AutoCloner

Multiple sequence alignment - TraesCS5A01G215200

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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	TraesCS5A01G215200	chr5A	100.000	4377	0	0	1	4377	430509452	430505076	0.000000e+00	8083.0
1	TraesCS5A01G215200	chr5A	87.626	1188	128	11	2442	3622	430957360	430956185	0.000000e+00	1362.0
2	TraesCS5A01G215200	chr5A	89.659	996	87	13	2635	3623	431029495	431028509	0.000000e+00	1254.0
3	TraesCS5A01G215200	chr5A	86.571	834	70	24	801	1617	431045269	431044461	0.000000e+00	881.0
4	TraesCS5A01G215200	chr5A	86.968	729	69	16	927	1654	430958691	430957988	0.000000e+00	797.0
5	TraesCS5A01G215200	chr5A	79.132	1083	172	30	1434	2500	666934158	666933114	0.000000e+00	699.0
6	TraesCS5A01G215200	chr5A	83.511	655	67	21	1751	2399	430957990	430957371	1.370000e-159	573.0
7	TraesCS5A01G215200	chr5A	82.547	636	54	29	1614	2243	431030126	431029542	1.400000e-139	507.0
8	TraesCS5A01G215200	chr5A	90.446	157	11	4	3637	3791	427318927	427318773	2.060000e-48	204.0
9	TraesCS5A01G215200	chr5B	94.239	4426	182	34	1	4377	378509552	378513953	0.000000e+00	6693.0
10	TraesCS5A01G215200	chr5B	87.791	1204	123	16	2438	3635	378069729	378070914	0.000000e+00	1387.0
11	TraesCS5A01G215200	chr5B	82.467	1654	164	64	792	2410	377978009	377979571	0.000000e+00	1332.0
12	TraesCS5A01G215200	chr5B	83.301	1545	140	61	920	2399	378068231	378069722	0.000000e+00	1315.0
13	TraesCS5A01G215200	chr5B	90.223	716	65	4	2611	3322	377979595	377980309	0.000000e+00	929.0
14	TraesCS5A01G215200	chr5B	87.525	505	49	12	1136	1634	377698698	377699194	4.910000e-159	571.0
15	TraesCS5A01G215200	chr5B	85.377	212	20	6	433	635	377976204	377976413	4.440000e-50	209.0
16	TraesCS5A01G215200	chr5B	85.000	80	6	3	793	867	378068140	378068218	4.690000e-10	76.8
17	TraesCS5A01G215200	chr5D	93.948	3701	138	41	1	3641	326117094	326120768	0.000000e+00	5515.0
18	TraesCS5A01G215200	chr5D	87.647	1020	101	9	2619	3635	325664861	325665858	0.000000e+00	1162.0
19	TraesCS5A01G215200	chr5D	94.553	716	29	5	3665	4371	326121027	326121741	0.000000e+00	1098.0
20	TraesCS5A01G215200	chr5D	90.209	766	63	9	2526	3283	325648105	325648866	0.000000e+00	989.0
21	TraesCS5A01G215200	chr5D	88.583	727	63	16	931	1652	325646757	325647468	0.000000e+00	865.0
22	TraesCS5A01G215200	chr5D	87.875	734	61	16	939	1669	325663603	325664311	0.000000e+00	837.0
23	TraesCS5A01G215200	chr5D	87.033	509	47	13	1136	1634	325422824	325423323	1.380000e-154	556.0
24	TraesCS5A01G215200	chr5D	83.712	528	48	21	1723	2243	325664331	325664827	8.570000e-127	464.0
25	TraesCS5A01G215200	chr5D	85.618	445	53	7	1961	2399	325647610	325648049	1.430000e-124	457.0
26	TraesCS5A01G215200	chr5D	86.478	318	29	8	3321	3635	325652098	325652404	1.950000e-88	337.0
27	TraesCS5A01G215200	chr5D	89.121	239	24	2	1959	2196	325423518	325423755	3.310000e-76	296.0
28	TraesCS5A01G215200	chr5D	81.818	88	10	3	793	875	325646666	325646752	7.850000e-08	69.4
29	TraesCS5A01G215200	chr7D	83.760	782	98	16	1724	2495	50650380	50651142	0.000000e+00	713.0
30	TraesCS5A01G215200	chr7D	90.385	156	13	2	3637	3791	549312704	549312550	2.060000e-48	204.0
31	TraesCS5A01G215200	chrUn	79.224	1083	172	29	1434	2500	30413611	30412566	0.000000e+00	704.0
32	TraesCS5A01G215200	chr4A	82.084	787	113	13	1724	2501	482875610	482874843	0.000000e+00	647.0
33	TraesCS5A01G215200	chr4A	90.000	160	13	3	3634	3791	503614219	503614377	2.060000e-48	204.0
34	TraesCS5A01G215200	chr6D	81.969	782	109	17	1724	2495	36220046	36220805	6.180000e-178	634.0
35	TraesCS5A01G215200	chr2D	90.968	155	13	1	3637	3791	533094319	533094166	1.600000e-49	207.0
36	TraesCS5A01G215200	chr6B	90.385	156	12	3	3637	3791	623719553	623719400	7.420000e-48	202.0
37	TraesCS5A01G215200	chr2A	89.809	157	16	0	3635	3791	163044351	163044507	7.420000e-48	202.0
38	TraesCS5A01G215200	chr2A	88.344	163	17	2	3629	3791	14590421	14590581	1.240000e-45	195.0
39	TraesCS5A01G215200	chr7B	87.574	169	17	4	3625	3791	463682100	463682266	4.470000e-45	193.0

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	TraesCS5A01G215200	chr5A	430505076	430509452	4376	True	8083.000000	8083	100.000000	1	4377	1	chr5A.!!$R2	4376
1	TraesCS5A01G215200	chr5A	430956185	430958691	2506	True	910.666667	1362	86.035000	927	3622	3	chr5A.!!$R5	2695
2	TraesCS5A01G215200	chr5A	431044461	431045269	808	True	881.000000	881	86.571000	801	1617	1	chr5A.!!$R3	816
3	TraesCS5A01G215200	chr5A	431028509	431030126	1617	True	880.500000	1254	86.103000	1614	3623	2	chr5A.!!$R6	2009
4	TraesCS5A01G215200	chr5A	666933114	666934158	1044	True	699.000000	699	79.132000	1434	2500	1	chr5A.!!$R4	1066
5	TraesCS5A01G215200	chr5B	378509552	378513953	4401	False	6693.000000	6693	94.239000	1	4377	1	chr5B.!!$F2	4376
6	TraesCS5A01G215200	chr5B	378068140	378070914	2774	False	926.266667	1387	85.364000	793	3635	3	chr5B.!!$F4	2842
7	TraesCS5A01G215200	chr5B	377976204	377980309	4105	False	823.333333	1332	86.022333	433	3322	3	chr5B.!!$F3	2889
8	TraesCS5A01G215200	chr5D	326117094	326121741	4647	False	3306.500000	5515	94.250500	1	4371	2	chr5D.!!$F4	4370
9	TraesCS5A01G215200	chr5D	325663603	325665858	2255	False	821.000000	1162	86.411333	939	3635	3	chr5D.!!$F3	2696
10	TraesCS5A01G215200	chr5D	325646666	325652404	5738	False	543.480000	989	86.541200	793	3635	5	chr5D.!!$F2	2842
11	TraesCS5A01G215200	chr5D	325422824	325423755	931	False	426.000000	556	88.077000	1136	2196	2	chr5D.!!$F1	1060
12	TraesCS5A01G215200	chr7D	50650380	50651142	762	False	713.000000	713	83.760000	1724	2495	1	chr7D.!!$F1	771
13	TraesCS5A01G215200	chrUn	30412566	30413611	1045	True	704.000000	704	79.224000	1434	2500	1	chrUn.!!$R1	1066
14	TraesCS5A01G215200	chr4A	482874843	482875610	767	True	647.000000	647	82.084000	1724	2501	1	chr4A.!!$R1	777
15	TraesCS5A01G215200	chr6D	36220046	36220805	759	False	634.000000	634	81.969000	1724	2495	1	chr6D.!!$F1	771

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
893	2389	0.036858	GTCCTGCTCACCTGACCTTC	60.037	60.0	0.00	0.0	0.00	3.46	F
1759	3345	0.109272	CACGTACGAGTGCCATCTGT	60.109	55.0	24.41	0.0	35.17	3.41	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1771	3357	0.671781	CAGGGGACAAGAACAGCTCG	60.672	60.0	0.0	0.0	0.0	5.03	R
3648	8514	0.392595	GGAACTCCCCACCGTGATTC	60.393	60.0	0.0	0.0	0.0	2.52	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
95	96	3.347405	CGGTAAAACGGGTGCGCA	61.347	61.111	5.66	5.66	0.00	6.09
149	150	4.989168	CAGGTAGTAACAACTCAGGTGTTC	59.011	45.833	12.59	4.13	0.00	3.18
159	160	7.264373	ACAACTCAGGTGTTCATAAGAAAAG	57.736	36.000	0.00	0.00	35.08	2.27
192	193	1.002544	CCAGGCCGTTCTCTTCTTCTT	59.997	52.381	0.00	0.00	0.00	2.52
216	217	5.577835	TGTTTGTTGATCTTGAAACTTCCG	58.422	37.500	12.30	0.00	31.03	4.30
248	249	4.452455	AGCAATTCACTCTACTTTTCACCG	59.548	41.667	0.00	0.00	0.00	4.94
279	280	5.865552	CCTGCACAAAGTCCAAATTAGAATG	59.134	40.000	0.00	0.00	0.00	2.67
293	294	7.341769	CCAAATTAGAATGTCCCAAGGTGAATA	59.658	37.037	0.00	0.00	0.00	1.75
304	305	6.882678	GTCCCAAGGTGAATAGTTTAGCTAAA	59.117	38.462	14.96	14.96	32.72	1.85
305	306	7.556635	GTCCCAAGGTGAATAGTTTAGCTAAAT	59.443	37.037	21.28	12.75	32.72	1.40
306	307	8.774183	TCCCAAGGTGAATAGTTTAGCTAAATA	58.226	33.333	21.28	14.28	32.72	1.40
307	308	9.403583	CCCAAGGTGAATAGTTTAGCTAAATAA	57.596	33.333	21.28	12.96	32.72	1.40
367	376	2.264794	GACCGGTCGTTCCTGCAT	59.735	61.111	20.85	0.00	0.00	3.96
389	398	0.941542	TGAAGCAACTGTTACACGGC	59.058	50.000	0.00	0.00	0.00	5.68
422	431	3.478540	GGGCTAAAGGCACCTGTAG	57.521	57.895	9.27	9.27	44.01	2.74
466	475	1.142474	GTAGCGCAAAACCACGTACT	58.858	50.000	11.47	0.00	0.00	2.73
469	478	0.110823	GCGCAAAACCACGTACTCTG	60.111	55.000	0.30	0.00	0.00	3.35
470	479	1.214367	CGCAAAACCACGTACTCTGT	58.786	50.000	0.00	0.00	0.00	3.41
471	480	1.595794	CGCAAAACCACGTACTCTGTT	59.404	47.619	0.00	0.00	0.00	3.16
472	481	2.796031	CGCAAAACCACGTACTCTGTTA	59.204	45.455	0.00	0.00	0.00	2.41
473	482	3.121126	CGCAAAACCACGTACTCTGTTAG	60.121	47.826	0.00	0.00	0.00	2.34
477	495	6.211515	CAAAACCACGTACTCTGTTAGTAGT	58.788	40.000	0.00	0.00	41.42	2.73
479	497	6.734104	AACCACGTACTCTGTTAGTAGTAG	57.266	41.667	0.00	0.00	41.42	2.57
508	526	9.208022	TGAATAGTCAATTTAATCATCCTAGCG	57.792	33.333	0.00	0.00	0.00	4.26
548	572	3.057806	CCCCGAACAACTTTTCACCATAC	60.058	47.826	0.00	0.00	0.00	2.39
744	2176	0.324275	GCCACCAACCACCACCATAT	60.324	55.000	0.00	0.00	0.00	1.78
766	2210	1.198759	CCTTCCCCTGTTTCCTCCGA	61.199	60.000	0.00	0.00	0.00	4.55
767	2211	0.912486	CTTCCCCTGTTTCCTCCGAT	59.088	55.000	0.00	0.00	0.00	4.18
768	2212	0.909623	TTCCCCTGTTTCCTCCGATC	59.090	55.000	0.00	0.00	0.00	3.69
769	2213	0.252513	TCCCCTGTTTCCTCCGATCA	60.253	55.000	0.00	0.00	0.00	2.92
770	2214	0.179000	CCCCTGTTTCCTCCGATCAG	59.821	60.000	0.00	0.00	0.00	2.90
786	2230	2.042843	AGAGTCCTACGGCAGGGG	60.043	66.667	5.58	0.00	45.58	4.79
874	2370	0.459489	CGCCTTCTCCTTCTCTCCAG	59.541	60.000	0.00	0.00	0.00	3.86
893	2389	0.036858	GTCCTGCTCACCTGACCTTC	60.037	60.000	0.00	0.00	0.00	3.46
894	2390	0.178921	TCCTGCTCACCTGACCTTCT	60.179	55.000	0.00	0.00	0.00	2.85
895	2391	0.248843	CCTGCTCACCTGACCTTCTC	59.751	60.000	0.00	0.00	0.00	2.87
896	2392	0.248843	CTGCTCACCTGACCTTCTCC	59.751	60.000	0.00	0.00	0.00	3.71
961	2459	3.370953	CGGGAAACATTCTTGATCCTCCT	60.371	47.826	0.00	0.00	34.71	3.69
983	2489	5.235831	CCTACGATATTGATATACGCGGAGA	59.764	44.000	12.47	0.00	33.44	3.71
994	2500	1.313812	ACGCGGAGATTCTCGGTTCT	61.314	55.000	12.47	3.41	34.09	3.01
1320	2838	2.254651	GTCGACGACAAGCTCCGT	59.745	61.111	22.66	8.23	42.17	4.69
1407	2925	2.746359	GAGTGGCTGGTGAGTGCT	59.254	61.111	0.00	0.00	0.00	4.40
1424	2945	0.879765	GCTGAACAGAGTGCAATGCT	59.120	50.000	6.82	0.00	0.00	3.79
1447	3001	1.004185	CGCCAGCAGATCAATTTCGAG	60.004	52.381	0.00	0.00	0.00	4.04
1456	3010	4.331168	CAGATCAATTTCGAGGTCTGGTTC	59.669	45.833	5.05	0.00	31.77	3.62
1465	3019	2.093500	CGAGGTCTGGTTCATGAATGGA	60.093	50.000	12.12	7.54	0.00	3.41
1526	3088	1.391157	TTGGGCAACTGAGGCACAAC	61.391	55.000	8.46	0.00	46.95	3.32
1690	3268	7.505585	TCATTCTGAGGATTAGTTTGTTTGGTT	59.494	33.333	0.00	0.00	0.00	3.67
1694	3272	6.568869	TGAGGATTAGTTTGTTTGGTTGTTG	58.431	36.000	0.00	0.00	0.00	3.33
1759	3345	0.109272	CACGTACGAGTGCCATCTGT	60.109	55.000	24.41	0.00	35.17	3.41
1771	3357	1.293924	CCATCTGTTCCATCAGCGAC	58.706	55.000	0.00	0.00	35.63	5.19
2009	3637	1.645710	ACGTGGAGGAGGAAACTGAT	58.354	50.000	0.00	0.00	44.43	2.90
2168	3813	2.613977	CCTCCAACATCTTGCTCGACTT	60.614	50.000	0.00	0.00	0.00	3.01
2327	3986	6.540205	ACTACAAAAGTGTCTGAAAAACGAC	58.460	36.000	0.00	0.00	39.30	4.34
2411	4074	6.127535	CCAAGATGCCATGTTTCTGAACTTAT	60.128	38.462	0.00	0.00	36.70	1.73
2412	4075	7.318141	CAAGATGCCATGTTTCTGAACTTATT	58.682	34.615	0.00	0.00	36.70	1.40
2413	4076	8.461222	CAAGATGCCATGTTTCTGAACTTATTA	58.539	33.333	0.00	0.00	36.70	0.98
2528	4192	9.176460	TGAGATACATTTAGCATTCAATGTCAA	57.824	29.630	0.00	0.00	41.67	3.18
3461	8327	4.810790	TGTCACATCGGTTTGTTTGTTTT	58.189	34.783	0.00	0.00	0.00	2.43
3735	8843	7.466804	ACTGATCCAGTTTATAAGGAAAACCA	58.533	34.615	0.00	0.00	42.59	3.67
3766	8874	3.570975	ACCTAAACAAATTGACCCCGTTC	59.429	43.478	0.00	0.00	0.00	3.95
3806	8914	1.260544	AACCAAAATGCCAGAGGAGC	58.739	50.000	0.00	0.00	0.00	4.70
3893	9001	9.902684	ATTTGCATAAATTTTGGTCCAATATCA	57.097	25.926	4.80	0.00	32.70	2.15
3903	9011	6.713762	TTGGTCCAATATCATCCATTGTTC	57.286	37.500	0.00	0.00	32.55	3.18
3919	9027	5.164031	CCATTGTTCGCAAATGAAATGAGTG	60.164	40.000	6.22	0.00	40.90	3.51
3920	9028	3.307674	TGTTCGCAAATGAAATGAGTGC	58.692	40.909	0.00	0.00	0.00	4.40
4177	9292	2.670905	TGACATATTGAAGGTTGACGCG	59.329	45.455	3.53	3.53	0.00	6.01
4184	9299	1.270625	TGAAGGTTGACGCGAAAGGAT	60.271	47.619	15.93	0.00	0.00	3.24
4253	9368	5.870433	TGAAACTGTACAGAAGAACGTTTGA	59.130	36.000	29.30	9.49	0.00	2.69
4328	9444	1.305297	TCACCCGTCCAGCTGAGAT	60.305	57.895	17.39	0.00	0.00	2.75
4329	9445	1.153489	CACCCGTCCAGCTGAGATG	60.153	63.158	17.39	15.36	0.00	2.90
4371	9487	2.222027	CAACCACCAGAACTGAAGGTC	58.778	52.381	14.70	0.00	36.83	3.85

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
25	26	6.816640	CCGAGTAAACATGATAGAAGTTCCAA	59.183	38.462	0.00	0.00	0.00	3.53
102	103	9.869844	CTGTATCTTTAAGAAATAGGCGAAATG	57.130	33.333	0.00	0.00	0.00	2.32
142	143	8.897752	GCTGAATATCTTTTCTTATGAACACCT	58.102	33.333	0.00	0.00	31.02	4.00
159	160	2.224305	ACGGCCTGGTAAGCTGAATATC	60.224	50.000	0.00	0.00	39.03	1.63
192	193	6.033341	CGGAAGTTTCAAGATCAACAAACAA	58.967	36.000	13.01	0.00	32.20	2.83
216	217	0.250513	AGTGAATTGCTCGAGGGACC	59.749	55.000	15.58	0.00	0.00	4.46
248	249	2.130073	GACTTTGTGCAGGCCGTTCC	62.130	60.000	0.00	0.00	0.00	3.62
256	257	6.449698	ACATTCTAATTTGGACTTTGTGCAG	58.550	36.000	0.00	0.00	34.96	4.41
279	280	4.844884	AGCTAAACTATTCACCTTGGGAC	58.155	43.478	0.00	0.00	0.00	4.46
293	294	5.127194	GCAGGGCCTTTTATTTAGCTAAACT	59.873	40.000	20.85	12.41	0.00	2.66
304	305	0.817654	GAAAGCGCAGGGCCTTTTAT	59.182	50.000	11.47	0.00	45.17	1.40
305	306	0.251165	AGAAAGCGCAGGGCCTTTTA	60.251	50.000	11.47	0.00	45.17	1.52
306	307	1.531602	AGAAAGCGCAGGGCCTTTT	60.532	52.632	11.47	0.87	45.17	2.27
307	308	2.116125	AGAAAGCGCAGGGCCTTT	59.884	55.556	11.47	0.00	45.17	3.11
354	355	2.032178	GCTTCAATATGCAGGAACGACC	59.968	50.000	0.00	0.00	39.35	4.79
367	376	3.187637	GCCGTGTAACAGTTGCTTCAATA	59.812	43.478	2.84	0.00	35.74	1.90
404	413	0.748367	GCTACAGGTGCCTTTAGCCC	60.748	60.000	20.17	0.79	42.99	5.19
416	425	3.118408	TGGGTTTATGCTACAGCTACAGG	60.118	47.826	2.44	0.00	42.66	4.00
420	429	2.159014	CCGTGGGTTTATGCTACAGCTA	60.159	50.000	2.44	0.00	42.66	3.32
421	430	1.406887	CCGTGGGTTTATGCTACAGCT	60.407	52.381	2.44	0.00	42.66	4.24
422	431	1.014352	CCGTGGGTTTATGCTACAGC	58.986	55.000	0.00	0.00	42.50	4.40
423	432	1.014352	GCCGTGGGTTTATGCTACAG	58.986	55.000	0.00	0.00	0.00	2.74
424	433	0.741574	CGCCGTGGGTTTATGCTACA	60.742	55.000	0.00	0.00	0.00	2.74
425	434	0.460635	TCGCCGTGGGTTTATGCTAC	60.461	55.000	0.00	0.00	0.00	3.58
466	475	9.524496	TTGACTATTCAACCTACTACTAACAGA	57.476	33.333	0.00	0.00	36.79	3.41
508	526	1.140375	GGTGGACCATCGGACGTAC	59.860	63.158	0.00	0.00	35.64	3.67
531	549	4.801516	GCGTTTGTATGGTGAAAAGTTGTT	59.198	37.500	0.00	0.00	0.00	2.83
744	2176	1.073098	GAGGAAACAGGGGAAGGGAA	58.927	55.000	0.00	0.00	0.00	3.97
874	2370	0.036858	GAAGGTCAGGTGAGCAGGAC	60.037	60.000	11.53	0.00	44.42	3.85
910	2408	2.667418	CTGTGAGTGCAGGGGAGG	59.333	66.667	0.00	0.00	33.11	4.30
961	2459	6.856135	ATCTCCGCGTATATCAATATCGTA	57.144	37.500	4.92	0.00	0.00	3.43
983	2489	2.094675	CCATGGCAAAGAACCGAGAAT	58.905	47.619	0.00	0.00	0.00	2.40
1278	2796	1.294138	CTTGTAGACCGGGCCGAAA	59.706	57.895	30.79	10.40	0.00	3.46
1407	2925	1.150827	CGAGCATTGCACTCTGTTCA	58.849	50.000	11.91	0.00	31.71	3.18
1424	2945	1.026182	AAATTGATCTGCTGGCGCGA	61.026	50.000	12.10	0.00	39.65	5.87
1447	3001	3.629398	GTCATCCATTCATGAACCAGACC	59.371	47.826	11.07	0.00	34.50	3.85
1456	3010	7.576287	GCAACCCATATAAGTCATCCATTCATG	60.576	40.741	0.00	0.00	0.00	3.07
1465	3019	6.006275	ACAAGAGCAACCCATATAAGTCAT	57.994	37.500	0.00	0.00	0.00	3.06
1526	3088	2.164219	CCCGATCAATTTCACCAGGTTG	59.836	50.000	0.00	0.00	0.00	3.77
1681	3256	2.420722	GGTCTCGACAACAACCAAACAA	59.579	45.455	0.00	0.00	0.00	2.83
1682	3257	2.011222	GGTCTCGACAACAACCAAACA	58.989	47.619	0.00	0.00	0.00	2.83
1690	3268	0.750249	TCTTGCTGGTCTCGACAACA	59.250	50.000	0.00	0.00	0.00	3.33
1694	3272	4.111375	TCTTTATCTTGCTGGTCTCGAC	57.889	45.455	0.00	0.00	0.00	4.20
1771	3357	0.671781	CAGGGGACAAGAACAGCTCG	60.672	60.000	0.00	0.00	0.00	5.03
2009	3637	5.104776	CCTGAAGATGGTAGGATGTTTCAGA	60.105	44.000	11.64	0.00	41.38	3.27
2168	3813	1.551883	GAAGTTACGGGAGGCTTACCA	59.448	52.381	0.00	0.00	39.06	3.25
2411	4074	1.198094	TAGCACACTGGGCCAGCTAA	61.198	55.000	33.04	10.29	35.11	3.09
2412	4075	0.982852	ATAGCACACTGGGCCAGCTA	60.983	55.000	33.04	27.22	41.46	3.32
2413	4076	2.304056	ATAGCACACTGGGCCAGCT	61.304	57.895	33.04	25.99	39.22	4.24
2518	4181	6.321717	GTGTTTCTGTGAACTTGACATTGAA	58.678	36.000	0.00	0.00	0.00	2.69
2528	4192	5.552870	ATCTGTAGGTGTTTCTGTGAACT	57.447	39.130	0.00	0.00	0.00	3.01
3461	8327	5.867903	AAGAAACACAATCCACAAATCCA	57.132	34.783	0.00	0.00	0.00	3.41
3641	8507	1.003118	CCCCACCGTGATTCTCAAAGA	59.997	52.381	0.00	0.00	0.00	2.52
3642	8508	1.003118	TCCCCACCGTGATTCTCAAAG	59.997	52.381	0.00	0.00	0.00	2.77
3643	8509	1.003118	CTCCCCACCGTGATTCTCAAA	59.997	52.381	0.00	0.00	0.00	2.69
3646	8512	0.613777	AACTCCCCACCGTGATTCTC	59.386	55.000	0.00	0.00	0.00	2.87
3647	8513	0.613777	GAACTCCCCACCGTGATTCT	59.386	55.000	0.00	0.00	0.00	2.40
3648	8514	0.392595	GGAACTCCCCACCGTGATTC	60.393	60.000	0.00	0.00	0.00	2.52
3649	8515	1.683441	GGAACTCCCCACCGTGATT	59.317	57.895	0.00	0.00	0.00	2.57
3650	8516	3.400188	GGAACTCCCCACCGTGAT	58.600	61.111	0.00	0.00	0.00	3.06
3709	8817	8.349568	GGTTTTCCTTATAAACTGGATCAGTT	57.650	34.615	7.41	7.41	45.31	3.16
3735	8843	7.931407	GGGTCAATTTGTTTAGGTTTTTGATCT	59.069	33.333	0.00	0.00	0.00	2.75
3766	8874	2.440247	GGCCCGGTTTCCCTCATG	60.440	66.667	0.00	0.00	0.00	3.07
3806	8914	8.726650	TTGATTTGTAAACAACATCTTGATCG	57.273	30.769	13.85	0.00	38.10	3.69
3893	9001	5.722263	TCATTTCATTTGCGAACAATGGAT	58.278	33.333	12.18	1.30	35.21	3.41
3903	9011	3.567530	TCAAGCACTCATTTCATTTGCG	58.432	40.909	0.00	0.00	38.26	4.85
3939	9047	6.723298	TTCTTAAAGAATCACAAAAGCCCA	57.277	33.333	0.00	0.00	0.00	5.36
4029	9137	7.012799	TCACAGTGTTAGTTTCATGTTGCATTA	59.987	33.333	0.00	0.00	0.00	1.90
4129	9244	0.618458	TGTACTTGCCCATCCCTCAC	59.382	55.000	0.00	0.00	0.00	3.51
4132	9247	1.212935	GACATGTACTTGCCCATCCCT	59.787	52.381	0.00	0.00	0.00	4.20
4177	9292	6.877611	TGTTGACTTGACCTTAATCCTTTC	57.122	37.500	0.00	0.00	0.00	2.62
4184	9299	4.973168	AGCTGATGTTGACTTGACCTTAA	58.027	39.130	0.00	0.00	0.00	1.85
4222	9337	5.116180	TCTTCTGTACAGTTTCACAGTTGG	58.884	41.667	21.99	0.00	42.28	3.77
4253	9368	6.471233	TCTATTGTCATGTAGCTAGCTTGT	57.529	37.500	24.88	6.46	0.00	3.16
4307	9423	1.305297	TCAGCTGGACGGGTGAGAT	60.305	57.895	15.13	0.00	38.55	2.75
4328	9444	4.019860	GCATTCCTATTGGGCTATCTCTCA	60.020	45.833	0.00	0.00	34.39	3.27
4329	9445	4.019860	TGCATTCCTATTGGGCTATCTCTC	60.020	45.833	0.00	0.00	34.39	3.20

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.