AutoCloner

Multiple sequence alignment - TraesCS2D01G419200

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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	TraesCS2D01G419200	chr2D	100.000	3423	0	0	1	3423	533164127	533167549	0.000000e+00	6322.0
1	TraesCS2D01G419200	chr2D	91.998	1662	97	15	1080	2712	533251638	533253292	0.000000e+00	2300.0
2	TraesCS2D01G419200	chr2D	84.869	1606	186	26	967	2556	533658119	533659683	0.000000e+00	1567.0
3	TraesCS2D01G419200	chr2D	78.506	1754	287	50	980	2697	533668306	533670005	0.000000e+00	1068.0
4	TraesCS2D01G419200	chr2D	79.037	1579	274	38	1150	2697	533831245	533832797	0.000000e+00	1029.0
5	TraesCS2D01G419200	chr2D	79.113	1489	231	44	967	2424	534135006	534136445	0.000000e+00	953.0
6	TraesCS2D01G419200	chr2D	78.963	1388	244	25	1176	2529	533662433	533663806	0.000000e+00	902.0
7	TraesCS2D01G419200	chr2D	82.883	222	6	8	865	1054	533251427	533251648	1.630000e-38	171.0
8	TraesCS2D01G419200	chr2B	93.876	2923	93	32	526	3423	632987594	632990455	0.000000e+00	4327.0
9	TraesCS2D01G419200	chr2B	84.075	1595	206	26	967	2530	633575153	633576730	0.000000e+00	1495.0
10	TraesCS2D01G419200	chr2B	78.992	1547	268	34	980	2510	633584651	633586156	0.000000e+00	1003.0
11	TraesCS2D01G419200	chr2B	86.140	570	58	15	226	781	632926768	632927330	2.270000e-166	595.0
12	TraesCS2D01G419200	chr2B	83.453	556	71	11	967	1514	633240587	633241129	6.600000e-137	497.0
13	TraesCS2D01G419200	chr2B	86.920	237	26	4	1	235	632926354	632926587	9.420000e-66	261.0
14	TraesCS2D01G419200	chr2A	91.840	2745	154	37	1	2703	677544981	677547697	0.000000e+00	3764.0
15	TraesCS2D01G419200	chr2A	85.052	194	27	2	32	224	669816557	669816365	2.690000e-46	196.0
16	TraesCS2D01G419200	chrUn	84.203	1323	180	17	1253	2557	26138820	26140131	0.000000e+00	1258.0
17	TraesCS2D01G419200	chrUn	88.333	240	18	3	967	1205	26119878	26120108	2.600000e-71	279.0
18	TraesCS2D01G419200	chr7B	76.952	1050	181	38	1246	2275	26034513	26033505	3.000000e-150	542.0
19	TraesCS2D01G419200	chr7B	85.217	115	11	3	963	1077	26034744	26034636	2.790000e-21	113.0
20	TraesCS2D01G419200	chr7B	100.000	29	0	0	1544	1572	723971038	723971066	2.000000e-03	54.7
21	TraesCS2D01G419200	chr7A	77.684	829	131	40	1623	2429	81916751	81915955	1.120000e-124	457.0
22	TraesCS2D01G419200	chr7A	87.692	65	6	2	3147	3210	49640358	49640295	1.320000e-09	75.0
23	TraesCS2D01G419200	chr6B	80.556	216	35	5	1	215	695196981	695197190	3.540000e-35	159.0
24	TraesCS2D01G419200	chr1B	86.014	143	18	2	78	218	301098384	301098526	5.920000e-33	152.0
25	TraesCS2D01G419200	chr1B	81.707	82	14	1	3143	3224	522830850	522830770	2.200000e-07	67.6
26	TraesCS2D01G419200	chr7D	81.046	153	23	4	963	1114	78799551	78799404	2.160000e-22	117.0
27	TraesCS2D01G419200	chr1A	89.610	77	8	0	3150	3226	495704656	495704732	7.820000e-17	99.0
28	TraesCS2D01G419200	chr1A	81.707	82	14	1	3143	3224	488202702	488202622	2.200000e-07	67.6
29	TraesCS2D01G419200	chr5B	87.879	66	7	1	3146	3211	686209499	686209563	3.660000e-10	76.8
30	TraesCS2D01G419200	chr3A	93.478	46	3	0	3147	3192	509887463	509887418	6.130000e-08	69.4
31	TraesCS2D01G419200	chr5D	89.091	55	5	1	150	203	232544337	232544391	2.200000e-07	67.6

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	TraesCS2D01G419200	chr2D	533164127	533167549	3422	False	6322.0	6322	100.0000	1	3423	1	chr2D.!!$F1	3422
1	TraesCS2D01G419200	chr2D	533251427	533253292	1865	False	1235.5	2300	87.4405	865	2712	2	chr2D.!!$F5	1847
2	TraesCS2D01G419200	chr2D	533658119	533663806	5687	False	1234.5	1567	81.9160	967	2556	2	chr2D.!!$F6	1589
3	TraesCS2D01G419200	chr2D	533668306	533670005	1699	False	1068.0	1068	78.5060	980	2697	1	chr2D.!!$F2	1717
4	TraesCS2D01G419200	chr2D	533831245	533832797	1552	False	1029.0	1029	79.0370	1150	2697	1	chr2D.!!$F3	1547
5	TraesCS2D01G419200	chr2D	534135006	534136445	1439	False	953.0	953	79.1130	967	2424	1	chr2D.!!$F4	1457
6	TraesCS2D01G419200	chr2B	632987594	632990455	2861	False	4327.0	4327	93.8760	526	3423	1	chr2B.!!$F1	2897
7	TraesCS2D01G419200	chr2B	633575153	633576730	1577	False	1495.0	1495	84.0750	967	2530	1	chr2B.!!$F3	1563
8	TraesCS2D01G419200	chr2B	633584651	633586156	1505	False	1003.0	1003	78.9920	980	2510	1	chr2B.!!$F4	1530
9	TraesCS2D01G419200	chr2B	633240587	633241129	542	False	497.0	497	83.4530	967	1514	1	chr2B.!!$F2	547
10	TraesCS2D01G419200	chr2B	632926354	632927330	976	False	428.0	595	86.5300	1	781	2	chr2B.!!$F5	780
11	TraesCS2D01G419200	chr2A	677544981	677547697	2716	False	3764.0	3764	91.8400	1	2703	1	chr2A.!!$F1	2702
12	TraesCS2D01G419200	chrUn	26138820	26140131	1311	False	1258.0	1258	84.2030	1253	2557	1	chrUn.!!$F2	1304
13	TraesCS2D01G419200	chr7B	26033505	26034744	1239	True	327.5	542	81.0845	963	2275	2	chr7B.!!$R1	1312
14	TraesCS2D01G419200	chr7A	81915955	81916751	796	True	457.0	457	77.6840	1623	2429	1	chr7A.!!$R2	806

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
630	636	0.103937	GAGCTGCGAGCATCTTAGGT	59.896	55.0	2.86	0.0	45.56	3.08	F
1061	1124	0.245266	TATTTCTCCTCACGCGCACA	59.755	50.0	5.73	0.0	0.00	4.57	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2077	2203	0.033991	TCTTCTCGCCAGGAGCTAGT	60.034	55.000	0.0	0.0	42.82	2.57	R
3055	4036	2.083774	CCCATTCGTGTGCAGTACAAT	58.916	47.619	0.0	0.0	41.89	2.71	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
21	22	4.850859	CGTGCTATTGTTTCGATAACCA	57.149	40.909	7.64	0.00	0.00	3.67
63	65	3.442273	AGTTCGCTCTTCACCAAAAACAA	59.558	39.130	0.00	0.00	0.00	2.83
70	72	6.640499	CGCTCTTCACCAAAAACAATCATTTA	59.360	34.615	0.00	0.00	0.00	1.40
80	82	7.094848	CCAAAAACAATCATTTATTTTCGCCCT	60.095	33.333	0.00	0.00	0.00	5.19
90	92	6.827586	TTTATTTTCGCCCTCACTTTGTAT	57.172	33.333	0.00	0.00	0.00	2.29
94	96	4.386867	TTCGCCCTCACTTTGTATAGAG	57.613	45.455	0.00	0.00	0.00	2.43
99	101	5.241949	CGCCCTCACTTTGTATAGAGTCTAT	59.758	44.000	16.75	16.75	0.00	1.98
130	132	8.755696	TTTGCAGACACAAATCCATAATTTAC	57.244	30.769	0.00	0.00	35.77	2.01
131	133	7.459795	TGCAGACACAAATCCATAATTTACA	57.540	32.000	0.00	0.00	35.77	2.41
145	147	7.029563	CCATAATTTACAAGAAGAGGCAACAC	58.970	38.462	0.00	0.00	41.41	3.32
147	149	2.561478	TACAAGAAGAGGCAACACCC	57.439	50.000	0.00	0.00	40.58	4.61
153	155	2.108952	AGAAGAGGCAACACCCAATTCT	59.891	45.455	0.00	0.00	40.58	2.40
155	157	2.242043	AGAGGCAACACCCAATTCTTG	58.758	47.619	0.00	0.00	40.58	3.02
158	160	1.412343	GGCAACACCCAATTCTTGTGT	59.588	47.619	0.00	0.00	44.63	3.72
162	164	2.316108	ACACCCAATTCTTGTGTTCCC	58.684	47.619	0.00	0.00	40.12	3.97
163	165	2.091333	ACACCCAATTCTTGTGTTCCCT	60.091	45.455	0.00	0.00	40.12	4.20
171	173	5.712152	ATTCTTGTGTTCCCTGTGAAATC	57.288	39.130	0.00	0.00	33.94	2.17
184	186	6.380274	TCCCTGTGAAATCGATACTCTTACTT	59.620	38.462	0.00	0.00	0.00	2.24
185	187	7.558807	TCCCTGTGAAATCGATACTCTTACTTA	59.441	37.037	0.00	0.00	0.00	2.24
228	231	3.868661	TGTACACTTACATGCCATTAGCG	59.131	43.478	0.00	0.00	37.54	4.26
229	232	5.213597	TGTACACTTACATGCCATTAGCGG	61.214	45.833	0.00	0.00	37.54	5.52
301	305	7.263100	ACACGTAAATCACATTGATGCATAT	57.737	32.000	0.00	0.00	37.15	1.78
305	309	8.835439	ACGTAAATCACATTGATGCATATACAA	58.165	29.630	0.00	0.00	37.15	2.41
316	320	7.686438	TGATGCATATACAATACATTCCCAC	57.314	36.000	0.00	0.00	0.00	4.61
318	322	7.391275	TGATGCATATACAATACATTCCCACAG	59.609	37.037	0.00	0.00	0.00	3.66
329	333	8.526147	CAATACATTCCCACAGAAAAGAAAGAT	58.474	33.333	0.00	0.00	38.21	2.40
331	335	6.752168	ACATTCCCACAGAAAAGAAAGATTG	58.248	36.000	0.00	0.00	38.21	2.67
336	340	5.218139	CCACAGAAAAGAAAGATTGACTGC	58.782	41.667	0.00	0.00	0.00	4.40
337	341	5.221106	CCACAGAAAAGAAAGATTGACTGCA	60.221	40.000	0.00	0.00	0.00	4.41
338	342	6.444633	CACAGAAAAGAAAGATTGACTGCAT	58.555	36.000	0.00	0.00	0.00	3.96
339	343	7.308770	CCACAGAAAAGAAAGATTGACTGCATA	60.309	37.037	0.00	0.00	0.00	3.14
341	345	8.457261	ACAGAAAAGAAAGATTGACTGCATATC	58.543	33.333	0.00	0.00	0.00	1.63
342	346	8.456471	CAGAAAAGAAAGATTGACTGCATATCA	58.544	33.333	0.00	0.00	0.00	2.15
343	347	9.017509	AGAAAAGAAAGATTGACTGCATATCAA	57.982	29.630	14.06	14.06	40.25	2.57
344	348	9.630098	GAAAAGAAAGATTGACTGCATATCAAA	57.370	29.630	15.29	2.76	39.43	2.69
381	385	7.827729	AGTGTTTAGCTAGTTTTGGGGTTATAG	59.172	37.037	0.00	0.00	0.00	1.31
382	386	7.825761	GTGTTTAGCTAGTTTTGGGGTTATAGA	59.174	37.037	0.00	0.00	0.00	1.98
423	427	0.918619	CGGTTTACCTACATGTCGCG	59.081	55.000	0.00	0.00	0.00	5.87
437	441	0.448379	GTCGCGTCGTTAGCAAACAC	60.448	55.000	5.77	0.00	35.16	3.32
458	462	1.604693	GCGAAGTGTTTTCCTCTCGGA	60.605	52.381	0.00	0.00	37.60	4.55
465	469	3.096852	TGTTTTCCTCTCGGATGCTAGA	58.903	45.455	0.00	0.00	39.58	2.43
466	470	3.131223	TGTTTTCCTCTCGGATGCTAGAG	59.869	47.826	8.60	8.60	39.58	2.43
480	484	4.803098	TGCTAGAGGACTGAAACCTTAC	57.197	45.455	0.00	0.00	37.93	2.34
484	488	1.897802	GAGGACTGAAACCTTACCCGA	59.102	52.381	0.00	0.00	37.93	5.14
485	489	1.622312	AGGACTGAAACCTTACCCGAC	59.378	52.381	0.00	0.00	33.55	4.79
487	491	1.000171	GACTGAAACCTTACCCGACGT	60.000	52.381	0.00	0.00	0.00	4.34
488	492	1.269936	ACTGAAACCTTACCCGACGTG	60.270	52.381	0.00	0.00	0.00	4.49
496	500	0.679002	TTACCCGACGTGAGGAGAGG	60.679	60.000	7.44	0.00	0.00	3.69
514	518	1.086634	GGCCACTCGCTAGCTTTCTG	61.087	60.000	13.93	2.57	37.74	3.02
516	520	0.247736	CCACTCGCTAGCTTTCTGGT	59.752	55.000	13.93	0.00	0.00	4.00
630	636	0.103937	GAGCTGCGAGCATCTTAGGT	59.896	55.000	2.86	0.00	45.56	3.08
642	648	7.203910	CGAGCATCTTAGGTACTTTTCTGTAT	58.796	38.462	0.00	0.00	41.75	2.29
669	675	1.678728	CCCTTCATGCGAGGTGCTTTA	60.679	52.381	12.29	0.00	46.63	1.85
672	678	3.248602	CCTTCATGCGAGGTGCTTTATAC	59.751	47.826	6.76	0.00	46.63	1.47
681	687	4.192317	GAGGTGCTTTATACTGTTGGAGG	58.808	47.826	0.00	0.00	0.00	4.30
713	719	0.398318	AGATCTGGGGGCTTATTCGC	59.602	55.000	0.00	0.00	0.00	4.70
727	733	4.737765	GCTTATTCGCAAAACAAAGTGACA	59.262	37.500	0.00	0.00	0.00	3.58
748	754	7.278868	GTGACAGGTAAATCACTTTAGATGGAG	59.721	40.741	0.00	0.00	41.69	3.86
800	817	8.419076	AATATATTCACCGCATTTCCAAAAAC	57.581	30.769	0.00	0.00	0.00	2.43
801	818	2.517650	TCACCGCATTTCCAAAAACC	57.482	45.000	0.00	0.00	0.00	3.27
810	832	6.591834	CCGCATTTCCAAAAACCAATAATACA	59.408	34.615	0.00	0.00	0.00	2.29
1061	1124	0.245266	TATTTCTCCTCACGCGCACA	59.755	50.000	5.73	0.00	0.00	4.57
1062	1125	1.291877	ATTTCTCCTCACGCGCACAC	61.292	55.000	5.73	0.00	0.00	3.82
1068	1131	2.050077	TCACGCGCACACAGAGAG	60.050	61.111	5.73	0.00	0.00	3.20
1176	1261	4.923942	CAGCGGCGCCATGGAGAT	62.924	66.667	30.40	4.96	0.00	2.75
1177	1262	4.923942	AGCGGCGCCATGGAGATG	62.924	66.667	30.40	11.18	0.00	2.90
1426	1529	2.145397	TCCTCTACAGCACCTACCAG	57.855	55.000	0.00	0.00	0.00	4.00
1524	1627	0.250295	TCTTTCTTGCCGTCCCACAG	60.250	55.000	0.00	0.00	0.00	3.66
1550	1653	3.907260	TACGTCGACCGGCTGGACT	62.907	63.158	21.41	0.00	42.24	3.85
1603	1715	5.377478	CACAAGTTCCCTTCTACTCCTTTT	58.623	41.667	0.00	0.00	0.00	2.27
1735	1853	1.541588	GCTCGTTTGGCTTTTGATCCT	59.458	47.619	0.00	0.00	0.00	3.24
2077	2203	1.675310	GCACTATGCTGCCACACCA	60.675	57.895	0.00	0.00	40.96	4.17
2575	3033	3.149005	TCCGAGCAAACCCTGTAAATT	57.851	42.857	0.00	0.00	0.00	1.82
2727	3550	2.556144	TGAATTCAGTCTGCTGCAGT	57.444	45.000	27.24	8.26	42.29	4.40
3055	4036	8.680001	TGATTACTATCGTTGTTTGTCTAGCTA	58.320	33.333	0.00	0.00	33.23	3.32
3111	4092	6.396829	AAATTATGCTTCTGTAATCTGGCC	57.603	37.500	0.00	0.00	0.00	5.36
3300	4298	6.500041	AGTCTATTTGATCTTAGTCGTCAGC	58.500	40.000	0.00	0.00	0.00	4.26

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
63	65	6.071391	ACAAAGTGAGGGCGAAAATAAATGAT	60.071	34.615	0.00	0.00	0.00	2.45
70	72	5.741011	TCTATACAAAGTGAGGGCGAAAAT	58.259	37.500	0.00	0.00	0.00	1.82
74	76	3.362706	ACTCTATACAAAGTGAGGGCGA	58.637	45.455	0.00	0.00	0.00	5.54
120	122	7.029563	GTGTTGCCTCTTCTTGTAAATTATGG	58.970	38.462	0.00	0.00	0.00	2.74
130	132	1.691196	TTGGGTGTTGCCTCTTCTTG	58.309	50.000	0.00	0.00	37.43	3.02
131	133	2.683211	ATTGGGTGTTGCCTCTTCTT	57.317	45.000	0.00	0.00	37.43	2.52
135	137	2.242043	CAAGAATTGGGTGTTGCCTCT	58.758	47.619	0.00	0.00	43.94	3.69
147	149	5.261209	TTTCACAGGGAACACAAGAATTG	57.739	39.130	0.00	0.00	43.62	2.32
153	155	3.201353	TCGATTTCACAGGGAACACAA	57.799	42.857	0.00	0.00	34.56	3.33
155	157	4.504858	AGTATCGATTTCACAGGGAACAC	58.495	43.478	1.71	0.00	34.56	3.32
158	160	5.677319	AAGAGTATCGATTTCACAGGGAA	57.323	39.130	1.71	0.00	42.67	3.97
160	162	6.150396	AGTAAGAGTATCGATTTCACAGGG	57.850	41.667	1.71	0.00	42.67	4.45
209	212	2.288666	CCGCTAATGGCATGTAAGTGT	58.711	47.619	0.00	0.00	41.91	3.55
267	270	6.275494	TGTGATTTACGTGTCCATCTAGAA	57.725	37.500	0.00	0.00	0.00	2.10
268	271	5.907866	TGTGATTTACGTGTCCATCTAGA	57.092	39.130	0.00	0.00	0.00	2.43
280	283	9.830294	ATTGTATATGCATCAATGTGATTTACG	57.170	29.630	0.19	0.00	34.28	3.18
301	305	8.698973	TTTCTTTTCTGTGGGAATGTATTGTA	57.301	30.769	0.00	0.00	33.53	2.41
305	309	8.526147	CAATCTTTCTTTTCTGTGGGAATGTAT	58.474	33.333	0.00	0.00	33.53	2.29
308	312	6.865205	GTCAATCTTTCTTTTCTGTGGGAATG	59.135	38.462	0.00	0.00	33.53	2.67
316	320	8.456471	TGATATGCAGTCAATCTTTCTTTTCTG	58.544	33.333	2.34	0.00	0.00	3.02
318	322	9.630098	TTTGATATGCAGTCAATCTTTCTTTTC	57.370	29.630	15.52	0.00	35.68	2.29
347	351	8.793592	CCAAAACTAGCTAAACACTTCCTATTT	58.206	33.333	0.00	0.00	0.00	1.40
348	352	7.393515	CCCAAAACTAGCTAAACACTTCCTATT	59.606	37.037	0.00	0.00	0.00	1.73
350	354	6.235664	CCCAAAACTAGCTAAACACTTCCTA	58.764	40.000	0.00	0.00	0.00	2.94
351	355	5.070685	CCCAAAACTAGCTAAACACTTCCT	58.929	41.667	0.00	0.00	0.00	3.36
352	356	4.217767	CCCCAAAACTAGCTAAACACTTCC	59.782	45.833	0.00	0.00	0.00	3.46
353	357	4.825634	ACCCCAAAACTAGCTAAACACTTC	59.174	41.667	0.00	0.00	0.00	3.01
354	358	4.800023	ACCCCAAAACTAGCTAAACACTT	58.200	39.130	0.00	0.00	0.00	3.16
355	359	4.448720	ACCCCAAAACTAGCTAAACACT	57.551	40.909	0.00	0.00	0.00	3.55
356	360	6.829229	ATAACCCCAAAACTAGCTAAACAC	57.171	37.500	0.00	0.00	0.00	3.32
357	361	7.825761	GTCTATAACCCCAAAACTAGCTAAACA	59.174	37.037	0.00	0.00	0.00	2.83
358	362	8.045507	AGTCTATAACCCCAAAACTAGCTAAAC	58.954	37.037	0.00	0.00	0.00	2.01
359	363	8.154420	AGTCTATAACCCCAAAACTAGCTAAA	57.846	34.615	0.00	0.00	0.00	1.85
381	385	3.181510	CCAGCCGCAAAGTATGTTTAGTC	60.182	47.826	0.00	0.00	0.00	2.59
382	386	2.747446	CCAGCCGCAAAGTATGTTTAGT	59.253	45.455	0.00	0.00	0.00	2.24
405	409	1.922545	GACGCGACATGTAGGTAAACC	59.077	52.381	15.93	0.00	0.00	3.27
412	416	0.838229	GCTAACGACGCGACATGTAG	59.162	55.000	15.93	9.34	0.00	2.74
423	427	0.230260	TTCGCGTGTTTGCTAACGAC	59.770	50.000	5.77	5.33	42.32	4.34
437	441	0.435008	CGAGAGGAAAACACTTCGCG	59.565	55.000	0.00	0.00	34.01	5.87
458	462	4.162509	GGTAAGGTTTCAGTCCTCTAGCAT	59.837	45.833	0.00	0.00	33.76	3.79
465	469	1.622312	GTCGGGTAAGGTTTCAGTCCT	59.378	52.381	0.00	0.00	36.81	3.85
466	470	1.670967	CGTCGGGTAAGGTTTCAGTCC	60.671	57.143	0.00	0.00	0.00	3.85
480	484	3.827898	GCCTCTCCTCACGTCGGG	61.828	72.222	0.00	0.00	0.00	5.14
484	488	1.979693	GAGTGGCCTCTCCTCACGT	60.980	63.158	21.90	0.00	36.60	4.49
485	489	2.888863	GAGTGGCCTCTCCTCACG	59.111	66.667	21.90	0.00	36.60	4.35
487	491	2.211468	TAGCGAGTGGCCTCTCCTCA	62.211	60.000	25.32	10.26	45.17	3.86
488	492	1.452145	CTAGCGAGTGGCCTCTCCTC	61.452	65.000	25.32	18.02	45.17	3.71
496	500	1.086634	CCAGAAAGCTAGCGAGTGGC	61.087	60.000	9.55	0.00	44.05	5.01
505	509	1.210478	GAGGATGGCACCAGAAAGCTA	59.790	52.381	8.48	0.00	0.00	3.32
514	518	2.187946	CCGTCAGAGGATGGCACC	59.812	66.667	0.00	0.00	43.03	5.01
555	559	0.916358	CCCCCTCACCATCAAGGACT	60.916	60.000	0.00	0.00	41.22	3.85
587	592	3.917300	AGCTACTAGGGCTCTAACACAT	58.083	45.455	6.65	0.00	34.70	3.21
617	622	5.411781	ACAGAAAAGTACCTAAGATGCTCG	58.588	41.667	0.00	0.00	0.00	5.03
648	654	1.841302	AAGCACCTCGCATGAAGGGA	61.841	55.000	16.42	0.00	46.13	4.20
658	664	3.857052	TCCAACAGTATAAAGCACCTCG	58.143	45.455	0.00	0.00	0.00	4.63
669	675	9.315363	CTTATTATAGAGGACCTCCAACAGTAT	57.685	37.037	18.32	10.35	38.89	2.12
672	678	7.841282	TCTTATTATAGAGGACCTCCAACAG	57.159	40.000	18.32	9.46	38.89	3.16
681	687	5.129650	GCCCCCAGATCTTATTATAGAGGAC	59.870	48.000	0.00	0.00	0.00	3.85
693	699	1.202818	GCGAATAAGCCCCCAGATCTT	60.203	52.381	0.00	0.00	0.00	2.40
713	719	7.449934	GTGATTTACCTGTCACTTTGTTTTG	57.550	36.000	0.00	0.00	41.10	2.44
727	733	6.674419	ACCTCTCCATCTAAAGTGATTTACCT	59.326	38.462	0.00	0.00	0.00	3.08
748	754	6.192360	GTGTACAATCAATGCGATTTACCTC	58.808	40.000	0.00	0.00	41.83	3.85
825	847	5.467735	ACTGCCATGCAATTTCTTTCTTTTC	59.532	36.000	0.00	0.00	38.41	2.29
836	858	2.336667	GCGTTTAACTGCCATGCAATT	58.663	42.857	0.00	0.00	38.41	2.32
1068	1131	4.445545	CGGGAAACAAGCTCGCGC	62.446	66.667	0.00	0.00	41.42	6.86
1077	1140	0.249573	GGACGAACTGACGGGAAACA	60.250	55.000	0.00	0.00	37.61	2.83
1081	1144	0.538977	AGAAGGACGAACTGACGGGA	60.539	55.000	0.00	0.00	37.61	5.14
1175	1260	1.614317	CGCAGAACTTTTCCCCTCCAT	60.614	52.381	0.00	0.00	0.00	3.41
1176	1261	0.250727	CGCAGAACTTTTCCCCTCCA	60.251	55.000	0.00	0.00	0.00	3.86
1177	1262	0.036306	TCGCAGAACTTTTCCCCTCC	59.964	55.000	0.00	0.00	0.00	4.30
1178	1263	1.807142	CTTCGCAGAACTTTTCCCCTC	59.193	52.381	0.00	0.00	45.90	4.30
1179	1264	1.420138	TCTTCGCAGAACTTTTCCCCT	59.580	47.619	0.00	0.00	45.90	4.79
1180	1265	1.892209	TCTTCGCAGAACTTTTCCCC	58.108	50.000	0.00	0.00	45.90	4.81
1524	1627	1.425428	CGGTCGACGTACCAGTACC	59.575	63.158	9.92	3.99	39.71	3.34
1550	1653	2.683465	GGAGGAGGCCATTGCAGGA	61.683	63.158	5.01	0.00	40.13	3.86
1603	1715	3.458163	GGCTCATCGTCGTCCCCA	61.458	66.667	0.00	0.00	0.00	4.96
1735	1853	0.605319	GGAAATGGGACGACACTGCA	60.605	55.000	0.00	0.00	0.00	4.41
2077	2203	0.033991	TCTTCTCGCCAGGAGCTAGT	60.034	55.000	0.00	0.00	42.82	2.57
2727	3550	8.741603	AACAGGTTAAGTAGCAGAAGTTAAAA	57.258	30.769	0.00	0.00	0.00	1.52
2925	3906	4.074970	GGATGGCATCATTTAGGTCGATT	58.925	43.478	27.39	0.00	32.98	3.34
3055	4036	2.083774	CCCATTCGTGTGCAGTACAAT	58.916	47.619	0.00	0.00	41.89	2.71

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.