AutoCloner

Multiple sequence alignment - TraesCS3B01G593200

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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	TraesCS3B01G593200	chr3B	100.000	3050	0	0	1	3050	816693077	816690028	0.000000e+00	5633.0
1	TraesCS3B01G593200	chr3B	94.860	1109	50	3	947	2053	816264530	816265633	0.000000e+00	1725.0
2	TraesCS3B01G593200	chr3B	88.480	408	34	5	2634	3031	816271819	816272223	5.910000e-132	481.0
3	TraesCS3B01G593200	chr3B	87.988	333	25	9	2092	2423	816265634	816265952	2.220000e-101	379.0
4	TraesCS3B01G593200	chr3B	95.205	146	5	2	2491	2636	816271565	816271708	2.370000e-56	230.0
5	TraesCS3B01G593200	chr3A	92.295	1778	95	18	425	2195	739735593	739733851	0.000000e+00	2486.0
6	TraesCS3B01G593200	chr3A	87.045	934	81	16	680	1601	739322282	739323187	0.000000e+00	1018.0
7	TraesCS3B01G593200	chr3A	83.636	825	70	26	2228	3000	739733766	739732955	0.000000e+00	715.0
8	TraesCS3B01G593200	chr3A	89.640	444	37	7	2427	2870	739325784	739326218	9.550000e-155	556.0
9	TraesCS3B01G593200	chr3A	89.552	402	35	7	1	398	739736339	739735941	1.260000e-138	503.0
10	TraesCS3B01G593200	chr3A	81.481	675	67	28	1541	2195	739323191	739323827	4.540000e-138	501.0
11	TraesCS3B01G593200	chr3A	86.728	324	14	13	2110	2423	739325411	739325715	1.750000e-87	333.0
12	TraesCS3B01G593200	chr3A	92.814	167	12	0	229	395	694387494	694387328	3.040000e-60	243.0
13	TraesCS3B01G593200	chr3A	88.535	157	17	1	2006	2162	739325239	739325394	4.010000e-44	189.0
14	TraesCS3B01G593200	chr3A	84.091	176	16	7	2865	3029	739324395	739324569	3.150000e-35	159.0
15	TraesCS3B01G593200	chr3A	97.778	45	1	0	620	664	712185219	712185263	9.070000e-11	78.7
16	TraesCS3B01G593200	chr3D	93.537	1439	72	9	732	2165	607310709	607309287	0.000000e+00	2122.0
17	TraesCS3B01G593200	chr3D	90.565	1505	103	14	668	2165	606929723	606931195	0.000000e+00	1956.0
18	TraesCS3B01G593200	chr3D	90.223	583	43	6	2427	3000	607308914	607308337	0.000000e+00	749.0
19	TraesCS3B01G593200	chr3D	91.558	308	21	3	2116	2423	606931215	606931517	1.310000e-113	420.0
20	TraesCS3B01G593200	chr3D	90.429	303	22	5	2113	2415	607309282	607308987	2.850000e-105	392.0
21	TraesCS3B01G593200	chr3D	88.854	323	31	3	3	325	607312290	607311973	2.850000e-105	392.0
22	TraesCS3B01G593200	chr3D	90.942	276	14	6	425	700	607310972	607310708	8.040000e-96	361.0
23	TraesCS3B01G593200	chr3D	90.254	236	13	5	2760	2995	606931814	606932039	1.780000e-77	300.0
24	TraesCS3B01G593200	chr3D	92.045	88	7	0	2638	2725	606931734	606931821	1.150000e-24	124.0
25	TraesCS3B01G593200	chr3D	78.906	128	17	7	425	544	137706079	137705954	9.070000e-11	78.7
26	TraesCS3B01G593200	chr1B	83.498	1418	159	30	679	2070	327024632	327023264	0.000000e+00	1253.0
27	TraesCS3B01G593200	chr1B	84.695	967	108	20	664	1604	435194076	435195028	0.000000e+00	929.0
28	TraesCS3B01G593200	chr1B	82.294	401	42	12	1681	2070	435195411	435195793	1.360000e-83	320.0
29	TraesCS3B01G593200	chr1B	93.293	164	11	0	229	392	619204448	619204611	3.040000e-60	243.0
30	TraesCS3B01G593200	chr1B	93.293	164	11	0	229	392	668824926	668824763	3.040000e-60	243.0
31	TraesCS3B01G593200	chr1A	83.138	1447	166	42	664	2070	406189441	406190849	0.000000e+00	1249.0
32	TraesCS3B01G593200	chr1D	86.809	887	98	12	679	1550	227130925	227130043	0.000000e+00	972.0
33	TraesCS3B01G593200	chr1D	84.995	973	113	18	668	1614	322285104	322286069	0.000000e+00	957.0
34	TraesCS3B01G593200	chr1D	82.933	416	46	8	1664	2070	227129632	227129233	4.840000e-93	351.0
35	TraesCS3B01G593200	chr1D	80.315	127	14	7	425	544	124623827	124623949	5.420000e-13	86.1
36	TraesCS3B01G593200	chr6B	93.293	164	11	0	229	392	151239130	151238967	3.040000e-60	243.0
37	TraesCS3B01G593200	chr6B	87.857	140	17	0	88	227	388357129	388357268	6.770000e-37	165.0
38	TraesCS3B01G593200	chr6B	85.965	57	6	2	605	660	621310392	621310447	3.280000e-05	60.2
39	TraesCS3B01G593200	chr6A	93.293	164	11	0	229	392	84427191	84427354	3.040000e-60	243.0
40	TraesCS3B01G593200	chr5B	93.293	164	11	0	229	392	713103337	713103500	3.040000e-60	243.0
41	TraesCS3B01G593200	chr5B	93.293	164	11	0	229	392	713104699	713104536	3.040000e-60	243.0
42	TraesCS3B01G593200	chr5B	88.571	140	16	0	88	227	667148024	667147885	1.450000e-38	171.0
43	TraesCS3B01G593200	chr5B	86.567	67	5	2	481	544	657040538	657040603	1.520000e-08	71.3
44	TraesCS3B01G593200	chr5A	93.293	164	11	0	229	392	157794739	157794902	3.040000e-60	243.0
45	TraesCS3B01G593200	chr2B	89.286	140	14	1	88	227	112853573	112853435	1.120000e-39	174.0
46	TraesCS3B01G593200	chr2B	88.571	140	16	0	88	227	751959896	751960035	1.450000e-38	171.0
47	TraesCS3B01G593200	chrUn	88.571	140	16	0	88	227	171035473	171035334	1.450000e-38	171.0
48	TraesCS3B01G593200	chrUn	90.244	41	4	0	620	660	138316240	138316200	2.000000e-03	54.7
49	TraesCS3B01G593200	chrUn	90.244	41	4	0	620	660	138389878	138389838	2.000000e-03	54.7
50	TraesCS3B01G593200	chrUn	90.244	41	4	0	620	660	138458897	138458857	2.000000e-03	54.7
51	TraesCS3B01G593200	chrUn	90.244	41	4	0	620	660	138526986	138526946	2.000000e-03	54.7
52	TraesCS3B01G593200	chrUn	94.286	35	2	0	620	654	172079721	172079755	2.000000e-03	54.7
53	TraesCS3B01G593200	chr4D	87.857	140	17	0	88	227	398049591	398049730	6.770000e-37	165.0
54	TraesCS3B01G593200	chr4B	87.857	140	17	0	88	227	209312011	209311872	6.770000e-37	165.0
55	TraesCS3B01G593200	chr4A	93.750	96	6	0	2904	2999	59277772	59277677	8.810000e-31	145.0
56	TraesCS3B01G593200	chr2A	93.814	97	4	2	2904	2999	65404005	65403910	8.810000e-31	145.0
57	TraesCS3B01G593200	chr7D	93.814	97	2	3	2904	2999	44702638	44702545	3.170000e-30	143.0
58	TraesCS3B01G593200	chr7A	90.654	107	7	2	2894	2999	47495738	47495842	4.100000e-29	139.0

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	TraesCS3B01G593200	chr3B	816690028	816693077	3049	True	5633.000000	5633	100.000000	1	3050	1	chr3B.!!$R1	3049
1	TraesCS3B01G593200	chr3B	816264530	816265952	1422	False	1052.000000	1725	91.424000	947	2423	2	chr3B.!!$F1	1476
2	TraesCS3B01G593200	chr3B	816271565	816272223	658	False	355.500000	481	91.842500	2491	3031	2	chr3B.!!$F2	540
3	TraesCS3B01G593200	chr3A	739732955	739736339	3384	True	1234.666667	2486	88.494333	1	3000	3	chr3A.!!$R2	2999
4	TraesCS3B01G593200	chr3A	739322282	739326218	3936	False	459.333333	1018	86.253333	680	3029	6	chr3A.!!$F2	2349
5	TraesCS3B01G593200	chr3D	607308337	607312290	3953	True	803.200000	2122	90.797000	3	3000	5	chr3D.!!$R2	2997
6	TraesCS3B01G593200	chr3D	606929723	606932039	2316	False	700.000000	1956	91.105500	668	2995	4	chr3D.!!$F1	2327
7	TraesCS3B01G593200	chr1B	327023264	327024632	1368	True	1253.000000	1253	83.498000	679	2070	1	chr1B.!!$R1	1391
8	TraesCS3B01G593200	chr1B	435194076	435195793	1717	False	624.500000	929	83.494500	664	2070	2	chr1B.!!$F2	1406
9	TraesCS3B01G593200	chr1A	406189441	406190849	1408	False	1249.000000	1249	83.138000	664	2070	1	chr1A.!!$F1	1406
10	TraesCS3B01G593200	chr1D	322285104	322286069	965	False	957.000000	957	84.995000	668	1614	1	chr1D.!!$F2	946
11	TraesCS3B01G593200	chr1D	227129233	227130925	1692	True	661.500000	972	84.871000	679	2070	2	chr1D.!!$R1	1391

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
771	1701	0.250338	GGCGACTGAGGGACTGTTTT	60.25	55.0	0.0	0.0	41.55	2.43	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2305	5403	0.538057	CACCACCACCTTCAGCATGT	60.538	55.0	0.0	0.0	37.4	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
25	26	3.884091	ACTCGTGTCTGTATCCCTGTATC	59.116	47.826	0.00	0.00	0.00	2.24
40	41	3.865745	CCTGTATCGGTGCTTCTTAGTTG	59.134	47.826	0.00	0.00	0.00	3.16
86	87	3.610677	GTCAAGTTTCACCAAACAAACCG	59.389	43.478	0.74	0.00	43.98	4.44
111	112	3.319755	CGAGTTTCAATGCAAAATGGCT	58.680	40.909	0.00	0.00	34.04	4.75
114	115	2.743664	GTTTCAATGCAAAATGGCTCCC	59.256	45.455	0.00	0.00	34.04	4.30
123	124	1.026718	AAATGGCTCCCGCTTCTTCG	61.027	55.000	0.00	0.00	36.09	3.79
137	138	3.365565	GCTTCTTCGGAAATAAAACGGCA	60.366	43.478	0.00	0.00	33.12	5.69
158	159	2.887152	AGGAAAATCAATATGGAGCCGC	59.113	45.455	0.00	0.00	0.00	6.53
240	241	4.977739	TGGAGGGGTTTCAAGATCTGATAT	59.022	41.667	0.00	0.00	32.78	1.63
282	283	2.229062	TGAGAGAGCAAGTACAAGGACG	59.771	50.000	0.00	0.00	0.00	4.79
424	1152	8.608317	CATTCCGGTTTGTTTAACAAGAAAAAT	58.392	29.630	10.51	6.27	39.53	1.82
484	1410	7.440523	TCTTTAAGAAGAGAAAATGCTGGAC	57.559	36.000	0.00	0.00	36.99	4.02
522	1448	7.124448	GGGAGATTCTAGAACAAAGGAGAAGTA	59.876	40.741	7.48	0.00	31.76	2.24
594	1520	8.610896	GCGTGGAATATTCTAGATAGTACGTAT	58.389	37.037	14.95	0.00	0.00	3.06
595	1521	9.917872	CGTGGAATATTCTAGATAGTACGTATG	57.082	37.037	14.95	0.00	0.00	2.39
600	1526	9.664332	AATATTCTAGATAGTACGTATGTCGGT	57.336	33.333	0.00	0.00	44.69	4.69
603	1529	8.471361	TTCTAGATAGTACGTATGTCGGTATG	57.529	38.462	0.00	0.00	44.69	2.39
660	1586	1.135527	CGGCCAACACTACTCGGATTA	59.864	52.381	2.24	0.00	0.00	1.75
769	1699	1.534235	AGGCGACTGAGGGACTGTT	60.534	57.895	0.00	0.00	41.55	3.16
771	1701	0.250338	GGCGACTGAGGGACTGTTTT	60.250	55.000	0.00	0.00	41.55	2.43
788	1718	8.592155	GGACTGTTTTTGTTAGTTGTTTCATTC	58.408	33.333	0.00	0.00	0.00	2.67
798	1728	8.575589	TGTTAGTTGTTTCATTCATAGCAATGT	58.424	29.630	0.00	0.00	35.56	2.71
875	1812	7.689446	TGATTGGACAAATACGTAATGGAAA	57.311	32.000	14.08	7.27	0.00	3.13
901	1838	2.376808	TGTTGCACCAAACAAACCAG	57.623	45.000	0.00	0.00	37.12	4.00
1167	2130	1.068474	GAATCCGTGACGACAACCAG	58.932	55.000	6.54	0.00	0.00	4.00
1251	2214	5.368989	CATTCCTCAAGTCAGGTTATACCC	58.631	45.833	0.00	0.00	39.75	3.69
1273	2236	1.074752	GCTCCGTGCAGAGAAAGAAG	58.925	55.000	7.13	0.00	42.31	2.85
1280	2243	4.023707	CCGTGCAGAGAAAGAAGTTGAATT	60.024	41.667	0.00	0.00	0.00	2.17
1589	2567	2.551071	GCTGAGTCTAAGTTGGTGGCTT	60.551	50.000	0.00	0.00	0.00	4.35
1761	3121	1.134461	CAGGCAGTGGAGAAGGATCTG	60.134	57.143	0.00	0.00	35.54	2.90
1884	3244	4.887071	ACTGAAAATCACTTGTGGCTAACA	59.113	37.500	0.64	0.00	36.85	2.41
2002	3384	0.526211	CTACACAGACAGGCGCTACA	59.474	55.000	7.64	0.00	0.00	2.74
2070	5038	2.977772	TTGGGCTTTTGGTTCTTGTG	57.022	45.000	0.00	0.00	0.00	3.33
2071	5039	1.118838	TGGGCTTTTGGTTCTTGTGG	58.881	50.000	0.00	0.00	0.00	4.17
2074	5042	1.484653	GGCTTTTGGTTCTTGTGGGTT	59.515	47.619	0.00	0.00	0.00	4.11
2165	5200	6.947733	TGTTCAGAAGATTGTAACCATGGATT	59.052	34.615	21.47	11.61	0.00	3.01
2204	5281	9.994432	CTTAGGAAGCAATTCATTGTACTTAAG	57.006	33.333	0.00	0.00	39.88	1.85
2225	5302	3.019564	GAGGATGTGGACCCTTTTGATG	58.980	50.000	0.00	0.00	31.84	3.07
2226	5303	2.379907	AGGATGTGGACCCTTTTGATGT	59.620	45.455	0.00	0.00	0.00	3.06
2240	5338	6.587608	CCCTTTTGATGTTGTTGCTAATCTTC	59.412	38.462	0.00	0.00	0.00	2.87
2305	5403	1.614903	AGCTTGCAATGCTGCTTTGTA	59.385	42.857	23.67	18.89	46.52	2.41
2315	5413	2.227149	TGCTGCTTTGTACATGCTGAAG	59.773	45.455	22.74	13.58	0.00	3.02
2316	5414	2.415090	GCTGCTTTGTACATGCTGAAGG	60.415	50.000	22.74	10.70	0.00	3.46
2317	5415	2.816087	CTGCTTTGTACATGCTGAAGGT	59.184	45.455	18.10	0.00	0.00	3.50
2380	5478	1.804748	ACCGATCTCGCCTTGTTTTTC	59.195	47.619	0.00	0.00	38.18	2.29
2387	5485	2.442424	TCGCCTTGTTTTTCGTTTTCG	58.558	42.857	0.00	0.00	45.64	3.46
2406	5504	7.479291	CGTTTTCGTAATACAAATTCGAATGGT	59.521	33.333	12.25	15.11	36.01	3.55
2408	5506	6.352682	TCGTAATACAAATTCGAATGGTGG	57.647	37.500	20.15	10.23	0.00	4.61
2419	5517	2.029470	TCGAATGGTGGATTTTTGTGGC	60.029	45.455	0.00	0.00	0.00	5.01
2423	5521	1.833630	TGGTGGATTTTTGTGGCACAA	59.166	42.857	28.09	28.09	44.16	3.33
2424	5522	2.158986	TGGTGGATTTTTGTGGCACAAG	60.159	45.455	29.58	0.00	44.16	3.16
2425	5523	2.158971	GGTGGATTTTTGTGGCACAAGT	60.159	45.455	29.58	20.55	44.16	3.16
2432	5595	1.110442	TTGTGGCACAAGTTTCAGGG	58.890	50.000	28.09	0.00	44.16	4.45
2473	5636	1.372582	GATGCCTCAGAATTGCGTGA	58.627	50.000	0.00	0.00	0.00	4.35
2521	5684	1.866601	TCAATGCAATCCGATAGTGCG	59.133	47.619	0.00	0.00	41.27	5.34
2641	5918	9.926751	GTCAAAATCTGAATCTATGTACATGTG	57.073	33.333	18.81	10.94	35.22	3.21
2661	5938	7.123098	ACATGTGTCATGTATGGTTTTCATGAT	59.877	33.333	12.74	0.00	45.79	2.45
2682	5959	8.915654	CATGATGAAAAGGCAAAGTTAAGTTAC	58.084	33.333	0.00	0.00	0.00	2.50
2683	5960	8.232913	TGATGAAAAGGCAAAGTTAAGTTACT	57.767	30.769	0.00	0.00	0.00	2.24
2772	6139	7.391148	TTTCCAGAGCATACCTTTTCATTAC	57.609	36.000	0.00	0.00	0.00	1.89
2802	6169	6.296026	ACAGACAGGTATAAACAAAGCTGAA	58.704	36.000	8.37	0.00	42.45	3.02
2870	6265	8.422577	TGTATTGCTCACTCCATACAGTATAT	57.577	34.615	0.00	0.00	0.00	0.86
2871	6266	9.528489	TGTATTGCTCACTCCATACAGTATATA	57.472	33.333	0.00	0.00	0.00	0.86
2875	6270	8.706322	TGCTCACTCCATACAGTATATAAGAA	57.294	34.615	0.00	0.00	0.00	2.52

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
25	26	2.288825	TGTCCTCAACTAAGAAGCACCG	60.289	50.000	0.00	0.00	0.00	4.94
40	41	6.761714	ACATATTCCACTTCGTATTTGTCCTC	59.238	38.462	0.00	0.00	0.00	3.71
86	87	4.621034	CCATTTTGCATTGAAACTCGGTAC	59.379	41.667	0.00	0.00	0.00	3.34
114	115	3.413558	CCGTTTTATTTCCGAAGAAGCG	58.586	45.455	0.00	0.00	32.35	4.68
123	124	5.474825	TGATTTTCCTGCCGTTTTATTTCC	58.525	37.500	0.00	0.00	0.00	3.13
134	135	3.006217	GGCTCCATATTGATTTTCCTGCC	59.994	47.826	0.00	0.00	0.00	4.85
137	138	2.887152	GCGGCTCCATATTGATTTTCCT	59.113	45.455	0.00	0.00	0.00	3.36
166	167	7.550597	TCTGGAAGTCATATCAGCAAGATAT	57.449	36.000	6.01	6.01	41.96	1.63
240	241	0.491823	TCCTGGGAGTCCTTCAAGGA	59.508	55.000	0.34	0.34	43.43	3.36
282	283	8.265108	ACCTCCTACCCTTAGAAAATAAGATC	57.735	38.462	0.00	0.00	0.00	2.75
328	932	4.522789	GGCTTTTCAAATCCACTCTAACCA	59.477	41.667	0.00	0.00	0.00	3.67
379	984	6.183360	CGGAATGCAGATTGAGTTGACTTATT	60.183	38.462	0.00	0.00	0.00	1.40
380	985	5.295292	CGGAATGCAGATTGAGTTGACTTAT	59.705	40.000	0.00	0.00	0.00	1.73
392	997	5.221342	TGTTAAACAAACCGGAATGCAGATT	60.221	36.000	9.46	3.34	37.27	2.40
394	999	3.632604	TGTTAAACAAACCGGAATGCAGA	59.367	39.130	9.46	0.00	37.27	4.26
395	1000	3.971150	TGTTAAACAAACCGGAATGCAG	58.029	40.909	9.46	0.00	37.27	4.41
396	1001	4.098044	TCTTGTTAAACAAACCGGAATGCA	59.902	37.500	9.46	0.00	37.69	3.96
397	1002	4.612943	TCTTGTTAAACAAACCGGAATGC	58.387	39.130	9.46	0.00	37.69	3.56
424	1152	9.809096	TGTTTTCAGTTTATTATTTCAAGTGCA	57.191	25.926	0.00	0.00	0.00	4.57
479	1405	7.995488	AGAATCTCCCATACTTTAATTGTCCAG	59.005	37.037	0.00	0.00	0.00	3.86
594	1520	2.030401	GTTGCCACGCATACCGACA	61.030	57.895	0.00	0.00	38.76	4.35
595	1521	2.030401	TGTTGCCACGCATACCGAC	61.030	57.895	0.00	0.00	38.76	4.79
596	1522	2.030401	GTGTTGCCACGCATACCGA	61.030	57.895	0.00	0.00	38.76	4.69
597	1523	2.478746	GTGTTGCCACGCATACCG	59.521	61.111	0.00	0.00	38.76	4.02
598	1524	1.674322	AGGTGTTGCCACGCATACC	60.674	57.895	3.69	10.81	42.48	2.73
599	1525	0.953471	TCAGGTGTTGCCACGCATAC	60.953	55.000	3.69	0.00	42.80	2.39
600	1526	0.035534	ATCAGGTGTTGCCACGCATA	60.036	50.000	3.69	0.00	42.80	3.14
601	1527	1.303561	ATCAGGTGTTGCCACGCAT	60.304	52.632	3.69	0.00	42.80	4.73
602	1528	2.112928	ATCAGGTGTTGCCACGCA	59.887	55.556	3.69	0.00	42.80	5.24
603	1529	0.953471	TACATCAGGTGTTGCCACGC	60.953	55.000	0.00	0.00	42.80	5.34
660	1586	1.884579	CATTTCTGCACAAGCCAGACT	59.115	47.619	0.00	0.00	41.13	3.24
769	1699	9.809096	TTGCTATGAATGAAACAACTAACAAAA	57.191	25.926	0.00	0.00	0.00	2.44
771	1701	9.409312	CATTGCTATGAATGAAACAACTAACAA	57.591	29.630	1.51	0.00	35.65	2.83
788	1718	4.201714	CCGACACACAAGTACATTGCTATG	60.202	45.833	6.59	6.59	43.15	2.23
791	1721	2.143122	CCGACACACAAGTACATTGCT	58.857	47.619	0.00	0.00	43.15	3.91
852	1789	7.217447	CGTTTTCCATTACGTATTTGTCCAATC	59.783	37.037	0.00	0.00	33.33	2.67
869	1806	2.288152	GGTGCAACATGACGTTTTCCAT	60.288	45.455	0.00	0.00	39.98	3.41
875	1812	1.474478	TGTTTGGTGCAACATGACGTT	59.526	42.857	4.62	0.00	39.98	3.99
886	1823	0.530431	CTGCCTGGTTTGTTTGGTGC	60.530	55.000	0.00	0.00	0.00	5.01
901	1838	1.989706	TAAGTGGTTGGTTTCCTGCC	58.010	50.000	0.00	0.00	0.00	4.85
1251	2214	0.795085	CTTTCTCTGCACGGAGCTTG	59.205	55.000	1.37	0.00	45.94	4.01
1273	2236	3.006247	GAGTCAGCTCCCTCAATTCAAC	58.994	50.000	4.61	0.00	35.76	3.18
1280	2243	0.324183	CCTCTGAGTCAGCTCCCTCA	60.324	60.000	15.72	10.59	40.95	3.86
1761	3121	1.410882	GACTCCTGAGCCATAGTCACC	59.589	57.143	0.00	0.00	38.56	4.02
1884	3244	9.984590	ACCCCTAAAAGTGTATTAAACATACAT	57.015	29.630	0.00	0.00	41.10	2.29
2002	3384	1.612442	ATGGTCCAGCACCCGTACT	60.612	57.895	0.00	0.00	46.18	2.73
2070	5038	2.736682	CGACGATGAACGCCAACCC	61.737	63.158	0.00	0.00	46.94	4.11
2071	5039	2.776072	CGACGATGAACGCCAACC	59.224	61.111	0.00	0.00	46.94	3.77
2089	5057	5.046529	CCAGAGATATCAGGAACTTTGTCG	58.953	45.833	5.32	0.00	34.60	4.35
2165	5200	2.070039	CCTAAGATGGCCCACGGGA	61.070	63.158	6.21	0.00	37.50	5.14
2204	5281	2.879103	TCAAAAGGGTCCACATCCTC	57.121	50.000	0.00	0.00	32.02	3.71
2225	5302	6.072508	TCACCAATCAGAAGATTAGCAACAAC	60.073	38.462	0.00	0.00	42.46	3.32
2226	5303	6.003326	TCACCAATCAGAAGATTAGCAACAA	58.997	36.000	0.00	0.00	42.46	2.83
2240	5338	5.345702	CAGGCAATAATGTTCACCAATCAG	58.654	41.667	0.00	0.00	0.00	2.90
2293	5391	2.439409	TCAGCATGTACAAAGCAGCAT	58.561	42.857	21.20	2.78	37.40	3.79
2305	5403	0.538057	CACCACCACCTTCAGCATGT	60.538	55.000	0.00	0.00	37.40	3.21
2315	5413	3.201266	TGTTATCCTTATCCACCACCACC	59.799	47.826	0.00	0.00	0.00	4.61
2316	5414	4.451900	CTGTTATCCTTATCCACCACCAC	58.548	47.826	0.00	0.00	0.00	4.16
2317	5415	3.118038	GCTGTTATCCTTATCCACCACCA	60.118	47.826	0.00	0.00	0.00	4.17
2380	5478	7.479291	ACCATTCGAATTTGTATTACGAAAACG	59.521	33.333	8.21	14.35	43.89	3.60
2387	5485	9.581099	AAAATCCACCATTCGAATTTGTATTAC	57.419	29.630	8.21	0.00	0.00	1.89
2406	5504	3.902881	AACTTGTGCCACAAAAATCCA	57.097	38.095	11.99	0.00	37.69	3.41
2408	5506	4.270808	CCTGAAACTTGTGCCACAAAAATC	59.729	41.667	11.99	9.85	37.69	2.17
2419	5517	2.223805	GCTTCAACCCCTGAAACTTGTG	60.224	50.000	0.00	0.00	43.54	3.33
2423	5521	1.064017	TGTGCTTCAACCCCTGAAACT	60.064	47.619	0.00	0.00	43.54	2.66
2424	5522	1.398692	TGTGCTTCAACCCCTGAAAC	58.601	50.000	0.00	0.00	43.54	2.78
2425	5523	2.031120	CTTGTGCTTCAACCCCTGAAA	58.969	47.619	0.00	0.00	43.54	2.69
2473	5636	9.490083	AGTAACAAACCTAACTACTCCATATCT	57.510	33.333	0.00	0.00	0.00	1.98
2661	5938	8.132995	GCTAAGTAACTTAACTTTGCCTTTTCA	58.867	33.333	10.67	0.00	46.05	2.69
2772	6139	9.341899	GCTTTGTTTATACCTGTCTGTAAATTG	57.658	33.333	0.00	0.00	0.00	2.32
2802	6169	1.862602	GAACGGGGCAGCGTTTTGAT	61.863	55.000	0.00	0.00	0.00	2.57
2871	6266	9.419297	GTTTCTTTTGGACAAGTTAGTTTTCTT	57.581	29.630	0.00	0.00	0.00	2.52
2872	6267	8.581578	TGTTTCTTTTGGACAAGTTAGTTTTCT	58.418	29.630	0.00	0.00	0.00	2.52
2873	6268	8.751302	TGTTTCTTTTGGACAAGTTAGTTTTC	57.249	30.769	0.00	0.00	0.00	2.29
2893	6290	4.273480	ACACCAGATGCGCTAATATGTTTC	59.727	41.667	9.73	0.00	0.00	2.78
2901	6298	1.134818	CCACTACACCAGATGCGCTAA	60.135	52.381	9.73	0.00	0.00	3.09
2902	6299	0.459899	CCACTACACCAGATGCGCTA	59.540	55.000	9.73	0.00	0.00	4.26

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.