AutoCloner

Multiple sequence alignment - TraesCS2A01G158600

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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	TraesCS2A01G158600	chr2A	100.000	2207	0	0	1	2207	105521854	105524060	0.000000e+00	4076.0
1	TraesCS2A01G158600	chr2A	85.888	659	70	15	789	1431	105531639	105532290	0.000000e+00	680.0
2	TraesCS2A01G158600	chr2A	84.474	380	49	5	922	1291	105541247	105541626	1.250000e-97	366.0
3	TraesCS2A01G158600	chr2A	91.398	186	11	4	322	502	105531150	105531335	1.310000e-62	250.0
4	TraesCS2A01G158600	chr2D	90.301	897	70	11	519	1402	109737186	109738078	0.000000e+00	1158.0
5	TraesCS2A01G158600	chr2D	86.835	790	83	13	1430	2207	575766026	575765246	0.000000e+00	863.0
6	TraesCS2A01G158600	chr2D	86.421	788	80	17	1434	2207	15520513	15519739	0.000000e+00	837.0
7	TraesCS2A01G158600	chr2D	85.552	616	70	15	828	1431	109830732	109831340	5.170000e-176	627.0
8	TraesCS2A01G158600	chr2D	81.242	805	76	29	1	795	109802792	109803531	4.080000e-162	580.0
9	TraesCS2A01G158600	chr2D	86.207	377	47	4	934	1305	109902020	109902396	9.490000e-109	403.0
10	TraesCS2A01G158600	chr2D	85.042	361	50	4	933	1290	109793373	109793732	4.480000e-97	364.0
11	TraesCS2A01G158600	chr2D	86.339	183	18	7	322	501	109792911	109793089	2.240000e-45	193.0
12	TraesCS2A01G158600	chr2D	100.000	29	0	0	800	828	109830634	109830662	1.000000e-03	54.7
13	TraesCS2A01G158600	chr4B	88.931	786	65	14	1435	2207	404845241	404844465	0.000000e+00	950.0
14	TraesCS2A01G158600	chr4B	86.300	781	80	18	1435	2206	624187876	624188638	0.000000e+00	824.0
15	TraesCS2A01G158600	chr3D	86.792	795	82	15	1427	2207	508553004	508553789	0.000000e+00	865.0
16	TraesCS2A01G158600	chr7D	86.912	787	81	12	1433	2207	39670116	39670892	0.000000e+00	863.0
17	TraesCS2A01G158600	chr7D	86.224	784	85	15	1436	2207	94795272	94796044	0.000000e+00	828.0
18	TraesCS2A01G158600	chr5B	86.780	764	82	11	1457	2207	696200928	696200171	0.000000e+00	833.0
19	TraesCS2A01G158600	chr6B	83.576	755	100	17	1434	2172	571621513	571622259	0.000000e+00	686.0
20	TraesCS2A01G158600	chr3B	82.188	786	115	22	1440	2207	736024545	736025323	0.000000e+00	652.0
21	TraesCS2A01G158600	chr3B	81.922	791	118	20	1434	2207	736151644	736152426	0.000000e+00	645.0
22	TraesCS2A01G158600	chr2B	81.965	804	71	29	1	795	159299182	159299920	4.030000e-172	614.0
23	TraesCS2A01G158600	chr2B	85.029	521	65	11	828	1337	159300062	159300580	3.250000e-143	518.0
24	TraesCS2A01G158600	chr2B	85.552	353	47	3	943	1291	159319085	159319437	1.250000e-97	366.0
25	TraesCS2A01G158600	chr2B	83.558	371	35	12	322	688	159318379	159318727	7.600000e-85	324.0
26	TraesCS2A01G158600	chr2B	100.000	32	0	0	797	828	159299962	159299993	2.370000e-05	60.2
27	TraesCS2A01G158600	chr6D	84.928	345	36	8	1435	1771	427705839	427706175	3.510000e-88	335.0

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	TraesCS2A01G158600	chr2A	105521854	105524060	2206	False	4076.00	4076	100.0000	1	2207	1	chr2A.!!$F1	2206
1	TraesCS2A01G158600	chr2A	105531150	105532290	1140	False	465.00	680	88.6430	322	1431	2	chr2A.!!$F3	1109
2	TraesCS2A01G158600	chr2D	109737186	109738078	892	False	1158.00	1158	90.3010	519	1402	1	chr2D.!!$F1	883
3	TraesCS2A01G158600	chr2D	575765246	575766026	780	True	863.00	863	86.8350	1430	2207	1	chr2D.!!$R2	777
4	TraesCS2A01G158600	chr2D	15519739	15520513	774	True	837.00	837	86.4210	1434	2207	1	chr2D.!!$R1	773
5	TraesCS2A01G158600	chr2D	109802792	109803531	739	False	580.00	580	81.2420	1	795	1	chr2D.!!$F2	794
6	TraesCS2A01G158600	chr2D	109830634	109831340	706	False	340.85	627	92.7760	800	1431	2	chr2D.!!$F5	631
7	TraesCS2A01G158600	chr2D	109792911	109793732	821	False	278.50	364	85.6905	322	1290	2	chr2D.!!$F4	968
8	TraesCS2A01G158600	chr4B	404844465	404845241	776	True	950.00	950	88.9310	1435	2207	1	chr4B.!!$R1	772
9	TraesCS2A01G158600	chr4B	624187876	624188638	762	False	824.00	824	86.3000	1435	2206	1	chr4B.!!$F1	771
10	TraesCS2A01G158600	chr3D	508553004	508553789	785	False	865.00	865	86.7920	1427	2207	1	chr3D.!!$F1	780
11	TraesCS2A01G158600	chr7D	39670116	39670892	776	False	863.00	863	86.9120	1433	2207	1	chr7D.!!$F1	774
12	TraesCS2A01G158600	chr7D	94795272	94796044	772	False	828.00	828	86.2240	1436	2207	1	chr7D.!!$F2	771
13	TraesCS2A01G158600	chr5B	696200171	696200928	757	True	833.00	833	86.7800	1457	2207	1	chr5B.!!$R1	750
14	TraesCS2A01G158600	chr6B	571621513	571622259	746	False	686.00	686	83.5760	1434	2172	1	chr6B.!!$F1	738
15	TraesCS2A01G158600	chr3B	736024545	736025323	778	False	652.00	652	82.1880	1440	2207	1	chr3B.!!$F1	767
16	TraesCS2A01G158600	chr3B	736151644	736152426	782	False	645.00	645	81.9220	1434	2207	1	chr3B.!!$F2	773
17	TraesCS2A01G158600	chr2B	159299182	159300580	1398	False	397.40	614	88.9980	1	1337	3	chr2B.!!$F1	1336
18	TraesCS2A01G158600	chr2B	159318379	159319437	1058	False	345.00	366	84.5550	322	1291	2	chr2B.!!$F2	969

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
896	1131	1.251251	GCTGGATTGAGTTGTGGCTT	58.749	50.0	0.0	0.0	0.0	4.35	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2151	2445	1.003118	TGGTGGTGACTGTAGATTGCC	59.997	52.381	0.0	0.0	0.0	4.52	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
23	24	4.639755	ACAATTTTGGGTTTCTGCCAAAAG	59.360	37.500	5.04	0.00	43.45	2.27
37	38	2.552315	GCCAAAAGCAGTGCTAGTAACA	59.448	45.455	20.09	0.00	38.25	2.41
40	41	5.106317	GCCAAAAGCAGTGCTAGTAACAATA	60.106	40.000	20.09	0.00	38.25	1.90
41	42	6.546395	CCAAAAGCAGTGCTAGTAACAATAG	58.454	40.000	20.09	0.00	38.25	1.73
42	43	6.149474	CCAAAAGCAGTGCTAGTAACAATAGT	59.851	38.462	20.09	0.00	38.25	2.12
43	44	6.969828	AAAGCAGTGCTAGTAACAATAGTC	57.030	37.500	20.09	0.00	38.25	2.59
48	49	7.760340	AGCAGTGCTAGTAACAATAGTCTTTAC	59.240	37.037	18.11	0.00	36.99	2.01
91	92	5.472137	ACGTCAAATTATACACAAAGTGGCT	59.528	36.000	1.93	0.00	37.94	4.75
138	139	6.462487	CCGTATCAGCTCCTCCAAACTTAATA	60.462	42.308	0.00	0.00	0.00	0.98
175	176	5.989777	GCAAGTTATCACGTCCTAACCATAT	59.010	40.000	11.35	0.00	0.00	1.78
207	209	2.358898	GACCCGCAATTTAGCATCACAT	59.641	45.455	0.00	0.00	0.00	3.21
228	232	6.510641	CACATTAGAAAAACGTTCGTTACTCG	59.489	38.462	10.89	6.64	41.41	4.18
235	239	3.557908	ACGTTCGTTACTCGTTTGTTG	57.442	42.857	0.00	0.00	40.80	3.33
236	240	2.283661	CGTTCGTTACTCGTTTGTTGC	58.716	47.619	0.00	0.00	40.80	4.17
237	241	2.034339	CGTTCGTTACTCGTTTGTTGCT	60.034	45.455	0.00	0.00	40.80	3.91
238	242	3.529085	GTTCGTTACTCGTTTGTTGCTC	58.471	45.455	0.00	0.00	40.80	4.26
239	243	2.129607	TCGTTACTCGTTTGTTGCTCC	58.870	47.619	0.00	0.00	40.80	4.70
240	244	2.132762	CGTTACTCGTTTGTTGCTCCT	58.867	47.619	0.00	0.00	34.52	3.69
265	269	6.073058	TGCAATGTCTCAGTTATCTTTGTGAC	60.073	38.462	0.00	0.00	37.96	3.67
270	274	5.808030	GTCTCAGTTATCTTTGTGACCTAGC	59.192	44.000	0.00	0.00	33.80	3.42
278	282	3.503363	TCTTTGTGACCTAGCTGCATTTG	59.497	43.478	1.02	0.00	0.00	2.32
292	296	5.757320	AGCTGCATTTGTATCTAGTCATCAC	59.243	40.000	1.02	0.00	0.00	3.06
294	298	6.925718	GCTGCATTTGTATCTAGTCATCACTA	59.074	38.462	0.00	0.00	33.62	2.74
295	299	7.601886	GCTGCATTTGTATCTAGTCATCACTAT	59.398	37.037	0.00	0.00	34.44	2.12
401	407	3.513515	GGGGCCTGAAATGTTGACAATAA	59.486	43.478	0.84	0.00	0.00	1.40
477	489	1.923204	CGGCTTCGAAACATCTCTCTG	59.077	52.381	0.00	0.00	35.61	3.35
497	509	8.752005	TCTCTGTTATTTATTTAGCATTGCCT	57.248	30.769	4.70	0.00	0.00	4.75
498	510	9.845740	TCTCTGTTATTTATTTAGCATTGCCTA	57.154	29.630	4.70	0.00	0.00	3.93
619	638	4.520874	TCACATAGAGGTACATAGAGCTGC	59.479	45.833	0.00	0.00	0.00	5.25
695	715	9.477484	TTCTATCTATTCTTCGGTTTAGAATGC	57.523	33.333	8.04	0.00	41.25	3.56
706	797	4.260990	CGGTTTAGAATGCCATTTATCGCA	60.261	41.667	0.00	0.00	39.79	5.10
765	856	5.494724	TCCATTGTCTTCTCTCTTTCCATG	58.505	41.667	0.00	0.00	0.00	3.66
896	1131	1.251251	GCTGGATTGAGTTGTGGCTT	58.749	50.000	0.00	0.00	0.00	4.35
920	1156	8.773404	TTAGCTAAAAGTGAAGCCTACTTAAG	57.227	34.615	2.97	0.00	39.64	1.85
1103	1349	3.756727	GGACCGACCGGACCTCAC	61.757	72.222	19.70	0.00	44.68	3.51
1104	1350	3.756727	GACCGACCGGACCTCACC	61.757	72.222	16.07	0.00	38.96	4.02
1111	1357	2.184322	CGGACCTCACCGTGGATG	59.816	66.667	0.00	0.00	46.70	3.51
1140	1389	3.438183	AGTAGGAACTAATGTGACGGGT	58.562	45.455	0.00	0.00	45.48	5.28
1147	1396	2.631062	ACTAATGTGACGGGTGAGTTCA	59.369	45.455	0.00	0.00	0.00	3.18
1150	1399	1.877637	TGTGACGGGTGAGTTCAATG	58.122	50.000	0.00	0.00	0.00	2.82
1151	1400	1.414550	TGTGACGGGTGAGTTCAATGA	59.585	47.619	0.00	0.00	0.00	2.57
1214	1464	1.098050	CGGATTGGCTAAGCTGCTTT	58.902	50.000	21.29	0.23	0.00	3.51
1227	1482	6.038271	GCTAAGCTGCTTTTAATTAGCCTACA	59.962	38.462	21.29	0.00	41.45	2.74
1234	1489	8.446599	TGCTTTTAATTAGCCTACAGGAATAC	57.553	34.615	0.00	0.00	37.85	1.89
1235	1490	8.272173	TGCTTTTAATTAGCCTACAGGAATACT	58.728	33.333	0.00	0.00	37.85	2.12
1246	1501	1.819632	GGAATACTGGCCCGTGCAG	60.820	63.158	10.50	0.00	40.13	4.41
1261	1516	0.900182	TGCAGGTCTCCACATCGTCT	60.900	55.000	0.00	0.00	0.00	4.18
1271	1526	5.007430	GTCTCCACATCGTCTAGTTAATCGA	59.993	44.000	0.00	0.00	36.77	3.59
1294	1549	3.554524	CGAATAAATAAGCATGGGCACG	58.445	45.455	0.00	0.00	44.61	5.34
1316	1575	6.315144	CACGGTCTGAAAAATGTATGGATGTA	59.685	38.462	0.00	0.00	0.00	2.29
1332	1591	7.792374	ATGGATGTACTATGTCATGTTGTTC	57.208	36.000	0.00	0.00	0.00	3.18
1352	1612	5.207768	GTTCTGTTGTGAGTTGTAAGCATG	58.792	41.667	0.00	0.00	0.00	4.06
1364	1624	8.882736	TGAGTTGTAAGCATGAGTAATATTGTG	58.117	33.333	0.00	0.00	0.00	3.33
1374	1634	4.130118	GAGTAATATTGTGGAGCCACTGG	58.870	47.826	19.47	0.00	46.30	4.00
1388	1648	5.123979	GGAGCCACTGGTTATTGTTTAAGAG	59.876	44.000	0.00	0.00	0.00	2.85
1472	1732	9.743581	AAGGATGAATTTTATTGGCTCAAAATT	57.256	25.926	13.17	13.17	43.50	1.82
1520	1780	3.206246	CACACACCCGGCGTTTGT	61.206	61.111	6.01	5.38	35.74	2.83
1563	1831	2.022623	CAACACACACGCACACCG	59.977	61.111	0.00	0.00	44.21	4.94
1590	1858	7.041098	ACAACTAGCAAAGTCATAAGACCAAAG	60.041	37.037	0.00	0.00	46.15	2.77
1660	1939	4.182693	TCGGTGATCGACAAACTACAAT	57.817	40.909	0.00	0.00	43.74	2.71
1695	1978	2.417924	GCACAAACCATTGACACCACAA	60.418	45.455	0.00	0.00	38.94	3.33
1777	2061	3.930229	CGTCATCGGATCTAACCACAAAA	59.070	43.478	0.00	0.00	0.00	2.44
1790	2074	7.001674	TCTAACCACAAAAGCCAGAATCTAAA	58.998	34.615	0.00	0.00	0.00	1.85
1799	2083	6.916360	AAGCCAGAATCTAAATTTTCACCA	57.084	33.333	0.00	0.00	0.00	4.17
1830	2116	0.597568	TCCAAGCAAACCGAGCAATG	59.402	50.000	0.00	0.00	0.00	2.82
1832	2118	1.010419	CAAGCAAACCGAGCAATGCC	61.010	55.000	0.00	0.00	39.59	4.40
1833	2119	1.181098	AAGCAAACCGAGCAATGCCT	61.181	50.000	0.00	0.00	39.59	4.75
1901	2191	1.104630	CTCGGGTCTGACCTAGGTTC	58.895	60.000	25.01	9.99	38.64	3.62
1923	2213	2.192443	CCCGGAGCTCGAGACCTA	59.808	66.667	18.75	0.00	42.43	3.08
1960	2250	4.393062	CACCATCCAAGTCATACAAGTGTC	59.607	45.833	0.00	0.00	0.00	3.67
1999	2290	3.018856	CAATCCCAGCAGCTACAATTGA	58.981	45.455	13.59	0.00	0.00	2.57
2000	2291	3.589951	ATCCCAGCAGCTACAATTGAT	57.410	42.857	13.59	0.00	0.00	2.57
2012	2304	1.003580	ACAATTGATCGCCACCACTCT	59.996	47.619	13.59	0.00	0.00	3.24
2044	2336	1.358877	TTGCGTCAAGTCATCATCCG	58.641	50.000	0.00	0.00	0.00	4.18
2054	2346	7.399523	GTCAAGTCATCATCCGTAATTTGTAC	58.600	38.462	0.00	0.00	0.00	2.90
2078	2372	5.455755	CCATATCACTGAAGTCATCCACCAT	60.456	44.000	0.00	0.00	0.00	3.55
2144	2438	2.036089	GTCGTGGATCCATAGGAAGTCC	59.964	54.545	19.62	0.00	34.34	3.85
2151	2445	1.839994	TCCATAGGAAGTCCTTGCAGG	59.160	52.381	4.91	3.33	46.09	4.85
2190	2484	4.223255	CACCATCTGGCAGATCTGATCTAT	59.777	45.833	26.62	10.59	36.86	1.98

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
23	24	6.969828	AAAGACTATTGTTACTAGCACTGC	57.030	37.500	0.00	0.00	0.00	4.40
48	49	9.590451	TTTGACGTATAACTTTACCCTCATAAG	57.410	33.333	0.00	0.00	0.00	1.73
68	69	5.938322	AGCCACTTTGTGTATAATTTGACG	58.062	37.500	0.00	0.00	0.00	4.35
150	151	2.601763	GGTTAGGACGTGATAACTTGCG	59.398	50.000	15.39	0.00	33.36	4.85
151	152	3.592059	TGGTTAGGACGTGATAACTTGC	58.408	45.455	15.39	4.39	33.36	4.01
175	176	1.697082	TTGCGGGTCAAGGTGTACCA	61.697	55.000	3.56	0.00	37.51	3.25
179	180	2.159382	CTAAATTGCGGGTCAAGGTGT	58.841	47.619	0.00	0.00	38.22	4.16
180	181	1.135402	GCTAAATTGCGGGTCAAGGTG	60.135	52.381	0.00	0.00	38.22	4.00
181	182	1.173913	GCTAAATTGCGGGTCAAGGT	58.826	50.000	0.00	0.00	38.22	3.50
207	209	6.567769	AACGAGTAACGAACGTTTTTCTAA	57.432	33.333	17.19	0.00	45.58	2.10
235	239	1.818642	AACTGAGACATTGCAGGAGC	58.181	50.000	0.00	0.00	42.57	4.70
236	240	5.021033	AGATAACTGAGACATTGCAGGAG	57.979	43.478	0.00	0.00	36.47	3.69
237	241	5.426689	AAGATAACTGAGACATTGCAGGA	57.573	39.130	0.00	0.00	36.47	3.86
238	242	5.413833	ACAAAGATAACTGAGACATTGCAGG	59.586	40.000	0.00	0.00	36.47	4.85
239	243	6.148315	TCACAAAGATAACTGAGACATTGCAG	59.852	38.462	0.00	0.00	38.10	4.41
240	244	5.997129	TCACAAAGATAACTGAGACATTGCA	59.003	36.000	0.00	0.00	0.00	4.08
245	249	5.808366	AGGTCACAAAGATAACTGAGACA	57.192	39.130	0.00	0.00	0.00	3.41
252	256	4.253685	TGCAGCTAGGTCACAAAGATAAC	58.746	43.478	0.00	0.00	0.00	1.89
265	269	5.847304	TGACTAGATACAAATGCAGCTAGG	58.153	41.667	9.92	0.00	31.90	3.02
311	315	9.748708	CAAAACCTTATCATCTTTCTGTCAAAA	57.251	29.630	0.00	0.00	0.00	2.44
312	316	8.359642	CCAAAACCTTATCATCTTTCTGTCAAA	58.640	33.333	0.00	0.00	0.00	2.69
313	317	7.505585	ACCAAAACCTTATCATCTTTCTGTCAA	59.494	33.333	0.00	0.00	0.00	3.18
314	318	7.004086	ACCAAAACCTTATCATCTTTCTGTCA	58.996	34.615	0.00	0.00	0.00	3.58
315	319	7.174946	TGACCAAAACCTTATCATCTTTCTGTC	59.825	37.037	0.00	0.00	0.00	3.51
316	320	7.004086	TGACCAAAACCTTATCATCTTTCTGT	58.996	34.615	0.00	0.00	0.00	3.41
317	321	7.452880	TGACCAAAACCTTATCATCTTTCTG	57.547	36.000	0.00	0.00	0.00	3.02
318	322	8.360390	GTTTGACCAAAACCTTATCATCTTTCT	58.640	33.333	0.00	0.00	42.06	2.52
319	323	8.520835	GTTTGACCAAAACCTTATCATCTTTC	57.479	34.615	0.00	0.00	42.06	2.62
401	407	0.662619	CGTGCATGTTGAGGTGTTGT	59.337	50.000	0.00	0.00	0.00	3.32
407	413	1.536766	ACATTCACGTGCATGTTGAGG	59.463	47.619	25.11	5.21	27.64	3.86
505	517	3.068024	AGGCAATGCTCTTTGTCGAAAAA	59.932	39.130	4.82	0.00	36.34	1.94
506	518	2.622942	AGGCAATGCTCTTTGTCGAAAA	59.377	40.909	4.82	0.00	36.34	2.29
507	519	2.229792	AGGCAATGCTCTTTGTCGAAA	58.770	42.857	4.82	0.00	36.34	3.46
508	520	1.896220	AGGCAATGCTCTTTGTCGAA	58.104	45.000	4.82	0.00	36.34	3.71
509	521	2.760634	TAGGCAATGCTCTTTGTCGA	57.239	45.000	4.82	0.00	36.34	4.20
510	522	5.484173	TTTATAGGCAATGCTCTTTGTCG	57.516	39.130	4.82	0.00	36.34	4.35
511	523	7.930217	TGTATTTATAGGCAATGCTCTTTGTC	58.070	34.615	4.82	0.00	0.00	3.18
512	524	7.013655	CCTGTATTTATAGGCAATGCTCTTTGT	59.986	37.037	4.82	0.00	0.00	2.83
513	525	7.365741	CCTGTATTTATAGGCAATGCTCTTTG	58.634	38.462	4.82	0.00	0.00	2.77
514	526	6.491403	CCCTGTATTTATAGGCAATGCTCTTT	59.509	38.462	4.82	0.00	33.67	2.52
515	527	6.006449	CCCTGTATTTATAGGCAATGCTCTT	58.994	40.000	4.82	0.00	33.67	2.85
516	528	5.564550	CCCTGTATTTATAGGCAATGCTCT	58.435	41.667	4.82	3.24	33.67	4.09
517	529	4.156739	GCCCTGTATTTATAGGCAATGCTC	59.843	45.833	4.82	0.00	33.67	4.26
588	607	6.814954	ATGTACCTCTATGTGATTTGGTCT	57.185	37.500	0.00	0.00	0.00	3.85
695	715	2.775890	AGAGATGCCTGCGATAAATGG	58.224	47.619	0.00	0.00	0.00	3.16
706	797	1.421480	TCATGCTGCTAGAGATGCCT	58.579	50.000	0.00	0.00	0.00	4.75
896	1131	7.817962	CACTTAAGTAGGCTTCACTTTTAGCTA	59.182	37.037	8.04	0.00	37.42	3.32
1050	1296	2.107141	GCCTCCTTGATCGTCCGG	59.893	66.667	0.00	0.00	0.00	5.14
1053	1299	1.066587	CTCCGCCTCCTTGATCGTC	59.933	63.158	0.00	0.00	0.00	4.20
1107	1353	2.572104	AGTTCCTACTGGGACAACATCC	59.428	50.000	0.00	0.00	44.49	3.51
1109	1355	5.250774	ACATTAGTTCCTACTGGGACAACAT	59.749	40.000	0.00	0.00	44.49	2.71
1110	1356	4.595781	ACATTAGTTCCTACTGGGACAACA	59.404	41.667	0.00	0.00	44.49	3.33
1111	1357	4.935808	CACATTAGTTCCTACTGGGACAAC	59.064	45.833	0.00	0.00	44.49	3.32
1119	1365	3.194968	CACCCGTCACATTAGTTCCTACT	59.805	47.826	0.00	0.00	38.44	2.57
1127	1373	3.313012	TGAACTCACCCGTCACATTAG	57.687	47.619	0.00	0.00	0.00	1.73
1130	1379	2.038426	TCATTGAACTCACCCGTCACAT	59.962	45.455	0.00	0.00	0.00	3.21
1147	1396	2.813908	GCGGACGCGGTTCTCATT	60.814	61.111	12.47	0.00	0.00	2.57
1195	1444	1.098050	AAAGCAGCTTAGCCAATCCG	58.902	50.000	8.45	0.00	34.23	4.18
1196	1445	4.718940	TTAAAAGCAGCTTAGCCAATCC	57.281	40.909	8.45	0.00	34.23	3.01
1214	1464	6.465321	GGCCAGTATTCCTGTAGGCTAATTAA	60.465	42.308	0.00	0.00	39.74	1.40
1227	1482	2.257409	CTGCACGGGCCAGTATTCCT	62.257	60.000	7.46	0.00	40.13	3.36
1234	1489	4.767255	GAGACCTGCACGGGCCAG	62.767	72.222	7.46	1.85	44.54	4.85
1246	1501	4.978083	TTAACTAGACGATGTGGAGACC	57.022	45.455	0.00	0.00	0.00	3.85
1261	1516	9.701098	ATGCTTATTTATTCGGTCGATTAACTA	57.299	29.630	7.07	4.86	0.00	2.24
1271	1526	3.317993	GTGCCCATGCTTATTTATTCGGT	59.682	43.478	0.00	0.00	38.71	4.69
1294	1549	7.865706	AGTACATCCATACATTTTTCAGACC	57.134	36.000	0.00	0.00	0.00	3.85
1316	1575	6.054941	TCACAACAGAACAACATGACATAGT	58.945	36.000	0.00	0.00	0.00	2.12
1323	1582	4.985413	ACAACTCACAACAGAACAACATG	58.015	39.130	0.00	0.00	0.00	3.21
1332	1591	4.512944	ACTCATGCTTACAACTCACAACAG	59.487	41.667	0.00	0.00	0.00	3.16
1364	1624	5.007682	TCTTAAACAATAACCAGTGGCTCC	58.992	41.667	9.78	0.00	0.00	4.70
1388	1648	9.944376	TGTCCTAATGCCAAAGTAGATTATATC	57.056	33.333	0.00	0.00	0.00	1.63
1438	1698	7.009540	GCCAATAAAATTCATCCTTTGTCGAAG	59.990	37.037	0.00	0.00	35.02	3.79
1472	1732	7.330262	TGTGTTATGTATTCTCTTGATGCTCA	58.670	34.615	0.00	0.00	0.00	4.26
1515	1775	7.095187	GGCTATGTGCATCCTAGTTATACAAAC	60.095	40.741	0.00	0.00	45.15	2.93
1520	1780	6.680148	TTGGCTATGTGCATCCTAGTTATA	57.320	37.500	0.00	0.00	45.15	0.98
1563	1831	5.932303	TGGTCTTATGACTTTGCTAGTTGTC	59.068	40.000	8.51	0.00	42.54	3.18
1590	1858	0.392461	TTCCTTGCCGACACATAGCC	60.392	55.000	0.00	0.00	0.00	3.93
1641	1920	5.637810	TCTCAATTGTAGTTTGTCGATCACC	59.362	40.000	5.13	0.00	0.00	4.02
1660	1939	3.006940	GTTTGTGCGGATATGGTCTCAA	58.993	45.455	0.00	0.00	0.00	3.02
1695	1978	6.997655	TGCTATTGAAGATCCTCGTTATCAT	58.002	36.000	0.00	0.00	0.00	2.45
1777	2061	6.664816	TCATGGTGAAAATTTAGATTCTGGCT	59.335	34.615	0.00	0.00	0.00	4.75
1790	2074	6.012113	TGGACTGATTCTTCATGGTGAAAAT	58.988	36.000	0.00	0.00	35.73	1.82
1799	2083	4.219288	GGTTTGCTTGGACTGATTCTTCAT	59.781	41.667	0.00	0.00	0.00	2.57
1832	2118	5.640218	TTTTACGTCGTTACCTTGTTGAG	57.360	39.130	1.78	0.00	0.00	3.02
1901	2191	3.522731	CTCGAGCTCCGGGGTGAG	61.523	72.222	8.47	4.42	39.14	3.51
1923	2213	3.209097	GGTGGTGTTGCGTGCACT	61.209	61.111	16.19	0.00	37.07	4.40
1999	2290	1.267121	AGTTGTAGAGTGGTGGCGAT	58.733	50.000	0.00	0.00	0.00	4.58
2000	2291	1.045407	AAGTTGTAGAGTGGTGGCGA	58.955	50.000	0.00	0.00	0.00	5.54
2012	2304	3.472283	TGACGCAAAGGGTAAGTTGTA	57.528	42.857	0.00	0.00	0.00	2.41
2054	2346	4.141642	TGGTGGATGACTTCAGTGATATGG	60.142	45.833	0.00	0.00	0.00	2.74
2078	2372	6.383147	ACTTCGGGAGGTTTTATCTCTTGATA	59.617	38.462	0.00	0.00	34.32	2.15
2151	2445	1.003118	TGGTGGTGACTGTAGATTGCC	59.997	52.381	0.00	0.00	0.00	4.52

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.