AutoCloner

Multiple sequence alignment - TraesCS3A01G392000

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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	TraesCS3A01G392000	chr3A	100.000	2552	0	0	1	2552	639619130	639621681	0.000000e+00	4713.0
1	TraesCS3A01G392000	chr3A	92.543	979	73	0	1574	2552	307660540	307659562	0.000000e+00	1404.0
2	TraesCS3A01G392000	chr3A	83.841	328	51	2	2	328	546698343	546698669	6.860000e-81	311.0
3	TraesCS3A01G392000	chr4D	95.020	984	42	3	1576	2552	419196656	419195673	0.000000e+00	1539.0
4	TraesCS3A01G392000	chr1D	93.807	985	59	2	1569	2552	451144012	451144995	0.000000e+00	1480.0
5	TraesCS3A01G392000	chr2A	93.245	977	65	1	1577	2552	469829715	469830691	0.000000e+00	1437.0
6	TraesCS3A01G392000	chr6B	92.536	978	71	2	1577	2552	646541753	646542730	0.000000e+00	1400.0
7	TraesCS3A01G392000	chr6B	91.709	977	79	2	1577	2552	126839815	126838840	0.000000e+00	1354.0
8	TraesCS3A01G392000	chr3B	91.011	979	81	7	1578	2552	806666203	806665228	0.000000e+00	1314.0
9	TraesCS3A01G392000	chr1B	90.414	991	86	8	1567	2551	611319029	611318042	0.000000e+00	1295.0
10	TraesCS3A01G392000	chr2B	89.468	978	99	4	1576	2552	303839343	303838369	0.000000e+00	1232.0
11	TraesCS3A01G392000	chr2B	80.480	333	61	2	4	336	206683158	206682830	4.210000e-63	252.0
12	TraesCS3A01G392000	chr2B	81.308	321	47	10	19	333	363504686	363504999	5.450000e-62	248.0
13	TraesCS3A01G392000	chr7A	87.690	723	61	9	872	1576	57095858	57096570	0.000000e+00	817.0
14	TraesCS3A01G392000	chr7A	84.298	726	75	17	872	1569	57156684	57157398	0.000000e+00	673.0
15	TraesCS3A01G392000	chr4A	85.534	712	66	17	872	1556	668351738	668352439	0.000000e+00	710.0
16	TraesCS3A01G392000	chr4A	88.360	189	20	2	1313	1500	668183567	668183754	2.550000e-55	226.0
17	TraesCS3A01G392000	chr4A	88.360	189	20	2	1313	1500	668218236	668218423	2.550000e-55	226.0
18	TraesCS3A01G392000	chr4A	97.727	44	1	0	827	870	668373210	668373253	2.720000e-10	76.8
19	TraesCS3A01G392000	chr7D	87.046	633	65	10	935	1557	53637837	53638462	0.000000e+00	699.0
20	TraesCS3A01G392000	chr7D	82.907	743	77	26	872	1569	53710891	53711628	7.750000e-175	623.0
21	TraesCS3A01G392000	chr7D	82.653	98	17	0	971	1068	46965670	46965767	1.260000e-13	87.9
22	TraesCS3A01G392000	chr7D	80.165	121	7	8	767	870	53710727	53710847	9.790000e-10	75.0
23	TraesCS3A01G392000	chr3D	89.062	448	45	4	2	446	500108641	500109087	1.030000e-153	553.0
24	TraesCS3A01G392000	chr3D	94.776	268	12	1	1232	1499	500110049	500110314	1.410000e-112	416.0
25	TraesCS3A01G392000	chr3D	86.189	391	31	5	439	817	500109273	500109652	3.950000e-108	401.0
26	TraesCS3A01G392000	chr3D	87.032	347	43	2	2	348	451232906	451233250	8.560000e-105	390.0
27	TraesCS3A01G392000	chr3D	85.546	339	46	3	2	338	342105236	342105573	4.040000e-93	351.0
28	TraesCS3A01G392000	chr3D	84.488	361	31	6	800	1137	500109672	500110030	1.460000e-87	333.0
29	TraesCS3A01G392000	chr5D	83.929	336	48	5	2	335	369421889	369421558	1.470000e-82	316.0
30	TraesCS3A01G392000	chr5B	83.284	335	54	2	2	335	650036032	650035699	8.870000e-80	307.0
31	TraesCS3A01G392000	chr5B	82.831	332	55	2	5	335	606586120	606585790	1.920000e-76	296.0
32	TraesCS3A01G392000	chrUn	88.360	189	20	2	1313	1500	402758570	402758757	2.550000e-55	226.0

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	TraesCS3A01G392000	chr3A	639619130	639621681	2551	False	4713.00	4713	100.00000	1	2552	1	chr3A.!!$F2	2551
1	TraesCS3A01G392000	chr3A	307659562	307660540	978	True	1404.00	1404	92.54300	1574	2552	1	chr3A.!!$R1	978
2	TraesCS3A01G392000	chr4D	419195673	419196656	983	True	1539.00	1539	95.02000	1576	2552	1	chr4D.!!$R1	976
3	TraesCS3A01G392000	chr1D	451144012	451144995	983	False	1480.00	1480	93.80700	1569	2552	1	chr1D.!!$F1	983
4	TraesCS3A01G392000	chr2A	469829715	469830691	976	False	1437.00	1437	93.24500	1577	2552	1	chr2A.!!$F1	975
5	TraesCS3A01G392000	chr6B	646541753	646542730	977	False	1400.00	1400	92.53600	1577	2552	1	chr6B.!!$F1	975
6	TraesCS3A01G392000	chr6B	126838840	126839815	975	True	1354.00	1354	91.70900	1577	2552	1	chr6B.!!$R1	975
7	TraesCS3A01G392000	chr3B	806665228	806666203	975	True	1314.00	1314	91.01100	1578	2552	1	chr3B.!!$R1	974
8	TraesCS3A01G392000	chr1B	611318042	611319029	987	True	1295.00	1295	90.41400	1567	2551	1	chr1B.!!$R1	984
9	TraesCS3A01G392000	chr2B	303838369	303839343	974	True	1232.00	1232	89.46800	1576	2552	1	chr2B.!!$R2	976
10	TraesCS3A01G392000	chr7A	57095858	57096570	712	False	817.00	817	87.69000	872	1576	1	chr7A.!!$F1	704
11	TraesCS3A01G392000	chr7A	57156684	57157398	714	False	673.00	673	84.29800	872	1569	1	chr7A.!!$F2	697
12	TraesCS3A01G392000	chr4A	668351738	668352439	701	False	710.00	710	85.53400	872	1556	1	chr4A.!!$F3	684
13	TraesCS3A01G392000	chr7D	53637837	53638462	625	False	699.00	699	87.04600	935	1557	1	chr7D.!!$F2	622
14	TraesCS3A01G392000	chr7D	53710727	53711628	901	False	349.00	623	81.53600	767	1569	2	chr7D.!!$F3	802
15	TraesCS3A01G392000	chr3D	500108641	500110314	1673	False	425.75	553	88.62875	2	1499	4	chr3D.!!$F3	1497

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
414	417	0.110486	ATCAAACCGACAAGTGGGCT	59.89	50.0	0.82	0.0	30.95	5.19	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1693	2081	0.303493	GCTTTCGTGCTTGTCGTTGA	59.697	50.0	0.0	0.0	0.0	3.18	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
38	39	1.883084	CGGCCCGAGCTTGACATAC	60.883	63.158	0.00	0.00	39.73	2.39
46	47	2.622436	GAGCTTGACATACTGTCCCAC	58.378	52.381	4.91	0.00	46.40	4.61
95	96	1.005037	AGTGGCGAGAAATGCGACA	60.005	52.632	3.12	0.00	45.85	4.35
105	106	0.976641	AAATGCGACAGAGGGAGTGA	59.023	50.000	0.00	0.00	0.00	3.41
116	117	0.978146	AGGGAGTGAGGAATCACGGG	60.978	60.000	2.94	0.00	44.71	5.28
118	119	0.976073	GGAGTGAGGAATCACGGGGA	60.976	60.000	2.94	0.00	44.71	4.81
119	120	0.902531	GAGTGAGGAATCACGGGGAA	59.097	55.000	2.94	0.00	44.71	3.97
120	121	1.278127	GAGTGAGGAATCACGGGGAAA	59.722	52.381	2.94	0.00	44.71	3.13
121	122	1.003233	AGTGAGGAATCACGGGGAAAC	59.997	52.381	2.94	0.00	44.71	2.78
170	171	2.607568	TATCTGCCCCGCAAACCCA	61.608	57.895	0.00	0.00	38.41	4.51
174	175	2.044352	GCCCCGCAAACCCATAGT	60.044	61.111	0.00	0.00	0.00	2.12
216	217	3.817655	GCGGGCCGCGGTAATTTT	61.818	61.111	37.09	0.00	44.55	1.82
217	218	2.879168	CGGGCCGCGGTAATTTTT	59.121	55.556	28.70	0.00	0.00	1.94
248	250	1.022735	ACGAGTATACGGGCTCTGTG	58.977	55.000	0.00	0.00	37.61	3.66
259	261	1.601759	GCTCTGTGCTGGCCAGAAA	60.602	57.895	37.21	20.59	38.42	2.52
263	265	1.614903	TCTGTGCTGGCCAGAAAATTG	59.385	47.619	37.21	18.82	36.07	2.32
277	279	2.005971	AAATTGAGCCGAGACCGTAC	57.994	50.000	0.00	0.00	0.00	3.67
278	280	0.892755	AATTGAGCCGAGACCGTACA	59.107	50.000	0.00	0.00	0.00	2.90
282	284	1.303074	AGCCGAGACCGTACACTCA	60.303	57.895	10.70	0.00	33.86	3.41
286	288	1.004595	CGAGACCGTACACTCATCGA	58.995	55.000	10.70	0.00	33.86	3.59
329	331	1.528542	CGGGGTCCGCTAGAGATGA	60.529	63.158	4.18	0.00	41.17	2.92
351	353	4.842531	TCTAAGTTGATCATCAAGCCCA	57.157	40.909	0.00	0.00	37.00	5.36
414	417	0.110486	ATCAAACCGACAAGTGGGCT	59.890	50.000	0.82	0.00	30.95	5.19
446	449	2.269940	AGCCTTGGAGAGAAAAGCCTA	58.730	47.619	0.00	0.00	0.00	3.93
469	665	3.067106	ACGCTTTGTGTGTAGAATCAGG	58.933	45.455	0.00	0.00	37.67	3.86
497	693	3.388272	GCTAGTAGCCCCTCAAAGC	57.612	57.895	11.33	0.00	34.48	3.51
498	694	0.541863	GCTAGTAGCCCCTCAAAGCA	59.458	55.000	11.33	0.00	34.48	3.91
499	695	1.065418	GCTAGTAGCCCCTCAAAGCAA	60.065	52.381	11.33	0.00	34.48	3.91
500	696	2.618045	GCTAGTAGCCCCTCAAAGCAAA	60.618	50.000	11.33	0.00	34.48	3.68
501	697	2.675658	AGTAGCCCCTCAAAGCAAAA	57.324	45.000	0.00	0.00	0.00	2.44
502	698	2.957474	AGTAGCCCCTCAAAGCAAAAA	58.043	42.857	0.00	0.00	0.00	1.94
503	699	3.510459	AGTAGCCCCTCAAAGCAAAAAT	58.490	40.909	0.00	0.00	0.00	1.82
512	708	5.530543	CCCTCAAAGCAAAAATAAAAAGGCA	59.469	36.000	0.00	0.00	0.00	4.75
513	709	6.039159	CCCTCAAAGCAAAAATAAAAAGGCAA	59.961	34.615	0.00	0.00	0.00	4.52
527	723	0.621082	AGGCAAAGAAGGGCTAGTCC	59.379	55.000	4.79	4.79	39.65	3.85
528	724	0.328258	GGCAAAGAAGGGCTAGTCCA	59.672	55.000	17.52	0.00	36.21	4.02
593	789	2.289565	CCCCGCTCAAAACCTAATCTC	58.710	52.381	0.00	0.00	0.00	2.75
598	794	2.289565	CTCAAAACCTAATCTCCCCGC	58.710	52.381	0.00	0.00	0.00	6.13
602	798	0.763223	AACCTAATCTCCCCGCCGAT	60.763	55.000	0.00	0.00	0.00	4.18
604	800	1.185618	CCTAATCTCCCCGCCGATCA	61.186	60.000	0.00	0.00	0.00	2.92
606	802	0.391597	TAATCTCCCCGCCGATCAAC	59.608	55.000	0.00	0.00	0.00	3.18
651	847	1.069204	GGCGGCTCTTGTGATCTGATA	59.931	52.381	0.00	0.00	0.00	2.15
654	850	3.491619	GCGGCTCTTGTGATCTGATAAGA	60.492	47.826	0.00	0.00	0.00	2.10
658	854	4.505922	GCTCTTGTGATCTGATAAGAACCG	59.494	45.833	0.00	0.00	0.00	4.44
683	884	1.858091	CCCAACTTGGATCGAGATCG	58.142	55.000	9.61	0.00	40.96	3.69
690	891	2.691409	TGGATCGAGATCGCCTTTTT	57.309	45.000	6.96	0.00	38.69	1.94
694	895	3.623510	GGATCGAGATCGCCTTTTTCTTT	59.376	43.478	6.96	0.00	38.69	2.52
695	896	4.260415	GGATCGAGATCGCCTTTTTCTTTC	60.260	45.833	6.96	0.00	38.69	2.62
712	913	2.779951	TTCGAGCTAGCTTTGGCGCA	62.780	55.000	20.42	5.16	44.37	6.09
718	919	2.098117	AGCTAGCTTTGGCGCATAAAAG	59.902	45.455	12.68	19.37	44.37	2.27
809	1026	1.152881	GATAACCTGCCTGCCCTGG	60.153	63.158	0.00	0.00	0.00	4.45
909	1206	3.695830	AATAAACGGCTCAACTCCTCA	57.304	42.857	0.00	0.00	0.00	3.86
975	1308	1.002430	CCTACTCTTTGCACTGAGCCA	59.998	52.381	13.28	3.48	44.83	4.75
995	1330	3.181491	CCATTTCGGCAAATAATCACGGT	60.181	43.478	0.00	0.00	30.51	4.83
1048	1383	0.318441	CCACCTCGAGAACAAGCTCA	59.682	55.000	15.71	0.00	34.56	4.26
1050	1385	0.039074	ACCTCGAGAACAAGCTCACG	60.039	55.000	15.71	0.00	34.56	4.35
1068	1403	2.740055	CTCGCCAAACGCTGCTCT	60.740	61.111	0.00	0.00	43.23	4.09
1098	1440	3.795688	AAGCAGGATCCACTTCTTCAA	57.204	42.857	15.82	0.00	0.00	2.69
1114	1461	7.589221	CACTTCTTCAAATTTCAGTTCAGCTAC	59.411	37.037	0.00	0.00	0.00	3.58
1120	1467	6.480651	TCAAATTTCAGTTCAGCTACGTTGTA	59.519	34.615	0.00	0.00	0.00	2.41
1133	1480	8.146412	TCAGCTACGTTGTATACTGATAGTCTA	58.854	37.037	4.17	0.00	0.00	2.59
1141	1488	9.881529	GTTGTATACTGATAGTCTAACAGTAGC	57.118	37.037	25.36	21.34	45.74	3.58
1142	1489	9.623000	TTGTATACTGATAGTCTAACAGTAGCA	57.377	33.333	25.36	22.84	45.74	3.49
1143	1490	9.623000	TGTATACTGATAGTCTAACAGTAGCAA	57.377	33.333	25.36	15.56	45.74	3.91
1171	1520	8.928733	GCAATGCATTTCTTTTCTTAATCTTCA	58.071	29.630	9.83	0.00	0.00	3.02
1184	1533	1.251527	ATCTTCACCAGAGGCGACGT	61.252	55.000	0.00	0.00	33.87	4.34
1249	1598	2.286523	CCCAACGGTGAGCTCCTCT	61.287	63.158	12.15	0.00	0.00	3.69
1255	1607	1.679305	GGTGAGCTCCTCTGTCCGA	60.679	63.158	12.15	0.00	0.00	4.55
1266	1618	3.515502	TCCTCTGTCCGAGATTTGTTGAT	59.484	43.478	0.00	0.00	42.62	2.57
1267	1619	4.020218	TCCTCTGTCCGAGATTTGTTGATT	60.020	41.667	0.00	0.00	42.62	2.57
1304	1678	4.518970	TGCTCTGGTTTTCATAACTGAACC	59.481	41.667	0.00	0.00	41.05	3.62
1398	1776	1.520120	CATCATCTGCACCGTCGCT	60.520	57.895	0.00	0.00	0.00	4.93
1416	1794	2.590821	GCTGGGATGGCATACTTCATT	58.409	47.619	10.07	0.00	0.00	2.57
1502	1880	3.502086	AGGACACCTCCTTCCATGT	57.498	52.632	0.00	0.00	45.77	3.21
1572	1956	8.317679	CCTTGAGCTAGTATTATCCTGCTAATT	58.682	37.037	0.00	0.00	0.00	1.40
1653	2041	3.192001	CACAGAGCAACCATAGCAACAAT	59.808	43.478	0.00	0.00	0.00	2.71
1712	2100	0.303493	TCAACGACAAGCACGAAAGC	59.697	50.000	0.00	0.00	34.70	3.51
1984	2376	7.441458	GGTTTAGTAGGATAAGCATGTTCGATT	59.559	37.037	0.00	0.00	0.00	3.34
1995	2387	7.566858	AAGCATGTTCGATTGTAAATTTGTC	57.433	32.000	0.00	0.00	0.00	3.18
2007	2399	5.265989	TGTAAATTTGTCCCTAATGGTCCC	58.734	41.667	0.00	0.00	34.77	4.46
2251	2645	5.183228	GGTCCATTCCTCTTACGAATTTGA	58.817	41.667	0.00	0.00	0.00	2.69
2291	2685	0.547712	TCTAAAGGCCTGCCAGAGGT	60.548	55.000	5.69	0.00	44.97	3.85
2373	2767	5.650543	GGCACCACCAATAAGTTTAGAATG	58.349	41.667	0.00	0.00	38.86	2.67
2512	2906	3.934391	AAGGGAGCGACGGAAAGCG	62.934	63.158	0.00	0.00	38.61	4.68
2538	2932	5.193679	GTCCCAATTATTAGCTGACACCTT	58.806	41.667	0.00	0.00	0.00	3.50

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
38	39	4.415150	AGCCGCCATGTGGGACAG	62.415	66.667	0.54	0.00	41.80	3.51
77	78	1.005037	TGTCGCATTTCTCGCCACT	60.005	52.632	0.00	0.00	0.00	4.00
79	80	0.737367	CTCTGTCGCATTTCTCGCCA	60.737	55.000	0.00	0.00	0.00	5.69
105	106	1.376812	GCGTTTCCCCGTGATTCCT	60.377	57.895	0.00	0.00	0.00	3.36
130	131	1.210538	GGTCGAAACCCTATCCCCTT	58.789	55.000	0.00	0.00	39.93	3.95
131	132	2.926539	GGTCGAAACCCTATCCCCT	58.073	57.895	0.00	0.00	39.93	4.79
170	171	3.050835	ACCCCCAAAGCCGTATAACTAT	58.949	45.455	0.00	0.00	0.00	2.12
174	175	2.173143	CCTTACCCCCAAAGCCGTATAA	59.827	50.000	0.00	0.00	0.00	0.98
215	216	5.120519	CGTATACTCGTTTGGCCTGTAAAAA	59.879	40.000	3.32	0.00	0.00	1.94
216	217	4.626604	CGTATACTCGTTTGGCCTGTAAAA	59.373	41.667	3.32	0.00	0.00	1.52
217	218	4.175516	CGTATACTCGTTTGGCCTGTAAA	58.824	43.478	3.32	0.00	0.00	2.01
220	221	1.134907	CCGTATACTCGTTTGGCCTGT	60.135	52.381	3.32	0.00	0.00	4.00
221	222	1.567504	CCGTATACTCGTTTGGCCTG	58.432	55.000	3.32	0.00	0.00	4.85
222	223	0.462789	CCCGTATACTCGTTTGGCCT	59.537	55.000	3.32	0.00	0.00	5.19
225	226	1.407979	AGAGCCCGTATACTCGTTTGG	59.592	52.381	0.56	0.00	37.99	3.28
227	228	2.097825	ACAGAGCCCGTATACTCGTTT	58.902	47.619	0.56	0.00	37.99	3.60
228	229	1.404391	CACAGAGCCCGTATACTCGTT	59.596	52.381	0.56	0.00	37.99	3.85
229	230	1.022735	CACAGAGCCCGTATACTCGT	58.977	55.000	0.56	0.00	37.99	4.18
230	231	0.317938	GCACAGAGCCCGTATACTCG	60.318	60.000	0.56	0.00	37.99	4.18
248	250	0.108472	GGCTCAATTTTCTGGCCAGC	60.108	55.000	28.91	13.67	42.08	4.85
259	261	0.892755	TGTACGGTCTCGGCTCAATT	59.107	50.000	0.00	0.00	41.39	2.32
263	265	1.303799	TGAGTGTACGGTCTCGGCTC	61.304	60.000	7.62	0.00	41.39	4.70
277	279	2.872245	ACCCGCATAATTTCGATGAGTG	59.128	45.455	0.00	0.00	0.00	3.51
278	280	3.131396	GACCCGCATAATTTCGATGAGT	58.869	45.455	0.00	0.00	0.00	3.41
282	284	1.508632	CGGACCCGCATAATTTCGAT	58.491	50.000	0.00	0.00	0.00	3.59
329	331	5.128919	GTGGGCTTGATGATCAACTTAGAT	58.871	41.667	3.29	0.00	32.21	1.98
361	364	5.537300	TTTTGGCATAGTTTGGTGCTTAA	57.463	34.783	0.00	0.00	41.04	1.85
386	389	4.821805	ACTTGTCGGTTTGATGATCAACTT	59.178	37.500	7.48	0.00	35.89	2.66
387	390	4.214119	CACTTGTCGGTTTGATGATCAACT	59.786	41.667	7.48	0.00	35.89	3.16
405	408	1.673665	GCTGGTCTGAGCCCACTTG	60.674	63.158	4.17	0.00	32.35	3.16
414	417	0.538057	CCAAGGCTTTGCTGGTCTGA	60.538	55.000	2.41	0.00	32.79	3.27
446	449	4.870426	CCTGATTCTACACACAAAGCGTAT	59.130	41.667	0.00	0.00	0.00	3.06
469	665	1.364536	GCTACTAGCCCTTCTCCGC	59.635	63.158	0.00	0.00	34.48	5.54
492	688	8.908172	TTCTTTGCCTTTTTATTTTTGCTTTG	57.092	26.923	0.00	0.00	0.00	2.77
493	689	8.190122	CCTTCTTTGCCTTTTTATTTTTGCTTT	58.810	29.630	0.00	0.00	0.00	3.51
494	690	7.201812	CCCTTCTTTGCCTTTTTATTTTTGCTT	60.202	33.333	0.00	0.00	0.00	3.91
495	691	6.262944	CCCTTCTTTGCCTTTTTATTTTTGCT	59.737	34.615	0.00	0.00	0.00	3.91
496	692	6.437928	CCCTTCTTTGCCTTTTTATTTTTGC	58.562	36.000	0.00	0.00	0.00	3.68
497	693	6.262944	AGCCCTTCTTTGCCTTTTTATTTTTG	59.737	34.615	0.00	0.00	0.00	2.44
498	694	6.364701	AGCCCTTCTTTGCCTTTTTATTTTT	58.635	32.000	0.00	0.00	0.00	1.94
499	695	5.940617	AGCCCTTCTTTGCCTTTTTATTTT	58.059	33.333	0.00	0.00	0.00	1.82
500	696	5.567037	AGCCCTTCTTTGCCTTTTTATTT	57.433	34.783	0.00	0.00	0.00	1.40
501	697	5.780282	ACTAGCCCTTCTTTGCCTTTTTATT	59.220	36.000	0.00	0.00	0.00	1.40
502	698	5.333581	ACTAGCCCTTCTTTGCCTTTTTAT	58.666	37.500	0.00	0.00	0.00	1.40
503	699	4.736473	ACTAGCCCTTCTTTGCCTTTTTA	58.264	39.130	0.00	0.00	0.00	1.52
527	723	4.415150	ACTGATGTGCCCCCGCTG	62.415	66.667	0.00	0.00	35.36	5.18
528	724	4.415150	CACTGATGTGCCCCCGCT	62.415	66.667	0.00	0.00	37.38	5.52
540	736	1.735360	GCAAAACTGGCAGCACTGA	59.265	52.632	15.89	0.00	0.00	3.41
547	743	2.725312	TTTGCGGGCAAAACTGGCA	61.725	52.632	15.82	0.00	42.16	4.92
548	744	2.107953	TTTGCGGGCAAAACTGGC	59.892	55.556	15.82	0.00	42.16	4.85
551	747	1.441311	CCAGTTTGCGGGCAAAACT	59.559	52.632	19.30	15.22	45.86	2.66
573	769	2.289565	GAGATTAGGTTTTGAGCGGGG	58.710	52.381	0.00	0.00	0.00	5.73
574	770	2.289565	GGAGATTAGGTTTTGAGCGGG	58.710	52.381	0.00	0.00	0.00	6.13
587	783	0.391597	GTTGATCGGCGGGGAGATTA	59.608	55.000	7.21	0.00	0.00	1.75
651	847	2.112029	GTTGGGCACAACGGTTCTT	58.888	52.632	17.51	0.00	46.50	2.52
672	868	2.827652	AGAAAAAGGCGATCTCGATCC	58.172	47.619	3.33	0.00	43.02	3.36
683	884	2.744741	AGCTAGCTCGAAAGAAAAAGGC	59.255	45.455	12.68	0.00	41.32	4.35
690	891	1.726853	GCCAAAGCTAGCTCGAAAGA	58.273	50.000	19.65	0.00	35.50	2.52
694	895	2.509336	GCGCCAAAGCTAGCTCGA	60.509	61.111	23.22	0.00	36.60	4.04
695	896	0.875908	TATGCGCCAAAGCTAGCTCG	60.876	55.000	19.65	17.94	38.13	5.03
712	913	3.094572	TCCTCCGTTCGTCCTCTTTTAT	58.905	45.455	0.00	0.00	0.00	1.40
718	919	0.667453	GGTATCCTCCGTTCGTCCTC	59.333	60.000	0.00	0.00	0.00	3.71
814	1066	2.531685	TTGGTGGGTGAGGAGGGG	60.532	66.667	0.00	0.00	0.00	4.79
821	1073	1.134220	GTGAACTGAGTTGGTGGGTGA	60.134	52.381	0.90	0.00	0.00	4.02
823	1075	0.182775	GGTGAACTGAGTTGGTGGGT	59.817	55.000	0.90	0.00	0.00	4.51
893	1190	0.250513	GGATGAGGAGTTGAGCCGTT	59.749	55.000	0.00	0.00	0.00	4.44
909	1206	2.097825	GTTGCTTGATGCTTCCAGGAT	58.902	47.619	0.00	0.00	43.37	3.24
931	1228	4.035814	TGATCAAGTGAGATGAGATGGGT	58.964	43.478	0.00	0.00	0.00	4.51
975	1308	3.692101	TCACCGTGATTATTTGCCGAAAT	59.308	39.130	0.00	0.00	35.83	2.17
984	1317	4.755411	ACGACATCTTCACCGTGATTATT	58.245	39.130	1.09	0.00	33.69	1.40
986	1319	3.729762	CGACGACATCTTCACCGTGATTA	60.730	47.826	1.09	0.00	35.22	1.75
987	1320	2.607187	GACGACATCTTCACCGTGATT	58.393	47.619	1.09	0.00	35.22	2.57
995	1330	1.154093	GCCGTCGACGACATCTTCA	60.154	57.895	37.65	0.00	43.02	3.02
1025	1360	2.154798	CTTGTTCTCGAGGTGGCCGA	62.155	60.000	13.56	0.00	34.61	5.54
1068	1403	4.168283	AGTGGATCCTGCTTACTACCTCTA	59.832	45.833	14.23	0.00	0.00	2.43
1098	1440	7.817962	AGTATACAACGTAGCTGAACTGAAATT	59.182	33.333	5.50	0.00	0.00	1.82
1120	1467	8.085296	GCATTGCTACTGTTAGACTATCAGTAT	58.915	37.037	24.09	13.70	41.64	2.12
1144	1491	8.836268	AAGATTAAGAAAAGAAATGCATTGCA	57.164	26.923	19.79	14.72	44.86	4.08
1283	1655	4.755123	ACGGTTCAGTTATGAAAACCAGAG	59.245	41.667	4.23	0.00	46.75	3.35
1304	1678	1.723870	GCCAGCTGCAGGATTAACG	59.276	57.895	17.12	0.00	40.77	3.18
1398	1776	2.309613	GCAATGAAGTATGCCATCCCA	58.690	47.619	0.00	0.00	36.56	4.37
1416	1794	3.982372	GATCGTCTTGTCGGCGGCA	62.982	63.158	11.51	11.51	0.00	5.69
1536	1920	2.027653	ACTAGCTCAAGGCCTGAAGAAC	60.028	50.000	5.69	0.10	43.05	3.01
1653	2041	3.948719	GTGGTGGCTTCGTCCCCA	61.949	66.667	0.00	0.00	0.00	4.96
1693	2081	0.303493	GCTTTCGTGCTTGTCGTTGA	59.697	50.000	0.00	0.00	0.00	3.18
1712	2100	1.229428	GGTGCCATGTATCCGTCATG	58.771	55.000	0.00	0.00	41.34	3.07
1949	2341	6.768381	GCTTATCCTACTAAACCAGCTGATTT	59.232	38.462	17.39	14.33	0.00	2.17
1984	2376	5.015817	AGGGACCATTAGGGACAAATTTACA	59.984	40.000	0.00	0.00	41.15	2.41
1995	2387	2.904697	GTCGTTAGGGACCATTAGGG	57.095	55.000	0.00	0.00	44.81	3.53
2017	2409	0.397675	TTGGTTTGGGTGCCATGTGA	60.398	50.000	0.00	0.00	34.37	3.58
2251	2645	4.514577	CGTCTTCCCGCGGCTGAT	62.515	66.667	22.85	0.00	0.00	2.90
2291	2685	6.662865	TGTGCCTCCAAAAATCAAAATCTA	57.337	33.333	0.00	0.00	0.00	1.98
2373	2767	2.157085	CGTTTCTCGGTTAAGTCCTTGC	59.843	50.000	0.00	0.00	35.71	4.01
2402	2796	1.004277	GGTGGTTTGGCCTCATACTGA	59.996	52.381	3.32	0.00	38.35	3.41
2438	2832	1.570501	TGCCTTATTCCCCATGCTCTT	59.429	47.619	0.00	0.00	0.00	2.85
2512	2906	4.816925	GTGTCAGCTAATAATTGGGACCTC	59.183	45.833	0.00	0.00	0.00	3.85

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.