AutoCloner

Multiple sequence alignment - TraesCS3D01G450200

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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	TraesCS3D01G450200	chr3D	100.000	4628	0	0	1	4628	558557429	558562056	0.000000e+00	8547.0
1	TraesCS3D01G450200	chr3D	95.327	535	20	2	281	813	179871287	179871818	0.000000e+00	845.0
2	TraesCS3D01G450200	chr3D	94.347	513	24	4	312	820	43537291	43537802	0.000000e+00	782.0
3	TraesCS3D01G450200	chr3D	83.539	243	9	7	1900	2111	236629042	236628800	1.020000e-46	198.0
4	TraesCS3D01G450200	chr3D	81.377	247	14	13	1894	2109	251409401	251409156	6.160000e-39	172.0
5	TraesCS3D01G450200	chr3D	97.590	83	2	0	1	83	558557508	558557426	4.830000e-30	143.0
6	TraesCS3D01G450200	chr3A	95.524	3664	112	12	821	4445	694965145	694968795	0.000000e+00	5810.0
7	TraesCS3D01G450200	chr3A	95.570	158	6	1	78	235	694964923	694965079	7.690000e-63	252.0
8	TraesCS3D01G450200	chr3A	92.800	125	5	2	4469	4592	694968878	694968999	1.320000e-40	178.0
9	TraesCS3D01G450200	chr3A	81.545	233	23	5	1898	2110	725447832	725447600	1.710000e-39	174.0
10	TraesCS3D01G450200	chr3A	97.368	38	1	0	244	281	694965108	694965145	1.070000e-06	65.8
11	TraesCS3D01G450200	chr3A	100.000	32	0	0	4597	4628	694969019	694969050	5.000000e-05	60.2
12	TraesCS3D01G450200	chr3B	91.678	1430	85	17	2108	3525	741302179	741303586	0.000000e+00	1951.0
13	TraesCS3D01G450200	chr3B	91.132	733	45	9	1174	1892	741301466	741302192	0.000000e+00	976.0
14	TraesCS3D01G450200	chr3B	87.197	742	64	11	3436	4172	741303586	741304301	0.000000e+00	815.0
15	TraesCS3D01G450200	chr3B	90.761	368	18	8	821	1176	741300981	741301344	1.160000e-130	477.0
16	TraesCS3D01G450200	chr3B	82.645	242	11	8	1900	2110	353997425	353997184	7.910000e-43	185.0
17	TraesCS3D01G450200	chr3B	98.780	82	1	0	1	82	825250108	825250027	3.730000e-31	147.0
18	TraesCS3D01G450200	chr3B	98.750	80	1	0	1	80	825250029	825250108	4.830000e-30	143.0
19	TraesCS3D01G450200	chr3B	84.177	158	12	3	78	235	741300770	741300914	1.740000e-29	141.0
20	TraesCS3D01G450200	chr3B	97.500	80	2	0	1	80	257512410	257512489	2.250000e-28	137.0
21	TraesCS3D01G450200	chr3B	97.500	80	2	0	1	80	257512489	257512410	2.250000e-28	137.0
22	TraesCS3D01G450200	chr3B	95.402	87	0	3	1	84	187335682	187335767	8.080000e-28	135.0
23	TraesCS3D01G450200	chr2D	98.088	523	8	2	280	800	14713943	14713421	0.000000e+00	909.0
24	TraesCS3D01G450200	chr2D	94.255	470	26	1	353	822	6530382	6530850	0.000000e+00	717.0
25	TraesCS3D01G450200	chr2B	90.091	656	39	11	2311	2962	304252312	304252945	0.000000e+00	828.0
26	TraesCS3D01G450200	chr6D	93.923	543	28	3	279	821	307884061	307884598	0.000000e+00	815.0
27	TraesCS3D01G450200	chr6D	79.747	237	19	6	1895	2110	82214019	82214247	1.340000e-30	145.0
28	TraesCS3D01G450200	chr4D	93.738	543	32	2	281	822	121351007	121350466	0.000000e+00	813.0
29	TraesCS3D01G450200	chr7A	92.279	544	39	3	280	823	153915653	153916193	0.000000e+00	769.0
30	TraesCS3D01G450200	chr7A	79.565	230	22	10	1900	2109	727459090	727459314	1.740000e-29	141.0
31	TraesCS3D01G450200	chr5A	91.636	538	31	3	274	809	606180783	606180258	0.000000e+00	732.0
32	TraesCS3D01G450200	chr5A	85.030	167	18	3	1899	2058	522884550	522884716	3.710000e-36	163.0
33	TraesCS3D01G450200	chr5D	92.116	482	35	3	312	793	206092822	206092344	0.000000e+00	676.0
34	TraesCS3D01G450200	chr1B	92.746	386	26	2	438	823	58030766	58031149	1.450000e-154	556.0
35	TraesCS3D01G450200	chr1B	77.083	240	31	13	1893	2108	394191001	394191240	2.930000e-22	117.0
36	TraesCS3D01G450200	chr1B	77.083	240	31	13	1893	2108	394275840	394276079	2.930000e-22	117.0
37	TraesCS3D01G450200	chr7B	83.190	232	15	12	1900	2117	720318687	720318908	1.700000e-44	191.0
38	TraesCS3D01G450200	chr1D	82.787	244	11	12	1899	2111	378551667	378551910	6.110000e-44	189.0
39	TraesCS3D01G450200	chr1D	93.458	107	7	0	1899	2005	11141351	11141245	4.790000e-35	159.0
40	TraesCS3D01G450200	chr4B	82.158	241	12	8	1900	2109	374722397	374722637	1.320000e-40	178.0
41	TraesCS3D01G450200	chr4B	81.443	194	16	9	1934	2109	127104812	127105003	1.740000e-29	141.0
42	TraesCS3D01G450200	chr7D	81.818	242	12	4	1900	2109	54151118	54150877	1.710000e-39	174.0
43	TraesCS3D01G450200	chr7D	89.231	65	7	0	2057	2121	101524419	101524355	1.070000e-11	82.4
44	TraesCS3D01G450200	chr4A	97.500	80	2	0	1	80	735552423	735552502	2.250000e-28	137.0
45	TraesCS3D01G450200	chr4A	97.500	80	2	0	1	80	735552502	735552423	2.250000e-28	137.0
46	TraesCS3D01G450200	chr2A	94.318	88	3	2	1	87	549890466	549890380	2.910000e-27	134.0

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	TraesCS3D01G450200	chr3D	558557429	558562056	4627	False	8547.0	8547	100.0000	1	4628	1	chr3D.!!$F3	4627
1	TraesCS3D01G450200	chr3D	179871287	179871818	531	False	845.0	845	95.3270	281	813	1	chr3D.!!$F2	532
2	TraesCS3D01G450200	chr3D	43537291	43537802	511	False	782.0	782	94.3470	312	820	1	chr3D.!!$F1	508
3	TraesCS3D01G450200	chr3A	694964923	694969050	4127	False	1273.2	5810	96.2524	78	4628	5	chr3A.!!$F1	4550
4	TraesCS3D01G450200	chr3B	741300770	741304301	3531	False	872.0	1951	88.9890	78	4172	5	chr3B.!!$F4	4094
5	TraesCS3D01G450200	chr2D	14713421	14713943	522	True	909.0	909	98.0880	280	800	1	chr2D.!!$R1	520
6	TraesCS3D01G450200	chr2B	304252312	304252945	633	False	828.0	828	90.0910	2311	2962	1	chr2B.!!$F1	651
7	TraesCS3D01G450200	chr6D	307884061	307884598	537	False	815.0	815	93.9230	279	821	1	chr6D.!!$F2	542
8	TraesCS3D01G450200	chr4D	121350466	121351007	541	True	813.0	813	93.7380	281	822	1	chr4D.!!$R1	541
9	TraesCS3D01G450200	chr7A	153915653	153916193	540	False	769.0	769	92.2790	280	823	1	chr7A.!!$F1	543
10	TraesCS3D01G450200	chr5A	606180258	606180783	525	True	732.0	732	91.6360	274	809	1	chr5A.!!$R1	535

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
21	22	1.344087	ACTCCCTCCGTCCCATAATGT	60.344	52.381	0.00	0.00	0.00	2.71	F
237	238	1.597742	TCTCCTTGCAGAAGTTGTGC	58.402	50.000	17.64	17.64	41.59	4.57	F
294	316	2.266279	AGGAGTACTAGCAAAAGGGCA	58.734	47.619	0.00	0.00	35.83	5.36	F
1859	2040	4.034410	GGTTTGATAAATAAGGGGGCCAA	58.966	43.478	4.39	0.00	0.00	4.52	F
2284	2485	0.598065	AGCTTGCGAAAATGTGGTCC	59.402	50.000	0.00	0.00	0.00	4.46	F

Position	MSA Position	Penalty	Sequence	TM	GC	Hairpin	End Stability	Orientation
1379	1546	2.442212	TGCGTCGATTGGTTAGAACA	57.558	45.000	0.00	3.18	R
2135	2336	5.717119	ACAAAGGCATTTCTTTAGCATCTG	58.283	37.500	35.44	2.90	R
2136	2337	5.990120	ACAAAGGCATTTCTTTAGCATCT	57.010	34.783	35.44	2.90	R
3338	3553	1.347707	CAACAGGAGTGGAGGCAGTAA	59.652	52.381	0.00	2.24	R
3926	4224	0.174845	CTGACCGGCCTAATGTTCGA	59.825	55.000	0.00	3.71	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
19	20	3.970426	ACTCCCTCCGTCCCATAAT	57.030	52.632	0.00	0.00	0.00	1.28
20	21	1.424638	ACTCCCTCCGTCCCATAATG	58.575	55.000	0.00	0.00	0.00	1.90
21	22	1.344087	ACTCCCTCCGTCCCATAATGT	60.344	52.381	0.00	0.00	0.00	2.71
22	23	2.090943	ACTCCCTCCGTCCCATAATGTA	60.091	50.000	0.00	0.00	0.00	2.29
23	24	2.969950	CTCCCTCCGTCCCATAATGTAA	59.030	50.000	0.00	0.00	0.00	2.41
24	25	2.969950	TCCCTCCGTCCCATAATGTAAG	59.030	50.000	0.00	0.00	0.00	2.34
25	26	2.969950	CCCTCCGTCCCATAATGTAAGA	59.030	50.000	0.00	0.00	0.00	2.10
26	27	3.244112	CCCTCCGTCCCATAATGTAAGAC	60.244	52.174	0.00	0.00	0.00	3.01
28	29	3.025978	TCCGTCCCATAATGTAAGACGT	58.974	45.455	9.63	0.00	46.62	4.34
29	30	3.448301	TCCGTCCCATAATGTAAGACGTT	59.552	43.478	9.63	0.00	46.62	3.99
30	31	4.081531	TCCGTCCCATAATGTAAGACGTTT	60.082	41.667	9.63	0.00	46.62	3.60
31	32	4.632688	CCGTCCCATAATGTAAGACGTTTT	59.367	41.667	9.63	0.00	46.62	2.43
32	33	5.122711	CCGTCCCATAATGTAAGACGTTTTT	59.877	40.000	9.63	0.00	46.62	1.94
72	73	3.720949	CGTCTTACATTATGGGACGGA	57.279	47.619	20.50	2.30	43.69	4.69
73	74	3.639538	CGTCTTACATTATGGGACGGAG	58.360	50.000	20.50	2.74	43.69	4.63
74	75	3.552273	CGTCTTACATTATGGGACGGAGG	60.552	52.174	20.50	5.87	43.69	4.30
75	76	2.969950	TCTTACATTATGGGACGGAGGG	59.030	50.000	0.00	0.00	0.00	4.30
76	77	2.779429	TACATTATGGGACGGAGGGA	57.221	50.000	0.00	0.00	0.00	4.20
235	236	4.889409	TCAAAATCTCCTTGCAGAAGTTGT	59.111	37.500	0.00	0.00	0.00	3.32
237	238	1.597742	TCTCCTTGCAGAAGTTGTGC	58.402	50.000	17.64	17.64	41.59	4.57
294	316	2.266279	AGGAGTACTAGCAAAAGGGCA	58.734	47.619	0.00	0.00	35.83	5.36
978	1021	7.341256	ACAGATATTTCCATTGCTTCAGTTCAT	59.659	33.333	0.00	0.00	0.00	2.57
1007	1050	5.163923	GGAGCAAAGCAGTAAAAATGAATGC	60.164	40.000	0.00	0.00	37.15	3.56
1196	1363	5.200368	ACCAGTGAAGCACTTAAATTTGG	57.800	39.130	0.00	0.00	42.59	3.28
1379	1546	5.730550	TCTATTGCCGAGTCAGTATTTGTT	58.269	37.500	0.00	0.00	0.00	2.83
1419	1586	6.183360	ACGCATTTAAGAGTGAGGAAATGATG	60.183	38.462	9.70	4.56	40.25	3.07
1462	1629	4.816925	ACTACTGACTTTTGTTTCCTCTGC	59.183	41.667	0.00	0.00	0.00	4.26
1619	1798	7.504238	ACCAAGTTACAAACCAGATAATGTGAA	59.496	33.333	0.00	0.00	0.00	3.18
1680	1859	6.544564	TGTTGTAAAGGGAAACTTGGAACTAG	59.455	38.462	0.00	0.00	39.96	2.57
1681	1860	6.503560	TGTAAAGGGAAACTTGGAACTAGA	57.496	37.500	0.00	0.00	39.96	2.43
1698	1877	9.638239	TGGAACTAGATTATTTGCATTTGAAAC	57.362	29.630	0.00	0.00	0.00	2.78
1700	1879	9.638239	GAACTAGATTATTTGCATTTGAAACCA	57.362	29.630	0.00	0.00	0.00	3.67
1859	2040	4.034410	GGTTTGATAAATAAGGGGGCCAA	58.966	43.478	4.39	0.00	0.00	4.52
2042	2243	4.037803	TGCTTTGTGTAACTTGCATGTCAT	59.962	37.500	5.61	0.00	38.04	3.06
2069	2270	4.737855	ATTGCTCTAAAGTTAGCCTCGA	57.262	40.909	0.00	0.00	37.97	4.04
2073	2274	4.929808	TGCTCTAAAGTTAGCCTCGAAAAG	59.070	41.667	0.00	0.00	37.97	2.27
2074	2275	4.930405	GCTCTAAAGTTAGCCTCGAAAAGT	59.070	41.667	0.00	0.00	32.40	2.66
2135	2336	8.992835	ATAATTTCCATGTTTCTCTTTGCTTC	57.007	30.769	0.00	0.00	0.00	3.86
2136	2337	5.850557	TTTCCATGTTTCTCTTTGCTTCA	57.149	34.783	0.00	0.00	0.00	3.02
2200	2401	5.065914	TCATTCTTCCCTCTGTTGACTTTG	58.934	41.667	0.00	0.00	0.00	2.77
2284	2485	0.598065	AGCTTGCGAAAATGTGGTCC	59.402	50.000	0.00	0.00	0.00	4.46
2450	2651	8.162245	GCGAGAAATATTTTTGTTTTCACATCC	58.838	33.333	1.43	0.00	32.94	3.51
2463	2665	9.582431	TTGTTTTCACATCCGTTTGTTTTTATA	57.418	25.926	0.00	0.00	31.06	0.98
3212	3426	8.811378	GCTTCTAAAATGCCAAAATAAGATGTC	58.189	33.333	0.00	0.00	0.00	3.06
3219	3433	6.558771	TGCCAAAATAAGATGTCGATATGG	57.441	37.500	0.00	0.00	0.00	2.74
3272	3487	7.967854	TCAATTAGCAAATGTCTTAATTGTCCG	59.032	33.333	12.72	0.00	36.70	4.79
3292	3507	3.368427	CCGAGACCACAGAAATTCAGCTA	60.368	47.826	0.00	0.00	0.00	3.32
3319	3534	6.050432	TGAATCATGCAAAATGCTATTTCCC	58.950	36.000	3.78	0.00	45.31	3.97
3336	3551	3.660501	TCCCGACATATTTCTGATCCG	57.339	47.619	0.00	0.00	0.00	4.18
3338	3553	3.386726	TCCCGACATATTTCTGATCCGTT	59.613	43.478	0.00	0.00	0.00	4.44
3480	3695	2.336554	GCACTTGCATCATCGTTTGT	57.663	45.000	0.00	0.00	41.59	2.83
3487	3702	5.932303	ACTTGCATCATCGTTTGTTACTACT	59.068	36.000	0.00	0.00	0.00	2.57
3639	3937	7.607991	AGTTACATGGAGTAGAAAGGAAATGTG	59.392	37.037	0.00	0.00	33.43	3.21
3659	3957	3.372206	GTGCTTCAGCTAACATTCATCGT	59.628	43.478	0.00	0.00	42.66	3.73
3777	4075	3.067461	GTGTACTGTGGATTTTGTTGGCA	59.933	43.478	0.00	0.00	0.00	4.92
3785	4083	3.198635	TGGATTTTGTTGGCAAGGTTTGA	59.801	39.130	0.00	0.00	35.82	2.69
3926	4224	6.018994	GGCAGTTTATTTTGATCGTCGTCTAT	60.019	38.462	0.00	0.00	0.00	1.98
3968	4266	2.103373	CCTAGCACTCTTAGTGGCTGA	58.897	52.381	8.99	0.00	46.01	4.26
4038	4338	1.239296	TGGTGTGCTTCTGATGCTGC	61.239	55.000	15.38	9.48	0.00	5.25
4127	4428	8.764558	TGCTAAACTGTAGATTAGATGGGTTTA	58.235	33.333	11.64	0.00	33.77	2.01
4133	4434	9.614792	ACTGTAGATTAGATGGGTTTATGTTTC	57.385	33.333	0.00	0.00	0.00	2.78
4142	4443	4.148838	TGGGTTTATGTTTCTTCCTGGTG	58.851	43.478	0.00	0.00	0.00	4.17
4209	4510	4.428209	CAGTGTGTGGTAATTGTTTGCAA	58.572	39.130	0.00	0.00	39.16	4.08
4246	4547	2.696707	ACCCAGCTTGCATTATGAATGG	59.303	45.455	0.00	0.00	39.31	3.16
4265	4566	5.825593	ATGGTTCATGGATCGTATACCTT	57.174	39.130	0.00	0.00	0.00	3.50
4266	4567	4.956085	TGGTTCATGGATCGTATACCTTG	58.044	43.478	0.00	0.00	34.17	3.61
4279	4582	4.201910	CGTATACCTTGTTGGCCTGATTTG	60.202	45.833	3.32	0.00	40.22	2.32
4291	4594	2.611292	GCCTGATTTGGAGTGATTCTCG	59.389	50.000	0.00	0.00	43.60	4.04
4319	4622	9.060347	AGCATAATCGTATGTGAATCTCATTTT	57.940	29.630	3.01	0.00	39.55	1.82
4376	4679	4.003584	AGAGGGTACTTGGCCATAGTAA	57.996	45.455	21.75	2.06	30.42	2.24
4385	4692	2.442413	TGGCCATAGTAACCTTTGCAC	58.558	47.619	0.00	0.00	0.00	4.57
4405	4712	7.233389	TGCACTCTCTTACTTTCTAGTGATT	57.767	36.000	0.00	0.00	37.18	2.57
4421	4728	9.807921	TTCTAGTGATTGATAAAGGGTTTTCTT	57.192	29.630	0.00	0.00	0.00	2.52
4452	4784	8.704849	TTGATTGAAAGAATAACCTTTGAGGA	57.295	30.769	0.07	0.00	37.67	3.71
4467	4799	5.397221	CCTTTGAGGAGAATATCAGCTTCCA	60.397	44.000	1.38	0.00	37.67	3.53
4470	4802	7.379059	TTGAGGAGAATATCAGCTTCCAATA	57.621	36.000	1.38	0.00	0.00	1.90
4471	4803	7.379059	TGAGGAGAATATCAGCTTCCAATAA	57.621	36.000	1.38	0.00	0.00	1.40
4524	4890	1.210478	ACTGCCAAGCGTATTCAGGAT	59.790	47.619	0.00	0.00	0.00	3.24
4525	4891	2.292267	CTGCCAAGCGTATTCAGGATT	58.708	47.619	0.00	0.00	0.00	3.01
4556	4922	6.563422	TGCACCATGAATCTTAATTACTTGC	58.437	36.000	0.00	0.00	0.00	4.01
4557	4923	6.152492	TGCACCATGAATCTTAATTACTTGCA	59.848	34.615	0.00	0.00	0.00	4.08
4558	4924	7.147863	TGCACCATGAATCTTAATTACTTGCAT	60.148	33.333	0.00	0.00	0.00	3.96
4559	4925	7.707893	GCACCATGAATCTTAATTACTTGCATT	59.292	33.333	0.00	0.00	0.00	3.56
4578	4944	4.260990	GCATTATTACCGCACACAAGCATA	60.261	41.667	0.00	0.00	0.00	3.14

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
0	1	2.090943	ACATTATGGGACGGAGGGAGTA	60.091	50.000	0.00	0.00	0.00	2.59
1	2	1.344087	ACATTATGGGACGGAGGGAGT	60.344	52.381	0.00	0.00	0.00	3.85
2	3	1.424638	ACATTATGGGACGGAGGGAG	58.575	55.000	0.00	0.00	0.00	4.30
3	4	2.779429	TACATTATGGGACGGAGGGA	57.221	50.000	0.00	0.00	0.00	4.20
4	5	2.969950	TCTTACATTATGGGACGGAGGG	59.030	50.000	0.00	0.00	0.00	4.30
5	6	3.552273	CGTCTTACATTATGGGACGGAGG	60.552	52.174	20.50	5.87	43.69	4.30
6	7	3.639538	CGTCTTACATTATGGGACGGAG	58.360	50.000	20.50	2.74	43.69	4.63
7	8	3.720949	CGTCTTACATTATGGGACGGA	57.279	47.619	20.50	2.30	43.69	4.69
47	48	5.122711	CCGTCCCATAATGTAAGACGTTTTT	59.877	40.000	9.63	0.00	46.62	1.94
48	49	4.632688	CCGTCCCATAATGTAAGACGTTTT	59.367	41.667	9.63	0.00	46.62	2.43
49	50	4.081531	TCCGTCCCATAATGTAAGACGTTT	60.082	41.667	9.63	0.00	46.62	3.60
50	51	3.448301	TCCGTCCCATAATGTAAGACGTT	59.552	43.478	9.63	0.00	46.62	3.99
51	52	3.025978	TCCGTCCCATAATGTAAGACGT	58.974	45.455	9.63	0.00	46.62	4.34
53	54	3.244112	CCCTCCGTCCCATAATGTAAGAC	60.244	52.174	0.00	0.00	0.00	3.01
54	55	2.969950	CCCTCCGTCCCATAATGTAAGA	59.030	50.000	0.00	0.00	0.00	2.10
55	56	2.969950	TCCCTCCGTCCCATAATGTAAG	59.030	50.000	0.00	0.00	0.00	2.34
56	57	2.969950	CTCCCTCCGTCCCATAATGTAA	59.030	50.000	0.00	0.00	0.00	2.41
57	58	2.090943	ACTCCCTCCGTCCCATAATGTA	60.091	50.000	0.00	0.00	0.00	2.29
58	59	1.344087	ACTCCCTCCGTCCCATAATGT	60.344	52.381	0.00	0.00	0.00	2.71
59	60	1.424638	ACTCCCTCCGTCCCATAATG	58.575	55.000	0.00	0.00	0.00	1.90
60	61	2.090943	TGTACTCCCTCCGTCCCATAAT	60.091	50.000	0.00	0.00	0.00	1.28
61	62	1.288633	TGTACTCCCTCCGTCCCATAA	59.711	52.381	0.00	0.00	0.00	1.90
62	63	0.928505	TGTACTCCCTCCGTCCCATA	59.071	55.000	0.00	0.00	0.00	2.74
63	64	0.042131	TTGTACTCCCTCCGTCCCAT	59.958	55.000	0.00	0.00	0.00	4.00
64	65	0.178926	TTTGTACTCCCTCCGTCCCA	60.179	55.000	0.00	0.00	0.00	4.37
65	66	0.248565	GTTTGTACTCCCTCCGTCCC	59.751	60.000	0.00	0.00	0.00	4.46
66	67	0.971386	TGTTTGTACTCCCTCCGTCC	59.029	55.000	0.00	0.00	0.00	4.79
67	68	2.825861	TTGTTTGTACTCCCTCCGTC	57.174	50.000	0.00	0.00	0.00	4.79
68	69	2.027469	GGATTGTTTGTACTCCCTCCGT	60.027	50.000	0.00	0.00	0.00	4.69
69	70	2.629051	GGATTGTTTGTACTCCCTCCG	58.371	52.381	0.00	0.00	0.00	4.63
70	71	2.629051	CGGATTGTTTGTACTCCCTCC	58.371	52.381	0.00	0.00	0.00	4.30
71	72	2.007608	GCGGATTGTTTGTACTCCCTC	58.992	52.381	0.00	0.00	0.00	4.30
72	73	1.339727	GGCGGATTGTTTGTACTCCCT	60.340	52.381	0.00	0.00	0.00	4.20
73	74	1.092348	GGCGGATTGTTTGTACTCCC	58.908	55.000	0.00	0.00	0.00	4.30
74	75	1.816074	TGGCGGATTGTTTGTACTCC	58.184	50.000	0.00	0.00	0.00	3.85
75	76	2.812011	ACTTGGCGGATTGTTTGTACTC	59.188	45.455	0.00	0.00	0.00	2.59
76	77	2.552315	CACTTGGCGGATTGTTTGTACT	59.448	45.455	0.00	0.00	0.00	2.73
191	192	4.149922	TGAAACTTCGTCTACGCATTTCAG	59.850	41.667	17.14	3.80	38.24	3.02
214	215	4.500375	GCACAACTTCTGCAAGGAGATTTT	60.500	41.667	0.00	0.00	44.80	1.82
235	236	1.272037	TGTTCCAGAAGCCATCATGCA	60.272	47.619	0.00	0.00	0.00	3.96
237	238	3.446161	ACAATGTTCCAGAAGCCATCATG	59.554	43.478	0.00	0.00	0.00	3.07
238	239	3.705051	ACAATGTTCCAGAAGCCATCAT	58.295	40.909	0.00	0.00	0.00	2.45
239	240	3.159213	ACAATGTTCCAGAAGCCATCA	57.841	42.857	0.00	0.00	0.00	3.07
240	241	7.516198	AATATACAATGTTCCAGAAGCCATC	57.484	36.000	0.00	0.00	0.00	3.51
242	243	7.498900	CACTAATATACAATGTTCCAGAAGCCA	59.501	37.037	0.00	0.00	0.00	4.75
978	1021	6.264292	TCATTTTTACTGCTTTGCTCCTACAA	59.736	34.615	0.00	0.00	0.00	2.41
1196	1363	8.783833	AAAGTATATGGACATATCATGAGCAC	57.216	34.615	8.01	0.70	35.71	4.40
1379	1546	2.442212	TGCGTCGATTGGTTAGAACA	57.558	45.000	0.00	0.00	0.00	3.18
1437	1604	6.511929	GCAGAGGAAACAAAAGTCAGTAGTTC	60.512	42.308	0.00	0.00	0.00	3.01
1569	1748	6.973229	TCAAGATGACACAACACTATGATG	57.027	37.500	0.00	0.00	0.00	3.07
2042	2243	9.856488	CGAGGCTAACTTTAGAGCAATAATATA	57.144	33.333	0.00	0.00	40.64	0.86
2073	2274	7.316393	TCCATATATATAGGGCCTAATGCAC	57.684	40.000	18.91	0.00	46.89	4.57
2074	2275	9.271921	CTATCCATATATATAGGGCCTAATGCA	57.728	37.037	18.91	2.57	43.89	3.96
2123	2324	6.233434	TCTTTAGCATCTGAAGCAAAGAGAA	58.767	36.000	18.99	6.84	35.86	2.87
2135	2336	5.717119	ACAAAGGCATTTCTTTAGCATCTG	58.283	37.500	0.00	0.00	35.44	2.90
2136	2337	5.990120	ACAAAGGCATTTCTTTAGCATCT	57.010	34.783	0.00	0.00	35.44	2.90
2165	2366	6.941436	AGAGGGAAGAATGATGCATATCTTTC	59.059	38.462	17.89	16.36	42.98	2.62
2200	2401	7.027760	GGCAAACCTAAGTAAATAAGCAGAAC	58.972	38.462	0.00	0.00	0.00	3.01
2463	2665	9.131791	AGGTAGAAAATGTGTAAGAAACATGTT	57.868	29.630	4.92	4.92	41.10	2.71
2588	2793	4.126437	GCTTTTAACAACAACCAGGCAAT	58.874	39.130	0.00	0.00	0.00	3.56
2673	2878	4.141205	TGCCCATCAAGATGTCCATATCAA	60.141	41.667	9.04	0.00	37.11	2.57
3052	3257	2.034124	AGGCAAACATGTTCAAGCTGT	58.966	42.857	22.01	12.26	0.00	4.40
3272	3487	4.826556	AGTAGCTGAATTTCTGTGGTCTC	58.173	43.478	0.00	0.00	0.00	3.36
3319	3534	6.562270	GCAGTAAACGGATCAGAAATATGTCG	60.562	42.308	0.00	0.00	0.00	4.35
3336	3551	1.348036	ACAGGAGTGGAGGCAGTAAAC	59.652	52.381	0.00	0.00	0.00	2.01
3338	3553	1.347707	CAACAGGAGTGGAGGCAGTAA	59.652	52.381	0.00	0.00	0.00	2.24
3505	3803	5.423704	TGGAATGGTTAGTCGTAATCCAA	57.576	39.130	0.00	0.00	33.06	3.53
3572	3870	1.722751	CGCTGTCAATTGTCAAGCGAC	60.723	52.381	30.32	13.05	45.53	5.19
3639	3937	4.606457	AACGATGAATGTTAGCTGAAGC	57.394	40.909	0.00	0.00	42.49	3.86
3659	3957	6.177610	CCTTCCTGTATGTAAGCTTGGTTAA	58.822	40.000	9.86	0.00	0.00	2.01
3751	4049	4.067972	ACAAAATCCACAGTACACGAGT	57.932	40.909	0.00	0.00	0.00	4.18
3777	4075	9.310716	GTATAGCGTTTAATCTAGTCAAACCTT	57.689	33.333	9.45	3.72	0.00	3.50
3785	4083	9.900710	CAGATTCAGTATAGCGTTTAATCTAGT	57.099	33.333	0.00	0.00	32.48	2.57
3926	4224	0.174845	CTGACCGGCCTAATGTTCGA	59.825	55.000	0.00	0.00	0.00	3.71
4007	4305	2.906897	ACACCAAAGGCACAGGCG	60.907	61.111	0.00	0.00	42.47	5.52
4127	4428	4.278419	GCAAACTACACCAGGAAGAAACAT	59.722	41.667	0.00	0.00	0.00	2.71
4133	4434	1.156736	CGGCAAACTACACCAGGAAG	58.843	55.000	0.00	0.00	0.00	3.46
4142	4443	1.198408	GCAACCTTACCGGCAAACTAC	59.802	52.381	0.00	0.00	35.61	2.73
4179	4480	1.419381	TACCACACACTGGCTCAAGA	58.581	50.000	0.00	0.00	45.32	3.02
4182	4483	2.158682	ACAATTACCACACACTGGCTCA	60.159	45.455	0.00	0.00	45.32	4.26
4209	4510	8.633561	GCAAGCTGGGTTTATAGAATCTAAAAT	58.366	33.333	0.00	0.00	0.00	1.82
4246	4547	5.236478	CCAACAAGGTATACGATCCATGAAC	59.764	44.000	0.00	0.00	0.00	3.18
4257	4558	4.097892	CCAAATCAGGCCAACAAGGTATAC	59.902	45.833	5.01	0.00	40.61	1.47
4265	4566	1.144708	TCACTCCAAATCAGGCCAACA	59.855	47.619	5.01	0.00	0.00	3.33
4266	4567	1.909700	TCACTCCAAATCAGGCCAAC	58.090	50.000	5.01	0.00	0.00	3.77
4279	4582	2.515926	TATGCTGCGAGAATCACTCC	57.484	50.000	0.00	0.00	42.18	3.85
4291	4594	5.406477	TGAGATTCACATACGATTATGCTGC	59.594	40.000	0.00	0.00	39.07	5.25
4319	4622	5.596361	TGAAATAGTTTCAGCACTTCCCAAA	59.404	36.000	1.24	0.00	44.21	3.28
4376	4679	5.297569	AGAAAGTAAGAGAGTGCAAAGGT	57.702	39.130	0.00	0.00	0.00	3.50
4405	4712	8.256356	TCAATTGGAAAGAAAACCCTTTATCA	57.744	30.769	5.42	0.00	36.58	2.15
4450	4782	8.131731	GTGTTTTATTGGAAGCTGATATTCTCC	58.868	37.037	0.00	0.00	0.00	3.71
4452	4784	8.462016	GTGTGTTTTATTGGAAGCTGATATTCT	58.538	33.333	0.00	0.00	0.00	2.40
4467	4799	8.723942	TGCCAATTAAAAGTGTGTGTTTTATT	57.276	26.923	0.00	0.00	31.19	1.40
4470	4802	7.440523	TTTGCCAATTAAAAGTGTGTGTTTT	57.559	28.000	0.00	0.00	0.00	2.43
4471	4803	7.622893	ATTTGCCAATTAAAAGTGTGTGTTT	57.377	28.000	0.00	0.00	0.00	2.83
4524	4890	4.160642	AGATTCATGGTGCATCTGCTAA	57.839	40.909	0.00	0.00	42.66	3.09
4525	4891	3.851458	AGATTCATGGTGCATCTGCTA	57.149	42.857	0.00	0.00	42.66	3.49
4556	4922	3.755965	TGCTTGTGTGCGGTAATAATG	57.244	42.857	0.00	0.00	35.36	1.90
4557	4923	6.633500	ATTATGCTTGTGTGCGGTAATAAT	57.367	33.333	0.00	0.00	35.36	1.28
4558	4924	7.737972	ATATTATGCTTGTGTGCGGTAATAA	57.262	32.000	0.00	0.00	34.96	1.40
4559	4925	7.547722	CCTATATTATGCTTGTGTGCGGTAATA	59.452	37.037	0.00	0.00	35.35	0.98
4565	4931	6.073058	ACAATCCTATATTATGCTTGTGTGCG	60.073	38.462	0.00	0.00	35.36	5.34
4595	4976	2.522185	AGGCACTGCATTTCACAAGAT	58.478	42.857	2.82	0.00	37.18	2.40

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.