AutoCloner

Multiple sequence alignment - TraesCS6D01G195100

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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	TraesCS6D01G195100	chr6D	100.000	5997	0	0	1	5997	270687328	270693324	0.000000e+00	11075.0
1	TraesCS6D01G195100	chr6D	99.804	5096	6	1	71	5162	270585423	270590518	0.000000e+00	9352.0
2	TraesCS6D01G195100	chr6D	98.607	359	4	1	5640	5997	270590831	270591189	8.480000e-178	634.0
3	TraesCS6D01G195100	chr6D	98.276	174	3	0	2012	2185	392896968	392897141	7.550000e-79	305.0
4	TraesCS6D01G195100	chr6D	97.333	150	4	0	5331	5480	270590689	270590838	7.710000e-64	255.0
5	TraesCS6D01G195100	chr6D	97.345	113	1	1	5202	5314	270590519	270590629	2.210000e-44	191.0
6	TraesCS6D01G195100	chr6D	98.305	59	1	0	1	59	270649736	270649794	2.960000e-18	104.0
7	TraesCS6D01G195100	chr6D	96.610	59	2	0	1	59	219161969	219162027	1.380000e-16	99.0
8	TraesCS6D01G195100	chr6D	96.610	59	2	0	1	59	233470164	233470222	1.380000e-16	99.0
9	TraesCS6D01G195100	chr6A	96.624	2962	53	12	2181	5123	386893863	386890930	0.000000e+00	4872.0
10	TraesCS6D01G195100	chr6A	98.294	1114	12	2	909	2022	386894970	386893864	0.000000e+00	1945.0
11	TraesCS6D01G195100	chr6A	99.690	646	2	0	71	716	386895807	386895162	0.000000e+00	1182.0
12	TraesCS6D01G195100	chr6A	80.380	790	81	37	5143	5874	386890942	386890169	3.180000e-147	532.0
13	TraesCS6D01G195100	chr6B	96.798	1655	43	4	3479	5123	423191248	423189594	0.000000e+00	2754.0
14	TraesCS6D01G195100	chr6B	96.661	1198	29	6	2365	3551	423192451	423191254	0.000000e+00	1980.0
15	TraesCS6D01G195100	chr6B	92.958	923	49	12	702	1614	423194366	423193450	0.000000e+00	1330.0
16	TraesCS6D01G195100	chr6B	92.488	639	44	4	71	706	423200916	423200279	0.000000e+00	911.0
17	TraesCS6D01G195100	chr6B	80.736	815	76	41	5120	5874	423189513	423188720	1.460000e-155	560.0
18	TraesCS6D01G195100	chr6B	91.283	413	27	4	1616	2022	423193417	423193008	6.790000e-154	555.0
19	TraesCS6D01G195100	chr6B	92.784	194	9	4	2180	2368	423193013	423192820	5.920000e-70	276.0
20	TraesCS6D01G195100	chr2A	94.377	1405	36	10	2365	3758	734976659	734975287	0.000000e+00	2117.0
21	TraesCS6D01G195100	chr2A	77.778	234	35	15	1500	1720	9138773	9138544	1.750000e-25	128.0
22	TraesCS6D01G195100	chr2A	87.654	81	9	1	1499	1578	16835802	16835882	6.400000e-15	93.5
23	TraesCS6D01G195100	chr2D	96.341	1230	24	3	71	1294	630684734	630683520	0.000000e+00	2002.0
24	TraesCS6D01G195100	chr3D	89.950	398	30	5	3345	3732	419585217	419584820	6.940000e-139	505.0
25	TraesCS6D01G195100	chr3D	93.469	245	16	0	3488	3732	459884672	459884428	1.230000e-96	364.0
26	TraesCS6D01G195100	chrUn	93.469	245	16	0	3488	3732	425657896	425658140	1.230000e-96	364.0
27	TraesCS6D01G195100	chr1D	93.469	245	16	0	3488	3732	156283767	156284011	1.230000e-96	364.0
28	TraesCS6D01G195100	chr1D	92.653	245	18	0	3488	3732	11357652	11357896	2.660000e-93	353.0
29	TraesCS6D01G195100	chr1D	98.235	170	3	0	2015	2184	331539433	331539264	1.260000e-76	298.0
30	TraesCS6D01G195100	chr1D	96.610	59	2	0	1	59	342764982	342764924	1.380000e-16	99.0
31	TraesCS6D01G195100	chr4D	97.727	176	2	2	2019	2192	477898795	477898970	9.770000e-78	302.0
32	TraesCS6D01G195100	chr4D	98.810	168	2	0	2019	2186	75782217	75782050	3.510000e-77	300.0
33	TraesCS6D01G195100	chr4D	94.709	189	7	3	2019	2206	46028701	46028515	2.110000e-74	291.0
34	TraesCS6D01G195100	chr4D	96.610	59	2	0	1	59	41889487	41889545	1.380000e-16	99.0
35	TraesCS6D01G195100	chr4D	96.610	59	2	0	1	59	346061510	346061568	1.380000e-16	99.0
36	TraesCS6D01G195100	chr2B	98.817	169	2	0	2019	2187	174794822	174794990	9.770000e-78	302.0
37	TraesCS6D01G195100	chr1B	98.246	171	3	0	2019	2189	628050851	628050681	3.510000e-77	300.0
38	TraesCS6D01G195100	chr1B	93.717	191	10	2	2016	2205	278469371	278469560	9.840000e-73	285.0
39	TraesCS6D01G195100	chr5B	88.971	136	11	4	3332	3466	509466949	509467081	1.340000e-36	165.0
40	TraesCS6D01G195100	chr5B	76.030	267	38	19	1509	1757	414830337	414830079	1.370000e-21	115.0
41	TraesCS6D01G195100	chr4B	91.379	116	8	2	2458	2572	178352851	178352965	2.240000e-34	158.0
42	TraesCS6D01G195100	chr4B	87.640	89	7	4	1506	1592	93286439	93286353	3.820000e-17	100.0
43	TraesCS6D01G195100	chr5A	79.878	164	26	7	1492	1650	314672223	314672062	4.910000e-21	113.0
44	TraesCS6D01G195100	chr5D	96.610	59	2	0	1	59	119231169	119231111	1.380000e-16	99.0
45	TraesCS6D01G195100	chr5D	96.610	59	2	0	1	59	352179183	352179241	1.380000e-16	99.0
46	TraesCS6D01G195100	chr5D	96.610	59	2	0	1	59	534131817	534131759	1.380000e-16	99.0
47	TraesCS6D01G195100	chr4A	87.356	87	8	3	1508	1592	533449010	533449095	4.950000e-16	97.1
48	TraesCS6D01G195100	chr7B	82.051	117	12	9	1492	1604	506016921	506017032	2.300000e-14	91.6

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	TraesCS6D01G195100	chr6D	270687328	270693324	5996	False	11075.00	11075	100.00000	1	5997	1	chr6D.!!$F4	5996
1	TraesCS6D01G195100	chr6D	270585423	270591189	5766	False	2608.00	9352	98.27225	71	5997	4	chr6D.!!$F6	5926
2	TraesCS6D01G195100	chr6A	386890169	386895807	5638	True	2132.75	4872	93.74700	71	5874	4	chr6A.!!$R1	5803
3	TraesCS6D01G195100	chr6B	423188720	423194366	5646	True	1242.50	2754	91.87000	702	5874	6	chr6B.!!$R2	5172
4	TraesCS6D01G195100	chr6B	423200279	423200916	637	True	911.00	911	92.48800	71	706	1	chr6B.!!$R1	635
5	TraesCS6D01G195100	chr2A	734975287	734976659	1372	True	2117.00	2117	94.37700	2365	3758	1	chr2A.!!$R2	1393
6	TraesCS6D01G195100	chr2D	630683520	630684734	1214	True	2002.00	2002	96.34100	71	1294	1	chr2D.!!$R1	1223

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	Hairpin	End Stability	Orientation
31	32	0.106819	GCTCCAGATGCCTTCCATGT	60.107	55.0	33.29	3.21	F
39	40	0.597568	TGCCTTCCATGTTTTGCGAG	59.402	50.0	0.00	5.03	F
40	41	0.598065	GCCTTCCATGTTTTGCGAGT	59.402	50.0	0.00	4.18	F

Position	MSA Position	Penalty	Sequence	TM	GC	Hairpin	End Stability	Orientation
2027	2105	9.907576	CTCTAGCAAGACAAATATTTAAGAACG	57.092	33.333	0.00	3.95	R
4965	5541	2.724454	TCGAGCTTAGAAGGTAGTGCT	58.276	47.619	36.78	4.40	R
5188	5845	4.876107	CCGAAGCAATAGGACAACAGTTAT	59.124	41.667	0.00	1.89	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
17	18	3.691342	CCCAAGACCGACGCTCCA	61.691	66.667	0.00	0.00	0.00	3.86
18	19	2.125912	CCAAGACCGACGCTCCAG	60.126	66.667	0.00	0.00	0.00	3.86
19	20	2.636412	CCAAGACCGACGCTCCAGA	61.636	63.158	0.00	0.00	0.00	3.86
20	21	1.513158	CAAGACCGACGCTCCAGAT	59.487	57.895	0.00	0.00	0.00	2.90
21	22	0.803768	CAAGACCGACGCTCCAGATG	60.804	60.000	0.00	0.00	0.00	2.90
22	23	2.564553	AAGACCGACGCTCCAGATGC	62.565	60.000	0.00	0.00	0.00	3.91
23	24	4.148825	ACCGACGCTCCAGATGCC	62.149	66.667	0.00	0.00	0.00	4.40
24	25	3.842923	CCGACGCTCCAGATGCCT	61.843	66.667	0.00	0.00	0.00	4.75
25	26	2.185350	CGACGCTCCAGATGCCTT	59.815	61.111	0.00	0.00	0.00	4.35
26	27	1.880340	CGACGCTCCAGATGCCTTC	60.880	63.158	0.00	0.00	0.00	3.46
27	28	1.522580	GACGCTCCAGATGCCTTCC	60.523	63.158	0.00	0.00	0.00	3.46
28	29	2.244117	GACGCTCCAGATGCCTTCCA	62.244	60.000	0.00	0.00	0.00	3.53
29	30	1.147824	CGCTCCAGATGCCTTCCAT	59.852	57.895	0.00	0.00	36.70	3.41
30	31	1.164662	CGCTCCAGATGCCTTCCATG	61.165	60.000	0.00	0.00	33.29	3.66
31	32	0.106819	GCTCCAGATGCCTTCCATGT	60.107	55.000	0.00	0.00	33.29	3.21
32	33	1.684248	GCTCCAGATGCCTTCCATGTT	60.684	52.381	0.00	0.00	33.29	2.71
33	34	2.731572	CTCCAGATGCCTTCCATGTTT	58.268	47.619	0.00	0.00	33.29	2.83
34	35	3.094572	CTCCAGATGCCTTCCATGTTTT	58.905	45.455	0.00	0.00	33.29	2.43
35	36	2.827322	TCCAGATGCCTTCCATGTTTTG	59.173	45.455	0.00	0.00	33.29	2.44
36	37	2.613691	CAGATGCCTTCCATGTTTTGC	58.386	47.619	0.00	0.00	33.29	3.68
37	38	1.203052	AGATGCCTTCCATGTTTTGCG	59.797	47.619	0.00	0.00	33.29	4.85
38	39	1.202114	GATGCCTTCCATGTTTTGCGA	59.798	47.619	0.00	0.00	33.29	5.10
39	40	0.597568	TGCCTTCCATGTTTTGCGAG	59.402	50.000	0.00	0.00	0.00	5.03
40	41	0.598065	GCCTTCCATGTTTTGCGAGT	59.402	50.000	0.00	0.00	0.00	4.18
41	42	1.401539	GCCTTCCATGTTTTGCGAGTC	60.402	52.381	0.00	0.00	0.00	3.36
42	43	1.879380	CCTTCCATGTTTTGCGAGTCA	59.121	47.619	0.00	0.00	0.00	3.41
43	44	2.095567	CCTTCCATGTTTTGCGAGTCAG	60.096	50.000	0.00	0.00	0.00	3.51
44	45	0.874390	TCCATGTTTTGCGAGTCAGC	59.126	50.000	0.00	0.00	37.71	4.26
45	46	0.877071	CCATGTTTTGCGAGTCAGCT	59.123	50.000	8.13	0.00	38.13	4.24
46	47	1.400629	CCATGTTTTGCGAGTCAGCTG	60.401	52.381	7.63	7.63	38.13	4.24
47	48	1.265095	CATGTTTTGCGAGTCAGCTGT	59.735	47.619	14.67	0.00	38.13	4.40
48	49	0.657312	TGTTTTGCGAGTCAGCTGTG	59.343	50.000	14.67	3.70	38.13	3.66
49	50	0.657840	GTTTTGCGAGTCAGCTGTGT	59.342	50.000	14.67	1.40	38.13	3.72
50	51	1.064060	GTTTTGCGAGTCAGCTGTGTT	59.936	47.619	14.67	0.00	38.13	3.32
51	52	2.232756	TTTGCGAGTCAGCTGTGTTA	57.767	45.000	14.67	0.00	38.13	2.41
52	53	2.455674	TTGCGAGTCAGCTGTGTTAT	57.544	45.000	14.67	0.00	38.13	1.89
53	54	2.455674	TGCGAGTCAGCTGTGTTATT	57.544	45.000	14.67	0.00	38.13	1.40
54	55	2.766313	TGCGAGTCAGCTGTGTTATTT	58.234	42.857	14.67	0.00	38.13	1.40
55	56	2.480037	TGCGAGTCAGCTGTGTTATTTG	59.520	45.455	14.67	0.00	38.13	2.32
56	57	2.480419	GCGAGTCAGCTGTGTTATTTGT	59.520	45.455	14.67	0.00	0.00	2.83
57	58	3.058914	GCGAGTCAGCTGTGTTATTTGTT	60.059	43.478	14.67	0.00	0.00	2.83
58	59	4.554723	GCGAGTCAGCTGTGTTATTTGTTT	60.555	41.667	14.67	0.00	0.00	2.83
59	60	5.510671	CGAGTCAGCTGTGTTATTTGTTTT	58.489	37.500	14.67	0.00	0.00	2.43
60	61	5.621228	CGAGTCAGCTGTGTTATTTGTTTTC	59.379	40.000	14.67	0.00	0.00	2.29
61	62	5.831997	AGTCAGCTGTGTTATTTGTTTTCC	58.168	37.500	14.67	0.00	0.00	3.13
62	63	4.982295	GTCAGCTGTGTTATTTGTTTTCCC	59.018	41.667	14.67	0.00	0.00	3.97
63	64	4.038642	TCAGCTGTGTTATTTGTTTTCCCC	59.961	41.667	14.67	0.00	0.00	4.81
64	65	3.964031	AGCTGTGTTATTTGTTTTCCCCA	59.036	39.130	0.00	0.00	0.00	4.96
65	66	4.592778	AGCTGTGTTATTTGTTTTCCCCAT	59.407	37.500	0.00	0.00	0.00	4.00
66	67	5.071653	AGCTGTGTTATTTGTTTTCCCCATT	59.928	36.000	0.00	0.00	0.00	3.16
67	68	6.268847	AGCTGTGTTATTTGTTTTCCCCATTA	59.731	34.615	0.00	0.00	0.00	1.90
68	69	7.038373	AGCTGTGTTATTTGTTTTCCCCATTAT	60.038	33.333	0.00	0.00	0.00	1.28
69	70	7.606073	GCTGTGTTATTTGTTTTCCCCATTATT	59.394	33.333	0.00	0.00	0.00	1.40
2027	2105	5.873146	AAGCATAAAGTAGTACTCCCTCC	57.127	43.478	2.58	0.00	0.00	4.30
4965	5541	1.792757	ATTCCAAGGCTGGCACCAGA	61.793	55.000	20.92	0.00	46.30	3.86
5337	6027	1.714899	GACACCCGATTTGGATGCCG	61.715	60.000	0.00	0.00	42.00	5.69
5360	6072	1.961277	CACGTGGCTCCACTTCCAC	60.961	63.158	16.15	1.54	46.95	4.02
5489	6201	2.512515	GAGCGGCCACTCCATCAC	60.513	66.667	9.82	0.00	34.01	3.06
5490	6202	3.315142	GAGCGGCCACTCCATCACA	62.315	63.158	9.82	0.00	34.01	3.58
5492	6204	2.665000	CGGCCACTCCATCACAGT	59.335	61.111	2.24	0.00	34.01	3.55
5495	6207	0.326264	GGCCACTCCATCACAGTCTT	59.674	55.000	0.00	0.00	34.01	3.01
5498	6210	2.693069	CCACTCCATCACAGTCTTGAC	58.307	52.381	0.00	0.00	0.00	3.18
5503	6215	1.446907	CATCACAGTCTTGACCTGCC	58.553	55.000	0.00	0.00	33.09	4.85
5512	6224	0.957395	CTTGACCTGCCGCATGAACT	60.957	55.000	0.00	0.00	0.00	3.01
5535	6279	1.296715	GTTCATGACTGGCCTCCGT	59.703	57.895	3.32	0.00	0.00	4.69
5578	6322	4.025401	CTTGTGCGGCGGTTGGTC	62.025	66.667	9.78	0.00	0.00	4.02
5584	6328	4.016706	CGGCGGTTGGTCCTCCTT	62.017	66.667	0.00	0.00	38.85	3.36
5585	6329	2.359975	GGCGGTTGGTCCTCCTTG	60.360	66.667	0.00	0.00	38.03	3.61
5586	6330	2.430367	GCGGTTGGTCCTCCTTGT	59.570	61.111	0.00	0.00	34.23	3.16
5587	6331	1.671379	GCGGTTGGTCCTCCTTGTC	60.671	63.158	0.00	0.00	34.23	3.18
5588	6332	1.374252	CGGTTGGTCCTCCTTGTCG	60.374	63.158	0.00	0.00	34.23	4.35
5589	6333	1.671379	GGTTGGTCCTCCTTGTCGC	60.671	63.158	0.00	0.00	34.23	5.19
5590	6334	1.671379	GTTGGTCCTCCTTGTCGCC	60.671	63.158	0.00	0.00	34.23	5.54
5591	6335	2.144078	TTGGTCCTCCTTGTCGCCA	61.144	57.895	0.00	0.00	34.23	5.69
5592	6336	2.111999	TTGGTCCTCCTTGTCGCCAG	62.112	60.000	0.00	0.00	34.23	4.85
5593	6337	2.283529	GGTCCTCCTTGTCGCCAGA	61.284	63.158	0.00	0.00	0.00	3.86
5594	6338	1.216710	GTCCTCCTTGTCGCCAGAG	59.783	63.158	0.00	0.00	0.00	3.35
5595	6339	1.984570	TCCTCCTTGTCGCCAGAGG	60.985	63.158	0.00	0.00	46.11	3.69
5596	6340	3.700109	CTCCTTGTCGCCAGAGGA	58.300	61.111	0.00	0.00	37.24	3.71
5597	6341	3.700109	TCCTTGTCGCCAGAGGAG	58.300	61.111	0.00	0.00	34.74	3.69
5598	6342	1.076727	TCCTTGTCGCCAGAGGAGA	59.923	57.895	0.00	0.00	34.74	3.71
5599	6343	0.324738	TCCTTGTCGCCAGAGGAGAT	60.325	55.000	0.00	0.00	34.74	2.75
5600	6344	0.179089	CCTTGTCGCCAGAGGAGATG	60.179	60.000	0.00	0.00	33.47	2.90
5601	6345	0.179089	CTTGTCGCCAGAGGAGATGG	60.179	60.000	0.00	0.00	41.04	3.51
5928	6672	3.036084	CGGTCGCTGTGTCCACAC	61.036	66.667	2.69	2.69	46.59	3.82

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
0	1	3.649277	CTGGAGCGTCGGTCTTGGG	62.649	68.421	22.48	7.93	0.00	4.12
1	2	1.949847	ATCTGGAGCGTCGGTCTTGG	61.950	60.000	22.48	13.14	0.00	3.61
2	3	0.803768	CATCTGGAGCGTCGGTCTTG	60.804	60.000	22.48	15.36	0.00	3.02
3	4	1.513158	CATCTGGAGCGTCGGTCTT	59.487	57.895	22.48	4.49	0.00	3.01
4	5	3.069980	GCATCTGGAGCGTCGGTCT	62.070	63.158	22.48	1.24	0.00	3.85
5	6	2.583593	GCATCTGGAGCGTCGGTC	60.584	66.667	15.95	15.95	0.00	4.79
6	7	4.148825	GGCATCTGGAGCGTCGGT	62.149	66.667	0.00	0.00	0.00	4.69
7	8	3.376935	AAGGCATCTGGAGCGTCGG	62.377	63.158	0.00	0.00	0.00	4.79
8	9	1.880340	GAAGGCATCTGGAGCGTCG	60.880	63.158	0.00	0.00	0.00	5.12
9	10	1.522580	GGAAGGCATCTGGAGCGTC	60.523	63.158	0.00	0.00	0.00	5.19
10	11	1.630126	ATGGAAGGCATCTGGAGCGT	61.630	55.000	0.00	0.00	0.00	5.07
11	12	1.147824	ATGGAAGGCATCTGGAGCG	59.852	57.895	0.00	0.00	0.00	5.03
12	13	0.106819	ACATGGAAGGCATCTGGAGC	60.107	55.000	0.00	0.00	0.00	4.70
13	14	2.431954	AACATGGAAGGCATCTGGAG	57.568	50.000	0.00	0.00	0.00	3.86
14	15	2.827322	CAAAACATGGAAGGCATCTGGA	59.173	45.455	0.00	0.00	0.00	3.86
15	16	2.675889	GCAAAACATGGAAGGCATCTGG	60.676	50.000	0.00	0.00	0.00	3.86
16	17	2.613691	GCAAAACATGGAAGGCATCTG	58.386	47.619	0.00	0.00	0.00	2.90
17	18	1.203052	CGCAAAACATGGAAGGCATCT	59.797	47.619	0.00	0.00	0.00	2.90
18	19	1.202114	TCGCAAAACATGGAAGGCATC	59.798	47.619	0.00	0.00	0.00	3.91
19	20	1.203052	CTCGCAAAACATGGAAGGCAT	59.797	47.619	0.00	0.00	0.00	4.40
20	21	0.597568	CTCGCAAAACATGGAAGGCA	59.402	50.000	0.00	0.00	0.00	4.75
21	22	0.598065	ACTCGCAAAACATGGAAGGC	59.402	50.000	0.00	0.00	0.00	4.35
22	23	1.879380	TGACTCGCAAAACATGGAAGG	59.121	47.619	0.00	0.00	0.00	3.46
23	24	2.666619	GCTGACTCGCAAAACATGGAAG	60.667	50.000	0.00	0.00	0.00	3.46
24	25	1.266718	GCTGACTCGCAAAACATGGAA	59.733	47.619	0.00	0.00	0.00	3.53
25	26	0.874390	GCTGACTCGCAAAACATGGA	59.126	50.000	0.00	0.00	0.00	3.41
26	27	0.877071	AGCTGACTCGCAAAACATGG	59.123	50.000	0.00	0.00	0.00	3.66
27	28	1.265095	ACAGCTGACTCGCAAAACATG	59.735	47.619	23.35	0.00	0.00	3.21
28	29	1.265095	CACAGCTGACTCGCAAAACAT	59.735	47.619	23.35	0.00	0.00	2.71
29	30	0.657312	CACAGCTGACTCGCAAAACA	59.343	50.000	23.35	0.00	0.00	2.83
30	31	0.657840	ACACAGCTGACTCGCAAAAC	59.342	50.000	23.35	0.00	0.00	2.43
31	32	1.378531	AACACAGCTGACTCGCAAAA	58.621	45.000	23.35	0.00	0.00	2.44
32	33	2.232756	TAACACAGCTGACTCGCAAA	57.767	45.000	23.35	0.00	0.00	3.68
33	34	2.455674	ATAACACAGCTGACTCGCAA	57.544	45.000	23.35	0.00	0.00	4.85
34	35	2.455674	AATAACACAGCTGACTCGCA	57.544	45.000	23.35	0.04	0.00	5.10
35	36	2.480419	ACAAATAACACAGCTGACTCGC	59.520	45.455	23.35	0.00	0.00	5.03
36	37	4.732285	AACAAATAACACAGCTGACTCG	57.268	40.909	23.35	8.16	0.00	4.18
37	38	5.915196	GGAAAACAAATAACACAGCTGACTC	59.085	40.000	23.35	0.00	0.00	3.36
38	39	5.221244	GGGAAAACAAATAACACAGCTGACT	60.221	40.000	23.35	6.45	0.00	3.41
39	40	4.982295	GGGAAAACAAATAACACAGCTGAC	59.018	41.667	23.35	0.00	0.00	3.51
40	41	4.038642	GGGGAAAACAAATAACACAGCTGA	59.961	41.667	23.35	0.00	0.00	4.26
41	42	4.202202	TGGGGAAAACAAATAACACAGCTG	60.202	41.667	13.48	13.48	0.00	4.24
42	43	3.964031	TGGGGAAAACAAATAACACAGCT	59.036	39.130	0.00	0.00	0.00	4.24
43	44	4.329462	TGGGGAAAACAAATAACACAGC	57.671	40.909	0.00	0.00	0.00	4.40
44	45	9.500785	AAATAATGGGGAAAACAAATAACACAG	57.499	29.630	0.00	0.00	0.00	3.66
59	60	9.400208	TGGAAGATATACTGTAAATAATGGGGA	57.600	33.333	0.00	0.00	0.00	4.81
2027	2105	9.907576	CTCTAGCAAGACAAATATTTAAGAACG	57.092	33.333	0.00	0.00	0.00	3.95
4965	5541	2.724454	TCGAGCTTAGAAGGTAGTGCT	58.276	47.619	0.00	0.00	36.78	4.40
5188	5845	4.876107	CCGAAGCAATAGGACAACAGTTAT	59.124	41.667	0.00	0.00	0.00	1.89
5192	5849	2.009774	CCCGAAGCAATAGGACAACAG	58.990	52.381	0.00	0.00	0.00	3.16
5376	6088	0.911045	TGAAGCAGGATCAGCCCTCA	60.911	55.000	5.84	6.70	37.37	3.86
5485	6197	0.036952	CGGCAGGTCAAGACTGTGAT	60.037	55.000	0.00	0.00	38.22	3.06
5489	6201	1.376424	ATGCGGCAGGTCAAGACTG	60.376	57.895	9.25	0.00	38.95	3.51
5490	6202	1.376424	CATGCGGCAGGTCAAGACT	60.376	57.895	9.25	0.00	0.00	3.24
5492	6204	0.955428	GTTCATGCGGCAGGTCAAGA	60.955	55.000	14.79	0.00	0.00	3.02
5495	6207	1.375908	GAGTTCATGCGGCAGGTCA	60.376	57.895	14.79	0.00	0.00	4.02
5498	6210	1.769098	CGATGAGTTCATGCGGCAGG	61.769	60.000	8.58	8.58	36.57	4.85
5512	6224	0.904649	AGGCCAGTCATGAACGATGA	59.095	50.000	5.01	0.00	38.87	2.92
5521	6233	2.362369	CCTCACGGAGGCCAGTCAT	61.362	63.158	5.01	0.00	43.29	3.06
5572	6316	1.671379	GGCGACAAGGAGGACCAAC	60.671	63.158	0.00	0.00	38.94	3.77
5573	6317	2.111999	CTGGCGACAAGGAGGACCAA	62.112	60.000	0.00	0.00	42.06	3.67
5574	6318	2.525629	TGGCGACAAGGAGGACCA	60.526	61.111	0.00	0.00	37.44	4.02
5575	6319	2.232298	CTCTGGCGACAAGGAGGACC	62.232	65.000	0.00	0.00	42.06	4.46
5576	6320	1.216710	CTCTGGCGACAAGGAGGAC	59.783	63.158	0.00	0.00	42.06	3.85
5577	6321	3.700109	CTCTGGCGACAAGGAGGA	58.300	61.111	0.00	0.00	42.06	3.71
5578	6322	2.581354	CCTCTGGCGACAAGGAGG	59.419	66.667	11.86	11.86	43.77	4.30
5579	6323	3.700109	TCCTCTGGCGACAAGGAG	58.300	61.111	15.60	9.00	40.43	3.69
5580	6324	0.324738	ATCTCCTCTGGCGACAAGGA	60.325	55.000	17.72	17.72	41.92	3.36
5581	6325	0.179089	CATCTCCTCTGGCGACAAGG	60.179	60.000	11.91	11.91	42.06	3.61
5582	6326	0.179089	CCATCTCCTCTGGCGACAAG	60.179	60.000	0.00	0.00	42.06	3.16
5583	6327	1.900351	CCATCTCCTCTGGCGACAA	59.100	57.895	0.00	0.00	42.06	3.18
5584	6328	3.621225	CCATCTCCTCTGGCGACA	58.379	61.111	0.00	0.00	39.59	4.35
5596	6340	2.848694	TCCAAGAAGGAGATTGCCATCT	59.151	45.455	0.00	0.00	43.07	2.90
5597	6341	3.287867	TCCAAGAAGGAGATTGCCATC	57.712	47.619	0.00	0.00	43.07	3.51
5888	6632	2.509336	CCTACTCCAGCCGTTGCG	60.509	66.667	0.00	0.00	44.33	4.85
5928	6672	2.230994	TAGGGACAGCGCTGCTTCAG	62.231	60.000	36.28	13.26	36.40	3.02

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.