AutoCloner

Multiple sequence alignment - TraesCS1D01G292200

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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	TraesCS1D01G292200	chr1D	100.000	3911	0	0	1	3911	391317737	391313827	0.000000e+00	7223.0
1	TraesCS1D01G292200	chr1D	92.793	111	7	1	2473	2583	391315160	391315051	4.040000e-35	159.0
2	TraesCS1D01G292200	chr1D	92.793	111	7	1	2578	2687	391315265	391315155	4.040000e-35	159.0
3	TraesCS1D01G292200	chr1D	91.667	60	5	0	2638	2697	391315265	391315206	2.500000e-12	84.2
4	TraesCS1D01G292200	chr1B	91.409	2747	120	48	1	2697	531205741	531208421	0.000000e+00	3659.0
5	TraesCS1D01G292200	chr1B	93.854	1448	63	15	2473	3911	531208257	531209687	0.000000e+00	2158.0
6	TraesCS1D01G292200	chr1B	87.363	182	8	1	2470	2636	531208299	531208480	1.110000e-45	195.0
7	TraesCS1D01G292200	chr1B	93.694	111	6	1	2473	2583	531208362	531208471	8.690000e-37	165.0
8	TraesCS1D01G292200	chr1B	91.228	114	9	1	2575	2687	531208194	531208307	1.880000e-33	154.0
9	TraesCS1D01G292200	chr4A	90.187	1498	93	22	1161	2635	590125829	590124363	0.000000e+00	1903.0
10	TraesCS1D01G292200	chr4A	85.440	1353	123	32	2533	3839	590124507	590123183	0.000000e+00	1339.0
11	TraesCS1D01G292200	chr4A	88.485	1129	84	21	1182	2281	590256664	590257775	0.000000e+00	1323.0
12	TraesCS1D01G292200	chr4A	84.812	665	64	17	1	641	590255056	590255707	5.510000e-178	634.0
13	TraesCS1D01G292200	chr4A	91.061	358	14	6	2279	2636	590257856	590258195	5.920000e-128	468.0
14	TraesCS1D01G292200	chr1A	92.661	981	57	3	2577	3557	493825471	493826436	0.000000e+00	1399.0
15	TraesCS1D01G292200	chr1A	95.221	544	26	0	1	544	493823096	493823639	0.000000e+00	861.0
16	TraesCS1D01G292200	chr1A	82.784	970	111	27	2687	3656	493823996	493824909	0.000000e+00	815.0
17	TraesCS1D01G292200	chr1A	95.909	220	9	0	3692	3911	493918007	493918226	1.340000e-94	357.0
18	TraesCS1D01G292200	chr1A	86.034	179	19	1	1611	1789	493824912	493825084	1.860000e-43	187.0
19	TraesCS1D01G292200	chr1A	91.406	128	10	1	2456	2583	493825395	493825521	1.440000e-39	174.0
20	TraesCS1D01G292200	chr1A	93.750	112	7	0	3583	3694	493826432	493826543	6.720000e-38	169.0
21	TraesCS1D01G292200	chr1A	90.244	123	12	0	2575	2697	493825409	493825531	1.120000e-35	161.0
22	TraesCS1D01G292200	chr1A	90.090	111	10	1	2473	2583	493825472	493825581	4.070000e-30	143.0
23	TraesCS1D01G292200	chr4D	86.072	1357	114	33	2533	3844	12418322	12416996	0.000000e+00	1389.0
24	TraesCS1D01G292200	chr4D	90.650	984	48	12	1679	2636	12419142	12418177	0.000000e+00	1267.0
25	TraesCS1D01G292200	chr4D	89.735	302	22	3	4	296	12419834	12419533	1.030000e-100	377.0
26	TraesCS1D01G292200	chr4D	86.574	216	14	4	1182	1397	12419337	12419137	1.410000e-54	224.0
27	TraesCS1D01G292200	chr4D	90.361	166	8	2	3682	3839	12356347	12356512	1.100000e-50	211.0
28	TraesCS1D01G292200	chr4D	97.674	43	1	0	598	640	12419409	12419367	1.510000e-09	75.0
29	TraesCS1D01G292200	chr4D	100.000	40	0	0	486	525	12419513	12419474	1.510000e-09	75.0
30	TraesCS1D01G292200	chr3B	90.943	541	42	4	2	535	702692060	702692600	0.000000e+00	721.0
31	TraesCS1D01G292200	chr4B	80.196	1020	130	36	2840	3844	22565545	22564583	0.000000e+00	699.0
32	TraesCS1D01G292200	chr4B	85.383	561	45	17	1237	1767	22566116	22565563	7.390000e-152	547.0
33	TraesCS1D01G292200	chr3A	90.203	541	46	2	2	535	665966638	665967178	0.000000e+00	699.0
34	TraesCS1D01G292200	chr3D	90.018	541	47	4	2	535	531367288	531367828	0.000000e+00	693.0
35	TraesCS1D01G292200	chr3D	89.483	542	50	2	1	535	426440828	426440287	0.000000e+00	678.0

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	TraesCS1D01G292200	chr1D	391313827	391317737	3910	True	1906.300000	7223	94.313250	1	3911	4	chr1D.!!$R1	3910
1	TraesCS1D01G292200	chr1B	531205741	531209687	3946	False	1266.200000	3659	91.509600	1	3911	5	chr1B.!!$F1	3910
2	TraesCS1D01G292200	chr4A	590123183	590125829	2646	True	1621.000000	1903	87.813500	1161	3839	2	chr4A.!!$R1	2678
3	TraesCS1D01G292200	chr4A	590255056	590258195	3139	False	808.333333	1323	88.119333	1	2636	3	chr4A.!!$F1	2635
4	TraesCS1D01G292200	chr1A	493823096	493826543	3447	False	488.625000	1399	90.273750	1	3694	8	chr1A.!!$F2	3693
5	TraesCS1D01G292200	chr4D	12416996	12419834	2838	True	567.833333	1389	91.784167	4	3844	6	chr4D.!!$R1	3840
6	TraesCS1D01G292200	chr3B	702692060	702692600	540	False	721.000000	721	90.943000	2	535	1	chr3B.!!$F1	533
7	TraesCS1D01G292200	chr4B	22564583	22566116	1533	True	623.000000	699	82.789500	1237	3844	2	chr4B.!!$R1	2607
8	TraesCS1D01G292200	chr3A	665966638	665967178	540	False	699.000000	699	90.203000	2	535	1	chr3A.!!$F1	533
9	TraesCS1D01G292200	chr3D	531367288	531367828	540	False	693.000000	693	90.018000	2	535	1	chr3D.!!$F1	533
10	TraesCS1D01G292200	chr3D	426440287	426440828	541	True	678.000000	678	89.483000	1	535	1	chr3D.!!$R1	534

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
553	580	0.101399	GATCCGATGATCGATCCCCG	59.899	60.0	22.31	22.12	43.74	5.73	F
643	689	0.176449	GCCAAATGCCATTCCACTCC	59.824	55.0	0.00	0.00	0.00	3.85	F
772	859	0.393132	GCTTAACCAGGTCAGGCTCC	60.393	60.0	0.00	0.00	0.00	4.70	F
1042	1142	0.521735	GTGGCTTCGGGTGATTTCAC	59.478	55.0	1.99	1.99	45.72	3.18	F
1123	1227	0.739112	GCGTGCTCTCTCCTCCAAAG	60.739	60.0	0.00	0.00	0.00	2.77	F
1612	2855	0.741915	TCTTTTTGGTTCGTGTGCCC	59.258	50.0	0.00	0.00	0.00	5.36	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1859	3367	0.466124	GCCATAGTCAGTGGAGGTCC	59.534	60.000	0.00	0.00	39.12	4.46	R
1874	3382	3.560025	GCCAGGTAATGTGCTATAGCCAT	60.560	47.826	21.84	19.49	41.18	4.40	R
2550	4162	5.747342	TCTTCCACAATGTGATCATCATCA	58.253	37.500	15.91	0.00	36.62	3.07	R
2886	4561	0.094216	CATTCAGCGTGTGAGCTTCG	59.906	55.000	0.00	0.00	46.80	3.79	R
2908	4583	1.271543	CCCAAACTCCACAGATGCTCA	60.272	52.381	0.00	0.00	0.00	4.26	R
3533	5229	0.250513	ACGAATCTCTTCCAGCCACC	59.749	55.000	0.00	0.00	0.00	4.61	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
79	83	2.738521	CTGGTTCACCTCGTGCCG	60.739	66.667	0.00	0.00	36.82	5.69
484	506	4.722700	GCGGTGTGGGATGGCACT	62.723	66.667	0.00	0.00	36.03	4.40
553	580	0.101399	GATCCGATGATCGATCCCCG	59.899	60.000	22.31	22.12	43.74	5.73
554	581	1.949847	ATCCGATGATCGATCCCCGC	61.950	60.000	22.31	8.16	43.74	6.13
555	582	2.504899	CGATGATCGATCCCCGCG	60.505	66.667	22.31	15.47	43.74	6.46
556	583	2.811317	GATGATCGATCCCCGCGC	60.811	66.667	22.31	0.00	38.37	6.86
557	584	4.379243	ATGATCGATCCCCGCGCC	62.379	66.667	22.31	0.00	38.37	6.53
590	635	9.511144	CCGCTTATACCCAAGTAAAATAAAAAG	57.489	33.333	0.00	0.00	30.59	2.27
642	688	3.746900	GCCAAATGCCATTCCACTC	57.253	52.632	0.00	0.00	0.00	3.51
643	689	0.176449	GCCAAATGCCATTCCACTCC	59.824	55.000	0.00	0.00	0.00	3.85
644	690	1.559368	CCAAATGCCATTCCACTCCA	58.441	50.000	0.00	0.00	0.00	3.86
658	704	4.270153	TCCACTCCACCCCTGCCT	62.270	66.667	0.00	0.00	0.00	4.75
659	705	4.039092	CCACTCCACCCCTGCCTG	62.039	72.222	0.00	0.00	0.00	4.85
662	708	3.721706	CTCCACCCCTGCCTGACC	61.722	72.222	0.00	0.00	0.00	4.02
719	782	1.226717	CAGAGGAGACGCCGCTAAC	60.227	63.158	0.31	0.00	45.92	2.34
772	859	0.393132	GCTTAACCAGGTCAGGCTCC	60.393	60.000	0.00	0.00	0.00	4.70
807	894	0.783206	TGATTCCTGGGCAAAAGGGA	59.217	50.000	0.00	0.00	35.35	4.20
816	910	1.263356	GGCAAAAGGGAGGGTTTACC	58.737	55.000	0.00	0.00	40.67	2.85
838	932	4.101119	CCTCTACTGTACTGTAAATGGGGG	59.899	50.000	12.92	7.51	0.00	5.40
839	933	4.950361	TCTACTGTACTGTAAATGGGGGA	58.050	43.478	12.92	3.60	0.00	4.81
891	985	4.832248	TCTTCTTGATTCCGTAGCACAAT	58.168	39.130	0.00	0.00	0.00	2.71
894	988	4.769688	TCTTGATTCCGTAGCACAATCAT	58.230	39.130	0.00	0.00	30.97	2.45
904	998	1.278985	AGCACAATCATCAGGTCGGAA	59.721	47.619	0.00	0.00	0.00	4.30
1041	1141	0.953471	CGTGGCTTCGGGTGATTTCA	60.953	55.000	0.00	0.00	0.00	2.69
1042	1142	0.521735	GTGGCTTCGGGTGATTTCAC	59.478	55.000	1.99	1.99	45.72	3.18
1099	1203	4.400567	CCTCCCATCAATCCACTTCTTTTC	59.599	45.833	0.00	0.00	0.00	2.29
1118	1222	3.423162	ATGCGCGTGCTCTCTCCTC	62.423	63.158	23.16	0.00	43.34	3.71
1119	1223	4.863925	GCGCGTGCTCTCTCCTCC	62.864	72.222	15.02	0.00	38.39	4.30
1120	1224	3.443925	CGCGTGCTCTCTCCTCCA	61.444	66.667	0.00	0.00	0.00	3.86
1121	1225	2.973899	GCGTGCTCTCTCCTCCAA	59.026	61.111	0.00	0.00	0.00	3.53
1122	1226	1.293498	GCGTGCTCTCTCCTCCAAA	59.707	57.895	0.00	0.00	0.00	3.28
1123	1227	0.739112	GCGTGCTCTCTCCTCCAAAG	60.739	60.000	0.00	0.00	0.00	2.77
1125	1229	1.001406	CGTGCTCTCTCCTCCAAAGTT	59.999	52.381	0.00	0.00	0.00	2.66
1126	1230	2.548920	CGTGCTCTCTCCTCCAAAGTTT	60.549	50.000	0.00	0.00	0.00	2.66
1225	1921	5.009010	CCACTACCATCATTGTGCTATTTCC	59.991	44.000	0.00	0.00	0.00	3.13
1226	1922	5.009010	CACTACCATCATTGTGCTATTTCCC	59.991	44.000	0.00	0.00	0.00	3.97
1227	1923	4.255510	ACCATCATTGTGCTATTTCCCT	57.744	40.909	0.00	0.00	0.00	4.20
1228	1924	4.613437	ACCATCATTGTGCTATTTCCCTT	58.387	39.130	0.00	0.00	0.00	3.95
1229	1925	4.646492	ACCATCATTGTGCTATTTCCCTTC	59.354	41.667	0.00	0.00	0.00	3.46
1296	1994	7.767250	TGTCCATAATGTGTGTTCCAAATAA	57.233	32.000	0.00	0.00	0.00	1.40
1297	1995	8.359875	TGTCCATAATGTGTGTTCCAAATAAT	57.640	30.769	0.00	0.00	0.00	1.28
1315	2013	8.205297	CCAAATAATCGAGTTTTTGTTTCGTTC	58.795	33.333	21.42	0.00	35.90	3.95
1370	2095	4.855531	AGCACGAAACTTAAATTGTCACC	58.144	39.130	0.00	0.00	0.00	4.02
1371	2096	4.336993	AGCACGAAACTTAAATTGTCACCA	59.663	37.500	0.00	0.00	0.00	4.17
1372	2097	4.439776	GCACGAAACTTAAATTGTCACCAC	59.560	41.667	0.00	0.00	0.00	4.16
1477	2203	3.069872	AGCATGATCTCTGAGACCATCAC	59.930	47.826	11.68	7.40	33.22	3.06
1549	2732	3.249917	GTGAGCTAGTTCTTCAGTCTGC	58.750	50.000	8.15	0.00	0.00	4.26
1609	2852	9.030301	AGAAAATTATTCTTTTTGGTTCGTGTG	57.970	29.630	0.00	0.00	0.00	3.82
1612	2855	0.741915	TCTTTTTGGTTCGTGTGCCC	59.258	50.000	0.00	0.00	0.00	5.36
1801	3305	2.099098	ACTTGTACTGTGCTTTTGTGGC	59.901	45.455	0.00	0.00	0.00	5.01
1859	3367	2.094026	TGTCTGATCCTGGACATGTTCG	60.094	50.000	0.00	0.00	37.52	3.95
1874	3382	1.202964	TGTTCGGACCTCCACTGACTA	60.203	52.381	0.00	0.00	35.14	2.59
2078	3605	5.367945	TGTTATTGACCCCATTCCTACTC	57.632	43.478	0.00	0.00	0.00	2.59
2090	3617	5.053145	CCATTCCTACTCTTCAAGATTCCG	58.947	45.833	0.00	0.00	0.00	4.30
2398	4010	5.415077	CAGAGAACCTCTTCATGCTTTGATT	59.585	40.000	0.00	0.00	38.99	2.57
2617	4229	5.587443	TCTGATGATGATCACATTGTGGAAC	59.413	40.000	16.46	8.86	36.82	3.62
2636	4248	5.774690	TGGAACAAGGCACTAGAAAATCATT	59.225	36.000	0.00	0.00	38.49	2.57
2833	4505	9.898152	TTTTCCTTTTATCAACTTCCAAATTGT	57.102	25.926	0.00	0.00	0.00	2.71
2886	4561	4.229876	GTTGTGCAAGCTTTTCAGGATAC	58.770	43.478	0.00	0.00	0.00	2.24
2908	4583	0.319728	AGCTCACACGCTGAATGAGT	59.680	50.000	2.72	0.00	41.62	3.41
3009	4684	6.480320	CCTACATTTTATCTGAAGGAAGGACG	59.520	42.308	0.00	0.00	0.00	4.79
3085	4760	8.311395	TCAATCTGAACTTCCTATCTATGTGT	57.689	34.615	0.00	0.00	0.00	3.72
3317	5009	3.818387	ACTGTACTGTACGTGTGAATCG	58.182	45.455	12.87	0.00	0.00	3.34
3483	5176	4.452733	GGAGGGAAGCACGACGGG	62.453	72.222	0.00	0.00	0.00	5.28
3533	5229	2.979814	TGGTATGAGGTGGATTCGTG	57.020	50.000	0.00	0.00	0.00	4.35
3546	5242	0.036010	ATTCGTGGTGGCTGGAAGAG	60.036	55.000	0.00	0.00	34.07	2.85
3675	5380	0.107945	GAGGTGTAGCTCAAGCCCTG	60.108	60.000	6.23	0.00	43.38	4.45
3767	5501	7.770897	GTGAACTTGTATCTCATTTGGGATAGT	59.229	37.037	0.30	0.00	0.00	2.12
3852	5602	3.585862	GATGTCTCGAGGTAAACTGCAA	58.414	45.455	13.56	0.00	0.00	4.08
3873	5623	5.215903	CAAACACCATTATGTTACGTGCAA	58.784	37.500	0.00	0.00	42.01	4.08
3899	5649	3.313526	GTGTTCAGCTGCGATTGGATTAT	59.686	43.478	9.47	0.00	0.00	1.28

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
457	479	3.991051	CACACCGCACTCTCCCGT	61.991	66.667	0.00	0.00	0.00	5.28
537	564	2.125912	GCGGGGATCGATCATCGG	60.126	66.667	28.16	22.18	40.88	4.18
560	587	2.203098	TTGGGTATAAGCGGCGGC	60.203	61.111	9.78	8.43	40.37	6.53
561	588	0.390124	TACTTGGGTATAAGCGGCGG	59.610	55.000	9.78	0.00	0.00	6.13
562	589	2.228138	TTACTTGGGTATAAGCGGCG	57.772	50.000	0.51	0.51	0.00	6.46
563	590	6.622833	TTATTTTACTTGGGTATAAGCGGC	57.377	37.500	0.00	0.00	0.00	6.53
564	591	9.511144	CTTTTTATTTTACTTGGGTATAAGCGG	57.489	33.333	0.00	0.00	0.00	5.52
590	635	5.006358	CAGCGACAAAACTGGGTATATGTAC	59.994	44.000	0.00	0.00	0.00	2.90
591	636	5.113383	CAGCGACAAAACTGGGTATATGTA	58.887	41.667	0.00	0.00	0.00	2.29
592	637	3.938963	CAGCGACAAAACTGGGTATATGT	59.061	43.478	0.00	0.00	0.00	2.29
593	638	3.938963	ACAGCGACAAAACTGGGTATATG	59.061	43.478	0.00	0.00	38.25	1.78
594	639	4.216411	ACAGCGACAAAACTGGGTATAT	57.784	40.909	0.00	0.00	38.25	0.86
635	681	1.846124	GGGGTGGAGTGGAGTGGAA	60.846	63.158	0.00	0.00	0.00	3.53
636	682	2.203938	GGGGTGGAGTGGAGTGGA	60.204	66.667	0.00	0.00	0.00	4.02
637	683	2.203998	AGGGGTGGAGTGGAGTGG	60.204	66.667	0.00	0.00	0.00	4.00
638	684	3.072476	CAGGGGTGGAGTGGAGTG	58.928	66.667	0.00	0.00	0.00	3.51
639	685	2.930562	GCAGGGGTGGAGTGGAGT	60.931	66.667	0.00	0.00	0.00	3.85
640	686	3.721706	GGCAGGGGTGGAGTGGAG	61.722	72.222	0.00	0.00	0.00	3.86
641	687	4.270153	AGGCAGGGGTGGAGTGGA	62.270	66.667	0.00	0.00	0.00	4.02
642	688	4.039092	CAGGCAGGGGTGGAGTGG	62.039	72.222	0.00	0.00	0.00	4.00
643	689	2.930019	TCAGGCAGGGGTGGAGTG	60.930	66.667	0.00	0.00	0.00	3.51
644	690	2.930562	GTCAGGCAGGGGTGGAGT	60.931	66.667	0.00	0.00	0.00	3.85
668	714	2.433318	AAACAGAGCTCGCTCGGC	60.433	61.111	16.98	0.00	46.90	5.54
713	776	1.752501	CGATCTGTTGGCCGTTAGCG	61.753	60.000	0.00	0.00	45.17	4.26
772	859	2.887151	ATCAAGAAGGAGGTGGTTGG	57.113	50.000	0.00	0.00	0.00	3.77
816	910	4.960469	TCCCCCATTTACAGTACAGTAGAG	59.040	45.833	0.00	0.00	0.00	2.43
817	911	4.950361	TCCCCCATTTACAGTACAGTAGA	58.050	43.478	0.00	0.00	0.00	2.59
821	915	6.663523	AGAAAAATCCCCCATTTACAGTACAG	59.336	38.462	0.00	0.00	33.16	2.74
838	932	4.864806	GCCATTTCCGGAAGAAGAAAAATC	59.135	41.667	17.97	0.00	35.40	2.17
839	933	4.528206	AGCCATTTCCGGAAGAAGAAAAAT	59.472	37.500	17.97	2.20	35.40	1.82
891	985	2.577059	GCCGTTCCGACCTGATGA	59.423	61.111	0.00	0.00	0.00	2.92
919	1013	1.010793	TCCTCTCCTCTCCTCTCCTCT	59.989	57.143	0.00	0.00	0.00	3.69
920	1014	1.421646	CTCCTCTCCTCTCCTCTCCTC	59.578	61.905	0.00	0.00	0.00	3.71
921	1015	1.522900	CTCCTCTCCTCTCCTCTCCT	58.477	60.000	0.00	0.00	0.00	3.69
922	1016	0.478507	CCTCCTCTCCTCTCCTCTCC	59.521	65.000	0.00	0.00	0.00	3.71
923	1017	1.421646	CTCCTCCTCTCCTCTCCTCTC	59.578	61.905	0.00	0.00	0.00	3.20
949	1043	3.402681	ACATGGTGGAGCTCCCGG	61.403	66.667	29.95	16.07	37.93	5.73
959	1053	0.968901	AATGCTGCCTCCACATGGTG	60.969	55.000	0.00	0.00	36.34	4.17
1041	1141	2.609610	ACCATACTGCGGGTGGGT	60.610	61.111	19.66	10.50	37.33	4.51
1042	1142	2.189521	GACCATACTGCGGGTGGG	59.810	66.667	19.66	9.92	37.57	4.61
1043	1143	1.153369	CTGACCATACTGCGGGTGG	60.153	63.158	15.46	15.46	37.57	4.61
1044	1144	0.036388	AACTGACCATACTGCGGGTG	60.036	55.000	0.00	0.00	37.57	4.61
1099	1203	3.260483	GGAGAGAGCACGCGCATG	61.260	66.667	5.73	2.46	42.27	4.06
1172	1709	8.452534	CAGAAGTGTAGTAAAGTAGGAGTACTG	58.547	40.741	0.00	0.00	39.60	2.74
1296	1994	4.525411	ACGAACGAAACAAAAACTCGAT	57.475	36.364	0.14	0.00	36.45	3.59
1297	1995	3.995412	ACGAACGAAACAAAAACTCGA	57.005	38.095	0.14	0.00	36.45	4.04
1315	2013	2.507339	ACAAAAGGACATGGCAAACG	57.493	45.000	0.00	0.00	0.00	3.60
1371	2096	2.501723	AGTCACAAGGTTCACTGTCTGT	59.498	45.455	0.00	0.00	0.00	3.41
1372	2097	3.126831	GAGTCACAAGGTTCACTGTCTG	58.873	50.000	0.00	0.00	0.00	3.51
1389	2114	5.715434	ACAAGGAAGACAGACTTAGAGTC	57.285	43.478	0.00	0.00	45.38	3.36
1477	2203	3.827008	TGCCATTAGGAGCTTCTAGTG	57.173	47.619	15.96	15.96	36.89	2.74
1549	2732	2.107950	TGCGACAAACTTATCCCAGG	57.892	50.000	0.00	0.00	0.00	4.45
1609	2852	0.992695	AAAGGTAGAGTTCCCAGGGC	59.007	55.000	0.00	0.00	0.00	5.19
1738	2981	4.750098	ACTAATTAATCTCACCATTCGGCG	59.250	41.667	0.00	0.00	34.57	6.46
1767	3012	7.067251	AGCACAGTACAAGTAGTATTAGACTCC	59.933	40.741	0.00	0.00	39.81	3.85
1768	3013	7.987649	AGCACAGTACAAGTAGTATTAGACTC	58.012	38.462	0.00	0.00	39.81	3.36
1801	3305	5.346551	CACATCAAGCACATTGTTACAATGG	59.653	40.000	32.69	24.21	40.05	3.16
1859	3367	0.466124	GCCATAGTCAGTGGAGGTCC	59.534	60.000	0.00	0.00	39.12	4.46
1874	3382	3.560025	GCCAGGTAATGTGCTATAGCCAT	60.560	47.826	21.84	19.49	41.18	4.40
2078	3605	5.779806	ATTACAACGACGGAATCTTGAAG	57.220	39.130	0.00	0.00	0.00	3.02
2398	4010	7.402054	TCTTGAGTGCTAGAAATATTTCCCAA	58.598	34.615	21.86	13.63	37.92	4.12
2550	4162	5.747342	TCTTCCACAATGTGATCATCATCA	58.253	37.500	15.91	0.00	36.62	3.07
2617	4229	7.856145	AGTAGAATGATTTTCTAGTGCCTTG	57.144	36.000	2.69	0.00	34.39	3.61
2636	4248	6.153510	AGCATCAGAACAACTCACATAGTAGA	59.846	38.462	0.00	0.00	37.50	2.59
2886	4561	0.094216	CATTCAGCGTGTGAGCTTCG	59.906	55.000	0.00	0.00	46.80	3.79
2908	4583	1.271543	CCCAAACTCCACAGATGCTCA	60.272	52.381	0.00	0.00	0.00	4.26
3009	4684	4.017808	TCTTCTCCACACTAGTTAGAGGC	58.982	47.826	11.70	0.00	0.00	4.70
3085	4760	2.039216	TCCGGCTTTTGGTCATTAGTGA	59.961	45.455	0.00	0.00	0.00	3.41
3317	5009	6.688578	TGTCTACTACTTCAGTGGAATGAAC	58.311	40.000	0.00	0.00	45.32	3.18
3533	5229	0.250513	ACGAATCTCTTCCAGCCACC	59.749	55.000	0.00	0.00	0.00	4.61
3755	5489	7.995488	AGATTAGACTCCAAACTATCCCAAATG	59.005	37.037	0.00	0.00	0.00	2.32
3767	5501	5.273208	ACTAGAGGCAGATTAGACTCCAAA	58.727	41.667	0.00	0.00	45.09	3.28
3852	5602	4.614993	GCTTGCACGTAACATAATGGTGTT	60.615	41.667	0.00	2.10	44.09	3.32
3888	5638	2.596452	ACGAGCGCTATAATCCAATCG	58.404	47.619	11.50	8.53	35.21	3.34

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.