AutoCloner

Multiple sequence alignment - TraesCS1B01G059700

Loading Multiple Alignment...

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	TraesCS1B01G059700	chr1B	100.000	2771	0	0	1	2771	42324627	42327397	0.000000e+00	5118.0
1	TraesCS1B01G059700	chr1B	81.848	617	95	13	1137	1740	42325679	42326291	1.150000e-138	503.0
2	TraesCS1B01G059700	chr1B	81.848	617	95	13	1053	1665	42325763	42326366	1.150000e-138	503.0
3	TraesCS1B01G059700	chr1B	79.926	543	88	16	1216	1740	42325677	42326216	2.010000e-101	379.0
4	TraesCS1B01G059700	chr1B	79.926	543	88	16	1051	1590	42325842	42326366	2.010000e-101	379.0
5	TraesCS1B01G059700	chr1B	74.098	471	89	28	1051	1515	42325923	42326366	2.210000e-36	163.0
6	TraesCS1B01G059700	chr1D	94.240	816	43	3	1	812	26675823	26676638	0.000000e+00	1243.0
7	TraesCS1B01G059700	chr1D	93.995	816	45	4	1	812	26689908	26690723	0.000000e+00	1232.0
8	TraesCS1B01G059700	chr1D	93.487	522	27	4	1502	2022	26677814	26678329	0.000000e+00	769.0
9	TraesCS1B01G059700	chr1D	93.256	519	28	4	1505	2022	26692185	26692697	0.000000e+00	758.0
10	TraesCS1B01G059700	chr1D	82.865	712	86	24	864	1561	26690854	26691543	8.490000e-170	606.0
11	TraesCS1B01G059700	chr1D	82.159	667	89	20	864	1519	26676769	26677416	1.880000e-151	545.0
12	TraesCS1B01G059700	chr1D	88.182	440	49	3	1047	1486	26691107	26691543	3.160000e-144	521.0
13	TraesCS1B01G059700	chr1D	87.688	398	46	3	1047	1444	26677022	26677416	6.990000e-126	460.0
14	TraesCS1B01G059700	chr1D	93.305	239	16	0	1427	1665	26677814	26678052	1.220000e-93	353.0
15	TraesCS1B01G059700	chr1D	92.797	236	17	0	1430	1665	26692185	26692420	2.640000e-90	342.0
16	TraesCS1B01G059700	chr1D	93.976	166	7	3	1577	1742	26677814	26677976	5.930000e-62	248.0
17	TraesCS1B01G059700	chr1D	94.410	161	9	0	1580	1740	26692185	26692345	5.930000e-62	248.0
18	TraesCS1B01G059700	chr1D	87.097	217	24	4	1376	1590	26677838	26678052	2.760000e-60	243.0
19	TraesCS1B01G059700	chr1D	87.037	216	26	2	1376	1590	26692206	26692420	2.760000e-60	243.0
20	TraesCS1B01G059700	chr1D	75.962	520	95	24	1216	1711	26691030	26691543	9.920000e-60	241.0
21	TraesCS1B01G059700	chr1D	77.091	275	56	6	1042	1314	26691183	26691452	4.780000e-33	152.0
22	TraesCS1B01G059700	chr1D	76.642	274	59	5	1042	1314	26677098	26677367	2.220000e-31	147.0
23	TraesCS1B01G059700	chr1D	83.916	143	21	2	1374	1515	26692279	26692420	4.810000e-28	135.0
24	TraesCS1B01G059700	chr1D	89.888	89	9	0	1652	1740	26677814	26677902	6.270000e-22	115.0
25	TraesCS1B01G059700	chr1D	90.698	86	8	0	1655	1740	26692185	26692270	6.270000e-22	115.0
26	TraesCS1B01G059700	chrUn	94.920	748	28	5	2024	2771	16211094	16211831	0.000000e+00	1162.0
27	TraesCS1B01G059700	chrUn	94.652	748	18	4	2024	2771	312209322	312210047	0.000000e+00	1140.0
28	TraesCS1B01G059700	chr2B	95.915	710	19	5	2063	2771	64801786	64801086	0.000000e+00	1142.0
29	TraesCS1B01G059700	chr6A	92.553	752	41	7	2024	2771	498068357	498069097	0.000000e+00	1064.0
30	TraesCS1B01G059700	chr6A	92.533	750	39	10	2027	2771	171324757	171324020	0.000000e+00	1059.0
31	TraesCS1B01G059700	chr6A	91.756	558	36	8	2193	2741	83462945	83463501	0.000000e+00	767.0
32	TraesCS1B01G059700	chr7D	82.650	317	47	6	143	455	107380847	107381159	9.780000e-70	274.0
33	TraesCS1B01G059700	chr4B	76.243	181	19	12	2019	2183	573224925	573224753	1.060000e-09	75.0
34	TraesCS1B01G059700	chr4A	83.582	67	10	1	2107	2172	544180054	544180120	8.290000e-06	62.1

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	TraesCS1B01G059700	chr1B	42324627	42327397	2770	False	1174.166667	5118	82.941000	1	2771	6	chr1B.!!$F1	2770
1	TraesCS1B01G059700	chr1D	26675823	26678329	2506	False	458.111111	1243	88.720222	1	2022	9	chr1D.!!$F1	2021
2	TraesCS1B01G059700	chr1D	26689908	26692697	2789	False	417.545455	1232	87.291727	1	2022	11	chr1D.!!$F2	2021
3	TraesCS1B01G059700	chrUn	16211094	16211831	737	False	1162.000000	1162	94.920000	2024	2771	1	chrUn.!!$F1	747
4	TraesCS1B01G059700	chrUn	312209322	312210047	725	False	1140.000000	1140	94.652000	2024	2771	1	chrUn.!!$F2	747
5	TraesCS1B01G059700	chr2B	64801086	64801786	700	True	1142.000000	1142	95.915000	2063	2771	1	chr2B.!!$R1	708
6	TraesCS1B01G059700	chr6A	498068357	498069097	740	False	1064.000000	1064	92.553000	2024	2771	1	chr6A.!!$F2	747
7	TraesCS1B01G059700	chr6A	171324020	171324757	737	True	1059.000000	1059	92.533000	2027	2771	1	chr6A.!!$R1	744
8	TraesCS1B01G059700	chr6A	83462945	83463501	556	False	767.000000	767	91.756000	2193	2741	1	chr6A.!!$F1	548

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
460	463	0.036858	AAAAGCTCGCACTCCTCTCC	60.037	55.0	0.00	0.0	0.00	3.71	F
1326	1508	0.110486	GGAAGGTGCCTTTCAGACCA	59.890	55.0	4.83	0.0	36.26	4.02	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1599	2404	0.321671	CCTTCCTGAGCACCGAGAAA	59.678	55.0	0.0	0.0	0.00	2.52	R
2678	3498	0.946221	GTCGCCGATCCATGATCACC	60.946	60.0	0.0	0.0	38.84	4.02	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
27	28	6.889722	CCCCTCCATGTAATCTTCTTTGTAAA	59.110	38.462	0.00	0.00	0.00	2.01
85	86	1.335872	GGAAAATGCCAACTGTGACCG	60.336	52.381	0.00	0.00	0.00	4.79
97	98	1.068281	CTGTGACCGATCTCATGGGAG	59.932	57.143	0.00	0.00	42.80	4.30
101	102	0.397675	ACCGATCTCATGGGAGCTCA	60.398	55.000	17.19	0.00	41.13	4.26
108	109	5.619220	GATCTCATGGGAGCTCAGTATTTT	58.381	41.667	17.19	0.00	41.13	1.82
109	110	5.441718	TCTCATGGGAGCTCAGTATTTTT	57.558	39.130	17.19	0.00	41.13	1.94
181	184	4.379394	CCATGGAAACTTGTACATGTTCCG	60.379	45.833	22.94	14.45	39.14	4.30
229	232	1.619827	ACATTGTGATTTGTGGGCTGG	59.380	47.619	0.00	0.00	0.00	4.85
230	233	1.619827	CATTGTGATTTGTGGGCTGGT	59.380	47.619	0.00	0.00	0.00	4.00
289	292	5.286082	GTGCATTTTAGAAATACGTGCTTGG	59.714	40.000	0.00	0.00	32.67	3.61
323	326	1.931709	GCCACGCGTGAAAGTGTACTA	60.932	52.381	39.10	0.00	36.69	1.82
352	355	8.291888	TGAATTTTTGCACACACATAATACAC	57.708	30.769	0.00	0.00	0.00	2.90
356	359	2.158645	TGCACACACATAATACACGTGC	59.841	45.455	17.22	0.00	46.38	5.34
379	382	7.894247	GTGCATGAATGTTCACAAAATATTTCG	59.106	33.333	0.10	0.00	40.49	3.46
384	387	9.393249	TGAATGTTCACAAAATATTTCGAGTTC	57.607	29.630	0.10	5.94	31.01	3.01
385	388	8.742554	AATGTTCACAAAATATTTCGAGTTCC	57.257	30.769	0.10	0.00	0.00	3.62
417	420	8.334632	CGCTGTAGAAAATTGGTTTTTGAAAAT	58.665	29.630	0.00	0.00	37.65	1.82
460	463	0.036858	AAAAGCTCGCACTCCTCTCC	60.037	55.000	0.00	0.00	0.00	3.71
619	625	9.489084	AAAATTTTACTCCAATTTAGGACTTGC	57.511	29.630	0.37	0.00	33.56	4.01
629	635	6.537301	CCAATTTAGGACTTGCTGAATACGTA	59.463	38.462	0.00	0.00	0.00	3.57
633	639	8.638685	TTTAGGACTTGCTGAATACGTATTAC	57.361	34.615	20.37	13.26	0.00	1.89
637	643	9.293404	AGGACTTGCTGAATACGTATTACTATA	57.707	33.333	20.37	6.32	0.00	1.31
851	952	0.173029	TTCTAAATACGGACGCGGCA	59.827	50.000	17.00	0.00	0.00	5.69
852	953	0.248743	TCTAAATACGGACGCGGCAG	60.249	55.000	17.00	14.22	0.00	4.85
853	954	1.213094	CTAAATACGGACGCGGCAGG	61.213	60.000	18.43	9.13	0.00	4.85
854	955	2.632136	TAAATACGGACGCGGCAGGG	62.632	60.000	18.43	6.16	0.00	4.45
904	1005	2.783288	CCGGACGGAGGGAGTAAGC	61.783	68.421	4.40	0.00	37.50	3.09
905	1006	2.050350	CGGACGGAGGGAGTAAGCA	61.050	63.158	0.00	0.00	0.00	3.91
906	1007	1.601419	CGGACGGAGGGAGTAAGCAA	61.601	60.000	0.00	0.00	0.00	3.91
907	1008	0.175989	GGACGGAGGGAGTAAGCAAG	59.824	60.000	0.00	0.00	0.00	4.01
908	1009	0.896226	GACGGAGGGAGTAAGCAAGT	59.104	55.000	0.00	0.00	0.00	3.16
909	1010	1.275573	GACGGAGGGAGTAAGCAAGTT	59.724	52.381	0.00	0.00	0.00	2.66
910	1011	1.002087	ACGGAGGGAGTAAGCAAGTTG	59.998	52.381	0.00	0.00	0.00	3.16
911	1012	1.454201	GGAGGGAGTAAGCAAGTTGC	58.546	55.000	20.44	20.44	45.46	4.17
986	1087	4.057943	ACCGGCGGTACTCCTCCT	62.058	66.667	33.31	0.74	36.51	3.69
987	1088	2.758737	CCGGCGGTACTCCTCCTT	60.759	66.667	19.97	0.00	36.51	3.36
988	1089	2.783288	CCGGCGGTACTCCTCCTTC	61.783	68.421	19.97	0.00	36.51	3.46
1095	1196	1.143073	GGACCAGACCCCATAATGTCC	59.857	57.143	0.00	0.00	34.61	4.02
1098	1199	1.202651	CCAGACCCCATAATGTCCGAC	60.203	57.143	0.00	0.00	31.76	4.79
1101	1202	0.622154	ACCCCATAATGTCCGACCCA	60.622	55.000	0.00	0.00	0.00	4.51
1183	1284	2.505407	CCAGACCCCATAACATCTGACA	59.495	50.000	1.71	0.00	40.92	3.58
1184	1285	3.535561	CAGACCCCATAACATCTGACAC	58.464	50.000	0.00	0.00	40.92	3.67
1191	1292	1.195442	TAACATCTGACACGCCCCCA	61.195	55.000	0.00	0.00	0.00	4.96
1326	1508	0.110486	GGAAGGTGCCTTTCAGACCA	59.890	55.000	4.83	0.00	36.26	4.02
1380	1562	1.669158	CGACAAGCGCTCACTTCTCG	61.669	60.000	12.06	7.15	32.99	4.04
1486	1668	0.321919	GGTTCCTACCGGACCAAACC	60.322	60.000	9.46	12.93	39.60	3.27
1487	1669	0.321919	GTTCCTACCGGACCAAACCC	60.322	60.000	9.46	0.00	39.60	4.11
1488	1670	0.767446	TTCCTACCGGACCAAACCCA	60.767	55.000	9.46	0.00	39.60	4.51
1489	1671	1.196104	TCCTACCGGACCAAACCCAG	61.196	60.000	9.46	0.00	33.30	4.45
1490	1672	1.196104	CCTACCGGACCAAACCCAGA	61.196	60.000	9.46	0.00	0.00	3.86
1491	1673	0.249398	CTACCGGACCAAACCCAGAG	59.751	60.000	9.46	0.00	0.00	3.35
1492	1674	0.178926	TACCGGACCAAACCCAGAGA	60.179	55.000	9.46	0.00	0.00	3.10
1493	1675	1.003718	CCGGACCAAACCCAGAGAC	60.004	63.158	0.00	0.00	0.00	3.36
1494	1676	1.374252	CGGACCAAACCCAGAGACG	60.374	63.158	0.00	0.00	0.00	4.18
1495	1677	1.752833	GGACCAAACCCAGAGACGT	59.247	57.895	0.00	0.00	0.00	4.34
1496	1678	0.320508	GGACCAAACCCAGAGACGTC	60.321	60.000	7.70	7.70	0.00	4.34
1497	1679	0.320508	GACCAAACCCAGAGACGTCC	60.321	60.000	13.01	3.77	0.00	4.79
1498	1680	1.374252	CCAAACCCAGAGACGTCCG	60.374	63.158	13.01	0.63	0.00	4.79
1499	1681	1.663739	CAAACCCAGAGACGTCCGA	59.336	57.895	13.01	0.00	0.00	4.55
1500	1682	0.666577	CAAACCCAGAGACGTCCGAC	60.667	60.000	13.01	4.38	0.00	4.79
1524	2329	3.391382	CCACCACCTCCGAGGGAC	61.391	72.222	18.99	0.00	40.58	4.46
1537	2342	2.182030	GGGACTTCTCGGTGCTCG	59.818	66.667	0.00	0.00	40.90	5.03
1565	2370	1.196104	CCTACCGGACCAAACCCAGA	61.196	60.000	9.46	0.00	0.00	3.86
1569	2374	1.374252	CGGACCAAACCCAGAGACG	60.374	63.158	0.00	0.00	0.00	4.18
1599	2404	2.365635	CCACCACCTCCGAGGGAT	60.366	66.667	18.99	0.52	40.58	3.85
1732	2537	1.576421	GTGACGTCCGACTTACCGT	59.424	57.895	14.12	0.00	36.04	4.83
1838	2643	8.461249	CTTGTAGTGTTAGCTACTAGGGAATA	57.539	38.462	0.00	0.00	41.27	1.75
1839	2644	8.827832	TTGTAGTGTTAGCTACTAGGGAATAA	57.172	34.615	0.00	0.00	41.27	1.40
1840	2645	9.430399	TTGTAGTGTTAGCTACTAGGGAATAAT	57.570	33.333	0.00	0.00	41.27	1.28
1844	2649	9.080097	AGTGTTAGCTACTAGGGAATAATAGTG	57.920	37.037	0.00	0.00	34.21	2.74
1845	2650	8.858094	GTGTTAGCTACTAGGGAATAATAGTGT	58.142	37.037	0.00	0.00	34.21	3.55
1851	2656	9.392259	GCTACTAGGGAATAATAGTGTTTTTGT	57.608	33.333	0.00	0.00	34.21	2.83
1873	2678	8.859517	TTGTGCGCTTACTTTTTAAGTATTTT	57.140	26.923	9.73	0.00	43.09	1.82
1896	2701	0.956633	ACGGAGTACTTGCAGTTCGA	59.043	50.000	0.00	0.00	41.94	3.71
1911	2716	0.319900	TTCGAGGCAGTTGACAGAGC	60.320	55.000	0.00	0.00	0.00	4.09
1919	2724	1.400846	CAGTTGACAGAGCCATGCATC	59.599	52.381	0.00	0.00	0.00	3.91
1921	2726	0.622136	TTGACAGAGCCATGCATCCT	59.378	50.000	0.00	0.00	0.00	3.24
1973	2779	1.135083	AGATGGTCGTTCGCTACTTGG	60.135	52.381	0.00	0.00	0.00	3.61
2005	2811	3.720949	TTGCATGCTATCTTGATTGCC	57.279	42.857	20.33	1.31	0.00	4.52
2022	2828	3.066291	TGCCGATCAATTAGTTGTGGT	57.934	42.857	0.00	0.00	36.69	4.16
2054	2860	3.788142	AGCCAGAAAATGAAGATAGGGGA	59.212	43.478	0.00	0.00	0.00	4.81
2095	2904	9.929180	GCACTAAAATCATAGTAGGATACATGA	57.071	33.333	0.00	0.00	46.26	3.07
2291	3102	4.558496	CGAGCTGGAAACAATTGGCTTAAA	60.558	41.667	10.83	0.00	38.15	1.52
2463	3281	0.964860	TATTGCCAGCACGCCATTGT	60.965	50.000	0.00	0.00	0.00	2.71
2464	3282	1.818959	ATTGCCAGCACGCCATTGTT	61.819	50.000	0.00	0.00	0.00	2.83
2713	3534	1.738099	GACACTACGGCTGCCTGTG	60.738	63.158	24.31	24.31	35.09	3.66

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
55	56	1.043116	GGCATTTTCCAGCCCCTACC	61.043	60.000	0.00	0.00	45.18	3.18
156	159	5.418840	GGAACATGTACAAGTTTCCATGGAT	59.581	40.000	17.06	1.24	39.14	3.41
181	184	1.185189	GGTTTTTCACACGTTCGTGC	58.815	50.000	22.35	6.76	39.53	5.34
229	232	5.606505	TGGGCCAGAATTTTGTCTTTTTAC	58.393	37.500	0.00	0.00	0.00	2.01
230	233	5.878406	TGGGCCAGAATTTTGTCTTTTTA	57.122	34.783	0.00	0.00	0.00	1.52
261	264	5.019498	CACGTATTTCTAAAATGCACCGAC	58.981	41.667	0.00	0.00	0.00	4.79
266	269	5.398169	CCAAGCACGTATTTCTAAAATGCA	58.602	37.500	0.00	0.00	34.03	3.96
279	282	4.775058	ACAAAATAATGCCAAGCACGTA	57.225	36.364	0.00	0.00	43.04	3.57
289	292	1.843753	GCGTGGCGTACAAAATAATGC	59.156	47.619	0.00	0.00	0.00	3.56
352	355	6.874297	ATATTTTGTGAACATTCATGCACG	57.126	33.333	0.00	0.00	39.73	5.34
356	359	9.345517	ACTCGAAATATTTTGTGAACATTCATG	57.654	29.630	19.62	0.00	39.73	3.07
379	382	3.299340	TCTACAGCGTGAAAGGAACTC	57.701	47.619	0.00	0.00	38.49	3.01
384	387	4.023193	ACCAATTTTCTACAGCGTGAAAGG	60.023	41.667	0.00	0.00	34.29	3.11
385	388	5.108385	ACCAATTTTCTACAGCGTGAAAG	57.892	39.130	0.00	0.00	34.29	2.62
483	486	2.106684	GGGACTCCCAAGTTTCAAGACT	59.893	50.000	9.53	0.00	44.65	3.24
484	487	2.505405	GGGACTCCCAAGTTTCAAGAC	58.495	52.381	9.53	0.00	44.65	3.01
593	599	9.489084	GCAAGTCCTAAATTGGAGTAAAATTTT	57.511	29.630	8.75	8.75	38.73	1.82
730	736	6.638021	AATATAGGGGTGGCCTAATTAGTC	57.362	41.667	11.50	0.00	0.00	2.59
732	738	8.159229	ACTTAATATAGGGGTGGCCTAATTAG	57.841	38.462	3.32	5.43	0.00	1.73
735	741	6.446110	GGTACTTAATATAGGGGTGGCCTAAT	59.554	42.308	3.32	0.00	0.00	1.73
736	742	5.786975	GGTACTTAATATAGGGGTGGCCTAA	59.213	44.000	3.32	0.00	0.00	2.69
829	930	0.850856	CGCGTCCGTATTTAGAAGGC	59.149	55.000	0.00	0.00	0.00	4.35
860	961	1.558294	GGGGTTTATATAGGGCCGGAG	59.442	57.143	5.05	0.00	0.00	4.63
861	962	1.660242	GGGGTTTATATAGGGCCGGA	58.340	55.000	5.05	0.00	0.00	5.14
862	963	0.251073	CGGGGTTTATATAGGGCCGG	59.749	60.000	0.00	0.00	0.00	6.13
863	964	0.251073	CCGGGGTTTATATAGGGCCG	59.749	60.000	0.00	0.00	0.00	6.13
864	965	1.280133	GTCCGGGGTTTATATAGGGCC	59.720	57.143	0.00	0.00	0.00	5.80
865	966	1.066645	CGTCCGGGGTTTATATAGGGC	60.067	57.143	0.00	0.00	0.00	5.19
866	967	1.066645	GCGTCCGGGGTTTATATAGGG	60.067	57.143	0.00	0.00	0.00	3.53
867	968	1.066645	GGCGTCCGGGGTTTATATAGG	60.067	57.143	0.00	0.00	0.00	2.57
868	969	1.403249	CGGCGTCCGGGGTTTATATAG	60.403	57.143	0.00	0.00	44.15	1.31
869	970	0.602562	CGGCGTCCGGGGTTTATATA	59.397	55.000	0.00	0.00	44.15	0.86
870	971	1.368579	CGGCGTCCGGGGTTTATAT	59.631	57.895	0.00	0.00	44.15	0.86
891	992	1.726853	CAACTTGCTTACTCCCTCCG	58.273	55.000	0.00	0.00	0.00	4.63
909	1010	1.019278	GGCTAGTTTGCTACTGCGCA	61.019	55.000	10.98	10.98	43.34	6.09
910	1011	1.019278	TGGCTAGTTTGCTACTGCGC	61.019	55.000	0.00	0.00	43.34	6.09
911	1012	1.394917	CTTGGCTAGTTTGCTACTGCG	59.605	52.381	2.79	0.00	43.34	5.18
986	1087	2.124983	GCATCAGCGGCAGGAGAA	60.125	61.111	1.45	0.00	0.00	2.87
1125	1226	0.950836	TCAGCACCGGAAAATGTGTG	59.049	50.000	9.46	0.00	34.94	3.82
1126	1227	1.238439	CTCAGCACCGGAAAATGTGT	58.762	50.000	9.46	0.00	34.94	3.72
1134	1235	2.203788	ACCTTCCTCAGCACCGGA	60.204	61.111	9.46	0.00	0.00	5.14
1135	1236	2.046892	CACCTTCCTCAGCACCGG	60.047	66.667	0.00	0.00	0.00	5.28
1176	1277	3.717294	GGTGGGGGCGTGTCAGAT	61.717	66.667	0.00	0.00	0.00	2.90
1245	1427	1.622312	GGGTCCGATGTTATAGGGTCC	59.378	57.143	0.00	0.00	0.00	4.46
1288	1470	1.284982	CGAAGCACCGAGAAGTGTGG	61.285	60.000	0.00	0.00	40.04	4.17
1326	1508	6.382570	GTGGAGCATAAGATACTATGGGATCT	59.617	42.308	0.00	0.00	33.75	2.75
1380	1562	2.987962	GGGACCTTCCGGAGAACC	59.012	66.667	3.34	7.36	37.43	3.62
1450	1632	1.254284	ACCTTCCTGAGCACCGAGAG	61.254	60.000	0.00	0.00	0.00	3.20
1486	1668	1.502640	GTGAGTCGGACGTCTCTGG	59.497	63.158	16.46	2.93	32.85	3.86
1487	1669	1.502640	GGTGAGTCGGACGTCTCTG	59.497	63.158	16.46	6.10	32.85	3.35
1488	1670	2.033755	CGGTGAGTCGGACGTCTCT	61.034	63.158	16.46	11.39	32.85	3.10
1489	1671	2.479650	CGGTGAGTCGGACGTCTC	59.520	66.667	16.46	11.10	0.00	3.36
1490	1672	3.735029	GCGGTGAGTCGGACGTCT	61.735	66.667	16.46	0.00	0.00	4.18
1491	1673	4.773117	GGCGGTGAGTCGGACGTC	62.773	72.222	7.13	7.13	0.00	4.34
1494	1676	4.736896	GGTGGCGGTGAGTCGGAC	62.737	72.222	0.00	0.00	0.00	4.79
1498	1680	3.591254	GAGGTGGTGGCGGTGAGTC	62.591	68.421	0.00	0.00	0.00	3.36
1499	1681	3.626924	GAGGTGGTGGCGGTGAGT	61.627	66.667	0.00	0.00	0.00	3.41
1500	1682	4.394712	GGAGGTGGTGGCGGTGAG	62.395	72.222	0.00	0.00	0.00	3.51
1509	2314	1.609794	GAAGTCCCTCGGAGGTGGT	60.610	63.158	22.07	5.00	31.93	4.16
1518	2323	1.513622	GAGCACCGAGAAGTCCCTC	59.486	63.158	0.00	0.00	0.00	4.30
1524	2329	1.153745	CTTCCCGAGCACCGAGAAG	60.154	63.158	7.99	7.99	44.47	2.85
1565	2370	3.735029	GCGGTGAGTCGGACGTCT	61.735	66.667	16.46	0.00	0.00	4.18
1569	2374	4.736896	GGTGGCGGTGAGTCGGAC	62.737	72.222	0.00	0.00	0.00	4.79
1599	2404	0.321671	CCTTCCTGAGCACCGAGAAA	59.678	55.000	0.00	0.00	0.00	2.52
1641	2446	4.773117	GGCGGTGAGTCGGACGTC	62.773	72.222	7.13	7.13	0.00	4.34
1671	2476	1.216710	CCTGAGCACCGAGAAGTCC	59.783	63.158	0.00	0.00	0.00	3.85
1680	2485	4.724262	GGAACCTTCCTGAGCACC	57.276	61.111	0.00	0.00	44.11	5.01
1715	2520	4.063529	ACGGTAAGTCGGACGTCA	57.936	55.556	18.91	0.00	33.92	4.35
1716	2521	4.753541	GACGGTAAGTCGGACGTC	57.246	61.111	7.13	7.13	46.89	4.34
1763	2568	1.011242	CGGTAATTGCATCACGCCG	60.011	57.895	0.00	0.00	41.33	6.46
1778	2583	3.986072	TAACATGCATGGCGCCGGT	62.986	57.895	29.41	10.60	41.33	5.28
1779	2584	3.208383	TAACATGCATGGCGCCGG	61.208	61.111	29.41	18.06	41.33	6.13
1838	2643	5.432885	AGTAAGCGCACAAAAACACTATT	57.567	34.783	11.47	0.00	0.00	1.73
1839	2644	5.432885	AAGTAAGCGCACAAAAACACTAT	57.567	34.783	11.47	0.00	0.00	2.12
1840	2645	4.886247	AAGTAAGCGCACAAAAACACTA	57.114	36.364	11.47	0.00	0.00	2.74
1841	2646	3.775661	AAGTAAGCGCACAAAAACACT	57.224	38.095	11.47	0.00	0.00	3.55
1842	2647	4.833469	AAAAGTAAGCGCACAAAAACAC	57.167	36.364	11.47	0.00	0.00	3.32
1843	2648	6.586844	ACTTAAAAAGTAAGCGCACAAAAACA	59.413	30.769	11.47	0.00	40.69	2.83
1844	2649	6.985013	ACTTAAAAAGTAAGCGCACAAAAAC	58.015	32.000	11.47	0.00	40.69	2.43
1845	2650	8.859517	ATACTTAAAAAGTAAGCGCACAAAAA	57.140	26.923	11.47	0.00	46.24	1.94
1896	2701	0.322277	CATGGCTCTGTCAACTGCCT	60.322	55.000	10.49	0.00	45.11	4.75
1911	2716	9.234827	TCTTATATAACATTTCAGGATGCATGG	57.765	33.333	2.46	0.00	32.60	3.66
2005	2811	3.623060	CCCTGACCACAACTAATTGATCG	59.377	47.826	0.00	0.00	39.30	3.69
2022	2828	1.125093	TTTTCTGGCTCCGTCCCTGA	61.125	55.000	0.00	0.00	0.00	3.86
2054	2860	0.394565	AGTGCTTCGAGTTCTTGCCT	59.605	50.000	0.00	0.00	0.00	4.75
2218	3029	4.846779	ACGAAATGCAACTAAACACCAT	57.153	36.364	0.00	0.00	0.00	3.55
2291	3102	8.765517	AGAAAGGGCTGAATCAATTCATATTTT	58.234	29.630	5.92	5.51	44.92	1.82
2463	3281	2.186532	TGGTGTGCAGGCGTATTTAA	57.813	45.000	0.00	0.00	0.00	1.52
2464	3282	2.411628	ATGGTGTGCAGGCGTATTTA	57.588	45.000	0.00	0.00	0.00	1.40
2678	3498	0.946221	GTCGCCGATCCATGATCACC	60.946	60.000	0.00	0.00	38.84	4.02
2713	3534	2.245438	CTCTTCGTTGAGGGGAGGGC	62.245	65.000	0.68	0.00	0.00	5.19

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.