AutoCloner

Multiple sequence alignment - TraesCS2A01G409500

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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	TraesCS2A01G409500	chr2A	100.000	4040	0	0	1	4040	667583084	667587123	0.000000e+00	7461.0
1	TraesCS2A01G409500	chr2A	91.477	176	14	1	3865	4040	375770091	375769917	1.450000e-59	241.0
2	TraesCS2A01G409500	chr6A	96.425	3329	103	12	725	4040	365556215	365552890	0.000000e+00	5474.0
3	TraesCS2A01G409500	chr6A	97.087	2506	68	5	992	3493	365563139	365560635	0.000000e+00	4218.0
4	TraesCS2A01G409500	chr6A	87.788	868	73	23	131	996	365578502	365577666	0.000000e+00	985.0
5	TraesCS2A01G409500	chr6A	96.477	511	16	2	3532	4040	365560635	365560125	0.000000e+00	843.0
6	TraesCS2A01G409500	chr6A	87.597	387	18	9	130	486	365557071	365556685	4.830000e-114	422.0
7	TraesCS2A01G409500	chr6A	84.184	392	45	10	181	563	155908797	155909180	8.250000e-97	364.0
8	TraesCS2A01G409500	chr6A	83.000	400	41	12	587	960	155933584	155933982	1.800000e-88	337.0
9	TraesCS2A01G409500	chr6A	88.172	93	10	1	123	214	518075644	518075552	4.270000e-20	110.0
10	TraesCS2A01G409500	chr4A	93.733	3367	169	22	686	4040	299912444	299909108	0.000000e+00	5011.0
11	TraesCS2A01G409500	chr4A	84.459	592	61	20	128	693	299921215	299920629	4.560000e-154	555.0
12	TraesCS2A01G409500	chr1D	88.845	1533	105	29	1355	2836	457880532	457879015	0.000000e+00	1823.0
13	TraesCS2A01G409500	chr1D	90.105	1233	95	17	2829	4040	237419976	237421202	0.000000e+00	1576.0
14	TraesCS2A01G409500	chr1D	88.889	549	46	13	3502	4040	237424577	237425120	0.000000e+00	662.0
15	TraesCS2A01G409500	chr1D	81.933	631	80	23	362	984	237419355	237419959	1.680000e-138	503.0
16	TraesCS2A01G409500	chr1D	82.785	395	21	25	982	1354	457881080	457880711	3.920000e-80	309.0
17	TraesCS2A01G409500	chr1D	96.000	125	5	0	4	128	30392029	30391905	1.900000e-48	204.0
18	TraesCS2A01G409500	chr1D	95.312	128	6	0	1	128	211256456	211256583	1.900000e-48	204.0
19	TraesCS2A01G409500	chr1D	95.312	128	6	0	1	128	476698501	476698628	1.900000e-48	204.0
20	TraesCS2A01G409500	chr1A	88.108	1438	106	35	1417	2836	550344274	550342884	0.000000e+00	1648.0
21	TraesCS2A01G409500	chr1A	88.133	809	61	13	3244	4040	232733562	232734347	0.000000e+00	929.0
22	TraesCS2A01G409500	chr1A	84.250	400	27	22	982	1357	550344976	550344589	1.380000e-94	357.0
23	TraesCS2A01G409500	chr1A	97.436	78	2	0	1355	1432	550344380	550344303	2.530000e-27	134.0
24	TraesCS2A01G409500	chr1A	86.000	100	13	1	121	219	309966910	309967009	5.520000e-19	106.0
25	TraesCS2A01G409500	chr3B	88.821	1154	100	18	2839	3976	42263496	42264636	0.000000e+00	1389.0
26	TraesCS2A01G409500	chr3B	89.593	884	72	13	2839	3712	40047320	40048193	0.000000e+00	1105.0
27	TraesCS2A01G409500	chr3B	78.281	884	114	33	135	984	40046435	40047274	7.800000e-137	497.0
28	TraesCS2A01G409500	chr3B	78.778	622	78	36	151	727	358654430	358653818	6.380000e-98	368.0
29	TraesCS2A01G409500	chr3B	87.762	286	30	4	431	713	42256942	42257225	3.010000e-86	329.0
30	TraesCS2A01G409500	chr3B	80.769	416	51	15	3625	4040	40048038	40048424	8.490000e-77	298.0
31	TraesCS2A01G409500	chr3B	88.559	236	26	1	750	984	42263215	42263450	6.610000e-73	285.0
32	TraesCS2A01G409500	chr1B	87.563	997	87	23	1358	2324	627947592	627946603	0.000000e+00	1120.0
33	TraesCS2A01G409500	chr1B	93.910	312	13	2	2525	2836	627946599	627946294	2.200000e-127	466.0
34	TraesCS2A01G409500	chr1B	91.950	323	15	7	982	1294	627948013	627947692	3.710000e-120	442.0
35	TraesCS2A01G409500	chr1B	89.286	56	5	1	2884	2939	376488366	376488420	7.250000e-08	69.4
36	TraesCS2A01G409500	chr7A	89.753	810	63	13	3244	4040	60645590	60644788	0.000000e+00	1018.0
37	TraesCS2A01G409500	chr7A	84.966	592	60	9	395	960	238553574	238552986	1.260000e-159	573.0
38	TraesCS2A01G409500	chr7A	86.667	105	8	6	121	222	429696565	429696666	1.190000e-20	111.0
39	TraesCS2A01G409500	chr5A	84.049	489	55	13	121	599	116897223	116896748	2.210000e-122	449.0
40	TraesCS2A01G409500	chr5A	87.059	255	30	3	709	960	116896313	116896059	6.610000e-73	285.0
41	TraesCS2A01G409500	chr5A	93.750	48	3	0	2892	2939	296728053	296728100	5.600000e-09	73.1
42	TraesCS2A01G409500	chr3D	86.641	262	30	4	304	563	286534828	286534570	6.610000e-73	285.0
43	TraesCS2A01G409500	chr3D	90.476	168	16	0	790	957	286534224	286534057	5.260000e-54	222.0
44	TraesCS2A01G409500	chr3D	96.000	125	5	0	4	128	52189055	52188931	1.900000e-48	204.0
45	TraesCS2A01G409500	chr3D	96.000	125	5	0	4	128	228843274	228843150	1.900000e-48	204.0
46	TraesCS2A01G409500	chr3D	83.436	163	15	7	121	277	286536442	286536286	1.510000e-29	141.0
47	TraesCS2A01G409500	chr4D	96.094	128	5	0	1	128	139397892	139398019	4.090000e-50	209.0
48	TraesCS2A01G409500	chr5D	95.312	128	6	0	1	128	357318856	357318983	1.900000e-48	204.0
49	TraesCS2A01G409500	chr5D	96.000	125	5	0	4	128	480306898	480306774	1.900000e-48	204.0
50	TraesCS2A01G409500	chr5D	95.312	128	6	0	1	128	529944758	529944885	1.900000e-48	204.0
51	TraesCS2A01G409500	chr5D	86.154	130	12	4	225	352	28370478	28370603	7.040000e-28	135.0
52	TraesCS2A01G409500	chr2B	94.737	114	6	0	1244	1357	425812011	425812124	1.150000e-40	178.0
53	TraesCS2A01G409500	chr2B	87.368	95	10	2	121	214	692736105	692736012	1.540000e-19	108.0
54	TraesCS2A01G409500	chr3A	93.750	48	3	0	2892	2939	6686666	6686619	5.600000e-09	73.1

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	TraesCS2A01G409500	chr2A	667583084	667587123	4039	False	7461.000000	7461	100.000000	1	4040	1	chr2A.!!$F1	4039
1	TraesCS2A01G409500	chr6A	365552890	365563139	10249	True	2739.250000	5474	94.396500	130	4040	4	chr6A.!!$R3	3910
2	TraesCS2A01G409500	chr6A	365577666	365578502	836	True	985.000000	985	87.788000	131	996	1	chr6A.!!$R1	865
3	TraesCS2A01G409500	chr4A	299909108	299912444	3336	True	5011.000000	5011	93.733000	686	4040	1	chr4A.!!$R1	3354
4	TraesCS2A01G409500	chr4A	299920629	299921215	586	True	555.000000	555	84.459000	128	693	1	chr4A.!!$R2	565
5	TraesCS2A01G409500	chr1D	457879015	457881080	2065	True	1066.000000	1823	85.815000	982	2836	2	chr1D.!!$R2	1854
6	TraesCS2A01G409500	chr1D	237419355	237425120	5765	False	913.666667	1576	86.975667	362	4040	3	chr1D.!!$F3	3678
7	TraesCS2A01G409500	chr1A	232733562	232734347	785	False	929.000000	929	88.133000	3244	4040	1	chr1A.!!$F1	796
8	TraesCS2A01G409500	chr1A	550342884	550344976	2092	True	713.000000	1648	89.931333	982	2836	3	chr1A.!!$R1	1854
9	TraesCS2A01G409500	chr3B	42263215	42264636	1421	False	837.000000	1389	88.690000	750	3976	2	chr3B.!!$F3	3226
10	TraesCS2A01G409500	chr3B	40046435	40048424	1989	False	633.333333	1105	82.881000	135	4040	3	chr3B.!!$F2	3905
11	TraesCS2A01G409500	chr3B	358653818	358654430	612	True	368.000000	368	78.778000	151	727	1	chr3B.!!$R1	576
12	TraesCS2A01G409500	chr1B	627946294	627948013	1719	True	676.000000	1120	91.141000	982	2836	3	chr1B.!!$R1	1854
13	TraesCS2A01G409500	chr7A	60644788	60645590	802	True	1018.000000	1018	89.753000	3244	4040	1	chr7A.!!$R1	796
14	TraesCS2A01G409500	chr7A	238552986	238553574	588	True	573.000000	573	84.966000	395	960	1	chr7A.!!$R2	565
15	TraesCS2A01G409500	chr5A	116896059	116897223	1164	True	367.000000	449	85.554000	121	960	2	chr5A.!!$R1	839
16	TraesCS2A01G409500	chr3D	286534057	286536442	2385	True	216.000000	285	86.851000	121	957	3	chr3D.!!$R3	836

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
64	65	0.537143	GGCAACTCATGTCACCCACA	60.537	55.000	0.00	40.18	4.17	F
318	7674	0.546598	CTTCCCCGAATTAGGCCACT	59.453	55.000	5.01	0.00	4.00	F
774	8488	0.618968	CTTGCCCCACTCCTAGGTCT	60.619	60.000	9.08	0.00	3.85	F
1445	9668	1.203063	ACTGCTGAGAGTGGACACCTA	60.203	52.381	0.00	0.00	3.08	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Hairpin	End Stability	Orientation
1916	10169	0.249238	GATCTCTTCGTCGGCATGCT	60.249	55.000	18.92	0.00	3.79	R
2076	10329	2.696526	TCCCAGTCAGTACCTTCACT	57.303	50.000	0.00	0.00	3.41	R
2259	10529	2.742053	CCATCTTGTCGATCCGTTTTGT	59.258	45.455	0.00	0.00	2.83	R
3066	11375	2.701587	TGGACAAACTCCAGCAACG	58.298	52.632	0.00	44.99	4.10	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
20	21	3.487563	GAGATTCGCCAAAACGGAATT	57.512	42.857	0.00	0.00	36.56	2.17
22	23	2.817258	AGATTCGCCAAAACGGAATTGA	59.183	40.909	0.00	0.00	36.56	2.57
25	26	3.210358	TCGCCAAAACGGAATTGAATC	57.790	42.857	0.00	0.00	36.56	2.52
27	28	2.413502	CGCCAAAACGGAATTGAATCGA	60.414	45.455	0.00	0.00	36.56	3.59
30	31	4.732784	CCAAAACGGAATTGAATCGACAT	58.267	39.130	0.00	0.00	36.56	3.06
31	32	5.160641	CCAAAACGGAATTGAATCGACATT	58.839	37.500	0.00	0.00	36.56	2.71
32	33	5.633182	CCAAAACGGAATTGAATCGACATTT	59.367	36.000	0.00	0.00	36.56	2.32
34	35	6.689178	AAACGGAATTGAATCGACATTTTG	57.311	33.333	0.00	0.00	0.00	2.44
35	36	5.621197	ACGGAATTGAATCGACATTTTGA	57.379	34.783	0.00	0.00	0.00	2.69
36	37	5.390613	ACGGAATTGAATCGACATTTTGAC	58.609	37.500	0.00	0.00	0.00	3.18
38	39	5.855925	CGGAATTGAATCGACATTTTGACAA	59.144	36.000	0.00	0.00	0.00	3.18
39	40	6.362016	CGGAATTGAATCGACATTTTGACAAA	59.638	34.615	0.00	0.00	0.00	2.83
40	41	7.096271	CGGAATTGAATCGACATTTTGACAAAA	60.096	33.333	15.39	15.39	34.41	2.44
44	45	9.689976	ATTGAATCGACATTTTGACAAAACATA	57.310	25.926	15.36	1.29	32.37	2.29
46	47	7.807433	TGAATCGACATTTTGACAAAACATAGG	59.193	33.333	15.36	6.14	32.37	2.57
47	48	5.457140	TCGACATTTTGACAAAACATAGGC	58.543	37.500	15.36	7.56	32.37	3.93
48	49	5.009110	TCGACATTTTGACAAAACATAGGCA	59.991	36.000	15.36	0.00	32.37	4.75
49	50	5.689514	CGACATTTTGACAAAACATAGGCAA	59.310	36.000	15.36	0.00	32.37	4.52
53	54	6.700960	CATTTTGACAAAACATAGGCAACTCA	59.299	34.615	15.36	0.00	39.94	3.41
55	56	7.385752	ATTTTGACAAAACATAGGCAACTCATG	59.614	33.333	15.36	0.00	39.94	3.07
62	63	4.819783	GGCAACTCATGTCACCCA	57.180	55.556	0.00	0.00	32.41	4.51
63	64	2.257353	GGCAACTCATGTCACCCAC	58.743	57.895	0.00	0.00	32.41	4.61
64	65	0.537143	GGCAACTCATGTCACCCACA	60.537	55.000	0.00	0.00	40.18	4.17
67	68	3.081061	GCAACTCATGTCACCCACATTA	58.919	45.455	0.00	0.00	43.89	1.90
68	69	3.696051	GCAACTCATGTCACCCACATTAT	59.304	43.478	0.00	0.00	43.89	1.28
69	70	4.158394	GCAACTCATGTCACCCACATTATT	59.842	41.667	0.00	0.00	43.89	1.40
71	72	6.324819	CAACTCATGTCACCCACATTATTTC	58.675	40.000	0.00	0.00	43.89	2.17
72	73	5.569355	ACTCATGTCACCCACATTATTTCA	58.431	37.500	0.00	0.00	43.89	2.69
74	75	6.319658	ACTCATGTCACCCACATTATTTCATC	59.680	38.462	0.00	0.00	43.89	2.92
75	76	6.186234	TCATGTCACCCACATTATTTCATCA	58.814	36.000	0.00	0.00	43.89	3.07
76	77	6.662663	TCATGTCACCCACATTATTTCATCAA	59.337	34.615	0.00	0.00	43.89	2.57
77	78	6.907853	TGTCACCCACATTATTTCATCAAA	57.092	33.333	0.00	0.00	0.00	2.69
79	80	8.586879	TGTCACCCACATTATTTCATCAAATA	57.413	30.769	0.00	0.00	33.95	1.40
80	81	8.465999	TGTCACCCACATTATTTCATCAAATAC	58.534	33.333	0.00	0.00	34.73	1.89
81	82	8.465999	GTCACCCACATTATTTCATCAAATACA	58.534	33.333	0.00	0.00	34.73	2.29
82	83	8.465999	TCACCCACATTATTTCATCAAATACAC	58.534	33.333	0.00	0.00	34.73	2.90
84	85	8.811017	ACCCACATTATTTCATCAAATACACAA	58.189	29.630	0.00	0.00	34.73	3.33
85	86	9.820725	CCCACATTATTTCATCAAATACACAAT	57.179	29.630	0.00	0.00	34.73	2.71
92	93	7.459795	TTTCATCAAATACACAATGTAGGCA	57.540	32.000	0.00	0.00	36.14	4.75
93	94	7.459795	TTCATCAAATACACAATGTAGGCAA	57.540	32.000	0.00	0.00	36.14	4.52
94	95	6.851609	TCATCAAATACACAATGTAGGCAAC	58.148	36.000	0.00	0.00	36.14	4.17
111	112	3.911868	GCAACTCAAATTATGCCACACA	58.088	40.909	0.00	0.00	32.73	3.72
112	113	3.674753	GCAACTCAAATTATGCCACACAC	59.325	43.478	0.00	0.00	32.73	3.82
113	114	4.795635	GCAACTCAAATTATGCCACACACA	60.796	41.667	0.00	0.00	32.73	3.72
114	115	5.288015	CAACTCAAATTATGCCACACACAA	58.712	37.500	0.00	0.00	0.00	3.33
115	116	5.726980	ACTCAAATTATGCCACACACAAT	57.273	34.783	0.00	0.00	0.00	2.71
117	118	6.523840	ACTCAAATTATGCCACACACAATTT	58.476	32.000	0.00	0.00	30.89	1.82
118	119	6.424509	ACTCAAATTATGCCACACACAATTTG	59.575	34.615	13.33	13.33	43.22	2.32
119	120	5.178996	TCAAATTATGCCACACACAATTTGC	59.821	36.000	14.27	0.00	42.32	3.68
232	6180	1.320344	TAGCCGAACTGCCACGATCT	61.320	55.000	0.00	0.00	0.00	2.75
318	7674	0.546598	CTTCCCCGAATTAGGCCACT	59.453	55.000	5.01	0.00	0.00	4.00
354	7740	4.329545	AATCGCGCCACCACCACT	62.330	61.111	0.00	0.00	0.00	4.00
516	7905	2.746375	GCCCACCGGACCTGATGAT	61.746	63.158	9.46	0.00	0.00	2.45
579	7968	1.598130	GCACTGTTGCGACCTTCCT	60.598	57.895	0.45	0.00	39.50	3.36
615	8004	2.532715	TTCCCCAGCTCTGCCCTT	60.533	61.111	0.00	0.00	0.00	3.95
616	8005	2.147433	CTTCCCCAGCTCTGCCCTTT	62.147	60.000	0.00	0.00	0.00	3.11
621	8010	0.825010	CCAGCTCTGCCCTTTGTTGT	60.825	55.000	0.00	0.00	0.00	3.32
774	8488	0.618968	CTTGCCCCACTCCTAGGTCT	60.619	60.000	9.08	0.00	0.00	3.85
843	8558	3.758088	ATAGCACACGAGCGCCGAG	62.758	63.158	22.10	17.10	41.76	4.63
912	8629	1.745890	CCGACATTATCCCGCCTCA	59.254	57.895	0.00	0.00	0.00	3.86
954	8671	3.100671	TCCTCTTCTGCCTAGAACTTCC	58.899	50.000	0.00	0.00	37.99	3.46
1072	8793	8.869109	AGGAATCGAGATGAATTCTATCTTCTT	58.131	33.333	16.49	12.05	35.14	2.52
1225	8969	5.067153	CAGTTTCTTGGATTGTTGGTGTGTA	59.933	40.000	0.00	0.00	0.00	2.90
1445	9668	1.203063	ACTGCTGAGAGTGGACACCTA	60.203	52.381	0.00	0.00	0.00	3.08
1685	9923	1.934410	TTTGGACCCAAAGAGGCCA	59.066	52.632	5.01	0.00	40.51	5.36
1762	10000	1.371558	GCGACTCCCACCAACTCTT	59.628	57.895	0.00	0.00	0.00	2.85
1876	10129	2.134789	ATGCCCTGGAAAGTTAGCAG	57.865	50.000	0.00	0.00	33.10	4.24
1916	10169	4.142609	AGAACTTCTTCACAGAGCACAA	57.857	40.909	0.00	0.00	0.00	3.33
2231	10500	6.207509	AGGCACTAGATTAGAGGACATCTA	57.792	41.667	0.00	0.00	36.64	1.98
2259	10529	3.550639	CCATCAAAAAGAAGCGCAAGTCA	60.551	43.478	11.47	0.00	41.68	3.41
2271	10549	1.721489	CGCAAGTCACAAAACGGATCG	60.721	52.381	0.00	0.00	0.00	3.69
2344	10623	7.666623	ACCACTAAGGAAAAACAATACAATGG	58.333	34.615	0.00	0.00	41.22	3.16
2651	10931	0.759346	GGAGAACCAGTGTGGACAGT	59.241	55.000	0.00	0.00	40.96	3.55
2873	11176	2.573869	CGCACCATGGACGTCTCT	59.426	61.111	21.47	0.00	0.00	3.10
3050	11359	4.286707	TGTAATGCCTGAGAACTAGCCTA	58.713	43.478	0.00	0.00	0.00	3.93
3066	11375	5.712917	ACTAGCCTAGGAATAGATGCAGTAC	59.287	44.000	21.99	0.00	0.00	2.73
3082	11391	2.221055	CAGTACGTTGCTGGAGTTTGTC	59.779	50.000	10.76	0.00	0.00	3.18
3178	11487	3.560896	GCAGTACCCAGTTAACGTTTTCA	59.439	43.478	5.91	0.00	0.00	2.69
3295	11605	6.595682	ACAAAGAGAGGAGTTCAAAGAATCA	58.404	36.000	0.00	0.00	0.00	2.57
3445	11759	8.741101	TGAAAAAGTGTGATATTACATTGCAC	57.259	30.769	3.37	0.00	32.43	4.57
3783	16051	3.770263	AAAATGGCGATGTCTGATGTG	57.230	42.857	0.00	0.00	0.00	3.21

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
0	1	3.119990	TCAATTCCGTTTTGGCGAATCTC	60.120	43.478	0.00	0.00	37.80	2.75
1	2	2.817258	TCAATTCCGTTTTGGCGAATCT	59.183	40.909	0.00	0.00	37.80	2.40
5	6	2.413502	CGATTCAATTCCGTTTTGGCGA	60.414	45.455	0.00	0.00	37.80	5.54
6	7	1.910819	CGATTCAATTCCGTTTTGGCG	59.089	47.619	0.00	0.00	37.80	5.69
7	8	2.914838	GTCGATTCAATTCCGTTTTGGC	59.085	45.455	0.00	0.00	37.80	4.52
9	10	6.689178	AAATGTCGATTCAATTCCGTTTTG	57.311	33.333	0.00	0.00	0.00	2.44
10	11	6.920758	TCAAAATGTCGATTCAATTCCGTTTT	59.079	30.769	0.00	0.00	0.00	2.43
11	12	6.362283	GTCAAAATGTCGATTCAATTCCGTTT	59.638	34.615	0.00	0.00	0.00	3.60
12	13	5.856455	GTCAAAATGTCGATTCAATTCCGTT	59.144	36.000	0.00	0.00	0.00	4.44
13	14	5.049060	TGTCAAAATGTCGATTCAATTCCGT	60.049	36.000	0.00	0.00	0.00	4.69
14	15	5.389778	TGTCAAAATGTCGATTCAATTCCG	58.610	37.500	0.00	0.00	0.00	4.30
15	16	7.636259	TTTGTCAAAATGTCGATTCAATTCC	57.364	32.000	0.00	0.00	0.00	3.01
16	17	8.538856	TGTTTTGTCAAAATGTCGATTCAATTC	58.461	29.630	13.65	0.00	32.22	2.17
17	18	8.417780	TGTTTTGTCAAAATGTCGATTCAATT	57.582	26.923	13.65	0.00	32.22	2.32
18	19	8.592105	ATGTTTTGTCAAAATGTCGATTCAAT	57.408	26.923	13.65	0.00	32.22	2.57
19	20	9.179552	CTATGTTTTGTCAAAATGTCGATTCAA	57.820	29.630	13.65	0.00	32.22	2.69
20	21	7.807433	CCTATGTTTTGTCAAAATGTCGATTCA	59.193	33.333	13.65	5.32	32.22	2.57
22	23	6.586082	GCCTATGTTTTGTCAAAATGTCGATT	59.414	34.615	13.65	0.00	32.22	3.34
25	26	5.218885	TGCCTATGTTTTGTCAAAATGTCG	58.781	37.500	13.65	4.28	32.22	4.35
27	28	6.581712	AGTTGCCTATGTTTTGTCAAAATGT	58.418	32.000	13.65	8.31	32.22	2.71
30	31	6.214191	TGAGTTGCCTATGTTTTGTCAAAA	57.786	33.333	6.65	6.65	0.00	2.44
31	32	5.843673	TGAGTTGCCTATGTTTTGTCAAA	57.156	34.783	0.00	0.00	0.00	2.69
32	33	5.301551	ACATGAGTTGCCTATGTTTTGTCAA	59.698	36.000	0.00	0.00	31.38	3.18
34	35	5.048782	TGACATGAGTTGCCTATGTTTTGTC	60.049	40.000	0.00	0.00	35.35	3.18
35	36	4.826733	TGACATGAGTTGCCTATGTTTTGT	59.173	37.500	0.00	0.00	35.35	2.83
36	37	5.156355	GTGACATGAGTTGCCTATGTTTTG	58.844	41.667	0.00	0.00	35.35	2.44
38	39	3.758554	GGTGACATGAGTTGCCTATGTTT	59.241	43.478	0.00	0.00	35.35	2.83
39	40	3.347216	GGTGACATGAGTTGCCTATGTT	58.653	45.455	0.00	0.00	35.35	2.71
40	41	2.356125	GGGTGACATGAGTTGCCTATGT	60.356	50.000	0.00	0.00	37.72	2.29
44	45	0.250901	GTGGGTGACATGAGTTGCCT	60.251	55.000	0.00	0.00	0.00	4.75
46	47	1.538047	ATGTGGGTGACATGAGTTGC	58.462	50.000	0.00	0.00	44.12	4.17
47	48	5.902613	AATAATGTGGGTGACATGAGTTG	57.097	39.130	0.00	0.00	45.12	3.16
48	49	6.009589	TGAAATAATGTGGGTGACATGAGTT	58.990	36.000	0.00	0.00	45.12	3.01
49	50	5.569355	TGAAATAATGTGGGTGACATGAGT	58.431	37.500	0.00	0.00	45.12	3.41
53	54	9.199645	TATTTGATGAAATAATGTGGGTGACAT	57.800	29.630	0.00	0.00	38.61	3.06
55	56	8.465999	TGTATTTGATGAAATAATGTGGGTGAC	58.534	33.333	0.00	0.00	36.10	3.67
56	57	8.465999	GTGTATTTGATGAAATAATGTGGGTGA	58.534	33.333	0.00	0.00	36.10	4.02
57	58	8.249638	TGTGTATTTGATGAAATAATGTGGGTG	58.750	33.333	0.00	0.00	36.10	4.61
59	60	9.820725	ATTGTGTATTTGATGAAATAATGTGGG	57.179	29.630	0.00	0.00	36.10	4.61
67	68	8.065473	TGCCTACATTGTGTATTTGATGAAAT	57.935	30.769	0.00	0.00	31.66	2.17
68	69	7.459795	TGCCTACATTGTGTATTTGATGAAA	57.540	32.000	0.00	0.00	31.66	2.69
69	70	7.176515	AGTTGCCTACATTGTGTATTTGATGAA	59.823	33.333	0.00	0.00	31.66	2.57
71	72	6.855836	AGTTGCCTACATTGTGTATTTGATG	58.144	36.000	0.00	0.00	31.66	3.07
72	73	6.658816	TGAGTTGCCTACATTGTGTATTTGAT	59.341	34.615	0.00	0.00	31.66	2.57
74	75	6.252967	TGAGTTGCCTACATTGTGTATTTG	57.747	37.500	0.00	0.00	31.66	2.32
75	76	6.892658	TTGAGTTGCCTACATTGTGTATTT	57.107	33.333	0.00	0.00	31.66	1.40
76	77	6.892658	TTTGAGTTGCCTACATTGTGTATT	57.107	33.333	0.00	0.00	31.66	1.89
77	78	7.466746	AATTTGAGTTGCCTACATTGTGTAT	57.533	32.000	0.00	0.00	31.66	2.29
79	80	5.789643	AATTTGAGTTGCCTACATTGTGT	57.210	34.783	0.00	0.00	0.00	3.72
80	81	6.254157	GCATAATTTGAGTTGCCTACATTGTG	59.746	38.462	0.00	0.00	0.00	3.33
81	82	6.332630	GCATAATTTGAGTTGCCTACATTGT	58.667	36.000	0.00	0.00	0.00	2.71
82	83	6.817270	GCATAATTTGAGTTGCCTACATTG	57.183	37.500	0.00	0.00	0.00	2.82
90	91	3.674753	GTGTGTGGCATAATTTGAGTTGC	59.325	43.478	0.00	0.00	0.00	4.17
91	92	4.869215	TGTGTGTGGCATAATTTGAGTTG	58.131	39.130	0.00	0.00	0.00	3.16
92	93	5.528043	TTGTGTGTGGCATAATTTGAGTT	57.472	34.783	0.00	0.00	0.00	3.01
93	94	5.726980	ATTGTGTGTGGCATAATTTGAGT	57.273	34.783	0.00	0.00	35.77	3.41
98	99	4.897140	AGCAAATTGTGTGTGGCATAATT	58.103	34.783	0.00	0.00	46.30	1.40
99	100	4.540359	AGCAAATTGTGTGTGGCATAAT	57.460	36.364	0.00	0.00	40.02	1.28
100	101	5.657826	ATAGCAAATTGTGTGTGGCATAA	57.342	34.783	0.00	0.00	32.81	1.90
101	102	6.957920	ATATAGCAAATTGTGTGTGGCATA	57.042	33.333	0.00	0.00	0.00	3.14
102	103	5.857471	ATATAGCAAATTGTGTGTGGCAT	57.143	34.783	0.00	0.00	0.00	4.40
103	104	6.957920	ATATATAGCAAATTGTGTGTGGCA	57.042	33.333	0.00	0.00	0.00	4.92
104	105	8.322906	TCTATATATAGCAAATTGTGTGTGGC	57.677	34.615	14.03	0.00	0.00	5.01
105	106	9.494271	ACTCTATATATAGCAAATTGTGTGTGG	57.506	33.333	14.03	0.00	0.00	4.17
169	6110	1.131693	CATATAGGGCGCGTCGTGATA	59.868	52.381	17.25	8.19	0.00	2.15
232	6180	0.548197	ATGGGTCGGGGTTAGGAACA	60.548	55.000	0.00	0.00	0.00	3.18
370	7758	4.664267	TGGGAGGCCAGGAGCTGT	62.664	66.667	5.01	0.00	43.05	4.40
474	7862	0.980231	GAGATCAGGCAGTGGAGGGT	60.980	60.000	0.00	0.00	0.00	4.34
513	7902	2.046023	CAAGGGTGGCGCTGATCA	60.046	61.111	7.64	0.00	0.00	2.92
563	7952	1.546476	CTCTAGGAAGGTCGCAACAGT	59.454	52.381	0.00	0.00	0.00	3.55
567	7956	0.976073	CCCCTCTAGGAAGGTCGCAA	60.976	60.000	0.00	0.00	38.24	4.85
568	7957	1.381327	CCCCTCTAGGAAGGTCGCA	60.381	63.158	0.00	0.00	38.24	5.10
570	7959	2.134933	GGCCCCTCTAGGAAGGTCG	61.135	68.421	0.00	0.00	38.24	4.79
843	8558	1.852157	TTGGGGACTGGCAGTGGATC	61.852	60.000	27.45	10.40	0.00	3.36
954	8671	1.072965	ACAAGGCAAGAGGTTGGAGAG	59.927	52.381	0.00	0.00	33.87	3.20
1072	8793	5.368145	AGATTAGGCGCAAATCAGATACAA	58.632	37.500	26.73	0.00	36.09	2.41
1164	8885	1.274712	CTTGGAGCTTGGAGAGAGGT	58.725	55.000	0.00	0.00	0.00	3.85
1445	9668	6.884836	CCCTTGTTCTACTTGCCTTATTAGTT	59.115	38.462	0.00	0.00	0.00	2.24
1685	9923	2.733858	CGCTAGCTCTTCTTCGCTTTCT	60.734	50.000	13.93	0.00	37.68	2.52
1762	10000	6.935208	GGTTAAAGAGAAGCAAAGAGGAACTA	59.065	38.462	0.00	0.00	41.55	2.24
1848	10101	4.990526	ACTTTCCAGGGCATATATTGAGG	58.009	43.478	0.00	0.00	0.00	3.86
1852	10105	5.952387	TGCTAACTTTCCAGGGCATATATT	58.048	37.500	0.00	0.00	0.00	1.28
1916	10169	0.249238	GATCTCTTCGTCGGCATGCT	60.249	55.000	18.92	0.00	0.00	3.79
2076	10329	2.696526	TCCCAGTCAGTACCTTCACT	57.303	50.000	0.00	0.00	0.00	3.41
2231	10500	4.458989	TGCGCTTCTTTTTGATGGTTCTAT	59.541	37.500	9.73	0.00	0.00	1.98
2259	10529	2.742053	CCATCTTGTCGATCCGTTTTGT	59.258	45.455	0.00	0.00	0.00	2.83
2271	10549	7.440523	AGAATTAGTTGTCAACCATCTTGTC	57.559	36.000	12.17	1.98	0.00	3.18
2344	10623	3.686241	TGAATGTGATGCTGCTAGTTCAC	59.314	43.478	14.29	14.29	39.11	3.18
2651	10931	4.641645	CCTGAGGCCGGTTGTGCA	62.642	66.667	1.90	0.00	0.00	4.57
2971	11280	3.840594	AGCGGCGGCGGTACAATA	61.841	61.111	35.05	0.00	46.35	1.90
3050	11359	3.133003	AGCAACGTACTGCATCTATTCCT	59.867	43.478	14.28	0.00	45.18	3.36
3066	11375	2.701587	TGGACAAACTCCAGCAACG	58.298	52.632	0.00	0.00	44.99	4.10
3273	11583	9.225436	GTTATGATTCTTTGAACTCCTCTCTTT	57.775	33.333	0.00	0.00	0.00	2.52
3385	11698	7.540400	CCAAATGTTTTTGCGAATGACATACTA	59.460	33.333	13.60	0.00	40.77	1.82
3590	11923	7.911205	CCGCACCGATATTTTAATTTGAACTTA	59.089	33.333	0.00	0.00	0.00	2.24
3793	16061	6.035327	GGGAAATCATTCTTTGCTCAAATTCG	59.965	38.462	0.00	0.00	35.79	3.34

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.