AutoCloner

Multiple sequence alignment - TraesCS6D01G134500

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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	TraesCS6D01G134500	chr6D	100.000	5645	0	0	1	5645	102252478	102246834	0.000000e+00	10425
1	TraesCS6D01G134500	chr6D	95.108	2719	112	5	140	2839	277340136	277337420	0.000000e+00	4265
2	TraesCS6D01G134500	chr6D	92.821	390	26	2	4922	5310	102247460	102247072	1.060000e-156	564
3	TraesCS6D01G134500	chr6D	89.616	443	35	11	4922	5358	102247509	102247072	2.300000e-153	553
4	TraesCS6D01G134500	chr6D	89.616	443	35	11	4970	5407	102247557	102247121	2.300000e-153	553
5	TraesCS6D01G134500	chr4D	95.611	5514	142	41	140	5645	122726628	122721207	0.000000e+00	8750
6	TraesCS6D01G134500	chr4D	95.382	2252	67	4	3087	5309	122723712	122721469	0.000000e+00	3548
7	TraesCS6D01G134500	chr7D	97.288	5052	79	22	141	5188	362367312	362372309	0.000000e+00	8517
8	TraesCS6D01G134500	chr7D	97.572	4324	73	13	141	4452	95100903	95096600	0.000000e+00	7374
9	TraesCS6D01G134500	chr7D	96.815	4333	83	17	141	4452	590592671	590588373	0.000000e+00	7186
10	TraesCS6D01G134500	chr7D	96.352	2138	60	10	2696	4829	550666249	550668372	0.000000e+00	3500
11	TraesCS6D01G134500	chr7D	94.221	1021	28	10	4219	5232	590588471	590587475	0.000000e+00	1530
12	TraesCS6D01G134500	chr7D	94.826	831	18	4	4219	5045	95096743	95095934	0.000000e+00	1273
13	TraesCS6D01G134500	chr7D	95.674	601	3	2	5068	5645	362372405	362373005	0.000000e+00	944
14	TraesCS6D01G134500	chr7D	93.805	565	11	3	5105	5645	95095596	95095032	0.000000e+00	828
15	TraesCS6D01G134500	chr7D	92.514	521	14	9	5149	5645	550680797	550681316	0.000000e+00	723
16	TraesCS6D01G134500	chr7D	94.395	446	2	2	5223	5645	95094362	95093917	0.000000e+00	664
17	TraesCS6D01G134500	chr7D	93.237	414	5	2	5255	5645	590578335	590577922	6.300000e-164	588
18	TraesCS6D01G134500	chr7D	89.489	333	29	6	4931	5260	362372414	362372743	3.150000e-112	416
19	TraesCS6D01G134500	chr3D	98.889	3961	40	2	301	4261	53788544	53792500	0.000000e+00	7068
20	TraesCS6D01G134500	chr3D	98.512	2823	28	2	140	2959	5493960	5496771	0.000000e+00	4968
21	TraesCS6D01G134500	chr3D	93.743	943	27	9	4219	5155	5497478	5498394	0.000000e+00	1386
22	TraesCS6D01G134500	chr3D	95.357	840	17	3	4219	5057	53811393	53812211	0.000000e+00	1315
23	TraesCS6D01G134500	chr3D	94.130	460	4	2	5209	5645	5498823	5499282	0.000000e+00	678
24	TraesCS6D01G134500	chr3D	94.130	460	4	2	5209	5645	53812847	53813306	0.000000e+00	678
25	TraesCS6D01G134500	chr2A	96.364	4318	106	10	141	4443	2356026	2360307	0.000000e+00	7057
26	TraesCS6D01G134500	chr2A	91.763	607	27	2	5062	5645	2360834	2361440	0.000000e+00	822
27	TraesCS6D01G134500	chr2A	95.053	283	13	1	4844	5126	712849947	712849666	1.440000e-120	444
28	TraesCS6D01G134500	chr1A	96.131	4316	136	16	139	4443	582348667	582352962	0.000000e+00	7016
29	TraesCS6D01G134500	chrUn	98.682	2201	28	1	2093	4293	108019461	108021660	0.000000e+00	3903
30	TraesCS6D01G134500	chr5A	94.634	1994	73	9	2462	4443	35060153	35062124	0.000000e+00	3059
31	TraesCS6D01G134500	chr5A	90.152	660	39	5	5011	5645	273993042	273992384	0.000000e+00	835
32	TraesCS6D01G134500	chr5A	91.020	490	20	3	5180	5645	35083659	35084148	1.710000e-179	640
33	TraesCS6D01G134500	chr5A	91.379	406	32	3	4844	5248	273993811	273993408	2.300000e-153	553
34	TraesCS6D01G134500	chr5A	88.451	381	40	4	4931	5309	273993024	273992646	1.850000e-124	457
35	TraesCS6D01G134500	chr1D	93.322	1198	48	5	3958	5154	386771763	386770597	0.000000e+00	1740
36	TraesCS6D01G134500	chr1D	90.515	485	23	2	5184	5645	386770255	386769771	2.230000e-173	619
37	TraesCS6D01G134500	chr5D	98.603	859	12	0	141	999	42992384	42993242	0.000000e+00	1520
38	TraesCS6D01G134500	chr4A	93.054	907	49	9	4219	5122	84939684	84940579	0.000000e+00	1314
39	TraesCS6D01G134500	chr3B	90.278	144	13	1	1	143	372909607	372909464	2.690000e-43	187
40	TraesCS6D01G134500	chr2B	89.583	144	14	1	1	143	418678761	418678904	1.250000e-41	182

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	TraesCS6D01G134500	chr6D	102246834	102252478	5644	True	10425.000000	10425	100.000000	1	5645	1	chr6D.!!$R1	5644
1	TraesCS6D01G134500	chr6D	277337420	277340136	2716	True	4265.000000	4265	95.108000	140	2839	1	chr6D.!!$R2	2699
2	TraesCS6D01G134500	chr4D	122721207	122726628	5421	True	8750.000000	8750	95.611000	140	5645	1	chr4D.!!$R1	5505
3	TraesCS6D01G134500	chr4D	122721469	122723712	2243	True	3548.000000	3548	95.382000	3087	5309	1	chr4D.!!$R2	2222
4	TraesCS6D01G134500	chr7D	590587475	590592671	5196	True	4358.000000	7186	95.518000	141	5232	2	chr7D.!!$R3	5091
5	TraesCS6D01G134500	chr7D	550666249	550668372	2123	False	3500.000000	3500	96.352000	2696	4829	1	chr7D.!!$F1	2133
6	TraesCS6D01G134500	chr7D	362367312	362373005	5693	False	3292.333333	8517	94.150333	141	5645	3	chr7D.!!$F3	5504
7	TraesCS6D01G134500	chr7D	95093917	95100903	6986	True	2534.750000	7374	95.149500	141	5645	4	chr7D.!!$R2	5504
8	TraesCS6D01G134500	chr7D	550680797	550681316	519	False	723.000000	723	92.514000	5149	5645	1	chr7D.!!$F2	496
9	TraesCS6D01G134500	chr3D	53788544	53792500	3956	False	7068.000000	7068	98.889000	301	4261	1	chr3D.!!$F1	3960
10	TraesCS6D01G134500	chr3D	5493960	5499282	5322	False	2344.000000	4968	95.461667	140	5645	3	chr3D.!!$F2	5505
11	TraesCS6D01G134500	chr3D	53811393	53813306	1913	False	996.500000	1315	94.743500	4219	5645	2	chr3D.!!$F3	1426
12	TraesCS6D01G134500	chr2A	2356026	2361440	5414	False	3939.500000	7057	94.063500	141	5645	2	chr2A.!!$F1	5504
13	TraesCS6D01G134500	chr1A	582348667	582352962	4295	False	7016.000000	7016	96.131000	139	4443	1	chr1A.!!$F1	4304
14	TraesCS6D01G134500	chrUn	108019461	108021660	2199	False	3903.000000	3903	98.682000	2093	4293	1	chrUn.!!$F1	2200
15	TraesCS6D01G134500	chr5A	35060153	35062124	1971	False	3059.000000	3059	94.634000	2462	4443	1	chr5A.!!$F1	1981
16	TraesCS6D01G134500	chr5A	273992384	273993811	1427	True	615.000000	835	89.994000	4844	5645	3	chr5A.!!$R1	801
17	TraesCS6D01G134500	chr1D	386769771	386771763	1992	True	1179.500000	1740	91.918500	3958	5645	2	chr1D.!!$R1	1687
18	TraesCS6D01G134500	chr5D	42992384	42993242	858	False	1520.000000	1520	98.603000	141	999	1	chr5D.!!$F1	858
19	TraesCS6D01G134500	chr4A	84939684	84940579	895	False	1314.000000	1314	93.054000	4219	5122	1	chr4A.!!$F1	903

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
29	30	0.179073	TAGAAATCCTCGCAGCAGGC	60.179	55.0	6.12	0.00	39.90	4.85	F
45	46	0.246635	AGGCAACGTGAATCGCTACT	59.753	50.0	0.00	0.00	44.19	2.57	F
68	69	0.605589	AAACGCAGTAGGTCCAAGCC	60.606	55.0	0.00	0.00	45.00	4.35	F
72	73	0.678048	GCAGTAGGTCCAAGCCAAGG	60.678	60.0	0.00	0.00	0.00	3.61	F
73	74	0.678048	CAGTAGGTCCAAGCCAAGGC	60.678	60.0	2.02	2.02	42.33	4.35	F
2546	2608	1.181098	GCAAAGAGGGCAGCAAAGGA	61.181	55.0	0.00	0.00	0.00	3.36	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2088	2150	6.212388	ACCTCTTCTTCATCTTCTTTGCTCTA	59.788	38.462	0.00	0.00	0.00	2.43	R
2371	2433	8.410673	ACTTTAGTGTTCTCTGACATAGAAGA	57.589	34.615	3.65	0.32	33.75	2.87	R
2506	2568	1.473677	CCTGTATGCCATGTGTGTTGG	59.526	52.381	0.00	0.00	37.31	3.77	R
2546	2608	4.974645	TTCTGGTCTCCTAACACAACAT	57.025	40.909	0.00	0.00	0.00	2.71	R
2776	2838	7.485913	CACATGAAATCAAACATTAGTAGCACC	59.514	37.037	0.00	0.00	0.00	5.01	R
4769	5213	0.396435	TCATCACAACCGAACTGGCT	59.604	50.000	0.00	0.00	43.94	4.75	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
25	26	2.423926	TCGATAGAAATCCTCGCAGC	57.576	50.000	0.00	0.00	46.15	5.25
26	27	1.681264	TCGATAGAAATCCTCGCAGCA	59.319	47.619	0.00	0.00	46.15	4.41
27	28	2.057316	CGATAGAAATCCTCGCAGCAG	58.943	52.381	0.00	0.00	39.76	4.24
28	29	2.411904	GATAGAAATCCTCGCAGCAGG	58.588	52.381	4.87	4.87	34.40	4.85
29	30	0.179073	TAGAAATCCTCGCAGCAGGC	60.179	55.000	6.12	0.00	39.90	4.85
30	31	1.746615	GAAATCCTCGCAGCAGGCA	60.747	57.895	6.12	0.00	45.17	4.75
31	32	1.303561	AAATCCTCGCAGCAGGCAA	60.304	52.632	6.12	0.00	45.17	4.52
32	33	1.589716	AAATCCTCGCAGCAGGCAAC	61.590	55.000	6.12	0.00	45.17	4.17
35	36	4.081030	CTCGCAGCAGGCAACGTG	62.081	66.667	0.00	0.98	45.17	4.49
36	37	4.600576	TCGCAGCAGGCAACGTGA	62.601	61.111	0.00	0.00	45.17	4.35
37	38	3.648982	CGCAGCAGGCAACGTGAA	61.649	61.111	0.00	0.00	45.17	3.18
38	39	2.956987	GCAGCAGGCAACGTGAAT	59.043	55.556	0.00	0.00	43.97	2.57
39	40	1.154150	GCAGCAGGCAACGTGAATC	60.154	57.895	0.00	0.00	43.97	2.52
40	41	1.133253	CAGCAGGCAACGTGAATCG	59.867	57.895	0.00	0.00	46.39	3.34
41	42	2.202349	GCAGGCAACGTGAATCGC	60.202	61.111	0.00	0.00	44.19	4.58
42	43	2.680913	GCAGGCAACGTGAATCGCT	61.681	57.895	0.00	0.00	44.19	4.93
43	44	1.358725	GCAGGCAACGTGAATCGCTA	61.359	55.000	0.00	0.00	44.19	4.26
44	45	0.370273	CAGGCAACGTGAATCGCTAC	59.630	55.000	0.00	0.00	44.19	3.58
45	46	0.246635	AGGCAACGTGAATCGCTACT	59.753	50.000	0.00	0.00	44.19	2.57
46	47	1.475280	AGGCAACGTGAATCGCTACTA	59.525	47.619	0.00	0.00	44.19	1.82
47	48	2.094390	AGGCAACGTGAATCGCTACTAA	60.094	45.455	0.00	0.00	44.19	2.24
48	49	2.669434	GGCAACGTGAATCGCTACTAAA	59.331	45.455	0.00	0.00	44.19	1.85
49	50	3.123959	GGCAACGTGAATCGCTACTAAAA	59.876	43.478	0.00	0.00	44.19	1.52
50	51	4.377635	GGCAACGTGAATCGCTACTAAAAA	60.378	41.667	0.00	0.00	44.19	1.94
67	68	1.235724	AAAACGCAGTAGGTCCAAGC	58.764	50.000	0.00	0.00	45.00	4.01
68	69	0.605589	AAACGCAGTAGGTCCAAGCC	60.606	55.000	0.00	0.00	45.00	4.35
69	70	1.764571	AACGCAGTAGGTCCAAGCCA	61.765	55.000	0.00	0.00	45.00	4.75
70	71	1.003839	CGCAGTAGGTCCAAGCCAA	60.004	57.895	0.00	0.00	0.00	4.52
71	72	1.021390	CGCAGTAGGTCCAAGCCAAG	61.021	60.000	0.00	0.00	0.00	3.61
72	73	0.678048	GCAGTAGGTCCAAGCCAAGG	60.678	60.000	0.00	0.00	0.00	3.61
73	74	0.678048	CAGTAGGTCCAAGCCAAGGC	60.678	60.000	2.02	2.02	42.33	4.35
97	98	4.657824	CAACGTCAGGGTCCGCGT	62.658	66.667	4.92	0.00	39.37	6.01
98	99	4.353437	AACGTCAGGGTCCGCGTC	62.353	66.667	4.92	0.00	36.51	5.19
101	102	4.477975	GTCAGGGTCCGCGTCGAG	62.478	72.222	4.92	0.00	0.00	4.04
120	121	4.759096	GCAACGCCATCACGCACC	62.759	66.667	0.00	0.00	36.19	5.01
121	122	4.444024	CAACGCCATCACGCACCG	62.444	66.667	0.00	0.00	36.19	4.94
137	138	2.896443	CGGGAGGAAGAGGTCAGC	59.104	66.667	0.00	0.00	0.00	4.26
495	531	1.226407	CGAAGTCGAGCGATGCTGA	60.226	57.895	0.00	0.00	39.88	4.26
624	669	2.203070	GGCCAGATCATTCGCCGT	60.203	61.111	0.00	0.00	0.00	5.68
1471	1518	4.080695	AGAGCAGAATAAATGTGAGCCTGA	60.081	41.667	0.00	0.00	0.00	3.86
2088	2150	3.964031	TGTTGCCCAATGGTAGAAAAAGT	59.036	39.130	0.00	0.00	0.00	2.66
2506	2568	3.871594	GAGCAAGTATGGTGTGGACATAC	59.128	47.826	7.33	7.33	46.88	2.39
2546	2608	1.181098	GCAAAGAGGGCAGCAAAGGA	61.181	55.000	0.00	0.00	0.00	3.36
4078	4213	6.479660	CACCAACTGTAATGTTGCTTTGAATT	59.520	34.615	0.00	0.00	44.12	2.17
4103	4238	4.206375	TCACTGGCAATGAGAAAGAACAA	58.794	39.130	0.00	0.00	0.00	2.83
4416	4854	2.842394	CTACAGCACCTGGACCAGCG	62.842	65.000	16.72	11.75	35.51	5.18
4500	4944	1.930371	GCTGCTGCAAAGGGTAAAACG	60.930	52.381	11.11	0.00	39.41	3.60
4769	5213	8.687242	TGGTTGTGTCAAAATACTGTCAAATTA	58.313	29.630	0.00	0.00	0.00	1.40
4996	5938	2.163010	CGACAAAGCCATCAAAGATGCT	59.837	45.455	1.52	0.83	35.08	3.79
5031	6021	3.932710	GTGATGGCTAGATGTCGACAAAA	59.067	43.478	24.13	9.89	0.00	2.44
5037	6027	3.000322	GCTAGATGTCGACAAAACCATCG	60.000	47.826	24.13	6.97	38.91	3.84
5046	6036	2.749621	GACAAAACCATCGAAGATGCCT	59.250	45.455	4.60	0.00	45.12	4.75
5050	6040	5.242838	ACAAAACCATCGAAGATGCCTAAAA	59.757	36.000	4.60	0.00	45.12	1.52
5061	6052	5.514500	AGATGCCTAAAAACCCTAGTGAA	57.486	39.130	0.00	0.00	0.00	3.18

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
0	1	3.854045	GCGAGGATTTCTATCGACCAGTC	60.854	52.174	9.02	0.00	38.72	3.51
1	2	2.034812	GCGAGGATTTCTATCGACCAGT	59.965	50.000	9.02	0.00	38.72	4.00
4	5	2.667137	CTGCGAGGATTTCTATCGACC	58.333	52.381	9.02	0.00	38.72	4.79
5	6	2.055100	GCTGCGAGGATTTCTATCGAC	58.945	52.381	9.02	3.27	38.72	4.20
6	7	1.681264	TGCTGCGAGGATTTCTATCGA	59.319	47.619	9.02	0.00	38.72	3.59
7	8	2.057316	CTGCTGCGAGGATTTCTATCG	58.943	52.381	0.00	0.00	39.40	2.92
8	9	2.411904	CCTGCTGCGAGGATTTCTATC	58.588	52.381	11.25	0.00	34.69	2.08
9	10	1.542108	GCCTGCTGCGAGGATTTCTAT	60.542	52.381	18.30	0.00	34.69	1.98
10	11	0.179073	GCCTGCTGCGAGGATTTCTA	60.179	55.000	18.30	0.00	34.69	2.10
11	12	1.451028	GCCTGCTGCGAGGATTTCT	60.451	57.895	18.30	0.00	34.69	2.52
12	13	1.308069	TTGCCTGCTGCGAGGATTTC	61.308	55.000	18.30	5.01	45.60	2.17
13	14	1.303561	TTGCCTGCTGCGAGGATTT	60.304	52.632	18.30	0.00	45.60	2.17
14	15	2.042831	GTTGCCTGCTGCGAGGATT	61.043	57.895	18.30	0.00	45.60	3.01
15	16	2.437359	GTTGCCTGCTGCGAGGAT	60.437	61.111	18.30	0.00	45.60	3.24
18	19	4.081030	CACGTTGCCTGCTGCGAG	62.081	66.667	11.43	0.00	45.60	5.03
19	20	4.600576	TCACGTTGCCTGCTGCGA	62.601	61.111	11.43	0.00	45.60	5.10
20	21	2.839324	GATTCACGTTGCCTGCTGCG	62.839	60.000	0.00	4.85	45.60	5.18
21	22	1.154150	GATTCACGTTGCCTGCTGC	60.154	57.895	0.00	0.00	41.77	5.25
22	23	1.133253	CGATTCACGTTGCCTGCTG	59.867	57.895	0.00	0.00	37.22	4.41
23	24	2.680913	GCGATTCACGTTGCCTGCT	61.681	57.895	0.00	0.00	44.60	4.24
24	25	1.358725	TAGCGATTCACGTTGCCTGC	61.359	55.000	0.00	0.00	44.60	4.85
25	26	0.370273	GTAGCGATTCACGTTGCCTG	59.630	55.000	0.00	0.00	44.60	4.85
26	27	0.246635	AGTAGCGATTCACGTTGCCT	59.753	50.000	0.00	0.00	44.60	4.75
27	28	1.917273	TAGTAGCGATTCACGTTGCC	58.083	50.000	0.00	0.00	44.60	4.52
28	29	3.984018	TTTAGTAGCGATTCACGTTGC	57.016	42.857	0.00	0.00	44.60	4.17
47	48	1.607148	GCTTGGACCTACTGCGTTTTT	59.393	47.619	0.00	0.00	0.00	1.94
48	49	1.235724	GCTTGGACCTACTGCGTTTT	58.764	50.000	0.00	0.00	0.00	2.43
49	50	0.605589	GGCTTGGACCTACTGCGTTT	60.606	55.000	0.00	0.00	0.00	3.60
50	51	1.003718	GGCTTGGACCTACTGCGTT	60.004	57.895	0.00	0.00	0.00	4.84
51	52	1.764571	TTGGCTTGGACCTACTGCGT	61.765	55.000	0.00	0.00	0.00	5.24
52	53	1.003839	TTGGCTTGGACCTACTGCG	60.004	57.895	0.00	0.00	0.00	5.18
53	54	0.678048	CCTTGGCTTGGACCTACTGC	60.678	60.000	0.00	0.00	0.00	4.40
54	55	0.678048	GCCTTGGCTTGGACCTACTG	60.678	60.000	4.11	0.00	0.00	2.74
55	56	1.685820	GCCTTGGCTTGGACCTACT	59.314	57.895	4.11	0.00	0.00	2.57
56	57	1.745489	CGCCTTGGCTTGGACCTAC	60.745	63.158	10.12	0.00	0.00	3.18
57	58	2.668632	CGCCTTGGCTTGGACCTA	59.331	61.111	10.12	0.00	0.00	3.08
60	61	3.435186	GAGCGCCTTGGCTTGGAC	61.435	66.667	2.29	0.00	44.93	4.02
74	75	4.681978	ACCCTGACGTTGCCGAGC	62.682	66.667	0.00	0.00	37.88	5.03
75	76	2.432628	GACCCTGACGTTGCCGAG	60.433	66.667	0.00	0.00	37.88	4.63
76	77	3.998672	GGACCCTGACGTTGCCGA	61.999	66.667	0.00	0.00	37.88	5.54
80	81	4.657824	ACGCGGACCCTGACGTTG	62.658	66.667	12.47	0.00	34.62	4.10
81	82	4.353437	GACGCGGACCCTGACGTT	62.353	66.667	12.47	0.00	39.16	3.99
84	85	4.477975	CTCGACGCGGACCCTGAC	62.478	72.222	12.47	0.00	0.00	3.51
103	104	4.759096	GGTGCGTGATGGCGTTGC	62.759	66.667	0.00	0.00	35.06	4.17
104	105	4.444024	CGGTGCGTGATGGCGTTG	62.444	66.667	0.00	0.00	35.06	4.10
109	110	4.838152	CCTCCCGGTGCGTGATGG	62.838	72.222	0.00	0.00	0.00	3.51
110	111	3.309436	TTCCTCCCGGTGCGTGATG	62.309	63.158	0.00	0.00	0.00	3.07
111	112	3.000819	TTCCTCCCGGTGCGTGAT	61.001	61.111	0.00	0.00	0.00	3.06
112	113	3.691342	CTTCCTCCCGGTGCGTGA	61.691	66.667	0.00	0.00	0.00	4.35
113	114	3.649277	CTCTTCCTCCCGGTGCGTG	62.649	68.421	0.00	0.00	0.00	5.34
114	115	3.382832	CTCTTCCTCCCGGTGCGT	61.383	66.667	0.00	0.00	0.00	5.24
115	116	4.148825	CCTCTTCCTCCCGGTGCG	62.149	72.222	0.00	0.00	0.00	5.34
116	117	3.003763	ACCTCTTCCTCCCGGTGC	61.004	66.667	0.00	0.00	0.00	5.01
117	118	1.608717	CTGACCTCTTCCTCCCGGTG	61.609	65.000	0.00	0.00	0.00	4.94
118	119	1.305381	CTGACCTCTTCCTCCCGGT	60.305	63.158	0.00	0.00	0.00	5.28
119	120	2.726351	GCTGACCTCTTCCTCCCGG	61.726	68.421	0.00	0.00	0.00	5.73
120	121	2.896443	GCTGACCTCTTCCTCCCG	59.104	66.667	0.00	0.00	0.00	5.14
121	122	2.726351	CCGCTGACCTCTTCCTCCC	61.726	68.421	0.00	0.00	0.00	4.30
122	123	2.726351	CCCGCTGACCTCTTCCTCC	61.726	68.421	0.00	0.00	0.00	4.30
123	124	1.671901	CTCCCGCTGACCTCTTCCTC	61.672	65.000	0.00	0.00	0.00	3.71
124	125	1.684049	CTCCCGCTGACCTCTTCCT	60.684	63.158	0.00	0.00	0.00	3.36
125	126	0.683504	TACTCCCGCTGACCTCTTCC	60.684	60.000	0.00	0.00	0.00	3.46
126	127	1.183549	TTACTCCCGCTGACCTCTTC	58.816	55.000	0.00	0.00	0.00	2.87
127	128	1.640917	TTTACTCCCGCTGACCTCTT	58.359	50.000	0.00	0.00	0.00	2.85
128	129	1.867363	ATTTACTCCCGCTGACCTCT	58.133	50.000	0.00	0.00	0.00	3.69
129	130	2.280628	CAATTTACTCCCGCTGACCTC	58.719	52.381	0.00	0.00	0.00	3.85
130	131	1.679032	GCAATTTACTCCCGCTGACCT	60.679	52.381	0.00	0.00	0.00	3.85
131	132	0.733150	GCAATTTACTCCCGCTGACC	59.267	55.000	0.00	0.00	0.00	4.02
132	133	1.398390	CTGCAATTTACTCCCGCTGAC	59.602	52.381	0.00	0.00	0.00	3.51
133	134	1.277842	TCTGCAATTTACTCCCGCTGA	59.722	47.619	0.00	0.00	0.00	4.26
134	135	1.737838	TCTGCAATTTACTCCCGCTG	58.262	50.000	0.00	0.00	0.00	5.18
135	136	2.489938	TTCTGCAATTTACTCCCGCT	57.510	45.000	0.00	0.00	0.00	5.52
136	137	3.242518	GTTTTCTGCAATTTACTCCCGC	58.757	45.455	0.00	0.00	0.00	6.13
137	138	3.254657	TGGTTTTCTGCAATTTACTCCCG	59.745	43.478	0.00	0.00	0.00	5.14
229	231	9.369904	GATCAGTGGTATTTGCAAATTGTTTAT	57.630	29.630	28.45	13.92	0.00	1.40
624	669	1.976474	GGATTTGCCTTCACCGCCA	60.976	57.895	0.00	0.00	0.00	5.69
2088	2150	6.212388	ACCTCTTCTTCATCTTCTTTGCTCTA	59.788	38.462	0.00	0.00	0.00	2.43
2371	2433	8.410673	ACTTTAGTGTTCTCTGACATAGAAGA	57.589	34.615	3.65	0.32	33.75	2.87
2506	2568	1.473677	CCTGTATGCCATGTGTGTTGG	59.526	52.381	0.00	0.00	37.31	3.77
2546	2608	4.974645	TTCTGGTCTCCTAACACAACAT	57.025	40.909	0.00	0.00	0.00	2.71
2776	2838	7.485913	CACATGAAATCAAACATTAGTAGCACC	59.514	37.037	0.00	0.00	0.00	5.01
3462	3594	4.030913	CCCTGACATCTAGAACCCACTTA	58.969	47.826	0.00	0.00	0.00	2.24
4078	4213	4.290711	TCTTTCTCATTGCCAGTGATGA	57.709	40.909	0.00	0.00	0.00	2.92
4103	4238	2.578021	AGGACATTGGTTACCTCATGCT	59.422	45.455	12.17	0.31	0.00	3.79
4500	4944	5.300792	AGCAGCTGAAGATCTAGTTACTACC	59.699	44.000	20.43	0.00	0.00	3.18
4769	5213	0.396435	TCATCACAACCGAACTGGCT	59.604	50.000	0.00	0.00	43.94	4.75
4935	5385	7.004086	CCTAGGGTATTTTGGCATCTTTGATA	58.996	38.462	0.00	0.00	0.00	2.15
4936	5386	5.835280	CCTAGGGTATTTTGGCATCTTTGAT	59.165	40.000	0.00	0.00	0.00	2.57
4937	5387	5.200483	CCTAGGGTATTTTGGCATCTTTGA	58.800	41.667	0.00	0.00	0.00	2.69
4938	5388	4.956075	ACCTAGGGTATTTTGGCATCTTTG	59.044	41.667	14.81	0.00	32.11	2.77
4939	5389	4.956075	CACCTAGGGTATTTTGGCATCTTT	59.044	41.667	14.81	0.00	32.11	2.52
4940	5390	4.229582	TCACCTAGGGTATTTTGGCATCTT	59.770	41.667	14.81	0.00	32.11	2.40
4941	5391	3.785887	TCACCTAGGGTATTTTGGCATCT	59.214	43.478	14.81	0.00	32.11	2.90
4942	5392	4.164843	TCACCTAGGGTATTTTGGCATC	57.835	45.455	14.81	0.00	32.11	3.91
4943	5393	4.473444	CATCACCTAGGGTATTTTGGCAT	58.527	43.478	14.81	0.00	32.11	4.40
4944	5394	3.372566	CCATCACCTAGGGTATTTTGGCA	60.373	47.826	14.81	0.00	32.11	4.92
4945	5395	3.222603	CCATCACCTAGGGTATTTTGGC	58.777	50.000	14.81	0.00	32.11	4.52
4946	5396	3.117512	AGCCATCACCTAGGGTATTTTGG	60.118	47.826	14.81	11.64	32.11	3.28
4947	5397	4.170468	AGCCATCACCTAGGGTATTTTG	57.830	45.455	14.81	0.59	32.11	2.44
4948	5398	5.224441	TCTAGCCATCACCTAGGGTATTTT	58.776	41.667	14.81	0.00	37.26	1.82
4949	5399	4.827789	TCTAGCCATCACCTAGGGTATTT	58.172	43.478	14.81	0.00	37.26	1.40
4950	5400	4.487282	TCTAGCCATCACCTAGGGTATT	57.513	45.455	14.81	0.00	37.26	1.89
4951	5401	4.202836	ACATCTAGCCATCACCTAGGGTAT	60.203	45.833	14.81	2.76	37.26	2.73
4952	5402	3.142217	ACATCTAGCCATCACCTAGGGTA	59.858	47.826	14.81	0.00	36.86	3.69
4953	5403	2.090494	ACATCTAGCCATCACCTAGGGT	60.090	50.000	14.81	0.00	39.33	4.34
4954	5404	2.564947	GACATCTAGCCATCACCTAGGG	59.435	54.545	14.81	2.03	34.43	3.53
4996	5938	6.387127	TCTAGCCATCACCTAGGGTATTTTA	58.613	40.000	14.81	0.00	37.26	1.52
5031	6021	3.694566	GGTTTTTAGGCATCTTCGATGGT	59.305	43.478	6.04	0.00	0.00	3.55
5037	6027	5.497474	TCACTAGGGTTTTTAGGCATCTTC	58.503	41.667	0.00	0.00	0.00	2.87
5061	6052	2.301870	TGGTTTTGTCGACATCTAGCCT	59.698	45.455	20.80	0.00	0.00	4.58

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.