AutoCloner

Multiple sequence alignment - TraesCS2D01G535100

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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	TraesCS2D01G535100	chr2D	100.000	3251	0	0	1	3251	618289590	618286340	0.000000e+00	6004.0
1	TraesCS2D01G535100	chr2D	82.706	1249	205	10	1010	2251	5747603	5748847	0.000000e+00	1099.0
2	TraesCS2D01G535100	chr2D	90.588	85	8	0	2582	2666	481141110	481141194	2.650000e-21	113.0
3	TraesCS2D01G535100	chr2A	95.726	2340	78	16	270	2596	749105339	749103009	0.000000e+00	3747.0
4	TraesCS2D01G535100	chr2A	82.767	1265	206	10	996	2251	4293809	4292548	0.000000e+00	1118.0
5	TraesCS2D01G535100	chr2A	91.827	624	31	7	2632	3251	749103007	749102400	0.000000e+00	852.0
6	TraesCS2D01G535100	chr2B	95.739	1502	42	10	845	2329	754928833	754927337	0.000000e+00	2399.0
7	TraesCS2D01G535100	chr2B	81.709	1252	212	16	1010	2251	5628374	5629618	0.000000e+00	1027.0
8	TraesCS2D01G535100	chr2B	85.174	634	66	16	1	630	754932033	754931424	2.750000e-175	625.0
9	TraesCS2D01G535100	chr2B	88.050	159	13	4	680	838	754931411	754931259	1.990000e-42	183.0
10	TraesCS2D01G535100	chr2B	89.412	85	9	0	2582	2666	457697556	457697640	1.230000e-19	108.0
11	TraesCS2D01G535100	chr5B	81.530	536	49	21	2680	3206	18065943	18065449	2.350000e-106	396.0
12	TraesCS2D01G535100	chr5B	83.133	166	19	6	2419	2582	18070528	18070370	3.380000e-30	143.0
13	TraesCS2D01G535100	chr6B	84.874	357	41	7	2905	3251	162562966	162563319	6.680000e-92	348.0
14	TraesCS2D01G535100	chr6B	81.481	216	17	9	2375	2589	162550499	162550692	4.340000e-34	156.0
15	TraesCS2D01G535100	chr3A	84.789	355	35	15	2909	3251	549909415	549909068	4.020000e-89	339.0
16	TraesCS2D01G535100	chr3A	90.110	91	7	2	2750	2840	549909512	549909424	2.050000e-22	117.0
17	TraesCS2D01G535100	chr3A	88.764	89	10	0	2582	2670	127266594	127266682	3.430000e-20	110.0
18	TraesCS2D01G535100	chr7A	84.722	144	21	1	6	149	527161186	527161328	3.380000e-30	143.0
19	TraesCS2D01G535100	chr7A	93.333	75	5	0	2592	2666	728022348	728022274	9.530000e-21	111.0
20	TraesCS2D01G535100	chr1B	84.328	134	17	3	10	139	528479762	528479895	9.470000e-26	128.0
21	TraesCS2D01G535100	chr1B	96.970	33	1	0	43	75	528479665	528479697	4.530000e-04	56.5
22	TraesCS2D01G535100	chr7B	83.582	134	21	1	6	139	494733342	494733210	1.220000e-24	124.0
23	TraesCS2D01G535100	chr7B	82.963	135	23	0	6	140	144817111	144817245	4.400000e-24	122.0
24	TraesCS2D01G535100	chr7D	85.345	116	14	3	47	159	137021720	137021835	2.050000e-22	117.0
25	TraesCS2D01G535100	chr7D	81.111	90	13	3	2819	2906	72116954	72117041	5.820000e-08	69.4
26	TraesCS2D01G535100	chr6D	89.130	92	8	1	2577	2666	382702861	382702952	2.650000e-21	113.0
27	TraesCS2D01G535100	chr6D	82.443	131	17	4	6	130	2528842	2528712	3.430000e-20	110.0
28	TraesCS2D01G535100	chr6D	89.412	85	9	0	2582	2666	60049531	60049615	1.230000e-19	108.0
29	TraesCS2D01G535100	chr3B	90.588	85	8	0	2589	2673	621334475	621334391	2.650000e-21	113.0
30	TraesCS2D01G535100	chr3D	89.412	85	9	0	2582	2666	23206183	23206099	1.230000e-19	108.0
31	TraesCS2D01G535100	chr3D	88.506	87	10	0	2580	2666	26166778	26166864	4.440000e-19	106.0
32	TraesCS2D01G535100	chr1D	84.043	94	8	7	2819	2906	104527945	104527853	2.080000e-12	84.2
33	TraesCS2D01G535100	chr4A	87.879	66	7	1	96	160	504193493	504193428	3.480000e-10	76.8
34	TraesCS2D01G535100	chr6A	83.544	79	13	0	21	99	49844154	49844232	1.250000e-09	75.0
35	TraesCS2D01G535100	chr5A	89.583	48	5	0	43	90	539953447	539953494	9.740000e-06	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	TraesCS2D01G535100	chr2D	618286340	618289590	3250	True	6004.0	6004	100.000000	1	3251	1	chr2D.!!$R1	3250
1	TraesCS2D01G535100	chr2D	5747603	5748847	1244	False	1099.0	1099	82.706000	1010	2251	1	chr2D.!!$F1	1241
2	TraesCS2D01G535100	chr2A	749102400	749105339	2939	True	2299.5	3747	93.776500	270	3251	2	chr2A.!!$R2	2981
3	TraesCS2D01G535100	chr2A	4292548	4293809	1261	True	1118.0	1118	82.767000	996	2251	1	chr2A.!!$R1	1255
4	TraesCS2D01G535100	chr2B	754927337	754932033	4696	True	1069.0	2399	89.654333	1	2329	3	chr2B.!!$R1	2328
5	TraesCS2D01G535100	chr2B	5628374	5629618	1244	False	1027.0	1027	81.709000	1010	2251	1	chr2B.!!$F1	1241

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
187	190	0.170561	TCTTCAGCCGCTCGTAGTTC	59.829	55.0	0.00	0.00	0.00	3.01	F
305	308	0.948141	GCTTATCTGGGCGCTAGCTG	60.948	60.0	13.93	7.67	44.37	4.24	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2022	4473	1.014564	CCTTGCCGAAGAAGTCCGTC	61.015	60.0	0.0	0.0	0.0	4.79	R
2324	4778	1.551452	CAATAGCCGGTCCCCAAAAA	58.449	50.0	1.9	0.0	0.0	1.94	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
33	34	3.463533	TTCACACAATATTTCACCGCG	57.536	42.857	0.00	0.00	0.00	6.46
40	41	1.567504	ATATTTCACCGCGTCTTCCG	58.432	50.000	4.92	0.00	40.40	4.30
67	68	9.490663	GTATGCCGCTCAATCATATTAATTTAC	57.509	33.333	0.00	0.00	0.00	2.01
89	90	2.190398	ACCATGTATGACCCAGGCTA	57.810	50.000	0.00	0.00	0.00	3.93
104	105	5.103515	ACCCAGGCTACCAAATTATTGAGAT	60.104	40.000	0.00	0.00	38.94	2.75
149	151	2.233922	ACACACAGGCACATACCTAGTC	59.766	50.000	0.00	0.00	38.26	2.59
165	168	4.158209	ACCTAGTCGAGCTAAAAAGGAGTC	59.842	45.833	8.22	0.00	0.00	3.36
167	170	2.818432	AGTCGAGCTAAAAAGGAGTCGA	59.182	45.455	0.00	0.00	34.26	4.20
177	180	0.457851	AAGGAGTCGATCTTCAGCCG	59.542	55.000	0.00	0.00	0.00	5.52
187	190	0.170561	TCTTCAGCCGCTCGTAGTTC	59.829	55.000	0.00	0.00	0.00	3.01
218	221	1.982073	GCAGCCCAATTTCGAGGACG	61.982	60.000	0.00	0.00	41.26	4.79
225	228	0.953960	AATTTCGAGGACGGTGGCAC	60.954	55.000	9.70	9.70	40.21	5.01
237	240	1.733526	GTGGCACCGACAGCTTTTT	59.266	52.632	6.29	0.00	0.00	1.94
247	250	4.216257	ACCGACAGCTTTTTCGTACTAGTA	59.784	41.667	0.00	0.00	33.23	1.82
305	308	0.948141	GCTTATCTGGGCGCTAGCTG	60.948	60.000	13.93	7.67	44.37	4.24
320	323	3.615110	GCTAGCTGCTTGTCAGTTGTCTA	60.615	47.826	7.79	0.00	44.66	2.59
327	330	2.768253	TGTCAGTTGTCTATGCCCTG	57.232	50.000	0.00	0.00	0.00	4.45
338	341	6.553953	TGTCTATGCCCTGTCTTTATGTTA	57.446	37.500	0.00	0.00	0.00	2.41
342	345	4.216411	TGCCCTGTCTTTATGTTACTCC	57.784	45.455	0.00	0.00	0.00	3.85
418	421	1.665679	CACCGATGAAAGATTGGACCG	59.334	52.381	0.00	0.00	0.00	4.79
486	489	9.491675	ACTTTTTGTATTTTGATTGATGCATGA	57.508	25.926	2.46	0.00	0.00	3.07
514	518	4.684703	CAGAAAGCCAGAAAGCTCAATTTG	59.315	41.667	0.00	0.00	44.11	2.32
517	521	4.773323	AGCCAGAAAGCTCAATTTGTAC	57.227	40.909	0.00	0.00	39.48	2.90
521	525	6.604795	AGCCAGAAAGCTCAATTTGTACATAT	59.395	34.615	0.00	0.00	39.48	1.78
522	526	7.775093	AGCCAGAAAGCTCAATTTGTACATATA	59.225	33.333	0.00	0.00	39.48	0.86
555	559	5.703130	AGTAAGAGCAAGTGGAATTTCAGTC	59.297	40.000	0.00	0.00	0.00	3.51
559	563	5.012561	AGAGCAAGTGGAATTTCAGTCTAGT	59.987	40.000	0.00	0.00	0.00	2.57
570	575	3.808834	TCAGTCTAGTCACAAGGAGGA	57.191	47.619	0.00	0.00	0.00	3.71
588	593	5.656416	AGGAGGATTGACTCTCTGTTAGAAG	59.344	44.000	0.00	0.00	37.63	2.85
645	650	6.223351	AGTCCTTTTTCTCTAATACTCCCG	57.777	41.667	0.00	0.00	0.00	5.14
646	651	4.809958	GTCCTTTTTCTCTAATACTCCCGC	59.190	45.833	0.00	0.00	0.00	6.13
664	669	4.512571	TCCCGCTGTAAACTTTTGTAAGAC	59.487	41.667	0.00	0.00	35.30	3.01
675	680	6.701432	ACTTTTGTAAGACCGTTTAGATCG	57.299	37.500	0.00	0.00	35.30	3.69
945	3384	2.531522	GTTGAGCAAACCCAGCAAAT	57.468	45.000	0.00	0.00	32.13	2.32
946	3385	2.837498	GTTGAGCAAACCCAGCAAATT	58.163	42.857	0.00	0.00	32.13	1.82
947	3386	3.988819	GTTGAGCAAACCCAGCAAATTA	58.011	40.909	0.00	0.00	32.13	1.40
948	3387	4.376146	GTTGAGCAAACCCAGCAAATTAA	58.624	39.130	0.00	0.00	32.13	1.40
1050	3501	2.196382	CTCGTCGTGTGTCGGTGGAT	62.196	60.000	0.00	0.00	40.32	3.41
1320	3771	1.006832	CCAGGTTCGACATTAAGCCG	58.993	55.000	0.00	0.00	0.00	5.52
2091	4542	3.681129	TGGAAGGGCCAGTTTGGA	58.319	55.556	6.18	0.00	43.33	3.53
2317	4771	2.025887	GGTCCTGGAATTGTGTGGAGAT	60.026	50.000	0.00	0.00	0.00	2.75
2322	4776	2.582172	TGGAATTGTGTGGAGATGGGAT	59.418	45.455	0.00	0.00	0.00	3.85
2323	4777	3.011595	TGGAATTGTGTGGAGATGGGATT	59.988	43.478	0.00	0.00	0.00	3.01
2324	4778	4.026052	GGAATTGTGTGGAGATGGGATTT	58.974	43.478	0.00	0.00	0.00	2.17
2384	4839	2.769663	ACTTGGGTCAGTGTGTAAGTCA	59.230	45.455	0.00	0.00	0.00	3.41
2385	4840	3.391296	ACTTGGGTCAGTGTGTAAGTCAT	59.609	43.478	0.00	0.00	0.00	3.06
2388	4843	4.133820	TGGGTCAGTGTGTAAGTCATTTG	58.866	43.478	0.00	0.00	0.00	2.32
2477	4934	1.746615	CAGGGCCTTGATCCACACG	60.747	63.158	9.80	0.00	0.00	4.49
2522	4981	0.719465	CGTACGTGCCATCCTGTTTC	59.281	55.000	7.22	0.00	0.00	2.78
2533	4992	3.623060	CCATCCTGTTTCGTATGGTTCAG	59.377	47.826	0.00	0.00	35.23	3.02
2570	5029	2.341846	ATCACAGTCACCGGTGTTTT	57.658	45.000	32.74	17.15	37.90	2.43
2596	5055	9.483489	TGTTACTTTATTACTCTATCTGTCCCA	57.517	33.333	0.00	0.00	0.00	4.37
2674	5133	7.332433	TGGGACAAAGGGAGTATTACTTTAA	57.668	36.000	0.00	0.00	33.47	1.52
2675	5134	7.757611	TGGGACAAAGGGAGTATTACTTTAAA	58.242	34.615	0.00	0.00	33.47	1.52
2693	5152	0.896940	AAGCCATTGCCCAGTGTCTG	60.897	55.000	0.00	0.00	38.69	3.51
2732	5191	4.382793	GGACGCTGGAAGGTTAAAGATAGT	60.383	45.833	0.00	0.00	0.00	2.12
2758	5217	9.868277	TCTTTTCAAATGTGTACTTTCAAATGT	57.132	25.926	0.00	0.00	0.00	2.71
2759	5218	9.904647	CTTTTCAAATGTGTACTTTCAAATGTG	57.095	29.630	0.00	0.00	0.00	3.21
2760	5219	8.994429	TTTCAAATGTGTACTTTCAAATGTGT	57.006	26.923	0.00	0.00	0.00	3.72
2762	5221	9.509855	TTCAAATGTGTACTTTCAAATGTGTAC	57.490	29.630	0.00	0.00	36.69	2.90
2763	5222	7.853437	TCAAATGTGTACTTTCAAATGTGTACG	59.147	33.333	0.00	0.00	38.35	3.67
2764	5223	5.660629	TGTGTACTTTCAAATGTGTACGG	57.339	39.130	0.00	0.00	38.35	4.02
2765	5224	5.358090	TGTGTACTTTCAAATGTGTACGGA	58.642	37.500	0.00	0.00	38.35	4.69
2797	5256	5.735766	AGCCTTCTAATACTTGTGAGTTCC	58.264	41.667	0.00	0.00	37.33	3.62
2827	5286	5.254901	AGCTATGTACCTATTACTCCCTCG	58.745	45.833	0.00	0.00	0.00	4.63
2844	5303	6.156429	ACTCCCTCGGTCTCAAAATAAGTATT	59.844	38.462	0.00	0.00	0.00	1.89
2932	5391	7.134815	GGGAATATTAGCTAATAATGCATGCG	58.865	38.462	25.90	0.00	35.63	4.73
3063	5522	8.344446	AGTGTCATTGGTATTACCCTTAAAAC	57.656	34.615	10.37	3.19	37.50	2.43
3190	5653	8.125728	ACAAAATTTGCACACAACTTACATAC	57.874	30.769	5.52	0.00	34.87	2.39

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
3	4	9.507280	GTGAAATATTGTGTGAAATCGAATGAT	57.493	29.630	0.00	0.00	35.98	2.45
20	21	1.931172	CGGAAGACGCGGTGAAATATT	59.069	47.619	12.47	0.00	34.82	1.28
40	41	6.683974	ATTAATATGATTGAGCGGCATACC	57.316	37.500	1.45	0.00	0.00	2.73
67	68	2.439507	AGCCTGGGTCATACATGGTAAG	59.560	50.000	0.00	0.00	0.00	2.34
76	77	5.922960	ATAATTTGGTAGCCTGGGTCATA	57.077	39.130	0.00	0.00	0.00	2.15
110	111	1.354031	TGTTGCCACAGGGTCACATAT	59.646	47.619	0.00	0.00	36.17	1.78
114	115	1.453015	TGTGTTGCCACAGGGTCAC	60.453	57.895	0.00	0.00	46.45	3.67
130	132	1.476891	CGACTAGGTATGTGCCTGTGT	59.523	52.381	0.00	0.00	39.60	3.72
133	135	1.269309	GCTCGACTAGGTATGTGCCTG	60.269	57.143	0.00	0.00	39.60	4.85
134	136	1.033574	GCTCGACTAGGTATGTGCCT	58.966	55.000	0.00	0.00	42.43	4.75
149	151	4.035278	AGATCGACTCCTTTTTAGCTCG	57.965	45.455	0.00	0.00	0.00	5.03
167	170	0.818296	AACTACGAGCGGCTGAAGAT	59.182	50.000	7.50	0.00	0.00	2.40
190	193	0.244721	AATTGGGCTGCGAGAAAAGC	59.755	50.000	0.00	0.00	38.76	3.51
198	201	1.745115	TCCTCGAAATTGGGCTGCG	60.745	57.895	0.00	0.00	0.00	5.18
203	206	1.024579	CCACCGTCCTCGAAATTGGG	61.025	60.000	0.00	0.00	39.71	4.12
218	221	1.734388	AAAAAGCTGTCGGTGCCACC	61.734	55.000	2.98	2.98	34.05	4.61
225	228	3.572584	ACTAGTACGAAAAAGCTGTCGG	58.427	45.455	16.33	3.94	41.56	4.79
230	233	8.738106	AGATGTAAGTACTAGTACGAAAAAGCT	58.262	33.333	23.87	14.72	40.80	3.74
247	250	7.093289	ACACCTACTGCTGAATTAGATGTAAGT	60.093	37.037	0.00	0.00	0.00	2.24
268	271	3.333029	AGCAAAACAAGCAAAACACCT	57.667	38.095	0.00	0.00	0.00	4.00
279	282	1.067915	GCGCCCAGATAAGCAAAACAA	60.068	47.619	0.00	0.00	0.00	2.83
305	308	1.740025	GGGCATAGACAACTGACAAGC	59.260	52.381	0.00	0.00	0.00	4.01
320	323	4.385310	GGGAGTAACATAAAGACAGGGCAT	60.385	45.833	0.00	0.00	0.00	4.40
327	330	6.625081	GCAAATGGTGGGAGTAACATAAAGAC	60.625	42.308	0.00	0.00	0.00	3.01
338	341	2.456577	GGTTATGCAAATGGTGGGAGT	58.543	47.619	0.00	0.00	0.00	3.85
342	345	3.056891	ACTTTCGGTTATGCAAATGGTGG	60.057	43.478	0.00	0.00	0.00	4.61
386	389	2.709213	TCATCGGTGCAACATCAATCA	58.291	42.857	0.98	0.00	39.98	2.57
400	403	2.309528	TCGGTCCAATCTTTCATCGG	57.690	50.000	0.00	0.00	0.00	4.18
418	421	2.034507	GCTGTAGACGCGTCATTGATTC	60.035	50.000	37.85	17.07	0.00	2.52
486	489	1.245732	CTTTCTGGCTTTCTGCAGCT	58.754	50.000	9.47	0.00	45.15	4.24
521	525	9.787435	TTCCACTTGCTCTTACTTTTCTTATTA	57.213	29.630	0.00	0.00	0.00	0.98
522	526	8.691661	TTCCACTTGCTCTTACTTTTCTTATT	57.308	30.769	0.00	0.00	0.00	1.40
524	528	8.691661	AATTCCACTTGCTCTTACTTTTCTTA	57.308	30.769	0.00	0.00	0.00	2.10
559	563	3.513119	CAGAGAGTCAATCCTCCTTGTGA	59.487	47.826	0.00	0.00	31.53	3.58
570	575	7.487822	TTCCATCTTCTAACAGAGAGTCAAT	57.512	36.000	0.00	0.00	34.93	2.57
576	581	5.940470	GGCTTTTTCCATCTTCTAACAGAGA	59.060	40.000	0.00	0.00	0.00	3.10
588	593	4.044426	GCGTGATAATGGCTTTTTCCATC	58.956	43.478	0.00	0.00	45.64	3.51
645	650	5.413969	ACGGTCTTACAAAAGTTTACAGC	57.586	39.130	0.00	0.00	34.13	4.40
646	651	8.819974	TCTAAACGGTCTTACAAAAGTTTACAG	58.180	33.333	0.00	0.00	34.29	2.74
664	669	6.090358	TGAAGAAAGCTTAACGATCTAAACGG	59.910	38.462	0.00	0.00	33.61	4.44
801	806	9.786105	CAAATTTAAAATGTTTCCAAAAGCACT	57.214	25.926	0.00	0.00	0.00	4.40
926	3361	2.531522	ATTTGCTGGGTTTGCTCAAC	57.468	45.000	0.00	0.00	34.18	3.18
970	3409	4.344865	GCTTCCTGGCCGGGTTGA	62.345	66.667	30.31	16.04	0.00	3.18
1050	3501	2.189257	CCGACGATGATTGGGCCA	59.811	61.111	0.00	0.00	0.00	5.36
1320	3771	1.782028	GCACGGTGGTGTTGAACTCC	61.782	60.000	10.60	9.36	46.13	3.85
2022	4473	1.014564	CCTTGCCGAAGAAGTCCGTC	61.015	60.000	0.00	0.00	0.00	4.79
2324	4778	1.551452	CAATAGCCGGTCCCCAAAAA	58.449	50.000	1.90	0.00	0.00	1.94
2477	4934	1.268743	GCGAGCAGATAAACCCAATGC	60.269	52.381	0.00	0.00	37.15	3.56
2522	4981	1.144969	AACACGTGCTGAACCATACG	58.855	50.000	17.22	0.00	41.86	3.06
2533	4992	5.444983	TGTGATTACAAACATAACACGTGC	58.555	37.500	17.22	0.00	32.88	5.34
2570	5029	9.483489	TGGGACAGATAGAGTAATAAAGTAACA	57.517	33.333	0.00	0.00	0.00	2.41
2637	5096	6.331572	TCCCTTTGTCCCATAATATAAGAGCA	59.668	38.462	0.00	0.00	0.00	4.26
2652	5111	7.148120	GGCTTTAAAGTAATACTCCCTTTGTCC	60.148	40.741	16.38	0.00	31.33	4.02
2653	5112	7.392393	TGGCTTTAAAGTAATACTCCCTTTGTC	59.608	37.037	16.38	0.00	31.33	3.18
2656	5115	8.749354	CAATGGCTTTAAAGTAATACTCCCTTT	58.251	33.333	16.38	7.94	33.32	3.11
2670	5129	2.298729	GACACTGGGCAATGGCTTTAAA	59.701	45.455	6.78	0.00	40.87	1.52
2674	5133	0.896940	CAGACACTGGGCAATGGCTT	60.897	55.000	6.78	0.00	40.87	4.35
2675	5134	1.303888	CAGACACTGGGCAATGGCT	60.304	57.895	6.78	0.00	40.87	4.75
2708	5167	1.076332	CTTTAACCTTCCAGCGTCCG	58.924	55.000	0.00	0.00	0.00	4.79
2732	5191	9.868277	ACATTTGAAAGTACACATTTGAAAAGA	57.132	25.926	0.00	0.00	28.94	2.52
2749	5208	7.455641	AATACCAATCCGTACACATTTGAAA	57.544	32.000	0.00	0.00	0.00	2.69
2750	5209	7.201661	GCTAATACCAATCCGTACACATTTGAA	60.202	37.037	0.00	0.00	0.00	2.69
2751	5210	6.259167	GCTAATACCAATCCGTACACATTTGA	59.741	38.462	0.00	0.00	0.00	2.69
2752	5211	6.427150	GCTAATACCAATCCGTACACATTTG	58.573	40.000	0.00	0.00	0.00	2.32
2753	5212	5.529800	GGCTAATACCAATCCGTACACATTT	59.470	40.000	0.00	0.00	0.00	2.32
2754	5213	5.061179	GGCTAATACCAATCCGTACACATT	58.939	41.667	0.00	0.00	0.00	2.71
2755	5214	4.347000	AGGCTAATACCAATCCGTACACAT	59.653	41.667	0.00	0.00	0.00	3.21
2756	5215	3.707611	AGGCTAATACCAATCCGTACACA	59.292	43.478	0.00	0.00	0.00	3.72
2757	5216	4.332428	AGGCTAATACCAATCCGTACAC	57.668	45.455	0.00	0.00	0.00	2.90
2758	5217	4.652421	AGAAGGCTAATACCAATCCGTACA	59.348	41.667	0.00	0.00	0.00	2.90
2759	5218	5.211174	AGAAGGCTAATACCAATCCGTAC	57.789	43.478	0.00	0.00	0.00	3.67
2760	5219	6.982160	TTAGAAGGCTAATACCAATCCGTA	57.018	37.500	0.00	0.00	31.81	4.02
2761	5220	5.881923	TTAGAAGGCTAATACCAATCCGT	57.118	39.130	0.00	0.00	31.81	4.69
2797	5256	8.732531	GGAGTAATAGGTACATAGCTTAGACAG	58.267	40.741	0.00	0.00	34.88	3.51
2901	5360	8.001292	GCATTATTAGCTAATATTCCCCCATCT	58.999	37.037	23.50	0.37	0.00	2.90
3103	5562	8.820831	TGCCATAATTCTTCCTTGGAATTTTTA	58.179	29.630	2.24	2.53	41.66	1.52
3105	5564	7.256494	TGCCATAATTCTTCCTTGGAATTTT	57.744	32.000	2.24	0.85	41.66	1.82
3106	5565	6.872585	TGCCATAATTCTTCCTTGGAATTT	57.127	33.333	2.24	1.16	41.66	1.82
3107	5566	7.441903	AATGCCATAATTCTTCCTTGGAATT	57.558	32.000	2.24	0.00	43.22	2.17
3108	5567	7.786464	ACTAATGCCATAATTCTTCCTTGGAAT	59.214	33.333	2.24	0.00	35.25	3.01
3124	5583	7.633018	TCTAGAAGGGAAATACTAATGCCAT	57.367	36.000	0.00	0.00	0.00	4.40
3161	5620	6.799926	AAGTTGTGTGCAAATTTTGTCTTT	57.200	29.167	10.65	0.00	39.49	2.52
3164	5623	6.639671	TGTAAGTTGTGTGCAAATTTTGTC	57.360	33.333	10.65	4.25	39.49	3.18
3166	5625	8.124586	TGTATGTAAGTTGTGTGCAAATTTTG	57.875	30.769	4.72	4.72	39.49	2.44
3206	5669	7.990917	TGTTCGGCTTATTCTTGCATATTAAA	58.009	30.769	0.00	0.00	0.00	1.52
3207	5670	7.561021	TGTTCGGCTTATTCTTGCATATTAA	57.439	32.000	0.00	0.00	0.00	1.40
3208	5671	7.744087	ATGTTCGGCTTATTCTTGCATATTA	57.256	32.000	0.00	0.00	0.00	0.98
3211	5674	6.202762	CACTATGTTCGGCTTATTCTTGCATA	59.797	38.462	0.00	0.00	0.00	3.14
3217	5680	5.353394	TTCCACTATGTTCGGCTTATTCT	57.647	39.130	0.00	0.00	0.00	2.40

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.