGTCCGACTATCAA	60.324	55.000	0.00	0.00	0.00	2.57	F
159	162	1.842381	GCTAACCCCTGGTGCAGTCT	61.842	60.000	0.00	0.00	35.34	3.24	F
420	424	1.990060	CCATGGTCGACCTCCCAGT	60.990	63.158	33.39	11.09	36.82	4.00	F
1568	1664	0.179215	GCAGGATCGTGAGTTTTGCG	60.179	55.000	19.26	0.00	0.00	4.85	F
2920	3092	2.086094	TGTATGCTGAGGTGTGCATTG	58.914	47.619	5.78	0.00	46.29	2.82	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1542	1583	0.529833	CTCACGATCCTGCAGAGTGT	59.470	55.000	17.39	5.11	34.71	3.55	R
1548	1589	0.874390	GCAAAACTCACGATCCTGCA	59.126	50.000	0.00	0.00	0.00	4.41	R
1961	2057	2.496899	ATGCCTTGTGTTCAGGTAGG	57.503	50.000	0.00	0.00	0.00	3.18	R
2937	3115	2.315176	CAACCCTCCACCAAACATTCA	58.685	47.619	0.00	0.00	0.00	2.57	R
4500	4742	3.536570	TCGTGAACTGTTTTGATCCACA	58.463	40.909	0.00	0.00	0.00	4.17	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
35	38	0.323633	TGACCCCGTCCGACTATCAA	60.324	55.000	0.00	0.00	0.00	2.57
68	71	6.709397	CACCACATCATCTACAAAGAGCATAT	59.291	38.462	0.00	0.00	34.49	1.78
75	78	7.966812	TCATCTACAAAGAGCATATACCATGT	58.033	34.615	0.00	0.00	34.49	3.21
159	162	1.842381	GCTAACCCCTGGTGCAGTCT	61.842	60.000	0.00	0.00	35.34	3.24
226	229	7.485418	AACACTTGTCACAACATTATCGTAA	57.515	32.000	0.00	0.00	34.73	3.18
274	277	3.872696	TGCTGAGACTTTGTGTTTCTCA	58.127	40.909	0.89	0.89	42.75	3.27
351	355	3.245229	TGAACACCATATGCAGGTCCTTT	60.245	43.478	0.00	0.00	37.23	3.11
352	356	3.456380	ACACCATATGCAGGTCCTTTT	57.544	42.857	0.00	0.00	37.23	2.27
420	424	1.990060	CCATGGTCGACCTCCCAGT	60.990	63.158	33.39	11.09	36.82	4.00
532	540	7.324935	TCGCCAGATTTCACAGTAATTAGTAA	58.675	34.615	0.00	0.00	0.00	2.24
555	563	6.569127	AAACTTTAAACATCCCCCTTGTTT	57.431	33.333	6.96	6.96	46.18	2.83
619	627	5.583457	AGCATCTTATTTGCCTGAAAAATGC	59.417	36.000	0.00	0.00	41.06	3.56
629	637	3.311048	GCCTGAAAAATGCGGTTGAAAAA	59.689	39.130	0.00	0.00	0.00	1.94
630	638	4.552572	GCCTGAAAAATGCGGTTGAAAAAG	60.553	41.667	0.00	0.00	0.00	2.27
644	652	7.627726	GCGGTTGAAAAAGTTAGTTAGCCATAT	60.628	37.037	0.00	0.00	0.00	1.78
673	681	3.151022	CTCCGAGGCCTCTCCACC	61.151	72.222	29.73	3.78	36.70	4.61
674	682	3.670629	CTCCGAGGCCTCTCCACCT	62.671	68.421	29.73	0.00	39.65	4.00
675	683	2.685380	CCGAGGCCTCTCCACCTT	60.685	66.667	29.73	0.00	36.05	3.50
676	684	2.726351	CCGAGGCCTCTCCACCTTC	61.726	68.421	29.73	1.67	36.05	3.46
715	723	6.975196	TTGCAATTATATTGTGCCACCTAT	57.025	33.333	0.00	0.00	37.48	2.57
826	854	2.693762	GCAGGCAATTCTCGCAGCA	61.694	57.895	0.00	0.00	33.66	4.41
1130	1165	2.347866	GGCGGCTCTATTAGGGCC	59.652	66.667	22.69	22.69	42.18	5.80
1395	1432	4.133078	GCGGAAGATCTTCTGGATTTGAT	58.867	43.478	34.69	0.71	44.13	2.57
1427	1464	7.095102	CCCAAATCAAACCAATTTTAGCTGAAG	60.095	37.037	0.00	0.00	0.00	3.02
1432	1469	6.646240	TCAAACCAATTTTAGCTGAAGATTGC	59.354	34.615	14.81	0.00	37.99	3.56
1434	1471	7.466746	AACCAATTTTAGCTGAAGATTGCTA	57.533	32.000	14.81	0.00	37.99	3.49
1435	1472	7.651027	ACCAATTTTAGCTGAAGATTGCTAT	57.349	32.000	14.81	0.00	40.81	2.97
1471	1508	9.346725	GAAGGAATAAACTGTGTCATTTTCATC	57.653	33.333	0.00	0.00	0.00	2.92
1473	1510	7.451255	AGGAATAAACTGTGTCATTTTCATCCA	59.549	33.333	13.38	0.00	30.66	3.41
1491	1528	4.989279	TCCATTTGGAATCTTGCTTAGC	57.011	40.909	0.00	0.00	42.18	3.09
1495	1532	2.489938	TGGAATCTTGCTTAGCGGTT	57.510	45.000	0.00	0.00	0.00	4.44
1512	1549	3.426292	GCGGTTTTCCTAGAGCATCAAAC	60.426	47.826	0.00	0.00	35.88	2.93
1517	1554	6.374578	GTTTTCCTAGAGCATCAAACTGTTC	58.625	40.000	0.00	0.00	37.82	3.18
1538	1579	7.269316	TGTTCGATGCTATGAATTTAGTGGTA	58.731	34.615	0.00	0.00	0.00	3.25
1539	1580	7.223971	TGTTCGATGCTATGAATTTAGTGGTAC	59.776	37.037	0.00	0.00	0.00	3.34
1540	1581	6.811954	TCGATGCTATGAATTTAGTGGTACA	58.188	36.000	0.00	0.00	0.00	2.90
1541	1582	7.269316	TCGATGCTATGAATTTAGTGGTACAA	58.731	34.615	0.00	0.00	44.16	2.41
1542	1583	7.766738	TCGATGCTATGAATTTAGTGGTACAAA	59.233	33.333	0.00	0.00	44.16	2.83
1547	1588	8.175716	GCTATGAATTTAGTGGTACAAACACTC	58.824	37.037	0.00	0.00	45.50	3.51
1548	1589	9.436957	CTATGAATTTAGTGGTACAAACACTCT	57.563	33.333	0.00	0.00	45.50	3.24
1568	1664	0.179215	GCAGGATCGTGAGTTTTGCG	60.179	55.000	19.26	0.00	0.00	4.85
1607	1703	2.358737	GTGCCCTTGACCGTGGAG	60.359	66.667	0.00	0.00	0.00	3.86
1646	1742	8.600449	AGAGTAGCTTATATCAACTGAATTGC	57.400	34.615	0.00	0.00	38.29	3.56
1659	1755	6.374053	TCAACTGAATTGCGGATTTCATTCTA	59.626	34.615	13.51	0.19	38.29	2.10
1660	1756	6.369059	ACTGAATTGCGGATTTCATTCTAG	57.631	37.500	13.51	5.70	0.00	2.43
1859	1955	8.692110	TGATCTTTGCATATCATTTTGTTGTC	57.308	30.769	0.00	0.00	0.00	3.18
1905	2001	2.735823	CTTCTTCTTGTTTGCCACAGC	58.264	47.619	0.00	0.00	36.48	4.40
1961	2057	8.000991	CGTATTCATTTGAACTCGATCTGAATC	58.999	37.037	11.08	0.91	36.80	2.52
2218	2330	8.702163	TGGAGTGTATATATGTATTTGCATCG	57.298	34.615	0.00	0.00	0.00	3.84
2328	2494	2.932614	GTCTGTTATGCTGTACTGCAGG	59.067	50.000	27.90	16.51	46.71	4.85
2357	2523	4.574674	TCCCTCTGCATGTTATGAACTT	57.425	40.909	0.00	0.00	0.00	2.66
2358	2524	4.922206	TCCCTCTGCATGTTATGAACTTT	58.078	39.130	0.00	0.00	0.00	2.66
2451	2618	2.106566	TGTTGTCCAATTGCTGGTTGT	58.893	42.857	0.00	0.00	46.51	3.32
2795	2967	5.817296	GTCAGCATTCACATGGTTACTATCA	59.183	40.000	0.00	0.00	39.19	2.15
2920	3092	2.086094	TGTATGCTGAGGTGTGCATTG	58.914	47.619	5.78	0.00	46.29	2.82
2937	3115	6.262944	TGTGCATTGTTCTTCTGAAACAGTAT	59.737	34.615	0.00	0.00	33.52	2.12
3188	3366	0.464036	AGATATCGGCCGAAGCAACA	59.536	50.000	34.66	13.37	42.56	3.33
3189	3367	0.582005	GATATCGGCCGAAGCAACAC	59.418	55.000	34.66	15.08	42.56	3.32
3192	3370	4.072088	CGGCCGAAGCAACACGAC	62.072	66.667	24.07	0.00	42.56	4.34
3195	3373	2.935955	CCGAAGCAACACGACCAC	59.064	61.111	0.00	0.00	0.00	4.16
3202	3380	0.814010	GCAACACGACCACAAGGAGT	60.814	55.000	0.00	0.00	38.69	3.85
3213	3391	4.266714	ACCACAAGGAGTCGAAAGAAAAA	58.733	39.130	0.00	0.00	39.53	1.94
3221	3399	6.055588	AGGAGTCGAAAGAAAAAGAACATGA	58.944	36.000	0.00	0.00	45.01	3.07
3225	3403	8.103948	AGTCGAAAGAAAAAGAACATGATCAT	57.896	30.769	1.18	1.18	45.01	2.45
3306	3484	5.062809	GGTCGAACAGAAGATTGATGAACTC	59.937	44.000	0.00	0.00	0.00	3.01
3311	3489	6.371595	ACAGAAGATTGATGAACTCTCCTT	57.628	37.500	0.00	0.00	0.00	3.36
3312	3490	6.777782	ACAGAAGATTGATGAACTCTCCTTT	58.222	36.000	0.00	0.00	0.00	3.11
3639	3822	5.903810	ACGGTGTTAGAACATCTCTAATCC	58.096	41.667	4.26	4.01	46.09	3.01
3820	4030	2.820037	TTGTGCGTGGCGTCAACA	60.820	55.556	0.00	0.00	0.00	3.33
3950	4160	1.322538	TGGAGAGCTGCGCAGATGTA	61.323	55.000	40.21	16.74	0.00	2.29
4058	4295	7.447374	AATCCAAAAATGTACACGATCTCAA	57.553	32.000	0.00	0.00	0.00	3.02
4075	4312	7.770433	ACGATCTCAATAAAGTCCATGAATTCA	59.230	33.333	11.26	11.26	0.00	2.57
4233	4473	7.651304	TGAGAAACGTTTATGTGCATGAAAAAT	59.349	29.630	13.73	0.00	0.00	1.82
4397	4637	8.326713	TGAATTTGAACATTGTTCACGAAATTG	58.673	29.630	28.46	0.00	0.00	2.32
4447	4689	6.869315	TTCACGAATAAGAAATGGTTGACA	57.131	33.333	0.00	0.00	0.00	3.58
4459	4701	8.558973	AGAAATGGTTGACAAATTTGAACAAA	57.441	26.923	24.64	14.55	33.26	2.83
4519	4761	5.406649	TGTTTGTGGATCAAAACAGTTCAC	58.593	37.500	13.51	2.36	45.84	3.18
4526	4768	5.818336	TGGATCAAAACAGTTCACGAAGTTA	59.182	36.000	0.00	0.00	41.61	2.24

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
35	38	2.103373	AGATGATGTGGTGCTAGTCGT	58.897	47.619	0.00	0.00	0.00	4.34
68	71	9.201989	GGATATACAAGGAGATATCACATGGTA	57.798	37.037	5.32	5.02	36.95	3.25
75	78	7.955750	TCACAAGGGATATACAAGGAGATATCA	59.044	37.037	5.32	0.00	36.95	2.15
159	162	7.827236	ACATTGATGACTTCCCGAGTAAAATAA	59.173	33.333	0.00	0.00	39.19	1.40
274	277	2.014010	AATGTCATGTGGTGGCCTTT	57.986	45.000	3.32	0.00	0.00	3.11
532	540	6.569127	AAACAAGGGGGATGTTTAAAGTTT	57.431	33.333	3.03	0.00	46.21	2.66
619	627	5.427036	TGGCTAACTAACTTTTTCAACCG	57.573	39.130	0.00	0.00	0.00	4.44
644	652	5.044772	AGAGGCCTCGGAGACATATCTATAA	60.045	44.000	26.95	0.00	32.51	0.98
650	658	1.549037	GGAGAGGCCTCGGAGACATAT	60.549	57.143	26.95	6.05	40.33	1.78
786	794	6.619744	TGCGATTACATGAACATGAACATTT	58.380	32.000	19.56	0.48	41.20	2.32
826	854	6.486253	AAAATAGATGATATGATGCGCGTT	57.514	33.333	8.43	0.00	0.00	4.84
889	918	6.440328	AGCCCAGGAATTTGAATTAGCTTTTA	59.560	34.615	0.00	0.00	0.00	1.52
894	923	3.068732	GGAGCCCAGGAATTTGAATTAGC	59.931	47.826	0.00	0.00	0.00	3.09
941	970	1.080569	GGCCGTGTCCAGCAATTTG	60.081	57.895	0.00	0.00	0.00	2.32
1130	1165	2.249535	CGGGATTCTGCTGCATCCG	61.250	63.158	14.34	12.32	40.13	4.18
1204	1239	1.987855	CCAGAACCCTAGCCACGGA	60.988	63.158	0.00	0.00	0.00	4.69
1273	1308	2.414785	TAGCTCGCGCTCCATGTCA	61.415	57.895	1.61	0.00	45.15	3.58
1294	1329	1.594836	GGGACGTACGTGTTTGGCA	60.595	57.895	28.16	0.00	0.00	4.92
1326	1361	2.945008	TCATTGGCTAAAATCGGCTGAG	59.055	45.455	0.00	0.00	0.00	3.35
1395	1432	7.566658	AAAATTGGTTTGATTTGGGGATCTA	57.433	32.000	0.00	0.00	0.00	1.98
1427	1464	8.860780	ATTCCTTCAAGGATAAGATAGCAATC	57.139	34.615	7.07	0.00	45.34	2.67
1434	1471	9.401058	CACAGTTTATTCCTTCAAGGATAAGAT	57.599	33.333	7.07	0.00	45.34	2.40
1435	1472	8.383175	ACACAGTTTATTCCTTCAAGGATAAGA	58.617	33.333	7.07	0.00	45.34	2.10
1457	1494	6.416631	TTCCAAATGGATGAAAATGACACA	57.583	33.333	2.38	0.00	44.98	3.72
1458	1495	7.325694	AGATTCCAAATGGATGAAAATGACAC	58.674	34.615	2.38	0.00	44.98	3.67
1461	1498	6.819649	GCAAGATTCCAAATGGATGAAAATGA	59.180	34.615	2.38	0.00	44.98	2.57
1471	1508	3.489738	CCGCTAAGCAAGATTCCAAATGG	60.490	47.826	0.00	0.00	0.00	3.16
1473	1510	3.356290	ACCGCTAAGCAAGATTCCAAAT	58.644	40.909	0.00	0.00	0.00	2.32
1491	1528	4.003648	AGTTTGATGCTCTAGGAAAACCG	58.996	43.478	0.00	0.00	0.00	4.44
1495	1532	4.690748	CGAACAGTTTGATGCTCTAGGAAA	59.309	41.667	0.00	0.00	0.00	3.13
1512	1549	6.258727	ACCACTAAATTCATAGCATCGAACAG	59.741	38.462	0.00	0.00	0.00	3.16
1517	1554	7.477144	TTGTACCACTAAATTCATAGCATCG	57.523	36.000	0.00	0.00	0.00	3.84
1538	1579	1.070758	ACGATCCTGCAGAGTGTTTGT	59.929	47.619	17.39	0.98	0.00	2.83
1539	1580	1.462283	CACGATCCTGCAGAGTGTTTG	59.538	52.381	17.39	0.90	0.00	2.93
1540	1581	1.344438	TCACGATCCTGCAGAGTGTTT	59.656	47.619	17.39	0.00	34.71	2.83
1541	1582	0.969149	TCACGATCCTGCAGAGTGTT	59.031	50.000	17.39	0.00	34.71	3.32
1542	1583	0.529833	CTCACGATCCTGCAGAGTGT	59.470	55.000	17.39	5.11	34.71	3.55
1547	1588	1.135859	GCAAAACTCACGATCCTGCAG	60.136	52.381	6.78	6.78	0.00	4.41
1548	1589	0.874390	GCAAAACTCACGATCCTGCA	59.126	50.000	0.00	0.00	0.00	4.41
1568	1664	4.202315	ACCCAGTTTCTGCAAAATTAACCC	60.202	41.667	0.00	0.00	0.00	4.11
1607	1703	5.394224	AGCTACTCTAAGTTCCTTGTGAC	57.606	43.478	0.00	0.00	0.00	3.67
1646	1742	7.171678	GGAAACATAGGACTAGAATGAAATCCG	59.828	40.741	0.00	0.00	34.46	4.18
1961	2057	2.496899	ATGCCTTGTGTTCAGGTAGG	57.503	50.000	0.00	0.00	0.00	3.18
2174	2284	9.241919	ACACTCCATTTCAATTTATGTGTCATA	57.758	29.630	0.00	0.00	31.64	2.15
2175	2285	8.125978	ACACTCCATTTCAATTTATGTGTCAT	57.874	30.769	0.00	0.00	31.64	3.06
2218	2330	4.963953	GCGCAATGTATTTATGTGTCTGAC	59.036	41.667	0.30	0.00	0.00	3.51
2357	2523	6.069905	TGGAACAGGACCAAACTATATGCTAA	60.070	38.462	0.00	0.00	34.25	3.09
2358	2524	5.427157	TGGAACAGGACCAAACTATATGCTA	59.573	40.000	0.00	0.00	34.25	3.49
2451	2618	3.538591	CAAGCAATCTAGATGAGCACCA	58.461	45.455	24.28	0.00	0.00	4.17
2664	2831	6.548171	TCGGCTATTGTGCAATTTAAGTAAC	58.452	36.000	2.56	0.00	32.50	2.50
2745	2912	7.919690	TGATGCTGCAGTTGATAACTATAAAC	58.080	34.615	16.64	0.00	40.46	2.01
2920	3092	9.173939	CAAACATTCATACTGTTTCAGAAGAAC	57.826	33.333	3.70	0.00	43.15	3.01
2937	3115	2.315176	CAACCCTCCACCAAACATTCA	58.685	47.619	0.00	0.00	0.00	2.57
3192	3370	4.574828	TCTTTTTCTTTCGACTCCTTGTGG	59.425	41.667	0.00	0.00	0.00	4.17
3195	3373	6.119144	TGTTCTTTTTCTTTCGACTCCTTG	57.881	37.500	0.00	0.00	0.00	3.61
3213	3391	6.471233	TTCGACTCCTTATGATCATGTTCT	57.529	37.500	18.72	0.00	0.00	3.01
3221	3399	8.669243	GTTCATTTTCTTTCGACTCCTTATGAT	58.331	33.333	0.00	0.00	0.00	2.45
3225	3403	7.659799	TGATGTTCATTTTCTTTCGACTCCTTA	59.340	33.333	0.00	0.00	0.00	2.69
3306	3484	2.681848	CAGCCTTGATACAGCAAAGGAG	59.318	50.000	4.88	0.00	0.00	3.69
3311	3489	3.515502	AGTACTCAGCCTTGATACAGCAA	59.484	43.478	0.00	0.00	31.68	3.91
3312	3490	3.099905	AGTACTCAGCCTTGATACAGCA	58.900	45.455	0.00	0.00	31.68	4.41
3639	3822	2.483538	GGATTGCCGGATTTTTGGGATG	60.484	50.000	5.05	0.00	0.00	3.51
4035	4272	7.630242	ATTGAGATCGTGTACATTTTTGGAT	57.370	32.000	0.00	0.00	0.00	3.41
4206	4446	5.681337	TCATGCACATAAACGTTTCTCAA	57.319	34.783	18.42	0.00	0.00	3.02
4208	4448	6.984740	TTTTCATGCACATAAACGTTTCTC	57.015	33.333	18.42	4.11	0.00	2.87
4308	4548	9.597170	TCATGAACATTTCTTTGAATTCACAAA	57.403	25.926	7.89	8.10	37.98	2.83
4309	4549	9.597170	TTCATGAACATTTCTTTGAATTCACAA	57.403	25.926	7.89	5.39	31.94	3.33
4310	4550	9.767228	ATTCATGAACATTTCTTTGAATTCACA	57.233	25.926	11.07	0.00	38.68	3.58
4435	4677	8.450180	ACTTTGTTCAAATTTGTCAACCATTTC	58.550	29.630	17.47	0.00	0.00	2.17
4482	4724	6.968263	TCCACAAACATTTATGGAAGTCAA	57.032	33.333	1.80	0.00	38.30	3.18
4498	4740	4.396478	TCGTGAACTGTTTTGATCCACAAA	59.604	37.500	0.00	0.00	45.22	2.83
4499	4741	3.942115	TCGTGAACTGTTTTGATCCACAA	59.058	39.130	0.00	0.00	36.65	3.33
4500	4742	3.536570	TCGTGAACTGTTTTGATCCACA	58.463	40.909	0.00	0.00	0.00	4.17
4501	4743	4.035208	ACTTCGTGAACTGTTTTGATCCAC	59.965	41.667	0.00	0.00	0.00	4.02

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.