AutoCloner

Multiple sequence alignment - TraesCS2D01G151700

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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	TraesCS2D01G151700	chr2D	100.000	3519	0	0	1	3519	95217156	95213638	0.000000e+00	6499
1	TraesCS2D01G151700	chr2D	99.165	1078	9	0	2442	3519	95208101	95207024	0.000000e+00	1941
2	TraesCS2D01G151700	chr2D	87.831	1134	120	11	1314	2444	95175441	95174323	0.000000e+00	1314
3	TraesCS2D01G151700	chr2D	97.739	575	9	4	2947	3519	430426134	430426706	0.000000e+00	987
4	TraesCS2D01G151700	chr2D	98.566	558	7	1	2962	3519	185902651	185902095	0.000000e+00	985
5	TraesCS2D01G151700	chr2D	97.387	574	12	3	2947	3519	541990103	541990674	0.000000e+00	974
6	TraesCS2D01G151700	chr2D	98.029	558	10	1	2962	3519	185895028	185894472	0.000000e+00	968
7	TraesCS2D01G151700	chr2D	92.652	626	46	0	1314	1939	95278616	95277991	0.000000e+00	902
8	TraesCS2D01G151700	chr2D	88.052	611	53	10	2	607	94929251	94928656	0.000000e+00	706
9	TraesCS2D01G151700	chr2D	93.235	340	22	1	2104	2443	95277993	95277655	1.890000e-137	499
10	TraesCS2D01G151700	chr2D	85.294	136	18	1	713	846	95177045	95176910	4.740000e-29	139
11	TraesCS2D01G151700	chr2D	94.872	78	4	0	1212	1289	95215868	95215791	4.770000e-24	122
12	TraesCS2D01G151700	chr2D	94.872	78	4	0	1289	1366	95215945	95215868	4.770000e-24	122
13	TraesCS2D01G151700	chr2B	96.546	1158	36	2	1289	2443	146781010	146779854	0.000000e+00	1914
14	TraesCS2D01G151700	chr2B	95.644	528	19	3	620	1145	146781725	146781200	0.000000e+00	845
15	TraesCS2D01G151700	chr2B	91.667	624	27	9	6	628	146818952	146818353	0.000000e+00	841
16	TraesCS2D01G151700	chr2B	93.939	528	28	3	620	1145	146805863	146805338	0.000000e+00	795
17	TraesCS2D01G151700	chr2B	88.449	606	60	6	6	607	146767138	146766539	0.000000e+00	723
18	TraesCS2D01G151700	chr2B	97.917	144	3	0	1146	1289	146781076	146780933	2.100000e-62	250
19	TraesCS2D01G151700	chr4D	97.156	1090	17	3	2443	3519	107181185	107182273	0.000000e+00	1829
20	TraesCS2D01G151700	chr3D	96.533	750	12	3	2442	3178	362892030	362891282	0.000000e+00	1229
21	TraesCS2D01G151700	chr3D	97.561	574	10	4	2947	3519	259481719	259482289	0.000000e+00	979
22	TraesCS2D01G151700	chr1D	96.267	750	14	6	2443	3180	385694527	385693780	0.000000e+00	1218
23	TraesCS2D01G151700	chr1D	94.927	749	11	7	2442	3178	358360834	358361567	0.000000e+00	1147
24	TraesCS2D01G151700	chr1D	97.387	574	12	3	2947	3519	358353756	358354327	0.000000e+00	974
25	TraesCS2D01G151700	chr1D	97.213	574	13	3	2947	3519	358361395	358361966	0.000000e+00	968
26	TraesCS2D01G151700	chr5D	95.393	738	18	7	2442	3178	454612151	454611429	0.000000e+00	1160
27	TraesCS2D01G151700	chr5D	95.073	751	11	6	2440	3178	217705391	217704655	0.000000e+00	1158
28	TraesCS2D01G151700	chr5D	94.558	735	14	6	2443	3165	248758670	248759390	0.000000e+00	1112
29	TraesCS2D01G151700	chr7D	94.793	749	12	7	2442	3178	304947134	304947867	0.000000e+00	1142
30	TraesCS2D01G151700	chrUn	98.208	558	9	1	2962	3519	466341529	466340973	0.000000e+00	974

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	TraesCS2D01G151700	chr2D	95213638	95217156	3518	True	2247.666667	6499	96.581333	1	3519	3	chr2D.!!$R6	3518
1	TraesCS2D01G151700	chr2D	95207024	95208101	1077	True	1941.000000	1941	99.165000	2442	3519	1	chr2D.!!$R2	1077
2	TraesCS2D01G151700	chr2D	430426134	430426706	572	False	987.000000	987	97.739000	2947	3519	1	chr2D.!!$F1	572
3	TraesCS2D01G151700	chr2D	185902095	185902651	556	True	985.000000	985	98.566000	2962	3519	1	chr2D.!!$R4	557
4	TraesCS2D01G151700	chr2D	541990103	541990674	571	False	974.000000	974	97.387000	2947	3519	1	chr2D.!!$F2	572
5	TraesCS2D01G151700	chr2D	185894472	185895028	556	True	968.000000	968	98.029000	2962	3519	1	chr2D.!!$R3	557
6	TraesCS2D01G151700	chr2D	95174323	95177045	2722	True	726.500000	1314	86.562500	713	2444	2	chr2D.!!$R5	1731
7	TraesCS2D01G151700	chr2D	94928656	94929251	595	True	706.000000	706	88.052000	2	607	1	chr2D.!!$R1	605
8	TraesCS2D01G151700	chr2D	95277655	95278616	961	True	700.500000	902	92.943500	1314	2443	2	chr2D.!!$R7	1129
9	TraesCS2D01G151700	chr2B	146779854	146781725	1871	True	1003.000000	1914	96.702333	620	2443	3	chr2B.!!$R4	1823
10	TraesCS2D01G151700	chr2B	146818353	146818952	599	True	841.000000	841	91.667000	6	628	1	chr2B.!!$R3	622
11	TraesCS2D01G151700	chr2B	146805338	146805863	525	True	795.000000	795	93.939000	620	1145	1	chr2B.!!$R2	525
12	TraesCS2D01G151700	chr2B	146766539	146767138	599	True	723.000000	723	88.449000	6	607	1	chr2B.!!$R1	601
13	TraesCS2D01G151700	chr4D	107181185	107182273	1088	False	1829.000000	1829	97.156000	2443	3519	1	chr4D.!!$F1	1076
14	TraesCS2D01G151700	chr3D	362891282	362892030	748	True	1229.000000	1229	96.533000	2442	3178	1	chr3D.!!$R1	736
15	TraesCS2D01G151700	chr3D	259481719	259482289	570	False	979.000000	979	97.561000	2947	3519	1	chr3D.!!$F1	572
16	TraesCS2D01G151700	chr1D	385693780	385694527	747	True	1218.000000	1218	96.267000	2443	3180	1	chr1D.!!$R1	737
17	TraesCS2D01G151700	chr1D	358360834	358361966	1132	False	1057.500000	1147	96.070000	2442	3519	2	chr1D.!!$F2	1077
18	TraesCS2D01G151700	chr1D	358353756	358354327	571	False	974.000000	974	97.387000	2947	3519	1	chr1D.!!$F1	572
19	TraesCS2D01G151700	chr5D	454611429	454612151	722	True	1160.000000	1160	95.393000	2442	3178	1	chr5D.!!$R2	736
20	TraesCS2D01G151700	chr5D	217704655	217705391	736	True	1158.000000	1158	95.073000	2440	3178	1	chr5D.!!$R1	738
21	TraesCS2D01G151700	chr5D	248758670	248759390	720	False	1112.000000	1112	94.558000	2443	3165	1	chr5D.!!$F1	722
22	TraesCS2D01G151700	chr7D	304947134	304947867	733	False	1142.000000	1142	94.793000	2442	3178	1	chr7D.!!$F1	736
23	TraesCS2D01G151700	chrUn	466340973	466341529	556	True	974.000000	974	98.208000	2962	3519	1	chrUn.!!$R1	557

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	Hairpin	End Stability	Orientation
71	72	1.461127	CCTTGCTGCAGAAGTTCGTAC	59.539	52.381	20.43	0.00	3.67	F
1081	2163	1.473278	ACTCGAGGATTCAGGTTCGTC	59.527	52.381	18.41	34.83	4.20	F
1689	2911	0.035439	CTAGGCTTTTCCCTCGCCAA	60.035	55.000	0.00	46.14	4.52	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Hairpin	End Stability	Orientation
1253	2458	0.036022	ACCTCAGTCTCAGGCAAAGC	59.964	55.000	0.00	33.84	3.51	R
2357	3581	0.937304	TTAATCGCGCTCTGAATGGC	59.063	50.000	5.56	0.00	4.40	R
2954	4180	1.903860	ACTCGTTTGGCACCCAGTATA	59.096	47.619	0.00	33.81	1.47	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
71	72	1.461127	CCTTGCTGCAGAAGTTCGTAC	59.539	52.381	20.43	0.00	0.00	3.67
85	86	4.370917	AGTTCGTACGTGTTACCAAACAT	58.629	39.130	16.05	0.00	46.84	2.71
109	110	5.673337	TTCACACATCTTACTGCTTGTTC	57.327	39.130	0.00	0.00	0.00	3.18
110	111	4.960938	TCACACATCTTACTGCTTGTTCT	58.039	39.130	0.00	0.00	0.00	3.01
111	112	5.368145	TCACACATCTTACTGCTTGTTCTT	58.632	37.500	0.00	0.00	0.00	2.52
112	113	5.822519	TCACACATCTTACTGCTTGTTCTTT	59.177	36.000	0.00	0.00	0.00	2.52
142	145	9.432982	TTGCATATCCCCTTGATAAAAACTAAT	57.567	29.630	0.00	0.00	39.36	1.73
285	290	2.005451	CCGAGCAAAATCTCTGGACTG	58.995	52.381	0.00	0.00	32.41	3.51
323	328	6.659242	TCTGTAATCTTTCCAATTTGAGGGAC	59.341	38.462	0.00	0.00	31.59	4.46
355	360	9.927668	CCAATGTAATTCTTCATTTTACCTTGT	57.072	29.630	0.00	0.00	31.22	3.16
595	600	5.513233	GGTATCTCCCTACCGATGGTTATA	58.487	45.833	0.00	0.00	37.09	0.98
596	601	5.593502	GGTATCTCCCTACCGATGGTTATAG	59.406	48.000	0.00	0.00	37.09	1.31
597	602	5.531753	ATCTCCCTACCGATGGTTATAGA	57.468	43.478	0.00	0.00	37.09	1.98
598	603	5.531753	TCTCCCTACCGATGGTTATAGAT	57.468	43.478	0.00	0.00	37.09	1.98
599	604	6.647461	TCTCCCTACCGATGGTTATAGATA	57.353	41.667	0.00	0.00	37.09	1.98
600	605	7.222180	TCTCCCTACCGATGGTTATAGATAT	57.778	40.000	0.00	0.00	37.09	1.63
790	798	1.581223	AGTCCCCTACTTAGGTTGCC	58.419	55.000	1.58	0.00	42.03	4.52
806	814	3.010420	GTTGCCTCTCATAAAGGTGGAC	58.990	50.000	0.00	0.00	36.21	4.02
846	854	2.041081	TGTGGCACCTAACTATTTGGCT	59.959	45.455	16.26	0.00	35.63	4.75
860	1849	1.979855	TTGGCTTGTCTTGCTGCTTA	58.020	45.000	0.00	0.00	0.00	3.09
891	1964	9.849166	TTAATTTCATAAACCTTTTGGATCGAC	57.151	29.630	0.00	0.00	44.07	4.20
919	1992	3.788227	AGTCACACTTCTTGGGCAATA	57.212	42.857	0.00	0.00	0.00	1.90
1054	2136	2.091775	GGGGAAGGAGAGACTAGCTACA	60.092	54.545	0.00	0.00	0.00	2.74
1065	2147	7.197071	AGAGACTAGCTACATCAATAACTCG	57.803	40.000	0.00	0.00	0.00	4.18
1081	2163	1.473278	ACTCGAGGATTCAGGTTCGTC	59.527	52.381	18.41	0.00	34.83	4.20
1210	2415	7.339721	GCCATATAGTAGGAGTAGATTGCACTA	59.660	40.741	0.00	0.00	0.00	2.74
1230	2435	9.120538	TGCACTATACTTTTAATCTGGATTTCC	57.879	33.333	1.01	0.00	32.50	3.13
1231	2436	9.343539	GCACTATACTTTTAATCTGGATTTCCT	57.656	33.333	1.01	0.00	36.82	3.36
1243	2448	8.953368	AATCTGGATTTCCTTTTCATTTATGC	57.047	30.769	0.00	0.00	36.82	3.14
1244	2449	6.877236	TCTGGATTTCCTTTTCATTTATGCC	58.123	36.000	0.00	0.00	36.82	4.40
1245	2450	6.440010	TCTGGATTTCCTTTTCATTTATGCCA	59.560	34.615	0.00	0.00	36.82	4.92
1246	2451	6.642430	TGGATTTCCTTTTCATTTATGCCAG	58.358	36.000	0.00	0.00	36.82	4.85
1247	2452	5.525012	GGATTTCCTTTTCATTTATGCCAGC	59.475	40.000	0.00	0.00	0.00	4.85
1248	2453	5.480642	TTTCCTTTTCATTTATGCCAGCA	57.519	34.783	0.00	0.00	0.00	4.41
1249	2454	5.480642	TTCCTTTTCATTTATGCCAGCAA	57.519	34.783	0.00	0.00	0.00	3.91
1250	2455	5.480642	TCCTTTTCATTTATGCCAGCAAA	57.519	34.783	0.00	0.00	0.00	3.68
1251	2456	5.862845	TCCTTTTCATTTATGCCAGCAAAA	58.137	33.333	0.00	0.00	0.00	2.44
1252	2457	6.294473	TCCTTTTCATTTATGCCAGCAAAAA	58.706	32.000	0.00	0.00	0.00	1.94
1253	2458	6.427547	TCCTTTTCATTTATGCCAGCAAAAAG	59.572	34.615	13.97	13.97	34.08	2.27
1254	2459	5.610235	TTTCATTTATGCCAGCAAAAAGC	57.390	34.783	0.00	0.00	46.19	3.51
1267	2472	3.722728	CAAAAAGCTTTGCCTGAGACT	57.277	42.857	13.54	0.00	35.81	3.24
1268	2473	3.378339	CAAAAAGCTTTGCCTGAGACTG	58.622	45.455	13.54	0.00	35.81	3.51
1269	2474	2.645838	AAAGCTTTGCCTGAGACTGA	57.354	45.000	11.80	0.00	0.00	3.41
1270	2475	2.181954	AAGCTTTGCCTGAGACTGAG	57.818	50.000	0.00	0.00	0.00	3.35
1271	2476	0.324285	AGCTTTGCCTGAGACTGAGG	59.676	55.000	3.15	3.15	0.00	3.86
1272	2477	0.036022	GCTTTGCCTGAGACTGAGGT	59.964	55.000	9.90	0.00	32.60	3.85
1273	2478	1.805869	CTTTGCCTGAGACTGAGGTG	58.194	55.000	9.90	0.00	32.60	4.00
1274	2479	0.397941	TTTGCCTGAGACTGAGGTGG	59.602	55.000	9.90	0.00	32.60	4.61
1275	2480	0.764369	TTGCCTGAGACTGAGGTGGT	60.764	55.000	9.90	0.00	32.60	4.16
1276	2481	0.114364	TGCCTGAGACTGAGGTGGTA	59.886	55.000	9.90	0.00	32.60	3.25
1277	2482	0.533032	GCCTGAGACTGAGGTGGTAC	59.467	60.000	9.90	0.00	32.60	3.34
1278	2483	1.893210	GCCTGAGACTGAGGTGGTACT	60.893	57.143	9.90	0.00	32.60	2.73
1279	2484	2.530701	CCTGAGACTGAGGTGGTACTT	58.469	52.381	0.00	0.00	0.00	2.24
1280	2485	2.232452	CCTGAGACTGAGGTGGTACTTG	59.768	54.545	0.00	0.00	0.00	3.16
1281	2486	3.157881	CTGAGACTGAGGTGGTACTTGA	58.842	50.000	0.00	0.00	0.00	3.02
1282	2487	3.157881	TGAGACTGAGGTGGTACTTGAG	58.842	50.000	0.00	0.00	0.00	3.02
1283	2488	3.181433	TGAGACTGAGGTGGTACTTGAGA	60.181	47.826	0.00	0.00	0.00	3.27
1284	2489	3.827302	GAGACTGAGGTGGTACTTGAGAA	59.173	47.826	0.00	0.00	0.00	2.87
1285	2490	3.829601	AGACTGAGGTGGTACTTGAGAAG	59.170	47.826	0.00	0.00	0.00	2.85
1286	2491	2.900546	ACTGAGGTGGTACTTGAGAAGG	59.099	50.000	0.00	0.00	0.00	3.46
1287	2492	1.623811	TGAGGTGGTACTTGAGAAGGC	59.376	52.381	0.00	0.00	0.00	4.35
1288	2493	1.903183	GAGGTGGTACTTGAGAAGGCT	59.097	52.381	0.00	0.00	0.00	4.58
1289	2494	3.097614	GAGGTGGTACTTGAGAAGGCTA	58.902	50.000	0.00	0.00	0.00	3.93
1290	2495	2.832733	AGGTGGTACTTGAGAAGGCTAC	59.167	50.000	0.00	0.00	0.00	3.58
1291	2496	2.832733	GGTGGTACTTGAGAAGGCTACT	59.167	50.000	0.00	0.00	0.00	2.57
1292	2497	3.261137	GGTGGTACTTGAGAAGGCTACTT	59.739	47.826	0.00	0.00	40.34	2.24
1293	2498	4.262938	GGTGGTACTTGAGAAGGCTACTTT	60.263	45.833	0.00	0.00	36.97	2.66
1294	2499	5.306394	GTGGTACTTGAGAAGGCTACTTTT	58.694	41.667	0.00	0.00	36.97	2.27
1295	2500	6.461640	GTGGTACTTGAGAAGGCTACTTTTA	58.538	40.000	0.00	0.00	36.97	1.52
1296	2501	6.932960	GTGGTACTTGAGAAGGCTACTTTTAA	59.067	38.462	0.00	0.00	36.97	1.52
1297	2502	7.606839	GTGGTACTTGAGAAGGCTACTTTTAAT	59.393	37.037	0.00	0.00	36.97	1.40
1298	2503	8.818860	TGGTACTTGAGAAGGCTACTTTTAATA	58.181	33.333	0.00	0.00	36.97	0.98
1299	2504	9.833917	GGTACTTGAGAAGGCTACTTTTAATAT	57.166	33.333	0.00	0.00	36.97	1.28
1301	2506	8.738645	ACTTGAGAAGGCTACTTTTAATATGG	57.261	34.615	0.00	0.00	36.97	2.74
1302	2507	7.283354	ACTTGAGAAGGCTACTTTTAATATGGC	59.717	37.037	0.00	0.00	36.97	4.40
1377	2590	2.298446	TGAGAAGGCTGTGAGAGAAGTG	59.702	50.000	0.00	0.00	0.00	3.16
1400	2616	1.229625	TGGATCTCCACCAGCCAGT	60.230	57.895	0.00	0.00	42.01	4.00
1435	2651	4.101114	TGATTTAGGGTGCTCTTCTGGTA	58.899	43.478	0.00	0.00	0.00	3.25
1474	2690	2.485814	GTCTCCAAGGTGATCAAAGTGC	59.514	50.000	0.00	0.00	0.00	4.40
1538	2754	3.683802	AGCTCCAGTTCTTTCTCAATGG	58.316	45.455	0.00	0.00	0.00	3.16
1625	2847	7.593825	ACAGCAAGACATAAAGAAAATACACC	58.406	34.615	0.00	0.00	0.00	4.16
1689	2911	0.035439	CTAGGCTTTTCCCTCGCCAA	60.035	55.000	0.00	0.00	46.14	4.52
1893	3115	0.895530	TTGCTAAGACTACGCCAGCT	59.104	50.000	0.00	0.00	33.38	4.24
2091	3313	4.159321	TCTCTGCAATCTCTTGTCGAAGAT	59.841	41.667	0.00	0.00	40.67	2.40
2206	3430	4.339530	GGTCTGGTGAAGAAAGAAAAGCTT	59.660	41.667	0.00	0.00	36.40	3.74
2257	3481	2.632377	TCGATCAATGAAGTGAAGGCC	58.368	47.619	0.00	0.00	0.00	5.19
2329	3553	1.839994	TCCAACTGGGATCCTCATGAC	59.160	52.381	12.58	0.00	42.15	3.06
2357	3581	1.771565	AGGGGATGATGCACACAATG	58.228	50.000	0.00	0.00	0.00	2.82
2396	3620	2.867624	ACATTGCAAAGAGCTTGAGGA	58.132	42.857	8.96	0.00	45.94	3.71
2486	3710	6.040504	GGATATAAATTCCCAGAAAAACGGCT	59.959	38.462	0.00	0.00	0.00	5.52
3050	4301	1.741401	CCTCGAGCGGACAATGCAA	60.741	57.895	6.99	0.00	33.85	4.08
3158	4467	0.735471	CTGAATGACTCCTCGAGCGA	59.265	55.000	6.99	5.16	32.04	4.93
3274	4641	0.397254	ACCGTCCCAGGGATACTCAG	60.397	60.000	12.84	0.00	32.73	3.35
3390	4758	5.186942	TCCATCCGAAAACCGATAATTCAA	58.813	37.500	0.00	0.00	41.76	2.69
3514	4882	7.440255	CCGAATACCGTTATCAAGATTTAACCT	59.560	37.037	0.00	0.00	36.31	3.50

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
85	86	7.161404	AGAACAAGCAGTAAGATGTGTGAATA	58.839	34.615	0.00	0.00	0.00	1.75
661	666	5.118286	GCAGGGGTAATCCATTTTTCAATG	58.882	41.667	0.00	0.00	39.79	2.82
662	667	4.164030	GGCAGGGGTAATCCATTTTTCAAT	59.836	41.667	0.00	0.00	37.22	2.57
790	798	3.133721	CCCTCTGTCCACCTTTATGAGAG	59.866	52.174	0.00	0.00	0.00	3.20
806	814	1.542915	CACAAAATGAGTGGCCCTCTG	59.457	52.381	18.49	12.29	41.11	3.35
846	854	9.410556	GAAATTAAAAGATAAGCAGCAAGACAA	57.589	29.630	0.00	0.00	0.00	3.18
880	1869	3.813166	GACTTGTTCCTGTCGATCCAAAA	59.187	43.478	0.00	0.00	0.00	2.44
891	1964	3.313526	CCAAGAAGTGTGACTTGTTCCTG	59.686	47.826	0.00	0.00	39.32	3.86
935	2008	0.895530	CTCGCCCTTGTGAAGACCTA	59.104	55.000	0.00	0.00	0.00	3.08
936	2009	1.122019	ACTCGCCCTTGTGAAGACCT	61.122	55.000	0.00	0.00	0.00	3.85
937	2010	0.951040	CACTCGCCCTTGTGAAGACC	60.951	60.000	0.00	0.00	36.38	3.85
938	2011	1.569479	GCACTCGCCCTTGTGAAGAC	61.569	60.000	0.00	0.00	36.38	3.01
1054	2136	5.878406	ACCTGAATCCTCGAGTTATTGAT	57.122	39.130	12.31	3.45	0.00	2.57
1065	2147	4.065789	ACTTTTGACGAACCTGAATCCTC	58.934	43.478	0.00	0.00	0.00	3.71
1226	2431	5.480642	TGCTGGCATAAATGAAAAGGAAA	57.519	34.783	0.00	0.00	0.00	3.13
1227	2432	5.480642	TTGCTGGCATAAATGAAAAGGAA	57.519	34.783	0.00	0.00	0.00	3.36
1228	2433	5.480642	TTTGCTGGCATAAATGAAAAGGA	57.519	34.783	0.00	0.00	0.00	3.36
1229	2434	6.557291	TTTTTGCTGGCATAAATGAAAAGG	57.443	33.333	7.00	0.00	0.00	3.11
1230	2435	6.081693	GCTTTTTGCTGGCATAAATGAAAAG	58.918	36.000	16.77	16.77	38.95	2.27
1231	2436	5.999721	GCTTTTTGCTGGCATAAATGAAAA	58.000	33.333	10.52	6.18	38.95	2.29
1232	2437	5.610235	GCTTTTTGCTGGCATAAATGAAA	57.390	34.783	10.52	0.00	38.95	2.69
1247	2452	3.067180	TCAGTCTCAGGCAAAGCTTTTTG	59.933	43.478	9.53	8.70	35.15	2.44
1248	2453	3.290710	TCAGTCTCAGGCAAAGCTTTTT	58.709	40.909	9.53	0.00	0.00	1.94
1249	2454	2.883386	CTCAGTCTCAGGCAAAGCTTTT	59.117	45.455	9.53	0.00	0.00	2.27
1250	2455	2.502295	CTCAGTCTCAGGCAAAGCTTT	58.498	47.619	5.69	5.69	0.00	3.51
1251	2456	1.271271	CCTCAGTCTCAGGCAAAGCTT	60.271	52.381	0.00	0.00	0.00	3.74
1252	2457	0.324285	CCTCAGTCTCAGGCAAAGCT	59.676	55.000	0.00	0.00	0.00	3.74
1253	2458	0.036022	ACCTCAGTCTCAGGCAAAGC	59.964	55.000	0.00	0.00	33.84	3.51
1254	2459	1.610102	CCACCTCAGTCTCAGGCAAAG	60.610	57.143	0.00	0.00	33.84	2.77
1255	2460	0.397941	CCACCTCAGTCTCAGGCAAA	59.602	55.000	0.00	0.00	33.84	3.68
1256	2461	0.764369	ACCACCTCAGTCTCAGGCAA	60.764	55.000	0.00	0.00	33.84	4.52
1257	2462	0.114364	TACCACCTCAGTCTCAGGCA	59.886	55.000	0.00	0.00	33.84	4.75
1258	2463	0.533032	GTACCACCTCAGTCTCAGGC	59.467	60.000	0.00	0.00	33.84	4.85
1259	2464	2.223803	AGTACCACCTCAGTCTCAGG	57.776	55.000	0.00	0.00	37.03	3.86
1260	2465	3.157881	TCAAGTACCACCTCAGTCTCAG	58.842	50.000	0.00	0.00	0.00	3.35
1261	2466	3.157881	CTCAAGTACCACCTCAGTCTCA	58.842	50.000	0.00	0.00	0.00	3.27
1262	2467	3.422796	TCTCAAGTACCACCTCAGTCTC	58.577	50.000	0.00	0.00	0.00	3.36
1263	2468	3.527507	TCTCAAGTACCACCTCAGTCT	57.472	47.619	0.00	0.00	0.00	3.24
1264	2469	3.056465	CCTTCTCAAGTACCACCTCAGTC	60.056	52.174	0.00	0.00	0.00	3.51
1265	2470	2.900546	CCTTCTCAAGTACCACCTCAGT	59.099	50.000	0.00	0.00	0.00	3.41
1266	2471	2.354203	GCCTTCTCAAGTACCACCTCAG	60.354	54.545	0.00	0.00	0.00	3.35
1267	2472	1.623811	GCCTTCTCAAGTACCACCTCA	59.376	52.381	0.00	0.00	0.00	3.86
1268	2473	1.903183	AGCCTTCTCAAGTACCACCTC	59.097	52.381	0.00	0.00	0.00	3.85
1269	2474	2.031495	AGCCTTCTCAAGTACCACCT	57.969	50.000	0.00	0.00	0.00	4.00
1270	2475	2.832733	AGTAGCCTTCTCAAGTACCACC	59.167	50.000	0.00	0.00	0.00	4.61
1271	2476	4.538746	AAGTAGCCTTCTCAAGTACCAC	57.461	45.455	0.00	0.00	0.00	4.16
1272	2477	5.562298	AAAAGTAGCCTTCTCAAGTACCA	57.438	39.130	0.00	0.00	0.00	3.25
1273	2478	9.833917	ATATTAAAAGTAGCCTTCTCAAGTACC	57.166	33.333	0.00	0.00	0.00	3.34
1275	2480	9.832445	CCATATTAAAAGTAGCCTTCTCAAGTA	57.168	33.333	0.00	0.00	0.00	2.24
1276	2481	7.283354	GCCATATTAAAAGTAGCCTTCTCAAGT	59.717	37.037	0.00	0.00	0.00	3.16
1277	2482	7.500559	AGCCATATTAAAAGTAGCCTTCTCAAG	59.499	37.037	0.00	0.00	0.00	3.02
1278	2483	7.346471	AGCCATATTAAAAGTAGCCTTCTCAA	58.654	34.615	0.00	0.00	0.00	3.02
1279	2484	6.900194	AGCCATATTAAAAGTAGCCTTCTCA	58.100	36.000	0.00	0.00	0.00	3.27
1280	2485	7.809546	AAGCCATATTAAAAGTAGCCTTCTC	57.190	36.000	0.00	0.00	0.00	2.87
1281	2486	7.285629	GGAAAGCCATATTAAAAGTAGCCTTCT	59.714	37.037	0.00	0.00	0.00	2.85
1282	2487	7.285629	AGGAAAGCCATATTAAAAGTAGCCTTC	59.714	37.037	0.00	0.00	36.29	3.46
1283	2488	7.126061	AGGAAAGCCATATTAAAAGTAGCCTT	58.874	34.615	0.00	0.00	36.29	4.35
1284	2489	6.673583	AGGAAAGCCATATTAAAAGTAGCCT	58.326	36.000	0.00	0.00	36.29	4.58
1285	2490	6.961360	AGGAAAGCCATATTAAAAGTAGCC	57.039	37.500	0.00	0.00	36.29	3.93
1286	2491	9.302345	GAAAAGGAAAGCCATATTAAAAGTAGC	57.698	33.333	0.00	0.00	36.29	3.58
1294	2499	9.762933	GCATAAATGAAAAGGAAAGCCATATTA	57.237	29.630	0.00	0.00	36.29	0.98
1295	2500	8.488668	AGCATAAATGAAAAGGAAAGCCATATT	58.511	29.630	0.00	0.00	36.29	1.28
1296	2501	8.026396	AGCATAAATGAAAAGGAAAGCCATAT	57.974	30.769	0.00	0.00	36.29	1.78
1297	2502	7.422465	AGCATAAATGAAAAGGAAAGCCATA	57.578	32.000	0.00	0.00	36.29	2.74
1298	2503	6.303903	AGCATAAATGAAAAGGAAAGCCAT	57.696	33.333	0.00	0.00	36.29	4.40
1299	2504	5.743636	AGCATAAATGAAAAGGAAAGCCA	57.256	34.783	0.00	0.00	36.29	4.75
1300	2505	5.750547	GCTAGCATAAATGAAAAGGAAAGCC	59.249	40.000	10.63	0.00	0.00	4.35
1301	2506	6.332630	TGCTAGCATAAATGAAAAGGAAAGC	58.667	36.000	14.93	0.00	0.00	3.51
1302	2507	8.761575	TTTGCTAGCATAAATGAAAAGGAAAG	57.238	30.769	20.13	0.00	0.00	2.62
1400	2616	5.647658	CACCCTAAATCAACAGCAGTCATTA	59.352	40.000	0.00	0.00	0.00	1.90
1435	2651	4.500035	GGAGACGAAGAAGAGTGTGTTCTT	60.500	45.833	0.00	0.00	45.05	2.52
1474	2690	4.322080	TTTCGTCACTATCATGGCCTAG	57.678	45.455	3.32	0.00	0.00	3.02
1538	2754	4.275196	GGTTGAAGTTGTTTCCTGGTAGAC	59.725	45.833	0.00	0.00	34.77	2.59
1625	2847	3.057456	AGCGATATAGAAAGGTGGTAGCG	60.057	47.826	0.00	0.00	0.00	4.26
1689	2911	3.118738	ACGAGTGAAAGAGGTGACAACTT	60.119	43.478	0.00	0.00	0.00	2.66
1893	3115	1.240256	GGTACAATTCCGCAACACCA	58.760	50.000	0.00	0.00	0.00	4.17
1923	3145	6.375174	TGAGGAACAATAACATGTCATTCTGG	59.625	38.462	0.00	0.00	31.81	3.86
2091	3313	6.563222	AAATTAACTTAAGGCTTACGCACA	57.437	33.333	6.43	0.00	38.10	4.57
2107	3329	8.173130	CAGTTCCGATAGTTGTGGTAAATTAAC	58.827	37.037	0.00	0.00	0.00	2.01
2206	3430	2.342406	TGGGGAGATTGAAGGAGTCA	57.658	50.000	0.00	0.00	0.00	3.41
2257	3481	1.082117	ACTCGCTTTGCCCGATTACG	61.082	55.000	0.00	0.00	33.83	3.18
2329	3553	1.945387	CATCATCCCCTTGTGAGTCG	58.055	55.000	0.00	0.00	0.00	4.18
2357	3581	0.937304	TTAATCGCGCTCTGAATGGC	59.063	50.000	5.56	0.00	0.00	4.40
2954	4180	1.903860	ACTCGTTTGGCACCCAGTATA	59.096	47.619	0.00	0.00	33.81	1.47
3050	4301	8.057536	TCGTTTGGCACCAGTATTATTATTTT	57.942	30.769	0.00	0.00	0.00	1.82
3158	4467	6.538021	TGCGGCATTATTATTTCTGCATTTTT	59.462	30.769	0.00	0.00	36.34	1.94
3390	4758	3.487372	TCGGATGGAGATACGACTTGAT	58.513	45.455	0.00	0.00	40.17	2.57

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.