AutoCloner

Multiple sequence alignment - TraesCS7A01G375600

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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	TraesCS7A01G375600	chr7A	100.000	4819	0	0	1	4819	548560901	548565719	0.000000e+00	8900.0
1	TraesCS7A01G375600	chr7A	95.723	678	27	1	253	928	295251117	295251794	0.000000e+00	1090.0
2	TraesCS7A01G375600	chr7A	94.860	681	30	2	253	928	724033059	724033739	0.000000e+00	1059.0
3	TraesCS7A01G375600	chr7A	93.109	682	39	5	249	928	624644496	624645171	0.000000e+00	992.0
4	TraesCS7A01G375600	chr7D	95.906	2003	56	7	1079	3061	481596913	481598909	0.000000e+00	3221.0
5	TraesCS7A01G375600	chr7D	93.434	1782	63	23	3062	4819	481598941	481600692	0.000000e+00	2593.0
6	TraesCS7A01G375600	chr7D	87.682	617	40	18	252	837	576852481	576851870	0.000000e+00	686.0
7	TraesCS7A01G375600	chr7D	89.464	541	39	13	2010	2547	595750361	595749836	0.000000e+00	667.0
8	TraesCS7A01G375600	chr7D	91.224	433	27	4	415	837	614668181	614667750	3.230000e-161	579.0
9	TraesCS7A01G375600	chr7D	90.306	196	6	3	57	249	481596045	481596230	1.340000e-60	244.0
10	TraesCS7A01G375600	chr7D	94.949	99	5	0	57	155	510388716	510388814	6.460000e-34	156.0
11	TraesCS7A01G375600	chr7D	100.000	28	0	0	983	1010	481596874	481596901	9.000000e-03	52.8
12	TraesCS7A01G375600	chr7B	95.515	1739	58	13	968	2695	506988836	506990565	0.000000e+00	2761.0
13	TraesCS7A01G375600	chr7B	88.880	1223	71	27	3062	4252	506991112	506992301	0.000000e+00	1445.0
14	TraesCS7A01G375600	chr7B	90.965	487	32	5	4335	4819	506992309	506992785	0.000000e+00	645.0
15	TraesCS7A01G375600	chr7B	89.460	389	18	5	2693	3058	506990689	506991077	2.030000e-128	470.0
16	TraesCS7A01G375600	chr7B	93.893	131	8	0	52	182	506988434	506988564	1.060000e-46	198.0
17	TraesCS7A01G375600	chr6A	94.845	679	33	1	252	928	561498103	561498781	0.000000e+00	1059.0
18	TraesCS7A01G375600	chr5A	96.230	557	21	0	252	808	523613045	523613601	0.000000e+00	913.0
19	TraesCS7A01G375600	chr1D	89.781	685	34	16	252	928	422870463	422869807	0.000000e+00	845.0
20	TraesCS7A01G375600	chr1D	96.667	60	2	0	75	134	21910933	21910992	3.070000e-17	100.0
21	TraesCS7A01G375600	chr1D	95.238	63	3	0	75	137	21913044	21912982	3.070000e-17	100.0
22	TraesCS7A01G375600	chr4B	87.500	688	47	16	252	928	645091217	645091876	0.000000e+00	758.0
23	TraesCS7A01G375600	chr5D	90.000	530	36	13	2010	2537	551104690	551105204	0.000000e+00	669.0
24	TraesCS7A01G375600	chr5D	89.642	531	40	12	2010	2537	481096323	481096841	0.000000e+00	662.0
25	TraesCS7A01G375600	chrUn	89.405	538	41	13	2004	2537	70735940	70736465	0.000000e+00	664.0
26	TraesCS7A01G375600	chr2B	89.279	541	39	15	2010	2547	684001185	684000661	0.000000e+00	660.0
27	TraesCS7A01G375600	chr2B	89.266	531	40	13	2010	2537	33602505	33603021	0.000000e+00	649.0
28	TraesCS7A01G375600	chr2B	90.795	239	19	2	693	928	98282516	98282278	2.800000e-82	316.0
29	TraesCS7A01G375600	chr2B	86.139	101	5	6	57	155	318213355	318213448	3.070000e-17	100.0
30	TraesCS7A01G375600	chr6B	88.512	531	44	14	2010	2537	241432490	241433006	1.140000e-175	627.0
31	TraesCS7A01G375600	chr3B	92.381	315	19	4	611	922	727320762	727321074	1.230000e-120	444.0
32	TraesCS7A01G375600	chr3B	90.149	335	22	4	252	577	727320036	727320368	4.460000e-115	425.0
33	TraesCS7A01G375600	chr3B	90.135	223	20	2	252	474	17630525	17630305	6.100000e-74	289.0
34	TraesCS7A01G375600	chr3B	90.361	83	7	1	53	134	804242751	804242669	1.830000e-19	108.0
35	TraesCS7A01G375600	chr5B	83.436	163	22	4	768	928	710240100	710240259	3.890000e-31	147.0
36	TraesCS7A01G375600	chr1B	95.238	63	3	0	75	137	37321706	37321644	3.070000e-17	100.0
37	TraesCS7A01G375600	chr3A	81.102	127	17	5	94	213	32244298	32244424	1.430000e-15	95.3
38	TraesCS7A01G375600	chr2D	93.182	44	2	1	57	99	563947243	563947200	4.030000e-06	63.9

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	TraesCS7A01G375600	chr7A	548560901	548565719	4818	False	8900.0	8900	100.0000	1	4819	1	chr7A.!!$F2	4818
1	TraesCS7A01G375600	chr7A	295251117	295251794	677	False	1090.0	1090	95.7230	253	928	1	chr7A.!!$F1	675
2	TraesCS7A01G375600	chr7A	724033059	724033739	680	False	1059.0	1059	94.8600	253	928	1	chr7A.!!$F4	675
3	TraesCS7A01G375600	chr7A	624644496	624645171	675	False	992.0	992	93.1090	249	928	1	chr7A.!!$F3	679
4	TraesCS7A01G375600	chr7D	481596045	481600692	4647	False	1527.7	3221	94.9115	57	4819	4	chr7D.!!$F2	4762
5	TraesCS7A01G375600	chr7D	576851870	576852481	611	True	686.0	686	87.6820	252	837	1	chr7D.!!$R1	585
6	TraesCS7A01G375600	chr7D	595749836	595750361	525	True	667.0	667	89.4640	2010	2547	1	chr7D.!!$R2	537
7	TraesCS7A01G375600	chr7B	506988434	506992785	4351	False	1103.8	2761	91.7426	52	4819	5	chr7B.!!$F1	4767
8	TraesCS7A01G375600	chr6A	561498103	561498781	678	False	1059.0	1059	94.8450	252	928	1	chr6A.!!$F1	676
9	TraesCS7A01G375600	chr5A	523613045	523613601	556	False	913.0	913	96.2300	252	808	1	chr5A.!!$F1	556
10	TraesCS7A01G375600	chr1D	422869807	422870463	656	True	845.0	845	89.7810	252	928	1	chr1D.!!$R2	676
11	TraesCS7A01G375600	chr4B	645091217	645091876	659	False	758.0	758	87.5000	252	928	1	chr4B.!!$F1	676
12	TraesCS7A01G375600	chr5D	551104690	551105204	514	False	669.0	669	90.0000	2010	2537	1	chr5D.!!$F2	527
13	TraesCS7A01G375600	chr5D	481096323	481096841	518	False	662.0	662	89.6420	2010	2537	1	chr5D.!!$F1	527
14	TraesCS7A01G375600	chrUn	70735940	70736465	525	False	664.0	664	89.4050	2004	2537	1	chrUn.!!$F1	533
15	TraesCS7A01G375600	chr2B	684000661	684001185	524	True	660.0	660	89.2790	2010	2547	1	chr2B.!!$R2	537
16	TraesCS7A01G375600	chr2B	33602505	33603021	516	False	649.0	649	89.2660	2010	2537	1	chr2B.!!$F1	527
17	TraesCS7A01G375600	chr6B	241432490	241433006	516	False	627.0	627	88.5120	2010	2537	1	chr6B.!!$F1	527
18	TraesCS7A01G375600	chr3B	727320036	727321074	1038	False	434.5	444	91.2650	252	922	2	chr3B.!!$F1	670

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
595	811	0.245266	CAGATGCAATGCCAAGCACA	59.755	50.000	1.53	43.04	4.57	F
942	1472	1.007387	GCTGCGGGTTTTTGTGAGG	60.007	57.895	0.00	0.00	3.86	F
1802	2907	1.781025	TTGAGGTTTTGGTCAGCGCG	61.781	55.000	0.00	0.00	6.86	F
3519	4814	0.389817	CTTACGCAGCAGTAGTGGCA	60.390	55.000	0.00	0.00	4.92	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Hairpin	End Stability	Orientation
2568	3676	1.462670	GCAACTTTCCAAGAGAGCTCG	59.537	52.381	8.37	34.09	5.03	R
2834	4081	1.081906	GCATGTGACAAGTGCGGTG	60.082	57.895	0.00	0.00	4.94	R
3611	4908	0.755079	CCATCCATTCTCGCTCCTCA	59.245	55.000	0.00	0.00	3.86	R
4677	6004	0.940126	GGACCATACAGATTGCAGCG	59.060	55.000	0.00	0.00	5.18	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
18	19	3.995526	TTATGATGCAGAGGCCGAG	57.004	52.632	0.00	0.00	40.13	4.63
19	20	0.394192	TTATGATGCAGAGGCCGAGG	59.606	55.000	0.00	0.00	40.13	4.63
20	21	1.475169	TATGATGCAGAGGCCGAGGG	61.475	60.000	0.00	0.00	40.13	4.30
21	22	3.474570	GATGCAGAGGCCGAGGGT	61.475	66.667	0.00	0.00	40.13	4.34
22	23	2.041922	ATGCAGAGGCCGAGGGTA	60.042	61.111	0.00	0.00	40.13	3.69
23	24	2.370647	GATGCAGAGGCCGAGGGTAC	62.371	65.000	0.00	0.00	40.13	3.34
24	25	4.208686	GCAGAGGCCGAGGGTACG	62.209	72.222	0.00	0.00	0.00	3.67
25	26	2.754658	CAGAGGCCGAGGGTACGT	60.755	66.667	0.00	0.00	0.00	3.57
26	27	2.439883	AGAGGCCGAGGGTACGTC	60.440	66.667	0.00	0.00	40.21	4.34
27	28	2.439883	GAGGCCGAGGGTACGTCT	60.440	66.667	0.00	0.00	41.61	4.18
28	29	2.439883	AGGCCGAGGGTACGTCTC	60.440	66.667	0.00	0.00	41.61	3.36
29	30	3.525545	GGCCGAGGGTACGTCTCC	61.526	72.222	0.00	0.00	41.61	3.71
30	31	2.753043	GCCGAGGGTACGTCTCCA	60.753	66.667	11.01	0.00	41.61	3.86
31	32	2.125961	GCCGAGGGTACGTCTCCAT	61.126	63.158	11.01	4.54	41.61	3.41
32	33	1.673808	GCCGAGGGTACGTCTCCATT	61.674	60.000	11.01	0.25	41.61	3.16
33	34	0.822164	CCGAGGGTACGTCTCCATTT	59.178	55.000	11.01	0.00	41.61	2.32
34	35	1.202382	CCGAGGGTACGTCTCCATTTC	60.202	57.143	11.01	5.48	41.61	2.17
35	36	1.202382	CGAGGGTACGTCTCCATTTCC	60.202	57.143	11.01	0.00	41.61	3.13
36	37	1.829222	GAGGGTACGTCTCCATTTCCA	59.171	52.381	11.01	0.00	40.48	3.53
37	38	2.235402	GAGGGTACGTCTCCATTTCCAA	59.765	50.000	11.01	0.00	40.48	3.53
38	39	2.640826	AGGGTACGTCTCCATTTCCAAA	59.359	45.455	11.01	0.00	0.00	3.28
39	40	3.073356	AGGGTACGTCTCCATTTCCAAAA	59.927	43.478	11.01	0.00	0.00	2.44
40	41	3.189910	GGGTACGTCTCCATTTCCAAAAC	59.810	47.826	11.01	0.00	0.00	2.43
41	42	3.816523	GGTACGTCTCCATTTCCAAAACA	59.183	43.478	0.00	0.00	0.00	2.83
42	43	4.276431	GGTACGTCTCCATTTCCAAAACAA	59.724	41.667	0.00	0.00	0.00	2.83
43	44	4.993029	ACGTCTCCATTTCCAAAACAAA	57.007	36.364	0.00	0.00	0.00	2.83
44	45	5.331876	ACGTCTCCATTTCCAAAACAAAA	57.668	34.783	0.00	0.00	0.00	2.44
45	46	5.725362	ACGTCTCCATTTCCAAAACAAAAA	58.275	33.333	0.00	0.00	0.00	1.94
249	374	1.136690	TAGTGCTCGCTTGTGTTTCG	58.863	50.000	0.00	0.00	0.00	3.46
308	434	1.273041	GGGAATTTAAGGTGGCTGGGT	60.273	52.381	0.00	0.00	0.00	4.51
353	479	4.463050	TGGACTTGGGAATTAACAAGGT	57.537	40.909	19.76	9.80	46.29	3.50
403	530	3.457380	CTCCCATCAATCTCTTCCTTGGA	59.543	47.826	0.00	0.00	0.00	3.53
423	568	1.605453	GGACCCTGGTAATTCCGCA	59.395	57.895	0.00	0.00	39.52	5.69
595	811	0.245266	CAGATGCAATGCCAAGCACA	59.755	50.000	1.53	0.00	43.04	4.57
688	1212	7.737972	TGATTCGTTTATCTTTCCTTCACAA	57.262	32.000	0.00	0.00	0.00	3.33
698	1222	2.198827	TCCTTCACAAACCGATGCAT	57.801	45.000	0.00	0.00	0.00	3.96
768	1296	7.201427	CGATTTTGTTTCAACATTTGTGTGTCT	60.201	33.333	0.00	0.00	38.95	3.41
863	1391	2.584835	AATAGTCCACTTGCCAAGCA	57.415	45.000	3.88	0.00	36.47	3.91
874	1402	3.228453	CTTGCCAAGCATAATCCCTCAT	58.772	45.455	0.00	0.00	38.76	2.90
875	1403	4.141181	ACTTGCCAAGCATAATCCCTCATA	60.141	41.667	3.88	0.00	38.76	2.15
942	1472	1.007387	GCTGCGGGTTTTTGTGAGG	60.007	57.895	0.00	0.00	0.00	3.86
1010	2110	2.644299	TCAAAGCTTCCATGGAGAAGGA	59.356	45.455	15.53	6.67	42.94	3.36
1089	2192	1.807495	CTTACTCCGGCGATCCCTCC	61.807	65.000	9.30	0.00	0.00	4.30
1378	2481	3.833442	CTTTCAGGTTCCATTTTACGGC	58.167	45.455	0.00	0.00	0.00	5.68
1444	2547	7.363793	CCGAATTTTATCAAGGGGAATTCAAGT	60.364	37.037	7.93	0.00	36.83	3.16
1592	2695	7.007697	GTGTGTAACGACTGTTGTTTATCATC	58.992	38.462	17.93	10.33	42.39	2.92
1740	2845	6.456501	CAGGTAAGTACAGTGGCCTATATTC	58.543	44.000	3.32	0.00	0.00	1.75
1783	2888	4.598257	GCACACGTATGCTGGTCT	57.402	55.556	12.49	0.00	42.62	3.85
1802	2907	1.781025	TTGAGGTTTTGGTCAGCGCG	61.781	55.000	0.00	0.00	0.00	6.86
1979	3084	6.072673	ACTGCAAAAATCTAAAGGTTCCTACG	60.073	38.462	0.00	0.00	0.00	3.51
2141	3248	4.100808	CCTGTCTGATTTTGTTTTCCCCAA	59.899	41.667	0.00	0.00	0.00	4.12
2339	3447	7.047460	TCTCGCTTATACCCCTACTAAAAAG	57.953	40.000	0.00	0.00	0.00	2.27
2481	3589	9.646427	GCTTATTACTTATAGATGTCTTGAGGG	57.354	37.037	0.00	0.00	0.00	4.30
2520	3628	6.882140	TGTTCTTTACAGTCCTCTTTTGTCAA	59.118	34.615	0.00	0.00	31.68	3.18
2764	4003	7.450014	TGCATTCTTAATGGTCTTGTTTAGGAA	59.550	33.333	2.11	0.00	39.31	3.36
2784	4023	5.045872	GGAATTGATTGCACTAAGGATTGC	58.954	41.667	0.00	0.00	39.33	3.56
2834	4081	6.442952	TGTTATGTAACACATGTTGCCTTTC	58.557	36.000	7.53	0.00	40.93	2.62
2892	4139	9.585099	TTTAATTCTGCCATTTCATTACATGAC	57.415	29.630	0.00	0.00	39.39	3.06
3316	4611	9.681062	TGGGCTATATACAATCTTTATTTAGGC	57.319	33.333	0.00	0.00	36.32	3.93
3357	4652	1.202348	GTAAGCCTGGGTTGCATGTTC	59.798	52.381	20.77	0.10	0.00	3.18
3358	4653	0.469705	AAGCCTGGGTTGCATGTTCA	60.470	50.000	10.87	0.00	0.00	3.18
3519	4814	0.389817	CTTACGCAGCAGTAGTGGCA	60.390	55.000	0.00	0.00	0.00	4.92
3611	4908	0.469705	AGGATGAGCGCAGGAGATCT	60.470	55.000	11.47	0.00	0.00	2.75
3671	4968	6.542821	TCACCACTTTGATTATGAGAAAGGT	58.457	36.000	0.00	0.00	32.07	3.50
3935	5233	8.530311	TCCAAATCATGTGCTGTTATACAATTT	58.470	29.630	0.00	0.00	0.00	1.82
3952	5254	4.036734	ACAATTTATTCTTCGATGCGCCAT	59.963	37.500	4.18	0.00	0.00	4.40
3999	5301	2.066340	CCCTGGTGGTTCAGCTACA	58.934	57.895	0.00	0.00	33.64	2.74
4002	5304	1.202758	CCTGGTGGTTCAGCTACAACA	60.203	52.381	9.36	4.27	33.64	3.33
4016	5318	3.628942	GCTACAACAATGATCATGCAGGA	59.371	43.478	9.46	2.36	0.00	3.86
4035	5337	1.100463	ACGTGCCACATCAAGCAACA	61.100	50.000	0.00	0.00	41.48	3.33
4085	5389	1.332375	TGCCACACAGCGACTAAAAAC	59.668	47.619	0.00	0.00	34.65	2.43
4095	5399	2.033832	GCGACTAAAAACCGAACGTTCA	60.034	45.455	26.71	5.63	31.78	3.18
4109	5413	5.910166	CCGAACGTTCAACAAACATATTTCA	59.090	36.000	26.71	0.00	37.77	2.69
4232	5557	5.813383	TGTTGTACGTTATTATTTCCCCCA	58.187	37.500	0.00	0.00	0.00	4.96
4237	5562	6.993902	TGTACGTTATTATTTCCCCCATCTTC	59.006	38.462	0.00	0.00	0.00	2.87
4250	5575	2.295885	CCATCTTCTGCTCACCAATCC	58.704	52.381	0.00	0.00	0.00	3.01
4276	5601	1.419762	TGGTGAGGCTAAGAGCACAAA	59.580	47.619	5.75	0.00	44.75	2.83
4294	5619	8.675705	AGCACAAATTTTTGCCTACTATTTTT	57.324	26.923	22.38	0.92	41.79	1.94
4307	5632	6.142817	CCTACTATTTTTGTCACTGCAACAC	58.857	40.000	0.00	0.00	0.00	3.32
4416	5741	1.039856	ACCACCACCATTTTGCAGTC	58.960	50.000	0.00	0.00	0.00	3.51
4479	5804	1.227438	CGGGTGTCAACGGAACTGT	60.227	57.895	0.00	0.00	0.00	3.55
4517	5842	7.214467	TGTTATCTGAAAATCAAGTCCAACC	57.786	36.000	0.00	0.00	0.00	3.77
4537	5862	3.005367	ACCTCCGTTTGGTTAATGCTTTG	59.995	43.478	0.00	0.00	33.34	2.77
4538	5863	3.574614	CTCCGTTTGGTTAATGCTTTGG	58.425	45.455	0.00	0.00	36.30	3.28
4693	6020	2.238942	TACCGCTGCAATCTGTATGG	57.761	50.000	0.00	0.00	0.00	2.74
4736	6063	2.910688	TCAGTGTTCAGAGTTCCCAC	57.089	50.000	0.00	0.00	0.00	4.61

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
0	1	0.394192	CCTCGGCCTCTGCATCATAA	59.606	55.000	0.00	0.00	40.13	1.90
2	3	2.815945	CCCTCGGCCTCTGCATCAT	61.816	63.158	0.00	0.00	40.13	2.45
6	7	3.075005	GTACCCTCGGCCTCTGCA	61.075	66.667	0.00	0.00	40.13	4.41
7	8	4.208686	CGTACCCTCGGCCTCTGC	62.209	72.222	0.00	0.00	0.00	4.26
8	9	2.754658	ACGTACCCTCGGCCTCTG	60.755	66.667	0.00	0.00	34.94	3.35
9	10	2.439883	GACGTACCCTCGGCCTCT	60.440	66.667	0.00	0.00	32.06	3.69
10	11	2.439883	AGACGTACCCTCGGCCTC	60.440	66.667	0.00	0.00	40.00	4.70
11	12	2.439883	GAGACGTACCCTCGGCCT	60.440	66.667	0.00	0.00	40.00	5.19
12	13	3.525545	GGAGACGTACCCTCGGCC	61.526	72.222	0.00	0.00	40.00	6.13
13	14	1.673808	AATGGAGACGTACCCTCGGC	61.674	60.000	8.47	0.00	39.37	5.54
14	15	0.822164	AAATGGAGACGTACCCTCGG	59.178	55.000	8.47	0.00	34.94	4.63
15	16	1.202382	GGAAATGGAGACGTACCCTCG	60.202	57.143	8.47	0.00	0.00	4.63
16	17	1.829222	TGGAAATGGAGACGTACCCTC	59.171	52.381	8.47	1.90	0.00	4.30
17	18	1.946984	TGGAAATGGAGACGTACCCT	58.053	50.000	8.47	0.00	0.00	4.34
18	19	2.773993	TTGGAAATGGAGACGTACCC	57.226	50.000	8.47	4.06	0.00	3.69
19	20	3.816523	TGTTTTGGAAATGGAGACGTACC	59.183	43.478	4.55	4.55	0.00	3.34
20	21	5.427036	TTGTTTTGGAAATGGAGACGTAC	57.573	39.130	0.00	0.00	0.00	3.67
21	22	6.452494	TTTTGTTTTGGAAATGGAGACGTA	57.548	33.333	0.00	0.00	0.00	3.57
22	23	4.993029	TTTGTTTTGGAAATGGAGACGT	57.007	36.364	0.00	0.00	0.00	4.34
45	46	9.646427	TGAAGCAAACACAGTTTAAACTATTTT	57.354	25.926	20.15	15.32	37.08	1.82
46	47	9.646427	TTGAAGCAAACACAGTTTAAACTATTT	57.354	25.926	20.15	16.59	37.08	1.40
47	48	9.646427	TTTGAAGCAAACACAGTTTAAACTATT	57.354	25.926	20.15	12.09	37.08	1.73
48	49	9.816354	ATTTGAAGCAAACACAGTTTAAACTAT	57.184	25.926	20.15	6.96	36.13	2.12
49	50	9.081997	CATTTGAAGCAAACACAGTTTAAACTA	57.918	29.630	20.15	0.60	36.13	2.24
50	51	7.816995	TCATTTGAAGCAAACACAGTTTAAACT	59.183	29.630	15.22	15.22	36.13	2.66
51	52	7.958674	TCATTTGAAGCAAACACAGTTTAAAC	58.041	30.769	10.47	10.47	36.13	2.01
52	53	8.539770	TTCATTTGAAGCAAACACAGTTTAAA	57.460	26.923	0.00	0.00	36.13	1.52
53	54	8.715191	ATTCATTTGAAGCAAACACAGTTTAA	57.285	26.923	0.00	0.00	36.13	1.52
54	55	8.715191	AATTCATTTGAAGCAAACACAGTTTA	57.285	26.923	0.00	0.00	36.13	2.01
55	56	7.614124	AATTCATTTGAAGCAAACACAGTTT	57.386	28.000	0.00	0.00	36.13	2.66
222	340	2.076100	CAAGCGAGCACTAATCCAACA	58.924	47.619	0.00	0.00	0.00	3.33
249	374	0.389025	CCCCAAACAAACAGGCTGAC	59.611	55.000	23.66	0.00	0.00	3.51
308	434	8.742777	CCATGAACCAATCAAGAGATTTTTAGA	58.257	33.333	0.00	0.00	42.46	2.10
353	479	3.637920	CCTCCTAATTCCCCTTCCCCTTA	60.638	52.174	0.00	0.00	0.00	2.69
403	530	1.632965	GCGGAATTACCAGGGTCCCT	61.633	60.000	3.85	3.85	38.90	4.20
423	568	1.250840	GCGCCAACTCCCATTCCTTT	61.251	55.000	0.00	0.00	0.00	3.11
595	811	2.366533	CCTCTTGCATGAGATGTGCTT	58.633	47.619	26.59	0.00	42.92	3.91
688	1212	5.505181	AGGGAAATAGATATGCATCGGTT	57.495	39.130	0.19	0.00	36.20	4.44
768	1296	7.689299	TCTAATGAACAATGGAGAAAGAAGGA	58.311	34.615	0.00	0.00	0.00	3.36
814	1342	1.452289	CACGTTTGGTGTGGGGTGA	60.452	57.895	0.00	0.00	41.89	4.02
863	1391	5.731924	AGAGGGAGTTGTATGAGGGATTAT	58.268	41.667	0.00	0.00	0.00	1.28
874	1402	5.729229	TGGGAATTTATGAGAGGGAGTTGTA	59.271	40.000	0.00	0.00	0.00	2.41
875	1403	4.540099	TGGGAATTTATGAGAGGGAGTTGT	59.460	41.667	0.00	0.00	0.00	3.32
1010	2110	4.862092	CCTCGATGCTCGTGCGCT	62.862	66.667	9.73	0.00	41.35	5.92
1030	2133	1.300233	GCCTAAGCCGTCGGATGAG	60.300	63.158	17.49	11.88	0.00	2.90
1378	2481	3.287867	AGCAATTCAGACACCTATGGG	57.712	47.619	0.00	0.00	38.88	4.00
1444	2547	2.813754	CAACCAGAAGCCGAATTCTTCA	59.186	45.455	3.52	0.00	41.68	3.02
1567	2670	6.276611	TGATAAACAACAGTCGTTACACAC	57.723	37.500	0.00	0.00	32.75	3.82
1568	2671	6.702282	TGATGATAAACAACAGTCGTTACACA	59.298	34.615	0.00	0.00	32.75	3.72
1592	2695	4.261741	CCGGGAGCCAATGAATTAAGATTG	60.262	45.833	0.00	0.00	0.00	2.67
1740	2845	4.943705	AGCCCATGTACATAACAAGTTCTG	59.056	41.667	8.32	0.00	42.70	3.02
1773	2878	3.181434	ACCAAAACCTCAAGACCAGCATA	60.181	43.478	0.00	0.00	0.00	3.14
1783	2888	1.781025	CGCGCTGACCAAAACCTCAA	61.781	55.000	5.56	0.00	0.00	3.02
1967	3072	4.914177	TTGGGTATTCGTAGGAACCTTT	57.086	40.909	0.00	0.00	34.37	3.11
2141	3248	1.642762	ACCTCCCCTGCAAATCTCAAT	59.357	47.619	0.00	0.00	0.00	2.57
2339	3447	2.159240	TGTCCTGCTGTACGATGTGATC	60.159	50.000	0.00	0.00	0.00	2.92
2474	3582	1.745141	GCCTGCTACATGACCCTCAAG	60.745	57.143	0.00	0.00	0.00	3.02
2481	3589	2.393271	AGAACAGCCTGCTACATGAC	57.607	50.000	0.00	0.00	0.00	3.06
2568	3676	1.462670	GCAACTTTCCAAGAGAGCTCG	59.537	52.381	8.37	0.00	34.09	5.03
2624	3732	8.482128	ACTTTTGGTCCATTTCAAATTAGTCAA	58.518	29.630	0.00	0.00	33.58	3.18
2625	3733	7.925483	CACTTTTGGTCCATTTCAAATTAGTCA	59.075	33.333	0.00	0.00	33.58	3.41
2626	3734	7.926018	ACACTTTTGGTCCATTTCAAATTAGTC	59.074	33.333	0.00	0.00	33.58	2.59
2627	3735	7.791029	ACACTTTTGGTCCATTTCAAATTAGT	58.209	30.769	0.00	0.00	33.58	2.24
2628	3736	9.191995	GTACACTTTTGGTCCATTTCAAATTAG	57.808	33.333	0.00	0.00	33.58	1.73
2764	4003	3.696051	ACGCAATCCTTAGTGCAATCAAT	59.304	39.130	0.00	0.00	46.89	2.57
2784	4023	5.607119	AAAACAGTGCCTAGATTGTAACG	57.393	39.130	0.00	0.00	0.00	3.18
2827	4074	1.444119	GACAAGTGCGGTGAAAGGCA	61.444	55.000	0.00	0.00	36.70	4.75
2834	4081	1.081906	GCATGTGACAAGTGCGGTG	60.082	57.895	0.00	0.00	0.00	4.94
3316	4611	8.989980	GCTTACATAAGTACCATAGCCTAAAAG	58.010	37.037	0.83	0.00	35.75	2.27
3357	4652	7.984002	TTCACGGTAAATTGCAAATATCATG	57.016	32.000	1.71	0.00	0.00	3.07
3358	4653	8.994429	TTTTCACGGTAAATTGCAAATATCAT	57.006	26.923	1.71	0.00	0.00	2.45
3498	4793	1.471676	GCCACTACTGCTGCGTAAGAT	60.472	52.381	0.00	0.00	43.02	2.40
3611	4908	0.755079	CCATCCATTCTCGCTCCTCA	59.245	55.000	0.00	0.00	0.00	3.86
3671	4968	4.142026	CCCCAGATTACATACGTCTTGTCA	60.142	45.833	7.28	0.00	0.00	3.58
3935	5233	2.135139	GACATGGCGCATCGAAGAATA	58.865	47.619	10.83	0.00	43.58	1.75
3952	5254	3.270027	CTTCACATAAATCGCAGGGACA	58.730	45.455	0.00	0.00	0.00	4.02
3999	5301	2.421073	CACGTCCTGCATGATCATTGTT	59.579	45.455	5.16	0.00	0.00	2.83
4002	5304	1.019673	GCACGTCCTGCATGATCATT	58.980	50.000	5.16	0.00	46.29	2.57
4016	5318	1.100463	TGTTGCTTGATGTGGCACGT	61.100	50.000	13.11	13.11	38.23	4.49
4035	5337	1.603802	CCATCAAATGCGCCGTAATCT	59.396	47.619	4.18	0.00	0.00	2.40
4085	5389	5.910166	TGAAATATGTTTGTTGAACGTTCGG	59.090	36.000	22.48	0.00	41.29	4.30
4232	5557	1.833630	TCGGATTGGTGAGCAGAAGAT	59.166	47.619	0.00	0.00	0.00	2.40
4237	5562	2.159338	CCATTTTCGGATTGGTGAGCAG	60.159	50.000	0.00	0.00	0.00	4.24
4250	5575	2.352960	GCTCTTAGCCTCACCATTTTCG	59.647	50.000	0.00	0.00	34.48	3.46
4276	5601	7.384932	GCAGTGACAAAAATAGTAGGCAAAAAT	59.615	33.333	0.00	0.00	0.00	1.82
4294	5619	2.549992	GGGTATCTGTGTTGCAGTGACA	60.550	50.000	0.00	0.00	45.23	3.58
4416	5741	2.874701	CGCCAATTCTACTTCTCATGGG	59.125	50.000	0.00	0.00	0.00	4.00
4517	5842	3.574614	CCAAAGCATTAACCAAACGGAG	58.425	45.455	0.00	0.00	0.00	4.63
4538	5863	4.382320	TGCGACGCTGTAACCCCC	62.382	66.667	22.08	0.00	0.00	5.40
4677	6004	0.940126	GGACCATACAGATTGCAGCG	59.060	55.000	0.00	0.00	0.00	5.18
4678	6005	1.945394	CTGGACCATACAGATTGCAGC	59.055	52.381	0.00	0.00	38.20	5.25
4736	6063	3.369892	CCCCGAGGATATTTGATAGCTGG	60.370	52.174	0.00	0.00	33.47	4.85

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.