AutoCloner

Multiple sequence alignment - TraesCS6B01G125900

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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	TraesCS6B01G125900	chr6B	100.000	3999	0	0	1	3999	121434689	121430691	0.000000e+00	7385
1	TraesCS6B01G125900	chr6B	84.218	1508	185	15	2013	3473	649832557	649831056	0.000000e+00	1417
2	TraesCS6B01G125900	chr6B	85.704	1378	155	20	2002	3363	121960085	121958734	0.000000e+00	1415
3	TraesCS6B01G125900	chr6B	84.576	1381	156	32	2002	3363	122186630	122185288	0.000000e+00	1317
4	TraesCS6B01G125900	chr6B	87.179	273	28	6	3469	3737	121958678	121958409	1.810000e-78	303
5	TraesCS6B01G125900	chr6B	86.477	281	30	7	3462	3737	122185240	122184963	6.500000e-78	302
6	TraesCS6B01G125900	chr6B	97.115	104	2	1	1	103	392389657	392389554	1.480000e-39	174
7	TraesCS6B01G125900	chr6B	97.115	104	2	1	1	103	526907247	526907144	1.480000e-39	174
8	TraesCS6B01G125900	chr6D	91.113	4051	291	24	1	3999	50177779	50181812	0.000000e+00	5422
9	TraesCS6B01G125900	chr6D	81.563	3135	432	75	319	3358	49181037	49184120	0.000000e+00	2453
10	TraesCS6B01G125900	chr6D	84.838	1385	184	11	1993	3360	50605088	50606463	0.000000e+00	1371
11	TraesCS6B01G125900	chr6D	88.358	481	46	9	3462	3935	50606514	50606991	1.610000e-158	569
12	TraesCS6B01G125900	chr6D	87.135	171	20	2	146	315	153811610	153811779	4.080000e-45	193
13	TraesCS6B01G125900	chr6D	82.075	212	34	3	319	526	457258144	457257933	1.140000e-40	178
14	TraesCS6B01G125900	chr6A	92.496	2852	184	15	1171	3999	64909290	64906446	0.000000e+00	4054
15	TraesCS6B01G125900	chr6A	84.761	1378	184	14	2002	3363	64679633	64678266	0.000000e+00	1358
16	TraesCS6B01G125900	chr6A	87.775	1137	112	11	2	1114	64910420	64909287	0.000000e+00	1304
17	TraesCS6B01G125900	chr6A	86.486	481	54	9	3462	3935	64678219	64677743	5.920000e-143	518
18	TraesCS6B01G125900	chr6A	74.706	510	93	29	1498	1998	577723885	577723403	1.130000e-45	195
19	TraesCS6B01G125900	chrUn	84.800	1375	183	14	2002	3360	277361311	277362675	0.000000e+00	1358
20	TraesCS6B01G125900	chrUn	85.531	546	60	10	2002	2534	373932978	373932439	1.620000e-153	553
21	TraesCS6B01G125900	chrUn	86.279	481	55	9	3462	3935	277362725	277363201	2.760000e-141	512
22	TraesCS6B01G125900	chr7B	82.203	1371	201	25	2013	3363	517933269	517931922	0.000000e+00	1140
23	TraesCS6B01G125900	chr7B	79.271	521	82	19	1494	2004	517933838	517933334	1.380000e-89	340
24	TraesCS6B01G125900	chr7B	78.736	522	86	16	1494	2003	509737120	509736612	3.850000e-85	326
25	TraesCS6B01G125900	chr7B	83.125	320	48	6	319	635	517935512	517935196	1.820000e-73	287
26	TraesCS6B01G125900	chr7B	80.142	282	40	14	316	594	517936027	517935759	3.150000e-46	196
27	TraesCS6B01G125900	chr7D	82.125	1365	206	22	2013	3360	489301837	489300494	0.000000e+00	1134
28	TraesCS6B01G125900	chr7D	84.013	319	46	5	319	635	489312658	489312343	6.500000e-78	302
29	TraesCS6B01G125900	chr7D	80.645	372	66	6	322	692	484073354	484072988	2.350000e-72	283
30	TraesCS6B01G125900	chr7D	85.514	214	22	7	1787	1998	535510772	535510978	8.700000e-52	215
31	TraesCS6B01G125900	chr7D	97.115	104	2	1	1	103	304183140	304183243	1.480000e-39	174
32	TraesCS6B01G125900	chr7D	80.603	232	38	5	1775	2003	489302130	489301903	5.310000e-39	172
33	TraesCS6B01G125900	chr7D	78.445	283	43	14	316	594	489313173	489312905	6.870000e-38	169
34	TraesCS6B01G125900	chr7A	84.130	523	67	11	3462	3976	591025626	591026140	3.590000e-135	492
35	TraesCS6B01G125900	chr7A	80.539	519	78	14	1494	2000	551543131	551542624	1.050000e-100	377
36	TraesCS6B01G125900	chr7A	84.013	319	44	6	3588	3899	616441783	616441465	2.340000e-77	300
37	TraesCS6B01G125900	chr7A	81.784	269	29	14	1744	1998	615785801	615786063	1.460000e-49	207
38	TraesCS6B01G125900	chr1A	90.503	179	15	2	146	323	91044688	91044865	6.680000e-58	235
39	TraesCS6B01G125900	chr1A	87.778	180	17	3	146	323	271622671	271622495	5.240000e-49	206
40	TraesCS6B01G125900	chr5D	88.701	177	18	2	146	321	250387578	250387753	8.700000e-52	215
41	TraesCS6B01G125900	chr5A	88.068	176	19	2	146	320	69192103	69192277	1.460000e-49	207
42	TraesCS6B01G125900	chr2A	86.517	178	21	2	146	321	715403723	715403899	4.080000e-45	193
43	TraesCS6B01G125900	chr2A	97.115	104	2	1	1	103	322408315	322408418	1.480000e-39	174
44	TraesCS6B01G125900	chr2A	97.115	104	2	1	1	103	388735305	388735408	1.480000e-39	174
45	TraesCS6B01G125900	chr3D	85.475	179	24	2	146	324	427044823	427044647	6.820000e-43	185
46	TraesCS6B01G125900	chr3B	100.000	97	0	0	1	97	341952349	341952445	3.180000e-41	180
47	TraesCS6B01G125900	chr3B	98.058	103	1	1	1	102	47375594	47375492	1.140000e-40	178
48	TraesCS6B01G125900	chr2D	100.000	97	0	0	1	97	463077551	463077455	3.180000e-41	180
49	TraesCS6B01G125900	chr1B	97.115	104	2	1	1	103	74011887	74011990	1.480000e-39	174

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	TraesCS6B01G125900	chr6B	121430691	121434689	3998	True	7385.00	7385	100.00000	1	3999	1	chr6B.!!$R1	3998
1	TraesCS6B01G125900	chr6B	649831056	649832557	1501	True	1417.00	1417	84.21800	2013	3473	1	chr6B.!!$R4	1460
2	TraesCS6B01G125900	chr6B	121958409	121960085	1676	True	859.00	1415	86.44150	2002	3737	2	chr6B.!!$R5	1735
3	TraesCS6B01G125900	chr6B	122184963	122186630	1667	True	809.50	1317	85.52650	2002	3737	2	chr6B.!!$R6	1735
4	TraesCS6B01G125900	chr6D	50177779	50181812	4033	False	5422.00	5422	91.11300	1	3999	1	chr6D.!!$F2	3998
5	TraesCS6B01G125900	chr6D	49181037	49184120	3083	False	2453.00	2453	81.56300	319	3358	1	chr6D.!!$F1	3039
6	TraesCS6B01G125900	chr6D	50605088	50606991	1903	False	970.00	1371	86.59800	1993	3935	2	chr6D.!!$F4	1942
7	TraesCS6B01G125900	chr6A	64906446	64910420	3974	True	2679.00	4054	90.13550	2	3999	2	chr6A.!!$R3	3997
8	TraesCS6B01G125900	chr6A	64677743	64679633	1890	True	938.00	1358	85.62350	2002	3935	2	chr6A.!!$R2	1933
9	TraesCS6B01G125900	chrUn	277361311	277363201	1890	False	935.00	1358	85.53950	2002	3935	2	chrUn.!!$F1	1933
10	TraesCS6B01G125900	chrUn	373932439	373932978	539	True	553.00	553	85.53100	2002	2534	1	chrUn.!!$R1	532
11	TraesCS6B01G125900	chr7B	517931922	517936027	4105	True	490.75	1140	81.18525	316	3363	4	chr7B.!!$R2	3047
12	TraesCS6B01G125900	chr7B	509736612	509737120	508	True	326.00	326	78.73600	1494	2003	1	chr7B.!!$R1	509
13	TraesCS6B01G125900	chr7D	489300494	489302130	1636	True	653.00	1134	81.36400	1775	3360	2	chr7D.!!$R2	1585
14	TraesCS6B01G125900	chr7D	489312343	489313173	830	True	235.50	302	81.22900	316	635	2	chr7D.!!$R3	319
15	TraesCS6B01G125900	chr7A	591025626	591026140	514	False	492.00	492	84.13000	3462	3976	1	chr7A.!!$F1	514
16	TraesCS6B01G125900	chr7A	551542624	551543131	507	True	377.00	377	80.53900	1494	2000	1	chr7A.!!$R1	506

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	Hairpin	End Stability	Orientation
577	936	0.405585	AAACCTGGATGGGGAGTGTG	59.594	55.0	41.11	3.82	F
1011	1910	1.024271	CAACCTTCATGTATGGCGGG	58.976	55.0	0.00	6.13	F
2807	4009	0.109342	CAACTCAGTGGTGCCTCCTT	59.891	55.0	37.07	3.36	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	End Stability	Orientation
2422	3612	1.280710	ACTATTGGTTCCCGTGATGCA	59.719	47.619	0.00	3.96	R
2914	4116	0.179032	TGTCCATGTTGCCAACGACT	60.179	50.000	13.00	4.18	R
3937	5194	0.836606	TCCACGCCATGTACATCCAT	59.163	50.000	5.07	3.41	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
122	146	2.139484	CAAAGCCCCCACTTGCCAA	61.139	57.895	0.00	0.00	0.00	4.52
218	243	5.356190	ACACATCTGCTGGTATTGATTTCAG	59.644	40.000	0.00	0.00	0.00	3.02
271	296	4.579869	TCTGGTCAAACTTTATGAGGCTC	58.420	43.478	7.79	7.79	0.00	4.70
279	304	4.537135	ACTTTATGAGGCTCGACTTCAA	57.463	40.909	10.42	0.00	0.00	2.69
281	306	4.691216	ACTTTATGAGGCTCGACTTCAAAC	59.309	41.667	10.42	0.00	0.00	2.93
294	319	8.604035	GCTCGACTTCAAACAAATCTTATATGA	58.396	33.333	0.00	0.00	0.00	2.15
370	566	6.054941	GGTCAAAAGTTTGGTTGGATGAATT	58.945	36.000	4.04	0.00	38.66	2.17
389	585	9.219603	GATGAATTCGTCCAATAAATCCAGATA	57.780	33.333	15.63	0.00	0.00	1.98
404	600	1.055040	AGATAGGAGGAGCATGCCAC	58.945	55.000	15.66	7.68	0.00	5.01
418	614	0.526211	TGCCACTAGTAGCACAGTCG	59.474	55.000	12.20	0.00	33.08	4.18
431	627	3.817084	AGCACAGTCGTACTACAAGTGTA	59.183	43.478	17.97	0.00	33.08	2.90
478	674	6.030548	TGGCATAACTAGCTATGAGTGATC	57.969	41.667	15.80	0.00	31.94	2.92
577	936	0.405585	AAACCTGGATGGGGAGTGTG	59.594	55.000	0.00	0.00	41.11	3.82
581	940	1.976132	CTGGATGGGGAGTGTGCGAT	61.976	60.000	0.00	0.00	0.00	4.58
647	1542	4.630111	TGAGCTAAAATTTGTTGGCTTGG	58.370	39.130	2.70	0.00	44.40	3.61
720	1615	6.354130	GGCAATACTAGAAATACCACTTCCA	58.646	40.000	0.00	0.00	0.00	3.53
730	1625	1.302511	CCACTTCCACCAAGGGTCG	60.303	63.158	0.00	0.00	32.92	4.79
772	1668	2.510768	AGAAACGCTCGTTCAGAACT	57.489	45.000	11.60	1.69	37.35	3.01
775	1671	1.217882	AACGCTCGTTCAGAACTTGG	58.782	50.000	11.60	2.79	32.09	3.61
792	1688	4.301505	GCTCGTGCCTTCCATTCA	57.698	55.556	0.00	0.00	0.00	2.57
910	1806	1.761174	CAACCCACACCTGCTACCT	59.239	57.895	0.00	0.00	0.00	3.08
925	1822	5.163713	CCTGCTACCTGCTTCACTAAAAATC	60.164	44.000	0.00	0.00	43.37	2.17
928	1825	5.416013	GCTACCTGCTTCACTAAAAATCCTT	59.584	40.000	0.00	0.00	38.95	3.36
929	1826	6.071896	GCTACCTGCTTCACTAAAAATCCTTT	60.072	38.462	0.00	0.00	38.95	3.11
946	1843	5.017093	TCCTTTCCCATTTACCAATTCCA	57.983	39.130	0.00	0.00	0.00	3.53
991	1890	2.226437	GACGACTACGACAAGGTACCAA	59.774	50.000	15.94	0.00	42.66	3.67
994	1893	3.550639	CGACTACGACAAGGTACCAACAA	60.551	47.826	15.94	0.00	42.66	2.83
1011	1910	1.024271	CAACCTTCATGTATGGCGGG	58.976	55.000	0.00	0.00	0.00	6.13
1049	1948	2.047655	GGTTCCGATGGTGACGCA	60.048	61.111	0.00	0.00	0.00	5.24
1050	1949	1.669760	GGTTCCGATGGTGACGCAA	60.670	57.895	0.00	0.00	0.00	4.85
1067	1966	2.565841	GCAAAAGGTGATAGAGGCGAT	58.434	47.619	0.00	0.00	0.00	4.58
1124	2023	2.986290	TGGGGACACGCGATTCAT	59.014	55.556	15.93	0.00	33.40	2.57
1133	2032	2.108976	GCGATTCATGGGGCTCGA	59.891	61.111	10.03	0.00	33.07	4.04
1177	2076	3.244561	GGATGACAACAAGGAGGACTTCA	60.245	47.826	0.00	0.00	37.29	3.02
1261	2160	1.839994	GGGTGGATGAGAAGGATGACA	59.160	52.381	0.00	0.00	0.00	3.58
1264	2163	3.307691	GGTGGATGAGAAGGATGACAACA	60.308	47.826	0.00	0.00	0.00	3.33
1291	2190	3.442273	GGTCATCAAAATAAAGCCCGTCA	59.558	43.478	0.00	0.00	0.00	4.35
1303	2202	1.669115	CCCGTCACTGCTGTCAAGG	60.669	63.158	0.00	0.00	0.00	3.61
1576	2664	5.046159	TCTGTTGTATTCGGTTGGTAGGATT	60.046	40.000	0.00	0.00	0.00	3.01
1593	2681	2.030274	GGATTTTTCCAACACTGTCCCG	60.030	50.000	0.00	0.00	0.00	5.14
1657	2745	4.707563	TGTGATTTATGCTTTTCGTGACG	58.292	39.130	0.00	0.00	0.00	4.35
1721	2809	4.302559	AGTAAATCCACAGAAAGGGTCC	57.697	45.455	0.00	0.00	0.00	4.46
1731	2819	2.027192	CAGAAAGGGTCCGATTTCTCCA	60.027	50.000	14.70	0.00	42.41	3.86
1785	2881	6.127168	CCTTATGATGGTTCTAGGTGTGTGTA	60.127	42.308	0.00	0.00	0.00	2.90
1840	2936	9.118300	CAGTCTAAAAGATTATTCTGCCAATCT	57.882	33.333	0.00	0.00	42.03	2.40
2104	3273	3.629398	GTCCCTCTTAGCATTGACATTGG	59.371	47.826	0.00	0.00	0.00	3.16
2130	3311	9.674824	GTCTTCCAATTATGATGATTTAAGCAG	57.325	33.333	0.00	0.00	0.00	4.24
2203	3393	3.009695	ACAAATTCAGGGGTATCCGTCAA	59.990	43.478	0.00	0.00	41.52	3.18
2280	3470	3.630312	GTCTGGCTTGGTACTTTCAACAA	59.370	43.478	0.00	0.00	0.00	2.83
2322	3512	3.670359	GCTTATGATGTTGAAGCACGCAA	60.670	43.478	1.13	0.00	44.05	4.85
2382	3572	1.490490	ACCAACAGTTCCTCAGAAGCA	59.510	47.619	0.00	0.00	30.91	3.91
2422	3612	2.642807	TCCTAAAGCACCCAAGCTAAGT	59.357	45.455	0.00	0.00	45.89	2.24
2483	3685	6.064060	CCAAATGCTTTCATCTACCCATCTA	58.936	40.000	0.00	0.00	31.27	1.98
2598	3800	1.552337	GAATCTGCACTCTGACCAGGA	59.448	52.381	0.00	0.00	0.00	3.86
2621	3823	3.173965	AGCAACTCCTTTGGCTACTCTA	58.826	45.455	0.00	0.00	35.51	2.43
2646	3848	3.696045	TGGGTTGGAATTATGACACCAG	58.304	45.455	0.00	0.00	33.85	4.00
2650	3852	3.644966	TGGAATTATGACACCAGGACC	57.355	47.619	0.00	0.00	0.00	4.46
2750	3952	3.213206	ACTCAGTGGTGATTGCTGAAA	57.787	42.857	0.00	0.00	38.58	2.69
2807	4009	0.109342	CAACTCAGTGGTGCCTCCTT	59.891	55.000	0.00	0.00	37.07	3.36
2876	4078	1.141881	GATGATGGCGTGGTCGAGT	59.858	57.895	0.00	0.00	39.71	4.18
2914	4116	2.214376	ATTTTGATGTGCCTCGGGAA	57.786	45.000	0.00	0.00	0.00	3.97
2989	4192	3.893753	TTTTCTGAGGGATCCAAACCA	57.106	42.857	15.23	4.36	0.00	3.67
2991	4195	4.402616	TTTCTGAGGGATCCAAACCATT	57.597	40.909	15.23	0.00	0.00	3.16
3011	4216	6.273965	ACCATTTATATAGGGACAAGGGGTAC	59.726	42.308	0.64	0.00	0.00	3.34
3131	4338	5.428253	GGAAGCACTATATTGTCACCTTCA	58.572	41.667	16.28	0.00	0.00	3.02
3380	4625	8.674607	CCTTTAATTGGTGATAGAAGTAACCAC	58.325	37.037	0.00	0.00	42.28	4.16
3441	4686	1.206371	GATTTTCCTGGCTGCTTGCAT	59.794	47.619	0.00	0.00	45.15	3.96
3447	4692	2.833338	TCCTGGCTGCTTGCATAATTTT	59.167	40.909	0.00	0.00	45.15	1.82
3499	4744	2.419159	GCGCATATCCTATGGATGCAGA	60.419	50.000	0.30	0.00	43.06	4.26
3518	4763	4.440250	GCAGAGGCTAGACGTTTCAATCTA	60.440	45.833	0.00	0.00	36.96	1.98
3521	4766	6.758886	CAGAGGCTAGACGTTTCAATCTATTT	59.241	38.462	0.00	0.00	0.00	1.40
3547	4792	4.992688	TGAAAAAGTGTGTGTTAAGCCAG	58.007	39.130	0.00	0.00	0.00	4.85
3549	4794	2.051334	AAGTGTGTGTTAAGCCAGCA	57.949	45.000	0.00	0.00	0.00	4.41
3570	4815	7.421599	CAGCATGTCCTCTATATTATACCTCG	58.578	42.308	0.00	0.00	0.00	4.63
3642	4887	6.779539	ACTAGATGTGTGATCATATGGAGTCA	59.220	38.462	0.00	2.85	0.00	3.41
3739	4988	4.872124	GGATTTTCCATTTCAGTGCATTCC	59.128	41.667	0.00	0.00	36.28	3.01
3857	5112	4.908601	AATTGGTGGTCTCATGTCACTA	57.091	40.909	0.00	0.00	0.00	2.74
3937	5194	8.114102	TCTTGATTAGAGGGTCAACTAGTTCTA	58.886	37.037	4.77	0.18	31.55	2.10
3969	5226	1.404035	GGCGTGGAAAGTTGTGAAGTT	59.596	47.619	0.00	0.00	0.00	2.66
3970	5227	2.540973	GGCGTGGAAAGTTGTGAAGTTC	60.541	50.000	0.00	0.00	0.00	3.01
3985	5242	5.242171	TGTGAAGTTCGAGTCCATAGTACAA	59.758	40.000	0.00	0.00	0.00	2.41

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
122	146	7.613801	TGATGTATAATTTTAGCAAGTGTGGGT	59.386	33.333	0.00	0.00	0.00	4.51
196	221	5.748402	TCTGAAATCAATACCAGCAGATGT	58.252	37.500	0.00	0.00	0.00	3.06
202	227	6.441093	TCACAATCTGAAATCAATACCAGC	57.559	37.500	0.00	0.00	0.00	4.85
249	274	4.579869	GAGCCTCATAAAGTTTGACCAGA	58.420	43.478	0.00	0.00	0.00	3.86
250	275	3.372206	CGAGCCTCATAAAGTTTGACCAG	59.628	47.826	0.00	0.00	0.00	4.00
264	289	2.613026	TTGTTTGAAGTCGAGCCTCA	57.387	45.000	0.00	0.00	0.00	3.86
294	319	3.585732	TCCCTCCGGTCATTTTTAGTTCT	59.414	43.478	0.00	0.00	0.00	3.01
370	566	5.246203	CCTCCTATCTGGATTTATTGGACGA	59.754	44.000	0.00	0.00	45.16	4.20
385	581	1.055040	GTGGCATGCTCCTCCTATCT	58.945	55.000	18.92	0.00	0.00	1.98
389	585	0.326048	ACTAGTGGCATGCTCCTCCT	60.326	55.000	18.92	8.74	0.00	3.69
478	674	8.572828	TGTGTGTAATGTTAAGATTTTTGCAG	57.427	30.769	2.84	0.00	0.00	4.41
647	1542	5.650543	TGTTTGACTTTCTTTCTTTGGAGC	58.349	37.500	0.00	0.00	0.00	4.70
704	1599	4.018779	CCCTTGGTGGAAGTGGTATTTCTA	60.019	45.833	0.00	0.00	38.35	2.10
720	1615	2.280592	GCGTGTTCGACCCTTGGT	60.281	61.111	0.00	0.00	39.44	3.67
730	1625	3.868661	ACTTGGGAAAATTTTGCGTGTTC	59.131	39.130	15.17	3.06	0.00	3.18
775	1671	0.955428	TGTGAATGGAAGGCACGAGC	60.955	55.000	0.00	0.00	41.10	5.03
910	1806	5.144100	TGGGAAAGGATTTTTAGTGAAGCA	58.856	37.500	0.00	0.00	39.27	3.91
925	1822	4.162131	CCTGGAATTGGTAAATGGGAAAGG	59.838	45.833	0.00	0.00	0.00	3.11
928	1825	3.338214	TCCCTGGAATTGGTAAATGGGAA	59.662	43.478	0.00	0.00	39.29	3.97
929	1826	2.929724	TCCCTGGAATTGGTAAATGGGA	59.070	45.455	0.00	0.00	39.87	4.37
960	1857	4.100084	TAGTCGTCGCCGGGGAGA	62.100	66.667	23.26	17.62	33.95	3.71
964	1861	4.527157	GTCGTAGTCGTCGCCGGG	62.527	72.222	2.18	0.00	38.33	5.73
965	1862	3.313007	TTGTCGTAGTCGTCGCCGG	62.313	63.158	0.00	0.00	38.33	6.13
991	1890	1.681780	CCCGCCATACATGAAGGTTGT	60.682	52.381	0.00	0.00	0.00	3.32
994	1893	1.531748	CCCCGCCATACATGAAGGT	59.468	57.895	0.00	0.00	0.00	3.50
997	1896	2.203139	CGCCCCGCCATACATGAA	60.203	61.111	0.00	0.00	0.00	2.57
1011	1910	3.959991	GAGGTCTGCAAGGGACGCC	62.960	68.421	0.00	0.00	34.82	5.68
1049	1948	4.762289	AGAATCGCCTCTATCACCTTTT	57.238	40.909	0.00	0.00	0.00	2.27
1050	1949	5.279708	CCATAGAATCGCCTCTATCACCTTT	60.280	44.000	3.81	0.00	36.66	3.11
1067	1966	2.747177	TCTTCTTCTCGGGCCATAGAA	58.253	47.619	15.88	15.88	0.00	2.10
1115	2014	3.341043	CGAGCCCCATGAATCGCG	61.341	66.667	0.00	0.00	0.00	5.87
1119	2018	1.457604	CCCATCGAGCCCCATGAAT	59.542	57.895	0.00	0.00	0.00	2.57
1152	2051	2.303022	GTCCTCCTTGTTGTCATCCAGA	59.697	50.000	0.00	0.00	0.00	3.86
1177	2076	2.484264	CGAATTCTTCAAACTCGGCCTT	59.516	45.455	0.00	0.00	0.00	4.35
1185	2084	2.073816	TCGGCCTCGAATTCTTCAAAC	58.926	47.619	0.00	0.00	43.03	2.93
1261	2160	6.295292	GGCTTTATTTTGATGACCTCCTTGTT	60.295	38.462	0.00	0.00	0.00	2.83
1264	2163	4.711846	GGGCTTTATTTTGATGACCTCCTT	59.288	41.667	0.00	0.00	0.00	3.36
1576	2664	2.018515	GAACGGGACAGTGTTGGAAAA	58.981	47.619	0.00	0.00	0.00	2.29
1593	2681	4.676924	CCAAAATCGCTTCTGTGAAAGAAC	59.323	41.667	0.00	0.00	40.09	3.01
1645	2733	1.461888	CCATCGAACGTCACGAAAAGC	60.462	52.381	18.48	0.00	42.80	3.51
1681	2769	3.242011	ACTACCCCTTTCGACTAAACCA	58.758	45.455	0.00	0.00	0.00	3.67
1682	2770	3.969287	ACTACCCCTTTCGACTAAACC	57.031	47.619	0.00	0.00	0.00	3.27
1691	2779	5.431179	TCTGTGGATTTACTACCCCTTTC	57.569	43.478	0.00	0.00	0.00	2.62
1721	2809	5.355350	ACCTCTAAGCAAAATGGAGAAATCG	59.645	40.000	0.00	0.00	0.00	3.34
1731	2819	9.301897	ACAATTTAAGAGACCTCTAAGCAAAAT	57.698	29.630	0.00	0.86	39.39	1.82
1773	2869	5.794894	AGAACAATCCTTACACACACCTAG	58.205	41.667	0.00	0.00	0.00	3.02
1785	2881	6.187727	TGAACCAAGTCTAGAACAATCCTT	57.812	37.500	0.00	0.00	0.00	3.36
2104	3273	9.674824	CTGCTTAAATCATCATAATTGGAAGAC	57.325	33.333	0.00	0.00	0.00	3.01
2280	3470	2.674033	TTGCAGCAGCTTCGGCAT	60.674	55.556	12.21	0.00	44.74	4.40
2382	3572	4.415332	CAGCACGGCGAGTACGGT	62.415	66.667	16.62	0.00	40.15	4.83
2422	3612	1.280710	ACTATTGGTTCCCGTGATGCA	59.719	47.619	0.00	0.00	0.00	3.96
2437	3627	4.709886	GGGTTGGCAAGGTTATTGACTATT	59.290	41.667	0.00	0.00	0.00	1.73
2446	3648	1.346068	GCATTTGGGTTGGCAAGGTTA	59.654	47.619	0.00	0.00	0.00	2.85
2483	3685	2.623416	GCTGGTTTGAGGCAAAGTTAGT	59.377	45.455	0.00	0.00	33.82	2.24
2518	3720	2.800544	AGGAACAAATGACACGTTCTCG	59.199	45.455	11.78	0.00	39.18	4.04
2598	3800	3.149981	GAGTAGCCAAAGGAGTTGCTTT	58.850	45.455	0.00	0.00	35.74	3.51
2621	3823	4.526650	GGTGTCATAATTCCAACCCAAGTT	59.473	41.667	0.00	0.00	36.33	2.66
2646	3848	2.434702	GTGGATGATATATCCGGGGTCC	59.565	54.545	10.25	9.78	41.03	4.46
2650	3852	2.768527	AGCAGTGGATGATATATCCGGG	59.231	50.000	10.25	0.00	41.03	5.73
2750	3952	2.753296	GAGCGCAATAGATTCAGCTCT	58.247	47.619	11.47	0.84	45.22	4.09
2762	3964	0.530744	TTACTCTGGACGAGCGCAAT	59.469	50.000	11.47	0.00	43.85	3.56
2763	3965	0.388134	GTTACTCTGGACGAGCGCAA	60.388	55.000	11.47	0.00	43.85	4.85
2807	4009	5.852282	TCGACATCATTGTTCTCCATAGA	57.148	39.130	0.00	0.00	35.79	1.98
2876	4078	6.823182	TCAAAATTCAGAAGGCTATCAATCGA	59.177	34.615	0.00	0.00	0.00	3.59
2914	4116	0.179032	TGTCCATGTTGCCAACGACT	60.179	50.000	13.00	0.00	0.00	4.18
2956	4158	4.284234	CCCTCAGAAAAATTCCCACACATT	59.716	41.667	0.00	0.00	0.00	2.71
2989	4192	5.046087	GCGTACCCCTTGTCCCTATATAAAT	60.046	44.000	0.00	0.00	0.00	1.40
2991	4195	3.834231	GCGTACCCCTTGTCCCTATATAA	59.166	47.826	0.00	0.00	0.00	0.98
3079	4285	8.662781	TCTTCCATAATCTTATTCCTGAAACG	57.337	34.615	0.00	0.00	0.00	3.60
3426	4671	2.148446	AATTATGCAAGCAGCCAGGA	57.852	45.000	0.00	0.00	44.83	3.86
3441	4686	8.749026	TTACCACACCTCTACAACAAAAATTA	57.251	30.769	0.00	0.00	0.00	1.40
3447	4692	9.661563	CTATAATTTACCACACCTCTACAACAA	57.338	33.333	0.00	0.00	0.00	2.83
3499	4744	7.923414	AAAAATAGATTGAAACGTCTAGCCT	57.077	32.000	0.00	0.00	31.05	4.58
3521	4766	6.706270	TGGCTTAACACACACTTTTTCAAAAA	59.294	30.769	0.00	0.00	0.00	1.94
3547	4792	7.067129	TGACGAGGTATAATATAGAGGACATGC	59.933	40.741	0.00	0.00	0.00	4.06
3549	4794	9.702253	AATGACGAGGTATAATATAGAGGACAT	57.298	33.333	0.00	0.00	0.00	3.06
3570	4815	9.185192	GTATATTTTGCCATAGCTTGAAATGAC	57.815	33.333	0.00	0.00	40.80	3.06
3642	4887	7.118971	GTGAGAAGAACTACATGCAGAAAGAAT	59.881	37.037	0.00	0.00	0.00	2.40
3806	5061	8.919145	TGAAGGTTTTGGTAATAAATCAAGTGT	58.081	29.630	0.00	0.00	0.00	3.55
3857	5112	7.415541	CCAATCAAATCAAGGACGTAACATGAT	60.416	37.037	0.00	5.05	32.36	2.45
3937	5194	0.836606	TCCACGCCATGTACATCCAT	59.163	50.000	5.07	0.00	0.00	3.41
3969	5226	6.682113	GCAAACCTATTGTACTATGGACTCGA	60.682	42.308	2.34	0.00	0.00	4.04
3970	5227	5.462398	GCAAACCTATTGTACTATGGACTCG	59.538	44.000	2.34	0.00	0.00	4.18

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.