AutoCloner

Multiple sequence alignment - TraesCS7A01G435300

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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	TraesCS7A01G435300	chr7A	100.000	5192	0	0	1	5192	628868273	628863082	0.000000e+00	9588.0
1	TraesCS7A01G435300	chr7A	88.399	1974	227	2	1082	3054	628653234	628655206	0.000000e+00	2375.0
2	TraesCS7A01G435300	chr7A	87.003	1762	218	6	1116	2875	594452613	594454365	0.000000e+00	1975.0
3	TraesCS7A01G435300	chr7A	87.079	1455	183	5	1572	3024	169952411	169950960	0.000000e+00	1640.0
4	TraesCS7A01G435300	chr7A	82.609	253	28	14	4504	4744	628839814	628839566	5.270000e-50	209.0
5	TraesCS7A01G435300	chr7A	83.251	203	21	7	4215	4417	628863859	628863670	1.920000e-39	174.0
6	TraesCS7A01G435300	chr7A	83.251	203	21	7	4415	4604	628864059	628863857	1.920000e-39	174.0
7	TraesCS7A01G435300	chr7D	95.373	5209	186	24	1	5192	546130939	546125769	0.000000e+00	8233.0
8	TraesCS7A01G435300	chr7D	94.216	2645	130	7	421	3054	545659442	545662074	0.000000e+00	4015.0
9	TraesCS7A01G435300	chr7D	87.738	1941	234	4	1116	3054	545654853	545656791	0.000000e+00	2263.0
10	TraesCS7A01G435300	chr7D	93.082	318	22	0	2558	2875	518779182	518779499	2.830000e-127	466.0
11	TraesCS7A01G435300	chr7D	83.744	203	20	5	4215	4417	546126532	546126343	4.130000e-41	180.0
12	TraesCS7A01G435300	chr7D	84.699	183	18	6	4415	4587	546126730	546126548	1.920000e-39	174.0
13	TraesCS7A01G435300	chr7B	93.796	4852	230	28	390	5192	590108180	590103351	0.000000e+00	7227.0
14	TraesCS7A01G435300	chr7B	85.527	1907	268	8	1121	3023	589899260	589901162	0.000000e+00	1986.0
15	TraesCS7A01G435300	chr7B	86.606	1538	203	3	1095	2630	589939952	589941488	0.000000e+00	1696.0
16	TraesCS7A01G435300	chr7B	92.214	411	31	1	2644	3054	589942917	589943326	9.690000e-162	580.0
17	TraesCS7A01G435300	chr7B	89.759	332	12	9	21	342	590108510	590108191	6.260000e-109	405.0
18	TraesCS7A01G435300	chr6B	80.662	786	145	6	3322	4102	156526628	156525845	2.070000e-168	603.0
19	TraesCS7A01G435300	chr6B	78.672	919	181	13	3272	4181	156373775	156372863	9.620000e-167	597.0
20	TraesCS7A01G435300	chr6A	78.703	925	182	12	3272	4187	98062712	98061794	2.070000e-168	603.0
21	TraesCS7A01G435300	chr6A	78.846	832	168	7	3331	4157	98247690	98246862	5.870000e-154	555.0
22	TraesCS7A01G435300	chr6D	78.587	892	180	10	3272	4156	81671633	81670746	3.490000e-161	579.0
23	TraesCS7A01G435300	chr6D	79.537	821	161	6	3287	4102	81757449	81756631	3.490000e-161	579.0
24	TraesCS7A01G435300	chr6D	78.311	876	183	6	3287	4157	81761680	81760807	4.540000e-155	558.0
25	TraesCS7A01G435300	chr6D	80.000	180	28	5	4240	4418	456825287	456825459	5.460000e-25	126.0
26	TraesCS7A01G435300	chr1B	82.514	183	26	3	4240	4421	305536840	305536663	6.960000e-34	156.0
27	TraesCS7A01G435300	chr3B	78.689	183	31	5	4240	4421	738623539	738623364	1.180000e-21	115.0
28	TraesCS7A01G435300	chr1D	77.778	180	32	5	4240	4418	482244495	482244667	2.560000e-18	104.0
29	TraesCS7A01G435300	chr1A	88.608	79	9	0	4240	4318	301862265	301862187	4.280000e-16	97.1

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	TraesCS7A01G435300	chr7A	628863082	628868273	5191	True	9588.0	9588	100.0000	1	5192	1	chr7A.!!$R3	5191
1	TraesCS7A01G435300	chr7A	628653234	628655206	1972	False	2375.0	2375	88.3990	1082	3054	1	chr7A.!!$F2	1972
2	TraesCS7A01G435300	chr7A	594452613	594454365	1752	False	1975.0	1975	87.0030	1116	2875	1	chr7A.!!$F1	1759
3	TraesCS7A01G435300	chr7A	169950960	169952411	1451	True	1640.0	1640	87.0790	1572	3024	1	chr7A.!!$R1	1452
4	TraesCS7A01G435300	chr7D	546125769	546130939	5170	True	8233.0	8233	95.3730	1	5192	1	chr7D.!!$R1	5191
5	TraesCS7A01G435300	chr7D	545654853	545662074	7221	False	3139.0	4015	90.9770	421	3054	2	chr7D.!!$F2	2633
6	TraesCS7A01G435300	chr7B	590103351	590108510	5159	True	3816.0	7227	91.7775	21	5192	2	chr7B.!!$R1	5171
7	TraesCS7A01G435300	chr7B	589899260	589901162	1902	False	1986.0	1986	85.5270	1121	3023	1	chr7B.!!$F1	1902
8	TraesCS7A01G435300	chr7B	589939952	589943326	3374	False	1138.0	1696	89.4100	1095	3054	2	chr7B.!!$F2	1959
9	TraesCS7A01G435300	chr6B	156525845	156526628	783	True	603.0	603	80.6620	3322	4102	1	chr6B.!!$R2	780
10	TraesCS7A01G435300	chr6B	156372863	156373775	912	True	597.0	597	78.6720	3272	4181	1	chr6B.!!$R1	909
11	TraesCS7A01G435300	chr6A	98061794	98062712	918	True	603.0	603	78.7030	3272	4187	1	chr6A.!!$R1	915
12	TraesCS7A01G435300	chr6A	98246862	98247690	828	True	555.0	555	78.8460	3331	4157	1	chr6A.!!$R2	826
13	TraesCS7A01G435300	chr6D	81670746	81671633	887	True	579.0	579	78.5870	3272	4156	1	chr6D.!!$R1	884
14	TraesCS7A01G435300	chr6D	81756631	81761680	5049	True	568.5	579	78.9240	3287	4157	2	chr6D.!!$R2	870

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
388	402	0.028902	ATTTTCTTATTCCGCGCGCC	59.971	50.0	27.36	8.11	0.00	6.53	F
1214	1268	0.105224	AACGTGTCATGGGTGAACGA	59.895	50.0	14.92	0.00	39.23	3.85	F
1719	7056	0.170561	GCTCCATGCTGAAAGTGCTG	59.829	55.0	0.00	0.00	38.95	4.41	F
3387	14372	0.811616	GCTGCGGAGGTAATGGTCTG	60.812	60.0	5.93	0.00	0.00	3.51	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Hairpin	End Stability	Orientation
1272	1326	1.004560	TCTGGAAGGCAGCAAGACG	60.005	57.895	0.00	0.00	4.18	R
3114	9868	0.962356	AGAACAGAATGGCAAGCCCG	60.962	55.000	8.89	43.62	6.13	R
3408	14393	0.471591	TGGCAAGCTTGGGTCCATTT	60.472	50.000	27.10	0.00	2.32	R
4594	15587	1.098712	GCGTGTCAACCCACTTTCCA	61.099	55.000	0.00	33.07	3.53	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
38	39	1.081509	CAATCAAACCACGCACCCG	60.082	57.895	0.00	0.00	41.14	5.28
55	61	1.127817	CGCACACATCAACGACGTC	59.872	57.895	5.18	5.18	0.00	4.34
85	91	5.963004	GCGACGTTAATCATTGATTGCTTTA	59.037	36.000	19.81	0.00	33.95	1.85
112	118	1.528586	GATCAGATTATGTGCGCGCTT	59.471	47.619	33.29	18.43	0.00	4.68
116	122	1.528586	AGATTATGTGCGCGCTTCATC	59.471	47.619	32.32	24.40	0.00	2.92
250	256	1.964373	GACGCCCGCCTTTCTTTCA	60.964	57.895	0.00	0.00	0.00	2.69
260	266	3.976942	CGCCTTTCTTTCACTGTTCAATG	59.023	43.478	0.00	0.00	0.00	2.82
273	284	6.547141	TCACTGTTCAATGATGAAAGAAACCT	59.453	34.615	0.00	0.00	46.66	3.50
388	402	0.028902	ATTTTCTTATTCCGCGCGCC	59.971	50.000	27.36	8.11	0.00	6.53
428	442	1.869767	CGGCTATCAAGTCAATGGCTC	59.130	52.381	0.00	0.00	31.85	4.70
438	452	3.942829	AGTCAATGGCTCTCGATTTTCA	58.057	40.909	0.00	0.00	0.00	2.69
461	475	2.222796	CGGTGACATGCAAATACTGACG	60.223	50.000	0.00	0.00	0.00	4.35
541	577	8.087303	TGAGCCAGAAAGATATGCATAGATAT	57.913	34.615	12.79	0.00	0.00	1.63
542	578	9.205513	TGAGCCAGAAAGATATGCATAGATATA	57.794	33.333	12.79	0.00	0.00	0.86
544	580	9.999660	AGCCAGAAAGATATGCATAGATATATG	57.000	33.333	12.79	2.86	0.00	1.78
605	641	2.733956	TCAACACCAACTTCCAAAGCT	58.266	42.857	0.00	0.00	0.00	3.74
683	729	2.811431	TGGACTTTTGCATACCAGAACG	59.189	45.455	0.00	0.00	0.00	3.95
684	730	3.071479	GGACTTTTGCATACCAGAACGA	58.929	45.455	0.00	0.00	0.00	3.85
685	731	3.500680	GGACTTTTGCATACCAGAACGAA	59.499	43.478	0.00	0.00	0.00	3.85
686	732	4.464112	GACTTTTGCATACCAGAACGAAC	58.536	43.478	0.00	0.00	0.00	3.95
766	815	2.620108	GCAGCATTCTCCTTTTCCTCCT	60.620	50.000	0.00	0.00	0.00	3.69
767	816	3.277715	CAGCATTCTCCTTTTCCTCCTC	58.722	50.000	0.00	0.00	0.00	3.71
768	817	3.054508	CAGCATTCTCCTTTTCCTCCTCT	60.055	47.826	0.00	0.00	0.00	3.69
848	897	0.107654	GTCCATAGCGCCTCACCTTT	60.108	55.000	2.29	0.00	0.00	3.11
853	902	2.196997	TAGCGCCTCACCTTTGCCAT	62.197	55.000	2.29	0.00	0.00	4.40
861	910	3.575687	CCTCACCTTTGCCATTTTTCTCT	59.424	43.478	0.00	0.00	0.00	3.10
914	966	4.299547	TGCTCTGCGCCACGAACT	62.300	61.111	4.18	0.00	38.05	3.01
1038	1092	2.425592	TGCCGTAGCAGCAACAGT	59.574	55.556	0.00	0.00	46.52	3.55
1060	1114	1.931172	GATACACCACCAAATCGTCCG	59.069	52.381	0.00	0.00	0.00	4.79
1062	1116	1.963855	CACCACCAAATCGTCCGCA	60.964	57.895	0.00	0.00	0.00	5.69
1093	1147	4.947147	TTGTCGCTGCCGCCCTTT	62.947	61.111	0.00	0.00	0.00	3.11
1101	1155	2.985847	GCCGCCCTTTTGCTCTGT	60.986	61.111	0.00	0.00	0.00	3.41
1114	1168	1.215647	CTCTGTTTCGTCTCCCCGG	59.784	63.158	0.00	0.00	0.00	5.73
1117	1171	4.772687	GTTTCGTCTCCCCGGCCC	62.773	72.222	0.00	0.00	0.00	5.80
1214	1268	0.105224	AACGTGTCATGGGTGAACGA	59.895	50.000	14.92	0.00	39.23	3.85
1282	1336	2.355837	TCACGGACGTCTTGCTGC	60.356	61.111	16.46	0.00	0.00	5.25
1302	1356	0.823460	CTTCCAGAGGTCTCAGAGGC	59.177	60.000	0.00	0.00	0.00	4.70
1318	1372	3.532155	GCCTCGTCTCGCCATCCT	61.532	66.667	0.00	0.00	0.00	3.24
1356	1410	2.345244	CTGCGCCTCAACCTGTCT	59.655	61.111	4.18	0.00	0.00	3.41
1448	1502	2.511600	CAACCGCCTCGATGGTCC	60.512	66.667	4.80	0.00	37.54	4.46
1622	6959	6.426328	GGACAAATACCATCTTCTATCTGCAG	59.574	42.308	7.63	7.63	0.00	4.41
1719	7056	0.170561	GCTCCATGCTGAAAGTGCTG	59.829	55.000	0.00	0.00	38.95	4.41
1809	7147	4.082125	AGCTCTCCTTACCCAACAATTTG	58.918	43.478	0.00	0.00	0.00	2.32
2185	7523	5.786311	CTTTCAATCAATTTCAAGGCCAGA	58.214	37.500	5.01	0.00	0.00	3.86
3114	9868	2.007608	GGATTAGGTGTGTTCTTCGGC	58.992	52.381	0.00	0.00	0.00	5.54
3387	14372	0.811616	GCTGCGGAGGTAATGGTCTG	60.812	60.000	5.93	0.00	0.00	3.51
3402	14387	2.173782	TGGTCTGGTTTACAAGGCAGAA	59.826	45.455	0.00	0.00	0.00	3.02
3507	14492	1.885850	ACTCACCGTGGCGAAACAC	60.886	57.895	0.00	0.00	37.99	3.32
3750	14738	2.746362	CAAGTCCAGCAACATCCTTCTC	59.254	50.000	0.00	0.00	0.00	2.87
3972	14960	0.898789	TCGAGGTCCTGTCCAAGTCC	60.899	60.000	0.00	0.00	0.00	3.85
4093	15081	1.949525	TGAAGGTGCTTGAAGTTGCTC	59.050	47.619	0.00	0.00	0.00	4.26
4187	15175	0.586802	GTGAACCTGCAGACGGAAAC	59.413	55.000	17.39	1.85	0.00	2.78
4263	15251	7.317722	AGGTGTAAACTGAGTAGAAGGATTT	57.682	36.000	0.00	0.00	0.00	2.17
4296	15284	2.212652	TCGTACAGTCGTGTGTGTAGT	58.787	47.619	0.00	0.00	37.52	2.73
4392	15382	3.069443	TGGAAACATTTCAGCTCCAAACC	59.931	43.478	6.68	0.00	38.92	3.27
4400	15390	2.114411	GCTCCAAACCCGGTTCCA	59.886	61.111	2.46	0.00	0.00	3.53
4546	15538	7.807977	ACGAGACCATATATTCAATTTTGCT	57.192	32.000	0.00	0.00	0.00	3.91
4588	15581	2.670148	GCTCCAGACCCCGTTCCAT	61.670	63.158	0.00	0.00	0.00	3.41
4594	15587	2.106511	CCAGACCCCGTTCCATGATTAT	59.893	50.000	0.00	0.00	0.00	1.28
4611	15604	4.764823	TGATTATGGAAAGTGGGTTGACAC	59.235	41.667	0.00	0.00	41.63	3.67
4689	15683	8.644318	AATTCATCTTCATTTATTTGAGCTGC	57.356	30.769	0.00	0.00	0.00	5.25
4700	15694	2.745492	GAGCTGCCTCAGTGCACC	60.745	66.667	14.63	0.00	38.03	5.01
4724	15718	3.558505	CGAGAACAATCCTGCAAAACAG	58.441	45.455	0.00	0.00	46.77	3.16
4740	15734	2.276732	ACAGAGTGGGAACATGTTGG	57.723	50.000	17.58	0.00	46.14	3.77
4750	15744	2.287915	GGAACATGTTGGTATGCTAGCG	59.712	50.000	17.58	0.00	0.00	4.26
4790	15789	3.536498	GAAAGGCGCACAACGTGGG	62.536	63.158	10.83	6.80	46.85	4.61
4811	15810	3.412386	GAAGTCCAACATTACAGCACCT	58.588	45.455	0.00	0.00	0.00	4.00
4836	15835	6.456501	AGTTGACTAGTTGTTCCTATGACAC	58.543	40.000	0.00	0.00	0.00	3.67
4839	15838	5.047306	TGACTAGTTGTTCCTATGACACTGG	60.047	44.000	0.00	0.00	0.00	4.00
4893	15892	4.017177	GGCTTTACCAAGTCCTAACTGT	57.983	45.455	0.00	0.00	38.86	3.55
4910	15909	0.901827	TGTTGCCATCGGAGAGCTAA	59.098	50.000	0.00	0.00	43.63	3.09
4924	15923	5.393135	CGGAGAGCTAATTTCAGTACTGTGA	60.393	44.000	21.99	12.31	0.00	3.58
5102	16114	0.248702	GCACCGCACCGAAAGAAAAA	60.249	50.000	0.00	0.00	0.00	1.94
5133	16145	4.552378	CGGCAACAACAACCAAATCAAATG	60.552	41.667	0.00	0.00	0.00	2.32
5149	16161	5.036117	TCAAATGCCTAGGGTATCAAGTC	57.964	43.478	11.72	0.00	0.00	3.01

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
3	4	1.172180	TTGCTCAACTCAAAGGCGGG	61.172	55.000	0.00	0.00	0.00	6.13
38	39	1.491563	GGACGTCGTTGATGTGTGC	59.508	57.895	9.92	0.00	31.35	4.57
61	67	3.940303	AGCAATCAATGATTAACGTCGC	58.060	40.909	8.29	6.86	30.44	5.19
85	91	5.290400	CGCGCACATAATCTGATCTGATAAT	59.710	40.000	14.70	4.12	0.00	1.28
112	118	3.122480	TGGAGCTTATCTTTGGGGATGA	58.878	45.455	0.00	0.00	0.00	2.92
116	122	3.019564	CACTTGGAGCTTATCTTTGGGG	58.980	50.000	0.00	0.00	0.00	4.96
250	256	6.736794	GCAGGTTTCTTTCATCATTGAACAGT	60.737	38.462	0.00	0.00	41.50	3.55
260	266	4.074970	TGAGAAGGCAGGTTTCTTTCATC	58.925	43.478	0.00	0.00	35.14	2.92
273	284	0.607489	GCCTCTTTGCTGAGAAGGCA	60.607	55.000	17.05	0.00	38.61	4.75
388	402	2.128035	GTTGATAGAATCTCACCGCGG	58.872	52.381	26.86	26.86	0.00	6.46
399	413	5.592104	TGACTTGATAGCCGTTGATAGAA	57.408	39.130	0.00	0.00	0.00	2.10
428	442	1.790755	TGTCACCGGTGAAAATCGAG	58.209	50.000	37.75	7.73	41.85	4.04
438	452	2.083774	CAGTATTTGCATGTCACCGGT	58.916	47.619	0.00	0.00	0.00	5.28
461	475	9.659830	CAAACTGTAAACTATCAACAACTTACC	57.340	33.333	0.00	0.00	0.00	2.85
542	578	9.635520	GTATAATAATTCACCAGCTACGTACAT	57.364	33.333	0.00	0.00	0.00	2.29
543	579	7.804600	CGTATAATAATTCACCAGCTACGTACA	59.195	37.037	0.00	0.00	0.00	2.90
544	580	7.272084	CCGTATAATAATTCACCAGCTACGTAC	59.728	40.741	0.00	0.00	0.00	3.67
605	641	1.283905	TGTCTAGGATCTCGTCACCCA	59.716	52.381	0.00	0.00	0.00	4.51
766	815	1.810151	GCGTGTTTTTCAGCCCATAGA	59.190	47.619	0.00	0.00	0.00	1.98
767	816	1.812571	AGCGTGTTTTTCAGCCCATAG	59.187	47.619	0.00	0.00	0.00	2.23
768	817	1.904287	AGCGTGTTTTTCAGCCCATA	58.096	45.000	0.00	0.00	0.00	2.74
848	897	3.157087	GTTCCCTCAGAGAAAAATGGCA	58.843	45.455	0.00	0.00	0.00	4.92
853	902	1.142060	TGCCGTTCCCTCAGAGAAAAA	59.858	47.619	0.00	0.00	0.00	1.94
861	910	4.020617	CTGCCTGCCGTTCCCTCA	62.021	66.667	0.00	0.00	0.00	3.86
914	966	1.378382	CAACCACCATGGGCGATGA	60.378	57.895	18.09	0.00	43.37	2.92
941	993	2.799371	CGCTACTCGGACCCTGAC	59.201	66.667	0.00	0.00	33.78	3.51
1034	1088	4.222145	ACGATTTGGTGGTGTATCTACTGT	59.778	41.667	0.00	0.00	0.00	3.55
1038	1092	3.181484	CGGACGATTTGGTGGTGTATCTA	60.181	47.826	0.00	0.00	0.00	1.98
1062	1116	4.250305	ACAAGGCTGGCGAACGGT	62.250	61.111	0.00	0.00	0.00	4.83
1093	1147	0.034896	GGGGAGACGAAACAGAGCAA	59.965	55.000	0.00	0.00	0.00	3.91
1214	1268	1.968017	CATTGGCAGCAGTCCGTGT	60.968	57.895	0.00	0.00	0.00	4.49
1269	1323	2.035442	GGAAGGCAGCAAGACGTCC	61.035	63.158	13.01	1.54	46.90	4.79
1272	1326	1.004560	TCTGGAAGGCAGCAAGACG	60.005	57.895	0.00	0.00	0.00	4.18
1302	1356	1.066587	GAAGGATGGCGAGACGAGG	59.933	63.158	0.00	0.00	0.00	4.63
1318	1372	2.186903	GCCAGGAAGATCGCCGAA	59.813	61.111	0.00	0.00	0.00	4.30
1356	1410	2.355756	GCTGCCTTCAAGCGAATTATGA	59.644	45.455	0.00	0.00	34.65	2.15
1459	1513	1.475034	GCCGGTATCTGAGGATTGCAA	60.475	52.381	0.00	0.00	33.71	4.08
1622	6959	2.028925	CAAACAAGGGGGCGTTGC	59.971	61.111	0.00	0.00	33.25	4.17
1635	6972	4.045636	ACAAAGGTCAAGCATGTCAAAC	57.954	40.909	0.00	0.00	0.00	2.93
1809	7147	3.445096	AGCCATCAATAACTCCTTGCAAC	59.555	43.478	0.00	0.00	0.00	4.17
2544	7883	2.907042	AGCTGGTATATCCCCTGTAAGC	59.093	50.000	0.00	0.00	34.77	3.09
3114	9868	0.962356	AGAACAGAATGGCAAGCCCG	60.962	55.000	8.89	0.00	43.62	6.13
3387	14372	2.706555	GCAGTTCTGCCTTGTAAACC	57.293	50.000	13.11	0.00	0.00	3.27
3402	14387	1.187567	GCTTGGGTCCATTTGGCAGT	61.188	55.000	0.00	0.00	34.44	4.40
3408	14393	0.471591	TGGCAAGCTTGGGTCCATTT	60.472	50.000	27.10	0.00	0.00	2.32
3507	14492	2.002586	CATAGAGGCACAAGGTTGTCG	58.997	52.381	0.00	0.00	39.91	4.35
3750	14738	6.414408	ACATAAGCTTTGAAATCTCTGTCG	57.586	37.500	3.20	0.00	0.00	4.35
3972	14960	1.133792	ACCCACTGGACAAGTTCCTTG	60.134	52.381	0.00	2.54	46.10	3.61
4093	15081	6.861065	AGGATTATGGTTTATACACTTGCG	57.139	37.500	0.00	0.00	0.00	4.85
4181	15169	7.379529	TCTGTTCTACTTTTAACTACGTTTCCG	59.620	37.037	0.00	0.00	40.83	4.30
4187	15175	9.286946	CCTGTATCTGTTCTACTTTTAACTACG	57.713	37.037	0.00	0.00	0.00	3.51
4263	15251	6.361481	CACGACTGTACGATCTGTTAGAAAAA	59.639	38.462	0.00	0.00	37.03	1.94
4277	15265	2.286595	ACACTACACACACGACTGTACG	60.287	50.000	0.00	0.00	39.31	3.67
4392	15382	1.810959	TTCCGTAATTGTGGAACCGG	58.189	50.000	0.00	0.00	39.29	5.28
4400	15390	7.033185	GCAAGAATACCATTTTCCGTAATTGT	58.967	34.615	0.00	0.00	0.00	2.71
4523	15515	9.520204	AAAAGCAAAATTGAATATATGGTCTCG	57.480	29.630	0.00	0.00	0.00	4.04
4554	15547	2.622942	TGGAGCTGAAATGTTTCCACAC	59.377	45.455	0.00	0.00	35.03	3.82
4588	15581	4.764823	GTGTCAACCCACTTTCCATAATCA	59.235	41.667	0.00	0.00	32.50	2.57
4594	15587	1.098712	GCGTGTCAACCCACTTTCCA	61.099	55.000	0.00	0.00	33.07	3.53
4689	15683	1.536073	TTCTCGGAGGTGCACTGAGG	61.536	60.000	17.98	4.53	40.11	3.86
4700	15694	2.099141	TTGCAGGATTGTTCTCGGAG	57.901	50.000	0.00	0.00	0.00	4.63
4724	15718	2.423538	GCATACCAACATGTTCCCACTC	59.576	50.000	8.48	0.00	0.00	3.51
4740	15734	6.648725	ATCGAAATTATTCCGCTAGCATAC	57.351	37.500	16.45	0.00	31.52	2.39
4750	15744	9.928236	CTTTCTCAGAGAAATCGAAATTATTCC	57.072	33.333	23.24	0.00	42.66	3.01
4786	15780	2.488153	GCTGTAATGTTGGACTTCCCAC	59.512	50.000	0.00	0.00	46.62	4.61
4790	15789	3.412386	AGGTGCTGTAATGTTGGACTTC	58.588	45.455	0.00	0.00	0.00	3.01
4811	15810	7.450634	AGTGTCATAGGAACAACTAGTCAACTA	59.549	37.037	0.00	0.00	0.00	2.24
4836	15835	4.582869	TGTGGTCTCAGAAATGAATCCAG	58.417	43.478	0.00	0.00	0.00	3.86
4839	15838	6.549952	GTGATTGTGGTCTCAGAAATGAATC	58.450	40.000	0.00	0.00	29.78	2.52
4893	15892	3.206150	GAAATTAGCTCTCCGATGGCAA	58.794	45.455	0.00	0.00	0.00	4.52
4910	15909	7.550551	CACCTCATATTGTCACAGTACTGAAAT	59.449	37.037	29.30	21.14	0.00	2.17
4948	15947	2.613133	GTGCTCTGGAATCTGAATCTGC	59.387	50.000	0.00	0.00	0.00	4.26
5102	16114	1.943116	TTGTTGTTGCCGCTGCTGTT	61.943	50.000	0.70	0.00	38.71	3.16
5112	16124	4.281264	GCATTTGATTTGGTTGTTGTTGC	58.719	39.130	0.00	0.00	0.00	4.17
5115	16127	4.420522	AGGCATTTGATTTGGTTGTTGT	57.579	36.364	0.00	0.00	0.00	3.32
5133	16145	3.243670	GGTAACGACTTGATACCCTAGGC	60.244	52.174	2.05	0.00	39.47	3.93

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.