AutoCloner

Multiple sequence alignment - TraesCS2D01G213300

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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	TraesCS2D01G213300	chr2D	100.000	2321	0	0	1	2321	174238833	174241153	0.000000e+00	4287.0
1	TraesCS2D01G213300	chr2D	98.291	117	1	1	901	1017	174239630	174239745	1.090000e-48	204.0
2	TraesCS2D01G213300	chr2D	98.291	117	1	1	798	913	174239733	174239849	1.090000e-48	204.0
3	TraesCS2D01G213300	chr2A	96.138	1424	45	4	901	2321	173783678	173785094	0.000000e+00	2316.0
4	TraesCS2D01G213300	chr2A	98.400	125	2	0	789	913	173783669	173783793	1.080000e-53	220.0
5	TraesCS2D01G213300	chr2B	96.646	1133	36	2	938	2069	222093433	222094564	0.000000e+00	1881.0
6	TraesCS2D01G213300	chr2B	96.470	1133	38	2	938	2069	222088810	222089941	0.000000e+00	1869.0
7	TraesCS2D01G213300	chr2B	90.180	611	50	9	1	607	644558506	644557902	0.000000e+00	787.0
8	TraesCS2D01G213300	chr2B	94.553	257	12	1	2067	2321	222094680	222094936	1.670000e-106	396.0
9	TraesCS2D01G213300	chr2B	94.323	229	9	2	2067	2293	222090057	222090283	4.750000e-92	348.0
10	TraesCS2D01G213300	chr2B	82.286	350	39	14	411	745	639529161	639529502	4.880000e-72	281.0
11	TraesCS2D01G213300	chr2B	94.624	93	4	1	753	844	222088687	222088779	2.400000e-30	143.0
12	TraesCS2D01G213300	chr2B	100.000	77	0	0	834	910	222088810	222088886	2.400000e-30	143.0
13	TraesCS2D01G213300	chr2B	100.000	77	0	0	834	910	222093433	222093509	2.400000e-30	143.0
14	TraesCS2D01G213300	chr2B	87.129	101	2	4	655	745	73977797	73977698	1.130000e-18	104.0
15	TraesCS2D01G213300	chr2B	100.000	38	0	0	2224	2261	677805571	677805608	1.150000e-08	71.3
16	TraesCS2D01G213300	chr2B	91.667	48	3	1	901	948	222088733	222088779	5.350000e-07	65.8
17	TraesCS2D01G213300	chr2B	97.059	34	1	0	1823	1856	793461939	793461906	8.960000e-05	58.4
18	TraesCS2D01G213300	chr6A	91.540	721	40	18	1	708	549403068	549402356	0.000000e+00	974.0
19	TraesCS2D01G213300	chr5A	91.690	710	46	11	1	703	561682110	561682813	0.000000e+00	972.0
20	TraesCS2D01G213300	chr7A	91.408	710	48	11	1	703	655441406	655442109	0.000000e+00	961.0
21	TraesCS2D01G213300	chr7A	90.821	719	45	9	1	703	177003585	177004298	0.000000e+00	942.0
22	TraesCS2D01G213300	chr7A	92.343	653	37	11	1	646	671217937	671218583	0.000000e+00	917.0
23	TraesCS2D01G213300	chr3A	91.201	716	50	10	1	708	641813156	641812446	0.000000e+00	961.0
24	TraesCS2D01G213300	chr3A	90.704	710	53	11	1	703	65796010	65796713	0.000000e+00	933.0
25	TraesCS2D01G213300	chr5B	86.907	611	66	11	1	605	486363647	486364249	0.000000e+00	673.0
26	TraesCS2D01G213300	chr5B	88.095	84	1	4	671	745	533440954	533441037	8.830000e-15	91.6
27	TraesCS2D01G213300	chr5B	97.059	34	1	0	1823	1856	24283028	24282995	8.960000e-05	58.4
28	TraesCS2D01G213300	chr7D	87.644	348	24	14	410	743	536311112	536310770	1.010000e-103	387.0
29	TraesCS2D01G213300	chr7D	83.442	308	31	15	451	744	1245588	1245889	3.800000e-68	268.0
30	TraesCS2D01G213300	chr1D	91.525	236	15	4	465	697	462049620	462049853	1.030000e-83	320.0
31	TraesCS2D01G213300	chr1D	97.674	43	1	0	2219	2261	394676813	394676771	8.890000e-10	75.0
32	TraesCS2D01G213300	chr4D	81.562	320	37	13	439	744	417397754	417397443	6.410000e-61	244.0
33	TraesCS2D01G213300	chr1B	86.547	223	16	10	532	744	14934733	14934515	1.390000e-57	233.0
34	TraesCS2D01G213300	chr3B	86.139	101	3	3	655	745	751097081	751097180	5.280000e-17	99.0
35	TraesCS2D01G213300	chr7B	83.838	99	7	2	655	744	611506021	611505923	4.110000e-13	86.1
36	TraesCS2D01G213300	chr7B	86.301	73	7	2	2189	2260	23560033	23560103	2.470000e-10	76.8
37	TraesCS2D01G213300	chr7B	97.561	41	1	0	2221	2261	371734280	371734240	1.150000e-08	71.3
38	TraesCS2D01G213300	chr4B	97.561	41	1	0	2221	2261	656162662	656162622	1.150000e-08	71.3
39	TraesCS2D01G213300	chr3D	95.349	43	1	1	2220	2261	136724274	136724232	1.490000e-07	67.6
40	TraesCS2D01G213300	chrUn	97.059	34	1	0	1823	1856	50555800	50555767	8.960000e-05	58.4
41	TraesCS2D01G213300	chrUn	97.059	34	1	0	1823	1856	401384211	401384178	8.960000e-05	58.4
42	TraesCS2D01G213300	chrUn	97.059	34	1	0	1823	1856	436530158	436530125	8.960000e-05	58.4
43	TraesCS2D01G213300	chr4A	97.059	34	1	0	1823	1856	704303532	704303499	8.960000e-05	58.4

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	TraesCS2D01G213300	chr2D	174238833	174241153	2320	False	1565.0	4287	98.860667	1	2321	3	chr2D.!!$F1	2320
1	TraesCS2D01G213300	chr2A	173783669	173785094	1425	False	1268.0	2316	97.269000	789	2321	2	chr2A.!!$F1	1532
2	TraesCS2D01G213300	chr2B	644557902	644558506	604	True	787.0	787	90.180000	1	607	1	chr2B.!!$R2	606
3	TraesCS2D01G213300	chr2B	222088687	222094936	6249	False	623.6	1881	96.035375	753	2321	8	chr2B.!!$F3	1568
4	TraesCS2D01G213300	chr6A	549402356	549403068	712	True	974.0	974	91.540000	1	708	1	chr6A.!!$R1	707
5	TraesCS2D01G213300	chr5A	561682110	561682813	703	False	972.0	972	91.690000	1	703	1	chr5A.!!$F1	702
6	TraesCS2D01G213300	chr7A	655441406	655442109	703	False	961.0	961	91.408000	1	703	1	chr7A.!!$F2	702
7	TraesCS2D01G213300	chr7A	177003585	177004298	713	False	942.0	942	90.821000	1	703	1	chr7A.!!$F1	702
8	TraesCS2D01G213300	chr7A	671217937	671218583	646	False	917.0	917	92.343000	1	646	1	chr7A.!!$F3	645
9	TraesCS2D01G213300	chr3A	641812446	641813156	710	True	961.0	961	91.201000	1	708	1	chr3A.!!$R1	707
10	TraesCS2D01G213300	chr3A	65796010	65796713	703	False	933.0	933	90.704000	1	703	1	chr3A.!!$F1	702
11	TraesCS2D01G213300	chr5B	486363647	486364249	602	False	673.0	673	86.907000	1	605	1	chr5B.!!$F1	604

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
931	1503	0.033504	GTCGTTTCTGACCAGGCAGA	59.966	55.0	0.0	0.0	42.81	4.26	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2148	6850	1.795286	CTCGGTGCTCTCTTTTCACAC	59.205	52.381	0.0	0.0	32.69	3.82	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
144	145	2.285743	GGGCCAAGAGGAGGGAGT	60.286	66.667	4.39	0.00	36.89	3.85
153	154	1.356398	AGAGGAGGGAGTCGAAGAAGT	59.644	52.381	0.00	0.00	39.69	3.01
333	346	2.771639	CGACGGGGATGAGAAGCGA	61.772	63.158	0.00	0.00	0.00	4.93
407	425	4.166888	GAGGCAGAGATGGCGGCA	62.167	66.667	16.34	16.34	39.53	5.69
523	543	3.136626	GGAGCCACTGTGATTTATACCCT	59.863	47.826	9.86	0.00	0.00	4.34
526	547	4.018415	AGCCACTGTGATTTATACCCTTGT	60.018	41.667	9.86	0.00	0.00	3.16
528	549	5.253330	CCACTGTGATTTATACCCTTGTGT	58.747	41.667	9.86	0.00	0.00	3.72
540	561	2.951642	ACCCTTGTGTGTGAAATGACAG	59.048	45.455	0.00	0.00	0.00	3.51
590	611	3.103911	CGGTGGCACGAACGAGAC	61.104	66.667	12.17	0.00	35.47	3.36
610	631	3.454375	ACGGTAACTATTCATTCCAGCG	58.546	45.455	0.00	0.00	0.00	5.18
620	641	5.722021	ATTCATTCCAGCGGTAACTTTTT	57.278	34.783	0.00	0.00	0.00	1.94
641	663	0.107508	TTATCCGACGGACGAGGTCT	60.108	55.000	21.02	3.66	45.77	3.85
647	669	1.935327	GACGGACGAGGTCTTCCAGG	61.935	65.000	0.00	0.00	34.26	4.45
648	670	1.677966	CGGACGAGGTCTTCCAGGA	60.678	63.158	3.63	0.00	34.26	3.86
651	673	2.272918	GACGAGGTCTTCCAGGAGCG	62.273	65.000	0.00	0.00	38.56	5.03
652	674	2.046864	CGAGGTCTTCCAGGAGCGA	61.047	63.158	0.00	0.00	38.56	4.93
653	675	1.388065	CGAGGTCTTCCAGGAGCGAT	61.388	60.000	0.00	0.00	38.56	4.58
658	680	1.964223	GTCTTCCAGGAGCGATATCCA	59.036	52.381	0.00	0.00	42.26	3.41
663	685	0.389391	CAGGAGCGATATCCAACGGT	59.611	55.000	0.00	0.00	42.26	4.83
665	687	3.196613	GAGCGATATCCAACGGTCC	57.803	57.895	0.00	0.00	46.47	4.46
666	688	0.387929	GAGCGATATCCAACGGTCCA	59.612	55.000	0.00	0.00	46.47	4.02
667	689	0.389391	AGCGATATCCAACGGTCCAG	59.611	55.000	0.00	0.00	35.37	3.86
669	691	1.202486	GCGATATCCAACGGTCCAGAA	60.202	52.381	0.00	0.00	0.00	3.02
670	692	2.470821	CGATATCCAACGGTCCAGAAC	58.529	52.381	0.00	0.00	0.00	3.01
680	702	0.955428	GGTCCAGAACGCATCAAGCA	60.955	55.000	0.00	0.00	46.13	3.91
690	712	0.248215	GCATCAAGCAAACCGATCCG	60.248	55.000	0.00	0.00	44.79	4.18
703	725	3.183776	GATCCGACGGCCGAGAGTC	62.184	68.421	35.90	18.40	41.76	3.36
705	727	4.180946	CCGACGGCCGAGAGTCTG	62.181	72.222	35.90	11.61	41.76	3.51
706	728	3.125573	CGACGGCCGAGAGTCTGA	61.126	66.667	35.90	0.00	41.76	3.27
708	730	2.752238	ACGGCCGAGAGTCTGAGG	60.752	66.667	35.90	1.66	0.00	3.86
709	731	2.438614	CGGCCGAGAGTCTGAGGA	60.439	66.667	24.07	0.00	0.00	3.71
710	732	2.477176	CGGCCGAGAGTCTGAGGAG	61.477	68.421	24.07	4.69	0.00	3.69
711	733	2.124693	GGCCGAGAGTCTGAGGAGG	61.125	68.421	13.85	3.79	0.00	4.30
712	734	2.781158	GCCGAGAGTCTGAGGAGGC	61.781	68.421	13.85	9.21	36.08	4.70
713	735	1.077068	CCGAGAGTCTGAGGAGGCT	60.077	63.158	0.00	0.00	36.62	4.58
714	736	0.682855	CCGAGAGTCTGAGGAGGCTT	60.683	60.000	0.00	0.00	32.84	4.35
715	737	0.455410	CGAGAGTCTGAGGAGGCTTG	59.545	60.000	0.00	0.00	32.84	4.01
716	738	1.555967	GAGAGTCTGAGGAGGCTTGT	58.444	55.000	0.00	0.00	32.84	3.16
717	739	2.729194	GAGAGTCTGAGGAGGCTTGTA	58.271	52.381	0.00	0.00	32.84	2.41
718	740	2.687935	GAGAGTCTGAGGAGGCTTGTAG	59.312	54.545	0.00	0.00	32.84	2.74
719	741	1.754226	GAGTCTGAGGAGGCTTGTAGG	59.246	57.143	0.00	0.00	32.84	3.18
720	742	1.359474	AGTCTGAGGAGGCTTGTAGGA	59.641	52.381	0.00	0.00	25.13	2.94
721	743	1.754226	GTCTGAGGAGGCTTGTAGGAG	59.246	57.143	0.00	0.00	0.00	3.69
722	744	1.118838	CTGAGGAGGCTTGTAGGAGG	58.881	60.000	0.00	0.00	0.00	4.30
723	745	0.413832	TGAGGAGGCTTGTAGGAGGT	59.586	55.000	0.00	0.00	0.00	3.85
724	746	1.203313	TGAGGAGGCTTGTAGGAGGTT	60.203	52.381	0.00	0.00	0.00	3.50
725	747	1.909986	GAGGAGGCTTGTAGGAGGTTT	59.090	52.381	0.00	0.00	0.00	3.27
726	748	1.909986	AGGAGGCTTGTAGGAGGTTTC	59.090	52.381	0.00	0.00	0.00	2.78
727	749	1.628846	GGAGGCTTGTAGGAGGTTTCA	59.371	52.381	0.00	0.00	0.00	2.69
728	750	2.239907	GGAGGCTTGTAGGAGGTTTCAT	59.760	50.000	0.00	0.00	0.00	2.57
729	751	3.536570	GAGGCTTGTAGGAGGTTTCATC	58.463	50.000	0.00	0.00	0.00	2.92
730	752	3.185455	AGGCTTGTAGGAGGTTTCATCT	58.815	45.455	0.00	0.00	0.00	2.90
731	753	3.198853	AGGCTTGTAGGAGGTTTCATCTC	59.801	47.826	0.00	0.00	0.00	2.75
732	754	3.198853	GGCTTGTAGGAGGTTTCATCTCT	59.801	47.826	0.00	0.00	0.00	3.10
733	755	4.323868	GGCTTGTAGGAGGTTTCATCTCTT	60.324	45.833	0.00	0.00	0.00	2.85
734	756	5.104900	GGCTTGTAGGAGGTTTCATCTCTTA	60.105	44.000	0.00	0.00	0.00	2.10
735	757	6.408662	GGCTTGTAGGAGGTTTCATCTCTTAT	60.409	42.308	0.00	0.00	0.00	1.73
736	758	7.051000	GCTTGTAGGAGGTTTCATCTCTTATT	58.949	38.462	0.00	0.00	0.00	1.40
737	759	7.554476	GCTTGTAGGAGGTTTCATCTCTTATTT	59.446	37.037	0.00	0.00	0.00	1.40
738	760	9.103861	CTTGTAGGAGGTTTCATCTCTTATTTC	57.896	37.037	0.00	0.00	0.00	2.17
739	761	8.380742	TGTAGGAGGTTTCATCTCTTATTTCT	57.619	34.615	0.00	0.00	0.00	2.52
740	762	8.260818	TGTAGGAGGTTTCATCTCTTATTTCTG	58.739	37.037	0.00	0.00	0.00	3.02
741	763	6.657875	AGGAGGTTTCATCTCTTATTTCTGG	58.342	40.000	0.00	0.00	0.00	3.86
742	764	6.445139	AGGAGGTTTCATCTCTTATTTCTGGA	59.555	38.462	0.00	0.00	0.00	3.86
743	765	7.128573	AGGAGGTTTCATCTCTTATTTCTGGAT	59.871	37.037	0.00	0.00	0.00	3.41
744	766	7.228308	GGAGGTTTCATCTCTTATTTCTGGATG	59.772	40.741	0.00	0.00	36.21	3.51
745	767	7.865820	AGGTTTCATCTCTTATTTCTGGATGA	58.134	34.615	0.00	0.00	40.29	2.92
746	768	7.992033	AGGTTTCATCTCTTATTTCTGGATGAG	59.008	37.037	0.00	0.00	42.05	2.90
747	769	7.255070	GGTTTCATCTCTTATTTCTGGATGAGC	60.255	40.741	0.00	0.00	42.05	4.26
748	770	5.862845	TCATCTCTTATTTCTGGATGAGCC	58.137	41.667	0.00	0.00	38.14	4.70
749	771	5.605908	TCATCTCTTATTTCTGGATGAGCCT	59.394	40.000	0.00	0.00	38.14	4.58
750	772	5.543507	TCTCTTATTTCTGGATGAGCCTC	57.456	43.478	0.00	0.00	37.63	4.70
751	773	5.215069	TCTCTTATTTCTGGATGAGCCTCT	58.785	41.667	0.00	0.00	37.63	3.69
923	1495	3.774702	GCGGCGGTCGTTTCTGAC	61.775	66.667	9.78	0.00	41.72	3.51
930	1502	2.533318	GTCGTTTCTGACCAGGCAG	58.467	57.895	0.00	0.00	37.24	4.85
931	1503	0.033504	GTCGTTTCTGACCAGGCAGA	59.966	55.000	0.00	0.00	42.81	4.26
932	1504	0.033504	TCGTTTCTGACCAGGCAGAC	59.966	55.000	1.72	0.00	44.08	3.51
934	1506	0.108585	GTTTCTGACCAGGCAGACCA	59.891	55.000	1.72	0.00	44.08	4.02
935	1507	0.108585	TTTCTGACCAGGCAGACCAC	59.891	55.000	1.72	0.00	44.08	4.16
936	1508	1.768684	TTCTGACCAGGCAGACCACC	61.769	60.000	1.72	0.00	44.08	4.61
1200	5783	2.110835	TGCGTGGTGAGCATGTGT	59.889	55.556	5.69	0.00	40.01	3.72
1299	5882	2.194212	GCGCATCGACCTCTCCCTA	61.194	63.158	0.30	0.00	0.00	3.53
1336	5919	1.199097	CATGACCTACGCAACCCAAAC	59.801	52.381	0.00	0.00	0.00	2.93
1403	5986	9.897744	GATTTTCTGTAAATTCACTGATGTTGA	57.102	29.630	0.00	0.00	36.59	3.18
1603	6186	6.539649	TTATCTCCTTGTCACTTTGAAACG	57.460	37.500	0.00	0.00	0.00	3.60
1618	6201	9.055248	CACTTTGAAACGATGAATATTGTCTTC	57.945	33.333	0.00	0.00	30.40	2.87
1659	6242	5.469760	TCTCTCATTTTTCTGATTCACGCAA	59.530	36.000	0.00	0.00	0.00	4.85
1696	6279	6.369890	AGTGTTGCTGATTAGTGATTACAGTG	59.630	38.462	0.00	0.00	0.00	3.66
1769	6352	1.349688	TCGGGCTTCCACATAACTGTT	59.650	47.619	0.00	0.00	31.62	3.16
1789	6372	9.623000	AACTGTTTTACTATGAAACCTTGTACT	57.377	29.630	0.00	0.00	36.43	2.73
2125	6827	4.024302	GTCCCTAAAAGAAAGAACACACGG	60.024	45.833	0.00	0.00	0.00	4.94
2130	6832	6.636850	CCTAAAAGAAAGAACACACGGAATTG	59.363	38.462	0.00	0.00	0.00	2.32
2148	6850	7.651704	ACGGAATTGTTTATGGTTCTTTTCAAG	59.348	33.333	0.00	0.00	0.00	3.02
2165	6867	3.206150	TCAAGTGTGAAAAGAGAGCACC	58.794	45.455	0.00	0.00	0.00	5.01
2189	6893	3.844211	AGGGACATAAGTTTACTCCAGCA	59.156	43.478	0.00	0.00	0.00	4.41
2208	6912	2.441750	GCATTGATAACTACCCCCTCCA	59.558	50.000	0.00	0.00	0.00	3.86
2236	6940	9.979578	CCCATAATATAAATAGCTTGCAAAACA	57.020	29.630	0.00	0.00	0.00	2.83

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
58	59	1.133761	TCACCCTGTAGAGAGGATCGG	60.134	57.143	0.00	0.00	42.67	4.18
153	154	1.669604	CTCCCTCTTCTCATCGACGA	58.330	55.000	0.00	0.00	0.00	4.20
267	280	4.271016	GGCGGCCCTCCCTTATGG	62.271	72.222	8.12	0.00	0.00	2.74
333	346	2.124487	CGCTCGTCCTCCTCCTCT	60.124	66.667	0.00	0.00	0.00	3.69
508	528	5.937540	TCACACACAAGGGTATAAATCACAG	59.062	40.000	0.00	0.00	0.00	3.66
523	543	5.042593	GCATTTCTGTCATTTCACACACAA	58.957	37.500	0.00	0.00	0.00	3.33
526	547	3.005684	GGGCATTTCTGTCATTTCACACA	59.994	43.478	0.00	0.00	0.00	3.72
528	549	3.499338	AGGGCATTTCTGTCATTTCACA	58.501	40.909	0.00	0.00	0.00	3.58
563	584	2.125633	TGCCACCGCGCGTAATTA	60.126	55.556	29.95	9.20	38.08	1.40
590	611	2.800544	CCGCTGGAATGAATAGTTACCG	59.199	50.000	0.00	0.00	0.00	4.02
620	641	1.133025	GACCTCGTCCGTCGGATAAAA	59.867	52.381	18.75	2.60	40.32	1.52
641	663	1.068588	CGTTGGATATCGCTCCTGGAA	59.931	52.381	0.00	0.00	36.20	3.53
647	669	0.387929	TGGACCGTTGGATATCGCTC	59.612	55.000	0.00	0.00	0.00	5.03
648	670	0.389391	CTGGACCGTTGGATATCGCT	59.611	55.000	0.00	0.00	0.00	4.93
651	673	2.470821	CGTTCTGGACCGTTGGATATC	58.529	52.381	0.00	0.00	0.00	1.63
652	674	1.472728	GCGTTCTGGACCGTTGGATAT	60.473	52.381	0.00	0.00	0.00	1.63
653	675	0.108520	GCGTTCTGGACCGTTGGATA	60.109	55.000	0.00	0.00	0.00	2.59
658	680	0.250124	TTGATGCGTTCTGGACCGTT	60.250	50.000	0.00	0.00	0.00	4.44
663	685	1.266718	GTTTGCTTGATGCGTTCTGGA	59.733	47.619	0.00	0.00	46.63	3.86
665	687	1.689959	GGTTTGCTTGATGCGTTCTG	58.310	50.000	0.00	0.00	46.63	3.02
666	688	0.238289	CGGTTTGCTTGATGCGTTCT	59.762	50.000	0.00	0.00	46.63	3.01
667	689	0.237235	TCGGTTTGCTTGATGCGTTC	59.763	50.000	0.00	0.00	46.63	3.95
669	691	0.447801	GATCGGTTTGCTTGATGCGT	59.552	50.000	0.00	0.00	46.63	5.24
670	692	0.248215	GGATCGGTTTGCTTGATGCG	60.248	55.000	0.00	0.00	46.63	4.73
671	693	0.248215	CGGATCGGTTTGCTTGATGC	60.248	55.000	0.00	0.00	43.25	3.91
690	712	2.766400	CCTCAGACTCTCGGCCGTC	61.766	68.421	27.15	15.64	0.00	4.79
703	725	1.118838	CCTCCTACAAGCCTCCTCAG	58.881	60.000	0.00	0.00	0.00	3.35
705	727	1.574263	AACCTCCTACAAGCCTCCTC	58.426	55.000	0.00	0.00	0.00	3.71
706	728	1.909986	GAAACCTCCTACAAGCCTCCT	59.090	52.381	0.00	0.00	0.00	3.69
708	730	3.198853	AGATGAAACCTCCTACAAGCCTC	59.801	47.826	0.00	0.00	0.00	4.70
709	731	3.185455	AGATGAAACCTCCTACAAGCCT	58.815	45.455	0.00	0.00	0.00	4.58
710	732	3.198853	AGAGATGAAACCTCCTACAAGCC	59.801	47.826	0.00	0.00	0.00	4.35
711	733	4.479786	AGAGATGAAACCTCCTACAAGC	57.520	45.455	0.00	0.00	0.00	4.01
712	734	9.103861	GAAATAAGAGATGAAACCTCCTACAAG	57.896	37.037	0.00	0.00	0.00	3.16
713	735	8.826765	AGAAATAAGAGATGAAACCTCCTACAA	58.173	33.333	0.00	0.00	0.00	2.41
714	736	8.260818	CAGAAATAAGAGATGAAACCTCCTACA	58.739	37.037	0.00	0.00	0.00	2.74
715	737	7.713073	CCAGAAATAAGAGATGAAACCTCCTAC	59.287	40.741	0.00	0.00	0.00	3.18
716	738	7.623677	TCCAGAAATAAGAGATGAAACCTCCTA	59.376	37.037	0.00	0.00	0.00	2.94
717	739	6.445139	TCCAGAAATAAGAGATGAAACCTCCT	59.555	38.462	0.00	0.00	0.00	3.69
718	740	6.653989	TCCAGAAATAAGAGATGAAACCTCC	58.346	40.000	0.00	0.00	0.00	4.30
719	741	7.989741	TCATCCAGAAATAAGAGATGAAACCTC	59.010	37.037	0.00	0.00	40.14	3.85
720	742	7.865820	TCATCCAGAAATAAGAGATGAAACCT	58.134	34.615	0.00	0.00	40.14	3.50
721	743	7.255070	GCTCATCCAGAAATAAGAGATGAAACC	60.255	40.741	0.00	0.00	41.90	3.27
722	744	7.255070	GGCTCATCCAGAAATAAGAGATGAAAC	60.255	40.741	0.00	0.00	41.90	2.78
723	745	6.769822	GGCTCATCCAGAAATAAGAGATGAAA	59.230	38.462	0.00	0.00	41.90	2.69
724	746	6.100859	AGGCTCATCCAGAAATAAGAGATGAA	59.899	38.462	0.00	0.00	41.90	2.57
725	747	5.605908	AGGCTCATCCAGAAATAAGAGATGA	59.394	40.000	0.00	0.00	40.65	2.92
726	748	5.867330	AGGCTCATCCAGAAATAAGAGATG	58.133	41.667	0.00	0.00	37.29	2.90
727	749	5.845614	AGAGGCTCATCCAGAAATAAGAGAT	59.154	40.000	18.26	0.00	37.29	2.75
728	750	5.070180	CAGAGGCTCATCCAGAAATAAGAGA	59.930	44.000	18.26	0.00	37.29	3.10
729	751	5.299148	CAGAGGCTCATCCAGAAATAAGAG	58.701	45.833	18.26	0.00	37.29	2.85
730	752	4.102210	CCAGAGGCTCATCCAGAAATAAGA	59.898	45.833	18.26	0.00	37.29	2.10
731	753	4.387598	CCAGAGGCTCATCCAGAAATAAG	58.612	47.826	18.26	0.00	37.29	1.73
732	754	3.137176	CCCAGAGGCTCATCCAGAAATAA	59.863	47.826	18.26	0.00	37.29	1.40
733	755	2.707791	CCCAGAGGCTCATCCAGAAATA	59.292	50.000	18.26	0.00	37.29	1.40
734	756	1.493871	CCCAGAGGCTCATCCAGAAAT	59.506	52.381	18.26	0.00	37.29	2.17
735	757	0.914644	CCCAGAGGCTCATCCAGAAA	59.085	55.000	18.26	0.00	37.29	2.52
736	758	2.612760	CCCAGAGGCTCATCCAGAA	58.387	57.895	18.26	0.00	37.29	3.02
737	759	4.388465	CCCAGAGGCTCATCCAGA	57.612	61.111	18.26	0.00	37.29	3.86
747	769	2.108566	CATGAGCTCGCCCAGAGG	59.891	66.667	9.64	0.00	46.91	3.69
749	771	3.473647	CCCATGAGCTCGCCCAGA	61.474	66.667	9.64	0.00	0.00	3.86
755	777	4.899239	GGTCGGCCCATGAGCTCG	62.899	72.222	9.64	1.37	0.00	5.03
913	1485	0.033504	GTCTGCCTGGTCAGAAACGA	59.966	55.000	18.19	0.00	43.89	3.85
923	1495	0.754957	TTTGTTGGTGGTCTGCCTGG	60.755	55.000	0.00	0.00	35.27	4.45
926	1498	0.603065	GGATTTGTTGGTGGTCTGCC	59.397	55.000	0.00	0.00	0.00	4.85
928	1500	3.221771	TCTTGGATTTGTTGGTGGTCTG	58.778	45.455	0.00	0.00	0.00	3.51
930	1502	2.029918	GCTCTTGGATTTGTTGGTGGTC	60.030	50.000	0.00	0.00	0.00	4.02
931	1503	1.963515	GCTCTTGGATTTGTTGGTGGT	59.036	47.619	0.00	0.00	0.00	4.16
932	1504	1.068333	CGCTCTTGGATTTGTTGGTGG	60.068	52.381	0.00	0.00	0.00	4.61
934	1506	1.202879	TCCGCTCTTGGATTTGTTGGT	60.203	47.619	0.00	0.00	31.53	3.67
935	1507	1.470098	CTCCGCTCTTGGATTTGTTGG	59.530	52.381	0.00	0.00	37.41	3.77
936	1508	1.470098	CCTCCGCTCTTGGATTTGTTG	59.530	52.381	0.00	0.00	37.41	3.33
1179	5762	1.668793	CATGCTCACCACGCACTCA	60.669	57.895	0.00	0.00	40.65	3.41
1336	5919	0.764890	ATGTACCGGATCACATGGGG	59.235	55.000	9.46	0.00	34.15	4.96
1403	5986	1.002134	CCGAACCAGGCCACATCTT	60.002	57.895	5.01	0.00	0.00	2.40
1603	6186	6.041296	AGGGCAAATGGAAGACAATATTCATC	59.959	38.462	0.00	0.00	0.00	2.92
1618	6201	3.629087	AGAGAGATGAAAGGGCAAATGG	58.371	45.455	0.00	0.00	0.00	3.16
1659	6242	5.661056	TCAGCAACACTAGCTATAACTGT	57.339	39.130	0.00	0.00	41.14	3.55
1696	6279	4.742438	TGCTTCGACCTTTAAATCACAC	57.258	40.909	0.00	0.00	0.00	3.82
1769	6352	9.616156	TTTCACAGTACAAGGTTTCATAGTAAA	57.384	29.630	0.00	0.00	0.00	2.01
1789	6372	9.495572	AAACTTTTACTTGGACAAAATTTCACA	57.504	25.926	0.00	0.00	0.00	3.58
2148	6850	1.795286	CTCGGTGCTCTCTTTTCACAC	59.205	52.381	0.00	0.00	32.69	3.82
2165	6867	4.683832	CTGGAGTAAACTTATGTCCCTCG	58.316	47.826	0.00	0.00	0.00	4.63
2189	6893	3.916989	GGATGGAGGGGGTAGTTATCAAT	59.083	47.826	0.00	0.00	0.00	2.57
2236	6940	6.156429	GTCCCTCCGTCCCATAATATAAGATT	59.844	42.308	0.00	0.00	0.00	2.40

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.