AutoCloner

Multiple sequence alignment - TraesCS6A01G057100

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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	TraesCS6A01G057100	chr6A	100.000	2205	0	0	726	2930	30036730	30034526	0.000000e+00	4072.0
1	TraesCS6A01G057100	chr6A	100.000	409	0	0	1	409	30037455	30037047	0.000000e+00	756.0
2	TraesCS6A01G057100	chr6A	82.343	606	102	4	990	1591	30422617	30423221	3.350000e-144	521.0
3	TraesCS6A01G057100	chr6A	78.468	483	98	5	1014	1491	31044151	31044632	7.890000e-81	311.0
4	TraesCS6A01G057100	chr6A	72.153	966	217	36	1004	1932	34178212	34179162	2.260000e-61	246.0
5	TraesCS6A01G057100	chr6A	84.103	195	27	2	1302	1492	30263655	30263461	4.990000e-43	185.0
6	TraesCS6A01G057100	chr6A	79.182	269	41	8	1656	1922	30263337	30263082	3.880000e-39	172.0
7	TraesCS6A01G057100	chr6A	77.509	289	50	8	1656	1942	30282820	30282545	3.020000e-35	159.0
8	TraesCS6A01G057100	chr6A	73.804	439	89	20	1706	2131	39877243	39876818	1.820000e-32	150.0
9	TraesCS6A01G057100	chr6A	74.315	292	60	13	1843	2129	33256040	33256321	3.090000e-20	110.0
10	TraesCS6A01G057100	chr6D	93.714	2227	98	19	729	2930	27845066	27847275	0.000000e+00	3299.0
11	TraesCS6A01G057100	chr6D	81.391	1150	151	24	1805	2930	28326642	28325532	0.000000e+00	880.0
12	TraesCS6A01G057100	chr6D	75.450	1112	239	20	1018	2116	28415994	28414904	7.240000e-141	510.0
13	TraesCS6A01G057100	chr6D	81.208	596	112	0	996	1591	27683726	27683131	5.680000e-132	481.0
14	TraesCS6A01G057100	chr6D	87.224	407	29	6	1	407	27844378	27844761	2.680000e-120	442.0
15	TraesCS6A01G057100	chr6D	81.319	546	82	15	1650	2192	27711724	27712252	2.700000e-115	425.0
16	TraesCS6A01G057100	chr6D	80.000	585	101	11	996	1577	27711107	27711678	4.520000e-113	418.0
17	TraesCS6A01G057100	chr6D	100.000	28	0	0	726	753	318989201	318989174	5.000000e-03	52.8
18	TraesCS6A01G057100	chr6B	92.259	1434	99	8	904	2334	51732015	51733439	0.000000e+00	2023.0
19	TraesCS6A01G057100	chr6B	91.562	557	37	5	2373	2928	51733434	51733981	0.000000e+00	760.0
20	TraesCS6A01G057100	chr6B	80.435	1058	136	32	1905	2930	52369487	52368469	0.000000e+00	741.0
21	TraesCS6A01G057100	chr6B	80.375	586	111	3	1008	1591	51435765	51435182	2.680000e-120	442.0
22	TraesCS6A01G057100	chr6B	82.413	489	83	3	996	1483	51537981	51538467	9.710000e-115	424.0
23	TraesCS6A01G057100	chr6B	72.951	976	201	49	1011	1951	75671083	75670136	6.180000e-72	281.0
24	TraesCS6A01G057100	chr6B	72.253	1092	240	52	1001	2059	61789942	61791003	2.220000e-71	279.0
25	TraesCS6A01G057100	chr6B	75.068	365	68	16	1139	1492	49701278	49700926	6.540000e-32	148.0
26	TraesCS6A01G057100	chr6B	80.435	92	16	2	1650	1740	51538607	51538697	5.240000e-08	69.4
27	TraesCS6A01G057100	chr3A	82.410	415	63	9	3	409	640842624	640842212	1.290000e-93	353.0
28	TraesCS6A01G057100	chr3A	78.744	414	81	4	2	409	8608580	8608168	1.340000e-68	270.0
29	TraesCS6A01G057100	chr1B	80.676	414	72	6	3	409	520780776	520780364	6.100000e-82	315.0
30	TraesCS6A01G057100	chrUn	79.333	450	87	5	1014	1458	76751769	76751321	7.890000e-81	311.0
31	TraesCS6A01G057100	chrUn	71.441	1166	262	53	1004	2129	101886091	101887225	2.920000e-60	243.0
32	TraesCS6A01G057100	chrUn	86.957	184	24	0	1007	1190	27447746	27447929	1.060000e-49	207.0
33	TraesCS6A01G057100	chr3D	80.203	394	73	4	9	397	501309519	501309126	1.030000e-74	291.0
34	TraesCS6A01G057100	chr1D	79.469	414	75	7	4	409	396946404	396946815	4.780000e-73	285.0
35	TraesCS6A01G057100	chr7B	81.739	345	57	3	46	384	513819021	513819365	1.720000e-72	283.0
36	TraesCS6A01G057100	chr5D	80.403	347	58	6	45	384	456591349	456591006	3.750000e-64	255.0
37	TraesCS6A01G057100	chr7A	80.678	295	51	4	120	409	35627189	35627482	1.060000e-54	224.0
38	TraesCS6A01G057100	chr4B	100.000	28	0	0	726	753	69321171	69321144	5.000000e-03	52.8

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	TraesCS6A01G057100	chr6A	30034526	30037455	2929	True	2414.0	4072	100.0000	1	2930	2	chr6A.!!$R3	2929
1	TraesCS6A01G057100	chr6A	30422617	30423221	604	False	521.0	521	82.3430	990	1591	1	chr6A.!!$F1	601
2	TraesCS6A01G057100	chr6A	34178212	34179162	950	False	246.0	246	72.1530	1004	1932	1	chr6A.!!$F4	928
3	TraesCS6A01G057100	chr6D	27844378	27847275	2897	False	1870.5	3299	90.4690	1	2930	2	chr6D.!!$F2	2929
4	TraesCS6A01G057100	chr6D	28325532	28326642	1110	True	880.0	880	81.3910	1805	2930	1	chr6D.!!$R2	1125
5	TraesCS6A01G057100	chr6D	28414904	28415994	1090	True	510.0	510	75.4500	1018	2116	1	chr6D.!!$R3	1098
6	TraesCS6A01G057100	chr6D	27683131	27683726	595	True	481.0	481	81.2080	996	1591	1	chr6D.!!$R1	595
7	TraesCS6A01G057100	chr6D	27711107	27712252	1145	False	421.5	425	80.6595	996	2192	2	chr6D.!!$F1	1196
8	TraesCS6A01G057100	chr6B	51732015	51733981	1966	False	1391.5	2023	91.9105	904	2928	2	chr6B.!!$F3	2024
9	TraesCS6A01G057100	chr6B	52368469	52369487	1018	True	741.0	741	80.4350	1905	2930	1	chr6B.!!$R3	1025
10	TraesCS6A01G057100	chr6B	51435182	51435765	583	True	442.0	442	80.3750	1008	1591	1	chr6B.!!$R2	583
11	TraesCS6A01G057100	chr6B	75670136	75671083	947	True	281.0	281	72.9510	1011	1951	1	chr6B.!!$R4	940
12	TraesCS6A01G057100	chr6B	61789942	61791003	1061	False	279.0	279	72.2530	1001	2059	1	chr6B.!!$F1	1058
13	TraesCS6A01G057100	chr6B	51537981	51538697	716	False	246.7	424	81.4240	996	1740	2	chr6B.!!$F2	744
14	TraesCS6A01G057100	chrUn	101886091	101887225	1134	False	243.0	243	71.4410	1004	2129	1	chrUn.!!$F2	1125

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
994	1010	0.180171	CGAGCTCTGAGGAGAGGAGA	59.82	60.0	12.85	0.0	45.4	3.71	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2563	2647	0.457851	CGATCGAGTCCAGCCTCTTT	59.542	55.0	10.26	0.0	0.0	2.52	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
32	33	1.660575	CACGGCAAGAACGAGTCGT	60.661	57.895	13.56	13.56	43.97	4.34
33	34	1.371389	ACGGCAAGAACGAGTCGTC	60.371	57.895	20.18	12.37	39.99	4.20
59	60	2.962253	GCTGTCGCCGCTCCATAC	60.962	66.667	0.00	0.00	0.00	2.39
78	79	1.308069	CCGGAGCCACATTGACCTTG	61.308	60.000	0.00	0.00	0.00	3.61
81	82	1.545428	GGAGCCACATTGACCTTGTCA	60.545	52.381	0.00	0.00	41.09	3.58
96	97	2.198827	TGTCAATGACAGCCGGAAAT	57.801	45.000	12.63	0.00	37.67	2.17
108	109	1.269517	GCCGGAAATTCTTTGTGCACA	60.270	47.619	17.42	17.42	0.00	4.57
114	115	3.665745	AATTCTTTGTGCACATGTCCC	57.334	42.857	22.39	0.00	0.00	4.46
168	169	4.097741	CGCCATTGAACCCTTGAATCAATA	59.902	41.667	0.00	0.00	40.75	1.90
169	170	5.221303	CGCCATTGAACCCTTGAATCAATAT	60.221	40.000	0.00	0.00	40.75	1.28
171	172	6.183360	GCCATTGAACCCTTGAATCAATATGA	60.183	38.462	0.00	0.00	40.75	2.15
172	173	7.633334	GCCATTGAACCCTTGAATCAATATGAA	60.633	37.037	0.00	0.00	40.75	2.57
174	175	8.689061	CATTGAACCCTTGAATCAATATGAAGA	58.311	33.333	0.00	0.00	40.75	2.87
175	176	8.648698	TTGAACCCTTGAATCAATATGAAGAA	57.351	30.769	0.00	0.00	0.00	2.52
176	177	8.827832	TGAACCCTTGAATCAATATGAAGAAT	57.172	30.769	0.00	0.00	0.00	2.40
178	179	9.129532	GAACCCTTGAATCAATATGAAGAATCT	57.870	33.333	0.00	0.00	0.00	2.40
179	180	8.461249	ACCCTTGAATCAATATGAAGAATCTG	57.539	34.615	0.00	0.00	0.00	2.90
180	181	7.504911	ACCCTTGAATCAATATGAAGAATCTGG	59.495	37.037	0.00	0.00	0.00	3.86
181	182	7.368833	CCTTGAATCAATATGAAGAATCTGGC	58.631	38.462	0.00	0.00	0.00	4.85
182	183	7.013942	CCTTGAATCAATATGAAGAATCTGGCA	59.986	37.037	0.00	0.00	0.00	4.92
183	184	8.473358	TTGAATCAATATGAAGAATCTGGCAT	57.527	30.769	0.00	4.65	0.00	4.40
184	185	8.107399	TGAATCAATATGAAGAATCTGGCATC	57.893	34.615	2.72	0.00	0.00	3.91
185	186	7.722285	TGAATCAATATGAAGAATCTGGCATCA	59.278	33.333	2.72	0.00	0.00	3.07
186	187	8.473358	AATCAATATGAAGAATCTGGCATCAA	57.527	30.769	2.72	0.00	0.00	2.57
187	188	7.885009	TCAATATGAAGAATCTGGCATCAAA	57.115	32.000	2.72	0.00	0.00	2.69
188	189	8.473358	TCAATATGAAGAATCTGGCATCAAAT	57.527	30.769	2.72	0.00	0.00	2.32
189	190	8.573885	TCAATATGAAGAATCTGGCATCAAATC	58.426	33.333	2.72	0.00	0.00	2.17
190	191	8.577296	CAATATGAAGAATCTGGCATCAAATCT	58.423	33.333	2.72	0.00	0.00	2.40
191	192	8.707796	ATATGAAGAATCTGGCATCAAATCTT	57.292	30.769	2.72	0.00	0.00	2.40
192	193	6.203808	TGAAGAATCTGGCATCAAATCTTG	57.796	37.500	0.00	0.00	0.00	3.02
193	194	5.713389	TGAAGAATCTGGCATCAAATCTTGT	59.287	36.000	0.00	0.00	0.00	3.16
194	195	6.885918	TGAAGAATCTGGCATCAAATCTTGTA	59.114	34.615	0.00	0.00	0.00	2.41
195	196	6.939132	AGAATCTGGCATCAAATCTTGTAG	57.061	37.500	0.00	0.00	0.00	2.74
196	197	6.421485	AGAATCTGGCATCAAATCTTGTAGT	58.579	36.000	0.00	0.00	0.00	2.73
197	198	6.888632	AGAATCTGGCATCAAATCTTGTAGTT	59.111	34.615	0.00	0.00	0.00	2.24
198	199	5.885230	TCTGGCATCAAATCTTGTAGTTG	57.115	39.130	0.00	0.00	34.46	3.16
199	200	4.156556	TCTGGCATCAAATCTTGTAGTTGC	59.843	41.667	0.00	0.00	33.18	4.17
200	201	3.119884	TGGCATCAAATCTTGTAGTTGCG	60.120	43.478	0.00	0.00	33.18	4.85
201	202	3.119849	GGCATCAAATCTTGTAGTTGCGT	60.120	43.478	0.00	0.00	33.18	5.24
202	203	3.848019	GCATCAAATCTTGTAGTTGCGTG	59.152	43.478	0.00	0.00	33.18	5.34
229	230	1.271217	ACAAGAAACCCTAACCTCGCC	60.271	52.381	0.00	0.00	0.00	5.54
230	231	1.061546	AAGAAACCCTAACCTCGCCA	58.938	50.000	0.00	0.00	0.00	5.69
252	253	2.443394	CGAGGGGCTGGCAGGAATA	61.443	63.158	17.64	0.00	0.00	1.75
304	305	3.762823	ACGAAGAAACTTAGGATCGGAGT	59.237	43.478	0.00	0.00	34.81	3.85
305	306	4.220163	ACGAAGAAACTTAGGATCGGAGTT	59.780	41.667	0.00	2.30	35.27	3.01
334	335	1.335964	TGACTCGAAGAAGAAGCACCG	60.336	52.381	0.00	0.00	34.09	4.94
341	342	1.377202	GAAGAAGCACCGCCATCCA	60.377	57.895	0.00	0.00	0.00	3.41
343	344	1.033746	AAGAAGCACCGCCATCCATG	61.034	55.000	0.00	0.00	0.00	3.66
359	360	0.960364	CATGTAAGCGCCACCCTTGT	60.960	55.000	2.29	0.00	0.00	3.16
387	388	6.402456	ACTAAAACCCTACCTATCTAAGCG	57.598	41.667	0.00	0.00	0.00	4.68
407	408	1.996070	GAGGCACCAGGAATACCCCC	61.996	65.000	0.00	0.00	36.73	5.40
758	759	9.706691	ACTTCTCAATTAGTGATTTCGAAACTA	57.293	29.630	13.81	8.41	35.07	2.24
787	788	6.069905	GGAAACCCTAGAGGAAAATTCTCTCT	60.070	42.308	14.41	14.41	41.37	3.10
789	790	5.346270	ACCCTAGAGGAAAATTCTCTCTGT	58.654	41.667	17.28	9.13	41.37	3.41
855	856	1.268625	GGGTAGCCCGTGAAGTTTTTG	59.731	52.381	0.00	0.00	32.13	2.44
857	858	2.359848	GGTAGCCCGTGAAGTTTTTGTT	59.640	45.455	0.00	0.00	0.00	2.83
858	859	3.181484	GGTAGCCCGTGAAGTTTTTGTTT	60.181	43.478	0.00	0.00	0.00	2.83
859	860	3.603158	AGCCCGTGAAGTTTTTGTTTT	57.397	38.095	0.00	0.00	0.00	2.43
861	862	3.682377	AGCCCGTGAAGTTTTTGTTTTTG	59.318	39.130	0.00	0.00	0.00	2.44
862	863	3.433957	GCCCGTGAAGTTTTTGTTTTTGT	59.566	39.130	0.00	0.00	0.00	2.83
863	864	4.083749	GCCCGTGAAGTTTTTGTTTTTGTT	60.084	37.500	0.00	0.00	0.00	2.83
864	865	5.561145	GCCCGTGAAGTTTTTGTTTTTGTTT	60.561	36.000	0.00	0.00	0.00	2.83
865	866	6.431278	CCCGTGAAGTTTTTGTTTTTGTTTT	58.569	32.000	0.00	0.00	0.00	2.43
866	867	6.358294	CCCGTGAAGTTTTTGTTTTTGTTTTG	59.642	34.615	0.00	0.00	0.00	2.44
887	888	9.520204	GTTTTGTTTTTGAGATGATGAGAAGAA	57.480	29.630	0.00	0.00	0.00	2.52
913	929	2.936498	CAGCCCGTGACCTTTACTTATG	59.064	50.000	0.00	0.00	0.00	1.90
994	1010	0.180171	CGAGCTCTGAGGAGAGGAGA	59.820	60.000	12.85	0.00	45.40	3.71
1727	1786	4.268359	GAGTTTGATTTGGAGAGGCAGAT	58.732	43.478	0.00	0.00	0.00	2.90
1744	1803	3.366883	GCAGATCCTAGATGTGATCCGAC	60.367	52.174	5.96	0.00	38.50	4.79
1770	1829	2.909006	ACCATGTCTGTCTGAAGTGGAT	59.091	45.455	14.69	2.13	35.93	3.41
1773	1832	4.431809	CATGTCTGTCTGAAGTGGATCTC	58.568	47.826	0.00	0.00	0.00	2.75
1922	1982	6.852420	ACTATTGAACTGGACAAGCTACTA	57.148	37.500	0.00	0.00	0.00	1.82
1994	2065	5.092781	GCCGAGTACAATAATGTGGTTTTG	58.907	41.667	0.00	0.00	40.84	2.44
2282	2357	7.305474	GTGTTGTTTTGAATATTCCGACATCT	58.695	34.615	12.90	0.00	0.00	2.90
2352	2427	5.581085	GGAAGCGACTAACACATCAAATACT	59.419	40.000	0.00	0.00	0.00	2.12
2427	2511	6.175471	TCTCTGCTGATCTTGCTAAAAATCA	58.825	36.000	11.38	0.00	0.00	2.57
2551	2635	1.618343	TGTCATCCGAAGTCTGAAGCA	59.382	47.619	0.00	0.00	0.00	3.91
2581	2665	1.478510	TCAAAGAGGCTGGACTCGATC	59.521	52.381	0.00	0.00	42.31	3.69
2620	2704	6.488006	GGAATTGCATGTGAAGTAGACCATAT	59.512	38.462	0.00	0.00	0.00	1.78
2653	2737	4.685169	ATGTGTTCTAACTTGCCATTCG	57.315	40.909	0.00	0.00	0.00	3.34
2663	2747	1.061131	CTTGCCATTCGTACGAGCTTG	59.939	52.381	23.18	18.71	0.00	4.01
2664	2748	1.348594	GCCATTCGTACGAGCTTGC	59.651	57.895	18.64	15.25	0.00	4.01
2665	2749	1.358725	GCCATTCGTACGAGCTTGCA	61.359	55.000	18.64	2.47	0.00	4.08
2666	2750	1.290203	CCATTCGTACGAGCTTGCAT	58.710	50.000	18.64	5.02	0.00	3.96
2668	2752	1.926510	CATTCGTACGAGCTTGCATGA	59.073	47.619	18.64	0.04	0.00	3.07
2669	2753	2.293677	TTCGTACGAGCTTGCATGAT	57.706	45.000	18.64	0.00	0.00	2.45
2671	2755	2.616960	TCGTACGAGCTTGCATGATTT	58.383	42.857	15.28	0.00	0.00	2.17
2672	2756	3.776340	TCGTACGAGCTTGCATGATTTA	58.224	40.909	15.28	0.00	0.00	1.40
2726	2812	0.613777	CCGAAGAGGCCCTTAGTTGT	59.386	55.000	0.00	0.00	34.68	3.32
2798	2892	4.740934	GCCTTCTCGTATCTATGTGGCTTT	60.741	45.833	0.00	0.00	35.44	3.51
2873	2968	2.034066	ACGAGCATTGGTGGTGGG	59.966	61.111	2.56	0.00	36.09	4.61

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
17	18	1.081641	TCGACGACTCGTTCTTGCC	60.082	57.895	5.37	0.00	41.37	4.52
59	60	1.002134	AAGGTCAATGTGGCTCCGG	60.002	57.895	0.00	0.00	0.00	5.14
78	79	2.749621	AGAATTTCCGGCTGTCATTGAC	59.250	45.455	9.93	9.93	0.00	3.18
81	82	3.573967	ACAAAGAATTTCCGGCTGTCATT	59.426	39.130	0.00	0.00	35.03	2.57
96	97	2.363306	AGGGACATGTGCACAAAGAA	57.637	45.000	25.72	0.00	0.00	2.52
114	115	1.153349	GCCGGAAGCTGGTCCTTAG	60.153	63.158	5.05	0.00	38.99	2.18
168	169	6.380274	ACAAGATTTGATGCCAGATTCTTCAT	59.620	34.615	0.00	0.00	0.00	2.57
169	170	5.713389	ACAAGATTTGATGCCAGATTCTTCA	59.287	36.000	0.00	0.00	0.00	3.02
171	172	6.888632	ACTACAAGATTTGATGCCAGATTCTT	59.111	34.615	0.00	0.00	0.00	2.52
172	173	6.421485	ACTACAAGATTTGATGCCAGATTCT	58.579	36.000	0.00	0.00	0.00	2.40
174	175	6.626623	GCAACTACAAGATTTGATGCCAGATT	60.627	38.462	0.00	0.00	0.00	2.40
175	176	5.163581	GCAACTACAAGATTTGATGCCAGAT	60.164	40.000	0.00	0.00	0.00	2.90
176	177	4.156556	GCAACTACAAGATTTGATGCCAGA	59.843	41.667	0.00	0.00	0.00	3.86
178	179	3.119884	CGCAACTACAAGATTTGATGCCA	60.120	43.478	0.00	0.00	0.00	4.92
179	180	3.119849	ACGCAACTACAAGATTTGATGCC	60.120	43.478	0.00	0.00	0.00	4.40
180	181	3.848019	CACGCAACTACAAGATTTGATGC	59.152	43.478	0.00	0.00	0.00	3.91
181	182	5.281693	TCACGCAACTACAAGATTTGATG	57.718	39.130	0.00	0.00	0.00	3.07
182	183	4.142816	GCTCACGCAACTACAAGATTTGAT	60.143	41.667	0.00	0.00	35.78	2.57
183	184	3.186409	GCTCACGCAACTACAAGATTTGA	59.814	43.478	0.00	0.00	35.78	2.69
184	185	3.058983	TGCTCACGCAACTACAAGATTTG	60.059	43.478	0.00	0.00	44.62	2.32
185	186	3.138304	TGCTCACGCAACTACAAGATTT	58.862	40.909	0.00	0.00	44.62	2.17
186	187	2.766313	TGCTCACGCAACTACAAGATT	58.234	42.857	0.00	0.00	44.62	2.40
187	188	2.455674	TGCTCACGCAACTACAAGAT	57.544	45.000	0.00	0.00	44.62	2.40
188	189	3.978460	TGCTCACGCAACTACAAGA	57.022	47.368	0.00	0.00	44.62	3.02
198	199	1.400242	GGTTTCTTGTCATGCTCACGC	60.400	52.381	0.00	0.00	0.00	5.34
199	200	1.197721	GGGTTTCTTGTCATGCTCACG	59.802	52.381	0.00	0.00	0.00	4.35
200	201	2.508526	AGGGTTTCTTGTCATGCTCAC	58.491	47.619	0.00	0.00	0.00	3.51
201	202	2.957402	AGGGTTTCTTGTCATGCTCA	57.043	45.000	0.00	0.00	0.00	4.26
202	203	3.440522	GGTTAGGGTTTCTTGTCATGCTC	59.559	47.826	0.00	0.00	0.00	4.26
211	212	1.061546	TGGCGAGGTTAGGGTTTCTT	58.938	50.000	0.00	0.00	0.00	2.52
239	240	0.955919	GGCGTATATTCCTGCCAGCC	60.956	60.000	0.00	0.00	46.76	4.85
243	244	0.389948	CTCCGGCGTATATTCCTGCC	60.390	60.000	6.01	0.00	44.09	4.85
252	253	2.195741	TAGACATAGCTCCGGCGTAT	57.804	50.000	6.01	0.00	44.37	3.06
277	278	2.517959	TCCTAAGTTTCTTCGTCGGGA	58.482	47.619	0.00	0.00	0.00	5.14
284	285	4.799428	CGAACTCCGATCCTAAGTTTCTTC	59.201	45.833	4.17	0.00	41.76	2.87
304	305	2.501261	TCTTCGAGTCAGTCTTCCGAA	58.499	47.619	0.00	0.00	37.61	4.30
305	306	2.180432	TCTTCGAGTCAGTCTTCCGA	57.820	50.000	0.00	0.00	0.00	4.55
334	335	1.823470	TGGCGCTTACATGGATGGC	60.823	57.895	7.64	0.00	0.00	4.40
341	342	0.960364	CACAAGGGTGGCGCTTACAT	60.960	55.000	7.64	0.00	41.45	2.29
343	344	1.298859	CTCACAAGGGTGGCGCTTAC	61.299	60.000	7.64	7.11	45.32	2.34
359	360	9.198475	CTTAGATAGGTAGGGTTTTAGTTCTCA	57.802	37.037	0.00	0.00	0.00	3.27
387	388	1.532238	GGGTATTCCTGGTGCCTCC	59.468	63.158	0.00	0.00	0.00	4.30
800	801	7.535139	ACGACACAGGGAATTAACAATTAATG	58.465	34.615	0.00	0.00	36.06	1.90
830	831	1.133730	ACTTCACGGGCTACCCAAAAA	60.134	47.619	3.08	0.00	45.83	1.94
831	832	0.475044	ACTTCACGGGCTACCCAAAA	59.525	50.000	3.08	0.00	45.83	2.44
857	858	9.650539	TCTCATCATCTCAAAAACAAAACAAAA	57.349	25.926	0.00	0.00	0.00	2.44
858	859	9.650539	TTCTCATCATCTCAAAAACAAAACAAA	57.349	25.926	0.00	0.00	0.00	2.83
859	860	9.304731	CTTCTCATCATCTCAAAAACAAAACAA	57.695	29.630	0.00	0.00	0.00	2.83
861	862	9.520204	TTCTTCTCATCATCTCAAAAACAAAAC	57.480	29.630	0.00	0.00	0.00	2.43
862	863	9.740239	CTTCTTCTCATCATCTCAAAAACAAAA	57.260	29.630	0.00	0.00	0.00	2.44
863	864	9.123902	TCTTCTTCTCATCATCTCAAAAACAAA	57.876	29.630	0.00	0.00	0.00	2.83
864	865	8.681486	TCTTCTTCTCATCATCTCAAAAACAA	57.319	30.769	0.00	0.00	0.00	2.83
865	866	7.389884	CCTCTTCTTCTCATCATCTCAAAAACA	59.610	37.037	0.00	0.00	0.00	2.83
866	867	7.626028	GCCTCTTCTTCTCATCATCTCAAAAAC	60.626	40.741	0.00	0.00	0.00	2.43
872	873	4.624015	CTGCCTCTTCTTCTCATCATCTC	58.376	47.826	0.00	0.00	0.00	2.75
913	929	1.380380	CCAATGGAGGAAGCCCACC	60.380	63.158	0.00	0.00	42.77	4.61
994	1010	3.893763	CGCCGGAGACATCTCGCT	61.894	66.667	5.05	0.00	43.76	4.93
1695	1754	3.848019	CCAAATCAAACTCGAGAATTGCG	59.152	43.478	21.68	11.64	0.00	4.85
1727	1786	3.137728	TGGTAGTCGGATCACATCTAGGA	59.862	47.826	0.00	0.00	0.00	2.94
1744	1803	3.259374	ACTTCAGACAGACATGGTGGTAG	59.741	47.826	0.00	0.00	0.00	3.18
1770	1829	0.609957	TAACCGCGAACTGGAGGAGA	60.610	55.000	8.23	0.00	0.00	3.71
1773	1832	1.429148	GCATAACCGCGAACTGGAGG	61.429	60.000	8.23	0.00	0.00	4.30
1868	1927	0.518636	CCATGAAGCAACACCGTGAG	59.481	55.000	5.28	0.00	0.00	3.51
1870	1929	1.580942	CCCATGAAGCAACACCGTG	59.419	57.895	0.00	0.00	0.00	4.94
1872	1931	0.680921	ATCCCCATGAAGCAACACCG	60.681	55.000	0.00	0.00	0.00	4.94
1994	2065	1.406069	CCATCACCACCTGTAGTCAGC	60.406	57.143	0.00	0.00	40.09	4.26
2102	2176	5.241506	GGCAATGCTATTACCTGCAGAATAA	59.758	40.000	17.39	13.70	42.74	1.40
2221	2295	8.200120	CCCTAAACTAGGTACCACTAACAATAC	58.800	40.741	15.94	0.00	44.73	1.89
2252	2327	5.234752	GGAATATTCAAAACAACACCACCC	58.765	41.667	17.07	0.00	0.00	4.61
2306	2381	6.539173	TCCTGTTAGTTTTCATGTACCACAT	58.461	36.000	0.00	0.00	39.91	3.21
2352	2427	6.036735	GCTTCCAAATGTACGTATTGAGCTAA	59.963	38.462	8.61	0.00	0.00	3.09
2363	2438	5.049680	ACACAAGTAAGCTTCCAAATGTACG	60.050	40.000	0.00	0.00	31.49	3.67
2400	2484	8.921353	ATTTTTAGCAAGATCAGCAGAGATAT	57.079	30.769	11.97	0.00	0.00	1.63
2458	2542	3.110447	GGCACAACCAAACATCATGTT	57.890	42.857	0.00	0.00	43.41	2.71
2563	2647	0.457851	CGATCGAGTCCAGCCTCTTT	59.542	55.000	10.26	0.00	0.00	2.52
2570	2654	4.184629	AGGAAAATTTCGATCGAGTCCAG	58.815	43.478	18.54	0.00	0.00	3.86
2581	2665	5.921004	TGCAATTCCAAAGGAAAATTTCG	57.079	34.783	2.16	0.00	45.41	3.46
2620	2704	3.806949	AGAACACATAGGCCCTTTTCA	57.193	42.857	0.00	0.00	0.00	2.69
2653	2737	7.740519	AAAAATAAATCATGCAAGCTCGTAC	57.259	32.000	0.00	0.00	0.00	3.67
2798	2892	5.191727	ACAACCAATGACATTCCTATGGA	57.808	39.130	9.60	0.00	36.01	3.41
2873	2968	3.057033	ACAAAAGTTCAGCTCCATCATGC	60.057	43.478	0.00	0.00	0.00	4.06

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.