AutoCloner

Multiple sequence alignment - TraesCS2B01G593800

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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	TraesCS2B01G593800	chr2B	100.000	2747	0	0	1	2747	778477961	778475215	0.000000e+00	5073.0
1	TraesCS2B01G593800	chr2B	96.217	2009	51	11	757	2747	778450576	778452577	0.000000e+00	3265.0
2	TraesCS2B01G593800	chr2B	97.612	670	15	1	88	756	778420521	778421190	0.000000e+00	1147.0
3	TraesCS2B01G593800	chr2B	83.778	937	117	21	824	1746	778293426	778292511	0.000000e+00	856.0
4	TraesCS2B01G593800	chr2B	80.576	973	168	11	803	1762	778778959	778779923	0.000000e+00	730.0
5	TraesCS2B01G593800	chr2A	89.727	2346	131	37	472	2747	778562988	778565293	0.000000e+00	2896.0
6	TraesCS2B01G593800	chr2A	83.333	876	118	16	897	1761	778457598	778456740	0.000000e+00	784.0
7	TraesCS2B01G593800	chr2A	87.113	582	74	1	2167	2747	138922381	138922962	0.000000e+00	658.0
8	TraesCS2B01G593800	chr2A	92.604	338	17	4	129	462	778552027	778552360	1.910000e-131	479.0
9	TraesCS2B01G593800	chrUn	81.762	965	138	22	812	1761	217850428	217849487	0.000000e+00	773.0
10	TraesCS2B01G593800	chrUn	81.762	965	138	22	812	1761	331471440	331470499	0.000000e+00	773.0
11	TraesCS2B01G593800	chrUn	82.692	572	85	11	809	1374	345946492	345947055	1.900000e-136	496.0
12	TraesCS2B01G593800	chrUn	82.692	572	85	11	809	1374	345948882	345949445	1.900000e-136	496.0
13	TraesCS2B01G593800	chrUn	82.692	572	85	11	809	1374	436326431	436326994	1.900000e-136	496.0
14	TraesCS2B01G593800	chrUn	79.587	387	63	10	1368	1747	345948116	345948493	2.100000e-66	263.0
15	TraesCS2B01G593800	chrUn	79.587	387	63	10	1368	1747	345950506	345950883	2.100000e-66	263.0
16	TraesCS2B01G593800	chrUn	79.487	390	64	10	1368	1750	447184094	447183714	2.100000e-66	263.0
17	TraesCS2B01G593800	chrUn	94.286	105	6	0	1	105	278087255	278087151	7.870000e-36	161.0
18	TraesCS2B01G593800	chr4A	87.629	582	71	1	2167	2747	69306108	69305527	0.000000e+00	675.0
19	TraesCS2B01G593800	chr3D	87.500	584	68	5	2167	2747	56362592	56362011	0.000000e+00	669.0
20	TraesCS2B01G593800	chr3D	94.792	96	5	0	2	97	607570337	607570432	1.700000e-32	150.0
21	TraesCS2B01G593800	chr3D	93.878	98	6	0	2	99	517156263	517156360	6.130000e-32	148.0
22	TraesCS2B01G593800	chr1B	87.457	582	72	1	2167	2747	453521965	453522546	0.000000e+00	669.0
23	TraesCS2B01G593800	chr3B	87.285	582	71	3	2167	2747	12765071	12765650	0.000000e+00	662.0
24	TraesCS2B01G593800	chr7A	86.927	589	75	2	2160	2747	10422944	10423531	0.000000e+00	660.0
25	TraesCS2B01G593800	chr6A	87.113	582	74	1	2167	2747	590370891	590371472	0.000000e+00	658.0
26	TraesCS2B01G593800	chr5B	87.136	583	72	3	2167	2747	638783201	638783782	0.000000e+00	658.0
27	TraesCS2B01G593800	chr7B	76.750	800	169	14	883	1669	719097484	719096689	5.430000e-117	431.0
28	TraesCS2B01G593800	chr3A	97.980	99	2	0	2	100	14077519	14077421	3.640000e-39	172.0
29	TraesCS2B01G593800	chr7D	94.286	105	6	0	1	105	15947688	15947584	7.870000e-36	161.0
30	TraesCS2B01G593800	chr7D	94.286	105	6	0	1	105	16034289	16034185	7.870000e-36	161.0
31	TraesCS2B01G593800	chr6D	93.939	99	6	0	2	100	457473672	457473574	1.700000e-32	150.0
32	TraesCS2B01G593800	chr6D	93.333	45	3	0	436	480	437332600	437332644	1.770000e-07	67.6
33	TraesCS2B01G593800	chr6B	91.919	99	8	0	2	100	15809927	15809829	3.690000e-29	139.0
34	TraesCS2B01G593800	chr1D	92.632	95	7	0	2	96	463162504	463162598	1.330000e-28	137.0
35	TraesCS2B01G593800	chr1D	88.889	54	5	1	429	481	6139953	6139900	6.350000e-07	65.8

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	TraesCS2B01G593800	chr2B	778475215	778477961	2746	True	5073.0	5073	100.0000	1	2747	1	chr2B.!!$R2	2746
1	TraesCS2B01G593800	chr2B	778450576	778452577	2001	False	3265.0	3265	96.2170	757	2747	1	chr2B.!!$F2	1990
2	TraesCS2B01G593800	chr2B	778420521	778421190	669	False	1147.0	1147	97.6120	88	756	1	chr2B.!!$F1	668
3	TraesCS2B01G593800	chr2B	778292511	778293426	915	True	856.0	856	83.7780	824	1746	1	chr2B.!!$R1	922
4	TraesCS2B01G593800	chr2B	778778959	778779923	964	False	730.0	730	80.5760	803	1762	1	chr2B.!!$F3	959
5	TraesCS2B01G593800	chr2A	778562988	778565293	2305	False	2896.0	2896	89.7270	472	2747	1	chr2A.!!$F3	2275
6	TraesCS2B01G593800	chr2A	778456740	778457598	858	True	784.0	784	83.3330	897	1761	1	chr2A.!!$R1	864
7	TraesCS2B01G593800	chr2A	138922381	138922962	581	False	658.0	658	87.1130	2167	2747	1	chr2A.!!$F1	580
8	TraesCS2B01G593800	chrUn	217849487	217850428	941	True	773.0	773	81.7620	812	1761	1	chrUn.!!$R1	949
9	TraesCS2B01G593800	chrUn	331470499	331471440	941	True	773.0	773	81.7620	812	1761	1	chrUn.!!$R3	949
10	TraesCS2B01G593800	chrUn	436326431	436326994	563	False	496.0	496	82.6920	809	1374	1	chrUn.!!$F1	565
11	TraesCS2B01G593800	chrUn	345946492	345950883	4391	False	379.5	496	81.1395	809	1747	4	chrUn.!!$F2	938
12	TraesCS2B01G593800	chr4A	69305527	69306108	581	True	675.0	675	87.6290	2167	2747	1	chr4A.!!$R1	580
13	TraesCS2B01G593800	chr3D	56362011	56362592	581	True	669.0	669	87.5000	2167	2747	1	chr3D.!!$R1	580
14	TraesCS2B01G593800	chr1B	453521965	453522546	581	False	669.0	669	87.4570	2167	2747	1	chr1B.!!$F1	580
15	TraesCS2B01G593800	chr3B	12765071	12765650	579	False	662.0	662	87.2850	2167	2747	1	chr3B.!!$F1	580
16	TraesCS2B01G593800	chr7A	10422944	10423531	587	False	660.0	660	86.9270	2160	2747	1	chr7A.!!$F1	587
17	TraesCS2B01G593800	chr6A	590370891	590371472	581	False	658.0	658	87.1130	2167	2747	1	chr6A.!!$F1	580
18	TraesCS2B01G593800	chr5B	638783201	638783782	581	False	658.0	658	87.1360	2167	2747	1	chr5B.!!$F1	580
19	TraesCS2B01G593800	chr7B	719096689	719097484	795	True	431.0	431	76.7500	883	1669	1	chr7B.!!$R1	786

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
52	53	0.032678	ACGCTGAGCCATCGGATTAG	59.967	55.0	0.0	0.0	33.17	1.73	F
53	54	0.315251	CGCTGAGCCATCGGATTAGA	59.685	55.0	0.0	0.0	33.17	2.10	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1485	2608	2.187163	GCCAGCGTAGTCTTCCCC	59.813	66.667	0.0	0.0	0.00	4.81	R
1977	3172	5.704515	GCCTCTGTTGATGCTATATTCATGT	59.295	40.000	0.0	0.0	32.28	3.21	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
18	19	2.212327	ATACTCCCTGCCACTTCCG	58.788	57.895	0.00	0.00	0.00	4.30
19	20	0.617820	ATACTCCCTGCCACTTCCGT	60.618	55.000	0.00	0.00	0.00	4.69
20	21	0.834687	TACTCCCTGCCACTTCCGTT	60.835	55.000	0.00	0.00	0.00	4.44
21	22	1.672356	CTCCCTGCCACTTCCGTTG	60.672	63.158	0.00	0.00	0.00	4.10
22	23	2.672996	CCCTGCCACTTCCGTTGG	60.673	66.667	0.00	0.00	0.00	3.77
23	24	2.429930	CCTGCCACTTCCGTTGGA	59.570	61.111	0.00	0.00	0.00	3.53
24	25	1.672356	CCTGCCACTTCCGTTGGAG	60.672	63.158	0.00	0.00	31.21	3.86
25	26	1.071471	CTGCCACTTCCGTTGGAGT	59.929	57.895	0.00	0.00	31.21	3.85
26	27	0.320374	CTGCCACTTCCGTTGGAGTA	59.680	55.000	0.00	0.00	31.21	2.59
27	28	0.034337	TGCCACTTCCGTTGGAGTAC	59.966	55.000	0.00	0.00	31.21	2.73
28	29	0.672711	GCCACTTCCGTTGGAGTACC	60.673	60.000	0.00	0.00	31.21	3.34
29	30	0.036671	CCACTTCCGTTGGAGTACCC	60.037	60.000	0.00	0.00	31.21	3.69
30	31	0.682852	CACTTCCGTTGGAGTACCCA	59.317	55.000	0.00	0.00	44.93	4.51
31	32	1.278127	CACTTCCGTTGGAGTACCCAT	59.722	52.381	4.19	0.00	46.10	4.00
32	33	1.982958	ACTTCCGTTGGAGTACCCATT	59.017	47.619	4.19	0.00	46.10	3.16
33	34	3.055675	CACTTCCGTTGGAGTACCCATTA	60.056	47.826	4.19	0.00	46.10	1.90
34	35	3.055602	ACTTCCGTTGGAGTACCCATTAC	60.056	47.826	4.19	0.95	46.10	1.89
35	36	1.477700	TCCGTTGGAGTACCCATTACG	59.522	52.381	15.22	15.22	46.10	3.18
36	37	1.283736	CGTTGGAGTACCCATTACGC	58.716	55.000	11.91	0.00	46.10	4.42
37	38	1.134907	CGTTGGAGTACCCATTACGCT	60.135	52.381	11.91	0.00	46.10	5.07
38	39	2.277084	GTTGGAGTACCCATTACGCTG	58.723	52.381	4.19	0.00	46.10	5.18
39	40	1.855295	TGGAGTACCCATTACGCTGA	58.145	50.000	0.00	0.00	40.82	4.26
40	41	1.754803	TGGAGTACCCATTACGCTGAG	59.245	52.381	0.00	0.00	40.82	3.35
41	42	1.538419	GGAGTACCCATTACGCTGAGC	60.538	57.143	0.00	0.00	35.61	4.26
42	43	0.464452	AGTACCCATTACGCTGAGCC	59.536	55.000	0.00	0.00	35.61	4.70
43	44	0.177141	GTACCCATTACGCTGAGCCA	59.823	55.000	0.00	0.00	0.00	4.75
44	45	1.128200	TACCCATTACGCTGAGCCAT	58.872	50.000	0.00	0.00	0.00	4.40
45	46	0.179045	ACCCATTACGCTGAGCCATC	60.179	55.000	0.00	0.00	0.00	3.51
46	47	1.224069	CCCATTACGCTGAGCCATCG	61.224	60.000	0.00	0.00	0.00	3.84
47	48	1.224069	CCATTACGCTGAGCCATCGG	61.224	60.000	0.00	0.00	34.66	4.18
48	49	0.249447	CATTACGCTGAGCCATCGGA	60.249	55.000	0.00	0.00	33.17	4.55
49	50	0.681733	ATTACGCTGAGCCATCGGAT	59.318	50.000	0.00	0.00	33.17	4.18
50	51	0.464036	TTACGCTGAGCCATCGGATT	59.536	50.000	0.00	0.00	33.17	3.01
51	52	1.324383	TACGCTGAGCCATCGGATTA	58.676	50.000	0.00	0.00	33.17	1.75
52	53	0.032678	ACGCTGAGCCATCGGATTAG	59.967	55.000	0.00	0.00	33.17	1.73
53	54	0.315251	CGCTGAGCCATCGGATTAGA	59.685	55.000	0.00	0.00	33.17	2.10
54	55	1.269778	CGCTGAGCCATCGGATTAGAA	60.270	52.381	0.00	0.00	33.17	2.10
55	56	2.139118	GCTGAGCCATCGGATTAGAAC	58.861	52.381	0.00	0.00	33.17	3.01
56	57	2.483714	GCTGAGCCATCGGATTAGAACA	60.484	50.000	0.00	0.00	33.17	3.18
57	58	3.797039	CTGAGCCATCGGATTAGAACAA	58.203	45.455	0.00	0.00	33.17	2.83
58	59	4.191544	CTGAGCCATCGGATTAGAACAAA	58.808	43.478	0.00	0.00	33.17	2.83
59	60	4.780815	TGAGCCATCGGATTAGAACAAAT	58.219	39.130	0.00	0.00	0.00	2.32
60	61	4.576053	TGAGCCATCGGATTAGAACAAATG	59.424	41.667	0.00	0.00	0.00	2.32
61	62	3.885297	AGCCATCGGATTAGAACAAATGG	59.115	43.478	0.00	0.00	36.19	3.16
62	63	3.882888	GCCATCGGATTAGAACAAATGGA	59.117	43.478	2.77	0.00	35.30	3.41
63	64	4.261197	GCCATCGGATTAGAACAAATGGAC	60.261	45.833	2.77	0.00	35.30	4.02
64	65	4.024893	CCATCGGATTAGAACAAATGGACG	60.025	45.833	0.00	0.00	35.30	4.79
65	66	3.527533	TCGGATTAGAACAAATGGACGG	58.472	45.455	0.00	0.00	0.00	4.79
66	67	3.196039	TCGGATTAGAACAAATGGACGGA	59.804	43.478	0.00	0.00	0.00	4.69
67	68	4.127171	CGGATTAGAACAAATGGACGGAT	58.873	43.478	0.00	0.00	0.00	4.18
68	69	4.211374	CGGATTAGAACAAATGGACGGATC	59.789	45.833	0.00	0.00	0.00	3.36
69	70	5.123227	GGATTAGAACAAATGGACGGATCA	58.877	41.667	0.00	0.00	0.00	2.92
70	71	5.765182	GGATTAGAACAAATGGACGGATCAT	59.235	40.000	0.00	0.00	0.00	2.45
71	72	6.934645	GGATTAGAACAAATGGACGGATCATA	59.065	38.462	0.00	0.00	0.00	2.15
72	73	7.607991	GGATTAGAACAAATGGACGGATCATAT	59.392	37.037	0.00	0.00	0.00	1.78
73	74	8.924511	ATTAGAACAAATGGACGGATCATATT	57.075	30.769	0.00	0.00	0.00	1.28
74	75	8.746052	TTAGAACAAATGGACGGATCATATTT	57.254	30.769	0.00	0.00	0.00	1.40
75	76	9.839817	TTAGAACAAATGGACGGATCATATTTA	57.160	29.630	0.00	0.00	0.00	1.40
76	77	8.154649	AGAACAAATGGACGGATCATATTTAC	57.845	34.615	0.00	0.00	0.00	2.01
77	78	7.993183	AGAACAAATGGACGGATCATATTTACT	59.007	33.333	0.00	0.00	0.00	2.24
78	79	8.519799	AACAAATGGACGGATCATATTTACTT	57.480	30.769	0.00	0.00	0.00	2.24
79	80	8.154649	ACAAATGGACGGATCATATTTACTTC	57.845	34.615	0.00	0.00	0.00	3.01
80	81	7.773224	ACAAATGGACGGATCATATTTACTTCA	59.227	33.333	0.00	0.00	0.00	3.02
81	82	7.969536	AATGGACGGATCATATTTACTTCAG	57.030	36.000	0.00	0.00	0.00	3.02
82	83	5.853936	TGGACGGATCATATTTACTTCAGG	58.146	41.667	0.00	0.00	0.00	3.86
83	84	5.221641	TGGACGGATCATATTTACTTCAGGG	60.222	44.000	0.00	0.00	0.00	4.45
84	85	5.221661	GGACGGATCATATTTACTTCAGGGT	60.222	44.000	0.00	0.00	0.00	4.34
85	86	6.014840	GGACGGATCATATTTACTTCAGGGTA	60.015	42.308	0.00	0.00	0.00	3.69
86	87	7.310485	GGACGGATCATATTTACTTCAGGGTAT	60.310	40.741	0.00	0.00	0.00	2.73
103	104	5.063060	CAGGGTATTGTAAAAGTGCTCGTAC	59.937	44.000	0.00	0.00	0.00	3.67
154	155	4.201656	GCCGACCGTGTAAGAAATACTTTC	60.202	45.833	0.00	0.00	39.72	2.62
217	218	0.539051	CTGTCTAACCCTCTGCCCAG	59.461	60.000	0.00	0.00	0.00	4.45
311	312	2.614983	TGTTGGCGAAAGGTTTACTGAC	59.385	45.455	0.00	0.00	0.00	3.51
343	344	1.138266	GTTGCCTATACTTCTGCCGGA	59.862	52.381	5.05	0.00	0.00	5.14
399	400	0.669625	AAGTCGGCAACTTACGAGGC	60.670	55.000	2.15	0.00	46.55	4.70
404	405	0.796927	GGCAACTTACGAGGCAGTTC	59.203	55.000	0.00	0.00	30.48	3.01
451	452	6.427547	ACTTTAGATATACTCCCTTCGTCTCG	59.572	42.308	0.00	0.00	0.00	4.04
459	460	9.896645	ATATACTCCCTTCGTCTCGTAATATAA	57.103	33.333	0.00	0.00	0.00	0.98
1137	1169	0.828022	TTTACATCCTCCGCATCCGT	59.172	50.000	0.00	0.00	0.00	4.69
1725	2852	3.327757	ACCTCACTAACATGCTCAAGGAA	59.672	43.478	0.00	0.00	0.00	3.36
1854	3043	4.636249	AGACACTCAGGAAGTTTCATGTC	58.364	43.478	6.44	0.00	39.74	3.06
1977	3172	1.552792	TGCCCACATCACGTAAGATCA	59.447	47.619	0.00	0.00	43.62	2.92
2025	3220	7.387948	GGCTTGATTAAGTCTAAGTCAACTGAA	59.612	37.037	0.00	0.00	35.64	3.02
2120	3315	7.571357	AGATTACCCACACTAATTACCCTACAT	59.429	37.037	0.00	0.00	0.00	2.29
2230	3437	5.221087	GGCAGTACATAGAACACTAGAGGTC	60.221	48.000	0.00	0.00	0.00	3.85
2396	3612	1.248101	GCCCCAAAGTACCAACGCAT	61.248	55.000	0.00	0.00	0.00	4.73
2615	3872	7.234355	GGATAGGATGTGGGAGACATTATTTT	58.766	38.462	0.00	0.00	45.90	1.82
2691	3948	5.330233	ACAAAAATTAGAACGGGATCCCTT	58.670	37.500	28.42	17.44	0.00	3.95

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
2	3	2.526873	ACGGAAGTGGCAGGGAGT	60.527	61.111	0.00	0.00	46.97	3.85
21	22	1.538419	GCTCAGCGTAATGGGTACTCC	60.538	57.143	0.00	0.00	0.00	3.85
22	23	1.538419	GGCTCAGCGTAATGGGTACTC	60.538	57.143	0.00	0.00	0.00	2.59
23	24	0.464452	GGCTCAGCGTAATGGGTACT	59.536	55.000	0.00	0.00	0.00	2.73
24	25	0.177141	TGGCTCAGCGTAATGGGTAC	59.823	55.000	0.00	0.00	0.00	3.34
25	26	1.070134	GATGGCTCAGCGTAATGGGTA	59.930	52.381	0.00	0.00	0.00	3.69
26	27	0.179045	GATGGCTCAGCGTAATGGGT	60.179	55.000	0.00	0.00	0.00	4.51
27	28	1.224069	CGATGGCTCAGCGTAATGGG	61.224	60.000	4.92	0.00	38.50	4.00
28	29	1.224069	CCGATGGCTCAGCGTAATGG	61.224	60.000	10.99	0.00	41.89	3.16
29	30	0.249447	TCCGATGGCTCAGCGTAATG	60.249	55.000	10.99	0.00	41.89	1.90
30	31	0.681733	ATCCGATGGCTCAGCGTAAT	59.318	50.000	10.99	3.20	41.89	1.89
31	32	0.464036	AATCCGATGGCTCAGCGTAA	59.536	50.000	10.99	1.25	41.89	3.18
32	33	1.269723	CTAATCCGATGGCTCAGCGTA	59.730	52.381	10.99	0.00	41.89	4.42
33	34	0.032678	CTAATCCGATGGCTCAGCGT	59.967	55.000	10.99	0.00	41.89	5.07
34	35	0.315251	TCTAATCCGATGGCTCAGCG	59.685	55.000	5.95	5.95	43.13	5.18
35	36	2.139118	GTTCTAATCCGATGGCTCAGC	58.861	52.381	0.00	0.00	0.00	4.26
36	37	3.459232	TGTTCTAATCCGATGGCTCAG	57.541	47.619	0.00	0.00	0.00	3.35
37	38	3.904800	TTGTTCTAATCCGATGGCTCA	57.095	42.857	0.00	0.00	0.00	4.26
38	39	4.023707	CCATTTGTTCTAATCCGATGGCTC	60.024	45.833	0.00	0.00	0.00	4.70
39	40	3.885297	CCATTTGTTCTAATCCGATGGCT	59.115	43.478	0.00	0.00	0.00	4.75
40	41	3.882888	TCCATTTGTTCTAATCCGATGGC	59.117	43.478	0.00	0.00	34.11	4.40
41	42	4.024893	CGTCCATTTGTTCTAATCCGATGG	60.025	45.833	0.00	0.00	35.13	3.51
42	43	4.024893	CCGTCCATTTGTTCTAATCCGATG	60.025	45.833	0.00	0.00	0.00	3.84
43	44	4.127171	CCGTCCATTTGTTCTAATCCGAT	58.873	43.478	0.00	0.00	0.00	4.18
44	45	3.196039	TCCGTCCATTTGTTCTAATCCGA	59.804	43.478	0.00	0.00	0.00	4.55
45	46	3.527533	TCCGTCCATTTGTTCTAATCCG	58.472	45.455	0.00	0.00	0.00	4.18
46	47	5.123227	TGATCCGTCCATTTGTTCTAATCC	58.877	41.667	0.00	0.00	0.00	3.01
47	48	6.867662	ATGATCCGTCCATTTGTTCTAATC	57.132	37.500	0.00	0.00	0.00	1.75
48	49	8.924511	AATATGATCCGTCCATTTGTTCTAAT	57.075	30.769	0.00	0.00	0.00	1.73
49	50	8.746052	AAATATGATCCGTCCATTTGTTCTAA	57.254	30.769	0.00	0.00	0.00	2.10
50	51	9.268268	GTAAATATGATCCGTCCATTTGTTCTA	57.732	33.333	0.00	0.00	0.00	2.10
51	52	7.993183	AGTAAATATGATCCGTCCATTTGTTCT	59.007	33.333	0.00	0.00	0.00	3.01
52	53	8.154649	AGTAAATATGATCCGTCCATTTGTTC	57.845	34.615	0.00	0.00	0.00	3.18
53	54	8.519799	AAGTAAATATGATCCGTCCATTTGTT	57.480	30.769	0.00	0.00	0.00	2.83
54	55	7.773224	TGAAGTAAATATGATCCGTCCATTTGT	59.227	33.333	0.00	0.00	0.00	2.83
55	56	8.153479	TGAAGTAAATATGATCCGTCCATTTG	57.847	34.615	0.00	0.00	0.00	2.32
56	57	7.445402	CCTGAAGTAAATATGATCCGTCCATTT	59.555	37.037	0.00	0.00	0.00	2.32
57	58	6.936900	CCTGAAGTAAATATGATCCGTCCATT	59.063	38.462	0.00	0.00	0.00	3.16
58	59	6.467677	CCTGAAGTAAATATGATCCGTCCAT	58.532	40.000	0.00	0.00	0.00	3.41
59	60	5.221641	CCCTGAAGTAAATATGATCCGTCCA	60.222	44.000	0.00	0.00	0.00	4.02
60	61	5.221661	ACCCTGAAGTAAATATGATCCGTCC	60.222	44.000	0.00	0.00	0.00	4.79
61	62	5.855045	ACCCTGAAGTAAATATGATCCGTC	58.145	41.667	0.00	0.00	0.00	4.79
62	63	5.888982	ACCCTGAAGTAAATATGATCCGT	57.111	39.130	0.00	0.00	0.00	4.69
63	64	7.878127	ACAATACCCTGAAGTAAATATGATCCG	59.122	37.037	0.00	0.00	0.00	4.18
71	72	8.520351	GCACTTTTACAATACCCTGAAGTAAAT	58.480	33.333	0.00	0.00	35.39	1.40
72	73	7.722285	AGCACTTTTACAATACCCTGAAGTAAA	59.278	33.333	0.00	0.00	34.09	2.01
73	74	7.228590	AGCACTTTTACAATACCCTGAAGTAA	58.771	34.615	0.00	0.00	0.00	2.24
74	75	6.775708	AGCACTTTTACAATACCCTGAAGTA	58.224	36.000	0.00	0.00	0.00	2.24
75	76	5.631119	AGCACTTTTACAATACCCTGAAGT	58.369	37.500	0.00	0.00	0.00	3.01
76	77	5.163854	CGAGCACTTTTACAATACCCTGAAG	60.164	44.000	0.00	0.00	0.00	3.02
77	78	4.693566	CGAGCACTTTTACAATACCCTGAA	59.306	41.667	0.00	0.00	0.00	3.02
78	79	4.250464	CGAGCACTTTTACAATACCCTGA	58.750	43.478	0.00	0.00	0.00	3.86
79	80	4.000988	ACGAGCACTTTTACAATACCCTG	58.999	43.478	0.00	0.00	0.00	4.45
80	81	4.281898	ACGAGCACTTTTACAATACCCT	57.718	40.909	0.00	0.00	0.00	4.34
81	82	4.032104	CGTACGAGCACTTTTACAATACCC	59.968	45.833	10.44	0.00	0.00	3.69
82	83	4.032104	CCGTACGAGCACTTTTACAATACC	59.968	45.833	18.76	0.00	0.00	2.73
83	84	4.491441	GCCGTACGAGCACTTTTACAATAC	60.491	45.833	18.76	0.00	0.00	1.89
84	85	3.613737	GCCGTACGAGCACTTTTACAATA	59.386	43.478	18.76	0.00	0.00	1.90
85	86	2.414138	GCCGTACGAGCACTTTTACAAT	59.586	45.455	18.76	0.00	0.00	2.71
86	87	1.794116	GCCGTACGAGCACTTTTACAA	59.206	47.619	18.76	0.00	0.00	2.41
154	155	2.300152	TGGTTAGAGAGCAGTTGGACAG	59.700	50.000	0.00	0.00	0.00	3.51
164	165	2.111384	TCCTGATGGTGGTTAGAGAGC	58.889	52.381	0.00	0.00	34.23	4.09
217	218	1.192146	TGTAGACAGACCTGGGTGGC	61.192	60.000	0.00	0.00	40.22	5.01
311	312	8.099537	AGAAGTATAGGCAACATCCATATTCTG	58.900	37.037	0.00	0.00	41.41	3.02
343	344	6.782494	AGGTAATCTGTCATGGAAAACCTTTT	59.218	34.615	0.00	0.00	31.94	2.27
399	400	2.676839	AGCTGATCATTGAAGCGAACTG	59.323	45.455	0.00	0.00	41.88	3.16
404	405	4.808077	ATGTTAGCTGATCATTGAAGCG	57.192	40.909	0.00	0.00	41.88	4.68
1249	1281	3.075998	CGCATGACGCTCACTGAC	58.924	61.111	0.00	0.00	39.08	3.51
1485	2608	2.187163	GCCAGCGTAGTCTTCCCC	59.813	66.667	0.00	0.00	0.00	4.81
1725	2852	5.825593	TTTACCTCATGTCCTTCAGAAGT	57.174	39.130	9.41	0.00	0.00	3.01
1854	3043	7.596248	CACACCTATGTTTTTCTTCCTTGATTG	59.404	37.037	0.00	0.00	36.72	2.67
1977	3172	5.704515	GCCTCTGTTGATGCTATATTCATGT	59.295	40.000	0.00	0.00	32.28	3.21
2014	3209	6.570378	CGGGATTGCTAAATTTCAGTTGACTT	60.570	38.462	0.00	0.00	0.00	3.01
2069	3264	9.911788	CTAATTGCAATTATACCTAGATCCCAT	57.088	33.333	27.56	3.30	31.03	4.00
2080	3275	9.893305	GTGTGGGTAATCTAATTGCAATTATAC	57.107	33.333	27.56	24.49	31.03	1.47
2182	3389	8.192774	GCCATGATTGATGAGTAGATTGAAAAA	58.807	33.333	0.00	0.00	33.31	1.94
2240	3449	5.905331	ACTAGATGGTCCATGAATCTGGTTA	59.095	40.000	9.76	0.00	38.53	2.85
2249	3458	7.066781	TGTAGTCATAACTAGATGGTCCATGA	58.933	38.462	9.76	0.00	38.66	3.07
2396	3612	0.955428	GGCGATGGTTGTTGCTCTGA	60.955	55.000	0.00	0.00	0.00	3.27
2500	3757	1.519455	CGATCGGTGCTGGTCTTCC	60.519	63.158	7.38	0.00	0.00	3.46
2615	3872	1.899814	AGTGGCGATGTCCTTCAGTAA	59.100	47.619	0.00	0.00	0.00	2.24

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.