AutoCloner

Multiple sequence alignment - TraesCS7B01G245800

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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	TraesCS7B01G245800	chr7B	100.000	5231	0	0	1	5231	454246807	454241577	0.000000e+00	9660.0
1	TraesCS7B01G245800	chr7D	96.319	3993	101	16	662	4618	437431398	437427416	0.000000e+00	6517.0
2	TraesCS7B01G245800	chr7D	90.086	464	14	8	4616	5065	437427186	437426741	1.630000e-159	573.0
3	TraesCS7B01G245800	chr7D	91.935	124	7	2	4770	4893	364737736	364737856	2.500000e-38	171.0
4	TraesCS7B01G245800	chr7D	95.146	103	5	0	5088	5190	437426681	437426579	4.190000e-36	163.0
5	TraesCS7B01G245800	chr7A	94.966	3675	134	22	767	4434	487637858	487634228	0.000000e+00	5714.0
6	TraesCS7B01G245800	chr7A	87.736	318	19	8	4735	5051	487634227	487633929	2.320000e-93	353.0
7	TraesCS7B01G245800	chr7A	90.977	133	9	3	4770	4902	607606115	607606244	5.380000e-40	176.0
8	TraesCS7B01G245800	chr4D	77.255	2106	457	19	1743	3840	143578812	143580903	0.000000e+00	1216.0
9	TraesCS7B01G245800	chr4D	81.016	374	55	9	241	600	363251637	363251266	3.080000e-72	283.0
10	TraesCS7B01G245800	chr4A	77.171	2107	457	21	1743	3840	325195091	325193000	0.000000e+00	1205.0
11	TraesCS7B01G245800	chr4B	77.113	2106	460	19	1743	3840	214924370	214926461	0.000000e+00	1199.0
12	TraesCS7B01G245800	chr4B	81.915	564	98	4	24	586	618376241	618376801	1.700000e-129	473.0
13	TraesCS7B01G245800	chr4B	78.837	619	94	20	44	653	83308319	83307729	2.960000e-102	383.0
14	TraesCS7B01G245800	chr3D	83.728	633	89	11	31	653	291755616	291756244	2.100000e-163	586.0
15	TraesCS7B01G245800	chr2D	82.059	641	96	11	25	653	617110603	617111236	3.590000e-146	529.0
16	TraesCS7B01G245800	chr2D	78.378	629	96	26	38	653	9099393	9099994	6.400000e-99	372.0
17	TraesCS7B01G245800	chr3B	81.911	586	99	5	39	620	384724530	384725112	6.090000e-134	488.0
18	TraesCS7B01G245800	chr3B	100.000	37	0	0	5050	5086	475141191	475141155	9.400000e-08	69.4
19	TraesCS7B01G245800	chr1D	80.386	622	109	11	39	654	404550725	404551339	1.330000e-125	460.0
20	TraesCS7B01G245800	chr1D	86.770	257	20	8	4798	5051	37451360	37451605	1.860000e-69	274.0
21	TraesCS7B01G245800	chr5D	79.876	646	102	13	25	653	329793738	329794372	1.030000e-121	448.0
22	TraesCS7B01G245800	chr5D	79.360	625	95	18	37	648	222986019	222985416	4.880000e-110	409.0
23	TraesCS7B01G245800	chr6A	79.968	634	104	14	37	653	140541851	140542478	3.720000e-121	446.0
24	TraesCS7B01G245800	chr6A	88.722	133	12	2	4770	4902	212052135	212052006	5.420000e-35	159.0
25	TraesCS7B01G245800	chr2A	78.548	620	113	12	37	653	707738763	707738161	1.770000e-104	390.0
26	TraesCS7B01G245800	chr5A	77.409	633	121	17	31	653	244765504	244764884	1.790000e-94	357.0
27	TraesCS7B01G245800	chr5A	87.970	133	14	2	4770	4902	272284364	272284494	7.010000e-34	156.0
28	TraesCS7B01G245800	chr6D	76.442	624	107	29	41	648	273087032	273087631	8.510000e-78	302.0
29	TraesCS7B01G245800	chr6B	81.293	294	40	8	326	616	127315388	127315107	1.900000e-54	224.0
30	TraesCS7B01G245800	chr6B	93.617	47	2	1	4770	4816	615325689	615325644	9.400000e-08	69.4
31	TraesCS7B01G245800	chr1A	85.946	185	17	6	4798	4980	36760684	36760861	6.920000e-44	189.0
32	TraesCS7B01G245800	chr5B	90.977	133	9	2	4770	4902	629257437	629257308	5.380000e-40	176.0
33	TraesCS7B01G245800	chr5B	85.938	64	9	0	590	653	710592476	710592539	9.400000e-08	69.4

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	TraesCS7B01G245800	chr7B	454241577	454246807	5230	True	9660.000000	9660	100.000000	1	5231	1	chr7B.!!$R1	5230
1	TraesCS7B01G245800	chr7D	437426579	437431398	4819	True	2417.666667	6517	93.850333	662	5190	3	chr7D.!!$R1	4528
2	TraesCS7B01G245800	chr7A	487633929	487637858	3929	True	3033.500000	5714	91.351000	767	5051	2	chr7A.!!$R1	4284
3	TraesCS7B01G245800	chr4D	143578812	143580903	2091	False	1216.000000	1216	77.255000	1743	3840	1	chr4D.!!$F1	2097
4	TraesCS7B01G245800	chr4A	325193000	325195091	2091	True	1205.000000	1205	77.171000	1743	3840	1	chr4A.!!$R1	2097
5	TraesCS7B01G245800	chr4B	214924370	214926461	2091	False	1199.000000	1199	77.113000	1743	3840	1	chr4B.!!$F1	2097
6	TraesCS7B01G245800	chr4B	618376241	618376801	560	False	473.000000	473	81.915000	24	586	1	chr4B.!!$F2	562
7	TraesCS7B01G245800	chr4B	83307729	83308319	590	True	383.000000	383	78.837000	44	653	1	chr4B.!!$R1	609
8	TraesCS7B01G245800	chr3D	291755616	291756244	628	False	586.000000	586	83.728000	31	653	1	chr3D.!!$F1	622
9	TraesCS7B01G245800	chr2D	617110603	617111236	633	False	529.000000	529	82.059000	25	653	1	chr2D.!!$F2	628
10	TraesCS7B01G245800	chr2D	9099393	9099994	601	False	372.000000	372	78.378000	38	653	1	chr2D.!!$F1	615
11	TraesCS7B01G245800	chr3B	384724530	384725112	582	False	488.000000	488	81.911000	39	620	1	chr3B.!!$F1	581
12	TraesCS7B01G245800	chr1D	404550725	404551339	614	False	460.000000	460	80.386000	39	654	1	chr1D.!!$F2	615
13	TraesCS7B01G245800	chr5D	329793738	329794372	634	False	448.000000	448	79.876000	25	653	1	chr5D.!!$F1	628
14	TraesCS7B01G245800	chr5D	222985416	222986019	603	True	409.000000	409	79.360000	37	648	1	chr5D.!!$R1	611
15	TraesCS7B01G245800	chr6A	140541851	140542478	627	False	446.000000	446	79.968000	37	653	1	chr6A.!!$F1	616
16	TraesCS7B01G245800	chr2A	707738161	707738763	602	True	390.000000	390	78.548000	37	653	1	chr2A.!!$R1	616
17	TraesCS7B01G245800	chr5A	244764884	244765504	620	True	357.000000	357	77.409000	31	653	1	chr5A.!!$R1	622
18	TraesCS7B01G245800	chr6D	273087032	273087631	599	False	302.000000	302	76.442000	41	648	1	chr6D.!!$F1	607

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
191	192	0.041047	CCTTGCGTCATGTGTGTGTG	60.041	55.000	0.00	0.00	3.82	F
635	703	0.318614	CACGTGTGGACAAAATGGGC	60.319	55.000	7.58	0.00	5.36	F
659	727	0.378257	GCGGTGGAGTTGCACATATG	59.622	55.000	0.00	0.00	1.78	F
2280	2392	0.328258	AGCAGCTTCCCATTTACCGT	59.672	50.000	0.00	0.00	4.83	F
2402	2514	1.414181	TGAGGCAGGCTATACTGAAGC	59.586	52.381	0.00	40.97	3.86	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2049	2161	0.107800	GCAATGCTCTCTGCTCCTGA	60.108	55.000	0.00	0.00	43.37	3.86	R
2198	2310	0.033894	TCCGGTTTTCCCATAAGCCC	60.034	55.000	0.00	0.00	36.42	5.19	R
2481	2593	1.341383	CCAACTTCCTCTCCCAATGGG	60.341	57.143	13.28	13.28	46.11	4.00	R
4132	4244	0.523072	TTCCGCTTGCTCATCTTTGC	59.477	50.000	0.00	0.00	0.00	3.68	R
4272	4384	5.542779	ACTACTCAAACTTACAGCAAGGAG	58.457	41.667	0.00	0.00	38.70	3.69	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
21	22	2.485814	GGCATATTTCCTTCATCTCCGC	59.514	50.000	0.00	0.00	0.00	5.54
22	23	2.485814	GCATATTTCCTTCATCTCCGCC	59.514	50.000	0.00	0.00	0.00	6.13
33	34	4.135153	CTCCGCCTCCACGACCAG	62.135	72.222	0.00	0.00	34.06	4.00
78	79	2.619849	GGCCAAGGTTTAACCCTAGGTC	60.620	54.545	10.93	8.14	39.75	3.85
79	80	2.040679	GCCAAGGTTTAACCCTAGGTCA	59.959	50.000	10.93	0.00	39.75	4.02
181	182	2.357034	GCTTCGTCCCTTGCGTCA	60.357	61.111	0.00	0.00	0.00	4.35
191	192	0.041047	CCTTGCGTCATGTGTGTGTG	60.041	55.000	0.00	0.00	0.00	3.82
324	345	1.893919	GACAGAGGTGAGGCTGGACC	61.894	65.000	0.00	0.00	36.47	4.46
429	496	1.000717	GGAAAATGGTGGTCGTTGTGG	60.001	52.381	0.00	0.00	0.00	4.17
514	582	2.411547	CCGACGCAAATGAGACTCAAAC	60.412	50.000	9.70	0.00	0.00	2.93
520	588	3.305608	GCAAATGAGACTCAAACTTGGGG	60.306	47.826	9.70	0.00	31.29	4.96
537	605	1.451387	GGCGGAAATGGGTCGACAT	60.451	57.895	18.91	0.00	31.36	3.06
635	703	0.318614	CACGTGTGGACAAAATGGGC	60.319	55.000	7.58	0.00	0.00	5.36
656	724	3.049674	CGCGGTGGAGTTGCACAT	61.050	61.111	0.00	0.00	0.00	3.21
657	725	1.739929	CGCGGTGGAGTTGCACATA	60.740	57.895	0.00	0.00	0.00	2.29
658	726	1.089481	CGCGGTGGAGTTGCACATAT	61.089	55.000	0.00	0.00	0.00	1.78
659	727	0.378257	GCGGTGGAGTTGCACATATG	59.622	55.000	0.00	0.00	0.00	1.78
660	728	2.011548	GCGGTGGAGTTGCACATATGA	61.012	52.381	10.38	0.00	0.00	2.15
707	775	6.108015	CAGGGCAGCAAATTTTACATGTAAT	58.892	36.000	18.69	3.55	0.00	1.89
729	797	9.767684	GTAATTTTTATGTTTAAAAGGCCATGC	57.232	29.630	5.01	0.00	38.26	4.06
764	832	0.881118	CAACCCCACGACCAAATCTG	59.119	55.000	0.00	0.00	0.00	2.90
805	873	8.627487	TGGTATTTTCGATGAATAAAATGTGC	57.373	30.769	0.00	0.00	36.31	4.57
930	1006	1.291877	ACTCGAGCAACAACGCATCC	61.292	55.000	13.61	0.00	0.00	3.51
931	1007	1.291184	CTCGAGCAACAACGCATCCA	61.291	55.000	0.00	0.00	0.00	3.41
950	1026	1.306642	ACGCCGACTCTGACGAATCT	61.307	55.000	0.00	0.00	0.00	2.40
1197	1285	0.671781	CCAAGCTCAAGGACCACGAG	60.672	60.000	5.93	5.93	0.00	4.18
1350	1462	1.460273	GCGATGAGGAGGAGGAGGAC	61.460	65.000	0.00	0.00	0.00	3.85
1368	1480	4.523282	GAGGGGGAGGATGGGGCT	62.523	72.222	0.00	0.00	0.00	5.19
1533	1645	2.224113	GGAGGTGTTTGTCAAGGTCGTA	60.224	50.000	0.00	0.00	0.00	3.43
1825	1937	2.283173	TGAGAGACTGCCCTGCGA	60.283	61.111	0.00	0.00	0.00	5.10
1865	1977	4.390264	GGGATACATTACCAGGAAGAAGC	58.610	47.826	0.00	0.00	39.74	3.86
1932	2044	1.278238	CGCCGTTCTTATCTGGACAC	58.722	55.000	0.00	0.00	0.00	3.67
2049	2161	2.542411	GGAACGGCGTGATATTCGTAGT	60.542	50.000	15.70	0.00	35.26	2.73
2198	2310	0.673644	ATGCCGGAGTGGAAGAAACG	60.674	55.000	5.05	0.00	42.00	3.60
2265	2377	1.117994	TACAGGATCAGAGGCAGCAG	58.882	55.000	0.00	0.00	0.00	4.24
2280	2392	0.328258	AGCAGCTTCCCATTTACCGT	59.672	50.000	0.00	0.00	0.00	4.83
2296	2408	2.693069	ACCGTCTGAAGAATGAGCTTG	58.307	47.619	0.00	0.00	0.00	4.01
2298	2410	2.414481	CCGTCTGAAGAATGAGCTTGTG	59.586	50.000	0.00	0.00	0.00	3.33
2402	2514	1.414181	TGAGGCAGGCTATACTGAAGC	59.586	52.381	0.00	0.00	40.97	3.86
2406	2518	1.414181	GCAGGCTATACTGAAGCTGGA	59.586	52.381	0.00	0.00	40.97	3.86
2481	2593	1.807142	GTAGCAGAGGAGTTTGGTTGC	59.193	52.381	0.00	0.00	0.00	4.17
2916	3028	5.485353	AGGTGATATCCTCTTGTTCTTGACA	59.515	40.000	0.00	0.00	32.09	3.58
3705	3817	1.561076	CCAGAAGGGGATCACATCACA	59.439	52.381	0.00	0.00	33.20	3.58
3957	4069	1.834263	GGAGGATACAGGACACTTGCT	59.166	52.381	0.00	0.00	41.41	3.91
4107	4219	4.056125	CTCGTCGAGCTGGCACCA	62.056	66.667	9.74	0.00	0.00	4.17
4272	4384	2.362077	TGCTTCTTTCTTGGCACCTTTC	59.638	45.455	0.00	0.00	0.00	2.62
4286	4398	3.744660	CACCTTTCTCCTTGCTGTAAGT	58.255	45.455	4.81	0.00	35.30	2.24
4455	4567	5.680619	ACGAATGCAGATAAGTTATTCCCA	58.319	37.500	0.00	0.00	0.00	4.37
4479	4591	8.190784	CCATCACGAAGCTTTATTTTCCTTAAT	58.809	33.333	0.00	0.00	0.00	1.40
4523	4635	6.470235	GGAACACTTTGAATTGCTATGATTCG	59.530	38.462	0.00	0.00	36.52	3.34
4565	4677	0.250467	GCAGGCAAGTCTTGAGACCA	60.250	55.000	16.99	0.00	45.85	4.02
4566	4678	1.805869	CAGGCAAGTCTTGAGACCAG	58.194	55.000	16.99	1.61	45.85	4.00
4598	4710	2.161609	CAGTATTGAACCGAGCAAACCC	59.838	50.000	0.00	0.00	0.00	4.11
4618	4730	2.432444	CCAGAATTACTCGCCAAACCA	58.568	47.619	0.00	0.00	0.00	3.67
4620	4732	3.181497	CCAGAATTACTCGCCAAACCATG	60.181	47.826	0.00	0.00	0.00	3.66
4703	5047	3.801050	CGATAAGATGCACTTGGTCAGAG	59.199	47.826	10.59	0.00	39.38	3.35
4721	5076	5.918011	GTCAGAGAGGTTAGCGATGATAAAG	59.082	44.000	0.00	0.00	0.00	1.85
4810	5165	1.134371	GTGCTACCACCTTCCTGATCC	60.134	57.143	0.00	0.00	35.92	3.36
4816	5171	3.189606	ACCACCTTCCTGATCCACATTA	58.810	45.455	0.00	0.00	0.00	1.90
4893	5249	4.019950	TGATCCGATGCCAGACATATGAAT	60.020	41.667	10.38	0.00	39.84	2.57
4915	5271	2.370519	TGTTAGTTGCTAGGGCTGTTGA	59.629	45.455	0.00	0.00	39.59	3.18
5006	5365	5.311265	TGCTGAACTCAGTCTTTCATCAAT	58.689	37.500	8.46	0.00	45.45	2.57
5062	5421	1.324005	GCAAGCTACTCCCTCCGTCT	61.324	60.000	0.00	0.00	0.00	4.18
5065	5424	0.553819	AGCTACTCCCTCCGTCTCAT	59.446	55.000	0.00	0.00	0.00	2.90
5066	5425	0.955905	GCTACTCCCTCCGTCTCATC	59.044	60.000	0.00	0.00	0.00	2.92
5069	5428	1.407936	ACTCCCTCCGTCTCATCATG	58.592	55.000	0.00	0.00	0.00	3.07
5070	5429	1.342474	ACTCCCTCCGTCTCATCATGT	60.342	52.381	0.00	0.00	0.00	3.21
5071	5430	2.091830	ACTCCCTCCGTCTCATCATGTA	60.092	50.000	0.00	0.00	0.00	2.29
5072	5431	2.959030	CTCCCTCCGTCTCATCATGTAA	59.041	50.000	0.00	0.00	0.00	2.41
5074	5433	2.959030	CCCTCCGTCTCATCATGTAAGA	59.041	50.000	0.00	0.00	0.00	2.10
5148	5544	8.427276	TGACTGTATCATTTATGCTCTTCAGAT	58.573	33.333	0.00	0.00	29.99	2.90
5178	5574	3.274288	GGAATGCTAGTCCTGAACCTTG	58.726	50.000	0.00	0.00	31.94	3.61
5183	5579	3.198872	GCTAGTCCTGAACCTTGTATGC	58.801	50.000	0.00	0.00	0.00	3.14
5187	5583	3.073062	AGTCCTGAACCTTGTATGCTGTT	59.927	43.478	0.00	0.00	0.00	3.16
5190	5586	4.892934	TCCTGAACCTTGTATGCTGTTTTT	59.107	37.500	0.00	0.00	0.00	1.94
5216	5612	5.606348	TTTTGGAACCTTTTATGCTGTGT	57.394	34.783	0.00	0.00	0.00	3.72
5217	5613	5.606348	TTTGGAACCTTTTATGCTGTGTT	57.394	34.783	0.00	0.00	0.00	3.32
5218	5614	4.846779	TGGAACCTTTTATGCTGTGTTC	57.153	40.909	0.00	0.00	33.20	3.18
5219	5615	4.211125	TGGAACCTTTTATGCTGTGTTCA	58.789	39.130	0.00	0.00	35.09	3.18
5220	5616	4.646945	TGGAACCTTTTATGCTGTGTTCAA	59.353	37.500	0.00	0.00	35.09	2.69
5221	5617	5.304101	TGGAACCTTTTATGCTGTGTTCAAT	59.696	36.000	0.00	0.00	35.09	2.57
5222	5618	6.183360	TGGAACCTTTTATGCTGTGTTCAATT	60.183	34.615	0.00	0.00	35.09	2.32
5223	5619	6.705825	GGAACCTTTTATGCTGTGTTCAATTT	59.294	34.615	0.00	0.00	35.09	1.82
5224	5620	7.870445	GGAACCTTTTATGCTGTGTTCAATTTA	59.130	33.333	0.00	0.00	35.09	1.40
5225	5621	9.255304	GAACCTTTTATGCTGTGTTCAATTTAA	57.745	29.630	0.00	0.00	33.93	1.52
5226	5622	9.777297	AACCTTTTATGCTGTGTTCAATTTAAT	57.223	25.926	0.00	0.00	0.00	1.40

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
0	1	2.485814	GCGGAGATGAAGGAAATATGCC	59.514	50.000	0.00	0.00	0.00	4.40
1	2	2.485814	GGCGGAGATGAAGGAAATATGC	59.514	50.000	0.00	0.00	0.00	3.14
2	3	3.999663	GAGGCGGAGATGAAGGAAATATG	59.000	47.826	0.00	0.00	0.00	1.78
3	4	3.008485	GGAGGCGGAGATGAAGGAAATAT	59.992	47.826	0.00	0.00	0.00	1.28
4	5	2.368875	GGAGGCGGAGATGAAGGAAATA	59.631	50.000	0.00	0.00	0.00	1.40
5	6	1.141858	GGAGGCGGAGATGAAGGAAAT	59.858	52.381	0.00	0.00	0.00	2.17
6	7	0.541863	GGAGGCGGAGATGAAGGAAA	59.458	55.000	0.00	0.00	0.00	3.13
7	8	0.617535	TGGAGGCGGAGATGAAGGAA	60.618	55.000	0.00	0.00	0.00	3.36
8	9	1.001631	TGGAGGCGGAGATGAAGGA	59.998	57.895	0.00	0.00	0.00	3.36
9	10	1.144936	GTGGAGGCGGAGATGAAGG	59.855	63.158	0.00	0.00	0.00	3.46
10	11	1.227089	CGTGGAGGCGGAGATGAAG	60.227	63.158	0.00	0.00	0.00	3.02
11	12	1.680989	TCGTGGAGGCGGAGATGAA	60.681	57.895	0.00	0.00	0.00	2.57
12	13	2.044352	TCGTGGAGGCGGAGATGA	60.044	61.111	0.00	0.00	0.00	2.92
13	14	2.105128	GTCGTGGAGGCGGAGATG	59.895	66.667	0.00	0.00	0.00	2.90
14	15	3.148279	GGTCGTGGAGGCGGAGAT	61.148	66.667	0.00	0.00	0.00	2.75
15	16	4.671590	TGGTCGTGGAGGCGGAGA	62.672	66.667	0.00	0.00	0.00	3.71
16	17	4.135153	CTGGTCGTGGAGGCGGAG	62.135	72.222	0.00	0.00	0.00	4.63
19	20	4.436998	GTCCTGGTCGTGGAGGCG	62.437	72.222	0.00	0.00	33.78	5.52
20	21	4.436998	CGTCCTGGTCGTGGAGGC	62.437	72.222	5.15	0.00	33.58	4.70
21	22	3.760035	CCGTCCTGGTCGTGGAGG	61.760	72.222	12.10	0.00	38.70	4.30
22	23	4.436998	GCCGTCCTGGTCGTGGAG	62.437	72.222	12.10	0.00	41.21	3.86
181	182	1.070786	GGGTCGGACACACACACAT	59.929	57.895	10.76	0.00	0.00	3.21
191	192	1.597461	CCAAGAGGAAGGGTCGGAC	59.403	63.158	0.00	0.00	36.89	4.79
239	240	1.308783	CCGCCCAAGAAGAAGAAGCC	61.309	60.000	0.00	0.00	0.00	4.35
284	296	1.589716	CCTCCGCCAAAGGAAAGCAG	61.590	60.000	0.00	0.00	40.25	4.24
285	297	1.603455	CCTCCGCCAAAGGAAAGCA	60.603	57.895	0.00	0.00	40.25	3.91
514	582	2.037208	ACCCATTTCCGCCCCAAG	59.963	61.111	0.00	0.00	0.00	3.61
520	588	1.721487	CATGTCGACCCATTTCCGC	59.279	57.895	14.12	0.00	0.00	5.54
537	605	2.932905	GTCCGCTTTTCGTTCGCA	59.067	55.556	0.00	0.00	36.19	5.10
586	654	2.602878	GTCATCGCGGACAGAAAAGTA	58.397	47.619	6.13	0.00	37.73	2.24
643	711	3.338249	ACTGTCATATGTGCAACTCCAC	58.662	45.455	1.90	0.00	38.04	4.02
657	725	8.207545	GGTTCTAATTCCAGAGATAACTGTCAT	58.792	37.037	0.00	0.00	36.30	3.06
658	726	7.180229	TGGTTCTAATTCCAGAGATAACTGTCA	59.820	37.037	0.00	0.00	36.30	3.58
659	727	7.556844	TGGTTCTAATTCCAGAGATAACTGTC	58.443	38.462	0.00	0.00	36.30	3.51
660	728	7.496346	TGGTTCTAATTCCAGAGATAACTGT	57.504	36.000	0.00	0.00	36.30	3.55
707	775	6.809630	GGCATGGCCTTTTAAACATAAAAA	57.190	33.333	8.35	0.00	46.69	1.94
724	792	5.907866	TGAATCATTGCATATAGGCATGG	57.092	39.130	13.56	8.54	44.48	3.66
729	797	5.047802	GTGGGGTTGAATCATTGCATATAGG	60.048	44.000	0.00	0.00	0.00	2.57
736	804	1.135402	GTCGTGGGGTTGAATCATTGC	60.135	52.381	0.00	0.00	0.00	3.56
764	832	1.867363	ACCAGAGTCTGTGGGGATAC	58.133	55.000	19.64	0.00	39.65	2.24
817	892	5.446875	GGTTTCGTGTCGAGTTCTTTTTCTT	60.447	40.000	0.00	0.00	37.14	2.52
818	893	4.033702	GGTTTCGTGTCGAGTTCTTTTTCT	59.966	41.667	0.00	0.00	37.14	2.52
819	894	4.269312	GGTTTCGTGTCGAGTTCTTTTTC	58.731	43.478	0.00	0.00	37.14	2.29
930	1006	1.134530	GATTCGTCAGAGTCGGCGTG	61.135	60.000	6.85	0.00	0.00	5.34
931	1007	1.136984	GATTCGTCAGAGTCGGCGT	59.863	57.895	6.85	0.00	0.00	5.68
950	1026	4.771356	CCGCGGCGAGAGAACGAA	62.771	66.667	25.92	0.00	35.49	3.85
1338	1450	2.123640	CCCTCGTCCTCCTCCTCC	60.124	72.222	0.00	0.00	0.00	4.30
1371	1483	3.649277	CTGGTGAAGCTCCGGACCG	62.649	68.421	6.99	6.99	33.49	4.79
1533	1645	3.286694	ATTGCCCCACTGCACGGAT	62.287	57.895	0.00	0.00	41.88	4.18
1614	1726	1.405933	CGAACAGCATCCTGACCATCA	60.406	52.381	0.00	0.00	41.77	3.07
1865	1977	3.631250	AGCTCCTCCTCTACTTCTTCTG	58.369	50.000	0.00	0.00	0.00	3.02
1932	2044	3.833645	TCAATCGAGGACCGGCCG	61.834	66.667	21.04	21.04	43.43	6.13
2023	2135	2.684001	ATATCACGCCGTTCCTTGAA	57.316	45.000	0.00	0.00	0.00	2.69
2049	2161	0.107800	GCAATGCTCTCTGCTCCTGA	60.108	55.000	0.00	0.00	43.37	3.86
2198	2310	0.033894	TCCGGTTTTCCCATAAGCCC	60.034	55.000	0.00	0.00	36.42	5.19
2265	2377	2.396590	TCAGACGGTAAATGGGAAGC	57.603	50.000	0.00	0.00	0.00	3.86
2280	2392	5.936686	CTTTCACAAGCTCATTCTTCAGA	57.063	39.130	0.00	0.00	0.00	3.27
2296	2408	4.507710	TGATGGTGATGTAGAGCTTTCAC	58.492	43.478	0.00	0.00	0.00	3.18
2298	2410	5.181748	ACTTGATGGTGATGTAGAGCTTTC	58.818	41.667	0.00	0.00	0.00	2.62
2481	2593	1.341383	CCAACTTCCTCTCCCAATGGG	60.341	57.143	13.28	13.28	46.11	4.00
2916	3028	2.438763	CTGATCAATCTCTTCCTGGCCT	59.561	50.000	3.32	0.00	0.00	5.19
3489	3601	1.742308	TTCTCCCCAGCTTGGTAAGT	58.258	50.000	2.68	0.00	35.17	2.24
3705	3817	3.447586	ACGCCTGATACACAGTGAGTAAT	59.552	43.478	7.81	0.00	44.40	1.89
3816	3928	2.396608	CTGTCCATGATCTCCAGGAGT	58.603	52.381	16.65	3.81	0.00	3.85
3903	4015	4.780815	TCTTGGCAGAGTTGAAGAAGAAA	58.219	39.130	0.00	0.00	0.00	2.52
3957	4069	4.840115	TGGATATACACCTGCTGATGATCA	59.160	41.667	0.00	0.00	0.00	2.92
4107	4219	2.496470	GTCCACGGATCTGTAGAACCTT	59.504	50.000	6.92	0.00	35.13	3.50
4132	4244	0.523072	TTCCGCTTGCTCATCTTTGC	59.477	50.000	0.00	0.00	0.00	3.68
4272	4384	5.542779	ACTACTCAAACTTACAGCAAGGAG	58.457	41.667	0.00	0.00	38.70	3.69
4455	4567	8.122952	CGATTAAGGAAAATAAAGCTTCGTGAT	58.877	33.333	0.00	0.00	0.00	3.06
4479	4591	3.086282	TCCACTCAGCAGTTATACACGA	58.914	45.455	0.00	0.00	0.00	4.35
4489	4601	2.564771	TCAAAGTGTTCCACTCAGCAG	58.435	47.619	0.00	0.00	44.62	4.24
4523	4635	0.605589	ACGAGGCCTAAACCAAGTGC	60.606	55.000	4.42	0.00	0.00	4.40
4565	4677	5.067954	GGTTCAATACTGGTACACCAAACT	58.932	41.667	2.14	0.00	46.97	2.66
4566	4678	4.083696	CGGTTCAATACTGGTACACCAAAC	60.084	45.833	2.14	3.08	46.97	2.93
4575	4687	2.812011	GTTTGCTCGGTTCAATACTGGT	59.188	45.455	0.00	0.00	33.68	4.00
4598	4710	2.432444	TGGTTTGGCGAGTAATTCTGG	58.568	47.619	0.00	0.00	0.00	3.86
4618	4730	1.620524	CCAAGGAAGGCCAATGACCAT	60.621	52.381	5.01	0.00	36.29	3.55
4620	4732	0.251787	ACCAAGGAAGGCCAATGACC	60.252	55.000	5.01	0.01	36.29	4.02
4621	4733	0.890683	CACCAAGGAAGGCCAATGAC	59.109	55.000	5.01	0.00	36.29	3.06
4623	4735	0.890683	GACACCAAGGAAGGCCAATG	59.109	55.000	5.01	0.00	36.29	2.82
4624	4736	0.779997	AGACACCAAGGAAGGCCAAT	59.220	50.000	5.01	0.00	36.29	3.16
4625	4737	0.555769	AAGACACCAAGGAAGGCCAA	59.444	50.000	5.01	0.00	36.29	4.52
4626	4738	0.555769	AAAGACACCAAGGAAGGCCA	59.444	50.000	5.01	0.00	36.29	5.36
4627	4739	2.437413	CTAAAGACACCAAGGAAGGCC	58.563	52.381	0.00	0.00	0.00	5.19
4675	5019	4.051922	CCAAGTGCATCTTATCGACTACC	58.948	47.826	0.00	0.00	34.66	3.18
4703	5047	9.646427	AAGAATATCTTTATCATCGCTAACCTC	57.354	33.333	0.00	0.00	31.57	3.85
4810	5165	6.968904	GGACAATTGCAATGTCTAGTAATGTG	59.031	38.462	26.59	15.53	45.13	3.21
4816	5171	6.655078	AAAAGGACAATTGCAATGTCTAGT	57.345	33.333	26.59	16.43	45.13	2.57
4893	5249	3.146066	CAACAGCCCTAGCAACTAACAA	58.854	45.455	0.00	0.00	43.56	2.83
4954	5313	8.650490	AACAATTCATTTTATGTTCAAGGGACT	58.350	29.630	0.00	0.00	32.58	3.85
5083	5442	9.812725	TAGGTTATCCAATACTCCCTCCGAGTC	62.813	48.148	0.00	0.00	42.86	3.36
5084	5443	7.420294	AGGTTATCCAATACTCCCTCCGAGT	62.420	48.000	0.00	0.00	44.61	4.18
5085	5444	3.258622	GGTTATCCAATACTCCCTCCGAG	59.741	52.174	0.00	0.00	44.95	4.63
5086	5445	3.116862	AGGTTATCCAATACTCCCTCCGA	60.117	47.826	0.00	0.00	35.89	4.55
5100	5496	5.891551	TCAAAAGGCATTTCCTAGGTTATCC	59.108	40.000	9.08	5.30	46.94	2.59
5148	5544	4.586421	CAGGACTAGCATTCCAGATAGTGA	59.414	45.833	0.00	0.00	40.50	3.41
5193	5589	5.983540	ACACAGCATAAAAGGTTCCAAAAA	58.016	33.333	0.00	0.00	0.00	1.94
5194	5590	5.606348	ACACAGCATAAAAGGTTCCAAAA	57.394	34.783	0.00	0.00	0.00	2.44
5195	5591	5.127845	TGAACACAGCATAAAAGGTTCCAAA	59.872	36.000	0.00	0.00	35.09	3.28
5196	5592	4.646945	TGAACACAGCATAAAAGGTTCCAA	59.353	37.500	0.00	0.00	35.09	3.53
5197	5593	4.211125	TGAACACAGCATAAAAGGTTCCA	58.789	39.130	0.00	0.00	35.09	3.53
5198	5594	4.846779	TGAACACAGCATAAAAGGTTCC	57.153	40.909	0.00	0.00	35.09	3.62
5199	5595	7.713764	AAATTGAACACAGCATAAAAGGTTC	57.286	32.000	0.00	0.00	36.18	3.62
5200	5596	9.777297	ATTAAATTGAACACAGCATAAAAGGTT	57.223	25.926	0.00	0.00	0.00	3.50

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.