AutoCloner

Multiple sequence alignment - TraesCS1D01G052900

Loading Multiple Alignment...

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	TraesCS1D01G052900	chr1D	100.000	2345	0	0	1	2345	33704663	33707007	0.000000e+00	4331.0
1	TraesCS1D01G052900	chr1D	82.874	689	49	34	64	728	33668432	33669075	2.630000e-154	555.0
2	TraesCS1D01G052900	chr1D	82.534	584	58	29	836	1384	33712126	33712700	7.580000e-130	473.0
3	TraesCS1D01G052900	chr1D	81.659	229	16	11	629	837	33663189	33663411	1.440000e-37	167.0
4	TraesCS1D01G052900	chr1D	84.252	127	9	2	719	834	33642702	33642828	1.900000e-21	113.0
5	TraesCS1D01G052900	chr1D	95.385	65	3	0	1	65	3287678	3287742	1.150000e-18	104.0
6	TraesCS1D01G052900	chr1D	94.030	67	4	0	1	67	418567785	418567719	4.120000e-18	102.0
7	TraesCS1D01G052900	chr1A	88.664	1535	89	27	838	2325	32451232	32452728	0.000000e+00	1792.0
8	TraesCS1D01G052900	chr1A	83.838	495	48	12	954	1421	32291407	32291896	2.140000e-120	442.0
9	TraesCS1D01G052900	chr1A	81.449	566	66	21	837	1384	32302065	32302609	5.990000e-116	427.0
10	TraesCS1D01G052900	chr1A	80.790	557	63	32	828	1368	32376246	32376774	1.690000e-106	396.0
11	TraesCS1D01G052900	chr1A	82.672	479	21	21	289	720	32305053	32305516	3.680000e-98	368.0
12	TraesCS1D01G052900	chr1A	82.766	441	44	14	973	1402	32454444	32454863	4.760000e-97	364.0
13	TraesCS1D01G052900	chr1A	91.584	202	8	4	555	755	32450812	32451005	1.070000e-68	270.0
14	TraesCS1D01G052900	chr1A	84.191	272	22	9	1490	1757	32302675	32302929	6.470000e-61	244.0
15	TraesCS1D01G052900	chr1A	84.146	246	6	10	494	728	32380163	32380386	8.490000e-50	207.0
16	TraesCS1D01G052900	chr1A	88.439	173	12	5	75	240	32304878	32305049	3.950000e-48	202.0
17	TraesCS1D01G052900	chr1A	86.339	183	20	5	1496	1675	32424574	32424754	6.610000e-46	195.0
18	TraesCS1D01G052900	chr1A	86.782	174	7	3	494	651	32296234	32296407	1.850000e-41	180.0
19	TraesCS1D01G052900	chr1A	81.308	214	20	10	629	827	32290760	32290968	3.120000e-34	156.0
20	TraesCS1D01G052900	chr1A	95.082	61	3	0	482	542	32435838	32435898	1.920000e-16	97.1
21	TraesCS1D01G052900	chr1A	87.500	72	8	1	697	767	32296804	32296875	5.370000e-12	82.4
22	TraesCS1D01G052900	chr1A	92.683	41	1	2	836	876	32454299	32454337	9.050000e-05	58.4
23	TraesCS1D01G052900	chr1B	83.509	1043	89	42	836	1848	51538848	51539837	0.000000e+00	896.0
24	TraesCS1D01G052900	chr1B	82.737	950	92	28	836	1757	51546252	51547157	0.000000e+00	780.0
25	TraesCS1D01G052900	chr1B	87.191	445	34	12	935	1368	51323242	51323674	3.500000e-133	484.0
26	TraesCS1D01G052900	chr1B	84.026	457	50	16	941	1384	51299875	51300321	3.600000e-113	418.0
27	TraesCS1D01G052900	chr1B	85.859	396	22	13	75	463	51317845	51318213	7.860000e-105	390.0
28	TraesCS1D01G052900	chr1B	90.732	205	7	5	464	661	51319590	51319789	1.790000e-66	263.0
29	TraesCS1D01G052900	chr1B	92.090	177	9	3	653	826	51320996	51321170	6.470000e-61	244.0
30	TraesCS1D01G052900	chr1B	85.427	199	13	7	494	687	51443843	51444030	2.380000e-45	193.0
31	TraesCS1D01G052900	chr1B	79.931	289	34	11	2072	2344	51539969	51540249	8.550000e-45	191.0
32	TraesCS1D01G052900	chr1B	77.296	392	43	23	1450	1835	51300345	51300696	3.080000e-44	189.0
33	TraesCS1D01G052900	chr1B	80.074	271	37	10	1566	1835	51502456	51502710	3.980000e-43	185.0
34	TraesCS1D01G052900	chr1B	79.085	306	35	15	2058	2344	51563615	51563910	1.430000e-42	183.0
35	TraesCS1D01G052900	chr1B	90.299	134	8	3	619	748	51322532	51322664	1.110000e-38	171.0
36	TraesCS1D01G052900	chr1B	91.346	104	6	2	726	827	51299341	51299443	3.140000e-29	139.0
37	TraesCS1D01G052900	chr1B	82.895	152	13	3	696	834	51143537	51143688	8.800000e-25	124.0
38	TraesCS1D01G052900	chr1B	86.207	116	11	3	2080	2191	51315079	51315193	1.140000e-23	121.0
39	TraesCS1D01G052900	chr1B	82.278	158	10	7	1552	1692	51323782	51323938	1.140000e-23	121.0
40	TraesCS1D01G052900	chr1B	89.535	86	9	0	1763	1848	51563412	51563497	2.460000e-20	110.0
41	TraesCS1D01G052900	chr1B	79.861	144	15	6	838	981	51321353	51321482	2.480000e-15	93.5
42	TraesCS1D01G052900	chr1B	100.000	38	0	0	836	873	51323134	51323171	1.160000e-08	71.3
43	TraesCS1D01G052900	chr6D	96.825	63	2	0	1	63	468825517	468825579	3.190000e-19	106.0
44	TraesCS1D01G052900	chr6D	95.385	65	1	2	1	64	452672123	452672186	4.120000e-18	102.0
45	TraesCS1D01G052900	chr7A	95.385	65	3	0	1	65	8670930	8670866	1.150000e-18	104.0
46	TraesCS1D01G052900	chr7A	96.774	62	2	0	1	62	46055079	46055140	1.150000e-18	104.0
47	TraesCS1D01G052900	chr2B	94.203	69	1	3	1	67	759515863	759515930	4.120000e-18	102.0
48	TraesCS1D01G052900	chr2D	95.238	63	3	0	1	63	17243018	17243080	1.480000e-17	100.0
49	TraesCS1D01G052900	chr6A	95.161	62	3	0	2	63	34558007	34557946	5.330000e-17	99.0

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	TraesCS1D01G052900	chr1D	33704663	33707007	2344	False	4331.000000	4331	100.000000	1	2345	1	chr1D.!!$F5	2344
1	TraesCS1D01G052900	chr1D	33668432	33669075	643	False	555.000000	555	82.874000	64	728	1	chr1D.!!$F4	664
2	TraesCS1D01G052900	chr1D	33712126	33712700	574	False	473.000000	473	82.534000	836	1384	1	chr1D.!!$F6	548
3	TraesCS1D01G052900	chr1A	32450812	32454863	4051	False	621.100000	1792	88.924250	555	2325	4	chr1A.!!$F7	1770
4	TraesCS1D01G052900	chr1A	32302065	32305516	3451	False	310.250000	427	84.187750	75	1757	4	chr1A.!!$F5	1682
5	TraesCS1D01G052900	chr1A	32376246	32380386	4140	False	301.500000	396	82.468000	494	1368	2	chr1A.!!$F6	874
6	TraesCS1D01G052900	chr1A	32290760	32291896	1136	False	299.000000	442	82.573000	629	1421	2	chr1A.!!$F3	792
7	TraesCS1D01G052900	chr1B	51546252	51547157	905	False	780.000000	780	82.737000	836	1757	1	chr1B.!!$F4	921
8	TraesCS1D01G052900	chr1B	51538848	51540249	1401	False	543.500000	896	81.720000	836	2344	2	chr1B.!!$F7	1508
9	TraesCS1D01G052900	chr1B	51299341	51300696	1355	False	248.666667	418	84.222667	726	1835	3	chr1B.!!$F5	1109
10	TraesCS1D01G052900	chr1B	51315079	51323938	8859	False	217.644444	484	88.279667	75	2191	9	chr1B.!!$F6	2116

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
899	6613	0.03213	TGCTTCTCACTCGTGTCCAC	59.968	55.0	0.0	0.0	0.0	4.02	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2154	10103	0.737715	CTGCACGGTTAGACTCTGGC	60.738	60.0	0.0	0.0	0.0	4.85	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	1.897802	GTTCCAGAACCGGGACTAGAA	59.102	52.381	6.32	6.66	35.36	2.10
22	23	1.848652	TCCAGAACCGGGACTAGAAG	58.151	55.000	6.32	0.00	0.00	2.85
23	24	0.175989	CCAGAACCGGGACTAGAAGC	59.824	60.000	6.32	0.00	0.00	3.86
24	25	0.175989	CAGAACCGGGACTAGAAGCC	59.824	60.000	6.32	0.00	0.00	4.35
25	26	0.976590	AGAACCGGGACTAGAAGCCC	60.977	60.000	6.32	3.28	41.11	5.19
26	27	0.976590	GAACCGGGACTAGAAGCCCT	60.977	60.000	6.32	1.03	42.40	5.19
28	29	0.561680	ACCGGGACTAGAAGCCCTAT	59.438	55.000	6.32	3.92	42.40	2.57
29	30	0.969894	CCGGGACTAGAAGCCCTATG	59.030	60.000	14.91	3.72	42.40	2.23
30	31	0.969894	CGGGACTAGAAGCCCTATGG	59.030	60.000	14.91	0.00	42.40	2.74
31	32	1.480683	CGGGACTAGAAGCCCTATGGA	60.481	57.143	14.91	0.00	42.40	3.41
32	33	2.690840	GGGACTAGAAGCCCTATGGAA	58.309	52.381	0.00	0.00	41.31	3.53
33	34	2.369203	GGGACTAGAAGCCCTATGGAAC	59.631	54.545	0.00	0.00	41.31	3.62
34	35	2.369203	GGACTAGAAGCCCTATGGAACC	59.631	54.545	0.00	0.00	0.00	3.62
35	36	2.036089	GACTAGAAGCCCTATGGAACCG	59.964	54.545	0.00	0.00	0.00	4.44
37	38	1.148498	GAAGCCCTATGGAACCGGG	59.852	63.158	6.32	0.00	41.06	5.73
38	39	1.307517	AAGCCCTATGGAACCGGGA	60.308	57.895	6.32	0.00	40.55	5.14
40	41	2.070650	GCCCTATGGAACCGGGACT	61.071	63.158	6.32	0.00	40.55	3.85
41	42	0.761702	GCCCTATGGAACCGGGACTA	60.762	60.000	6.32	0.00	40.55	2.59
42	43	1.797320	CCCTATGGAACCGGGACTAA	58.203	55.000	6.32	0.00	40.55	2.24
44	45	2.104281	CCCTATGGAACCGGGACTAAAG	59.896	54.545	6.32	0.00	40.55	1.85
45	46	2.104281	CCTATGGAACCGGGACTAAAGG	59.896	54.545	6.32	1.66	0.00	3.11
46	47	0.255033	ATGGAACCGGGACTAAAGGC	59.745	55.000	6.32	0.00	0.00	4.35
53	54	3.351609	GGGACTAAAGGCCCGTTTT	57.648	52.632	4.78	0.00	34.00	2.43
54	55	1.171308	GGGACTAAAGGCCCGTTTTC	58.829	55.000	4.78	0.00	34.00	2.29
55	56	1.271762	GGGACTAAAGGCCCGTTTTCT	60.272	52.381	4.78	0.00	34.00	2.52
57	58	3.005554	GGACTAAAGGCCCGTTTTCTAC	58.994	50.000	0.00	0.00	0.00	2.59
58	59	3.307269	GGACTAAAGGCCCGTTTTCTACT	60.307	47.826	0.00	0.00	0.00	2.57
60	61	5.082251	ACTAAAGGCCCGTTTTCTACTAG	57.918	43.478	0.00	0.00	0.00	2.57
62	63	3.329929	AAGGCCCGTTTTCTACTAGTG	57.670	47.619	5.39	0.00	0.00	2.74
114	2813	2.171840	GTGTGCTCCCTCTTCTCTACA	58.828	52.381	0.00	0.00	0.00	2.74
123	2822	5.690865	TCCCTCTTCTCTACATCTCTCTTC	58.309	45.833	0.00	0.00	0.00	2.87
139	2839	6.393990	TCTCTCTTCATTTTCTTTCTCTCCG	58.606	40.000	0.00	0.00	0.00	4.63
235	2941	3.554934	ACTTGAAGCTCATGGTTGTTGA	58.445	40.909	0.00	0.00	33.64	3.18
248	2954	4.389374	TGGTTGTTGAGAACTTGAGATCC	58.611	43.478	0.00	0.00	0.00	3.36
251	2957	4.963318	TGTTGAGAACTTGAGATCCTGT	57.037	40.909	0.00	0.00	0.00	4.00
257	2963	6.401394	TGAGAACTTGAGATCCTGTAACATG	58.599	40.000	0.00	0.00	0.00	3.21
265	2971	9.350357	CTTGAGATCCTGTAACATGAAAAATTG	57.650	33.333	0.00	0.00	0.00	2.32
269	2975	6.968263	TCCTGTAACATGAAAAATTGGTGA	57.032	33.333	0.00	0.00	0.00	4.02
296	3002	9.467258	TTCGTAAATTATTATCTACAACTCCCG	57.533	33.333	0.00	0.00	0.00	5.14
307	3013	0.602905	CAACTCCCGTCTTCCACACC	60.603	60.000	0.00	0.00	0.00	4.16
324	3030	0.966920	ACCCTCCTACTGTCAACACG	59.033	55.000	0.00	0.00	0.00	4.49
373	3080	2.574006	TATCTGCTTGGGATGGATGC	57.426	50.000	0.00	0.00	0.00	3.91
412	3119	3.308188	GGCAGGTCCATGGTTAAAGTACT	60.308	47.826	12.58	0.00	34.01	2.73
413	3120	4.080751	GGCAGGTCCATGGTTAAAGTACTA	60.081	45.833	12.58	0.00	34.01	1.82
414	3121	5.116882	GCAGGTCCATGGTTAAAGTACTAG	58.883	45.833	12.58	0.00	0.00	2.57
439	3146	5.357257	AGTATTAAGTGCATTGGTCCTACG	58.643	41.667	0.00	0.00	0.00	3.51
443	3150	3.350219	AGTGCATTGGTCCTACGATTT	57.650	42.857	0.00	0.00	0.00	2.17
613	4700	6.312487	CAGCACTATATTCATTGCATACAGC	58.688	40.000	0.00	0.00	45.96	4.40
679	5987	1.613437	CACCCACCAGTTTTGATGGAC	59.387	52.381	0.00	0.00	40.51	4.02
709	6032	1.630126	ATCTGTTCGGCCTGCCTGAT	61.630	55.000	6.60	0.11	0.00	2.90
733	6056	2.708051	CAGCATGTGACCTTGATGACT	58.292	47.619	0.00	0.00	34.95	3.41
768	6094	1.322538	AATCCAGCCCGTGAAATGGC	61.323	55.000	0.00	0.00	43.51	4.40
804	6140	2.415893	CCAGTTTCGACATGGAAATGGC	60.416	50.000	0.79	0.00	38.12	4.40
821	6157	6.267471	GGAAATGGCATGAAATAATGGACCTA	59.733	38.462	0.00	0.00	0.00	3.08
879	6587	5.071923	GTCTGCCTATATAAACCCCACTCTT	59.928	44.000	0.00	0.00	0.00	2.85
899	6613	0.032130	TGCTTCTCACTCGTGTCCAC	59.968	55.000	0.00	0.00	0.00	4.02
996	8558	1.457346	GGGTGAACAAGATCAGCAGG	58.543	55.000	10.85	0.00	46.89	4.85
1113	8710	1.004745	GCTTCCTCTGGTTCATTCCCA	59.995	52.381	0.00	0.00	0.00	4.37
1424	9102	1.526887	CATCCGTGCCGTTAGCTAATG	59.473	52.381	17.33	17.33	44.23	1.90
1543	9257	0.815734	CGTCGGTGTGTCCCTCTTAT	59.184	55.000	0.00	0.00	0.00	1.73
1546	9260	3.067742	CGTCGGTGTGTCCCTCTTATATT	59.932	47.826	0.00	0.00	0.00	1.28
1558	9282	9.804977	TGTCCCTCTTATATTAGTAGTAGAACC	57.195	37.037	0.00	0.00	0.00	3.62
1610	9337	3.631145	AGTTTACTTCGCTGTACGTCA	57.369	42.857	0.00	0.00	44.19	4.35
1678	9422	2.821969	GTTTCAGCATGGATGGACTTGT	59.178	45.455	0.00	0.00	36.16	3.16
1679	9423	2.118313	TCAGCATGGATGGACTTGTG	57.882	50.000	0.00	0.00	36.16	3.33
1680	9424	0.454600	CAGCATGGATGGACTTGTGC	59.545	55.000	0.00	0.00	0.00	4.57
1681	9425	0.330604	AGCATGGATGGACTTGTGCT	59.669	50.000	0.00	0.00	38.03	4.40
1682	9426	0.454600	GCATGGATGGACTTGTGCTG	59.545	55.000	0.00	0.00	0.00	4.41
1683	9427	1.830279	CATGGATGGACTTGTGCTGT	58.170	50.000	0.00	0.00	0.00	4.40
1684	9428	2.165167	CATGGATGGACTTGTGCTGTT	58.835	47.619	0.00	0.00	0.00	3.16
1685	9429	1.608055	TGGATGGACTTGTGCTGTTG	58.392	50.000	0.00	0.00	0.00	3.33
1725	9471	1.971357	CCCCTGTCTCTGTGTAAGTGT	59.029	52.381	0.00	0.00	0.00	3.55
1726	9472	2.289072	CCCCTGTCTCTGTGTAAGTGTG	60.289	54.545	0.00	0.00	0.00	3.82
1874	9786	4.499037	ACCTTGTCAAGAATTTAACGCC	57.501	40.909	14.42	0.00	0.00	5.68
1875	9787	3.058501	ACCTTGTCAAGAATTTAACGCCG	60.059	43.478	14.42	0.00	0.00	6.46
1877	9789	1.807742	TGTCAAGAATTTAACGCCGGG	59.192	47.619	2.18	0.00	0.00	5.73
1885	9797	0.683973	TTTAACGCCGGGTTGTAGGA	59.316	50.000	15.93	0.00	39.75	2.94
2154	10103	0.729140	GAACAATTCCGCACAAGCCG	60.729	55.000	0.00	0.00	37.52	5.52
2170	10119	1.153823	CCGCCAGAGTCTAACCGTG	60.154	63.158	0.00	0.00	0.00	4.94
2205	10160	1.327690	AAAGCGCTCCGGATACTCCA	61.328	55.000	12.06	0.00	35.91	3.86
2211	10166	1.912417	CTCCGGATACTCCACCTAGG	58.088	60.000	3.57	7.41	35.91	3.02
2237	10192	1.225855	GATGTGTCGTTGACTTGGCA	58.774	50.000	0.00	0.00	33.15	4.92
2242	10197	1.971167	TCGTTGACTTGGCATGGGC	60.971	57.895	5.31	0.00	40.13	5.36
2295	10269	4.872691	ACACACTATAAGCAGAGACAATGC	59.127	41.667	0.00	0.00	44.18	3.56
2298	10272	5.939883	ACACTATAAGCAGAGACAATGCAAA	59.060	36.000	0.00	0.00	46.31	3.68

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
1	2	1.553706	TCTAGTCCCGGTTCTGGAAC	58.446	55.000	0.00	5.02	40.45	3.62
3	4	1.848652	CTTCTAGTCCCGGTTCTGGA	58.151	55.000	0.00	2.73	0.00	3.86
4	5	0.175989	GCTTCTAGTCCCGGTTCTGG	59.824	60.000	0.00	0.00	0.00	3.86
5	6	0.175989	GGCTTCTAGTCCCGGTTCTG	59.824	60.000	0.00	0.00	0.00	3.02
6	7	0.976590	GGGCTTCTAGTCCCGGTTCT	60.977	60.000	0.00	0.15	32.63	3.01
7	8	0.976590	AGGGCTTCTAGTCCCGGTTC	60.977	60.000	0.00	0.00	42.20	3.62
8	9	0.337428	TAGGGCTTCTAGTCCCGGTT	59.663	55.000	0.00	0.00	42.20	4.44
9	10	0.561680	ATAGGGCTTCTAGTCCCGGT	59.438	55.000	0.00	0.00	42.20	5.28
10	11	0.969894	CATAGGGCTTCTAGTCCCGG	59.030	60.000	0.00	0.00	42.20	5.73
13	14	2.369203	GGTTCCATAGGGCTTCTAGTCC	59.631	54.545	0.00	0.00	41.32	3.85
14	15	2.036089	CGGTTCCATAGGGCTTCTAGTC	59.964	54.545	0.00	0.00	0.00	2.59
15	16	2.040178	CGGTTCCATAGGGCTTCTAGT	58.960	52.381	0.00	0.00	0.00	2.57
16	17	1.344763	CCGGTTCCATAGGGCTTCTAG	59.655	57.143	0.00	0.00	0.00	2.43
18	19	1.345715	CCCGGTTCCATAGGGCTTCT	61.346	60.000	0.00	0.00	38.51	2.85
21	22	2.070650	GTCCCGGTTCCATAGGGCT	61.071	63.158	0.00	0.00	44.70	5.19
22	23	0.761702	TAGTCCCGGTTCCATAGGGC	60.762	60.000	0.00	0.00	44.70	5.19
23	24	1.797320	TTAGTCCCGGTTCCATAGGG	58.203	55.000	0.00	0.00	46.40	3.53
24	25	2.104281	CCTTTAGTCCCGGTTCCATAGG	59.896	54.545	0.00	0.00	0.00	2.57
25	26	2.484947	GCCTTTAGTCCCGGTTCCATAG	60.485	54.545	0.00	0.00	0.00	2.23
26	27	1.487558	GCCTTTAGTCCCGGTTCCATA	59.512	52.381	0.00	0.00	0.00	2.74
28	29	1.681076	GCCTTTAGTCCCGGTTCCA	59.319	57.895	0.00	0.00	0.00	3.53
29	30	1.077930	GGCCTTTAGTCCCGGTTCC	60.078	63.158	0.00	0.00	0.00	3.62
30	31	1.077930	GGGCCTTTAGTCCCGGTTC	60.078	63.158	0.84	0.00	32.00	3.62
31	32	3.084304	GGGCCTTTAGTCCCGGTT	58.916	61.111	0.84	0.00	32.00	4.44
35	36	1.171308	GAAAACGGGCCTTTAGTCCC	58.829	55.000	0.84	0.00	39.17	4.46
37	38	3.935315	AGTAGAAAACGGGCCTTTAGTC	58.065	45.455	0.84	0.00	0.00	2.59
38	39	4.529769	ACTAGTAGAAAACGGGCCTTTAGT	59.470	41.667	0.84	0.00	0.00	2.24
40	41	4.284234	ACACTAGTAGAAAACGGGCCTTTA	59.716	41.667	0.84	0.00	0.00	1.85
41	42	3.072038	ACACTAGTAGAAAACGGGCCTTT	59.928	43.478	0.84	0.00	0.00	3.11
42	43	2.636403	ACACTAGTAGAAAACGGGCCTT	59.364	45.455	0.84	0.00	0.00	4.35
44	45	2.756840	ACACTAGTAGAAAACGGGCC	57.243	50.000	3.59	0.00	0.00	5.80
45	46	4.814147	AGTTACACTAGTAGAAAACGGGC	58.186	43.478	3.59	0.00	0.00	6.13
46	47	5.405797	GGAGTTACACTAGTAGAAAACGGG	58.594	45.833	3.59	0.00	0.00	5.28
49	50	4.861462	GGCGGAGTTACACTAGTAGAAAAC	59.139	45.833	3.59	5.24	0.00	2.43
51	52	4.081406	TGGCGGAGTTACACTAGTAGAAA	58.919	43.478	3.59	0.00	0.00	2.52
52	53	3.441572	GTGGCGGAGTTACACTAGTAGAA	59.558	47.826	3.59	0.00	32.58	2.10
53	54	3.012518	GTGGCGGAGTTACACTAGTAGA	58.987	50.000	3.59	0.00	32.58	2.59
54	55	3.015327	AGTGGCGGAGTTACACTAGTAG	58.985	50.000	0.00	0.00	43.13	2.57
55	56	3.077484	AGTGGCGGAGTTACACTAGTA	57.923	47.619	0.00	0.00	43.13	1.82
58	59	3.077484	ACTAGTGGCGGAGTTACACTA	57.923	47.619	0.00	0.00	43.13	2.74
60	61	2.230750	AGAACTAGTGGCGGAGTTACAC	59.769	50.000	0.00	0.00	36.04	2.90
62	63	3.251571	CAAGAACTAGTGGCGGAGTTAC	58.748	50.000	0.00	0.00	36.04	2.50
67	68	2.522185	ACTACAAGAACTAGTGGCGGA	58.478	47.619	0.00	0.00	0.00	5.54
70	71	5.175859	TGCAATACTACAAGAACTAGTGGC	58.824	41.667	0.00	0.00	0.00	5.01
114	2813	7.041107	CGGAGAGAAAGAAAATGAAGAGAGAT	58.959	38.462	0.00	0.00	0.00	2.75
123	2822	4.486090	TCGAGACGGAGAGAAAGAAAATG	58.514	43.478	0.00	0.00	0.00	2.32
139	2839	0.963225	GGAAGCCCTAGGATCGAGAC	59.037	60.000	11.48	0.00	0.00	3.36
235	2941	6.611613	TCATGTTACAGGATCTCAAGTTCT	57.388	37.500	0.00	0.00	0.00	3.01
248	2954	7.594758	ACGAATCACCAATTTTTCATGTTACAG	59.405	33.333	0.00	0.00	0.00	2.74
251	2957	9.967346	TTTACGAATCACCAATTTTTCATGTTA	57.033	25.926	0.00	0.00	0.00	2.41
296	3002	1.550976	CAGTAGGAGGGTGTGGAAGAC	59.449	57.143	0.00	0.00	0.00	3.01
307	3013	3.512680	GATTCGTGTTGACAGTAGGAGG	58.487	50.000	0.00	0.00	0.00	4.30
324	3030	4.284829	TGAAAAGGGCCAAAATGGATTC	57.715	40.909	6.18	0.00	40.96	2.52
373	3080	1.021390	GCCATCCTCAACCTCACACG	61.021	60.000	0.00	0.00	0.00	4.49
412	3119	7.670605	AGGACCAATGCACTTAATACTACTA	57.329	36.000	0.00	0.00	0.00	1.82
413	3120	6.561519	AGGACCAATGCACTTAATACTACT	57.438	37.500	0.00	0.00	0.00	2.57
414	3121	6.420008	CGTAGGACCAATGCACTTAATACTAC	59.580	42.308	0.00	0.00	0.00	2.73
439	3146	9.651718	CAATATAACTCCGCTTAGTCAAAAATC	57.348	33.333	0.00	0.00	0.00	2.17
443	3150	7.101054	ACACAATATAACTCCGCTTAGTCAAA	58.899	34.615	0.00	0.00	0.00	2.69
613	4700	3.357079	GGCAACACTCACGGGCTG	61.357	66.667	0.00	0.00	0.00	4.85
679	5987	3.321497	GCCGAACAGATTATAGCTGGAG	58.679	50.000	0.00	1.70	37.69	3.86
709	6032	0.397564	TCAAGGTCACATGCTGCTCA	59.602	50.000	0.00	0.00	0.00	4.26
733	6056	5.305585	GCTGGATTTCCTTACCGATGAATA	58.694	41.667	0.00	0.00	36.82	1.75
768	6094	2.687200	TGGTGGATGGGGACTCGG	60.687	66.667	0.00	0.00	0.00	4.63
804	6140	4.520492	GCCACCTAGGTCCATTATTTCATG	59.480	45.833	12.84	0.00	40.61	3.07
821	6157	0.816421	GGTGTTACACGTTGCCACCT	60.816	55.000	9.52	0.00	41.83	4.00
879	6587	0.750249	TGGACACGAGTGAGAAGCAA	59.250	50.000	10.50	0.00	0.00	3.91
899	6613	1.110442	AGCGAATGGAGTGGAGAGAG	58.890	55.000	0.00	0.00	0.00	3.20
996	8558	2.352915	CGAGAGAGCGCCATCGAC	60.353	66.667	2.29	1.90	37.35	4.20
1106	8703	1.860950	CTAAGCATCGTCGTGGGAATG	59.139	52.381	0.00	0.00	0.00	2.67
1113	8710	2.080286	AAGCAACTAAGCATCGTCGT	57.920	45.000	0.00	0.00	36.85	4.34
1377	9003	1.001268	CTATCATGGGACGTGTCTCGG	60.001	57.143	0.00	0.00	44.69	4.63
1378	9004	1.600663	GCTATCATGGGACGTGTCTCG	60.601	57.143	0.00	0.00	46.00	4.04
1379	9005	1.683917	AGCTATCATGGGACGTGTCTC	59.316	52.381	0.00	0.00	0.00	3.36
1380	9006	1.781786	AGCTATCATGGGACGTGTCT	58.218	50.000	0.00	0.00	0.00	3.41
1383	9009	3.507622	TGATCTAGCTATCATGGGACGTG	59.492	47.826	0.00	0.00	30.92	4.49
1424	9102	5.460419	CGACCAACAGAACAGATATAAGCTC	59.540	44.000	0.00	0.00	0.00	4.09
1558	9282	7.996385	ACCCCGATTGATTTTCTACTTTATTG	58.004	34.615	0.00	0.00	0.00	1.90
1610	9337	3.132646	ACACACAAATCAGGCACAAACAT	59.867	39.130	0.00	0.00	0.00	2.71
1678	9422	0.038067	GGATGCATTGCACAACAGCA	60.038	50.000	14.66	12.80	43.04	4.41
1679	9423	0.738412	GGGATGCATTGCACAACAGC	60.738	55.000	14.66	0.00	43.04	4.40
1680	9424	0.108520	GGGGATGCATTGCACAACAG	60.109	55.000	14.66	0.00	43.04	3.16
1681	9425	1.543065	GGGGGATGCATTGCACAACA	61.543	55.000	14.66	0.00	43.04	3.33
1682	9426	1.218854	GGGGGATGCATTGCACAAC	59.781	57.895	14.66	8.47	43.04	3.32
1683	9427	0.544833	AAGGGGGATGCATTGCACAA	60.545	50.000	14.66	0.00	43.04	3.33
1684	9428	0.544833	AAAGGGGGATGCATTGCACA	60.545	50.000	14.66	0.00	43.04	4.57
1685	9429	0.176449	GAAAGGGGGATGCATTGCAC	59.824	55.000	14.66	7.99	43.04	4.57
1725	9471	5.560760	GCATTTCTCTTTGAACACGATCACA	60.561	40.000	0.00	0.00	33.88	3.58
1726	9472	4.848299	GCATTTCTCTTTGAACACGATCAC	59.152	41.667	0.00	0.00	33.88	3.06
1849	9761	6.432107	GCGTTAAATTCTTGACAAGGTTACA	58.568	36.000	15.13	0.00	0.00	2.41
1863	9775	2.096335	CCTACAACCCGGCGTTAAATTC	59.904	50.000	6.01	0.00	31.77	2.17
1874	9786	3.679824	AGAGAAAAGTCCTACAACCCG	57.320	47.619	0.00	0.00	0.00	5.28
1875	9787	9.511272	TTTTAATAGAGAAAAGTCCTACAACCC	57.489	33.333	0.00	0.00	0.00	4.11
1951	9887	9.765795	AAGTTATACTCATGTTAATGCTCTACC	57.234	33.333	0.00	0.00	33.47	3.18
1996	9932	8.711457	GTGCACATAAAAATTTCACATAAAGCT	58.289	29.630	13.17	0.00	0.00	3.74
1999	9935	8.986847	CCAGTGCACATAAAAATTTCACATAAA	58.013	29.630	21.04	0.00	0.00	1.40
2148	10096	0.741221	GGTTAGACTCTGGCGGCTTG	60.741	60.000	11.43	3.13	0.00	4.01
2154	10103	0.737715	CTGCACGGTTAGACTCTGGC	60.738	60.000	0.00	0.00	0.00	4.85
2170	10119	4.035675	AGCGCTTTACCAAAATATCTCTGC	59.964	41.667	2.64	0.00	0.00	4.26
2205	10160	4.287552	ACGACACATCCTTATTCCTAGGT	58.712	43.478	9.08	0.00	34.29	3.08
2211	10166	5.163854	CCAAGTCAACGACACATCCTTATTC	60.164	44.000	0.00	0.00	34.60	1.75
2237	10192	3.811152	ATATCCATCCTCCTAGCCCAT	57.189	47.619	0.00	0.00	0.00	4.00

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.