AutoCloner

Multiple sequence alignment - TraesCS1B01G022400

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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	TraesCS1B01G022400	chr1B	100.000	4925	0	0	1	4925	10071884	10076808	0.000000e+00	9095.0
1	TraesCS1B01G022400	chr1B	92.129	1766	120	11	2268	4023	9595153	9593397	0.000000e+00	2473.0
2	TraesCS1B01G022400	chr1B	91.341	1663	122	11	2506	4153	10084412	10086067	0.000000e+00	2254.0
3	TraesCS1B01G022400	chr1B	82.702	1214	142	28	986	2173	9596684	9595513	0.000000e+00	1016.0
4	TraesCS1B01G022400	chr1B	82.668	877	117	22	986	1831	10083092	10083964	0.000000e+00	745.0
5	TraesCS1B01G022400	chr1B	84.818	303	36	5	1890	2187	10083991	10084288	3.730000e-76	296.0
6	TraesCS1B01G022400	chr1B	100.000	35	0	0	2194	2228	10084334	10084368	1.140000e-06	65.8
7	TraesCS1B01G022400	chr1D	94.048	3965	167	33	986	4925	7877403	7881323	0.000000e+00	5951.0
8	TraesCS1B01G022400	chr1D	90.473	1606	107	23	2506	4071	7900986	7902585	0.000000e+00	2076.0
9	TraesCS1B01G022400	chr1D	89.826	1376	106	15	2752	4102	7205731	7204365	0.000000e+00	1735.0
10	TraesCS1B01G022400	chr1D	85.766	1644	181	33	2539	4143	7348855	7347226	0.000000e+00	1690.0
11	TraesCS1B01G022400	chr1D	84.309	854	106	17	948	1792	7207689	7206855	0.000000e+00	809.0
12	TraesCS1B01G022400	chr1D	83.409	886	109	22	986	1836	7899677	7900559	0.000000e+00	787.0
13	TraesCS1B01G022400	chr1D	80.587	886	133	21	950	1818	7350911	7350048	0.000000e+00	647.0
14	TraesCS1B01G022400	chr1D	80.866	277	41	4	1890	2163	7900582	7900849	1.800000e-49	207.0
15	TraesCS1B01G022400	chr1D	81.102	254	35	7	525	775	7208298	7208055	1.810000e-44	191.0
16	TraesCS1B01G022400	chr1D	96.970	66	2	0	51	116	7891171	7891236	1.450000e-20	111.0
17	TraesCS1B01G022400	chr1D	89.231	65	6	1	4783	4846	7203357	7203293	4.090000e-11	80.5
18	TraesCS1B01G022400	chr1D	80.870	115	7	7	4810	4924	7204113	7204014	5.290000e-10	76.8
19	TraesCS1B01G022400	chr1A	92.034	2222	109	28	2232	4437	9362070	9364239	0.000000e+00	3061.0
20	TraesCS1B01G022400	chr1A	89.748	1824	134	28	2293	4084	9555288	9557090	0.000000e+00	2283.0
21	TraesCS1B01G022400	chr1A	89.338	1238	100	11	955	2187	9359184	9360394	0.000000e+00	1526.0
22	TraesCS1B01G022400	chr1A	93.348	902	54	4	1	902	9552976	9553871	0.000000e+00	1328.0
23	TraesCS1B01G022400	chr1A	83.446	1329	121	44	903	2187	9553913	9555186	0.000000e+00	1144.0
24	TraesCS1B01G022400	chr1A	78.045	706	79	35	946	1638	34975598	34974956	4.650000e-100	375.0
25	TraesCS1B01G022400	chr1A	81.975	405	38	18	525	907	9357854	9358245	1.330000e-80	311.0
26	TraesCS1B01G022400	chr1A	82.400	250	34	6	525	774	9358567	9358806	5.000000e-50	209.0
27	TraesCS1B01G022400	chr1A	82.723	191	24	3	2607	2790	9174542	9174730	1.420000e-35	161.0
28	TraesCS1B01G022400	chr1A	82.723	191	24	3	2607	2790	9201936	9202124	1.420000e-35	161.0
29	TraesCS1B01G022400	chr3A	85.622	1078	151	4	2842	3917	10956448	10957523	0.000000e+00	1129.0
30	TraesCS1B01G022400	chr3D	94.636	261	11	3	4444	4702	604126816	604127075	7.680000e-108	401.0
31	TraesCS1B01G022400	chr3D	92.278	259	18	2	4444	4701	565163418	565163675	2.800000e-97	366.0
32	TraesCS1B01G022400	chr6B	94.595	259	13	1	4444	4701	715294016	715294274	2.760000e-107	399.0
33	TraesCS1B01G022400	chr6B	91.923	260	20	1	4444	4702	9480616	9480357	3.620000e-96	363.0
34	TraesCS1B01G022400	chr5D	93.156	263	16	2	4441	4701	505431515	505431253	7.730000e-103	385.0
35	TraesCS1B01G022400	chr5D	92.193	269	18	3	4440	4705	491845033	491845301	1.290000e-100	377.0
36	TraesCS1B01G022400	chr5D	91.078	269	21	3	4439	4706	21677065	21676799	1.300000e-95	361.0
37	TraesCS1B01G022400	chr7D	91.571	261	21	1	4443	4702	42402043	42401783	4.690000e-95	359.0
38	TraesCS1B01G022400	chrUn	82.199	191	25	3	2607	2790	395190862	395190674	6.600000e-34	156.0
39	TraesCS1B01G022400	chrUn	76.667	240	36	14	947	1181	238781887	238781663	1.120000e-21	115.0
40	TraesCS1B01G022400	chrUn	76.667	240	36	14	947	1181	240354387	240354611	1.120000e-21	115.0
41	TraesCS1B01G022400	chr5B	79.426	209	16	12	3896	4084	103634548	103634347	6.690000e-24	122.0

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	TraesCS1B01G022400	chr1B	10071884	10076808	4924	False	9095.000000	9095	100.000000	1	4925	1	chr1B.!!$F1	4924
1	TraesCS1B01G022400	chr1B	9593397	9596684	3287	True	1744.500000	2473	87.415500	986	4023	2	chr1B.!!$R1	3037
2	TraesCS1B01G022400	chr1B	10083092	10086067	2975	False	840.200000	2254	89.706750	986	4153	4	chr1B.!!$F2	3167
3	TraesCS1B01G022400	chr1D	7877403	7881323	3920	False	5951.000000	5951	94.048000	986	4925	1	chr1D.!!$F1	3939
4	TraesCS1B01G022400	chr1D	7347226	7350911	3685	True	1168.500000	1690	83.176500	950	4143	2	chr1D.!!$R2	3193
5	TraesCS1B01G022400	chr1D	7899677	7902585	2908	False	1023.333333	2076	84.916000	986	4071	3	chr1D.!!$F3	3085
6	TraesCS1B01G022400	chr1D	7203293	7208298	5005	True	578.460000	1735	85.067600	525	4924	5	chr1D.!!$R1	4399
7	TraesCS1B01G022400	chr1A	9552976	9557090	4114	False	1585.000000	2283	88.847333	1	4084	3	chr1A.!!$F4	4083
8	TraesCS1B01G022400	chr1A	9357854	9364239	6385	False	1276.750000	3061	86.436750	525	4437	4	chr1A.!!$F3	3912
9	TraesCS1B01G022400	chr1A	34974956	34975598	642	True	375.000000	375	78.045000	946	1638	1	chr1A.!!$R1	692
10	TraesCS1B01G022400	chr3A	10956448	10957523	1075	False	1129.000000	1129	85.622000	2842	3917	1	chr3A.!!$F1	1075

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	Hairpin	End Stability	Orientation
449	450	0.396811	AAAGAGGGTGAAGGGACACG	59.603	55.0	0.00	41.12	4.49	F
1494	2481	0.249120	CACCTGGTGTTGCCGATAGA	59.751	55.0	18.76	41.21	1.98	F
2279	6134	0.827925	AGAGAACCGACTGCCACTGA	60.828	55.0	0.00	0.00	3.41	F
2362	6218	5.337330	GGCCTTAAGTTGACTCTAACTGCTA	60.337	44.0	0.00	40.58	3.49	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2187	4083	0.111253	ATTCCATCAATCCCCGCTCC	59.889	55.000	0.00	0.0	0.00	4.70	R
2547	6467	1.153628	CTACCGTGGCTGCAGTACC	60.154	63.158	16.64	9.6	0.00	3.34	R
3210	7211	3.188667	GTCTCATCCCTTCGGAACAAAAC	59.811	47.826	0.00	0.0	43.10	2.43	R
4086	8114	3.890756	ACAAGTCCAATTGTGAATCTGCA	59.109	39.130	4.43	0.0	41.76	4.41	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
30	31	1.338484	GGGGAAAGAGGGTTCGTGTAC	60.338	57.143	0.00	0.00	0.00	2.90
85	86	9.060347	CACTAACAAATAGTCCTTGCATCATAT	57.940	33.333	0.00	0.00	43.12	1.78
119	120	4.088634	TCCTTCCATTGAAAGGTTGATGG	58.911	43.478	1.24	0.00	40.28	3.51
147	148	7.527457	CAACTAAACTATTAGGTTGGTCAAGC	58.473	38.462	10.49	4.89	35.46	4.01
151	152	5.099042	ACTATTAGGTTGGTCAAGCGAAT	57.901	39.130	19.26	19.26	43.16	3.34
164	165	1.153449	GCGAATGTCCCCACGATGA	60.153	57.895	0.00	0.00	0.00	2.92
197	198	3.560902	TGCTAGACTCAACTTCAGTCG	57.439	47.619	0.00	0.00	44.40	4.18
236	237	9.996554	ATAAGGAACAAAAACAAAAGGGATTAG	57.003	29.630	0.00	0.00	0.00	1.73
237	238	7.669089	AGGAACAAAAACAAAAGGGATTAGA	57.331	32.000	0.00	0.00	0.00	2.10
246	247	2.757894	AAGGGATTAGAGCTCTCGGA	57.242	50.000	22.17	8.22	34.09	4.55
266	267	1.843851	ACTGACACAACTCTCCCCAAA	59.156	47.619	0.00	0.00	0.00	3.28
270	271	5.222130	ACTGACACAACTCTCCCCAAATTAT	60.222	40.000	0.00	0.00	0.00	1.28
279	280	7.757242	ACTCTCCCCAAATTATAAGAGTCTT	57.243	36.000	10.87	10.87	39.27	3.01
358	359	7.773224	TCTTTGACAAAGAAGTGATACCAAAGA	59.227	33.333	24.92	0.00	44.10	2.52
385	386	6.652900	CCTTGGGAGTTTGAAAAACTTGAAAA	59.347	34.615	6.81	0.83	0.00	2.29
423	424	5.748630	ACAAGAAAAGAATTTGAAACGCTCC	59.251	36.000	0.00	0.00	39.02	4.70
449	450	0.396811	AAAGAGGGTGAAGGGACACG	59.603	55.000	0.00	0.00	41.12	4.49
461	462	2.835027	AGGGACACGACAAGAACTTTC	58.165	47.619	0.00	0.00	0.00	2.62
466	467	2.030457	ACACGACAAGAACTTTCGCAAG	59.970	45.455	14.03	0.00	36.18	4.01
523	524	6.146510	ACGATTGCTTACGAAACAAATGACTA	59.853	34.615	0.00	0.00	0.00	2.59
536	537	4.225042	ACAAATGACTAGTGAGCACCCATA	59.775	41.667	0.00	0.00	0.00	2.74
537	538	5.104360	ACAAATGACTAGTGAGCACCCATAT	60.104	40.000	0.00	0.00	0.00	1.78
549	550	1.846439	CACCCATATTCTCCACCCTGT	59.154	52.381	0.00	0.00	0.00	4.00
601	602	3.006247	GGAGAAGACAGTGAAGGATTGC	58.994	50.000	0.00	0.00	0.00	3.56
614	615	8.180267	CAGTGAAGGATTGCAAAGTAATAGAAG	58.820	37.037	1.71	0.00	0.00	2.85
820	840	3.563390	GTGCAGAAGAGGGAAATATGCTC	59.437	47.826	0.00	0.00	33.47	4.26
975	1901	5.495926	TCTTCTTCTTCCTCTTGCTCAAT	57.504	39.130	0.00	0.00	0.00	2.57
1051	1981	1.693606	TGCTGTCTCTGATCAACCACA	59.306	47.619	0.00	0.00	0.00	4.17
1128	2058	1.466025	CCAACTGCAGCCAACATGGT	61.466	55.000	15.27	0.00	40.46	3.55
1173	2103	4.202040	TGCCTTGAATCCAGCAATAAATCG	60.202	41.667	0.00	0.00	30.97	3.34
1174	2104	4.202050	GCCTTGAATCCAGCAATAAATCGT	60.202	41.667	0.00	0.00	0.00	3.73
1175	2105	5.514279	CCTTGAATCCAGCAATAAATCGTC	58.486	41.667	0.00	0.00	0.00	4.20
1176	2106	4.794248	TGAATCCAGCAATAAATCGTCG	57.206	40.909	0.00	0.00	0.00	5.12
1177	2107	4.188462	TGAATCCAGCAATAAATCGTCGT	58.812	39.130	0.00	0.00	0.00	4.34
1178	2108	4.270084	TGAATCCAGCAATAAATCGTCGTC	59.730	41.667	0.00	0.00	0.00	4.20
1179	2109	3.239587	TCCAGCAATAAATCGTCGTCA	57.760	42.857	0.00	0.00	0.00	4.35
1180	2110	3.792401	TCCAGCAATAAATCGTCGTCAT	58.208	40.909	0.00	0.00	0.00	3.06
1181	2111	3.802139	TCCAGCAATAAATCGTCGTCATC	59.198	43.478	0.00	0.00	0.00	2.92
1300	2266	5.405935	TGTCAGCGCCATAGATTACATAT	57.594	39.130	2.29	0.00	0.00	1.78
1339	2305	0.974010	CCCGCTTGTAGACCCCTGTA	60.974	60.000	0.00	0.00	0.00	2.74
1425	2391	3.244215	ACGATGAGAAGCCAAGTCTTCAA	60.244	43.478	6.33	0.00	43.64	2.69
1426	2392	3.937706	CGATGAGAAGCCAAGTCTTCAAT	59.062	43.478	6.33	0.33	43.64	2.57
1427	2393	4.394300	CGATGAGAAGCCAAGTCTTCAATT	59.606	41.667	6.33	0.00	43.64	2.32
1431	2397	6.507023	TGAGAAGCCAAGTCTTCAATTTTTC	58.493	36.000	6.33	0.00	43.64	2.29
1432	2398	5.523369	AGAAGCCAAGTCTTCAATTTTTCG	58.477	37.500	6.33	0.00	43.64	3.46
1439	2408	6.363357	CCAAGTCTTCAATTTTTCGAATGGAC	59.637	38.462	0.00	0.00	0.00	4.02
1446	2427	7.979444	TCAATTTTTCGAATGGACTTCTACT	57.021	32.000	0.00	0.00	0.00	2.57
1447	2428	7.806690	TCAATTTTTCGAATGGACTTCTACTG	58.193	34.615	0.00	0.00	0.00	2.74
1494	2481	0.249120	CACCTGGTGTTGCCGATAGA	59.751	55.000	18.76	0.00	41.21	1.98
1639	2626	1.945819	GCGGCCTGATACCCATGTATG	60.946	57.143	0.00	0.00	37.80	2.39
1655	2642	3.395639	TGTATGAGTTTGACGACCCAAC	58.604	45.455	0.00	0.00	0.00	3.77
1735	2728	5.404366	GCTGAGACGACAGTGTATTTGTTTA	59.596	40.000	0.00	0.00	39.73	2.01
1748	2744	8.696175	AGTGTATTTGTTTAATTACTTTTGCGC	58.304	29.630	0.00	0.00	0.00	6.09
1802	2798	2.166459	TCAGCTCACAAAGGGATAGACG	59.834	50.000	0.00	0.00	0.00	4.18
1815	2811	2.548707	GGATAGACGATTCTGCATGCCA	60.549	50.000	16.68	2.21	32.75	4.92
1967	3390	3.078837	TGGGATTTTCGGTCAACTAAGC	58.921	45.455	0.00	0.00	0.00	3.09
2021	3476	1.701847	AGCAATCACACTGAAGGACCT	59.298	47.619	0.00	0.00	0.00	3.85
2086	3553	7.602644	TGTTTTGTTCATCTATCAGACACTACC	59.397	37.037	0.00	0.00	0.00	3.18
2187	4083	3.800863	CTGCTGCTGCGCTTGAGG	61.801	66.667	9.73	0.00	43.34	3.86
2190	4086	2.818714	CTGCTGCGCTTGAGGGAG	60.819	66.667	9.73	0.00	0.00	4.30
2245	5772	2.674754	GGCGAATTGGGGAGGACA	59.325	61.111	0.00	0.00	0.00	4.02
2279	6134	0.827925	AGAGAACCGACTGCCACTGA	60.828	55.000	0.00	0.00	0.00	3.41
2362	6218	5.337330	GGCCTTAAGTTGACTCTAACTGCTA	60.337	44.000	0.00	0.00	40.58	3.49
2406	6265	5.940470	AGAAAAACTAATAGGCCAGTCACTG	59.060	40.000	5.01	0.00	0.00	3.66
2440	6299	5.762711	GCACCAAAACAATACAAATTTCCCT	59.237	36.000	0.00	0.00	0.00	4.20
2467	6326	5.405935	AGGAAATTGGGTTGATAAGTTGC	57.594	39.130	0.00	0.00	0.00	4.17
2547	6467	5.808366	TGTTCCTGATATACTAGGGCAAG	57.192	43.478	0.00	0.00	34.76	4.01
3647	7649	0.253327	GTGAGCGGGAGGAGGAATTT	59.747	55.000	0.00	0.00	0.00	1.82
4086	8114	6.525629	ACTCTACTAGTTGTTTGCAAGACAT	58.474	36.000	0.00	4.89	33.35	3.06
4200	8255	4.907269	TCCACTCCCATATTTCTCTGCATA	59.093	41.667	0.00	0.00	0.00	3.14
4473	8529	1.287425	ATCGCGGGAGAAACGATTTC	58.713	50.000	6.13	0.00	43.55	2.17
4474	8530	0.038067	TCGCGGGAGAAACGATTTCA	60.038	50.000	6.13	0.00	42.10	2.69
4476	8532	1.153353	GCGGGAGAAACGATTTCACA	58.847	50.000	11.33	0.00	42.10	3.58
4565	8621	6.874278	TCTGGTGGAAGAGATGATTTCTAA	57.126	37.500	0.00	0.00	33.74	2.10
4566	8622	7.257790	TCTGGTGGAAGAGATGATTTCTAAA	57.742	36.000	0.00	0.00	33.74	1.85
4567	8623	7.334090	TCTGGTGGAAGAGATGATTTCTAAAG	58.666	38.462	0.00	0.00	33.74	1.85
4568	8624	6.418101	TGGTGGAAGAGATGATTTCTAAAGG	58.582	40.000	0.00	0.00	33.74	3.11
4569	8625	5.825151	GGTGGAAGAGATGATTTCTAAAGGG	59.175	44.000	0.00	0.00	33.74	3.95
4570	8626	6.418946	GTGGAAGAGATGATTTCTAAAGGGT	58.581	40.000	0.00	0.00	33.74	4.34
4571	8627	6.887002	GTGGAAGAGATGATTTCTAAAGGGTT	59.113	38.462	0.00	0.00	33.74	4.11
4682	8738	3.057734	GCAGTTATAGCGGCTATTTCGT	58.942	45.455	26.01	6.56	0.00	3.85

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
35	36	4.451096	GTGTAATCAATATGGACCGCGAAT	59.549	41.667	8.23	0.00	0.00	3.34
41	42	7.051623	TGTTAGTGGTGTAATCAATATGGACC	58.948	38.462	0.00	0.00	0.00	4.46
85	86	5.818887	TCAATGGAAGGATCTCATGTTCAA	58.181	37.500	0.00	0.00	0.00	2.69
119	120	4.393990	ACCAACCTAATAGTTTAGTTGCGC	59.606	41.667	0.00	0.00	34.20	6.09
147	148	1.732941	TTTCATCGTGGGGACATTCG	58.267	50.000	0.00	0.00	46.14	3.34
151	152	4.561500	TTAAGATTTCATCGTGGGGACA	57.438	40.909	0.00	0.00	38.70	4.02
164	165	9.678260	AGTTGAGTCTAGCATGATTTAAGATTT	57.322	29.630	0.00	0.00	0.00	2.17
211	212	9.203163	TCTAATCCCTTTTGTTTTTGTTCCTTA	57.797	29.630	0.00	0.00	0.00	2.69
236	237	0.598562	TTGTGTCAGTCCGAGAGCTC	59.401	55.000	5.27	5.27	0.00	4.09
237	238	0.315568	GTTGTGTCAGTCCGAGAGCT	59.684	55.000	0.00	0.00	0.00	4.09
246	247	1.507140	TTGGGGAGAGTTGTGTCAGT	58.493	50.000	0.00	0.00	0.00	3.41
266	267	8.049117	TGAATCTTGTGGCAAGACTCTTATAAT	58.951	33.333	17.32	0.00	0.00	1.28
270	271	5.012046	TCTGAATCTTGTGGCAAGACTCTTA	59.988	40.000	17.32	6.53	0.00	2.10
279	280	5.850557	TTTTCTTTCTGAATCTTGTGGCA	57.149	34.783	0.00	0.00	34.24	4.92
307	308	4.096532	GCAACTTATAGCCAAACCTCTTCC	59.903	45.833	0.00	0.00	0.00	3.46
314	315	6.582672	GTCAAAGAAGCAACTTATAGCCAAAC	59.417	38.462	0.00	0.00	0.00	2.93
318	319	5.880054	TGTCAAAGAAGCAACTTATAGCC	57.120	39.130	0.00	0.00	0.00	3.93
358	359	5.247337	TCAAGTTTTTCAAACTCCCAAGGTT	59.753	36.000	2.42	0.00	30.46	3.50
389	390	9.874205	TCAAATTCTTTTCTTGTCTTTCATGTT	57.126	25.926	0.00	0.00	0.00	2.71
390	391	9.874205	TTCAAATTCTTTTCTTGTCTTTCATGT	57.126	25.926	0.00	0.00	0.00	3.21
407	408	1.165270	CCCGGAGCGTTTCAAATTCT	58.835	50.000	0.73	0.00	0.00	2.40
423	424	1.523758	CTTCACCCTCTTTTCACCCG	58.476	55.000	0.00	0.00	0.00	5.28
449	450	3.304057	CCCTTCTTGCGAAAGTTCTTGTC	60.304	47.826	2.29	0.00	0.00	3.18
461	462	4.153475	TCGAAGTTTTATTCCCTTCTTGCG	59.847	41.667	0.00	0.00	33.94	4.85
466	467	7.624554	GCTTTCTCTCGAAGTTTTATTCCCTTC	60.625	40.741	0.00	0.00	33.00	3.46
495	496	4.539509	TTGTTTCGTAAGCAATCGTGTT	57.460	36.364	0.00	0.00	37.18	3.32
508	509	4.211374	GTGCTCACTAGTCATTTGTTTCGT	59.789	41.667	0.00	0.00	0.00	3.85
523	524	2.171448	GTGGAGAATATGGGTGCTCACT	59.829	50.000	0.00	0.00	0.00	3.41
536	537	0.994247	TCATGCACAGGGTGGAGAAT	59.006	50.000	0.00	0.00	37.30	2.40
537	538	0.994247	ATCATGCACAGGGTGGAGAA	59.006	50.000	0.00	0.00	37.30	2.87
563	564	5.529430	TCTTCTCCGTCATTTGCAGTTTTTA	59.471	36.000	0.00	0.00	0.00	1.52
575	576	2.232452	CCTTCACTGTCTTCTCCGTCAT	59.768	50.000	0.00	0.00	0.00	3.06
576	577	1.613925	CCTTCACTGTCTTCTCCGTCA	59.386	52.381	0.00	0.00	0.00	4.35
579	580	3.257393	CAATCCTTCACTGTCTTCTCCG	58.743	50.000	0.00	0.00	0.00	4.63
601	602	7.917505	GGTGCATTTCATCCTTCTATTACTTTG	59.082	37.037	0.00	0.00	0.00	2.77
614	615	2.424956	GGAACTCTGGTGCATTTCATCC	59.575	50.000	0.00	0.00	0.00	3.51
690	694	7.093068	TGCCCAGTGATTAATCAGTACTCTTAA	60.093	37.037	22.43	8.77	38.35	1.85
691	695	6.382859	TGCCCAGTGATTAATCAGTACTCTTA	59.617	38.462	22.43	7.48	38.35	2.10
692	696	5.189736	TGCCCAGTGATTAATCAGTACTCTT	59.810	40.000	22.43	0.00	38.35	2.85
820	840	2.359214	TGCTCCTAGCTACACAATCGAG	59.641	50.000	0.03	0.00	42.97	4.04
975	1901	6.436218	TCTTTCTGTACTGCTGTACCAAGATA	59.564	38.462	25.51	17.37	46.19	1.98
1023	1953	0.541530	TCAGAGACAGCAGCAGGAGT	60.542	55.000	0.00	0.00	0.00	3.85
1036	1966	5.954752	AGTAGATTCTGTGGTTGATCAGAGA	59.045	40.000	0.00	0.00	40.91	3.10
1051	1981	0.107654	GCCGTGGCCAAGTAGATTCT	60.108	55.000	17.81	0.00	34.56	2.40
1128	2058	2.118403	AAGGAAACCTGACCTCTGGA	57.882	50.000	5.30	0.00	38.22	3.86
1173	2103	4.151867	CCACATGATGATGATGATGACGAC	59.848	45.833	0.00	0.00	33.36	4.34
1174	2104	4.039488	TCCACATGATGATGATGATGACGA	59.961	41.667	0.00	0.00	33.36	4.20
1175	2105	4.312443	TCCACATGATGATGATGATGACG	58.688	43.478	0.00	0.00	33.36	4.35
1425	2391	5.123979	GGCAGTAGAAGTCCATTCGAAAAAT	59.876	40.000	0.00	0.00	43.16	1.82
1426	2392	4.454504	GGCAGTAGAAGTCCATTCGAAAAA	59.545	41.667	0.00	0.00	43.16	1.94
1427	2393	4.000988	GGCAGTAGAAGTCCATTCGAAAA	58.999	43.478	0.00	0.00	43.16	2.29
1431	2397	1.482593	AGGGCAGTAGAAGTCCATTCG	59.517	52.381	0.00	0.00	43.16	3.34
1432	2398	3.707102	ACTAGGGCAGTAGAAGTCCATTC	59.293	47.826	0.00	0.00	34.98	2.67
1439	2408	2.033550	CAGCGTACTAGGGCAGTAGAAG	59.966	54.545	0.00	0.00	40.48	2.85
1446	2427	0.970640	TTGAACAGCGTACTAGGGCA	59.029	50.000	0.00	0.00	0.00	5.36
1447	2428	1.203994	TCTTGAACAGCGTACTAGGGC	59.796	52.381	0.00	0.00	0.00	5.19
1484	2465	1.024271	GCCAGCAATTCTATCGGCAA	58.976	50.000	0.00	0.00	39.38	4.52
1494	2481	1.000396	GGAGACTGGGCCAGCAATT	60.000	57.895	33.04	14.25	34.37	2.32
1639	2626	2.981997	ACGTTGGGTCGTCAAACTC	58.018	52.632	0.00	0.00	40.04	3.01
1655	2642	1.000827	ACACTGAGAGCTTGTCTGACG	60.001	52.381	2.98	0.00	34.71	4.35
1735	2728	5.119931	TCACATTCTGCGCAAAAGTAATT	57.880	34.783	13.05	0.00	0.00	1.40
1742	2738	0.660005	GCGTTCACATTCTGCGCAAA	60.660	50.000	13.05	9.55	46.23	3.68
1748	2744	0.518636	CCCACTGCGTTCACATTCTG	59.481	55.000	0.00	0.00	0.00	3.02
1802	2798	2.496291	GGGCCTGGCATGCAGAATC	61.496	63.158	22.05	1.47	0.00	2.52
1815	2811	0.839946	GACTCATACCATGTGGGCCT	59.160	55.000	4.53	0.00	42.05	5.19
2021	3476	2.435372	ACTGCTCAGGTTTTTGTCCA	57.565	45.000	1.66	0.00	0.00	4.02
2086	3553	5.368989	AGAGTTCCAGATTATTTAAGGCCG	58.631	41.667	0.00	0.00	0.00	6.13
2187	4083	0.111253	ATTCCATCAATCCCCGCTCC	59.889	55.000	0.00	0.00	0.00	4.70
2188	4084	1.986882	AATTCCATCAATCCCCGCTC	58.013	50.000	0.00	0.00	0.00	5.03
2189	4085	2.034124	CAAATTCCATCAATCCCCGCT	58.966	47.619	0.00	0.00	0.00	5.52
2190	4086	1.069049	CCAAATTCCATCAATCCCCGC	59.931	52.381	0.00	0.00	0.00	6.13
2192	4088	1.417517	GCCCAAATTCCATCAATCCCC	59.582	52.381	0.00	0.00	0.00	4.81
2245	5772	3.361786	GTTCTCTCCCTTACTCTGCTCT	58.638	50.000	0.00	0.00	0.00	4.09
2362	6218	8.789825	TTTTCTAACATTTTTGCCATGCATAT	57.210	26.923	0.00	0.00	38.76	1.78
2406	6265	9.632807	TTGTATTGTTTTGGTGCTATTTATGAC	57.367	29.630	0.00	0.00	0.00	3.06
2440	6299	9.771534	CAACTTATCAACCCAATTTCCTTTTTA	57.228	29.630	0.00	0.00	0.00	1.52
2453	6312	2.695359	TCTGTCGCAACTTATCAACCC	58.305	47.619	0.00	0.00	0.00	4.11
2547	6467	1.153628	CTACCGTGGCTGCAGTACC	60.154	63.158	16.64	9.60	0.00	3.34
2626	6573	7.175104	ACCTGCAAATACCAAGAAAGAGAATA	58.825	34.615	0.00	0.00	0.00	1.75
3210	7211	3.188667	GTCTCATCCCTTCGGAACAAAAC	59.811	47.826	0.00	0.00	43.10	2.43
3225	7226	5.784177	TCATAAATAAGAGCCCGTCTCATC	58.216	41.667	4.99	0.00	44.35	2.92
4086	8114	3.890756	ACAAGTCCAATTGTGAATCTGCA	59.109	39.130	4.43	0.00	41.76	4.41
4200	8255	9.295825	CATAAGAGGAGATCTACTAACTGTCAT	57.704	37.037	7.68	0.00	37.23	3.06
4473	8529	4.463879	CTGGGAGAGGCCGCTGTG	62.464	72.222	16.07	0.00	37.63	3.66
4522	8578	5.289434	CCAGAAAAATTTCCGCTATTTGCTC	59.711	40.000	2.37	0.00	37.92	4.26
4651	8707	4.274421	CGCTATAACTGCGCTATAGCTA	57.726	45.455	29.35	10.86	46.44	3.32
4682	8738	9.342308	CTTAAAGTCATAGATTCAAATAGCCCA	57.658	33.333	0.00	0.00	0.00	5.36
4874	8930	1.893801	CACAGTTTCGGACCTACTCCT	59.106	52.381	0.00	0.00	36.80	3.69
4882	8938	1.003718	CCCTCCCACAGTTTCGGAC	60.004	63.158	0.00	0.00	0.00	4.79

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.