AutoCloner

Multiple sequence alignment - TraesCS6B01G315200

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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	TraesCS6B01G315200	chr6B	100.000	5259	0	0	1	5259	563136828	563131570	0.000000e+00	9712.0
1	TraesCS6B01G315200	chr6B	95.610	2756	101	13	2516	5259	563146206	563143459	0.000000e+00	4401.0
2	TraesCS6B01G315200	chr6B	94.346	1238	42	5	1	1213	563148623	563147389	0.000000e+00	1873.0
3	TraesCS6B01G315200	chr6B	92.926	1244	42	16	1195	2419	563147449	563146233	0.000000e+00	1768.0
4	TraesCS6B01G315200	chr6B	90.811	1295	48	20	2140	3406	60605325	60604074	0.000000e+00	1666.0
5	TraesCS6B01G315200	chr6B	88.692	1300	92	27	3454	4743	60604074	60602820	0.000000e+00	1535.0
6	TraesCS6B01G315200	chr6B	88.534	907	59	21	2147	3040	25454414	25453540	0.000000e+00	1057.0
7	TraesCS6B01G315200	chr6B	88.436	908	60	21	2147	3041	25429122	25428247	0.000000e+00	1053.0
8	TraesCS6B01G315200	chr6B	86.327	746	62	10	1303	2034	60606036	60605317	0.000000e+00	776.0
9	TraesCS6B01G315200	chr6B	84.720	733	79	19	1316	2034	25433691	25432978	0.000000e+00	702.0
10	TraesCS6B01G315200	chr6B	84.038	733	82	9	1316	2034	25376384	25375673	0.000000e+00	673.0
11	TraesCS6B01G315200	chr6B	82.249	738	92	12	1315	2034	25455128	25454412	7.540000e-168	601.0
12	TraesCS6B01G315200	chr6B	86.322	541	28	13	8	515	60607321	60606794	9.960000e-152	547.0
13	TraesCS6B01G315200	chr6B	94.375	320	15	2	516	834	60606684	60606367	6.120000e-134	488.0
14	TraesCS6B01G315200	chr6B	88.515	357	24	4	857	1213	60606392	60606053	2.930000e-112	416.0
15	TraesCS6B01G315200	chr6B	87.463	335	16	7	2147	2471	25398055	25397737	3.870000e-96	363.0
16	TraesCS6B01G315200	chr6B	97.959	49	1	0	1165	1213	563135619	563135571	9.380000e-13	86.1
17	TraesCS6B01G315200	chr6B	97.959	49	1	0	1210	1258	563135664	563135616	9.380000e-13	86.1
18	TraesCS6B01G315200	chr6D	95.598	5180	138	28	126	5259	376977414	376972279	0.000000e+00	8220.0
19	TraesCS6B01G315200	chr6D	94.383	5305	172	47	1	5259	376948601	376943377	0.000000e+00	8030.0
20	TraesCS6B01G315200	chr6D	90.716	2639	135	44	2140	4736	29114109	29116679	0.000000e+00	3415.0
21	TraesCS6B01G315200	chr6D	88.204	746	60	8	1303	2034	29113386	29114117	0.000000e+00	865.0
22	TraesCS6B01G315200	chr6D	85.871	729	70	5	1319	2034	13947759	13947051	0.000000e+00	745.0
23	TraesCS6B01G315200	chr6D	84.636	729	79	12	1319	2034	13959042	13958334	0.000000e+00	695.0
24	TraesCS6B01G315200	chr6D	89.507	467	26	12	61	515	29112176	29112631	2.130000e-158	569.0
25	TraesCS6B01G315200	chr6D	93.189	323	16	3	513	834	29112738	29113055	2.220000e-128	470.0
26	TraesCS6B01G315200	chr6D	89.916	357	19	4	857	1213	29113030	29113369	1.340000e-120	444.0
27	TraesCS6B01G315200	chr6D	89.216	204	6	3	1	189	376977659	376977457	1.890000e-59	241.0
28	TraesCS6B01G315200	chr6D	85.870	184	18	6	4743	4919	29116730	29116912	6.950000e-44	189.0
29	TraesCS6B01G315200	chr6D	97.959	49	1	0	1165	1213	376976319	376976271	9.380000e-13	86.1
30	TraesCS6B01G315200	chr6A	93.879	5293	206	50	1	5259	518600970	518595762	0.000000e+00	7871.0
31	TraesCS6B01G315200	chr6A	94.281	4861	173	40	1	4832	518552879	518548095	0.000000e+00	7339.0
32	TraesCS6B01G315200	chr6A	90.409	2638	131	50	2140	4743	33294314	33291765	0.000000e+00	3358.0
33	TraesCS6B01G315200	chr6A	87.131	746	56	10	1303	2034	33295025	33294306	0.000000e+00	809.0
34	TraesCS6B01G315200	chr6A	83.519	807	85	21	2763	3553	14522588	14521814	0.000000e+00	710.0
35	TraesCS6B01G315200	chr6A	84.853	647	77	7	1316	1949	14586576	14585938	2.670000e-177	632.0
36	TraesCS6B01G315200	chr6A	87.386	547	27	17	5	515	33296330	33295790	1.630000e-164	590.0
37	TraesCS6B01G315200	chr6A	88.222	433	29	9	4834	5259	518548066	518547649	1.020000e-136	497.0
38	TraesCS6B01G315200	chr6A	93.146	321	20	2	516	834	33295680	33295360	2.220000e-128	470.0
39	TraesCS6B01G315200	chr6A	87.812	361	23	6	857	1213	33295385	33295042	2.280000e-108	403.0
40	TraesCS6B01G315200	chr6A	89.362	141	12	3	1195	1335	518551770	518551633	1.950000e-39	174.0
41	TraesCS6B01G315200	chrUn	89.303	832	58	20	2224	3041	355299260	355298446	0.000000e+00	1014.0
42	TraesCS6B01G315200	chr3D	90.196	153	13	2	124	275	196949582	196949733	1.160000e-46	198.0
43	TraesCS6B01G315200	chr5A	89.677	155	12	4	670	823	214918580	214918731	1.490000e-45	195.0
44	TraesCS6B01G315200	chr3A	89.542	153	14	2	124	275	251339781	251339932	5.370000e-45	193.0

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	TraesCS6B01G315200	chr6B	563131570	563136828	5258	True	3294.733333	9712	98.639333	1	5259	3	chr6B.!!$R6	5258
1	TraesCS6B01G315200	chr6B	563143459	563148623	5164	True	2680.666667	4401	94.294000	1	5259	3	chr6B.!!$R7	5258
2	TraesCS6B01G315200	chr6B	60602820	60607321	4501	True	904.666667	1666	89.173667	8	4743	6	chr6B.!!$R5	4735
3	TraesCS6B01G315200	chr6B	25428247	25433691	5444	True	877.500000	1053	86.578000	1316	3041	2	chr6B.!!$R3	1725
4	TraesCS6B01G315200	chr6B	25453540	25455128	1588	True	829.000000	1057	85.391500	1315	3040	2	chr6B.!!$R4	1725
5	TraesCS6B01G315200	chr6B	25375673	25376384	711	True	673.000000	673	84.038000	1316	2034	1	chr6B.!!$R1	718
6	TraesCS6B01G315200	chr6D	376943377	376948601	5224	True	8030.000000	8030	94.383000	1	5259	1	chr6D.!!$R3	5258
7	TraesCS6B01G315200	chr6D	376972279	376977659	5380	True	2849.033333	8220	94.257667	1	5259	3	chr6D.!!$R4	5258
8	TraesCS6B01G315200	chr6D	29112176	29116912	4736	False	992.000000	3415	89.567000	61	4919	6	chr6D.!!$F1	4858
9	TraesCS6B01G315200	chr6D	13947051	13947759	708	True	745.000000	745	85.871000	1319	2034	1	chr6D.!!$R1	715
10	TraesCS6B01G315200	chr6D	13958334	13959042	708	True	695.000000	695	84.636000	1319	2034	1	chr6D.!!$R2	715
11	TraesCS6B01G315200	chr6A	518595762	518600970	5208	True	7871.000000	7871	93.879000	1	5259	1	chr6A.!!$R3	5258
12	TraesCS6B01G315200	chr6A	518547649	518552879	5230	True	2670.000000	7339	90.621667	1	5259	3	chr6A.!!$R5	5258
13	TraesCS6B01G315200	chr6A	33291765	33296330	4565	True	1126.000000	3358	89.176800	5	4743	5	chr6A.!!$R4	4738
14	TraesCS6B01G315200	chr6A	14521814	14522588	774	True	710.000000	710	83.519000	2763	3553	1	chr6A.!!$R1	790
15	TraesCS6B01G315200	chr6A	14585938	14586576	638	True	632.000000	632	84.853000	1316	1949	1	chr6A.!!$R2	633
16	TraesCS6B01G315200	chrUn	355298446	355299260	814	True	1014.000000	1014	89.303000	2224	3041	1	chrUn.!!$R1	817

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
24	25	0.543883	TGCTCTGCAGAGGAAGGTCT	60.544	55.000	37.86	0.00	39.60	3.85	F
1232	1652	0.397816	CCCTCGGTCATCTCTCCCTT	60.398	60.000	0.00	0.00	0.00	3.95	F
1239	1659	0.537188	TCATCTCTCCCTTTCACGGC	59.463	55.000	0.00	0.00	0.00	5.68	F
1312	1786	0.549950	CATCTCCTTCCCCATGCACT	59.450	55.000	0.00	0.00	0.00	4.40	F
1563	2073	2.348411	ACACAAACCTGAACCTGAGG	57.652	50.000	0.00	0.00	36.57	3.86	F
3734	8282	1.946768	TCGTTTGACAAGGCCTTTCAG	59.053	47.619	17.61	7.61	0.00	3.02	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1246	1666	0.038599	TCCTGCGTGTAGTGGAGGTA	59.961	55.000	0.43	0.00	44.54	3.08	R
2925	7351	1.208706	TTGACTTGGAGTGTGTGGGA	58.791	50.000	0.00	0.00	0.00	4.37	R
3633	8181	6.443934	ACGCCACATAAACAATTATTAGCA	57.556	33.333	0.00	0.00	29.08	3.49	R
3654	8202	2.476619	CACAAGCTAACAGACTGGAACG	59.523	50.000	7.51	0.00	0.00	3.95	R
3831	8379	0.241749	AACTGCATGACCACAATGCG	59.758	50.000	0.00	2.32	43.69	4.73	R
4709	9272	2.031120	TGAAAAACTGCACCCAGAAGG	58.969	47.619	0.00	0.00	41.77	3.46	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
24	25	0.543883	TGCTCTGCAGAGGAAGGTCT	60.544	55.000	37.86	0.00	39.60	3.85
566	880	4.957759	AACACACACTACAACCTTGTTC	57.042	40.909	0.00	0.00	42.35	3.18
602	916	3.804325	CGTGGAATGGAGTGATGTACATC	59.196	47.826	25.95	25.95	38.29	3.06
711	1028	1.805428	GCATGGGTGCGTGGAAGTTT	61.805	55.000	0.00	0.00	42.28	2.66
850	1191	3.662454	GCACAATTGAAGTGAAATTGCGC	60.662	43.478	13.59	0.00	45.02	6.09
1066	1407	2.499827	CCCGATCCTCCCTTCGACC	61.500	68.421	0.00	0.00	37.55	4.79
1213	1633	3.408853	GCCCCTACCTCCACCACC	61.409	72.222	0.00	0.00	0.00	4.61
1214	1634	2.691252	CCCCTACCTCCACCACCC	60.691	72.222	0.00	0.00	0.00	4.61
1215	1635	2.691252	CCCTACCTCCACCACCCC	60.691	72.222	0.00	0.00	0.00	4.95
1216	1636	2.454941	CCTACCTCCACCACCCCT	59.545	66.667	0.00	0.00	0.00	4.79
1217	1637	1.689582	CCTACCTCCACCACCCCTC	60.690	68.421	0.00	0.00	0.00	4.30
1218	1638	2.038329	TACCTCCACCACCCCTCG	59.962	66.667	0.00	0.00	0.00	4.63
1219	1639	3.612115	TACCTCCACCACCCCTCGG	62.612	68.421	0.00	0.00	0.00	4.63
1221	1641	3.391382	CTCCACCACCCCTCGGTC	61.391	72.222	0.00	0.00	42.04	4.79
1222	1642	4.242586	TCCACCACCCCTCGGTCA	62.243	66.667	0.00	0.00	42.04	4.02
1223	1643	3.009115	CCACCACCCCTCGGTCAT	61.009	66.667	0.00	0.00	42.04	3.06
1224	1644	2.584608	CACCACCCCTCGGTCATC	59.415	66.667	0.00	0.00	42.04	2.92
1225	1645	1.990060	CACCACCCCTCGGTCATCT	60.990	63.158	0.00	0.00	42.04	2.90
1226	1646	1.686110	ACCACCCCTCGGTCATCTC	60.686	63.158	0.00	0.00	42.04	2.75
1227	1647	1.381872	CCACCCCTCGGTCATCTCT	60.382	63.158	0.00	0.00	42.04	3.10
1228	1648	1.395826	CCACCCCTCGGTCATCTCTC	61.396	65.000	0.00	0.00	42.04	3.20
1229	1649	1.075896	ACCCCTCGGTCATCTCTCC	60.076	63.158	0.00	0.00	38.28	3.71
1230	1650	1.834822	CCCCTCGGTCATCTCTCCC	60.835	68.421	0.00	0.00	0.00	4.30
1231	1651	1.231641	CCCTCGGTCATCTCTCCCT	59.768	63.158	0.00	0.00	0.00	4.20
1232	1652	0.397816	CCCTCGGTCATCTCTCCCTT	60.398	60.000	0.00	0.00	0.00	3.95
1233	1653	1.490574	CCTCGGTCATCTCTCCCTTT	58.509	55.000	0.00	0.00	0.00	3.11
1234	1654	1.410882	CCTCGGTCATCTCTCCCTTTC	59.589	57.143	0.00	0.00	0.00	2.62
1235	1655	2.103373	CTCGGTCATCTCTCCCTTTCA	58.897	52.381	0.00	0.00	0.00	2.69
1236	1656	1.825474	TCGGTCATCTCTCCCTTTCAC	59.175	52.381	0.00	0.00	0.00	3.18
1237	1657	1.469940	CGGTCATCTCTCCCTTTCACG	60.470	57.143	0.00	0.00	0.00	4.35
1238	1658	1.134670	GGTCATCTCTCCCTTTCACGG	60.135	57.143	0.00	0.00	0.00	4.94
1239	1659	0.537188	TCATCTCTCCCTTTCACGGC	59.463	55.000	0.00	0.00	0.00	5.68
1240	1660	0.807667	CATCTCTCCCTTTCACGGCG	60.808	60.000	4.80	4.80	0.00	6.46
1241	1661	1.961180	ATCTCTCCCTTTCACGGCGG	61.961	60.000	13.24	0.00	0.00	6.13
1242	1662	4.388499	TCTCCCTTTCACGGCGGC	62.388	66.667	13.24	0.00	0.00	6.53
1247	1667	4.090588	CTTTCACGGCGGCCCCTA	62.091	66.667	14.55	0.00	0.00	3.53
1248	1668	4.397832	TTTCACGGCGGCCCCTAC	62.398	66.667	14.55	0.00	0.00	3.18
1256	1676	2.281091	CGGCCCCTACCTCCACTA	59.719	66.667	0.00	0.00	0.00	2.74
1257	1677	2.132352	CGGCCCCTACCTCCACTAC	61.132	68.421	0.00	0.00	0.00	2.73
1267	1687	0.537188	CCTCCACTACACGCAGGATT	59.463	55.000	0.00	0.00	0.00	3.01
1312	1786	0.549950	CATCTCCTTCCCCATGCACT	59.450	55.000	0.00	0.00	0.00	4.40
1563	2073	2.348411	ACACAAACCTGAACCTGAGG	57.652	50.000	0.00	0.00	36.57	3.86
1856	2386	2.739379	GAGAAGTTGAGCTTTCGAAGGG	59.261	50.000	9.52	2.81	37.59	3.95
1878	2408	6.937465	AGGGAAGTTTAGAGTTTGACAGATTC	59.063	38.462	0.00	0.00	0.00	2.52
2620	7043	9.056005	TGCTCATAGTTGATGTTATTTACCATC	57.944	33.333	0.00	0.00	36.84	3.51
3060	7497	3.438216	TCATCCATTCAAGAGTTGCCA	57.562	42.857	0.00	0.00	0.00	4.92
3654	8202	7.973388	TGTTCTGCTAATAATTGTTTATGTGGC	59.027	33.333	0.00	0.00	0.00	5.01
3734	8282	1.946768	TCGTTTGACAAGGCCTTTCAG	59.053	47.619	17.61	7.61	0.00	3.02
3819	8367	7.725251	TCCTTCGTTTTGGTTAAGAACTAGTA	58.275	34.615	0.00	0.00	0.00	1.82
3820	8368	8.203485	TCCTTCGTTTTGGTTAAGAACTAGTAA	58.797	33.333	0.00	0.00	0.00	2.24
3821	8369	8.996271	CCTTCGTTTTGGTTAAGAACTAGTAAT	58.004	33.333	0.00	0.00	0.00	1.89
3842	8390	7.815068	AGTAATATTAGAGATCGCATTGTGGTC	59.185	37.037	2.12	2.12	0.00	4.02
3844	8392	2.996249	AGAGATCGCATTGTGGTCAT	57.004	45.000	12.73	0.00	0.00	3.06
4098	8647	2.014857	TGATACCGTCTCTCAAGGTCG	58.985	52.381	0.00	0.00	39.31	4.79
4403	8959	2.639065	GGCAATGAAGGATCCGTAACA	58.361	47.619	5.98	5.93	0.00	2.41
4454	9010	3.679980	TGAAATCGAGCTCTTTCTTTCGG	59.320	43.478	22.08	2.38	33.50	4.30
4486	9044	7.817418	AATCAAGTTGTGTGTATGTAAACCT	57.183	32.000	2.11	0.00	0.00	3.50
4581	9141	2.812011	CTGCCGGTTTAGCTAGTTGTTT	59.188	45.455	1.90	0.00	0.00	2.83
4692	9255	4.082787	GCATTTCTGCTTGCCTGTTTACTA	60.083	41.667	0.00	0.00	45.32	1.82
4709	9272	7.478322	TGTTTACTATTCTGTGAGTCGTATCC	58.522	38.462	0.00	0.00	0.00	2.59
4728	9292	2.800881	CCTTCTGGGTGCAGTTTTTC	57.199	50.000	0.00	0.00	0.00	2.29
4751	9360	6.184789	TCACTTCTAGTTTGGGTTTTCTGTT	58.815	36.000	0.00	0.00	0.00	3.16
4768	9377	1.014564	GTTGACGGCAGCTCTGGTAC	61.015	60.000	0.00	0.00	0.00	3.34
4801	9410	6.039493	TGAATTTGTAGGTTCAGCGGTTTTAA	59.961	34.615	0.00	0.00	31.24	1.52
4866	9502	9.862371	TTGAATTTGTAGTTTCAGCAGTTTTAA	57.138	25.926	0.00	0.00	33.68	1.52
4946	9591	9.733556	TGTTTCATACATTGTTATTCCTGTAGT	57.266	29.630	0.00	0.00	0.00	2.73
4982	9627	9.559958	CATGTGTTTATTCTATTCCTGTGTTTC	57.440	33.333	0.00	0.00	0.00	2.78
5006	9651	7.445121	TCGAGAATCCTATACATCAAAGCAAT	58.555	34.615	0.00	0.00	0.00	3.56
5020	9665	4.396166	TCAAAGCAATCCTTAGCTAAGCAC	59.604	41.667	25.38	12.89	40.90	4.40
5046	9691	9.846248	CTTTGTTCTTAGGAATCCAACATAAAG	57.154	33.333	0.61	1.78	33.71	1.85
5089	9738	5.919755	TGGTTTTATTTTTCACCCTTCACC	58.080	37.500	0.00	0.00	0.00	4.02
5156	9808	4.702131	ACTGATAGGTGATCAAAGTTTGCC	59.298	41.667	10.90	6.33	44.14	4.52
5197	9849	1.816224	TGAACCGCTAAGCAAATTCCC	59.184	47.619	0.00	0.00	0.00	3.97
5202	9854	1.134946	CGCTAAGCAAATTCCCCCTTG	59.865	52.381	0.00	0.00	0.00	3.61
5229	9881	5.046231	AGACATCCCTGTTTTCCTAGTTCTC	60.046	44.000	0.00	0.00	35.14	2.87

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
24	25	3.364460	ACATGCCCTACATTAACAGCA	57.636	42.857	0.00	0.00	36.64	4.41
566	880	3.624326	TTCCACGCATTTCAACAAGAG	57.376	42.857	0.00	0.00	0.00	2.85
602	916	6.648310	CCCAGTACAATATGCAGACTTGATAG	59.352	42.308	11.36	0.00	0.00	2.08
668	985	5.192927	CCATGGCTAGTTCTTTGGTGATAA	58.807	41.667	0.00	0.00	0.00	1.75
711	1028	0.391130	GTTCTGCCACGTGGATAGCA	60.391	55.000	38.30	25.47	37.39	3.49
850	1191	4.564281	GCAATTTTACTTTATTTGCGCCG	58.436	39.130	4.18	0.00	34.09	6.46
1066	1407	2.810650	CGAACCGAAGAGAATACCCAG	58.189	52.381	0.00	0.00	0.00	4.45
1146	1503	1.262640	GGGAGTAAGGGCTGAACGGA	61.263	60.000	0.00	0.00	0.00	4.69
1213	1633	0.397816	AAGGGAGAGATGACCGAGGG	60.398	60.000	0.00	0.00	0.00	4.30
1214	1634	1.410882	GAAAGGGAGAGATGACCGAGG	59.589	57.143	0.00	0.00	0.00	4.63
1215	1635	2.103373	TGAAAGGGAGAGATGACCGAG	58.897	52.381	0.00	0.00	0.00	4.63
1216	1636	1.825474	GTGAAAGGGAGAGATGACCGA	59.175	52.381	0.00	0.00	0.00	4.69
1217	1637	1.469940	CGTGAAAGGGAGAGATGACCG	60.470	57.143	0.00	0.00	0.00	4.79
1218	1638	2.301577	CGTGAAAGGGAGAGATGACC	57.698	55.000	0.00	0.00	0.00	4.02
1230	1650	4.090588	TAGGGGCCGCCGTGAAAG	62.091	66.667	17.56	0.00	0.00	2.62
1231	1651	4.397832	GTAGGGGCCGCCGTGAAA	62.398	66.667	17.56	0.00	0.00	2.69
1239	1659	2.132352	GTAGTGGAGGTAGGGGCCG	61.132	68.421	0.00	0.00	0.00	6.13
1240	1660	1.002533	TGTAGTGGAGGTAGGGGCC	59.997	63.158	0.00	0.00	0.00	5.80
1241	1661	1.673808	CGTGTAGTGGAGGTAGGGGC	61.674	65.000	0.00	0.00	0.00	5.80
1242	1662	1.673808	GCGTGTAGTGGAGGTAGGGG	61.674	65.000	0.00	0.00	0.00	4.79
1243	1663	0.968901	TGCGTGTAGTGGAGGTAGGG	60.969	60.000	0.00	0.00	0.00	3.53
1244	1664	0.456221	CTGCGTGTAGTGGAGGTAGG	59.544	60.000	0.00	0.00	0.00	3.18
1245	1665	0.456221	CCTGCGTGTAGTGGAGGTAG	59.544	60.000	0.00	0.00	39.84	3.18
1246	1666	0.038599	TCCTGCGTGTAGTGGAGGTA	59.961	55.000	0.43	0.00	44.54	3.08
1247	1667	0.614979	ATCCTGCGTGTAGTGGAGGT	60.615	55.000	0.43	0.00	44.54	3.85
1248	1668	0.537188	AATCCTGCGTGTAGTGGAGG	59.463	55.000	0.00	0.00	45.50	4.30
1249	1669	2.386661	AAATCCTGCGTGTAGTGGAG	57.613	50.000	0.00	0.00	31.59	3.86
1250	1670	2.037902	TGAAAATCCTGCGTGTAGTGGA	59.962	45.455	0.00	0.00	0.00	4.02
1251	1671	2.422597	TGAAAATCCTGCGTGTAGTGG	58.577	47.619	0.00	0.00	0.00	4.00
1252	1672	3.063997	GGATGAAAATCCTGCGTGTAGTG	59.936	47.826	0.00	0.00	37.73	2.74
1253	1673	3.270877	GGATGAAAATCCTGCGTGTAGT	58.729	45.455	0.00	0.00	37.73	2.73
1254	1674	2.614057	GGGATGAAAATCCTGCGTGTAG	59.386	50.000	4.81	0.00	40.54	2.74
1255	1675	2.639065	GGGATGAAAATCCTGCGTGTA	58.361	47.619	4.81	0.00	40.54	2.90
1256	1676	1.463674	GGGATGAAAATCCTGCGTGT	58.536	50.000	4.81	0.00	40.54	4.49
1257	1677	0.740737	GGGGATGAAAATCCTGCGTG	59.259	55.000	4.81	0.00	40.54	5.34
1267	1687	0.628968	TGGGGCATAGGGGGATGAAA	60.629	55.000	0.00	0.00	0.00	2.69
1400	1894	1.971357	AGCAGGGTATGAAGTATCGGG	59.029	52.381	0.00	0.00	0.00	5.14
1779	2292	8.574737	TGTAAAATCATCAATCATCACACAACA	58.425	29.630	0.00	0.00	0.00	3.33
1856	2386	7.971183	AGGAATCTGTCAAACTCTAAACTTC	57.029	36.000	0.00	0.00	0.00	3.01
1878	2408	5.710099	TCCTGCAAGAATAAAACAGGTAAGG	59.290	40.000	7.19	0.00	46.49	2.69
2230	6640	3.614616	GTGCTAGCAGACACAAGTGATAC	59.385	47.826	20.03	0.00	36.77	2.24
2790	7214	8.259411	TCAACTATCCGGTAAATTTTAGTGCTA	58.741	33.333	0.00	0.00	0.00	3.49
2925	7351	1.208706	TTGACTTGGAGTGTGTGGGA	58.791	50.000	0.00	0.00	0.00	4.37
3633	8181	6.443934	ACGCCACATAAACAATTATTAGCA	57.556	33.333	0.00	0.00	29.08	3.49
3654	8202	2.476619	CACAAGCTAACAGACTGGAACG	59.523	50.000	7.51	0.00	0.00	3.95
3734	8282	7.327032	GTGAAGTGATTTCCTTCTTTTGCATAC	59.673	37.037	0.00	0.00	39.24	2.39
3819	8367	6.524734	TGACCACAATGCGATCTCTAATATT	58.475	36.000	0.00	0.00	0.00	1.28
3820	8368	6.101650	TGACCACAATGCGATCTCTAATAT	57.898	37.500	0.00	0.00	0.00	1.28
3821	8369	5.529581	TGACCACAATGCGATCTCTAATA	57.470	39.130	0.00	0.00	0.00	0.98
3831	8379	0.241749	AACTGCATGACCACAATGCG	59.758	50.000	0.00	2.32	43.69	4.73
3842	8390	3.986572	TGGCGAAACAATTTAACTGCATG	59.013	39.130	0.00	0.00	0.00	4.06
3844	8392	3.717400	TGGCGAAACAATTTAACTGCA	57.283	38.095	0.00	0.00	0.00	4.41
4235	8790	7.556635	GGTTCACTTGGAGGCTTTTATATTAGT	59.443	37.037	0.00	0.00	0.00	2.24
4403	8959	1.573108	CATACACCACAGAGACCCCT	58.427	55.000	0.00	0.00	0.00	4.79
4454	9010	0.243636	CACAACTTGATTTCGGCCCC	59.756	55.000	0.00	0.00	0.00	5.80
4486	9044	3.512035	CACACAGGTGCACAGCAA	58.488	55.556	20.43	0.00	41.47	3.91
4581	9141	6.048732	TGGCAATTCAGAGTACATCACTTA	57.951	37.500	0.00	0.00	37.72	2.24
4683	9246	7.644551	GGATACGACTCACAGAATAGTAAACAG	59.355	40.741	0.00	0.00	0.00	3.16
4692	9255	4.098654	CAGAAGGGATACGACTCACAGAAT	59.901	45.833	0.00	0.00	37.60	2.40
4709	9272	2.031120	TGAAAAACTGCACCCAGAAGG	58.969	47.619	0.00	0.00	41.77	3.46
4728	9292	6.094881	TCAACAGAAAACCCAAACTAGAAGTG	59.905	38.462	0.00	0.00	0.00	3.16
4751	9360	2.970639	GTACCAGAGCTGCCGTCA	59.029	61.111	0.00	0.00	0.00	4.35
4768	9377	4.155826	TGAACCTACAAATTCATTCTGCCG	59.844	41.667	0.00	0.00	29.89	5.69
4801	9410	5.730550	TGTTGGATTGCTAATCGTTCTAGT	58.269	37.500	0.00	0.00	38.82	2.57
4982	9627	7.148507	GGATTGCTTTGATGTATAGGATTCTCG	60.149	40.741	0.00	0.00	0.00	4.04
5006	9651	5.228945	AGAACAAAGTGCTTAGCTAAGGA	57.771	39.130	29.93	26.39	33.95	3.36
5020	9665	9.846248	CTTTATGTTGGATTCCTAAGAACAAAG	57.154	33.333	9.59	6.91	33.97	2.77
5202	9854	3.441500	AGGAAAACAGGGATGTCTTCC	57.558	47.619	5.52	5.52	44.62	3.46
5229	9881	3.262915	AGGTCAGAGAAAGGACTCAATGG	59.737	47.826	0.00	0.00	39.14	3.16

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.