AutoCloner

Multiple sequence alignment - TraesCS2D01G109700

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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	TraesCS2D01G109700	chr2D	100.000	4475	0	0	1	4475	60794254	60789780	0.000000e+00	8264.0
1	TraesCS2D01G109700	chr2B	96.316	3692	96	20	815	4475	95545160	95541478	0.000000e+00	6028.0
2	TraesCS2D01G109700	chr2B	86.174	622	66	9	1	614	95554287	95553678	0.000000e+00	654.0
3	TraesCS2D01G109700	chr2B	89.706	136	8	6	696	827	95550851	95550718	7.700000e-38	169.0
4	TraesCS2D01G109700	chr2A	94.508	2713	75	17	1773	4440	61385918	61383235	0.000000e+00	4117.0
5	TraesCS2D01G109700	chr2A	85.649	1526	127	42	25	1514	61387685	61386216	0.000000e+00	1520.0
6	TraesCS2D01G109700	chr2A	87.556	225	12	3	1568	1776	61386212	61385988	3.460000e-61	246.0
7	TraesCS2D01G109700	chr2A	96.429	56	2	0	3312	3367	61353634	61353579	4.770000e-15	93.5
8	TraesCS2D01G109700	chr3B	88.158	760	72	7	2734	3476	775476506	775475748	0.000000e+00	889.0
9	TraesCS2D01G109700	chr3B	84.633	436	42	12	2231	2659	775477400	775476983	1.160000e-110	411.0
10	TraesCS2D01G109700	chr3B	79.000	300	47	10	1237	1525	775478006	775477712	1.640000e-44	191.0
11	TraesCS2D01G109700	chr3D	87.615	654	64	7	2734	3371	580331760	580331108	0.000000e+00	743.0
12	TraesCS2D01G109700	chr3D	85.321	436	39	12	2231	2659	580332860	580332443	1.150000e-115	427.0
13	TraesCS2D01G109700	chr3D	79.412	306	44	9	1238	1532	580333451	580333154	9.820000e-47	198.0
14	TraesCS2D01G109700	chr3D	89.189	111	10	2	3368	3477	580330949	580330840	2.170000e-28	137.0
15	TraesCS2D01G109700	chr3A	83.131	824	106	14	2674	3476	715646541	715645730	0.000000e+00	721.0
16	TraesCS2D01G109700	chr3A	90.415	313	18	5	2231	2538	715647484	715647179	6.970000e-108	401.0
17	TraesCS2D01G109700	chr3A	82.812	256	26	5	1170	1407	715648143	715647888	3.510000e-51	213.0
18	TraesCS2D01G109700	chr4A	90.974	421	28	7	1	413	534181351	534181769	3.910000e-155	558.0
19	TraesCS2D01G109700	chr4A	85.992	514	44	14	987	1495	534200173	534200663	3.970000e-145	525.0
20	TraesCS2D01G109700	chr4A	91.892	111	5	2	889	996	534182563	534182672	7.750000e-33	152.0
21	TraesCS2D01G109700	chr7D	89.091	110	10	2	4358	4467	18405142	18405035	7.810000e-28	135.0
22	TraesCS2D01G109700	chr5B	76.395	233	32	11	4219	4436	419614609	419614833	2.200000e-18	104.0
23	TraesCS2D01G109700	chr5B	90.411	73	6	1	4218	4290	484833376	484833305	1.330000e-15	95.3
24	TraesCS2D01G109700	chr6D	84.694	98	13	2	4218	4314	461497248	461497152	3.680000e-16	97.1
25	TraesCS2D01G109700	chr6A	73.810	252	52	9	4212	4459	186279975	186280216	2.220000e-13	87.9
26	TraesCS2D01G109700	chr5A	88.462	52	5	1	4218	4268	505488837	505488786	1.340000e-05	62.1

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	TraesCS2D01G109700	chr2D	60789780	60794254	4474	True	8264.00	8264	100.000000	1	4475	1	chr2D.!!$R1	4474
1	TraesCS2D01G109700	chr2B	95541478	95545160	3682	True	6028.00	6028	96.316000	815	4475	1	chr2B.!!$R1	3660
2	TraesCS2D01G109700	chr2B	95550718	95554287	3569	True	411.50	654	87.940000	1	827	2	chr2B.!!$R2	826
3	TraesCS2D01G109700	chr2A	61383235	61387685	4450	True	1961.00	4117	89.237667	25	4440	3	chr2A.!!$R2	4415
4	TraesCS2D01G109700	chr3B	775475748	775478006	2258	True	497.00	889	83.930333	1237	3476	3	chr3B.!!$R1	2239
5	TraesCS2D01G109700	chr3D	580330840	580333451	2611	True	376.25	743	85.384250	1238	3477	4	chr3D.!!$R1	2239
6	TraesCS2D01G109700	chr3A	715645730	715648143	2413	True	445.00	721	85.452667	1170	3476	3	chr3A.!!$R1	2306
7	TraesCS2D01G109700	chr4A	534181351	534182672	1321	False	355.00	558	91.433000	1	996	2	chr4A.!!$F2	995

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
473	1053	0.032017	TTGTCTCCTCCTCCTAGCCC	60.032	60.0	0.00	0.00	0.00	5.19	F
1060	4411	0.037303	CCTGCTTTCCTCCTCTGCAA	59.963	55.0	0.00	0.00	33.07	4.08	F
1539	4923	0.514255	CAGTGAATATGCGCATCCGG	59.486	55.0	29.11	7.82	34.32	5.14	F
1545	4929	0.961019	ATATGCGCATCCGGCAATTT	59.039	45.0	29.11	1.29	44.66	1.82	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1347	4716	1.423921	AGTGTCCAGATTTTCCCCGTT	59.576	47.619	0.00	0.00	0.00	4.44	R
1946	5422	2.919666	ATTCACGGCGAAATTTCTGG	57.080	45.000	16.62	7.39	37.12	3.86	R
2550	6255	7.926018	ACATTTTTAAGTTCGCAGGAAGAAATT	59.074	29.630	0.00	0.00	38.98	1.82	R
3671	8189	4.600012	AACGTCAGCACTGCATAAATAC	57.400	40.909	3.30	0.00	0.00	1.89	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
27	29	2.086610	AGCCAACACATGTCCCTTTT	57.913	45.000	0.00	0.00	0.00	2.27
31	33	2.597455	CAACACATGTCCCTTTTCCCT	58.403	47.619	0.00	0.00	0.00	4.20
82	84	1.671901	CCGTTGGCCAAAACACACCT	61.672	55.000	22.47	0.00	0.00	4.00
204	213	6.471942	TTCCCCAAGGTTTTAAGAAGGATA	57.528	37.500	0.00	0.00	0.00	2.59
205	214	6.074698	TCCCCAAGGTTTTAAGAAGGATAG	57.925	41.667	0.00	0.00	0.00	2.08
326	335	8.598202	TTTCAGTACCAGTGGTATGATAACTA	57.402	34.615	24.66	10.79	40.54	2.24
366	376	2.172293	AGAAGATGGCTGGATGTTCCTC	59.828	50.000	0.00	0.00	37.46	3.71
378	389	0.250858	TGTTCCTCTGCCATGTGGTG	60.251	55.000	0.35	0.00	37.57	4.17
404	415	1.063642	TGACGAGGAGATCATCAGGGT	60.064	52.381	0.00	0.00	0.00	4.34
405	416	2.174854	TGACGAGGAGATCATCAGGGTA	59.825	50.000	0.00	0.00	0.00	3.69
434	445	1.714899	CCAACATCGATCCCAACCGC	61.715	60.000	0.00	0.00	0.00	5.68
473	1053	0.032017	TTGTCTCCTCCTCCTAGCCC	60.032	60.000	0.00	0.00	0.00	5.19
476	1056	2.698788	TCCTCCTCCTAGCCCCGA	60.699	66.667	0.00	0.00	0.00	5.14
500	1083	1.002134	CCGGCTCATCCCTGTTGTT	60.002	57.895	0.00	0.00	0.00	2.83
527	1110	1.224075	CGCTCGTCTCCGTTATCCTA	58.776	55.000	0.00	0.00	35.01	2.94
539	1122	4.581824	TCCGTTATCCTACGCTCAAATAGT	59.418	41.667	0.00	0.00	40.10	2.12
549	1132	4.855531	ACGCTCAAATAGTTGTTGTTTCC	58.144	39.130	2.43	0.00	36.07	3.13
553	1136	5.682943	TCAAATAGTTGTTGTTTCCCTCG	57.317	39.130	2.43	0.00	36.07	4.63
557	1140	2.835027	AGTTGTTGTTTCCCTCGTCTC	58.165	47.619	0.00	0.00	0.00	3.36
563	1146	0.733223	GTTTCCCTCGTCTCTGTCGC	60.733	60.000	0.00	0.00	0.00	5.19
569	1152	1.088306	CTCGTCTCTGTCGCCTAGTT	58.912	55.000	0.00	0.00	0.00	2.24
575	1158	0.803117	TCTGTCGCCTAGTTGTCTCG	59.197	55.000	0.00	0.00	0.00	4.04
585	1168	0.531974	AGTTGTCTCGCCGCTCAAAA	60.532	50.000	0.00	0.00	0.00	2.44
587	1170	1.069227	GTTGTCTCGCCGCTCAAAATT	60.069	47.619	0.00	0.00	0.00	1.82
588	1171	0.516877	TGTCTCGCCGCTCAAAATTG	59.483	50.000	0.00	0.00	0.00	2.32
614	1197	2.748465	GCAAACCAACCACCTCTACACT	60.748	50.000	0.00	0.00	0.00	3.55
659	3471	2.268920	CCTGTGCCAGTACCGCAT	59.731	61.111	8.35	0.00	38.76	4.73
685	3497	4.042809	TGACAAATGTGTGGATTAGGACCT	59.957	41.667	0.00	0.00	38.41	3.85
736	4065	2.119029	GGGGACGGTTTATGCAGGC	61.119	63.158	0.00	0.00	0.00	4.85
738	4067	1.077716	GGACGGTTTATGCAGGCCT	60.078	57.895	0.00	0.00	0.00	5.19
780	4112	6.090763	CGTACAAGACATATGTGCTTTCTTCA	59.909	38.462	14.43	0.00	32.10	3.02
829	4166	6.040504	GGTAAATGTTCTTTCCTTCAACTGGT	59.959	38.462	0.00	0.00	0.00	4.00
835	4172	1.133363	TTCCTTCAACTGGTCCGGAA	58.867	50.000	5.23	0.00	0.00	4.30
836	4173	1.133363	TCCTTCAACTGGTCCGGAAA	58.867	50.000	5.23	0.00	0.00	3.13
837	4174	1.202722	TCCTTCAACTGGTCCGGAAAC	60.203	52.381	5.23	2.37	0.00	2.78
838	4175	1.202770	CCTTCAACTGGTCCGGAAACT	60.203	52.381	5.23	0.00	0.00	2.66
839	4176	2.038033	CCTTCAACTGGTCCGGAAACTA	59.962	50.000	5.23	0.00	0.00	2.24
841	4178	2.600790	TCAACTGGTCCGGAAACTAGA	58.399	47.619	5.23	0.00	32.53	2.43
842	4179	2.298163	TCAACTGGTCCGGAAACTAGAC	59.702	50.000	5.23	0.00	32.53	2.59
843	4180	2.299297	CAACTGGTCCGGAAACTAGACT	59.701	50.000	5.23	0.00	32.53	3.24
844	4181	3.446442	ACTGGTCCGGAAACTAGACTA	57.554	47.619	5.23	0.00	32.53	2.59
845	4182	3.087781	ACTGGTCCGGAAACTAGACTAC	58.912	50.000	5.23	0.00	32.53	2.73
847	4184	3.762823	CTGGTCCGGAAACTAGACTACTT	59.237	47.826	5.23	0.00	33.27	2.24
866	4207	3.005791	ACTTTCTTTGGGCCATTTCTTCG	59.994	43.478	7.26	0.00	0.00	3.79
867	4208	0.887933	TCTTTGGGCCATTTCTTCGC	59.112	50.000	7.26	0.00	0.00	4.70
1056	4407	0.620121	CCTCCCTGCTTTCCTCCTCT	60.620	60.000	0.00	0.00	0.00	3.69
1057	4408	0.540923	CTCCCTGCTTTCCTCCTCTG	59.459	60.000	0.00	0.00	0.00	3.35
1059	4410	1.681666	CCTGCTTTCCTCCTCTGCA	59.318	57.895	0.00	0.00	0.00	4.41
1060	4411	0.037303	CCTGCTTTCCTCCTCTGCAA	59.963	55.000	0.00	0.00	33.07	4.08
1061	4412	1.340795	CCTGCTTTCCTCCTCTGCAAT	60.341	52.381	0.00	0.00	33.07	3.56
1062	4413	2.444421	CTGCTTTCCTCCTCTGCAATT	58.556	47.619	0.00	0.00	33.07	2.32
1250	4619	4.653004	GAGGTCGCTCTTGCTTTTTAATC	58.347	43.478	0.00	0.00	36.97	1.75
1255	4624	6.092259	GGTCGCTCTTGCTTTTTAATCTCTAA	59.908	38.462	0.00	0.00	36.97	2.10
1273	4642	7.938140	TCTCTAACCCATGTTTTAATCAAGG	57.062	36.000	0.00	0.00	35.87	3.61
1320	4689	6.695713	GTGTTGTTCCTTATGGTTTCTTGTTC	59.304	38.462	0.00	0.00	34.23	3.18
1411	4783	2.161211	GCTTTGCTGGTCAGTGAATCTC	59.839	50.000	0.00	0.00	0.00	2.75
1419	4793	5.152623	TGGTCAGTGAATCTCTTGGTTAG	57.847	43.478	0.00	0.00	0.00	2.34
1422	4796	4.859798	GTCAGTGAATCTCTTGGTTAGTCG	59.140	45.833	0.00	0.00	0.00	4.18
1443	4817	5.639506	GTCGGTGCTATACATAGATGCATTT	59.360	40.000	0.00	0.00	36.04	2.32
1496	4876	1.069022	TGCTTTCTGTTCAGCATTCGC	60.069	47.619	0.00	0.00	41.20	4.70
1539	4923	0.514255	CAGTGAATATGCGCATCCGG	59.486	55.000	29.11	7.82	34.32	5.14
1545	4929	0.961019	ATATGCGCATCCGGCAATTT	59.039	45.000	29.11	1.29	44.66	1.82
1562	4946	6.322491	GGCAATTTCAGTAAGAGCGTTAAAT	58.678	36.000	0.00	0.00	0.00	1.40
1563	4947	6.806739	GGCAATTTCAGTAAGAGCGTTAAATT	59.193	34.615	0.00	0.00	0.00	1.82
1721	5121	5.895636	TGACATGACATAAATGTGTTCCC	57.104	39.130	0.00	0.00	41.95	3.97
1785	5258	6.290605	TGAGCTATGCAAGTATATTGCTGAA	58.709	36.000	13.19	0.00	45.13	3.02
1946	5422	5.458779	ACATGTTTCTTAAGCGCTGTTTTTC	59.541	36.000	12.58	0.00	0.00	2.29
1948	5424	4.142359	TGTTTCTTAAGCGCTGTTTTTCCA	60.142	37.500	12.58	0.36	0.00	3.53
2550	6255	7.093024	CCTTTCTATGTACTTCTTAACCAGGGA	60.093	40.741	0.00	0.00	0.00	4.20
2577	6282	5.997385	TCTTCCTGCGAACTTAAAAATGTC	58.003	37.500	0.00	0.00	0.00	3.06
3592	8110	3.981071	TGGTTGTTCAGACAGATAGGG	57.019	47.619	0.00	0.00	37.04	3.53
3754	8272	4.463891	GTGATTGTTGGGGATCAGAATTGT	59.536	41.667	0.00	0.00	33.27	2.71
3829	8347	2.281970	CAGTGCAGAGCCTGGCAA	60.282	61.111	22.65	0.00	42.45	4.52
4098	8616	6.672147	AGACATCAAACTATGAAACACAAGC	58.328	36.000	0.00	0.00	42.54	4.01
4255	8785	7.409449	GCGACAAACATAGTCTAGCATAATACG	60.409	40.741	0.00	0.00	33.89	3.06
4343	8873	9.606631	AAAATAAAAGTGCTGATACAAAAACCA	57.393	25.926	0.00	0.00	0.00	3.67
4394	8924	3.004944	GGCGTAAGTCATTTTGTCCCAAA	59.995	43.478	0.00	0.00	45.31	3.28
4395	8925	4.500035	GGCGTAAGTCATTTTGTCCCAAAA	60.500	41.667	4.76	4.76	45.31	2.44
4443	8974	4.588528	ACCATGTATGTTGCCAAGAAGTTT	59.411	37.500	0.00	0.00	0.00	2.66
4447	8978	7.655328	CCATGTATGTTGCCAAGAAGTTTAAAA	59.345	33.333	0.00	0.00	0.00	1.52

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
27	29	7.070322	GGTACTTTCTACCATTGTGTATAGGGA	59.930	40.741	0.00	0.00	37.53	4.20
31	33	7.983166	AGGGTACTTTCTACCATTGTGTATA	57.017	36.000	0.00	0.00	39.31	1.47
179	184	5.330233	TCCTTCTTAAAACCTTGGGGAATC	58.670	41.667	0.00	0.00	36.25	2.52
182	191	5.793763	TCTATCCTTCTTAAAACCTTGGGGA	59.206	40.000	0.00	0.00	36.25	4.81
240	249	4.368969	TGACCACCTAGACCTCTAGTAGA	58.631	47.826	8.27	0.00	43.34	2.59
300	309	7.913789	AGTTATCATACCACTGGTACTGAAAA	58.086	34.615	10.28	6.19	41.31	2.29
309	318	6.323996	TGAACCTCTAGTTATCATACCACTGG	59.676	42.308	0.00	0.00	39.40	4.00
320	329	6.497259	TCTGAACCACTTGAACCTCTAGTTAT	59.503	38.462	0.00	0.00	39.40	1.89
326	335	3.309296	TCTCTGAACCACTTGAACCTCT	58.691	45.455	0.00	0.00	0.00	3.69
366	376	0.389296	CATTGTGCACCACATGGCAG	60.389	55.000	15.69	0.00	44.16	4.85
378	389	2.299993	TGATCTCCTCGTCATTGTGC	57.700	50.000	0.00	0.00	0.00	4.57
404	415	0.038067	CGATGTTGGTGGTCCACGTA	60.038	55.000	15.93	4.74	44.22	3.57
405	416	1.301401	CGATGTTGGTGGTCCACGT	60.301	57.895	15.93	0.00	44.22	4.49
448	459	2.476199	AGGAGGAGGAGACAATTGAGG	58.524	52.381	13.59	0.00	0.00	3.86
476	1056	4.115199	GGGATGAGCCGGGTTGCT	62.115	66.667	8.00	0.00	46.37	3.91
480	1060	2.610859	AACAGGGATGAGCCGGGT	60.611	61.111	5.45	5.45	37.63	5.28
484	1064	2.489938	TACAACAACAGGGATGAGCC	57.510	50.000	0.00	0.00	0.00	4.70
500	1083	2.704108	GGAGACGAGCGGAGATACA	58.296	57.895	0.00	0.00	0.00	2.29
527	1110	4.261447	GGGAAACAACAACTATTTGAGCGT	60.261	41.667	0.00	0.00	36.48	5.07
539	1122	2.169769	ACAGAGACGAGGGAAACAACAA	59.830	45.455	0.00	0.00	0.00	2.83
549	1132	0.745128	ACTAGGCGACAGAGACGAGG	60.745	60.000	0.00	0.00	0.00	4.63
553	1136	1.813786	AGACAACTAGGCGACAGAGAC	59.186	52.381	0.00	0.00	0.00	3.36
557	1140	0.798771	GCGAGACAACTAGGCGACAG	60.799	60.000	0.00	0.00	0.00	3.51
563	1146	1.226717	GAGCGGCGAGACAACTAGG	60.227	63.158	12.98	0.00	0.00	3.02
569	1152	0.516877	CAATTTTGAGCGGCGAGACA	59.483	50.000	12.98	3.75	0.00	3.41
575	1158	1.154035	CCGGACAATTTTGAGCGGC	60.154	57.895	0.00	0.00	0.00	6.53
585	1168	0.757188	TGGTTGGTTTGCCGGACAAT	60.757	50.000	5.05	0.00	38.31	2.71
587	1170	2.122167	GTGGTTGGTTTGCCGGACA	61.122	57.895	5.05	0.00	37.67	4.02
588	1171	2.725641	GTGGTTGGTTTGCCGGAC	59.274	61.111	5.05	0.00	37.67	4.79
659	3471	5.647658	GTCCTAATCCACACATTTGTCATCA	59.352	40.000	0.00	0.00	31.66	3.07
685	3497	6.855763	ACAAGATTAAAATCATGCCCTCAA	57.144	33.333	7.62	0.00	37.57	3.02
696	3508	8.490311	TCCCCAAAAACAGAACAAGATTAAAAT	58.510	29.630	0.00	0.00	0.00	1.82
803	4137	6.447162	CAGTTGAAGGAAAGAACATTTACCC	58.553	40.000	0.00	0.00	0.00	3.69
813	4150	1.071699	CCGGACCAGTTGAAGGAAAGA	59.928	52.381	0.00	0.00	0.00	2.52
819	4156	2.256117	AGTTTCCGGACCAGTTGAAG	57.744	50.000	1.83	0.00	0.00	3.02
829	4166	6.453092	CAAAGAAAGTAGTCTAGTTTCCGGA	58.547	40.000	26.36	0.00	45.06	5.14
835	4172	4.349930	TGGCCCAAAGAAAGTAGTCTAGTT	59.650	41.667	0.00	0.00	0.00	2.24
836	4173	3.908103	TGGCCCAAAGAAAGTAGTCTAGT	59.092	43.478	0.00	0.00	0.00	2.57
837	4174	4.553330	TGGCCCAAAGAAAGTAGTCTAG	57.447	45.455	0.00	0.00	0.00	2.43
838	4175	5.514500	AATGGCCCAAAGAAAGTAGTCTA	57.486	39.130	0.00	0.00	0.00	2.59
839	4176	4.388577	AATGGCCCAAAGAAAGTAGTCT	57.611	40.909	0.00	0.00	0.00	3.24
841	4178	4.740902	AGAAATGGCCCAAAGAAAGTAGT	58.259	39.130	0.00	0.00	0.00	2.73
842	4179	5.619981	CGAAGAAATGGCCCAAAGAAAGTAG	60.620	44.000	0.00	0.00	0.00	2.57
843	4180	4.217550	CGAAGAAATGGCCCAAAGAAAGTA	59.782	41.667	0.00	0.00	0.00	2.24
844	4181	3.005791	CGAAGAAATGGCCCAAAGAAAGT	59.994	43.478	0.00	0.00	0.00	2.66
845	4182	3.578688	CGAAGAAATGGCCCAAAGAAAG	58.421	45.455	0.00	0.00	0.00	2.62
847	4184	1.272212	GCGAAGAAATGGCCCAAAGAA	59.728	47.619	0.00	0.00	0.00	2.52
866	4207	5.334957	GCTTAAGAAAGTAGTCCAGTTTGGC	60.335	44.000	6.67	0.00	34.62	4.52
867	4208	5.181433	GGCTTAAGAAAGTAGTCCAGTTTGG	59.819	44.000	6.67	0.00	35.39	3.28
1056	4407	0.965363	GGCGGGAAGAGGAAATTGCA	60.965	55.000	0.00	0.00	0.00	4.08
1057	4408	1.667154	GGGCGGGAAGAGGAAATTGC	61.667	60.000	0.00	0.00	0.00	3.56
1059	4410	0.631212	ATGGGCGGGAAGAGGAAATT	59.369	50.000	0.00	0.00	0.00	1.82
1060	4411	0.106519	CATGGGCGGGAAGAGGAAAT	60.107	55.000	0.00	0.00	0.00	2.17
1061	4412	1.302949	CATGGGCGGGAAGAGGAAA	59.697	57.895	0.00	0.00	0.00	3.13
1062	4413	2.998097	CATGGGCGGGAAGAGGAA	59.002	61.111	0.00	0.00	0.00	3.36
1218	4569	1.956629	GAGCGACCTCGAATTGGGGA	61.957	60.000	0.00	0.00	43.02	4.81
1250	4619	7.703058	ACCTTGATTAAAACATGGGTTAGAG	57.297	36.000	16.39	0.00	35.82	2.43
1255	4624	6.739331	TTCAACCTTGATTAAAACATGGGT	57.261	33.333	16.39	10.68	37.00	4.51
1273	4642	1.668047	GCAGCAACATGAGGCTTCAAC	60.668	52.381	1.33	0.00	38.56	3.18
1320	4689	2.743752	CGGGAGCTGCACAATCACG	61.744	63.158	7.79	0.00	32.98	4.35
1347	4716	1.423921	AGTGTCCAGATTTTCCCCGTT	59.576	47.619	0.00	0.00	0.00	4.44
1411	4783	4.380841	TGTATAGCACCGACTAACCAAG	57.619	45.455	0.00	0.00	0.00	3.61
1419	4793	4.174411	TGCATCTATGTATAGCACCGAC	57.826	45.455	0.00	0.00	0.00	4.79
1446	4820	6.855914	CGCTAACTTTTTCAGTCATTAAAGCA	59.144	34.615	0.00	0.00	32.94	3.91
1496	4876	4.645588	CCCTAGTCTAACTGAGGGTAACAG	59.354	50.000	10.86	0.00	43.32	3.16
1539	4923	7.796958	AATTTAACGCTCTTACTGAAATTGC	57.203	32.000	0.00	0.00	0.00	3.56
1574	4958	4.330250	CCACCAGTCAATGATCAGAAAGT	58.670	43.478	0.09	0.00	0.00	2.66
1721	5121	5.123979	CCCAGCATCATCATCAACATATCAG	59.876	44.000	0.00	0.00	0.00	2.90
1946	5422	2.919666	ATTCACGGCGAAATTTCTGG	57.080	45.000	16.62	7.39	37.12	3.86
1948	5424	5.622770	AAACTATTCACGGCGAAATTTCT	57.377	34.783	16.62	0.00	37.12	2.52
2550	6255	7.926018	ACATTTTTAAGTTCGCAGGAAGAAATT	59.074	29.630	0.00	0.00	38.98	1.82
3671	8189	4.600012	AACGTCAGCACTGCATAAATAC	57.400	40.909	3.30	0.00	0.00	1.89
3754	8272	3.417101	ACGCCAACAATCTGTTTATCCA	58.583	40.909	0.00	0.00	38.77	3.41
3829	8347	2.169978	GAGCTACGGGTAGAATTTGGGT	59.830	50.000	9.94	0.00	35.21	4.51
3886	8404	6.362248	ACAGTTGGTACTATTTCCTTGTGTT	58.638	36.000	0.00	0.00	31.96	3.32
3984	8502	4.753610	GCTGATGCTCTCTGTTTATATGCA	59.246	41.667	0.00	0.00	36.03	3.96
4084	8602	5.182001	AGCTAAAGTGGCTTGTGTTTCATAG	59.818	40.000	0.00	0.00	36.56	2.23
4098	8616	9.502091	TTTGCAATATAGGTATAGCTAAAGTGG	57.498	33.333	15.25	6.28	0.00	4.00
4255	8785	8.942924	CATTTTGTTCCGAAACTTTAAAAATGC	58.057	29.630	7.49	0.00	37.74	3.56
4317	8847	9.606631	TGGTTTTTGTATCAGCACTTTTATTTT	57.393	25.926	0.00	0.00	0.00	1.82
4343	8873	4.630940	CCAAGCAAAAACGCCATTATTCAT	59.369	37.500	0.00	0.00	0.00	2.57
4394	8924	9.826574	TCTAGCATAATACTCACGGTAAAAATT	57.173	29.630	0.00	0.00	33.74	1.82
4395	8925	9.257651	GTCTAGCATAATACTCACGGTAAAAAT	57.742	33.333	0.00	0.00	33.74	1.82

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.