AutoCloner

Multiple sequence alignment - TraesCS5A01G413500

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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	TraesCS5A01G413500	chr5A	100.000	4754	0	0	1	4754	601678916	601683669	0.000000e+00	8780.0
1	TraesCS5A01G413500	chr5A	80.162	247	30	8	4479	4725	601628680	601628907	2.940000e-37	167.0
2	TraesCS5A01G413500	chr5A	100.000	28	0	0	355	382	408929327	408929354	9.000000e-03	52.8
3	TraesCS5A01G413500	chr5B	93.021	4585	229	31	211	4744	591520725	591525269	0.000000e+00	6610.0
4	TraesCS5A01G413500	chr5B	88.914	884	67	13	149	1010	591514718	591515592	0.000000e+00	1061.0
5	TraesCS5A01G413500	chr5B	85.616	146	21	0	4514	4659	591492513	591492658	2.290000e-33	154.0
6	TraesCS5A01G413500	chr5B	96.875	32	1	0	350	381	581145737	581145768	2.000000e-03	54.7
7	TraesCS5A01G413500	chr5D	96.843	2819	83	2	1226	4042	482142244	482145058	0.000000e+00	4708.0
8	TraesCS5A01G413500	chr5D	90.578	467	26	9	210	664	482141298	482141758	1.890000e-168	603.0
9	TraesCS5A01G413500	chr5D	83.117	693	66	19	4067	4732	482145051	482145719	6.860000e-163	584.0
10	TraesCS5A01G413500	chr5D	94.044	319	19	0	4436	4754	482166736	482167054	7.150000e-133	484.0
11	TraesCS5A01G413500	chr5D	94.488	254	9	2	97	348	482116379	482116629	2.080000e-103	387.0
12	TraesCS5A01G413500	chr5D	97.561	205	5	0	1	205	482140840	482141044	7.570000e-93	351.0
13	TraesCS5A01G413500	chr5D	94.258	209	11	1	3887	4095	482151034	482151241	7.680000e-83	318.0
14	TraesCS5A01G413500	chr7A	86.667	2640	322	25	1278	3896	20492157	20494787	0.000000e+00	2898.0
15	TraesCS5A01G413500	chr7A	84.542	2937	409	33	887	3789	20659540	20662465	0.000000e+00	2867.0
16	TraesCS5A01G413500	chr7A	83.836	2920	420	34	874	3762	20650690	20653588	0.000000e+00	2730.0
17	TraesCS5A01G413500	chr7A	83.683	2862	438	25	968	3812	20966266	20969115	0.000000e+00	2671.0
18	TraesCS5A01G413500	chr2A	84.918	2798	397	24	977	3761	733087777	733090562	0.000000e+00	2806.0
19	TraesCS5A01G413500	chr2D	84.626	2810	413	17	980	3778	598814078	598816879	0.000000e+00	2778.0
20	TraesCS5A01G413500	chr2D	83.621	116	10	5	414	522	592625117	592625004	3.030000e-17	100.0
21	TraesCS5A01G413500	chr2B	84.536	2813	408	23	980	3778	727686036	727688835	0.000000e+00	2760.0
22	TraesCS5A01G413500	chr2B	84.615	104	12	1	423	522	465132337	465132440	3.030000e-17	100.0
23	TraesCS5A01G413500	chr2B	83.186	113	13	6	408	516	174396327	174396217	1.090000e-16	99.0
24	TraesCS5A01G413500	chr7D	83.977	2796	423	22	977	3761	20460420	20463201	0.000000e+00	2658.0
25	TraesCS5A01G413500	chr7D	85.088	114	12	4	408	517	193770553	193770441	1.400000e-20	111.0
26	TraesCS5A01G413500	chr7D	96.875	32	0	1	351	382	37659001	37659031	9.000000e-03	52.8
27	TraesCS5A01G413500	chr7B	87.805	123	11	1	408	526	327272941	327273063	1.780000e-29	141.0
28	TraesCS5A01G413500	chr4A	85.714	112	11	3	415	522	381220583	381220473	3.890000e-21	113.0
29	TraesCS5A01G413500	chr3B	83.036	112	16	3	414	522	753962454	753962565	1.090000e-16	99.0
30	TraesCS5A01G413500	chr3B	87.037	54	6	1	354	407	399508164	399508216	5.140000e-05	60.2
31	TraesCS5A01G413500	chr3B	100.000	28	0	0	354	381	564243958	564243931	9.000000e-03	52.8
32	TraesCS5A01G413500	chr1D	100.000	28	0	0	347	374	367413286	367413259	9.000000e-03	52.8

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	TraesCS5A01G413500	chr5A	601678916	601683669	4753	False	8780.0	8780	100.00000	1	4754	1	chr5A.!!$F3	4753
1	TraesCS5A01G413500	chr5B	591520725	591525269	4544	False	6610.0	6610	93.02100	211	4744	1	chr5B.!!$F4	4533
2	TraesCS5A01G413500	chr5B	591514718	591515592	874	False	1061.0	1061	88.91400	149	1010	1	chr5B.!!$F3	861
3	TraesCS5A01G413500	chr5D	482140840	482145719	4879	False	1561.5	4708	92.02475	1	4732	4	chr5D.!!$F4	4731
4	TraesCS5A01G413500	chr7A	20492157	20494787	2630	False	2898.0	2898	86.66700	1278	3896	1	chr7A.!!$F1	2618
5	TraesCS5A01G413500	chr7A	20659540	20662465	2925	False	2867.0	2867	84.54200	887	3789	1	chr7A.!!$F3	2902
6	TraesCS5A01G413500	chr7A	20650690	20653588	2898	False	2730.0	2730	83.83600	874	3762	1	chr7A.!!$F2	2888
7	TraesCS5A01G413500	chr7A	20966266	20969115	2849	False	2671.0	2671	83.68300	968	3812	1	chr7A.!!$F4	2844
8	TraesCS5A01G413500	chr2A	733087777	733090562	2785	False	2806.0	2806	84.91800	977	3761	1	chr2A.!!$F1	2784
9	TraesCS5A01G413500	chr2D	598814078	598816879	2801	False	2778.0	2778	84.62600	980	3778	1	chr2D.!!$F1	2798
10	TraesCS5A01G413500	chr2B	727686036	727688835	2799	False	2760.0	2760	84.53600	980	3778	1	chr2B.!!$F2	2798
11	TraesCS5A01G413500	chr7D	20460420	20463201	2781	False	2658.0	2658	83.97700	977	3761	1	chr7D.!!$F1	2784

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	Hairpin	End Stability	Orientation
543	816	1.519408	AGATACGGCACCACACAAAC	58.481	50.000	0.00	0.00	2.93	F
1206	1508	1.001815	CGGAACCGCAACAATCAAGTT	60.002	47.619	0.00	0.00	2.66	F
1815	2126	2.118313	TGGACATCACATGCCTTGAG	57.882	50.000	0.00	0.00	3.02	F
2594	2905	2.421424	CACAAGAGGCTAAATGTGAGGC	59.579	50.000	17.22	44.52	4.70	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Hairpin	End Stability	Orientation
2274	2585	3.071479	GTGCGTTGGAAGGTAGATGAAA	58.929	45.455	0.00	0.00	2.69	R
2687	3001	2.423926	ACTATCGCCTGCTGTAATCG	57.576	50.000	0.00	0.00	3.34	R
3375	3689	2.898705	GTCAGCTGTGACCAAGATAGG	58.101	52.381	14.67	46.58	2.57	R
4034	4367	0.185901	AGGCAACATTGTCACACCCT	59.814	50.000	0.00	34.61	4.34	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
264	521	1.543944	CCCCAATTGCCACCCTTCAC	61.544	60.000	0.00	0.00	0.00	3.18
304	561	4.086457	TGGAATCAGTCTGCAGTGTAGTA	58.914	43.478	14.67	0.00	0.00	1.82
305	562	4.158579	TGGAATCAGTCTGCAGTGTAGTAG	59.841	45.833	14.67	0.26	0.00	2.57
306	563	4.158764	GGAATCAGTCTGCAGTGTAGTAGT	59.841	45.833	14.67	0.00	0.00	2.73
381	646	1.681264	CTCCGTCCCAAAAAGCTTGTT	59.319	47.619	0.00	0.00	0.00	2.83
392	657	7.279758	TCCCAAAAAGCTTGTTTTAGATTTGTG	59.720	33.333	0.00	0.00	38.09	3.33
543	816	1.519408	AGATACGGCACCACACAAAC	58.481	50.000	0.00	0.00	0.00	2.93
563	836	7.226720	CACAAACTTTTAGCCTTCTAGAGTCAA	59.773	37.037	0.00	0.00	0.00	3.18
565	838	5.471257	ACTTTTAGCCTTCTAGAGTCAACG	58.529	41.667	0.00	0.00	0.00	4.10
695	968	2.171003	GAACTGCCACCTTAGCCAATT	58.829	47.619	0.00	0.00	0.00	2.32
696	969	1.839424	ACTGCCACCTTAGCCAATTC	58.161	50.000	0.00	0.00	0.00	2.17
709	982	6.760770	CCTTAGCCAATTCTCTGAAAGTAGAG	59.239	42.308	0.00	0.00	44.42	2.43
753	1026	3.006217	GTCTTGCTTGCCTCAAATTTCCT	59.994	43.478	0.00	0.00	0.00	3.36
754	1027	3.006110	TCTTGCTTGCCTCAAATTTCCTG	59.994	43.478	0.00	0.00	0.00	3.86
755	1028	2.596346	TGCTTGCCTCAAATTTCCTGA	58.404	42.857	0.00	0.00	0.00	3.86
757	1030	3.194116	TGCTTGCCTCAAATTTCCTGATC	59.806	43.478	0.00	0.00	0.00	2.92
759	1032	4.439837	GCTTGCCTCAAATTTCCTGATCTC	60.440	45.833	0.00	0.00	0.00	2.75
760	1033	4.581309	TGCCTCAAATTTCCTGATCTCT	57.419	40.909	0.00	0.00	0.00	3.10
762	1035	3.066481	GCCTCAAATTTCCTGATCTCTGC	59.934	47.826	0.00	0.00	0.00	4.26
763	1036	4.525024	CCTCAAATTTCCTGATCTCTGCT	58.475	43.478	0.00	0.00	0.00	4.24
785	1063	4.687901	TTCTTGAACCTGAGATGTCACA	57.312	40.909	0.00	0.00	0.00	3.58
790	1068	4.832248	TGAACCTGAGATGTCACATTACC	58.168	43.478	0.00	0.00	0.00	2.85
791	1069	4.532126	TGAACCTGAGATGTCACATTACCT	59.468	41.667	0.00	0.00	0.00	3.08
868	1146	3.726291	AACACTAAATTTGCCGCAGTT	57.274	38.095	0.00	0.00	0.00	3.16
1164	1466	2.291465	GGAGCTTCGCATAATGCATGAA	59.709	45.455	0.00	0.00	45.36	2.57
1206	1508	1.001815	CGGAACCGCAACAATCAAGTT	60.002	47.619	0.00	0.00	0.00	2.66
1540	1851	3.588842	TGATGAAGAAGATCTTGTGGGGT	59.411	43.478	14.00	0.00	36.73	4.95
1815	2126	2.118313	TGGACATCACATGCCTTGAG	57.882	50.000	0.00	0.00	0.00	3.02
1909	2220	7.578310	ACATTTGATGATTTGTCTAGGATGG	57.422	36.000	0.00	0.00	0.00	3.51
2274	2585	6.860080	CATAAGGAATGTTTTGCATCTGAGT	58.140	36.000	0.00	0.00	36.67	3.41
2594	2905	2.421424	CACAAGAGGCTAAATGTGAGGC	59.579	50.000	17.22	0.00	44.52	4.70
2687	3001	3.289076	GTTTACAGCAACTTCGAAGTGC	58.711	45.455	30.33	29.77	39.66	4.40
3375	3689	7.255277	GGAGGGCAGAATTTGTATGAATTAGTC	60.255	40.741	0.00	0.00	29.75	2.59
3531	3845	2.752903	GGTTCTCTCTCTGACAGACCTC	59.247	54.545	0.00	0.00	0.00	3.85
3692	4006	0.892755	ATCACCGGCGACTTCTTGTA	59.107	50.000	9.30	0.00	0.00	2.41
3814	4133	3.074412	CCACAAACCAGCCAACTAGTAG	58.926	50.000	0.00	0.00	0.00	2.57
3873	4206	4.624024	ACGATGTTGTTTATGTAGGTGTCG	59.376	41.667	0.00	0.00	0.00	4.35
3874	4207	4.624024	CGATGTTGTTTATGTAGGTGTCGT	59.376	41.667	0.00	0.00	0.00	4.34
3903	4236	5.053140	GAAGGAAGATGCTTCCACTTTTC	57.947	43.478	23.76	15.85	38.66	2.29
3921	4254	5.417894	ACTTTTCGGTTTCCTCTGTTTCTTT	59.582	36.000	0.00	0.00	0.00	2.52
3942	4275	7.224297	TCTTTAAGATGGACTACTGCACTTTT	58.776	34.615	0.00	0.00	0.00	2.27
3968	4301	7.321153	TGCTGTTAGTTCCACTTCTACTTATC	58.679	38.462	0.00	0.00	0.00	1.75
3990	4323	0.950116	GCTTCACTTCTGCTGCAACT	59.050	50.000	3.02	0.00	0.00	3.16
4034	4367	2.535012	TGATTGTGTGCTCGGTTGTA	57.465	45.000	0.00	0.00	0.00	2.41
4054	4387	1.423541	AGGGTGTGACAATGTTGCCTA	59.576	47.619	0.00	0.00	0.00	3.93
4055	4388	1.539827	GGGTGTGACAATGTTGCCTAC	59.460	52.381	0.00	0.00	0.00	3.18
4058	4391	1.879380	TGTGACAATGTTGCCTACTGC	59.121	47.619	0.00	0.00	41.77	4.40
4060	4393	2.160417	GTGACAATGTTGCCTACTGCTC	59.840	50.000	0.00	0.00	42.00	4.26
4066	4399	2.436417	TGTTGCCTACTGCTCAATTCC	58.564	47.619	0.00	0.00	42.00	3.01
4068	4401	0.901827	TGCCTACTGCTCAATTCCGA	59.098	50.000	0.00	0.00	42.00	4.55
4240	4573	3.314541	AAGGCGACACTTACTGTAAGG	57.685	47.619	26.35	18.62	40.08	2.69
4247	4580	4.487019	GACACTTACTGTAAGGCTGAGAC	58.513	47.826	26.35	12.50	40.08	3.36
4248	4581	3.258622	ACACTTACTGTAAGGCTGAGACC	59.741	47.826	26.35	0.00	40.08	3.85
4253	4586	0.888619	TGTAAGGCTGAGACCGAGTG	59.111	55.000	0.00	0.00	33.69	3.51
4256	4589	1.629043	AAGGCTGAGACCGAGTGTTA	58.371	50.000	0.00	0.00	33.69	2.41
4289	4622	4.391830	TCAGACTAATTGCATTTCCACGAC	59.608	41.667	0.00	0.00	0.00	4.34
4293	4626	0.521291	ATTGCATTTCCACGACACCG	59.479	50.000	0.00	0.00	42.50	4.94
4318	4651	7.265673	GTTCCTGAAGTATGTACTGCTATTCA	58.734	38.462	0.00	0.00	36.50	2.57
4354	4687	4.851558	CAGCTGCGGATGTTAAACTTAAAC	59.148	41.667	0.00	0.00	0.00	2.01
4360	4693	6.693545	TGCGGATGTTAAACTTAAACACTTTG	59.306	34.615	0.00	0.00	0.00	2.77
4361	4694	6.913673	GCGGATGTTAAACTTAAACACTTTGA	59.086	34.615	0.00	0.00	0.00	2.69
4362	4695	7.593644	GCGGATGTTAAACTTAAACACTTTGAT	59.406	33.333	0.00	0.00	0.00	2.57
4367	4700	9.424319	TGTTAAACTTAAACACTTTGATTTGCA	57.576	25.926	0.00	0.00	0.00	4.08
4404	4737	3.388676	TCGGGTATTCATTTCCGGTATGT	59.611	43.478	15.57	4.30	42.44	2.29
4419	4752	4.547532	CGGTATGTTATGGCTACTGTCTC	58.452	47.826	0.00	0.00	0.00	3.36
4524	4884	6.889301	AATAATACACTGATGCAATGAGGG	57.111	37.500	0.00	0.00	36.83	4.30
4525	4885	2.715749	TACACTGATGCAATGAGGGG	57.284	50.000	0.00	0.00	34.14	4.79
4547	4909	3.386237	ACTGCCGGCTCTCACTCC	61.386	66.667	29.70	0.00	0.00	3.85
4548	4910	3.385384	CTGCCGGCTCTCACTCCA	61.385	66.667	29.70	1.91	0.00	3.86
4550	4912	4.828925	GCCGGCTCTCACTCCAGC	62.829	72.222	22.15	0.00	34.65	4.85
4558	4920	3.618780	CTCACTCCAGCCTGCCACC	62.619	68.421	0.00	0.00	0.00	4.61
4598	4960	1.144716	GATGATGCACCGAGCTGGA	59.855	57.895	8.91	0.00	45.94	3.86
4599	4961	0.462581	GATGATGCACCGAGCTGGAA	60.463	55.000	8.91	0.00	45.94	3.53
4604	4966	4.785453	CACCGAGCTGGAAGGGGC	62.785	72.222	8.91	0.00	42.00	5.80
4622	4984	1.202568	GGCCAGTGTCGATCATCATCA	60.203	52.381	0.00	0.00	0.00	3.07
4698	5060	8.755977	AGATAATGATTTGTGCCTTTTCTTGAT	58.244	29.630	0.00	0.00	0.00	2.57
4699	5061	8.712285	ATAATGATTTGTGCCTTTTCTTGATG	57.288	30.769	0.00	0.00	0.00	3.07
4704	5066	3.420893	TGTGCCTTTTCTTGATGTAGGG	58.579	45.455	0.00	0.00	0.00	3.53
4705	5067	2.164422	GTGCCTTTTCTTGATGTAGGGC	59.836	50.000	0.00	0.00	38.87	5.19
4708	5070	3.430453	CCTTTTCTTGATGTAGGGCCAA	58.570	45.455	6.18	0.00	0.00	4.52
4710	5072	4.142093	CCTTTTCTTGATGTAGGGCCAATG	60.142	45.833	6.18	0.00	0.00	2.82
4721	5083	0.178990	GGGCCAATGGGTTAGCTAGG	60.179	60.000	4.39	0.00	36.17	3.02
4726	5088	2.158755	CCAATGGGTTAGCTAGGACCTG	60.159	54.545	13.18	5.31	36.18	4.00
4744	5106	1.202099	TGCCACGGAAATGGGTAGGA	61.202	55.000	0.00	0.00	40.43	2.94
4745	5107	0.034863	GCCACGGAAATGGGTAGGAA	60.035	55.000	0.00	0.00	40.43	3.36
4746	5108	1.746470	CCACGGAAATGGGTAGGAAC	58.254	55.000	0.00	0.00	35.95	3.62
4747	5109	1.280998	CCACGGAAATGGGTAGGAACT	59.719	52.381	0.00	0.00	38.22	3.01
4748	5110	2.629051	CACGGAAATGGGTAGGAACTC	58.371	52.381	0.00	0.00	41.75	3.01
4749	5111	2.027561	CACGGAAATGGGTAGGAACTCA	60.028	50.000	0.00	0.00	41.40	3.41
4751	5113	4.035112	ACGGAAATGGGTAGGAACTCATA	58.965	43.478	0.00	0.00	46.50	2.15
4752	5114	4.658901	ACGGAAATGGGTAGGAACTCATAT	59.341	41.667	0.00	0.00	46.50	1.78
4753	5115	4.997395	CGGAAATGGGTAGGAACTCATATG	59.003	45.833	0.00	0.00	46.50	1.78

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
11	12	1.473434	CGTAGCCTTCCAGTTCCATCC	60.473	57.143	0.00	0.00	0.00	3.51
85	86	1.303282	GGTGTGGGAGGGATGGAAC	59.697	63.158	0.00	0.00	0.00	3.62
226	479	3.445987	GGGGAAATCAATTGGGTGGTAA	58.554	45.455	5.42	0.00	0.00	2.85
264	521	8.272545	TGATTCCAGATATTTGTCAGAAACAG	57.727	34.615	0.00	0.00	39.58	3.16
304	561	5.451908	CACGAACAAGCATTATCAACAACT	58.548	37.500	0.00	0.00	0.00	3.16
305	562	4.616802	CCACGAACAAGCATTATCAACAAC	59.383	41.667	0.00	0.00	0.00	3.32
306	563	4.277174	ACCACGAACAAGCATTATCAACAA	59.723	37.500	0.00	0.00	0.00	2.83
381	646	9.309516	GTACATCCGTATCTTCACAAATCTAAA	57.690	33.333	0.00	0.00	0.00	1.85
412	677	7.220030	AGACAGATCTAAGACAAGCTTTTTGA	58.780	34.615	0.00	0.00	38.05	2.69
543	816	5.471257	ACGTTGACTCTAGAAGGCTAAAAG	58.529	41.667	0.00	0.00	32.31	2.27
565	838	6.643770	TCAGGATTTACTCACGTAACAAGAAC	59.356	38.462	0.00	0.00	35.44	3.01
581	854	4.819105	ACGATGTCCACTTCAGGATTTA	57.181	40.909	0.00	0.00	40.42	1.40
695	968	5.728637	TTGACATGCTCTACTTTCAGAGA	57.271	39.130	4.35	0.00	44.11	3.10
696	969	6.981762	ATTTGACATGCTCTACTTTCAGAG	57.018	37.500	0.00	0.00	44.18	3.35
753	1026	4.040829	TCAGGTTCAAGAAAGCAGAGATCA	59.959	41.667	0.00	0.00	37.85	2.92
754	1027	4.573900	TCAGGTTCAAGAAAGCAGAGATC	58.426	43.478	0.00	0.00	37.85	2.75
755	1028	4.285517	TCTCAGGTTCAAGAAAGCAGAGAT	59.714	41.667	7.66	0.00	46.62	2.75
757	1030	4.000331	TCTCAGGTTCAAGAAAGCAGAG	58.000	45.455	3.80	3.80	45.34	3.35
759	1032	4.070716	ACATCTCAGGTTCAAGAAAGCAG	58.929	43.478	0.00	0.00	37.85	4.24
760	1033	4.067896	GACATCTCAGGTTCAAGAAAGCA	58.932	43.478	0.00	0.00	37.85	3.91
762	1035	5.059161	TGTGACATCTCAGGTTCAAGAAAG	58.941	41.667	0.00	0.00	0.00	2.62
763	1036	5.034852	TGTGACATCTCAGGTTCAAGAAA	57.965	39.130	0.00	0.00	0.00	2.52
790	1068	3.268330	ACTGAACATACATGCTCTGCAG	58.732	45.455	7.63	7.63	43.65	4.41
791	1069	3.339253	ACTGAACATACATGCTCTGCA	57.661	42.857	0.00	0.00	44.86	4.41
1164	1466	4.701765	GAATATCCATGTGACAGAGCACT	58.298	43.478	0.00	0.00	39.49	4.40
1206	1508	0.251916	CCTCCAACCAGCCGTCATAA	59.748	55.000	0.00	0.00	0.00	1.90
1458	1769	3.686241	TGACAATGTAATCACAGCTGCTC	59.314	43.478	15.27	0.00	38.30	4.26
1540	1851	5.659440	AGTTTTTCTCTGTTTTCAGCCAA	57.341	34.783	0.00	0.00	46.59	4.52
1815	2126	4.061596	CCAGAAAACTCTTCAGTGTCTCC	58.938	47.826	0.00	0.00	31.06	3.71
2274	2585	3.071479	GTGCGTTGGAAGGTAGATGAAA	58.929	45.455	0.00	0.00	0.00	2.69
2443	2754	5.633830	AGCATGTTTCTATCAACCAACTG	57.366	39.130	0.00	0.00	0.00	3.16
2594	2905	2.542618	CGTCCATCCATCTCAAGAGACG	60.543	54.545	1.20	0.00	40.75	4.18
2687	3001	2.423926	ACTATCGCCTGCTGTAATCG	57.576	50.000	0.00	0.00	0.00	3.34
3375	3689	2.898705	GTCAGCTGTGACCAAGATAGG	58.101	52.381	14.67	0.00	46.58	2.57
3531	3845	8.195436	TGTATCTCTAGACGTTTCAAATTAGGG	58.805	37.037	0.00	0.00	0.00	3.53
3873	4206	1.521681	CATCTTCCTTCCGGCCGAC	60.522	63.158	30.73	0.00	0.00	4.79
3874	4207	2.900273	CATCTTCCTTCCGGCCGA	59.100	61.111	30.73	10.38	0.00	5.54
3903	4236	6.348540	CCATCTTAAAGAAACAGAGGAAACCG	60.349	42.308	0.00	0.00	0.00	4.44
3921	4254	6.801539	CAAAAAGTGCAGTAGTCCATCTTA	57.198	37.500	0.00	0.00	0.00	2.10
3968	4301	1.206072	GCAGCAGAAGTGAAGCACG	59.794	57.895	0.00	0.00	39.64	5.34
4019	4352	1.369692	CCCTACAACCGAGCACACA	59.630	57.895	0.00	0.00	0.00	3.72
4034	4367	0.185901	AGGCAACATTGTCACACCCT	59.814	50.000	0.00	0.00	34.61	4.34
4054	4387	1.344438	TCACAGTCGGAATTGAGCAGT	59.656	47.619	0.00	0.00	0.00	4.40
4055	4388	2.084610	TCACAGTCGGAATTGAGCAG	57.915	50.000	0.00	0.00	0.00	4.24
4058	4391	6.368791	TCTTAACAATCACAGTCGGAATTGAG	59.631	38.462	6.40	0.00	0.00	3.02
4060	4393	6.147821	AGTCTTAACAATCACAGTCGGAATTG	59.852	38.462	0.00	0.00	0.00	2.32
4066	4399	3.181540	CGCAGTCTTAACAATCACAGTCG	60.182	47.826	0.00	0.00	0.00	4.18
4068	4401	3.990092	TCGCAGTCTTAACAATCACAGT	58.010	40.909	0.00	0.00	0.00	3.55
4240	4573	3.994392	TGAAAATAACACTCGGTCTCAGC	59.006	43.478	0.00	0.00	0.00	4.26
4247	4580	8.425577	AGTCTGAATATGAAAATAACACTCGG	57.574	34.615	0.00	0.00	0.00	4.63
4289	4622	4.174009	CAGTACATACTTCAGGAACGGTG	58.826	47.826	0.00	0.00	33.46	4.94
4293	4626	7.265673	TGAATAGCAGTACATACTTCAGGAAC	58.734	38.462	0.00	0.00	33.46	3.62
4295	4628	7.069950	ACATGAATAGCAGTACATACTTCAGGA	59.930	37.037	0.00	0.00	33.46	3.86
4371	4704	8.739972	GGAAATGAATACCCGAGCATTATTAAT	58.260	33.333	0.00	0.00	31.30	1.40
4404	4737	7.180408	AGGAAAAACTAGAGACAGTAGCCATAA	59.820	37.037	0.00	0.00	0.00	1.90
4419	4752	7.027778	AGCAAGTTACAACAGGAAAAACTAG	57.972	36.000	0.00	0.00	30.51	2.57
4480	4813	1.159285	TTGCTCAAGAAGACCATGCG	58.841	50.000	0.00	0.00	0.00	4.73
4524	4884	3.941657	GAGAGCCGGCAGTGTGTCC	62.942	68.421	31.54	6.53	0.00	4.02
4525	4885	2.433318	GAGAGCCGGCAGTGTGTC	60.433	66.667	31.54	16.55	0.00	3.67
4547	4909	1.672854	CCATCAATGGTGGCAGGCTG	61.673	60.000	10.94	10.94	43.05	4.85
4548	4910	1.380785	CCATCAATGGTGGCAGGCT	60.381	57.895	0.00	0.00	43.05	4.58
4574	4936	1.755179	CTCGGTGCATCATCCCTTTT	58.245	50.000	0.00	0.00	0.00	2.27
4575	4937	0.749454	GCTCGGTGCATCATCCCTTT	60.749	55.000	0.00	0.00	42.31	3.11
4576	4938	1.153086	GCTCGGTGCATCATCCCTT	60.153	57.895	0.00	0.00	42.31	3.95
4598	4960	1.274703	ATGATCGACACTGGCCCCTT	61.275	55.000	0.00	0.00	0.00	3.95
4599	4961	1.690219	GATGATCGACACTGGCCCCT	61.690	60.000	0.00	0.00	0.00	4.79
4604	4966	4.573607	ACAAATGATGATGATCGACACTGG	59.426	41.667	0.00	0.00	0.00	4.00
4606	4968	5.987953	CCTACAAATGATGATGATCGACACT	59.012	40.000	0.00	0.00	0.00	3.55
4610	4972	4.959723	TGCCTACAAATGATGATGATCGA	58.040	39.130	0.00	0.00	0.00	3.59
4639	5001	6.206634	GGAATACGAGATGCATAATTCCCAAA	59.793	38.462	17.90	0.00	37.48	3.28
4648	5010	9.901172	TCTAGTATAAGGAATACGAGATGCATA	57.099	33.333	0.00	0.00	43.66	3.14
4649	5011	8.809468	TCTAGTATAAGGAATACGAGATGCAT	57.191	34.615	0.00	0.00	43.66	3.96
4682	5044	3.826157	CCCTACATCAAGAAAAGGCACAA	59.174	43.478	0.00	0.00	0.00	3.33
4698	5060	0.257616	GCTAACCCATTGGCCCTACA	59.742	55.000	0.00	0.00	36.34	2.74
4699	5061	0.551396	AGCTAACCCATTGGCCCTAC	59.449	55.000	0.00	0.00	43.06	3.18
4704	5066	1.477014	GGTCCTAGCTAACCCATTGGC	60.477	57.143	3.51	0.00	42.41	4.52
4705	5067	2.127708	AGGTCCTAGCTAACCCATTGG	58.872	52.381	10.45	0.00	36.11	3.16
4708	5070	1.132500	GCAGGTCCTAGCTAACCCAT	58.868	55.000	10.45	0.00	36.11	4.00
4710	5072	0.981277	TGGCAGGTCCTAGCTAACCC	60.981	60.000	10.45	3.38	36.11	4.11
4721	5083	2.046285	CCCATTTCCGTGGCAGGTC	61.046	63.158	6.43	0.00	37.96	3.85
4726	5088	0.034863	TTCCTACCCATTTCCGTGGC	60.035	55.000	0.00	0.00	37.96	5.01

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.