AutoCloner

Multiple sequence alignment - TraesCS1B01G110600

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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	TraesCS1B01G110600	chr1B	100.000	3724	0	0	1	3724	123967852	123964129	0.000000e+00	6878
1	TraesCS1B01G110600	chr1B	80.819	1319	185	38	135	1419	123985983	123984699	0.000000e+00	972
2	TraesCS1B01G110600	chr1B	88.792	571	52	6	1805	2370	123974045	123973482	0.000000e+00	689
3	TraesCS1B01G110600	chr1B	91.406	128	11	0	4	131	123987520	123987393	3.820000e-40	176
4	TraesCS1B01G110600	chr1A	87.548	2867	309	21	1	2832	96462732	96465585	0.000000e+00	3273
5	TraesCS1B01G110600	chr1A	84.519	1828	218	18	1	1801	96470548	96472337	0.000000e+00	1748
6	TraesCS1B01G110600	chr1A	93.093	970	60	5	1802	2771	96472371	96473333	0.000000e+00	1413
7	TraesCS1B01G110600	chr1A	95.018	542	23	3	2778	3318	96473423	96473961	0.000000e+00	848
8	TraesCS1B01G110600	chr1D	92.123	1752	110	4	77	1801	78983090	78981340	0.000000e+00	2446
9	TraesCS1B01G110600	chr1D	92.519	1457	90	13	1802	3248	78981308	78979861	0.000000e+00	2069
10	TraesCS1B01G110600	chr1D	92.787	305	14	2	3234	3537	78979186	78978889	5.710000e-118	435
11	TraesCS1B01G110600	chr1D	91.558	154	7	3	3572	3724	78977785	78977637	1.360000e-49	207
12	TraesCS1B01G110600	chr1D	97.500	80	2	0	1	80	79010348	79010269	1.800000e-28	137
13	TraesCS1B01G110600	chr6A	83.528	1882	212	50	1	1801	574622	572758	0.000000e+00	1668
14	TraesCS1B01G110600	chr6A	87.350	917	92	9	1817	2724	572706	571805	0.000000e+00	1029
15	TraesCS1B01G110600	chr6A	81.109	974	121	31	1215	2167	1411840	1412771	0.000000e+00	721
16	TraesCS1B01G110600	chrUn	83.207	1715	220	40	133	1801	246307961	246306269	0.000000e+00	1509
17	TraesCS1B01G110600	chrUn	83.207	1715	220	40	133	1801	255506961	255505269	0.000000e+00	1509
18	TraesCS1B01G110600	chrUn	83.149	1715	221	40	133	1801	217766783	217765091	0.000000e+00	1504
19	TraesCS1B01G110600	chrUn	88.390	534	51	7	1817	2346	260128492	260129018	1.890000e-177	632
20	TraesCS1B01G110600	chrUn	88.202	534	52	7	1817	2346	246306217	246305691	8.780000e-176	627
21	TraesCS1B01G110600	chrUn	88.202	534	52	7	1817	2346	313906759	313907285	8.780000e-176	627
22	TraesCS1B01G110600	chrUn	88.914	451	46	3	2346	2793	217764395	217763946	1.510000e-153	553
23	TraesCS1B01G110600	chrUn	88.914	451	46	3	2346	2793	246305573	246305124	1.510000e-153	553
24	TraesCS1B01G110600	chrUn	89.213	445	44	3	2343	2784	313907400	313907843	1.510000e-153	553
25	TraesCS1B01G110600	chrUn	88.914	451	46	3	2346	2793	327119288	327118839	1.510000e-153	553
26	TraesCS1B01G110600	chrUn	82.870	216	15	11	2936	3148	217763860	217763664	1.370000e-39	174
27	TraesCS1B01G110600	chrUn	82.870	216	15	11	2936	3148	246305038	246304842	1.370000e-39	174
28	TraesCS1B01G110600	chrUn	82.870	216	15	11	2936	3148	327118753	327118557	1.370000e-39	174
29	TraesCS1B01G110600	chrUn	77.679	336	26	21	2816	3148	260129567	260129856	3.850000e-35	159
30	TraesCS1B01G110600	chrUn	77.679	336	26	21	2816	3148	313907845	313908134	3.850000e-35	159
31	TraesCS1B01G110600	chrUn	95.349	86	4	0	1	86	246308054	246307969	1.800000e-28	137
32	TraesCS1B01G110600	chrUn	95.349	86	4	0	1	86	255507054	255506969	1.800000e-28	137
33	TraesCS1B01G110600	chrUn	94.186	86	5	0	1	86	217766876	217766791	8.390000e-27	132
34	TraesCS1B01G110600	chrUn	87.234	94	10	2	2816	2909	217763953	217763862	5.090000e-19	106
35	TraesCS1B01G110600	chrUn	87.234	94	10	2	2816	2909	246305131	246305040	5.090000e-19	106
36	TraesCS1B01G110600	chrUn	87.234	94	10	2	2816	2909	327118846	327118755	5.090000e-19	106
37	TraesCS1B01G110600	chr2D	82.855	1569	203	30	278	1801	640044893	640043346	0.000000e+00	1347
38	TraesCS1B01G110600	chr2D	83.918	1368	203	10	1	1358	179661399	179662759	0.000000e+00	1291
39	TraesCS1B01G110600	chr2D	85.714	1015	127	13	1805	2809	640043189	640042183	0.000000e+00	1055
40	TraesCS1B01G110600	chr2B	84.137	1368	200	7	1	1358	236456492	236457852	0.000000e+00	1308
41	TraesCS1B01G110600	chr6B	83.819	1236	126	26	1813	3036	3823955	3822782	0.000000e+00	1107
42	TraesCS1B01G110600	chr6B	86.185	637	64	8	1186	1801	3824637	3824004	0.000000e+00	667
43	TraesCS1B01G110600	chr6B	89.213	445	44	3	2343	2784	4406715	4407158	1.510000e-153	553
44	TraesCS1B01G110600	chr6B	77.679	336	26	21	2816	3148	4407160	4407449	3.850000e-35	159
45	TraesCS1B01G110600	chr6B	97.500	80	2	0	1	80	4385837	4385916	1.800000e-28	137
46	TraesCS1B01G110600	chr5A	82.000	1250	188	25	1	1221	617255207	617253966	0.000000e+00	1027
47	TraesCS1B01G110600	chr5B	81.499	1254	193	23	1	1221	610664541	610663294	0.000000e+00	994
48	TraesCS1B01G110600	chr2A	85.342	730	92	5	1	721	194122138	194122861	0.000000e+00	741

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	TraesCS1B01G110600	chr1B	123964129	123967852	3723	True	6878.000000	6878	100.000000	1	3724	1	chr1B.!!$R1	3723
1	TraesCS1B01G110600	chr1B	123973482	123974045	563	True	689.000000	689	88.792000	1805	2370	1	chr1B.!!$R2	565
2	TraesCS1B01G110600	chr1B	123984699	123987520	2821	True	574.000000	972	86.112500	4	1419	2	chr1B.!!$R3	1415
3	TraesCS1B01G110600	chr1A	96462732	96465585	2853	False	3273.000000	3273	87.548000	1	2832	1	chr1A.!!$F1	2831
4	TraesCS1B01G110600	chr1A	96470548	96473961	3413	False	1336.333333	1748	90.876667	1	3318	3	chr1A.!!$F2	3317
5	TraesCS1B01G110600	chr1D	78977637	78983090	5453	True	1289.250000	2446	92.246750	77	3724	4	chr1D.!!$R2	3647
6	TraesCS1B01G110600	chr6A	571805	574622	2817	True	1348.500000	1668	85.439000	1	2724	2	chr6A.!!$R1	2723
7	TraesCS1B01G110600	chr6A	1411840	1412771	931	False	721.000000	721	81.109000	1215	2167	1	chr6A.!!$F1	952
8	TraesCS1B01G110600	chrUn	255505269	255507054	1785	True	823.000000	1509	89.278000	1	1801	2	chrUn.!!$R3	1800
9	TraesCS1B01G110600	chrUn	246304842	246308054	3212	True	517.666667	1509	87.629333	1	3148	6	chrUn.!!$R2	3147
10	TraesCS1B01G110600	chrUn	217763664	217766876	3212	True	493.800000	1504	87.270600	1	3148	5	chrUn.!!$R1	3147
11	TraesCS1B01G110600	chrUn	313906759	313908134	1375	False	446.333333	627	85.031333	1817	3148	3	chrUn.!!$F2	1331
12	TraesCS1B01G110600	chrUn	260128492	260129856	1364	False	395.500000	632	83.034500	1817	3148	2	chrUn.!!$F1	1331
13	TraesCS1B01G110600	chrUn	327118557	327119288	731	True	277.666667	553	86.339333	2346	3148	3	chrUn.!!$R4	802
14	TraesCS1B01G110600	chr2D	179661399	179662759	1360	False	1291.000000	1291	83.918000	1	1358	1	chr2D.!!$F1	1357
15	TraesCS1B01G110600	chr2D	640042183	640044893	2710	True	1201.000000	1347	84.284500	278	2809	2	chr2D.!!$R1	2531
16	TraesCS1B01G110600	chr2B	236456492	236457852	1360	False	1308.000000	1308	84.137000	1	1358	1	chr2B.!!$F1	1357
17	TraesCS1B01G110600	chr6B	3822782	3824637	1855	True	887.000000	1107	85.002000	1186	3036	2	chr6B.!!$R1	1850
18	TraesCS1B01G110600	chr6B	4406715	4407449	734	False	356.000000	553	83.446000	2343	3148	2	chr6B.!!$F2	805
19	TraesCS1B01G110600	chr5A	617253966	617255207	1241	True	1027.000000	1027	82.000000	1	1221	1	chr5A.!!$R1	1220
20	TraesCS1B01G110600	chr5B	610663294	610664541	1247	True	994.000000	994	81.499000	1	1221	1	chr5B.!!$R1	1220
21	TraesCS1B01G110600	chr2A	194122138	194122861	723	False	741.000000	741	85.342000	1	721	1	chr2A.!!$F1	720

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
572	2018	0.473886	AACTACTGGACCAGTGGCCT	60.474	55.000	33.24	19.78	44.89	5.19	F
755	2216	1.747355	GCTGTCATGGTTGGATTCCAG	59.253	52.381	5.36	0.00	38.42	3.86	F
2647	4655	0.179089	CCAGCCTTCTCTGACGGATG	60.179	60.000	2.03	2.03	37.17	3.51	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2261	4030	1.337823	CCCGTGACGATCTCCAAAACT	60.338	52.381	6.54	0.0	0.00	2.66	R
2668	4676	0.512952	CGAGGACGCCACTTTTGAAG	59.487	55.000	0.00	0.0	0.00	3.02	R
3585	7447	3.678072	ACACATGATACGAAAACACGGAG	59.322	43.478	0.00	0.0	37.61	4.63	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
75	79	2.303311	GTTCACCTTGGGCTTCTACTCT	59.697	50.000	0.00	0.00	0.00	3.24
214	1645	1.512694	GCCTCCTTGGAAATTGCCG	59.487	57.895	0.00	0.00	38.35	5.69
238	1669	1.084370	CGGCAATCTTGTCCTCCGTC	61.084	60.000	0.00	0.00	32.93	4.79
327	1761	3.077556	AGGGACAGCGGTAGCCTG	61.078	66.667	8.34	8.34	46.67	4.85
387	1821	1.942657	CAAAGCATAGACCATCCCACG	59.057	52.381	0.00	0.00	0.00	4.94
429	1863	2.331265	GCTCGGGCTGAACAAAACT	58.669	52.632	0.00	0.00	35.22	2.66
522	1968	3.443045	GACCCCAATGGCAGCACG	61.443	66.667	0.00	0.00	37.83	5.34
572	2018	0.473886	AACTACTGGACCAGTGGCCT	60.474	55.000	33.24	19.78	44.89	5.19
755	2216	1.747355	GCTGTCATGGTTGGATTCCAG	59.253	52.381	5.36	0.00	38.42	3.86
997	2476	4.657436	ACTCCGTCTGATAAGTTCCATC	57.343	45.455	0.00	0.00	0.00	3.51
1243	2791	4.440880	TCAGCAAAGGAACAAAACAATGG	58.559	39.130	0.00	0.00	0.00	3.16
1266	2814	3.070734	TCATTGGTTCAATTGTTGGTGGG	59.929	43.478	5.13	0.00	31.05	4.61
1286	2834	3.317150	GGGTTGCTGCAGTTTTGATAAC	58.683	45.455	16.64	9.10	0.00	1.89
1434	3000	7.761038	TCTTGATCTGTCAACACTAAGAGTA	57.239	36.000	0.00	0.00	39.36	2.59
1562	3138	9.730420	ATATTTACCAATGAGCGTGTATTTTTC	57.270	29.630	0.00	0.00	0.00	2.29
1563	3139	6.811253	TTACCAATGAGCGTGTATTTTTCT	57.189	33.333	0.00	0.00	0.00	2.52
1564	3140	5.705609	ACCAATGAGCGTGTATTTTTCTT	57.294	34.783	0.00	0.00	0.00	2.52
1565	3141	6.084326	ACCAATGAGCGTGTATTTTTCTTT	57.916	33.333	0.00	0.00	0.00	2.52
1568	3144	7.169140	ACCAATGAGCGTGTATTTTTCTTTTTC	59.831	33.333	0.00	0.00	0.00	2.29
1629	3205	8.161425	AGTAAAAAGGCTATGTAAGAGTTCCAA	58.839	33.333	0.00	0.00	0.00	3.53
1862	3617	5.343307	TCACTGCAATGCTGATACTTCTA	57.657	39.130	18.78	0.00	0.00	2.10
1935	3690	8.424918	GGAGATTCAAGATTATCAGTGGAGTTA	58.575	37.037	0.00	0.00	0.00	2.24
2026	3781	5.516339	GCAATATTTTGTTGGACCTCGATTG	59.484	40.000	0.00	0.00	35.17	2.67
2125	3880	2.540515	CGGGACATAGTAAGCACAGTG	58.459	52.381	0.00	0.00	0.00	3.66
2134	3889	2.816087	AGTAAGCACAGTGAGCATTTGG	59.184	45.455	15.15	0.00	0.00	3.28
2160	3921	6.641474	AGTTAGGCATCAAAGTAGAACCTAC	58.359	40.000	0.00	0.00	32.98	3.18
2192	3953	7.281774	CAGTTATGTTCTTCTTGCAGTGGATAT	59.718	37.037	0.00	0.00	0.00	1.63
2261	4030	1.262151	GCGTTCAGCTTCGGTGTTTTA	59.738	47.619	5.17	0.00	44.04	1.52
2385	4393	2.816958	CTGTGCGCGGCTGAATCT	60.817	61.111	8.83	0.00	0.00	2.40
2453	4461	1.158007	ACTGGACCAGGGGAAATGTT	58.842	50.000	25.34	0.00	35.51	2.71
2591	4599	0.647410	CGTCCGTGAATGTCATGCTC	59.353	55.000	0.00	0.00	32.19	4.26
2647	4655	0.179089	CCAGCCTTCTCTGACGGATG	60.179	60.000	2.03	2.03	37.17	3.51
2648	4656	0.534412	CAGCCTTCTCTGACGGATGT	59.466	55.000	1.02	0.00	33.61	3.06
2668	4676	6.591834	GGATGTAGTGGATGCAGTGATAATAC	59.408	42.308	4.57	0.00	0.00	1.89
2836	4932	9.513906	TTCATGGTTATGATGAAAAGTCTTACA	57.486	29.630	0.00	0.00	42.60	2.41
2837	4933	8.946085	TCATGGTTATGATGAAAAGTCTTACAC	58.054	33.333	0.00	0.00	38.37	2.90
2874	4970	2.016318	TCAGTGTCAGTTTTGCTGTGG	58.984	47.619	0.00	0.00	45.23	4.17
2876	4972	2.423185	CAGTGTCAGTTTTGCTGTGGAA	59.577	45.455	0.00	0.00	45.23	3.53
2913	5009	3.244526	TGCTGCTGGAGAAAATGTCAGTA	60.245	43.478	0.00	0.00	0.00	2.74
2948	5044	4.213906	TGTGATATGCGGCTCATACAAATG	59.786	41.667	0.00	0.00	40.22	2.32
2956	5052	3.312146	CGGCTCATACAAATGCATGTACA	59.688	43.478	0.00	0.00	38.53	2.90
2957	5053	4.023792	CGGCTCATACAAATGCATGTACAT	60.024	41.667	1.41	1.41	38.53	2.29
3000	5099	7.201947	GCCTTTCCATTTTGGCTATCTTCTAAT	60.202	37.037	0.00	0.00	41.92	1.73
3226	5328	8.072422	CCCTAAAACCTAGATAGGGCCCTTTT	62.072	46.154	34.04	23.12	46.92	2.27
3250	6041	5.899547	TGTAATCATACCTCACTGATGGTCT	59.100	40.000	4.09	0.00	37.74	3.85
3349	6140	5.913137	TTAACATGGGTCAAATTGCTAGG	57.087	39.130	0.00	0.00	0.00	3.02
3351	6142	4.255510	ACATGGGTCAAATTGCTAGGAT	57.744	40.909	0.00	0.00	0.00	3.24
3367	6158	8.929260	TTGCTAGGATGATGATCAATGTATTT	57.071	30.769	0.00	0.00	0.00	1.40
3378	6169	9.773328	GATGATCAATGTATTTTCGAACTCAAA	57.227	29.630	0.00	0.00	0.00	2.69
3394	6185	5.818678	ACTCAAACTGGGTGTACATAGAA	57.181	39.130	0.00	0.00	23.94	2.10
3404	6195	4.278419	GGGTGTACATAGAAAATGATGCCC	59.722	45.833	0.00	0.00	0.00	5.36
3405	6196	4.887071	GGTGTACATAGAAAATGATGCCCA	59.113	41.667	0.00	0.00	0.00	5.36
3406	6197	5.221048	GGTGTACATAGAAAATGATGCCCAC	60.221	44.000	0.00	0.00	0.00	4.61
3407	6198	4.574421	TGTACATAGAAAATGATGCCCACG	59.426	41.667	0.00	0.00	0.00	4.94
3408	6199	2.951642	ACATAGAAAATGATGCCCACGG	59.048	45.455	0.00	0.00	0.00	4.94
3409	6200	2.051334	TAGAAAATGATGCCCACGGG	57.949	50.000	0.00	0.00	38.57	5.28
3464	6255	4.617593	AGGCAGATCCATTTTCCTTTCAT	58.382	39.130	0.00	0.00	37.29	2.57
3490	6282	0.165944	GTCATCCCACGCTTTGTTCG	59.834	55.000	0.00	0.00	0.00	3.95
3501	6293	4.203563	CACGCTTTGTTCGGTTTAAGTTTC	59.796	41.667	0.00	0.00	0.00	2.78
3517	6309	9.736023	GTTTAAGTTTCAGAATCATCACTTTGT	57.264	29.630	3.11	0.00	0.00	2.83
3523	6315	8.299570	GTTTCAGAATCATCACTTTGTACCAAT	58.700	33.333	0.00	0.00	0.00	3.16
3537	6329	7.230510	ACTTTGTACCAATTTCAGCATTACAGA	59.769	33.333	0.00	0.00	0.00	3.41
3538	6330	7.517614	TTGTACCAATTTCAGCATTACAGAA	57.482	32.000	0.00	0.00	0.00	3.02
3540	6332	5.046910	ACCAATTTCAGCATTACAGAACG	57.953	39.130	0.00	0.00	0.00	3.95
3541	6333	4.759693	ACCAATTTCAGCATTACAGAACGA	59.240	37.500	0.00	0.00	0.00	3.85
3544	6336	6.808212	CCAATTTCAGCATTACAGAACGATTT	59.192	34.615	0.00	0.00	0.00	2.17
3547	6339	5.530519	TCAGCATTACAGAACGATTTGTC	57.469	39.130	0.00	0.00	0.00	3.18
3548	6340	5.237815	TCAGCATTACAGAACGATTTGTCT	58.762	37.500	0.00	0.00	0.00	3.41
3549	6341	5.700832	TCAGCATTACAGAACGATTTGTCTT	59.299	36.000	0.00	0.00	0.00	3.01
3550	6342	6.017933	CAGCATTACAGAACGATTTGTCTTC	58.982	40.000	0.00	0.00	0.00	2.87
3551	6343	5.122396	AGCATTACAGAACGATTTGTCTTCC	59.878	40.000	0.00	0.00	0.00	3.46
3553	6345	6.403636	GCATTACAGAACGATTTGTCTTCCAT	60.404	38.462	0.00	0.00	0.00	3.41
3554	6346	6.721571	TTACAGAACGATTTGTCTTCCATC	57.278	37.500	0.00	0.00	0.00	3.51
3555	6347	4.899502	ACAGAACGATTTGTCTTCCATCT	58.100	39.130	0.00	0.00	0.00	2.90
3556	6348	6.037786	ACAGAACGATTTGTCTTCCATCTA	57.962	37.500	0.00	0.00	0.00	1.98
3558	6350	7.782049	ACAGAACGATTTGTCTTCCATCTATA	58.218	34.615	0.00	0.00	0.00	1.31
3559	6351	8.258007	ACAGAACGATTTGTCTTCCATCTATAA	58.742	33.333	0.00	0.00	0.00	0.98
3560	6352	9.098355	CAGAACGATTTGTCTTCCATCTATAAA	57.902	33.333	0.00	0.00	0.00	1.40
3607	7469	3.655486	TCCGTGTTTTCGTATCATGTGT	58.345	40.909	0.00	0.00	0.00	3.72
3619	7481	8.731275	TTCGTATCATGTGTTCCAAAATAGAT	57.269	30.769	0.00	0.00	0.00	1.98
3622	7484	7.442364	CGTATCATGTGTTCCAAAATAGATCCT	59.558	37.037	0.00	0.00	0.00	3.24
3623	7485	9.125026	GTATCATGTGTTCCAAAATAGATCCTT	57.875	33.333	0.00	0.00	0.00	3.36
3625	7487	9.872684	ATCATGTGTTCCAAAATAGATCCTTAT	57.127	29.630	0.00	0.00	0.00	1.73
3626	7488	9.123902	TCATGTGTTCCAAAATAGATCCTTATG	57.876	33.333	0.00	0.00	0.00	1.90
3634	7496	9.670442	TCCAAAATAGATCCTTATGTACTACCT	57.330	33.333	0.00	0.00	0.00	3.08
3665	7527	8.272545	ACCTTTTACAAGACGTTTTTAGAGTT	57.727	30.769	0.00	0.00	30.57	3.01

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
214	1645	2.750888	GGACAAGATTGCCGTCGCC	61.751	63.158	0.00	0.00	0.00	5.54
225	1656	2.891580	GGCTATATGACGGAGGACAAGA	59.108	50.000	0.00	0.00	0.00	3.02
327	1761	0.539986	TGGAGGCATCGGTTAGTTCC	59.460	55.000	0.00	0.00	0.00	3.62
387	1821	2.505405	GACCCTGGAAGAAAGGTGTTC	58.495	52.381	0.00	0.00	34.07	3.18
429	1863	1.605058	GCTTCTGGCTCAGACCCGTA	61.605	60.000	4.59	0.00	40.46	4.02
522	1968	2.380084	TCCACCGAATGAAGTACTGC	57.620	50.000	0.00	0.00	0.00	4.40
572	2018	2.103094	CTGAATCTATTGCCGTCCCAGA	59.897	50.000	0.00	0.00	0.00	3.86
653	2108	7.553402	TCATCGAGTAGTAGAAGTAGCTTTCTT	59.447	37.037	6.00	4.92	38.35	2.52
755	2216	1.202698	AGAACAAGACCCACTGCTGTC	60.203	52.381	0.00	0.00	0.00	3.51
792	2253	2.493675	GAGAGCATACACCTCACACTGA	59.506	50.000	0.00	0.00	0.00	3.41
840	2307	2.584064	CAGTACGGCAGGGCATCA	59.416	61.111	0.00	0.00	0.00	3.07
997	2476	0.463295	AGGCGCACATCTTCCATGAG	60.463	55.000	10.83	0.00	0.00	2.90
1243	2791	4.057432	CCACCAACAATTGAACCAATGAC	58.943	43.478	13.59	0.00	34.04	3.06
1255	2803	1.757423	GCAGCAACCCCACCAACAAT	61.757	55.000	0.00	0.00	0.00	2.71
1266	2814	3.317150	GGTTATCAAAACTGCAGCAACC	58.683	45.455	15.27	11.66	0.00	3.77
1286	2834	3.457610	AGAACAACACAATTGCAAGGG	57.542	42.857	4.94	1.55	0.00	3.95
1434	3000	4.520492	CCTTCACCAAAGTCATTTGTAGCT	59.480	41.667	0.00	0.00	43.61	3.32
1562	3138	2.959465	AGGACTCCCTGTGGAAAAAG	57.041	50.000	0.00	0.00	42.42	2.27
1582	3158	2.745281	TGCTATTTGTTTACCGTCAGGC	59.255	45.455	0.00	0.00	42.76	4.85
1629	3205	5.333566	TTTCAGTTCCCCTATTCCTTGTT	57.666	39.130	0.00	0.00	0.00	2.83
1935	3690	5.480772	CGTGGAGATATTGTAATCCCCTAGT	59.519	44.000	0.00	0.00	0.00	2.57
2026	3781	6.127980	GCCAAAGTCAGAAATCTTAGGGTTAC	60.128	42.308	0.00	0.00	0.00	2.50
2125	3880	4.199310	TGATGCCTAACTACCAAATGCTC	58.801	43.478	0.00	0.00	0.00	4.26
2134	3889	6.641474	AGGTTCTACTTTGATGCCTAACTAC	58.359	40.000	0.00	0.00	0.00	2.73
2160	3921	7.041780	ACTGCAAGAAGAACATAACTGTTACTG	60.042	37.037	1.73	5.61	41.07	2.74
2192	3953	3.337358	CATGGCATATTCAGGCGACATA	58.663	45.455	0.00	0.00	30.30	2.29
2261	4030	1.337823	CCCGTGACGATCTCCAAAACT	60.338	52.381	6.54	0.00	0.00	2.66
2311	4080	9.599322	CAAGATTTACGAGATAAACATATTGCC	57.401	33.333	0.00	0.00	35.57	4.52
2576	4584	1.081094	TGCTGAGCATGACATTCACG	58.919	50.000	1.40	0.00	31.71	4.35
2591	4599	1.287730	GACGAGCACTCTGGTTGCTG	61.288	60.000	0.67	0.00	39.21	4.41
2647	4655	7.210174	TGAAGTATTATCACTGCATCCACTAC	58.790	38.462	0.00	0.00	28.52	2.73
2648	4656	7.360113	TGAAGTATTATCACTGCATCCACTA	57.640	36.000	0.00	0.00	28.52	2.74
2668	4676	0.512952	CGAGGACGCCACTTTTGAAG	59.487	55.000	0.00	0.00	0.00	3.02
2744	4752	5.803237	AAGTAACACTAGTACAAGCTGGT	57.197	39.130	0.00	0.00	0.00	4.00
2749	4757	9.962783	AAGACAGTAAAGTAACACTAGTACAAG	57.037	33.333	0.00	0.00	0.00	3.16
2835	4931	2.280628	GAAGATAACCTTGGAGGCGTG	58.719	52.381	0.00	0.00	39.63	5.34
2836	4932	1.906574	TGAAGATAACCTTGGAGGCGT	59.093	47.619	0.00	0.00	39.63	5.68
2837	4933	2.093447	ACTGAAGATAACCTTGGAGGCG	60.093	50.000	0.00	0.00	39.63	5.52
2874	4970	4.768968	AGCAGCAATACCATAATCCCATTC	59.231	41.667	0.00	0.00	0.00	2.67
2876	4972	4.084287	CAGCAGCAATACCATAATCCCAT	58.916	43.478	0.00	0.00	0.00	4.00
2913	5009	5.812642	GCCGCATATCACAGCTAATAATACT	59.187	40.000	0.00	0.00	0.00	2.12
2927	5023	3.189080	GCATTTGTATGAGCCGCATATCA	59.811	43.478	0.00	0.00	41.29	2.15
2934	5030	3.312146	TGTACATGCATTTGTATGAGCCG	59.688	43.478	14.39	0.00	39.98	5.52
2948	5044	8.854979	TGCAAATTAACTATTGATGTACATGC	57.145	30.769	14.43	7.22	0.00	4.06
2956	5052	7.093377	TGGAAAGGCTGCAAATTAACTATTGAT	60.093	33.333	0.50	0.00	0.00	2.57
2957	5053	6.210385	TGGAAAGGCTGCAAATTAACTATTGA	59.790	34.615	0.50	0.00	0.00	2.57
3226	5328	5.899547	AGACCATCAGTGAGGTATGATTACA	59.100	40.000	12.50	0.00	38.50	2.41
3250	6041	3.900966	ATGAGATGCTGCTTCAGTGTA	57.099	42.857	16.56	0.43	33.43	2.90
3322	6113	4.621034	GCAATTTGACCCATGTTAAAGACG	59.379	41.667	0.00	0.00	34.00	4.18
3349	6140	9.591404	GAGTTCGAAAATACATTGATCATCATC	57.409	33.333	0.00	0.00	0.00	2.92
3351	6142	8.491331	TGAGTTCGAAAATACATTGATCATCA	57.509	30.769	0.00	0.00	0.00	3.07
3367	6158	2.702592	ACACCCAGTTTGAGTTCGAA	57.297	45.000	0.00	0.00	0.00	3.71
3378	6169	5.590259	GCATCATTTTCTATGTACACCCAGT	59.410	40.000	0.00	0.00	0.00	4.00
3407	6198	2.443390	TAGTCTAGCCCGTGCCCC	60.443	66.667	0.00	0.00	38.69	5.80
3408	6199	1.041447	TTCTAGTCTAGCCCGTGCCC	61.041	60.000	1.60	0.00	38.69	5.36
3409	6200	0.822164	TTTCTAGTCTAGCCCGTGCC	59.178	55.000	1.60	0.00	38.69	5.01
3410	6201	1.803252	GCTTTCTAGTCTAGCCCGTGC	60.803	57.143	1.60	0.00	37.95	5.34
3422	6213	4.301628	CCTTGCAGTTTTTGGCTTTCTAG	58.698	43.478	0.00	0.00	0.00	2.43
3451	6242	5.518812	TGACACGTTGATGAAAGGAAAATG	58.481	37.500	0.00	0.00	0.00	2.32
3490	6282	9.185192	CAAAGTGATGATTCTGAAACTTAAACC	57.815	33.333	5.20	0.00	0.00	3.27
3517	6309	5.935206	TCGTTCTGTAATGCTGAAATTGGTA	59.065	36.000	0.00	0.00	36.91	3.25
3523	6315	6.204688	AGACAAATCGTTCTGTAATGCTGAAA	59.795	34.615	0.00	0.00	36.91	2.69
3585	7447	3.678072	ACACATGATACGAAAACACGGAG	59.322	43.478	0.00	0.00	37.61	4.63
3588	7450	4.084276	TGGAACACATGATACGAAAACACG	60.084	41.667	0.00	0.00	39.31	4.49
3619	7481	6.978261	AGGTTACAGAGGTAGTACATAAGGA	58.022	40.000	2.06	0.00	0.00	3.36
3623	7485	9.532494	TGTAAAAGGTTACAGAGGTAGTACATA	57.468	33.333	2.06	0.00	43.71	2.29
3624	7486	8.426569	TGTAAAAGGTTACAGAGGTAGTACAT	57.573	34.615	2.06	0.00	43.71	2.29
3625	7487	7.838079	TGTAAAAGGTTACAGAGGTAGTACA	57.162	36.000	2.06	0.00	43.71	2.90

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.