AutoCloner

Multiple sequence alignment - TraesCS6D01G001000

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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	TraesCS6D01G001000	chr6D	100.000	3535	0	0	1	3535	423985	420451	0.000000e+00	6529.0
1	TraesCS6D01G001000	chr6D	82.668	2983	423	52	1	2916	724460	721505	0.000000e+00	2558.0
2	TraesCS6D01G001000	chr6D	83.661	2491	378	16	1	2466	24750728	24748242	0.000000e+00	2318.0
3	TraesCS6D01G001000	chr6D	90.323	124	11	1	3374	3497	166709550	166709428	1.020000e-35	161.0
4	TraesCS6D01G001000	chr5B	86.108	2973	329	42	6	2909	35548278	35545321	0.000000e+00	3125.0
5	TraesCS6D01G001000	chr5B	90.345	145	7	2	2922	3060	35545043	35544900	2.170000e-42	183.0
6	TraesCS6D01G001000	chr6B	85.106	2981	367	42	1	2916	65090164	65087196	0.000000e+00	2974.0
7	TraesCS6D01G001000	chr6B	83.842	2488	376	14	1	2465	15276838	15274354	0.000000e+00	2344.0
8	TraesCS6D01G001000	chr6B	94.942	949	29	1	328	1257	2700688	2701636	0.000000e+00	1469.0
9	TraesCS6D01G001000	chr6B	96.407	334	12	0	1	334	2695138	2695471	5.160000e-153	551.0
10	TraesCS6D01G001000	chr6B	76.218	349	72	7	4	345	21931985	21931641	1.300000e-39	174.0
11	TraesCS6D01G001000	chr6B	87.671	146	9	4	2922	3060	65086920	65086777	1.020000e-35	161.0
12	TraesCS6D01G001000	chr6B	93.750	48	3	0	3080	3127	3326743	3326696	4.890000e-09	73.1
13	TraesCS6D01G001000	chr4B	83.458	2805	403	30	1	2750	650656599	650659397	0.000000e+00	2553.0
14	TraesCS6D01G001000	chr1B	85.324	2487	338	19	1	2464	2917566	2920048	0.000000e+00	2545.0
15	TraesCS6D01G001000	chr1B	90.756	119	10	1	3376	3494	30737178	30737295	1.310000e-34	158.0
16	TraesCS6D01G001000	chr5D	84.192	2600	367	32	1	2570	369019554	369022139	0.000000e+00	2484.0
17	TraesCS6D01G001000	chr5D	87.135	171	10	6	3374	3535	72209431	72209598	2.170000e-42	183.0
18	TraesCS6D01G001000	chr4D	87.222	2207	223	23	758	2924	19967992	19970179	0.000000e+00	2459.0
19	TraesCS6D01G001000	chr4D	94.010	384	14	6	3157	3535	19970652	19971031	1.100000e-159	573.0
20	TraesCS6D01G001000	chr4D	93.103	232	10	3	2922	3147	19970333	19970564	5.650000e-88	335.0
21	TraesCS6D01G001000	chr7D	83.253	2705	389	41	2	2663	9183094	9185777	0.000000e+00	2427.0
22	TraesCS6D01G001000	chr4A	83.554	2566	385	27	2	2538	730948298	730950855	0.000000e+00	2366.0
23	TraesCS6D01G001000	chr4A	85.057	174	12	5	3376	3535	533197896	533197723	7.850000e-37	165.0
24	TraesCS6D01G001000	chr6A	83.481	2488	382	23	4	2466	9014859	9012376	0.000000e+00	2290.0
25	TraesCS6D01G001000	chr6A	90.909	121	10	1	3374	3494	48087256	48087375	1.020000e-35	161.0
26	TraesCS6D01G001000	chr6A	90.741	54	5	0	3080	3133	256745	256692	4.890000e-09	73.1
27	TraesCS6D01G001000	chr3A	83.079	2559	389	29	6	2535	23648596	23646053	0.000000e+00	2287.0
28	TraesCS6D01G001000	chr3A	86.857	175	8	4	3376	3535	602855589	602855763	7.800000e-42	182.0
29	TraesCS6D01G001000	chrUn	83.918	1909	258	20	923	2797	254715641	254713748	0.000000e+00	1779.0
30	TraesCS6D01G001000	chr5A	89.072	851	64	11	2092	2916	29692534	29691687	0.000000e+00	1029.0
31	TraesCS6D01G001000	chr5A	87.429	175	7	7	3376	3535	275092474	275092300	1.680000e-43	187.0
32	TraesCS6D01G001000	chr5A	90.345	145	8	1	2922	3060	29691410	29691266	6.030000e-43	185.0
33	TraesCS6D01G001000	chr2B	88.000	175	7	7	3375	3535	701771341	701771515	1.000000e-45	195.0
34	TraesCS6D01G001000	chr2A	87.429	175	7	4	3376	3535	719783578	719783404	1.680000e-43	187.0
35	TraesCS6D01G001000	chr7A	86.857	175	8	7	3376	3535	31889754	31889580	7.800000e-42	182.0
36	TraesCS6D01G001000	chr7A	86.207	174	10	7	3376	3535	299432487	299432314	3.630000e-40	176.0
37	TraesCS6D01G001000	chr3B	85.632	174	11	2	3376	3535	723502814	723502641	1.690000e-38	171.0
38	TraesCS6D01G001000	chr3B	90.756	119	10	1	3376	3494	428106576	428106459	1.310000e-34	158.0
39	TraesCS6D01G001000	chr2D	90.244	123	11	1	3375	3497	633597900	633597779	3.650000e-35	159.0

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	TraesCS6D01G001000	chr6D	420451	423985	3534	True	6529.000000	6529	100.0000	1	3535	1	chr6D.!!$R1	3534
1	TraesCS6D01G001000	chr6D	721505	724460	2955	True	2558.000000	2558	82.6680	1	2916	1	chr6D.!!$R2	2915
2	TraesCS6D01G001000	chr6D	24748242	24750728	2486	True	2318.000000	2318	83.6610	1	2466	1	chr6D.!!$R3	2465
3	TraesCS6D01G001000	chr5B	35544900	35548278	3378	True	1654.000000	3125	88.2265	6	3060	2	chr5B.!!$R1	3054
4	TraesCS6D01G001000	chr6B	15274354	15276838	2484	True	2344.000000	2344	83.8420	1	2465	1	chr6B.!!$R2	2464
5	TraesCS6D01G001000	chr6B	65086777	65090164	3387	True	1567.500000	2974	86.3885	1	3060	2	chr6B.!!$R4	3059
6	TraesCS6D01G001000	chr6B	2700688	2701636	948	False	1469.000000	1469	94.9420	328	1257	1	chr6B.!!$F2	929
7	TraesCS6D01G001000	chr4B	650656599	650659397	2798	False	2553.000000	2553	83.4580	1	2750	1	chr4B.!!$F1	2749
8	TraesCS6D01G001000	chr1B	2917566	2920048	2482	False	2545.000000	2545	85.3240	1	2464	1	chr1B.!!$F1	2463
9	TraesCS6D01G001000	chr5D	369019554	369022139	2585	False	2484.000000	2484	84.1920	1	2570	1	chr5D.!!$F2	2569
10	TraesCS6D01G001000	chr4D	19967992	19971031	3039	False	1122.333333	2459	91.4450	758	3535	3	chr4D.!!$F1	2777
11	TraesCS6D01G001000	chr7D	9183094	9185777	2683	False	2427.000000	2427	83.2530	2	2663	1	chr7D.!!$F1	2661
12	TraesCS6D01G001000	chr4A	730948298	730950855	2557	False	2366.000000	2366	83.5540	2	2538	1	chr4A.!!$F1	2536
13	TraesCS6D01G001000	chr6A	9012376	9014859	2483	True	2290.000000	2290	83.4810	4	2466	1	chr6A.!!$R2	2462
14	TraesCS6D01G001000	chr3A	23646053	23648596	2543	True	2287.000000	2287	83.0790	6	2535	1	chr3A.!!$R1	2529
15	TraesCS6D01G001000	chrUn	254713748	254715641	1893	True	1779.000000	1779	83.9180	923	2797	1	chrUn.!!$R1	1874
16	TraesCS6D01G001000	chr5A	29691266	29692534	1268	True	607.000000	1029	89.7085	2092	3060	2	chr5A.!!$R2	968

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
392	396	0.409092	TGGAGGACAACTACCGGGTA	59.591	55.00	6.32	6.73	0.00	3.69	F
1240	1263	4.211125	TGTGAATTTGTGTGGTGGTACAT	58.789	39.13	0.00	0.00	44.52	2.29	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1240	1263	0.687354	GGAGCCAGGTGAAGTTGAGA	59.313	55.0	0.0	0.0	0.0	3.27	R
3204	3724	0.447801	GTTGCGTGCCATGTTCTAGG	59.552	55.0	0.0	0.0	0.0	3.02	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
30	31	6.352222	CCACCTTCTATCTACAACTGGTCATT	60.352	42.308	0.00	0.00	0.00	2.57
38	42	2.665165	ACAACTGGTCATTGCTGGAAA	58.335	42.857	0.00	0.00	0.00	3.13
39	43	2.362077	ACAACTGGTCATTGCTGGAAAC	59.638	45.455	0.00	0.00	0.00	2.78
58	62	5.408299	GGAAACATTTGATGTAGGGCAAAAC	59.592	40.000	0.00	0.00	44.07	2.43
64	68	4.782019	TGATGTAGGGCAAAACATGTTC	57.218	40.909	12.39	0.00	36.48	3.18
123	127	3.599046	CAAGTTGAGATATCTTGGCGC	57.401	47.619	6.70	0.00	36.09	6.53
139	143	1.303091	GCGCGGGTGGTAATCACTTT	61.303	55.000	8.83	0.00	45.38	2.66
142	146	1.662122	GCGGGTGGTAATCACTTTACG	59.338	52.381	0.00	0.00	45.38	3.18
181	185	6.078456	TCAATATCCAACATGTCTTCCCTT	57.922	37.500	0.00	0.00	0.00	3.95
186	190	4.651778	TCCAACATGTCTTCCCTTGTAAG	58.348	43.478	0.00	0.00	0.00	2.34
208	212	3.522553	ACTTAGCCTCGTGCAGAATAAC	58.477	45.455	0.00	0.00	44.83	1.89
217	221	5.142061	TCGTGCAGAATAACTTTAGTGGA	57.858	39.130	0.00	0.00	0.00	4.02
231	235	0.691078	AGTGGATACGTGCCTCCCAT	60.691	55.000	0.00	0.00	42.51	4.00
247	251	2.037847	ATGTTGGGGAAGCTGGGC	59.962	61.111	0.00	0.00	0.00	5.36
248	252	2.855770	ATGTTGGGGAAGCTGGGCA	61.856	57.895	0.00	0.00	0.00	5.36
257	261	1.163554	GAAGCTGGGCACTCTTCAAG	58.836	55.000	14.05	0.00	36.96	3.02
265	269	3.181440	TGGGCACTCTTCAAGAAGTGAAT	60.181	43.478	16.66	0.00	45.27	2.57
273	277	4.889409	TCTTCAAGAAGTGAATTTGGCAGT	59.111	37.500	9.44	0.00	45.27	4.40
289	293	2.159324	GGCAGTCAATAAGCTTGAAGCC	60.159	50.000	14.45	11.88	43.77	4.35
392	396	0.409092	TGGAGGACAACTACCGGGTA	59.591	55.000	6.32	6.73	0.00	3.69
1240	1263	4.211125	TGTGAATTTGTGTGGTGGTACAT	58.789	39.130	0.00	0.00	44.52	2.29
1268	1309	2.124403	CCTGGCTCCATGCTCCAC	60.124	66.667	0.00	0.00	42.39	4.02
1272	1322	1.751927	GGCTCCATGCTCCACAAGG	60.752	63.158	0.00	0.00	42.39	3.61
1291	1341	7.255942	CCACAAGGAAGAACAATAAAAGGATGT	60.256	37.037	0.00	0.00	36.89	3.06
1320	1370	7.100409	AGTCTCTTGTAATTTCTCTAGCAACC	58.900	38.462	0.00	0.00	0.00	3.77
1321	1371	7.038658	AGTCTCTTGTAATTTCTCTAGCAACCT	60.039	37.037	0.00	0.00	0.00	3.50
1328	1378	4.706842	TTTCTCTAGCAACCTTTGGAGT	57.293	40.909	0.00	0.00	0.00	3.85
1341	1391	4.283722	ACCTTTGGAGTAATCGTGTTCTCT	59.716	41.667	0.00	0.00	0.00	3.10
1344	1394	6.127703	CCTTTGGAGTAATCGTGTTCTCTCTA	60.128	42.308	0.00	0.00	0.00	2.43
1404	1454	5.416952	ACTCAAACCAAGCCAGAAGATATTG	59.583	40.000	0.00	0.00	0.00	1.90
1422	1473	7.995289	AGATATTGGCACGAAATTCAATTGTA	58.005	30.769	5.13	0.00	32.81	2.41
1431	1482	5.064707	ACGAAATTCAATTGTAGATGACCGG	59.935	40.000	0.00	0.00	0.00	5.28
1464	1515	3.584406	TCCCCTATCATGCATTACTGAGG	59.416	47.826	0.00	0.00	0.00	3.86
1686	1737	4.999950	ACTTCTTGTTCTAGCATCAACCAG	59.000	41.667	0.00	0.00	0.00	4.00
1759	1810	2.923121	TGGATAGCTGGCTTCATCAAC	58.077	47.619	0.00	0.00	0.00	3.18
1765	1816	1.404391	GCTGGCTTCATCAACCATCTG	59.596	52.381	0.00	0.00	31.79	2.90
1792	1843	1.070843	CCACTACAAACAACACGCTCG	60.071	52.381	0.00	0.00	0.00	5.03
1866	1917	0.250295	TGCACAACTACTGTCAGCCC	60.250	55.000	0.00	0.00	35.47	5.19
1929	1980	2.892425	GAAGACATGAGCGCCCGG	60.892	66.667	2.29	0.00	0.00	5.73
1979	2030	5.473504	TCCTTCAAGAAAATACAAGTGAGGC	59.526	40.000	0.00	0.00	0.00	4.70
2180	2238	6.923199	ATTTATAGCCTTGGCATATTGCTT	57.077	33.333	14.54	0.00	44.28	3.91
2277	2335	3.389329	GGATGCTCTTCCAGATAGAACCA	59.611	47.826	0.00	0.00	35.72	3.67
2287	2345	5.970289	TCCAGATAGAACCATGGAGATAGT	58.030	41.667	21.47	0.00	36.92	2.12
2317	2382	3.660111	GTGGTTGCACAGCGGACC	61.660	66.667	7.23	7.23	37.70	4.46
2327	2392	2.083774	CACAGCGGACCACACAATAAT	58.916	47.619	0.00	0.00	0.00	1.28
2335	2400	5.526111	GCGGACCACACAATAATACTACAAT	59.474	40.000	0.00	0.00	0.00	2.71
2472	2537	6.378710	TCAGAGATGTATACCTCAAGTTCG	57.621	41.667	10.32	0.00	32.07	3.95
2727	2827	4.431416	TCAAAACTGTACACATGGAGGT	57.569	40.909	0.00	0.00	0.00	3.85
2740	2845	7.865706	ACACATGGAGGTAACATTATTTCTC	57.134	36.000	0.00	0.00	41.41	2.87
2757	2862	4.365514	TTCTCCATGCTTCAGTAAACCA	57.634	40.909	0.00	0.00	0.00	3.67
2917	3140	9.900710	AAACATATGTTTCTTTTGCGTACAATA	57.099	25.926	24.88	0.00	44.15	1.90
2951	3385	4.319177	AGTAAAGTCAGGCTGCTTGTTAG	58.681	43.478	19.85	0.00	0.00	2.34
2989	3429	7.558161	TTCCATGTGCAGATACTAGAATTTG	57.442	36.000	0.00	0.00	0.00	2.32
2991	3431	5.824624	CCATGTGCAGATACTAGAATTTGGT	59.175	40.000	0.00	0.00	0.00	3.67
3009	3449	2.034066	GCACAAGCAGCCTACCCA	59.966	61.111	0.00	0.00	41.58	4.51
3078	3519	4.095483	CAGAAATGATAGCTCGCTTTGGTT	59.905	41.667	0.00	0.00	0.00	3.67
3082	3523	3.198068	TGATAGCTCGCTTTGGTTGATC	58.802	45.455	0.00	0.00	0.00	2.92
3111	3552	3.249189	AGCCGCCTTGGTGGAGAA	61.249	61.111	22.16	0.00	41.21	2.87
3151	3592	2.789409	AGGAGTTTCCTTCCCGATTG	57.211	50.000	0.00	0.00	46.91	2.67
3152	3593	1.282157	AGGAGTTTCCTTCCCGATTGG	59.718	52.381	0.00	0.00	46.91	3.16
3185	3705	5.410355	AATGCATTTGTGGTGCTTTAGAT	57.590	34.783	5.99	0.00	42.92	1.98
3188	3708	4.989797	TGCATTTGTGGTGCTTTAGATTTG	59.010	37.500	0.00	0.00	42.92	2.32
3271	3791	0.872388	AACAACTTCCACGAATCCGC	59.128	50.000	0.00	0.00	39.95	5.54
3282	3802	3.312421	CCACGAATCCGCAACTATTGAAT	59.688	43.478	0.00	0.00	39.95	2.57
3301	3821	3.863142	ATTGCAGCTGATTTCCAAGAC	57.137	42.857	20.43	0.00	0.00	3.01
3307	3827	4.562143	GCAGCTGATTTCCAAGACCAAAAT	60.562	41.667	20.43	0.00	0.00	1.82
3313	3833	7.173735	GCTGATTTCCAAGACCAAAATGATTTT	59.826	33.333	0.00	0.00	0.00	1.82
3318	3838	4.565444	CCAAGACCAAAATGATTTTCCCCC	60.565	45.833	0.00	0.00	0.00	5.40
3319	3839	3.868062	AGACCAAAATGATTTTCCCCCA	58.132	40.909	0.00	0.00	0.00	4.96
3321	3841	2.912295	ACCAAAATGATTTTCCCCCAGG	59.088	45.455	0.00	0.92	0.00	4.45
3322	3842	2.356022	CCAAAATGATTTTCCCCCAGGC	60.356	50.000	0.00	0.00	0.00	4.85
3325	3845	2.340721	ATGATTTTCCCCCAGGCAAA	57.659	45.000	0.00	0.00	32.57	3.68
3326	3846	1.643310	TGATTTTCCCCCAGGCAAAG	58.357	50.000	0.00	0.00	31.48	2.77
3378	3902	2.026822	CCGCCAAGCATTCCCTATCTAT	60.027	50.000	0.00	0.00	0.00	1.98
3450	3974	5.642686	CCCGATACGCCAATTTTCTAAAAA	58.357	37.500	0.00	0.00	0.00	1.94

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
14	15	3.264193	TCCAGCAATGACCAGTTGTAGAT	59.736	43.478	0.00	0.00	0.00	1.98
30	31	3.763360	CCCTACATCAAATGTTTCCAGCA	59.237	43.478	0.00	0.00	41.63	4.41
38	42	5.011943	ACATGTTTTGCCCTACATCAAATGT	59.988	36.000	0.00	0.00	46.92	2.71
39	43	5.481105	ACATGTTTTGCCCTACATCAAATG	58.519	37.500	0.00	0.00	32.88	2.32
58	62	1.672881	GGAATGCTTCCGGAGAACATG	59.327	52.381	14.45	0.00	40.59	3.21
122	126	1.662122	CGTAAAGTGATTACCACCCGC	59.338	52.381	0.00	0.00	46.87	6.13
123	127	2.273557	CCGTAAAGTGATTACCACCCG	58.726	52.381	0.00	0.00	46.87	5.28
157	161	6.078456	AGGGAAGACATGTTGGATATTGAA	57.922	37.500	0.00	0.00	0.00	2.69
181	185	1.890489	TGCACGAGGCTAAGTCTTACA	59.110	47.619	0.00	0.00	45.15	2.41
186	190	2.301577	ATTCTGCACGAGGCTAAGTC	57.698	50.000	0.00	0.00	45.15	3.01
208	212	2.483188	GGGAGGCACGTATCCACTAAAG	60.483	54.545	13.74	0.00	37.33	1.85
217	221	0.107214	CCAACATGGGAGGCACGTAT	60.107	55.000	0.00	0.00	32.67	3.06
231	235	3.506743	TGCCCAGCTTCCCCAACA	61.507	61.111	0.00	0.00	0.00	3.33
257	261	5.574443	GCTTATTGACTGCCAAATTCACTTC	59.426	40.000	0.00	0.00	38.43	3.01
265	269	4.559300	GCTTCAAGCTTATTGACTGCCAAA	60.559	41.667	0.71	0.00	38.45	3.28
273	277	4.766373	TGTCATTGGCTTCAAGCTTATTGA	59.234	37.500	9.83	8.23	41.99	2.57
289	293	0.968405	CCCACCCCTTGTTGTCATTG	59.032	55.000	0.00	0.00	0.00	2.82
392	396	3.560068	GTCGTTGAGAGGTTCACAATTGT	59.440	43.478	4.92	4.92	34.94	2.71
675	698	9.985730	AAATCAAGTGCATAGAGATTTTTCAAA	57.014	25.926	11.26	0.00	35.94	2.69
762	785	4.927267	TGACAAGTCCAAATACCAGGAT	57.073	40.909	0.00	0.00	36.11	3.24
765	788	7.630242	ATTGTATGACAAGTCCAAATACCAG	57.370	36.000	0.00	0.00	41.94	4.00
1240	1263	0.687354	GGAGCCAGGTGAAGTTGAGA	59.313	55.000	0.00	0.00	0.00	3.27
1268	1309	7.885297	TGACATCCTTTTATTGTTCTTCCTTG	58.115	34.615	0.00	0.00	0.00	3.61
1272	1322	9.399403	GACTTTGACATCCTTTTATTGTTCTTC	57.601	33.333	0.00	0.00	0.00	2.87
1291	1341	8.367911	TGCTAGAGAAATTACAAGAGACTTTGA	58.632	33.333	0.00	0.00	0.00	2.69
1320	1370	5.715070	AGAGAGAACACGATTACTCCAAAG	58.285	41.667	0.00	0.00	0.00	2.77
1321	1371	5.723672	AGAGAGAACACGATTACTCCAAA	57.276	39.130	0.00	0.00	0.00	3.28
1371	1421	2.860136	GCTTGGTTTGAGTTTCTTGCAC	59.140	45.455	0.00	0.00	0.00	4.57
1404	1454	5.739161	GTCATCTACAATTGAATTTCGTGCC	59.261	40.000	13.59	0.00	0.00	5.01
1409	1459	6.436843	ACCGGTCATCTACAATTGAATTTC	57.563	37.500	13.59	0.00	0.00	2.17
1422	1473	2.414994	TTCTCTCGTACCGGTCATCT	57.585	50.000	12.40	0.00	0.00	2.90
1431	1482	4.381079	GCATGATAGGGGATTCTCTCGTAC	60.381	50.000	0.00	0.00	0.00	3.67
1435	1486	4.840716	ATGCATGATAGGGGATTCTCTC	57.159	45.455	0.00	0.00	0.00	3.20
1464	1515	5.001874	ACTTCTGAAAATCCGTTAGTTCCC	58.998	41.667	0.00	0.00	0.00	3.97
1686	1737	1.268079	GCCTTGAACTCTTGACCTTGC	59.732	52.381	0.00	0.00	0.00	4.01
1759	1810	4.760530	TTGTAGTGGGATCTTCAGATGG	57.239	45.455	0.00	0.00	34.37	3.51
1765	1816	4.084013	CGTGTTGTTTGTAGTGGGATCTTC	60.084	45.833	0.00	0.00	0.00	2.87
1929	1980	3.620488	TGATATGCCAAAGTCTCCAACC	58.380	45.455	0.00	0.00	0.00	3.77
1979	2030	3.313249	TGAGCCATATGAAGTTTGCATCG	59.687	43.478	3.65	0.00	0.00	3.84
2065	2116	5.730550	TGCCATACTCGAGTGAAAAGTAAT	58.269	37.500	28.12	7.86	0.00	1.89
2180	2238	5.477607	TTCTTCCCGTAAACATCTCAAGA	57.522	39.130	0.00	0.00	0.00	3.02
2277	2335	2.747177	TGTCGGGTCAACTATCTCCAT	58.253	47.619	0.00	0.00	0.00	3.41
2287	2345	1.313772	CAACCACATTGTCGGGTCAA	58.686	50.000	0.00	0.00	32.67	3.18
2472	2537	1.050988	TCTGCTCCATGCTCCCCTAC	61.051	60.000	0.00	0.00	43.37	3.18
2538	2604	0.737219	GATCATGTCTTGTGCCAGCC	59.263	55.000	0.00	0.00	0.00	4.85
2584	2653	7.796054	ACATAGCTCTAAGAACATACATGGTT	58.204	34.615	0.00	0.00	0.00	3.67
2585	2654	7.366847	ACATAGCTCTAAGAACATACATGGT	57.633	36.000	0.00	0.00	0.00	3.55
2586	2655	9.363763	CATACATAGCTCTAAGAACATACATGG	57.636	37.037	0.00	0.00	0.00	3.66
2590	2659	8.704234	GCAACATACATAGCTCTAAGAACATAC	58.296	37.037	0.00	0.00	0.00	2.39
2631	2712	7.541783	CACAACACCATGGTTCTGTATTTATTG	59.458	37.037	22.47	11.90	0.00	1.90
2727	2827	9.679661	TTACTGAAGCATGGAGAAATAATGTTA	57.320	29.630	0.00	0.00	0.00	2.41
2811	2932	9.211485	ACAAATAAAATTGGATCTTTCTGCTTG	57.789	29.630	0.00	0.00	34.56	4.01
2917	3140	5.279556	GCCTGACTTTACTACCTCAAGTCTT	60.280	44.000	11.47	0.00	44.57	3.01
2951	3385	4.034510	GCACATGGAAAGTGTATACTCTGC	59.965	45.833	8.17	4.34	39.17	4.26
2961	3395	5.664457	TCTAGTATCTGCACATGGAAAGTG	58.336	41.667	0.00	0.00	39.92	3.16
2989	3429	2.335712	GGTAGGCTGCTTGTGCACC	61.336	63.158	15.69	0.00	45.31	5.01
3078	3519	0.741326	GGCTCACGCTCTACAGATCA	59.259	55.000	0.00	0.00	36.09	2.92
3147	3588	4.389890	TGCATTTCATAGGCAACCAATC	57.610	40.909	0.00	0.00	34.05	2.67
3148	3589	5.362105	AATGCATTTCATAGGCAACCAAT	57.638	34.783	5.99	0.00	41.43	3.16
3150	3591	4.020396	ACAAATGCATTTCATAGGCAACCA	60.020	37.500	21.70	0.00	41.43	3.67
3151	3592	4.330620	CACAAATGCATTTCATAGGCAACC	59.669	41.667	21.70	0.00	41.43	3.77
3152	3593	4.330620	CCACAAATGCATTTCATAGGCAAC	59.669	41.667	21.70	0.00	41.43	4.17
3185	3705	2.032528	CGGTGCTCTGCCCTCAAA	59.967	61.111	0.00	0.00	0.00	2.69
3204	3724	0.447801	GTTGCGTGCCATGTTCTAGG	59.552	55.000	0.00	0.00	0.00	3.02
3252	3772	0.872388	GCGGATTCGTGGAAGTTGTT	59.128	50.000	0.00	0.00	38.89	2.83
3271	3791	6.255020	GGAAATCAGCTGCAATTCAATAGTTG	59.745	38.462	20.26	0.00	0.00	3.16
3282	3802	1.888512	GGTCTTGGAAATCAGCTGCAA	59.111	47.619	9.47	6.19	0.00	4.08
3301	3821	2.356022	GCCTGGGGGAAAATCATTTTGG	60.356	50.000	0.00	0.00	31.94	3.28
3307	3827	1.148867	TCTTTGCCTGGGGGAAAATCA	59.851	47.619	4.93	0.00	42.12	2.57
3313	3833	0.624500	AGCTATCTTTGCCTGGGGGA	60.625	55.000	0.00	0.00	33.58	4.81
3318	3838	8.012241	GTCGATTATTTTAGCTATCTTTGCCTG	58.988	37.037	0.00	0.00	0.00	4.85
3319	3839	7.934120	AGTCGATTATTTTAGCTATCTTTGCCT	59.066	33.333	0.00	0.00	0.00	4.75
3355	3879	2.983725	ATAGGGAATGCTTGGCGGCC	62.984	60.000	13.32	13.32	0.00	6.13
3378	3902	2.779755	ATCCAAGTATCCGTGCAACA	57.220	45.000	0.00	0.00	35.74	3.33

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.