AutoCloner

Multiple sequence alignment - TraesCS2B01G448300

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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	TraesCS2B01G448300	chr2B	100.000	3164	0	0	1	3164	641076862	641073699	0.000000e+00	5843.0
1	TraesCS2B01G448300	chr2B	78.359	841	153	22	1137	1973	707731474	707732289	4.680000e-143	518.0
2	TraesCS2B01G448300	chr2B	78.868	530	92	7	1627	2154	90556540	90556029	1.090000e-89	340.0
3	TraesCS2B01G448300	chr2A	92.281	1425	85	8	836	2253	680502440	680501034	0.000000e+00	1999.0
4	TraesCS2B01G448300	chr2A	85.789	760	84	12	2415	3164	680501043	680500298	0.000000e+00	784.0
5	TraesCS2B01G448300	chr2A	83.250	597	94	5	1315	1908	58398879	58398286	7.720000e-151	544.0
6	TraesCS2B01G448300	chr2D	91.748	1430	90	9	836	2252	538272521	538271107	0.000000e+00	1962.0
7	TraesCS2B01G448300	chr2D	82.368	1140	162	26	1021	2154	57258989	57257883	0.000000e+00	955.0
8	TraesCS2B01G448300	chr2D	92.000	350	17	7	2686	3029	538270790	538270446	6.140000e-132	481.0
9	TraesCS2B01G448300	chr2D	90.813	283	22	4	2415	2697	538271115	538270837	2.980000e-100	375.0
10	TraesCS2B01G448300	chr2D	90.244	164	12	3	2255	2414	315491312	315491149	8.890000e-51	211.0
11	TraesCS2B01G448300	chr2D	93.269	104	7	0	3061	3164	538270219	538270116	1.520000e-33	154.0
12	TraesCS2B01G448300	chr2D	83.333	144	22	2	2012	2154	57168142	57168000	7.120000e-27	132.0
13	TraesCS2B01G448300	chr2D	84.722	72	6	5	768	836	370235153	370235222	2.040000e-07	67.6
14	TraesCS2B01G448300	chr5B	98.805	837	10	0	1	837	328220699	328219863	0.000000e+00	1491.0
15	TraesCS2B01G448300	chr1B	97.509	843	15	2	1	837	357339855	357339013	0.000000e+00	1435.0
16	TraesCS2B01G448300	chr1B	87.845	181	12	6	2243	2414	635929378	635929557	1.490000e-48	204.0
17	TraesCS2B01G448300	chr3B	95.154	846	29	4	1	837	124070222	124069380	0.000000e+00	1325.0
18	TraesCS2B01G448300	chr6A	83.190	1166	165	19	992	2155	534798828	534797692	0.000000e+00	1038.0
19	TraesCS2B01G448300	chr6D	83.162	1170	158	27	992	2155	388152806	388151670	0.000000e+00	1033.0
20	TraesCS2B01G448300	chr6D	86.111	72	10	0	768	839	84277224	84277153	9.410000e-11	78.7
21	TraesCS2B01G448300	chr6B	81.865	1169	173	28	992	2154	579888009	579886874	0.000000e+00	948.0
22	TraesCS2B01G448300	chr6B	83.824	68	11	0	768	835	584215120	584215053	7.330000e-07	65.8
23	TraesCS2B01G448300	chrUn	82.752	1032	146	16	1133	2154	361327630	361326621	0.000000e+00	891.0
24	TraesCS2B01G448300	chrUn	90.854	164	9	4	2255	2414	369332804	369332965	6.870000e-52	215.0
25	TraesCS2B01G448300	chrUn	90.303	165	9	5	2255	2414	281281953	281281791	3.200000e-50	209.0
26	TraesCS2B01G448300	chrUn	90.244	164	10	4	2255	2414	308142945	308142784	3.200000e-50	209.0
27	TraesCS2B01G448300	chr7B	81.845	1030	159	14	1133	2154	720537770	720536761	0.000000e+00	841.0
28	TraesCS2B01G448300	chr1A	90.854	164	9	4	2255	2414	588184716	588184877	6.870000e-52	215.0
29	TraesCS2B01G448300	chr1A	90.854	164	9	4	2255	2414	588191438	588191599	6.870000e-52	215.0
30	TraesCS2B01G448300	chr1A	90.244	164	10	4	2255	2414	588208268	588208429	3.200000e-50	209.0
31	TraesCS2B01G448300	chr1A	81.218	197	33	4	636	829	256698650	256698845	4.230000e-34	156.0
32	TraesCS2B01G448300	chr4D	89.941	169	8	5	2255	2414	29656472	29656640	3.200000e-50	209.0
33	TraesCS2B01G448300	chr4D	92.308	52	4	0	786	837	175811388	175811439	1.220000e-09	75.0
34	TraesCS2B01G448300	chr4A	84.286	70	9	2	768	836	702680579	702680647	2.040000e-07	67.6
35	TraesCS2B01G448300	chr3A	100.000	28	0	0	2566	2593	21319607	21319634	6.000000e-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	TraesCS2B01G448300	chr2B	641073699	641076862	3163	True	5843.0	5843	100.0000	1	3164	1	chr2B.!!$R2	3163
1	TraesCS2B01G448300	chr2B	707731474	707732289	815	False	518.0	518	78.3590	1137	1973	1	chr2B.!!$F1	836
2	TraesCS2B01G448300	chr2B	90556029	90556540	511	True	340.0	340	78.8680	1627	2154	1	chr2B.!!$R1	527
3	TraesCS2B01G448300	chr2A	680500298	680502440	2142	True	1391.5	1999	89.0350	836	3164	2	chr2A.!!$R2	2328
4	TraesCS2B01G448300	chr2A	58398286	58398879	593	True	544.0	544	83.2500	1315	1908	1	chr2A.!!$R1	593
5	TraesCS2B01G448300	chr2D	57257883	57258989	1106	True	955.0	955	82.3680	1021	2154	1	chr2D.!!$R2	1133
6	TraesCS2B01G448300	chr2D	538270116	538272521	2405	True	743.0	1962	91.9575	836	3164	4	chr2D.!!$R4	2328
7	TraesCS2B01G448300	chr5B	328219863	328220699	836	True	1491.0	1491	98.8050	1	837	1	chr5B.!!$R1	836
8	TraesCS2B01G448300	chr1B	357339013	357339855	842	True	1435.0	1435	97.5090	1	837	1	chr1B.!!$R1	836
9	TraesCS2B01G448300	chr3B	124069380	124070222	842	True	1325.0	1325	95.1540	1	837	1	chr3B.!!$R1	836
10	TraesCS2B01G448300	chr6A	534797692	534798828	1136	True	1038.0	1038	83.1900	992	2155	1	chr6A.!!$R1	1163
11	TraesCS2B01G448300	chr6D	388151670	388152806	1136	True	1033.0	1033	83.1620	992	2155	1	chr6D.!!$R2	1163
12	TraesCS2B01G448300	chr6B	579886874	579888009	1135	True	948.0	948	81.8650	992	2154	1	chr6B.!!$R1	1162
13	TraesCS2B01G448300	chrUn	361326621	361327630	1009	True	891.0	891	82.7520	1133	2154	1	chrUn.!!$R3	1021
14	TraesCS2B01G448300	chr7B	720536761	720537770	1009	True	841.0	841	81.8450	1133	2154	1	chr7B.!!$R1	1021

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
905	923	0.036022	TCGTGTCATGTCCATTGCCA	59.964	50.0	0.00	0.00	0.00	4.92	F
1505	1545	1.084370	GTGTACGAGCACATGGAGCC	61.084	60.0	8.57	1.08	39.07	4.70	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2073	2131	0.622665	CCCCTTCCAGCATCTTCACT	59.377	55.0	0.00	0.0	0.0	3.41	R
2922	3049	0.657840	GCAGCGGCGATGAGTAATTT	59.342	50.0	30.95	0.0	0.0	1.82	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
120	121	2.489938	TAGTGCTGCTAGGTTTTGGG	57.510	50.000	0.00	0.00	0.00	4.12
146	147	0.040204	CTCCTTGCCAATGGAAGGGT	59.960	55.000	21.84	0.00	39.49	4.34
442	457	3.117663	ACAACAAGGGGCTACAGAAGAAA	60.118	43.478	0.00	0.00	0.00	2.52
674	689	4.202367	CGGCCCAAATAAGGAGAGAACTAT	60.202	45.833	0.00	0.00	0.00	2.12
853	868	6.387041	AGTAATTGGATCTTACGACGATGA	57.613	37.500	0.00	0.00	34.88	2.92
862	877	1.934589	TACGACGATGATGGCAAAGG	58.065	50.000	0.00	0.00	0.00	3.11
882	900	2.113139	CCGCCACCACCTTCAGTT	59.887	61.111	0.00	0.00	0.00	3.16
885	903	1.966451	GCCACCACCTTCAGTTCCG	60.966	63.158	0.00	0.00	0.00	4.30
888	906	0.944311	CACCACCTTCAGTTCCGTCG	60.944	60.000	0.00	0.00	0.00	5.12
896	914	0.671796	TCAGTTCCGTCGTGTCATGT	59.328	50.000	0.00	0.00	0.00	3.21
905	923	0.036022	TCGTGTCATGTCCATTGCCA	59.964	50.000	0.00	0.00	0.00	4.92
922	940	2.819595	ATCGGTGAGCGCGCAAAT	60.820	55.556	35.10	13.58	0.00	2.32
924	942	3.787676	CGGTGAGCGCGCAAATCA	61.788	61.111	35.10	25.15	0.00	2.57
942	961	7.079475	GCAAATCAAAATTTTGGAATCCACAG	58.921	34.615	26.45	11.01	38.66	3.66
1129	1163	1.772836	GGGGATCACTACTGGTACGT	58.227	55.000	0.00	0.00	0.00	3.57
1130	1164	2.105766	GGGGATCACTACTGGTACGTT	58.894	52.381	0.00	0.00	0.00	3.99
1260	1294	2.158726	GGGGTTCACCAACAACTACTCA	60.159	50.000	0.00	0.00	42.91	3.41
1261	1295	2.876550	GGGTTCACCAACAACTACTCAC	59.123	50.000	0.00	0.00	39.85	3.51
1262	1296	3.433173	GGGTTCACCAACAACTACTCACT	60.433	47.826	0.00	0.00	39.85	3.41
1263	1297	4.202284	GGGTTCACCAACAACTACTCACTA	60.202	45.833	0.00	0.00	39.85	2.74
1264	1298	4.748600	GGTTCACCAACAACTACTCACTAC	59.251	45.833	0.00	0.00	33.70	2.73
1265	1299	5.452917	GGTTCACCAACAACTACTCACTACT	60.453	44.000	0.00	0.00	33.70	2.57
1266	1300	5.449107	TCACCAACAACTACTCACTACTC	57.551	43.478	0.00	0.00	0.00	2.59
1269	1303	5.009710	CACCAACAACTACTCACTACTCAGA	59.990	44.000	0.00	0.00	0.00	3.27
1336	1370	3.379445	TGCTCCCGAACGGACTCC	61.379	66.667	15.07	1.22	34.86	3.85
1442	1479	3.041940	CCACCACGTCAACCTCGC	61.042	66.667	0.00	0.00	0.00	5.03
1505	1545	1.084370	GTGTACGAGCACATGGAGCC	61.084	60.000	8.57	1.08	39.07	4.70
1544	1593	4.421479	CTTCGACTCTGCCGCCGT	62.421	66.667	0.00	0.00	0.00	5.68
2073	2131	2.986290	CCGACCATGGGCACAGTA	59.014	61.111	20.22	0.00	0.00	2.74
2098	2156	0.842635	GATGCTGGAAGGGGAGATGT	59.157	55.000	0.00	0.00	0.00	3.06
2111	2169	2.297597	GGGAGATGTACATTCCTCCTCG	59.702	54.545	29.14	0.00	43.50	4.63
2208	2266	1.282930	GGAGTGGTTCAAGACGCGAC	61.283	60.000	15.93	6.86	0.00	5.19
2226	2284	2.717044	CCACTCCATGGTCGCCGTA	61.717	63.158	12.58	0.00	44.46	4.02
2231	2289	1.611977	CTCCATGGTCGCCGTAGATAA	59.388	52.381	12.58	0.00	0.00	1.75
2243	2301	5.049198	TCGCCGTAGATAATTGAGTACGATT	60.049	40.000	13.70	0.00	40.53	3.34
2244	2302	5.628193	CGCCGTAGATAATTGAGTACGATTT	59.372	40.000	13.70	0.00	40.53	2.17
2245	2303	6.143438	CGCCGTAGATAATTGAGTACGATTTT	59.857	38.462	13.70	0.00	40.53	1.82
2246	2304	7.324375	CGCCGTAGATAATTGAGTACGATTTTA	59.676	37.037	13.70	0.00	40.53	1.52
2247	2305	8.636843	GCCGTAGATAATTGAGTACGATTTTAG	58.363	37.037	13.70	2.01	40.53	1.85
2248	2306	9.674824	CCGTAGATAATTGAGTACGATTTTAGT	57.325	33.333	13.70	0.00	40.53	2.24
2258	2316	9.710979	TTGAGTACGATTTTAGTTTTCTGTTTG	57.289	29.630	0.00	0.00	0.00	2.93
2259	2317	8.885722	TGAGTACGATTTTAGTTTTCTGTTTGT	58.114	29.630	0.00	0.00	0.00	2.83
2260	2318	9.366513	GAGTACGATTTTAGTTTTCTGTTTGTC	57.633	33.333	0.00	0.00	0.00	3.18
2261	2319	9.106070	AGTACGATTTTAGTTTTCTGTTTGTCT	57.894	29.630	0.00	0.00	0.00	3.41
2272	2330	9.125026	AGTTTTCTGTTTGTCTAATTCACATCT	57.875	29.630	0.00	0.00	0.00	2.90
2275	2333	9.996554	TTTCTGTTTGTCTAATTCACATCTAGA	57.003	29.630	0.00	0.00	0.00	2.43
2277	2335	9.591792	TCTGTTTGTCTAATTCACATCTAGATG	57.408	33.333	27.63	27.63	44.15	2.90
2304	2362	8.635765	TTTTTAAGGATGTCACATCTAAGCTT	57.364	30.769	17.46	13.56	0.00	3.74
2305	2363	7.849804	TTTAAGGATGTCACATCTAAGCTTC	57.150	36.000	17.46	0.00	0.00	3.86
2306	2364	4.414337	AGGATGTCACATCTAAGCTTCC	57.586	45.455	17.46	0.00	0.00	3.46
2307	2365	3.776969	AGGATGTCACATCTAAGCTTCCA	59.223	43.478	17.46	0.00	0.00	3.53
2308	2366	4.411540	AGGATGTCACATCTAAGCTTCCAT	59.588	41.667	17.46	0.00	0.00	3.41
2309	2367	5.604231	AGGATGTCACATCTAAGCTTCCATA	59.396	40.000	17.46	0.00	0.00	2.74
2310	2368	6.100279	AGGATGTCACATCTAAGCTTCCATAA	59.900	38.462	17.46	0.00	0.00	1.90
2311	2369	6.767902	GGATGTCACATCTAAGCTTCCATAAA	59.232	38.462	17.46	0.00	0.00	1.40
2312	2370	7.446625	GGATGTCACATCTAAGCTTCCATAAAT	59.553	37.037	17.46	0.00	0.00	1.40
2313	2371	9.494271	GATGTCACATCTAAGCTTCCATAAATA	57.506	33.333	10.81	0.00	0.00	1.40
2324	2382	8.807948	AAGCTTCCATAAATATATAATGCCGT	57.192	30.769	0.00	0.00	0.00	5.68
2325	2383	9.899661	AAGCTTCCATAAATATATAATGCCGTA	57.100	29.630	0.00	0.00	0.00	4.02
2326	2384	9.899661	AGCTTCCATAAATATATAATGCCGTAA	57.100	29.630	3.47	0.00	0.00	3.18
2376	2434	3.470709	CACAAACAGAGTGGACATCAGT	58.529	45.455	0.00	0.00	33.43	3.41
2377	2435	3.879295	CACAAACAGAGTGGACATCAGTT	59.121	43.478	0.00	0.00	33.43	3.16
2378	2436	4.336433	CACAAACAGAGTGGACATCAGTTT	59.664	41.667	0.00	0.00	37.00	2.66
2379	2437	5.527214	CACAAACAGAGTGGACATCAGTTTA	59.473	40.000	0.00	0.00	35.12	2.01
2380	2438	5.760253	ACAAACAGAGTGGACATCAGTTTAG	59.240	40.000	0.00	0.00	35.12	1.85
2381	2439	5.808366	AACAGAGTGGACATCAGTTTAGA	57.192	39.130	0.00	0.00	0.00	2.10
2382	2440	6.365970	AACAGAGTGGACATCAGTTTAGAT	57.634	37.500	0.00	0.00	0.00	1.98
2464	2522	5.429130	CTTAAGGACCCCACTACAAATCTC	58.571	45.833	0.00	0.00	0.00	2.75
2524	2582	2.755103	GAGGATGGCAAGTTTAGTTGGG	59.245	50.000	0.00	0.00	0.00	4.12
2533	2591	5.356426	GCAAGTTTAGTTGGGTGACAAATT	58.644	37.500	0.00	0.00	41.58	1.82
2541	2599	4.755123	AGTTGGGTGACAAATTCGTCTTAG	59.245	41.667	0.00	0.00	41.58	2.18
2547	2605	7.118680	TGGGTGACAAATTCGTCTTAGTTTATC	59.881	37.037	0.00	0.00	36.82	1.75
2549	2607	8.381387	GGTGACAAATTCGTCTTAGTTTATCTC	58.619	37.037	0.00	0.00	36.82	2.75
2601	2659	9.859427	ACTAAATTTGTTATCATCACACCAATG	57.141	29.630	0.00	0.00	0.00	2.82
2619	2677	7.013464	ACACCAATGCAAATTGACATGAAAAAT	59.987	29.630	0.00	0.00	33.55	1.82
2639	2697	6.851222	AAATGTCAGATTTATCGTGCCTAG	57.149	37.500	0.00	0.00	0.00	3.02
2659	2717	8.181573	TGCCTAGAAATTTGACGTCATATTTTC	58.818	33.333	33.02	29.04	37.53	2.29
2682	2740	6.550843	TCAGTGTTTTCATACAAAGTGTGTG	58.449	36.000	0.00	0.00	41.89	3.82
2683	2741	6.150307	TCAGTGTTTTCATACAAAGTGTGTGT	59.850	34.615	0.00	0.00	41.89	3.72
2684	2742	6.468956	CAGTGTTTTCATACAAAGTGTGTGTC	59.531	38.462	0.00	0.00	41.89	3.67
2685	2743	6.374333	AGTGTTTTCATACAAAGTGTGTGTCT	59.626	34.615	0.00	0.00	41.89	3.41
2686	2744	7.551262	AGTGTTTTCATACAAAGTGTGTGTCTA	59.449	33.333	0.00	0.00	41.89	2.59
2687	2745	8.342634	GTGTTTTCATACAAAGTGTGTGTCTAT	58.657	33.333	0.00	0.00	41.89	1.98
2688	2746	9.549078	TGTTTTCATACAAAGTGTGTGTCTATA	57.451	29.630	0.00	0.00	41.89	1.31
2802	2928	5.855740	AAAAAGGGACAATACACCGAAAA	57.144	34.783	0.00	0.00	0.00	2.29
2913	3039	5.305644	GCTGATCCCTTATCACCTTTAGAGA	59.694	44.000	0.00	0.00	39.77	3.10
2975	3102	0.896940	ACTCGAGTAGGGCCGTTTCA	60.897	55.000	18.46	0.00	0.00	2.69
3013	3144	1.004918	CGCGTCACCCTTCTTCCTT	60.005	57.895	0.00	0.00	0.00	3.36
3014	3145	0.245539	CGCGTCACCCTTCTTCCTTA	59.754	55.000	0.00	0.00	0.00	2.69
3023	3154	1.571919	CTTCTTCCTTATCCGCACCG	58.428	55.000	0.00	0.00	0.00	4.94
3030	3161	1.078072	TTATCCGCACCGCACCAAT	60.078	52.632	0.00	0.00	0.00	3.16
3047	3178	3.544503	ATGCCCAAACCCACCCCAG	62.545	63.158	0.00	0.00	0.00	4.45
3049	3180	2.117423	CCCAAACCCACCCCAGAC	59.883	66.667	0.00	0.00	0.00	3.51

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
120	121	1.134907	CCATTGGCAAGGAGTTGATGC	60.135	52.381	14.30	0.00	35.46	3.91
146	147	0.612174	AGGCTGGAAGTAGCGACTGA	60.612	55.000	0.00	0.00	44.60	3.41
567	582	3.243907	CCTCTCCAGACGAACAGTTTCTT	60.244	47.826	0.00	0.00	0.00	2.52
580	595	0.111446	CGCTATCCCTCCTCTCCAGA	59.889	60.000	0.00	0.00	0.00	3.86
718	733	3.681835	GTCTCAGGTCGCCCGTGT	61.682	66.667	0.00	0.00	35.12	4.49
870	888	1.366366	CGACGGAACTGAAGGTGGT	59.634	57.895	0.00	0.00	0.00	4.16
873	891	0.031721	GACACGACGGAACTGAAGGT	59.968	55.000	0.00	0.00	0.00	3.50
882	900	0.606096	AATGGACATGACACGACGGA	59.394	50.000	0.00	0.00	0.00	4.69
885	903	0.447801	GGCAATGGACATGACACGAC	59.552	55.000	0.00	0.00	0.00	4.34
888	906	1.064505	CGATGGCAATGGACATGACAC	59.935	52.381	0.00	0.00	44.92	3.67
896	914	1.451927	GCTCACCGATGGCAATGGA	60.452	57.895	14.50	0.00	0.00	3.41
905	923	2.813179	GATTTGCGCGCTCACCGAT	61.813	57.895	33.29	15.80	40.02	4.18
922	940	6.648192	ACAACTGTGGATTCCAAAATTTTGA	58.352	32.000	28.44	12.81	40.55	2.69
924	942	7.280652	CAGAACAACTGTGGATTCCAAAATTTT	59.719	33.333	7.05	0.00	41.30	1.82
942	961	6.611381	TGAGCAAAATGTATAGCAGAACAAC	58.389	36.000	0.00	0.00	0.00	3.32
1115	1149	1.336517	GCAGCAACGTACCAGTAGTGA	60.337	52.381	0.00	0.00	0.00	3.41
1260	1294	1.394618	GCCGATCCTGTCTGAGTAGT	58.605	55.000	0.00	0.00	0.00	2.73
1261	1295	0.309302	CGCCGATCCTGTCTGAGTAG	59.691	60.000	0.00	0.00	0.00	2.57
1262	1296	1.725557	GCGCCGATCCTGTCTGAGTA	61.726	60.000	0.00	0.00	0.00	2.59
1263	1297	3.069980	GCGCCGATCCTGTCTGAGT	62.070	63.158	0.00	0.00	0.00	3.41
1264	1298	2.279120	GCGCCGATCCTGTCTGAG	60.279	66.667	0.00	0.00	0.00	3.35
1265	1299	3.838271	GGCGCCGATCCTGTCTGA	61.838	66.667	12.58	0.00	0.00	3.27
1292	1326	0.169894	GTACACGACTCCCGACTTCC	59.830	60.000	0.00	0.00	41.76	3.46
1293	1327	0.877071	TGTACACGACTCCCGACTTC	59.123	55.000	0.00	0.00	41.76	3.01
1294	1328	0.879765	CTGTACACGACTCCCGACTT	59.120	55.000	0.00	0.00	41.76	3.01
1295	1329	0.959372	CCTGTACACGACTCCCGACT	60.959	60.000	0.00	0.00	41.76	4.18
1296	1330	1.505353	CCTGTACACGACTCCCGAC	59.495	63.158	0.00	0.00	41.76	4.79
1297	1331	1.676635	CCCTGTACACGACTCCCGA	60.677	63.158	0.00	0.00	41.76	5.14
1298	1332	2.707849	CCCCTGTACACGACTCCCG	61.708	68.421	0.00	0.00	45.44	5.14
1299	1333	3.015312	GCCCCTGTACACGACTCCC	62.015	68.421	0.00	0.00	0.00	4.30
1302	1336	2.599578	ACGCCCCTGTACACGACT	60.600	61.111	10.20	0.00	0.00	4.18
1332	1366	2.915659	TTCACAGCGACCGGGAGT	60.916	61.111	6.32	0.00	0.00	3.85
1442	1479	1.449246	CAGAAGCCGAAGAGCCTGG	60.449	63.158	0.00	0.00	0.00	4.45
1557	1606	1.153628	GGCGATGCCGTACAGAGTT	60.154	57.895	0.00	0.00	39.62	3.01
2069	2127	3.529533	CCTTCCAGCATCTTCACTACTG	58.470	50.000	0.00	0.00	0.00	2.74
2070	2128	2.503356	CCCTTCCAGCATCTTCACTACT	59.497	50.000	0.00	0.00	0.00	2.57
2073	2131	0.622665	CCCCTTCCAGCATCTTCACT	59.377	55.000	0.00	0.00	0.00	3.41
2098	2156	0.685131	TTCGGCCGAGGAGGAATGTA	60.685	55.000	29.20	6.31	45.00	2.29
2162	2220	1.696832	GGTGCTCGCTCGACCATTTC	61.697	60.000	0.00	0.00	0.00	2.17
2246	2304	9.125026	AGATGTGAATTAGACAAACAGAAAACT	57.875	29.630	0.00	0.00	0.00	2.66
2249	2307	9.996554	TCTAGATGTGAATTAGACAAACAGAAA	57.003	29.630	0.00	0.00	0.00	2.52
2251	2309	9.591792	CATCTAGATGTGAATTAGACAAACAGA	57.408	33.333	22.42	0.00	34.23	3.41
2279	2337	8.635765	AAGCTTAGATGTGACATCCTTAAAAA	57.364	30.769	21.05	6.46	0.00	1.94
2280	2338	7.336931	GGAAGCTTAGATGTGACATCCTTAAAA	59.663	37.037	21.05	8.00	0.00	1.52
2281	2339	6.823689	GGAAGCTTAGATGTGACATCCTTAAA	59.176	38.462	21.05	10.18	0.00	1.52
2282	2340	6.070251	TGGAAGCTTAGATGTGACATCCTTAA	60.070	38.462	21.05	13.11	0.00	1.85
2283	2341	5.425217	TGGAAGCTTAGATGTGACATCCTTA	59.575	40.000	21.05	6.22	0.00	2.69
2284	2342	4.225942	TGGAAGCTTAGATGTGACATCCTT	59.774	41.667	21.05	16.28	0.00	3.36
2285	2343	3.776969	TGGAAGCTTAGATGTGACATCCT	59.223	43.478	21.05	8.88	0.00	3.24
2286	2344	4.142609	TGGAAGCTTAGATGTGACATCC	57.857	45.455	21.05	6.31	0.00	3.51
2287	2345	7.792374	TTTATGGAAGCTTAGATGTGACATC	57.208	36.000	17.46	17.46	0.00	3.06
2298	2356	9.899661	ACGGCATTATATATTTATGGAAGCTTA	57.100	29.630	0.00	0.00	0.00	3.09
2299	2357	8.807948	ACGGCATTATATATTTATGGAAGCTT	57.192	30.769	0.00	0.00	0.00	3.74
2300	2358	9.899661	TTACGGCATTATATATTTATGGAAGCT	57.100	29.630	0.00	0.00	0.00	3.74
2355	2413	3.470709	ACTGATGTCCACTCTGTTTGTG	58.529	45.455	0.00	0.00	35.39	3.33
2356	2414	3.845781	ACTGATGTCCACTCTGTTTGT	57.154	42.857	0.00	0.00	0.00	2.83
2357	2415	5.991606	TCTAAACTGATGTCCACTCTGTTTG	59.008	40.000	14.59	7.92	41.71	2.93
2358	2416	6.174720	TCTAAACTGATGTCCACTCTGTTT	57.825	37.500	11.33	11.33	43.11	2.83
2359	2417	5.808366	TCTAAACTGATGTCCACTCTGTT	57.192	39.130	0.00	0.00	36.66	3.16
2360	2418	5.728471	CATCTAAACTGATGTCCACTCTGT	58.272	41.667	0.00	0.00	39.05	3.41
2408	2466	9.364989	CCTTTTGATTGAAAAACTAAAGACACA	57.635	29.630	0.00	0.00	41.36	3.72
2409	2467	8.328146	GCCTTTTGATTGAAAAACTAAAGACAC	58.672	33.333	0.00	0.00	41.36	3.67
2410	2468	8.037758	TGCCTTTTGATTGAAAAACTAAAGACA	58.962	29.630	0.00	0.00	41.36	3.41
2411	2469	8.419076	TGCCTTTTGATTGAAAAACTAAAGAC	57.581	30.769	0.00	0.00	41.36	3.01
2412	2470	9.612066	ATTGCCTTTTGATTGAAAAACTAAAGA	57.388	25.926	0.00	0.00	41.36	2.52
2418	2476	7.425577	AGCTATTGCCTTTTGATTGAAAAAC	57.574	32.000	0.00	0.00	40.80	2.43
2479	2537	7.911651	TCAAAGAATTTAATTTGCCCATGGTA	58.088	30.769	11.73	0.00	35.03	3.25
2480	2538	6.777782	TCAAAGAATTTAATTTGCCCATGGT	58.222	32.000	11.73	0.00	35.03	3.55
2482	2540	7.104939	TCCTCAAAGAATTTAATTTGCCCATG	58.895	34.615	0.00	0.00	35.03	3.66
2483	2541	7.256494	TCCTCAAAGAATTTAATTTGCCCAT	57.744	32.000	0.00	0.00	35.03	4.00
2484	2542	6.678568	TCCTCAAAGAATTTAATTTGCCCA	57.321	33.333	0.00	0.00	35.03	5.36
2485	2543	6.539826	CCATCCTCAAAGAATTTAATTTGCCC	59.460	38.462	0.00	0.00	35.03	5.36
2495	2553	5.813513	AAACTTGCCATCCTCAAAGAATT	57.186	34.783	0.00	0.00	0.00	2.17
2524	2582	9.141400	AGAGATAAACTAAGACGAATTTGTCAC	57.859	33.333	24.58	2.78	41.41	3.67
2533	2591	7.683437	TTCTGACAGAGATAAACTAAGACGA	57.317	36.000	5.10	0.00	0.00	4.20
2547	2605	6.369005	CAAGCACAGTAATTTTCTGACAGAG	58.631	40.000	5.10	0.00	36.81	3.35
2549	2607	4.913924	GCAAGCACAGTAATTTTCTGACAG	59.086	41.667	9.68	0.00	36.81	3.51
2586	2644	6.071503	TGTCAATTTGCATTGGTGTGATGATA	60.072	34.615	0.38	0.00	40.41	2.15
2619	2677	5.592104	TTCTAGGCACGATAAATCTGACA	57.408	39.130	0.00	0.00	0.00	3.58
2639	2697	8.728088	ACACTGAAAATATGACGTCAAATTTC	57.272	30.769	28.68	28.68	0.00	2.17
2659	2717	6.321717	ACACACACTTTGTATGAAAACACTG	58.678	36.000	0.00	0.00	35.67	3.66
2713	2837	7.988599	AGGTACTTTGTTGACATTGTACTAACA	59.011	33.333	17.99	8.72	36.30	2.41
2821	2947	3.071023	CAGGTTTGAGGGATCGGCTATAA	59.929	47.826	0.00	0.00	0.00	0.98
2922	3049	0.657840	GCAGCGGCGATGAGTAATTT	59.342	50.000	30.95	0.00	0.00	1.82
2923	3050	1.160329	GGCAGCGGCGATGAGTAATT	61.160	55.000	30.95	0.00	42.47	1.40
2938	3065	2.412089	GAGTAAATATAAGCGGCGGCAG	59.588	50.000	19.21	0.00	43.41	4.85
3013	3144	1.817520	CATTGGTGCGGTGCGGATA	60.818	57.895	0.00	0.00	0.00	2.59
3014	3145	3.133464	CATTGGTGCGGTGCGGAT	61.133	61.111	0.00	0.00	0.00	4.18
3030	3161	4.232061	CTGGGGTGGGTTTGGGCA	62.232	66.667	0.00	0.00	0.00	5.36
3049	3180	4.785453	GAGAGCGTTGGCAGGGGG	62.785	72.222	0.00	0.00	43.41	5.40
3141	3473	2.236223	ATCAGTGGCAGCGTCCTCTG	62.236	60.000	17.61	17.61	44.74	3.35
3142	3474	1.548357	AATCAGTGGCAGCGTCCTCT	61.548	55.000	0.00	0.00	0.00	3.69

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.