AutoCloner

Multiple sequence alignment - TraesCS5A01G287600

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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	TraesCS5A01G287600	chr5A	100.000	3040	0	0	1	3040	495360694	495357655	0.000000e+00	5614.0
1	TraesCS5A01G287600	chr5A	89.615	1040	70	18	1115	2142	495339920	495338907	0.000000e+00	1288.0
2	TraesCS5A01G287600	chr5A	89.342	319	25	6	203	514	495399913	495399597	2.840000e-105	392.0
3	TraesCS5A01G287600	chr5A	84.815	270	32	6	1308	1568	495840695	495840426	2.320000e-66	263.0
4	TraesCS5A01G287600	chr5D	94.619	2509	72	23	137	2615	393609529	393607054	0.000000e+00	3827.0
5	TraesCS5A01G287600	chr5D	89.453	1043	75	18	1115	2142	393569984	393568962	0.000000e+00	1284.0
6	TraesCS5A01G287600	chr5D	89.897	584	51	3	1168	1751	393712154	393711579	0.000000e+00	745.0
7	TraesCS5A01G287600	chr5D	93.706	429	24	2	2613	3038	393603386	393602958	9.190000e-180	640.0
8	TraesCS5A01G287600	chr5D	90.385	312	27	1	203	511	393636740	393636429	1.010000e-109	407.0
9	TraesCS5A01G287600	chr5D	85.025	394	44	6	1183	1566	393752901	393752513	1.320000e-103	387.0
10	TraesCS5A01G287600	chr5D	83.019	159	12	6	764	922	393712479	393712336	2.460000e-26	130.0
11	TraesCS5A01G287600	chr5B	90.251	1036	62	12	1154	2162	473291953	473290930	0.000000e+00	1317.0
12	TraesCS5A01G287600	chr5B	88.711	1063	83	14	1079	2134	473468051	473467019	0.000000e+00	1264.0
13	TraesCS5A01G287600	chr5B	88.128	1095	82	15	1079	2157	473448690	473447628	0.000000e+00	1258.0
14	TraesCS5A01G287600	chr5B	86.097	1007	61	33	117	1082	473449715	473448747	0.000000e+00	1011.0
15	TraesCS5A01G287600	chr5B	84.279	1075	64	38	53	1082	473469122	473468108	0.000000e+00	952.0
16	TraesCS5A01G287600	chr5B	85.533	394	42	6	1183	1566	473625833	473625445	6.110000e-107	398.0
17	TraesCS5A01G287600	chr5B	86.090	266	30	4	1308	1566	473454935	473454670	2.310000e-71	279.0
18	TraesCS5A01G287600	chr1B	87.324	568	65	4	2480	3040	646103253	646103820	0.000000e+00	643.0
19	TraesCS5A01G287600	chr1B	87.324	568	65	4	2480	3040	646133303	646133870	0.000000e+00	643.0
20	TraesCS5A01G287600	chr1B	85.211	568	73	6	2480	3038	139363743	139364308	9.450000e-160	573.0
21	TraesCS5A01G287600	chr1B	81.418	522	86	8	2512	3027	647207484	647208000	1.690000e-112	416.0
22	TraesCS5A01G287600	chr2D	84.425	565	76	5	2486	3038	571938814	571939378	2.060000e-151	545.0
23	TraesCS5A01G287600	chr2A	85.417	528	68	6	2518	3038	630463407	630462882	9.590000e-150	540.0
24	TraesCS5A01G287600	chr3A	82.982	570	74	9	2486	3037	74215329	74214765	7.570000e-136	494.0
25	TraesCS5A01G287600	chr3A	78.421	190	25	7	2160	2348	681348263	681348089	3.200000e-20	110.0
26	TraesCS5A01G287600	chr3D	86.022	465	58	7	2570	3032	295147179	295147638	2.720000e-135	492.0
27	TraesCS5A01G287600	chr1A	82.796	186	29	2	2160	2345	503464951	503465133	2.430000e-36	163.0
28	TraesCS5A01G287600	chr2B	74.194	155	38	1	2162	2316	397609895	397609743	2.530000e-06	63.9

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	TraesCS5A01G287600	chr5A	495357655	495360694	3039	True	5614.0	5614	100.0000	1	3040	1	chr5A.!!$R2	3039
1	TraesCS5A01G287600	chr5A	495338907	495339920	1013	True	1288.0	1288	89.6150	1115	2142	1	chr5A.!!$R1	1027
2	TraesCS5A01G287600	chr5D	393602958	393609529	6571	True	2233.5	3827	94.1625	137	3038	2	chr5D.!!$R4	2901
3	TraesCS5A01G287600	chr5D	393568962	393569984	1022	True	1284.0	1284	89.4530	1115	2142	1	chr5D.!!$R1	1027
4	TraesCS5A01G287600	chr5D	393711579	393712479	900	True	437.5	745	86.4580	764	1751	2	chr5D.!!$R5	987
5	TraesCS5A01G287600	chr5B	473290930	473291953	1023	True	1317.0	1317	90.2510	1154	2162	1	chr5B.!!$R1	1008
6	TraesCS5A01G287600	chr5B	473447628	473449715	2087	True	1134.5	1258	87.1125	117	2157	2	chr5B.!!$R4	2040
7	TraesCS5A01G287600	chr5B	473467019	473469122	2103	True	1108.0	1264	86.4950	53	2134	2	chr5B.!!$R5	2081
8	TraesCS5A01G287600	chr1B	646103253	646103820	567	False	643.0	643	87.3240	2480	3040	1	chr1B.!!$F2	560
9	TraesCS5A01G287600	chr1B	646133303	646133870	567	False	643.0	643	87.3240	2480	3040	1	chr1B.!!$F3	560
10	TraesCS5A01G287600	chr1B	139363743	139364308	565	False	573.0	573	85.2110	2480	3038	1	chr1B.!!$F1	558
11	TraesCS5A01G287600	chr1B	647207484	647208000	516	False	416.0	416	81.4180	2512	3027	1	chr1B.!!$F4	515
12	TraesCS5A01G287600	chr2D	571938814	571939378	564	False	545.0	545	84.4250	2486	3038	1	chr2D.!!$F1	552
13	TraesCS5A01G287600	chr2A	630462882	630463407	525	True	540.0	540	85.4170	2518	3038	1	chr2A.!!$R1	520
14	TraesCS5A01G287600	chr3A	74214765	74215329	564	True	494.0	494	82.9820	2486	3037	1	chr3A.!!$R1	551

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
40	41	0.393267	GCCAACGGCCATACCTGTTA	60.393	55.0	2.24	0.0	44.06	2.41	F
605	623	0.729690	GGGAGATCTGACTTTTGCGC	59.270	55.0	0.00	0.0	0.00	6.09	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1547	1714	0.030101	ATGTTTTGTCGTGGCGGTTG	59.97	50.0	0.00	0.0	0.00	3.77	R
2286	2503	0.110373	GATCGGCCACGTCAAAACAC	60.11	55.0	2.24	0.0	41.85	3.32	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	2.045340	GCCAACGGCCATACCTGT	60.045	61.111	2.24	0.00	44.06	4.00
39	40	1.677633	GCCAACGGCCATACCTGTT	60.678	57.895	2.24	0.00	44.06	3.16
40	41	0.393267	GCCAACGGCCATACCTGTTA	60.393	55.000	2.24	0.00	44.06	2.41
41	42	1.951424	GCCAACGGCCATACCTGTTAA	60.951	52.381	2.24	0.00	44.06	2.01
42	43	2.650322	CCAACGGCCATACCTGTTAAT	58.350	47.619	2.24	0.00	34.69	1.40
43	44	3.020984	CCAACGGCCATACCTGTTAATT	58.979	45.455	2.24	0.00	34.69	1.40
44	45	3.066203	CCAACGGCCATACCTGTTAATTC	59.934	47.826	2.24	0.00	34.69	2.17
45	46	2.927028	ACGGCCATACCTGTTAATTCC	58.073	47.619	2.24	0.00	35.61	3.01
46	47	1.871039	CGGCCATACCTGTTAATTCCG	59.129	52.381	2.24	0.00	35.61	4.30
47	48	2.227194	GGCCATACCTGTTAATTCCGG	58.773	52.381	0.00	0.00	34.51	5.14
48	49	2.422377	GGCCATACCTGTTAATTCCGGT	60.422	50.000	0.00	0.00	34.51	5.28
49	50	3.181452	GGCCATACCTGTTAATTCCGGTA	60.181	47.826	0.00	0.00	36.53	4.02
50	51	4.062991	GCCATACCTGTTAATTCCGGTAG	58.937	47.826	0.00	0.00	35.65	3.18
51	52	4.443881	GCCATACCTGTTAATTCCGGTAGT	60.444	45.833	0.00	0.00	35.65	2.73
79	81	5.009610	TGAGACCAAAGCAACTAAATTCCAC	59.990	40.000	0.00	0.00	0.00	4.02
83	85	5.221244	ACCAAAGCAACTAAATTCCACTGAC	60.221	40.000	0.00	0.00	0.00	3.51
84	86	5.221224	CCAAAGCAACTAAATTCCACTGACA	60.221	40.000	0.00	0.00	0.00	3.58
85	87	5.695851	AAGCAACTAAATTCCACTGACAG	57.304	39.130	0.00	0.00	0.00	3.51
86	88	4.973168	AGCAACTAAATTCCACTGACAGA	58.027	39.130	10.08	0.00	0.00	3.41
87	89	5.564550	AGCAACTAAATTCCACTGACAGAT	58.435	37.500	10.08	0.00	0.00	2.90
88	90	6.006449	AGCAACTAAATTCCACTGACAGATT	58.994	36.000	10.08	0.00	0.00	2.40
89	91	6.491403	AGCAACTAAATTCCACTGACAGATTT	59.509	34.615	10.08	7.22	0.00	2.17
90	92	6.803807	GCAACTAAATTCCACTGACAGATTTC	59.196	38.462	10.08	0.00	0.00	2.17
91	93	7.522073	GCAACTAAATTCCACTGACAGATTTCA	60.522	37.037	10.08	0.00	0.00	2.69
115	126	9.941325	TCAATGGTCAAGCAAATATTAATTGTT	57.059	25.926	0.00	0.00	0.00	2.83
119	130	9.941325	TGGTCAAGCAAATATTAATTGTTTCAT	57.059	25.926	0.00	0.00	30.20	2.57
133	144	9.912634	TTAATTGTTTCATTGAGAGATCCAAAC	57.087	29.630	0.00	0.00	0.00	2.93
134	145	6.957920	TTGTTTCATTGAGAGATCCAAACA	57.042	33.333	0.00	0.00	32.01	2.83
137	148	7.428020	TGTTTCATTGAGAGATCCAAACAAAG	58.572	34.615	0.00	0.00	31.18	2.77
147	162	8.242729	AGAGATCCAAACAAAGAAAGAAACAT	57.757	30.769	0.00	0.00	0.00	2.71
155	170	7.992180	AACAAAGAAAGAAACATACAAGCAG	57.008	32.000	0.00	0.00	0.00	4.24
328	343	1.374631	GATGACGCAGCACCAGTCA	60.375	57.895	3.65	3.65	46.99	3.41
605	623	0.729690	GGGAGATCTGACTTTTGCGC	59.270	55.000	0.00	0.00	0.00	6.09
717	738	1.676635	TATATAGACGCGGCGGGCT	60.677	57.895	27.37	23.42	40.44	5.19
809	856	3.441290	CGAGTCGGACCGAGGCTT	61.441	66.667	18.98	3.13	36.23	4.35
844	891	3.030168	ATGTCAGAATCGGGCCGCA	62.030	57.895	23.83	12.19	0.00	5.69
845	892	3.195698	GTCAGAATCGGGCCGCAC	61.196	66.667	23.83	14.59	0.00	5.34
846	893	4.812476	TCAGAATCGGGCCGCACG	62.812	66.667	23.83	9.27	0.00	5.34
929	982	2.208431	AGGACTAACGTAGACGATCGG	58.792	52.381	20.98	3.20	43.02	4.18
1226	1382	3.812262	TGCTAATGGTGATGTCTGGATG	58.188	45.455	0.00	0.00	0.00	3.51
1228	1384	3.181451	GCTAATGGTGATGTCTGGATGGA	60.181	47.826	0.00	0.00	0.00	3.41
1229	1385	4.506271	GCTAATGGTGATGTCTGGATGGAT	60.506	45.833	0.00	0.00	0.00	3.41
1230	1386	4.531357	AATGGTGATGTCTGGATGGATT	57.469	40.909	0.00	0.00	0.00	3.01
1231	1387	4.531357	ATGGTGATGTCTGGATGGATTT	57.469	40.909	0.00	0.00	0.00	2.17
1232	1388	3.623703	TGGTGATGTCTGGATGGATTTG	58.376	45.455	0.00	0.00	0.00	2.32
1233	1389	2.360165	GGTGATGTCTGGATGGATTTGC	59.640	50.000	0.00	0.00	0.00	3.68
1328	1486	1.746615	CTCGGAGTTCGTCCCCGTA	60.747	63.158	0.00	0.00	43.47	4.02
1391	1549	1.733399	GGTCCACGTCAGCTTCGTC	60.733	63.158	10.22	1.46	39.55	4.20
1433	1591	2.672996	AGCAAACGGAGGCGCAAT	60.673	55.556	10.83	0.00	34.54	3.56
1523	1684	1.134487	CGTCGAAACATGCGCCATT	59.866	52.632	4.18	0.00	0.00	3.16
1547	1714	1.014564	GTAAGCAGCGACCACACCTC	61.015	60.000	0.00	0.00	0.00	3.85
2007	2219	5.709164	GCCTTTGATGATAAGCATATGGACT	59.291	40.000	4.56	0.00	37.34	3.85
2008	2220	6.881065	GCCTTTGATGATAAGCATATGGACTA	59.119	38.462	4.56	0.00	37.34	2.59
2074	2286	7.928908	TCAATTTAAACACAATGAAGAGTGC	57.071	32.000	0.00	0.00	39.30	4.40
2108	2320	2.477825	CAAGGCCATGTATCAGACTCG	58.522	52.381	5.01	0.00	0.00	4.18
2193	2410	2.096406	CCACTTTCGCGCGTCATG	59.904	61.111	30.98	21.78	0.00	3.07
2204	2421	1.746727	CGCGTCATGGCTCTCGAAAG	61.747	60.000	0.00	0.00	0.00	2.62
2217	2434	4.327627	GCTCTCGAAAGACCATCACTTTAC	59.672	45.833	0.00	0.00	37.64	2.01
2229	2446	6.560711	ACCATCACTTTACAAAACTTGACAC	58.439	36.000	0.00	0.00	0.00	3.67
2238	2455	3.006323	ACAAAACTTGACACTTTGCACCA	59.994	39.130	0.00	0.00	34.15	4.17
2286	2503	2.993899	ACACTGATCCGTTTTCTAAGCG	59.006	45.455	0.00	0.00	0.00	4.68
2287	2504	2.993899	CACTGATCCGTTTTCTAAGCGT	59.006	45.455	0.00	0.00	0.00	5.07
2357	2574	2.277084	CGCTAACGCCCATTAACTCTT	58.723	47.619	0.00	0.00	0.00	2.85
2369	2586	3.462483	TTAACTCTTGTGTCCGAAGCA	57.538	42.857	0.00	0.00	0.00	3.91
2381	2598	4.147449	GAAGCAATTGGGCCGGCC	62.147	66.667	38.57	38.57	0.00	6.13
2431	2648	3.655777	TCTCCCTCTATCCCTCTTCTCTC	59.344	52.174	0.00	0.00	0.00	3.20
2438	2655	2.118404	CCCTCTTCTCTCTCGCGCT	61.118	63.158	5.56	0.00	0.00	5.92
2496	2718	2.112297	TCGACAAACTGGCCCCAC	59.888	61.111	0.00	0.00	0.00	4.61
2547	2783	1.224069	CTTGTGCGTGTCTCCACCTG	61.224	60.000	0.00	0.00	38.41	4.00
2666	6587	0.517755	CTATCGAGCGCGTAGTCCAT	59.482	55.000	10.30	0.00	38.98	3.41
2810	6735	0.460311	CGGGTGTACTCCTCATGGTC	59.540	60.000	13.44	0.00	34.23	4.02
2844	6772	2.875711	GCGCGCGCATGATGTTTT	60.876	55.556	46.11	0.00	41.49	2.43
2950	6878	2.880890	GCCTTGTCTTATCCGATGCAAT	59.119	45.455	0.00	0.00	0.00	3.56

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
22	23	2.116827	TTAACAGGTATGGCCGTTGG	57.883	50.000	0.77	0.00	43.70	3.77
23	24	3.066203	GGAATTAACAGGTATGGCCGTTG	59.934	47.826	0.77	0.00	43.70	4.10
24	25	3.284617	GGAATTAACAGGTATGGCCGTT	58.715	45.455	0.77	0.00	43.70	4.44
25	26	2.743838	CGGAATTAACAGGTATGGCCGT	60.744	50.000	1.35	1.35	43.70	5.68
26	27	1.871039	CGGAATTAACAGGTATGGCCG	59.129	52.381	0.00	0.00	43.70	6.13
27	28	2.227194	CCGGAATTAACAGGTATGGCC	58.773	52.381	0.00	0.00	37.58	5.36
28	29	2.927028	ACCGGAATTAACAGGTATGGC	58.073	47.619	9.46	0.00	36.66	4.40
29	30	5.054477	CACTACCGGAATTAACAGGTATGG	58.946	45.833	9.46	0.00	39.16	2.74
30	31	5.054477	CCACTACCGGAATTAACAGGTATG	58.946	45.833	9.46	0.00	39.16	2.39
31	32	4.964262	TCCACTACCGGAATTAACAGGTAT	59.036	41.667	9.46	0.00	39.16	2.73
32	33	4.352009	TCCACTACCGGAATTAACAGGTA	58.648	43.478	9.46	0.00	38.98	3.08
33	34	3.175594	TCCACTACCGGAATTAACAGGT	58.824	45.455	9.46	0.00	40.91	4.00
34	35	3.899052	TCCACTACCGGAATTAACAGG	57.101	47.619	9.46	0.00	29.93	4.00
35	36	5.018539	TCATCCACTACCGGAATTAACAG	57.981	43.478	9.46	0.00	38.95	3.16
36	37	4.712829	TCTCATCCACTACCGGAATTAACA	59.287	41.667	9.46	0.00	38.95	2.41
37	38	5.048507	GTCTCATCCACTACCGGAATTAAC	58.951	45.833	9.46	0.00	38.95	2.01
38	39	4.100498	GGTCTCATCCACTACCGGAATTAA	59.900	45.833	9.46	0.00	38.95	1.40
39	40	3.640029	GGTCTCATCCACTACCGGAATTA	59.360	47.826	9.46	0.00	38.95	1.40
40	41	2.434702	GGTCTCATCCACTACCGGAATT	59.565	50.000	9.46	0.00	38.95	2.17
41	42	2.040178	GGTCTCATCCACTACCGGAAT	58.960	52.381	9.46	0.00	38.95	3.01
42	43	1.272816	TGGTCTCATCCACTACCGGAA	60.273	52.381	9.46	0.00	38.95	4.30
43	44	0.333652	TGGTCTCATCCACTACCGGA	59.666	55.000	9.46	0.00	40.07	5.14
44	45	1.191535	TTGGTCTCATCCACTACCGG	58.808	55.000	0.00	0.00	37.20	5.28
45	46	2.893637	CTTTGGTCTCATCCACTACCG	58.106	52.381	0.00	0.00	37.20	4.02
46	47	2.027192	TGCTTTGGTCTCATCCACTACC	60.027	50.000	0.00	0.00	37.20	3.18
47	48	3.334583	TGCTTTGGTCTCATCCACTAC	57.665	47.619	0.00	0.00	37.20	2.73
48	49	3.327757	AGTTGCTTTGGTCTCATCCACTA	59.672	43.478	0.00	0.00	37.20	2.74
49	50	2.107204	AGTTGCTTTGGTCTCATCCACT	59.893	45.455	0.00	0.00	37.20	4.00
50	51	2.508526	AGTTGCTTTGGTCTCATCCAC	58.491	47.619	0.00	0.00	37.20	4.02
51	52	2.957402	AGTTGCTTTGGTCTCATCCA	57.043	45.000	0.00	0.00	35.49	3.41
79	81	4.216902	TGCTTGACCATTGAAATCTGTCAG	59.783	41.667	0.00	0.00	37.27	3.51
83	85	8.712285	AATATTTGCTTGACCATTGAAATCTG	57.288	30.769	0.00	0.00	0.00	2.90
88	90	9.941325	ACAATTAATATTTGCTTGACCATTGAA	57.059	25.926	0.00	0.00	0.00	2.69
89	91	9.941325	AACAATTAATATTTGCTTGACCATTGA	57.059	25.926	0.00	0.00	0.00	2.57
115	126	7.822161	TTCTTTGTTTGGATCTCTCAATGAA	57.178	32.000	0.00	5.50	33.29	2.57
119	130	7.880160	TTCTTTCTTTGTTTGGATCTCTCAA	57.120	32.000	0.00	0.00	0.00	3.02
133	144	5.403466	GCCTGCTTGTATGTTTCTTTCTTTG	59.597	40.000	0.00	0.00	0.00	2.77
134	145	5.068987	TGCCTGCTTGTATGTTTCTTTCTTT	59.931	36.000	0.00	0.00	0.00	2.52
137	148	4.503741	TGCCTGCTTGTATGTTTCTTTC	57.496	40.909	0.00	0.00	0.00	2.62
147	162	2.038426	TGCTCTAGTTTGCCTGCTTGTA	59.962	45.455	0.00	0.00	0.00	2.41
155	170	1.639298	CGTGCCTGCTCTAGTTTGCC	61.639	60.000	0.00	0.00	0.00	4.52
328	343	1.344942	GCGACGACAACTGCTTCGAT	61.345	55.000	0.00	0.00	38.63	3.59
560	578	3.777925	CAAGAGCAACGACGGCGG	61.778	66.667	18.49	0.00	43.17	6.13
605	623	1.932511	GCAAAAGCCAGATCTCTCTCG	59.067	52.381	0.00	0.00	0.00	4.04
661	679	1.301637	CCACGCCACTCATCACACA	60.302	57.895	0.00	0.00	0.00	3.72
809	856	0.673333	CATGTACCGCTCAACAGCCA	60.673	55.000	0.00	0.00	43.56	4.75
844	891	1.593296	GAAGCAGGGGAGACGTACGT	61.593	60.000	23.04	23.04	0.00	3.57
845	892	1.139095	GAAGCAGGGGAGACGTACG	59.861	63.158	15.01	15.01	0.00	3.67
846	893	1.255667	TGGAAGCAGGGGAGACGTAC	61.256	60.000	0.00	0.00	0.00	3.67
847	894	0.325296	ATGGAAGCAGGGGAGACGTA	60.325	55.000	0.00	0.00	0.00	3.57
929	982	2.163815	TGCCTCTCTTCTGTAACGCTAC	59.836	50.000	0.00	0.00	0.00	3.58
1226	1382	0.179092	GCTCCCTGCAATGCAAATCC	60.179	55.000	9.92	0.00	38.41	3.01
1228	1384	1.514087	CGCTCCCTGCAATGCAAAT	59.486	52.632	9.92	0.00	43.06	2.32
1229	1385	2.964174	CGCTCCCTGCAATGCAAA	59.036	55.556	9.92	0.00	43.06	3.68
1230	1386	3.751246	GCGCTCCCTGCAATGCAA	61.751	61.111	9.92	0.00	43.06	4.08
1233	1389	3.869272	GTCGCGCTCCCTGCAATG	61.869	66.667	5.56	0.00	43.06	2.82
1391	1549	1.205485	CGATCTTCTTCCTGCGAGCG	61.205	60.000	0.00	0.00	0.00	5.03
1523	1684	0.101759	GTGGTCGCTGCTTACCGATA	59.898	55.000	14.00	0.00	38.70	2.92
1547	1714	0.030101	ATGTTTTGTCGTGGCGGTTG	59.970	50.000	0.00	0.00	0.00	3.77
1673	1858	0.992802	GCGACGATTTCTCTGTGGAC	59.007	55.000	0.00	0.00	0.00	4.02
1805	1990	5.181245	CAGGTTCGTGAAATGTATGAAACCT	59.819	40.000	0.00	0.00	32.45	3.50
1861	2046	1.133976	CCTCCTTATTGCCTGGTCCAG	60.134	57.143	12.40	12.40	0.00	3.86
1872	2057	1.813092	CGCTGCTGCATCCTCCTTATT	60.813	52.381	16.29	0.00	39.64	1.40
1873	2058	0.250209	CGCTGCTGCATCCTCCTTAT	60.250	55.000	16.29	0.00	39.64	1.73
1874	2059	1.144716	CGCTGCTGCATCCTCCTTA	59.855	57.895	16.29	0.00	39.64	2.69
2007	2219	3.261897	GCTAGCTTTGCCCCTGATCTATA	59.738	47.826	7.70	0.00	0.00	1.31
2008	2220	2.039613	GCTAGCTTTGCCCCTGATCTAT	59.960	50.000	7.70	0.00	0.00	1.98
2074	2286	4.085357	TGGCCTTGCTATTACCATACAG	57.915	45.455	3.32	0.00	0.00	2.74
2108	2320	8.498054	TCTCATACATCAACTTCAAAATCTCC	57.502	34.615	0.00	0.00	0.00	3.71
2165	2382	1.130561	GCGAAAGTGGTGGTTCTATGC	59.869	52.381	0.00	0.00	0.00	3.14
2193	2410	1.205893	AGTGATGGTCTTTCGAGAGCC	59.794	52.381	0.00	3.99	35.63	4.70
2204	2421	6.691388	GTGTCAAGTTTTGTAAAGTGATGGTC	59.309	38.462	0.00	0.00	0.00	4.02
2217	2434	3.367630	GTGGTGCAAAGTGTCAAGTTTTG	59.632	43.478	0.00	2.81	35.47	2.44
2280	2497	1.659211	GCCACGTCAAAACACGCTTAG	60.659	52.381	0.00	0.00	43.93	2.18
2282	2499	1.063488	GCCACGTCAAAACACGCTT	59.937	52.632	0.00	0.00	43.93	4.68
2286	2503	0.110373	GATCGGCCACGTCAAAACAC	60.110	55.000	2.24	0.00	41.85	3.32
2287	2504	1.561717	CGATCGGCCACGTCAAAACA	61.562	55.000	7.38	0.00	41.85	2.83
2342	2559	2.423577	GACACAAGAGTTAATGGGCGT	58.576	47.619	0.00	0.00	0.00	5.68
2357	2574	1.523154	GCCCAATTGCTTCGGACACA	61.523	55.000	0.00	0.00	0.00	3.72
2381	2598	1.142748	GTGAGCGATGGGAGTGAGG	59.857	63.158	0.00	0.00	0.00	3.86
2450	2667	4.554036	GGATCCGGAGCTGCCACC	62.554	72.222	20.86	5.45	35.94	4.61
2496	2718	1.760268	GAAGAAGCTGCTCCGCATCG	61.760	60.000	1.00	0.00	38.13	3.84
2507	2729	2.940527	GCAGCATGAGGAAGAAGAAGCT	60.941	50.000	0.00	0.00	39.69	3.74
2750	6671	2.196749	CATTGATCGAGAACCTGGTCG	58.803	52.381	0.00	0.00	37.54	4.79
2840	6766	3.007635	ACCAGCGTTGCTATCCTAAAAC	58.992	45.455	0.00	0.00	36.40	2.43
2844	6772	1.191535	ACACCAGCGTTGCTATCCTA	58.808	50.000	0.00	0.00	36.40	2.94
2950	6878	0.669619	CTTCATTGCGCCATGGCATA	59.330	50.000	34.93	20.77	43.52	3.14

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.