AutoCloner

Multiple sequence alignment - TraesCS1B01G304200

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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	TraesCS1B01G304200	chr1B	100.000	3987	0	0	1	3987	526376963	526380949	0.000000e+00	7363.0
1	TraesCS1B01G304200	chr1B	81.649	752	104	17	1314	2036	526428739	526429485	9.540000e-166	593.0
2	TraesCS1B01G304200	chr1B	79.610	667	115	13	1327	1981	525894612	525895269	3.630000e-125	459.0
3	TraesCS1B01G304200	chr1B	73.356	593	106	29	729	1305	526428126	526428682	5.300000e-39	172.0
4	TraesCS1B01G304200	chr1B	90.400	125	12	0	533	657	526428693	526428817	8.860000e-37	165.0
5	TraesCS1B01G304200	chr1B	98.361	61	1	0	244	304	672857340	672857400	1.520000e-19	108.0
6	TraesCS1B01G304200	chr1B	97.778	45	1	0	486	530	526428625	526428669	1.190000e-10	78.7
7	TraesCS1B01G304200	chr1B	92.683	41	2	1	3630	3670	526430913	526430952	1.550000e-04	58.4
8	TraesCS1B01G304200	chr1D	91.819	1968	81	25	447	2368	395626961	395628894	0.000000e+00	2669.0
9	TraesCS1B01G304200	chr1D	92.708	1152	53	11	2364	3507	395628927	395630055	0.000000e+00	1633.0
10	TraesCS1B01G304200	chr1D	85.399	1493	106	47	2364	3827	395714534	395715943	0.000000e+00	1447.0
11	TraesCS1B01G304200	chr1D	91.383	499	27	8	3490	3987	395630073	395630556	0.000000e+00	669.0
12	TraesCS1B01G304200	chr1D	82.454	701	92	15	1314	1985	395877370	395878068	5.740000e-163	584.0
13	TraesCS1B01G304200	chr1D	95.000	220	11	0	24	243	395626566	395626785	2.950000e-91	346.0
14	TraesCS1B01G304200	chr1D	91.617	167	11	1	3821	3987	395797992	395798155	1.110000e-55	228.0
15	TraesCS1B01G304200	chr1D	90.854	164	14	1	81	243	395875046	395875209	6.710000e-53	219.0
16	TraesCS1B01G304200	chr1D	88.820	161	14	2	288	448	395626772	395626928	1.130000e-45	195.0
17	TraesCS1B01G304200	chr1D	75.375	333	63	11	987	1305	395876986	395877313	4.150000e-30	143.0
18	TraesCS1B01G304200	chr1D	96.552	58	0	2	245	302	450715156	450715101	1.180000e-15	95.3
19	TraesCS1B01G304200	chr1A	94.681	1410	62	4	960	2368	489921518	489922915	0.000000e+00	2176.0
20	TraesCS1B01G304200	chr1A	94.009	701	39	3	960	1659	490087083	490087781	0.000000e+00	1059.0
21	TraesCS1B01G304200	chr1A	82.119	755	98	18	1314	2036	490019051	490019800	2.630000e-171	612.0
22	TraesCS1B01G304200	chr1A	82.194	702	86	19	1314	1984	490109116	490109809	5.780000e-158	568.0
23	TraesCS1B01G304200	chr1A	81.371	569	98	5	1327	1888	489236511	489237078	1.310000e-124	457.0
24	TraesCS1B01G304200	chr1A	78.390	671	86	37	2929	3576	490020015	490020649	8.090000e-102	381.0
25	TraesCS1B01G304200	chr1A	78.241	671	87	37	2929	3576	490110073	490110707	3.760000e-100	375.0
26	TraesCS1B01G304200	chr1A	92.727	220	15	1	24	243	489918470	489918688	2.310000e-82	316.0
27	TraesCS1B01G304200	chr1A	91.818	220	17	1	24	243	490084074	490084292	5.010000e-79	305.0
28	TraesCS1B01G304200	chr1A	80.531	339	36	12	451	759	489919471	489919809	2.400000e-57	233.0
29	TraesCS1B01G304200	chr1A	79.941	339	38	13	451	759	490085074	490085412	5.190000e-54	222.0
30	TraesCS1B01G304200	chr1A	93.814	97	5	1	756	851	490086802	490086706	1.150000e-30	145.0
31	TraesCS1B01G304200	chr1A	95.918	49	2	0	2364	2412	489922947	489922995	3.300000e-11	80.5
32	TraesCS1B01G304200	chr6A	92.958	71	4	1	245	314	616113641	616113711	7.050000e-18	102.0
33	TraesCS1B01G304200	chr7D	96.667	60	1	1	245	304	529914250	529914192	9.120000e-17	99.0
34	TraesCS1B01G304200	chr7D	96.552	58	2	0	245	302	417925745	417925802	3.280000e-16	97.1
35	TraesCS1B01G304200	chr7A	96.667	60	1	1	244	302	78848990	78849049	9.120000e-17	99.0
36	TraesCS1B01G304200	chr3D	93.333	60	2	2	245	304	602062471	602062528	1.970000e-13	87.9
37	TraesCS1B01G304200	chr2A	92.063	63	3	2	244	304	766491379	766491317	1.970000e-13	87.9
38	TraesCS1B01G304200	chr3A	93.220	59	3	1	245	303	634185997	634185940	7.100000e-13	86.1

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	TraesCS1B01G304200	chr1B	526376963	526380949	3986	False	7363.000000	7363	100.000000	1	3987	1	chr1B.!!$F2	3986
1	TraesCS1B01G304200	chr1B	525894612	525895269	657	False	459.000000	459	79.610000	1327	1981	1	chr1B.!!$F1	654
2	TraesCS1B01G304200	chr1B	526428126	526430952	2826	False	213.420000	593	87.173200	486	3670	5	chr1B.!!$F4	3184
3	TraesCS1B01G304200	chr1D	395714534	395715943	1409	False	1447.000000	1447	85.399000	2364	3827	1	chr1D.!!$F1	1463
4	TraesCS1B01G304200	chr1D	395626566	395630556	3990	False	1102.400000	2669	91.946000	24	3987	5	chr1D.!!$F3	3963
5	TraesCS1B01G304200	chr1D	395875046	395878068	3022	False	315.333333	584	82.894333	81	1985	3	chr1D.!!$F4	1904
6	TraesCS1B01G304200	chr1A	489918470	489922995	4525	False	701.375000	2176	90.964250	24	2412	4	chr1A.!!$F2	2388
7	TraesCS1B01G304200	chr1A	490084074	490087781	3707	False	528.666667	1059	88.589333	24	1659	3	chr1A.!!$F4	1635
8	TraesCS1B01G304200	chr1A	490019051	490020649	1598	False	496.500000	612	80.254500	1314	3576	2	chr1A.!!$F3	2262
9	TraesCS1B01G304200	chr1A	490109116	490110707	1591	False	471.500000	568	80.217500	1314	3576	2	chr1A.!!$F5	2262
10	TraesCS1B01G304200	chr1A	489236511	489237078	567	False	457.000000	457	81.371000	1327	1888	1	chr1A.!!$F1	561

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
45	46	0.243365	TGCGTCATGGAAATTGCCAC	59.757	50.000	7.53	41.56	5.01	F
594	1254	1.736645	GCAGCTCGTCTACCGCAAA	60.737	57.895	0.00	36.19	3.68	F
624	1284	2.148916	TCGTCTGCAATCACGTCTTT	57.851	45.000	11.13	37.30	2.52	F
1546	4955	0.687757	CTCGGAGACAGGGGAATGGA	60.688	60.000	0.00	0.00	3.41	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1272	4609	1.376466	GCTCATGTGGGTGTCCAGT	59.624	57.895	0.00	0.00	45.05	4.00	R
1542	4951	1.599047	CAGGACCAGCTCGTTCCAT	59.401	57.895	7.39	0.00	0.00	3.41	R
2518	5988	2.296752	TGCCACAGACATGTTGGATTTG	59.703	45.455	17.52	4.95	37.65	2.32	R
3528	7540	0.952497	ATCAGCTAATCATGCCCGCG	60.952	55.000	0.00	0.00	0.00	6.46	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
19	20	2.169663	GCATGAGAGCGAACATTGTG	57.830	50.000	0.00	0.00	0.00	3.33
20	21	1.792993	GCATGAGAGCGAACATTGTGC	60.793	52.381	0.00	0.00	0.00	4.57
21	22	1.465777	CATGAGAGCGAACATTGTGCA	59.534	47.619	0.00	0.00	0.00	4.57
22	23	1.812235	TGAGAGCGAACATTGTGCAT	58.188	45.000	0.00	0.00	0.00	3.96
45	46	0.243365	TGCGTCATGGAAATTGCCAC	59.757	50.000	7.53	0.00	41.56	5.01
62	63	2.351350	GCCACGTGTCACCATTTTAAGG	60.351	50.000	15.65	0.00	0.00	2.69
77	78	7.231925	ACCATTTTAAGGTTCACTTACGGAATT	59.768	33.333	0.00	0.00	41.24	2.17
111	112	8.966868	CCTTAAAATTATGGAGGCTTCAAAGTA	58.033	33.333	0.00	0.00	31.49	2.24
116	117	9.646522	AAATTATGGAGGCTTCAAAGTATATGT	57.353	29.630	0.00	0.00	0.00	2.29
249	250	9.687210	TGCAGATTCATTCAAATATATTTCTGC	57.313	29.630	24.55	24.55	42.92	4.26
250	251	9.909644	GCAGATTCATTCAAATATATTTCTGCT	57.090	29.630	24.27	9.23	40.49	4.24
269	270	7.587037	TCTGCTTCAATCTATAAAATTGGGG	57.413	36.000	7.36	3.65	35.32	4.96
270	271	6.040842	TCTGCTTCAATCTATAAAATTGGGGC	59.959	38.462	7.36	10.53	35.32	5.80
271	272	5.660417	TGCTTCAATCTATAAAATTGGGGCA	59.340	36.000	15.56	15.56	38.41	5.36
272	273	6.183360	TGCTTCAATCTATAAAATTGGGGCAG	60.183	38.462	15.56	7.55	37.23	4.85
273	274	6.729690	TTCAATCTATAAAATTGGGGCAGG	57.270	37.500	7.36	0.00	35.32	4.85
274	275	5.147032	TCAATCTATAAAATTGGGGCAGGG	58.853	41.667	7.36	0.00	35.32	4.45
275	276	3.611025	TCTATAAAATTGGGGCAGGGG	57.389	47.619	0.00	0.00	0.00	4.79
276	277	2.178984	TCTATAAAATTGGGGCAGGGGG	59.821	50.000	0.00	0.00	0.00	5.40
297	298	3.483808	GGCAACCCCTTTCATTCAAAA	57.516	42.857	0.00	0.00	0.00	2.44
298	299	3.814625	GGCAACCCCTTTCATTCAAAAA	58.185	40.909	0.00	0.00	0.00	1.94
366	367	8.773645	TCATCAACCGACATTTCATTCATATAC	58.226	33.333	0.00	0.00	0.00	1.47
369	370	7.984617	TCAACCGACATTTCATTCATATACAGA	59.015	33.333	0.00	0.00	0.00	3.41
594	1254	1.736645	GCAGCTCGTCTACCGCAAA	60.737	57.895	0.00	0.00	36.19	3.68
624	1284	2.148916	TCGTCTGCAATCACGTCTTT	57.851	45.000	11.13	0.00	37.30	2.52
725	2493	6.501453	TCCCCAATTTGAATCTTTCCTTCAAT	59.499	34.615	0.00	0.00	41.03	2.57
772	4005	2.700773	GGAAGCATTGCCGGTCCAC	61.701	63.158	15.29	0.00	0.00	4.02
1272	4609	3.081409	GGCCACGGCTTCCTCCTA	61.081	66.667	8.20	0.00	41.60	2.94
1542	4951	1.000486	CTCCTCGGAGACAGGGGAA	60.000	63.158	6.58	0.00	44.53	3.97
1546	4955	0.687757	CTCGGAGACAGGGGAATGGA	60.688	60.000	0.00	0.00	0.00	3.41
2349	5773	2.627945	TGTTAGCTATTGCCTTGGTCG	58.372	47.619	0.00	0.00	40.80	4.79
2352	5776	4.141801	TGTTAGCTATTGCCTTGGTCGTAT	60.142	41.667	0.00	0.00	40.80	3.06
2392	5853	6.660949	ACAGCAATTTTTAGAGCTATGTTCCT	59.339	34.615	0.00	0.00	35.19	3.36
2420	5881	5.363005	CCTGGTACACTGTAGCTTAGGTTAT	59.637	44.000	17.19	0.00	0.00	1.89
2425	5886	7.286316	GGTACACTGTAGCTTAGGTTATTCCTA	59.714	40.741	10.57	0.00	46.10	2.94
2461	5922	6.037098	ACGTATTCTCAGTTATGAAGCTGTC	58.963	40.000	0.00	0.00	34.23	3.51
2475	5936	3.567478	AGCTGTCCACTTCTTTTCTGT	57.433	42.857	0.00	0.00	0.00	3.41
2499	5960	9.739276	TGTAACTATTTCTCAAATGGAGTTCAT	57.261	29.630	0.00	0.00	44.40	2.57
2518	5988	4.739793	TCATATGGGGATTTTCATGGGAC	58.260	43.478	2.13	0.00	0.00	4.46
2549	6019	1.541147	TGTCTGTGGCAATAGCTTTGC	59.459	47.619	19.20	19.20	44.22	3.68
2810	6289	2.403252	TTAGCTTCTGGTTGCTAGCC	57.597	50.000	13.29	0.00	41.89	3.93
3098	6602	6.599244	TCATCCACTCACATGTTTAGGATTTC	59.401	38.462	13.42	0.00	32.38	2.17
3269	6947	5.407387	GTCGTCATTGAAGTTAGCCTGTAAA	59.593	40.000	0.00	0.00	0.00	2.01
3277	6955	8.466617	TTGAAGTTAGCCTGTAAATGGTTAAA	57.533	30.769	0.00	0.00	33.29	1.52
3378	7083	9.854668	AGATCTCTGTAGAATGTTAGCTACTTA	57.145	33.333	0.00	0.00	38.21	2.24
3395	7100	5.763698	GCTACTTAAGTTTGTTCCTCCAGTT	59.236	40.000	14.49	0.00	0.00	3.16
3412	7119	3.741344	CCAGTTGTACAGTCTTGTGCTAC	59.259	47.826	0.00	3.17	42.58	3.58
3423	7130	6.320164	ACAGTCTTGTGCTACCAATTTGTAAA	59.680	34.615	0.00	0.00	35.83	2.01
3434	7141	7.817478	GCTACCAATTTGTAAACCTGCTAAAAT	59.183	33.333	0.00	0.00	0.00	1.82
3435	7142	7.961325	ACCAATTTGTAAACCTGCTAAAATG	57.039	32.000	0.00	0.00	0.00	2.32
3439	7146	9.469807	CAATTTGTAAACCTGCTAAAATGTACA	57.530	29.630	0.00	0.00	0.00	2.90
3552	7564	3.748083	GGGCATGATTAGCTGATGAAGA	58.252	45.455	0.00	0.00	0.00	2.87
3553	7565	3.501445	GGGCATGATTAGCTGATGAAGAC	59.499	47.826	0.00	0.00	0.00	3.01
3554	7566	4.132336	GGCATGATTAGCTGATGAAGACA	58.868	43.478	0.00	0.00	0.00	3.41
3555	7567	4.760715	GGCATGATTAGCTGATGAAGACAT	59.239	41.667	0.00	0.00	39.67	3.06
3556	7568	5.936372	GGCATGATTAGCTGATGAAGACATA	59.064	40.000	0.00	0.00	36.82	2.29
3557	7569	6.429078	GGCATGATTAGCTGATGAAGACATAA	59.571	38.462	0.00	0.00	36.82	1.90
3558	7570	7.040892	GGCATGATTAGCTGATGAAGACATAAA	60.041	37.037	0.00	0.00	36.82	1.40
3559	7571	8.016229	GCATGATTAGCTGATGAAGACATAAAG	58.984	37.037	0.00	0.00	36.82	1.85
3560	7572	9.053840	CATGATTAGCTGATGAAGACATAAAGT	57.946	33.333	0.00	0.00	36.82	2.66
3720	7861	5.811613	CACTTTTGAAAAGGACATGCTTTGA	59.188	36.000	20.48	0.00	0.00	2.69
3776	7917	7.260603	GCTCATTCTTTTACATGTGCCTAATT	58.739	34.615	9.11	0.00	35.01	1.40
3838	7979	0.464373	GATGCGTGATGGGTGATGGT	60.464	55.000	0.00	0.00	0.00	3.55
3855	7996	1.644786	GGTGGGACTCGGATTTTGCG	61.645	60.000	0.00	0.00	0.00	4.85
3857	7998	1.078708	GGGACTCGGATTTTGCGGA	60.079	57.895	0.00	0.00	0.00	5.54
3900	8041	6.418141	GTTTTGGGATTTTGATGTTTGTTCG	58.582	36.000	0.00	0.00	0.00	3.95
3915	8056	5.011329	TGTTTGTTCGGACTCCATACTAAGT	59.989	40.000	0.00	0.00	0.00	2.24
3917	8058	6.839124	TTGTTCGGACTCCATACTAAGTAA	57.161	37.500	0.00	0.00	0.00	2.24
3918	8059	6.199937	TGTTCGGACTCCATACTAAGTAAC	57.800	41.667	0.00	0.00	0.00	2.50
3937	8078	3.786101	CACGCTCATCCCTTCGTG	58.214	61.111	0.00	0.00	44.62	4.35
3939	8080	2.892425	CGCTCATCCCTTCGTGGC	60.892	66.667	0.00	0.00	0.00	5.01

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
0	1	1.792993	GCACAATGTTCGCTCTCATGC	60.793	52.381	0.00	0.00	0.00	4.06
5	6	2.294233	ACAAATGCACAATGTTCGCTCT	59.706	40.909	0.00	0.00	0.00	4.09
7	8	2.396601	CACAAATGCACAATGTTCGCT	58.603	42.857	0.00	0.00	0.00	4.93
8	9	2.841070	CACAAATGCACAATGTTCGC	57.159	45.000	0.00	0.00	0.00	4.70
20	21	3.181528	GCAATTTCCATGACGCACAAATG	60.182	43.478	0.00	0.00	0.00	2.32
21	22	2.995258	GCAATTTCCATGACGCACAAAT	59.005	40.909	0.00	0.00	0.00	2.32
22	23	2.402305	GCAATTTCCATGACGCACAAA	58.598	42.857	0.00	0.00	0.00	2.83
45	46	6.017770	TAAGTGAACCTTAAAATGGTGACACG	60.018	38.462	0.00	0.00	43.45	4.49
62	63	6.090783	GGAAAATCCAATTCCGTAAGTGAAC	58.909	40.000	0.00	0.00	37.22	3.18
77	78	7.623278	AGCCTCCATAATTTTAAGGAAAATCCA	59.377	33.333	0.00	0.00	43.10	3.41
111	112	7.792374	ACATCGATTCTTAGTTTGCACATAT	57.208	32.000	0.00	0.00	0.00	1.78
116	117	8.710835	TGTATTACATCGATTCTTAGTTTGCA	57.289	30.769	0.00	0.00	0.00	4.08
243	244	8.477256	CCCCAATTTTATAGATTGAAGCAGAAA	58.523	33.333	10.74	0.00	36.78	2.52
244	245	7.417797	GCCCCAATTTTATAGATTGAAGCAGAA	60.418	37.037	10.74	0.00	36.78	3.02
245	246	6.040842	GCCCCAATTTTATAGATTGAAGCAGA	59.959	38.462	10.74	0.00	36.78	4.26
246	247	6.183360	TGCCCCAATTTTATAGATTGAAGCAG	60.183	38.462	15.59	2.96	37.38	4.24
247	248	5.660417	TGCCCCAATTTTATAGATTGAAGCA	59.340	36.000	15.59	15.59	38.65	3.91
248	249	6.160576	TGCCCCAATTTTATAGATTGAAGC	57.839	37.500	10.74	11.89	36.78	3.86
249	250	6.239402	CCCTGCCCCAATTTTATAGATTGAAG	60.239	42.308	10.74	5.00	36.78	3.02
250	251	5.602145	CCCTGCCCCAATTTTATAGATTGAA	59.398	40.000	10.74	0.00	36.78	2.69
251	252	5.147032	CCCTGCCCCAATTTTATAGATTGA	58.853	41.667	10.74	0.00	36.78	2.57
252	253	4.284234	CCCCTGCCCCAATTTTATAGATTG	59.716	45.833	4.68	4.68	34.93	2.67
253	254	4.492646	CCCCTGCCCCAATTTTATAGATT	58.507	43.478	0.00	0.00	0.00	2.40
254	255	3.181407	CCCCCTGCCCCAATTTTATAGAT	60.181	47.826	0.00	0.00	0.00	1.98
255	256	2.178984	CCCCCTGCCCCAATTTTATAGA	59.821	50.000	0.00	0.00	0.00	1.98
256	257	2.608623	CCCCCTGCCCCAATTTTATAG	58.391	52.381	0.00	0.00	0.00	1.31
257	258	2.785357	CCCCCTGCCCCAATTTTATA	57.215	50.000	0.00	0.00	0.00	0.98
258	259	3.652886	CCCCCTGCCCCAATTTTAT	57.347	52.632	0.00	0.00	0.00	1.40
276	277	1.347062	TTGAATGAAAGGGGTTGCCC	58.653	50.000	0.00	0.00	44.51	5.36
277	278	3.483808	TTTTGAATGAAAGGGGTTGCC	57.516	42.857	0.00	0.00	0.00	4.52
300	301	9.956720	CTAATTCAGTGAGTCATTTTCAGTTTT	57.043	29.630	0.00	0.00	0.00	2.43
301	302	9.342308	TCTAATTCAGTGAGTCATTTTCAGTTT	57.658	29.630	0.00	0.00	0.00	2.66
302	303	8.908786	TCTAATTCAGTGAGTCATTTTCAGTT	57.091	30.769	0.00	0.00	0.00	3.16
314	315	6.312487	TCGTTCGTAGTTCTAATTCAGTGAG	58.688	40.000	0.00	0.00	0.00	3.51
323	324	6.529125	GGTTGATGAATCGTTCGTAGTTCTAA	59.471	38.462	0.00	0.00	0.00	2.10
366	367	1.268234	GCGATTCATTTTCCGCCTCTG	60.268	52.381	0.00	0.00	41.59	3.35
369	370	0.451783	GTGCGATTCATTTTCCGCCT	59.548	50.000	0.00	0.00	46.18	5.52
423	1007	4.832608	CCGACGCAACTAGCCCCC	62.833	72.222	0.00	0.00	41.38	5.40
427	1011	3.188786	CCTGCCGACGCAACTAGC	61.189	66.667	0.00	0.00	46.66	3.42
437	1021	0.749091	CATTGATTGAGCCCTGCCGA	60.749	55.000	0.00	0.00	0.00	5.54
725	2493	2.334946	CCCCGTCTCGTCGTGGTTA	61.335	63.158	0.00	0.00	0.00	2.85
772	4005	1.184970	ATCCCAACCGGCCAACTTTG	61.185	55.000	0.00	0.00	0.00	2.77
900	4169	2.280797	TGTGGCTGGTTCACGAGC	60.281	61.111	5.44	5.44	45.32	5.03
902	4171	2.280797	GCTGTGGCTGGTTCACGA	60.281	61.111	0.00	0.00	37.91	4.35
1272	4609	1.376466	GCTCATGTGGGTGTCCAGT	59.624	57.895	0.00	0.00	45.05	4.00
1398	4783	2.178521	CCGTCGGTCAAGGTCTCG	59.821	66.667	2.08	0.00	0.00	4.04
1423	4826	1.762460	CGTAGGCCTGGGTGAGGAT	60.762	63.158	17.99	0.00	46.33	3.24
1542	4951	1.599047	CAGGACCAGCTCGTTCCAT	59.401	57.895	7.39	0.00	0.00	3.41
1546	4955	2.456287	GAAGGCAGGACCAGCTCGTT	62.456	60.000	8.95	0.46	43.14	3.85
2169	5593	4.092279	TGGAGTCTCATCAACACATCTCT	58.908	43.478	1.47	0.00	0.00	3.10
2199	5623	8.834465	CATGAATTAGACTAAGCAAGTAAGCAT	58.166	33.333	0.73	0.00	39.07	3.79
2200	5624	7.824289	ACATGAATTAGACTAAGCAAGTAAGCA	59.176	33.333	0.00	0.00	39.07	3.91
2201	5625	8.119226	CACATGAATTAGACTAAGCAAGTAAGC	58.881	37.037	0.00	0.00	39.07	3.09
2202	5626	9.155975	ACACATGAATTAGACTAAGCAAGTAAG	57.844	33.333	0.00	0.00	39.07	2.34
2203	5627	8.935844	CACACATGAATTAGACTAAGCAAGTAA	58.064	33.333	0.00	0.00	39.07	2.24
2204	5628	8.094548	ACACACATGAATTAGACTAAGCAAGTA	58.905	33.333	0.00	0.00	39.07	2.24
2205	5629	6.936900	ACACACATGAATTAGACTAAGCAAGT	59.063	34.615	0.00	2.73	42.80	3.16
2206	5630	7.369803	ACACACATGAATTAGACTAAGCAAG	57.630	36.000	0.00	2.16	0.00	4.01
2207	5631	7.744087	AACACACATGAATTAGACTAAGCAA	57.256	32.000	0.00	0.00	0.00	3.91
2392	5853	2.605257	AGCTACAGTGTACCAGGACAA	58.395	47.619	0.00	0.00	0.00	3.18
2437	5898	5.967088	ACAGCTTCATAACTGAGAATACGT	58.033	37.500	0.00	0.00	37.35	3.57
2461	5922	9.273016	TGAGAAATAGTTACAGAAAAGAAGTGG	57.727	33.333	0.00	0.00	0.00	4.00
2499	5960	4.616671	TTGTCCCATGAAAATCCCCATA	57.383	40.909	0.00	0.00	0.00	2.74
2500	5961	3.488355	TTGTCCCATGAAAATCCCCAT	57.512	42.857	0.00	0.00	0.00	4.00
2518	5988	2.296752	TGCCACAGACATGTTGGATTTG	59.703	45.455	17.52	4.95	37.65	2.32
2534	6004	4.666237	CTTTAGAGCAAAGCTATTGCCAC	58.334	43.478	21.98	17.77	45.98	5.01
2849	6328	9.314501	GAACAGAATAGTAACACGAAACAATTC	57.685	33.333	0.00	0.00	0.00	2.17
3127	6796	4.201940	CGCAAGATCATAAAGTGCATGGAA	60.202	41.667	0.00	0.00	43.02	3.53
3269	6947	7.717875	TGCAACACTAACTAGAACTTTAACCAT	59.282	33.333	0.00	0.00	0.00	3.55
3277	6955	4.344102	TCCACTGCAACACTAACTAGAACT	59.656	41.667	0.00	0.00	0.00	3.01
3378	7083	4.850680	TGTACAACTGGAGGAACAAACTT	58.149	39.130	0.00	0.00	0.00	2.66
3380	7085	4.196971	ACTGTACAACTGGAGGAACAAAC	58.803	43.478	0.00	0.00	0.00	2.93
3395	7100	4.617253	ATTGGTAGCACAAGACTGTACA	57.383	40.909	0.00	0.00	33.22	2.90
3412	7119	7.961325	ACATTTTAGCAGGTTTACAAATTGG	57.039	32.000	0.00	0.00	0.00	3.16
3423	7130	6.648879	ACATGTTTGTACATTTTAGCAGGT	57.351	33.333	0.00	0.00	42.29	4.00
3451	7158	5.777449	TCCTAGATGAACAGTCCATCCTAA	58.223	41.667	0.00	0.00	40.85	2.69
3455	7162	6.909550	ATACTCCTAGATGAACAGTCCATC	57.090	41.667	0.00	0.00	40.40	3.51
3463	7170	9.522804	CAGAAAACACTATACTCCTAGATGAAC	57.477	37.037	0.00	0.00	0.00	3.18
3528	7540	0.952497	ATCAGCTAATCATGCCCGCG	60.952	55.000	0.00	0.00	0.00	6.46
3670	7808	9.261180	GAAATGAATAACGAGTTATCATCTGGA	57.739	33.333	8.71	0.00	34.90	3.86
3742	7883	8.680903	ACATGTAAAAGAATGAGCCATAGAAAG	58.319	33.333	0.00	0.00	0.00	2.62
3744	7885	7.415541	GCACATGTAAAAGAATGAGCCATAGAA	60.416	37.037	0.00	0.00	35.24	2.10
3745	7886	6.038603	GCACATGTAAAAGAATGAGCCATAGA	59.961	38.462	0.00	0.00	35.24	1.98
3746	7887	6.204359	GCACATGTAAAAGAATGAGCCATAG	58.796	40.000	0.00	0.00	35.24	2.23
3776	7917	5.544176	AGAAACCTGAGGATAGACACAAGAA	59.456	40.000	4.99	0.00	0.00	2.52
3838	7979	1.376683	CCGCAAAATCCGAGTCCCA	60.377	57.895	0.00	0.00	0.00	4.37
3855	7996	4.089361	ACCCAAACATCTCCAGATTTTCC	58.911	43.478	0.00	0.00	31.21	3.13
3857	7998	6.290605	CAAAACCCAAACATCTCCAGATTTT	58.709	36.000	0.00	0.00	31.21	1.82
3900	8041	4.202090	CGTGGGTTACTTAGTATGGAGTCC	60.202	50.000	0.73	0.73	0.00	3.85
3915	8056	0.539986	GAAGGGATGAGCGTGGGTTA	59.460	55.000	0.00	0.00	0.00	2.85
3917	8058	2.990479	GAAGGGATGAGCGTGGGT	59.010	61.111	0.00	0.00	0.00	4.51
3918	8059	2.202932	CGAAGGGATGAGCGTGGG	60.203	66.667	0.00	0.00	0.00	4.61
3937	8078	0.176449	GGATGCATCCACCTTTTGCC	59.824	55.000	35.93	9.33	46.38	4.52

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.