AutoCloner

Multiple sequence alignment - TraesCS2B01G435500

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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	TraesCS2B01G435500	chr2B	100.000	2562	0	0	1	2562	625912488	625915049	0.000000e+00	4732.0
1	TraesCS2B01G435500	chr2B	88.433	2533	246	30	68	2562	448077221	448079744	0.000000e+00	3011.0
2	TraesCS2B01G435500	chr2B	92.821	195	14	0	356	550	690252276	690252082	1.500000e-72	283.0
3	TraesCS2B01G435500	chr2B	92.000	75	6	0	1	75	76520320	76520394	3.490000e-19	106.0
4	TraesCS2B01G435500	chr2B	93.103	58	4	0	2505	2562	651601505	651601562	4.540000e-13	86.1
5	TraesCS2B01G435500	chr4B	89.355	2527	216	22	72	2555	48631819	48634335	0.000000e+00	3127.0
6	TraesCS2B01G435500	chr4B	89.255	2522	199	32	75	2562	221187432	221184949	0.000000e+00	3090.0
7	TraesCS2B01G435500	chr4B	87.426	2529	235	45	75	2562	87540945	87538459	0.000000e+00	2832.0
8	TraesCS2B01G435500	chr4B	88.889	72	8	0	7	78	623028239	623028168	3.510000e-14	89.8
9	TraesCS2B01G435500	chr1B	89.461	2505	200	21	98	2559	308912585	308915068	0.000000e+00	3105.0
10	TraesCS2B01G435500	chr1B	87.654	81	10	0	1	81	6868215	6868135	7.550000e-16	95.3
11	TraesCS2B01G435500	chr7B	88.580	2522	221	32	75	2557	724805163	724807656	0.000000e+00	3000.0
12	TraesCS2B01G435500	chr7B	87.179	78	10	0	1	78	700558833	700558756	3.510000e-14	89.8
13	TraesCS2B01G435500	chr4A	88.451	2537	216	35	73	2562	712563213	712560707	0.000000e+00	2990.0
14	TraesCS2B01G435500	chrUn	87.913	2515	232	39	72	2557	218124085	218121614	0.000000e+00	2894.0
15	TraesCS2B01G435500	chr3D	87.495	2559	215	40	73	2562	126392334	126394856	0.000000e+00	2856.0
16	TraesCS2B01G435500	chr2D	85.948	2569	266	47	70	2562	306627419	306624870	0.000000e+00	2656.0
17	TraesCS2B01G435500	chr2D	81.445	803	89	21	73	824	460867524	460866731	1.010000e-168	603.0
18	TraesCS2B01G435500	chr2D	83.333	78	13	0	1	78	36494064	36494141	3.540000e-09	73.1
19	TraesCS2B01G435500	chr7D	86.540	2214	232	35	73	2232	616482349	616484550	0.000000e+00	2377.0
20	TraesCS2B01G435500	chr6B	88.419	2012	178	16	75	2057	12602598	12600613	0.000000e+00	2374.0
21	TraesCS2B01G435500	chr3B	85.322	1458	148	24	115	1548	22891404	22892819	0.000000e+00	1447.0
22	TraesCS2B01G435500	chr3B	85.013	387	33	13	2176	2560	244663982	244663619	1.120000e-98	370.0
23	TraesCS2B01G435500	chr3B	87.879	66	6	2	14	78	227828267	227828203	2.730000e-10	76.8
24	TraesCS2B01G435500	chr5D	82.888	1198	119	29	75	1213	344691794	344690624	0.000000e+00	998.0
25	TraesCS2B01G435500	chr5D	92.308	78	6	0	1	78	400417645	400417568	7.490000e-21	111.0
26	TraesCS2B01G435500	chr5B	83.103	870	94	28	75	910	491616351	491617201	0.000000e+00	743.0
27	TraesCS2B01G435500	chr5A	86.621	441	48	9	75	512	504239077	504238645	6.410000e-131	477.0
28	TraesCS2B01G435500	chr3A	87.671	73	8	1	9	81	33274075	33274146	1.630000e-12	84.2
29	TraesCS2B01G435500	chr4D	83.544	79	12	1	1	78	506218442	506218520	3.540000e-09	73.1

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	TraesCS2B01G435500	chr2B	625912488	625915049	2561	False	4732	4732	100.000	1	2562	1	chr2B.!!$F3	2561
1	TraesCS2B01G435500	chr2B	448077221	448079744	2523	False	3011	3011	88.433	68	2562	1	chr2B.!!$F2	2494
2	TraesCS2B01G435500	chr4B	48631819	48634335	2516	False	3127	3127	89.355	72	2555	1	chr4B.!!$F1	2483
3	TraesCS2B01G435500	chr4B	221184949	221187432	2483	True	3090	3090	89.255	75	2562	1	chr4B.!!$R2	2487
4	TraesCS2B01G435500	chr4B	87538459	87540945	2486	True	2832	2832	87.426	75	2562	1	chr4B.!!$R1	2487
5	TraesCS2B01G435500	chr1B	308912585	308915068	2483	False	3105	3105	89.461	98	2559	1	chr1B.!!$F1	2461
6	TraesCS2B01G435500	chr7B	724805163	724807656	2493	False	3000	3000	88.580	75	2557	1	chr7B.!!$F1	2482
7	TraesCS2B01G435500	chr4A	712560707	712563213	2506	True	2990	2990	88.451	73	2562	1	chr4A.!!$R1	2489
8	TraesCS2B01G435500	chrUn	218121614	218124085	2471	True	2894	2894	87.913	72	2557	1	chrUn.!!$R1	2485
9	TraesCS2B01G435500	chr3D	126392334	126394856	2522	False	2856	2856	87.495	73	2562	1	chr3D.!!$F1	2489
10	TraesCS2B01G435500	chr2D	306624870	306627419	2549	True	2656	2656	85.948	70	2562	1	chr2D.!!$R1	2492
11	TraesCS2B01G435500	chr2D	460866731	460867524	793	True	603	603	81.445	73	824	1	chr2D.!!$R2	751
12	TraesCS2B01G435500	chr7D	616482349	616484550	2201	False	2377	2377	86.540	73	2232	1	chr7D.!!$F1	2159
13	TraesCS2B01G435500	chr6B	12600613	12602598	1985	True	2374	2374	88.419	75	2057	1	chr6B.!!$R1	1982
14	TraesCS2B01G435500	chr3B	22891404	22892819	1415	False	1447	1447	85.322	115	1548	1	chr3B.!!$F1	1433
15	TraesCS2B01G435500	chr5D	344690624	344691794	1170	True	998	998	82.888	75	1213	1	chr5D.!!$R1	1138
16	TraesCS2B01G435500	chr5B	491616351	491617201	850	False	743	743	83.103	75	910	1	chr5B.!!$F1	835

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
223	234	0.111446	TCCGACCCAATTTTGAGCCA	59.889	50.0	0.0	0.0	0.0	4.75	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1905	2111	0.038166	ATCATGCCCTTCACGGTTGT	59.962	50.0	0.0	0.0	0.0	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
18	19	3.487576	TTCGCCACAAAGGTCTTGT	57.512	47.368	0.00	0.00	40.61	3.16
19	20	1.757682	TTCGCCACAAAGGTCTTGTT	58.242	45.000	0.00	0.00	40.61	2.83
20	21	1.021202	TCGCCACAAAGGTCTTGTTG	58.979	50.000	0.00	0.00	40.61	3.33
21	22	0.738389	CGCCACAAAGGTCTTGTTGT	59.262	50.000	0.00	0.00	40.61	3.32
22	23	1.944024	CGCCACAAAGGTCTTGTTGTA	59.056	47.619	0.00	0.00	40.61	2.41
23	24	2.032030	CGCCACAAAGGTCTTGTTGTAG	60.032	50.000	0.00	0.00	40.61	2.74
24	25	3.211045	GCCACAAAGGTCTTGTTGTAGA	58.789	45.455	0.00	0.00	40.61	2.59
25	26	3.630312	GCCACAAAGGTCTTGTTGTAGAA	59.370	43.478	0.00	0.00	40.61	2.10
26	27	4.097286	GCCACAAAGGTCTTGTTGTAGAAA	59.903	41.667	0.00	0.00	40.61	2.52
27	28	5.393678	GCCACAAAGGTCTTGTTGTAGAAAA	60.394	40.000	0.00	0.00	40.61	2.29
28	29	6.682861	GCCACAAAGGTCTTGTTGTAGAAAAT	60.683	38.462	0.00	0.00	40.61	1.82
29	30	7.264947	CCACAAAGGTCTTGTTGTAGAAAATT	58.735	34.615	0.00	0.00	35.81	1.82
30	31	8.410141	CCACAAAGGTCTTGTTGTAGAAAATTA	58.590	33.333	0.00	0.00	35.81	1.40
31	32	9.450807	CACAAAGGTCTTGTTGTAGAAAATTAG	57.549	33.333	0.00	0.00	35.81	1.73
32	33	9.403583	ACAAAGGTCTTGTTGTAGAAAATTAGA	57.596	29.630	0.00	0.00	36.22	2.10
33	34	9.884465	CAAAGGTCTTGTTGTAGAAAATTAGAG	57.116	33.333	0.00	0.00	0.00	2.43
34	35	9.847224	AAAGGTCTTGTTGTAGAAAATTAGAGA	57.153	29.630	0.00	0.00	0.00	3.10
35	36	9.847224	AAGGTCTTGTTGTAGAAAATTAGAGAA	57.153	29.630	0.00	0.00	0.00	2.87
36	37	9.495572	AGGTCTTGTTGTAGAAAATTAGAGAAG	57.504	33.333	0.00	0.00	0.00	2.85
37	38	9.490379	GGTCTTGTTGTAGAAAATTAGAGAAGA	57.510	33.333	0.00	0.00	0.00	2.87
42	43	9.712305	TGTTGTAGAAAATTAGAGAAGAAGAGG	57.288	33.333	0.00	0.00	0.00	3.69
43	44	9.713713	GTTGTAGAAAATTAGAGAAGAAGAGGT	57.286	33.333	0.00	0.00	0.00	3.85
47	48	8.541133	AGAAAATTAGAGAAGAAGAGGTTTCG	57.459	34.615	0.00	0.00	0.00	3.46
48	49	8.151596	AGAAAATTAGAGAAGAAGAGGTTTCGT	58.848	33.333	0.00	0.00	0.00	3.85
49	50	9.420551	GAAAATTAGAGAAGAAGAGGTTTCGTA	57.579	33.333	0.00	0.00	0.00	3.43
50	51	9.774413	AAAATTAGAGAAGAAGAGGTTTCGTAA	57.226	29.630	0.00	0.00	0.00	3.18
51	52	8.760103	AATTAGAGAAGAAGAGGTTTCGTAAC	57.240	34.615	0.00	0.00	0.00	2.50
52	53	5.786264	AGAGAAGAAGAGGTTTCGTAACA	57.214	39.130	7.25	0.00	35.92	2.41
53	54	6.158023	AGAGAAGAAGAGGTTTCGTAACAA	57.842	37.500	7.25	0.00	35.92	2.83
54	55	6.217294	AGAGAAGAAGAGGTTTCGTAACAAG	58.783	40.000	7.25	0.00	35.92	3.16
55	56	6.040616	AGAGAAGAAGAGGTTTCGTAACAAGA	59.959	38.462	7.25	0.00	35.92	3.02
56	57	6.217294	AGAAGAAGAGGTTTCGTAACAAGAG	58.783	40.000	7.25	0.00	35.92	2.85
57	58	5.532664	AGAAGAGGTTTCGTAACAAGAGT	57.467	39.130	7.25	0.00	35.92	3.24
58	59	6.645790	AGAAGAGGTTTCGTAACAAGAGTA	57.354	37.500	7.25	0.00	35.92	2.59
59	60	7.229581	AGAAGAGGTTTCGTAACAAGAGTAT	57.770	36.000	7.25	0.00	35.92	2.12
60	61	7.668492	AGAAGAGGTTTCGTAACAAGAGTATT	58.332	34.615	7.25	0.00	35.92	1.89
61	62	7.599245	AGAAGAGGTTTCGTAACAAGAGTATTG	59.401	37.037	7.25	0.00	35.92	1.90
62	63	6.756221	AGAGGTTTCGTAACAAGAGTATTGT	58.244	36.000	7.25	0.00	35.92	2.71
63	64	7.215085	AGAGGTTTCGTAACAAGAGTATTGTT	58.785	34.615	18.99	18.99	44.03	2.83
64	65	7.170998	AGAGGTTTCGTAACAAGAGTATTGTTG	59.829	37.037	22.85	9.67	42.05	3.33
65	66	5.849604	GGTTTCGTAACAAGAGTATTGTTGC	59.150	40.000	22.85	20.40	42.05	4.17
66	67	6.423862	GTTTCGTAACAAGAGTATTGTTGCA	58.576	36.000	24.61	13.10	42.50	4.08
67	68	5.839262	TCGTAACAAGAGTATTGTTGCAG	57.161	39.130	24.61	18.42	42.50	4.41
68	69	5.534407	TCGTAACAAGAGTATTGTTGCAGA	58.466	37.500	24.61	19.86	42.50	4.26
223	234	0.111446	TCCGACCCAATTTTGAGCCA	59.889	50.000	0.00	0.00	0.00	4.75
279	302	2.494530	CGCCTACTCCTCTCCCTGC	61.495	68.421	0.00	0.00	0.00	4.85
322	358	1.689258	CCACCATTTCCCCTCATTCCC	60.689	57.143	0.00	0.00	0.00	3.97
344	393	3.979497	CCCAAAACCCTCCCGCCT	61.979	66.667	0.00	0.00	0.00	5.52
397	456	3.126225	GACCTCGACCTCGACGCT	61.126	66.667	0.00	0.00	44.22	5.07
802	982	2.363018	CTCTCGGGGGAGTGCTCA	60.363	66.667	1.41	0.00	0.00	4.26
820	1000	2.224159	ACCCGAGGTGAGCATGGTT	61.224	57.895	0.00	0.00	32.98	3.67
833	1025	0.321564	CATGGTTGCTCCTTCCACGA	60.322	55.000	0.00	0.00	37.07	4.35
900	1092	4.735132	CGGAGGCGCGAGGAAACA	62.735	66.667	12.10	0.00	0.00	2.83
910	1102	2.515057	AGGAAACACGTGCGGCAA	60.515	55.556	17.22	0.00	0.00	4.52
1124	1317	1.405933	CCTTCATGCGTGATCAGGTCA	60.406	52.381	15.84	14.22	33.56	4.02
1229	1422	0.034896	GGAGCCTTTGTTCGAGGACA	59.965	55.000	0.00	0.00	36.33	4.02
1279	1472	0.308684	CAAAGCACAAGAGCAAGCGA	59.691	50.000	0.00	0.00	36.85	4.93
1344	1540	3.266772	TGTTGGAGAGATATTGGGCAAGT	59.733	43.478	0.00	0.00	0.00	3.16
1409	1605	0.320374	TGTCCACCGTGAGTTCCATC	59.680	55.000	0.00	0.00	0.00	3.51
1525	1726	0.469494	TTGTGCCACTCTTGAGAGCA	59.531	50.000	7.91	13.12	45.79	4.26
1768	1973	1.896465	AGACGAGGAGAAGTTCAAGGG	59.104	52.381	5.50	0.00	0.00	3.95
1780	1986	4.255510	AGTTCAAGGGACAATATGCCAT	57.744	40.909	0.00	0.00	42.70	4.40
1809	2015	2.203480	GTGGTGGGAAGCAAGCCA	60.203	61.111	0.00	0.00	0.00	4.75
2027	2234	1.377202	GCTTGACATGGAGGCGGAA	60.377	57.895	0.00	0.00	0.00	4.30
2037	2244	1.598701	GGAGGCGGAAAAGCAAGCAT	61.599	55.000	0.00	0.00	39.27	3.79
2249	2490	6.482308	TCAAGTTCGACGATGAGTGATCTATA	59.518	38.462	0.00	0.00	0.00	1.31
2250	2491	7.173390	TCAAGTTCGACGATGAGTGATCTATAT	59.827	37.037	0.00	0.00	0.00	0.86
2251	2492	6.836953	AGTTCGACGATGAGTGATCTATATG	58.163	40.000	0.00	0.00	0.00	1.78
2253	2494	5.246307	TCGACGATGAGTGATCTATATGGT	58.754	41.667	0.00	0.00	0.00	3.55
2254	2495	5.122396	TCGACGATGAGTGATCTATATGGTG	59.878	44.000	0.00	0.00	0.00	4.17
2256	2497	4.081972	ACGATGAGTGATCTATATGGTGGC	60.082	45.833	0.00	0.00	0.00	5.01
2258	2499	3.496331	TGAGTGATCTATATGGTGGCGA	58.504	45.455	0.00	0.00	0.00	5.54
2264	2506	0.969149	CTATATGGTGGCGAGCCTCA	59.031	55.000	15.75	13.35	36.94	3.86
2266	2508	0.322975	ATATGGTGGCGAGCCTCATC	59.677	55.000	20.18	2.95	36.94	2.92
2298	2540	0.679002	GACAGGTGTGCTGGCATGAT	60.679	55.000	0.00	0.00	0.00	2.45
2305	2549	2.903855	GCTGGCATGATCACGGGG	60.904	66.667	0.00	0.00	0.00	5.73
2460	2715	2.903855	GCCGGCATGAGACATGGG	60.904	66.667	24.80	7.88	0.00	4.00

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
0	1	1.403679	CAACAAGACCTTTGTGGCGAA	59.596	47.619	0.00	0.00	40.22	4.70
2	3	0.738389	ACAACAAGACCTTTGTGGCG	59.262	50.000	0.00	0.00	40.22	5.69
3	4	3.211045	TCTACAACAAGACCTTTGTGGC	58.789	45.455	0.00	0.00	40.22	5.01
4	5	5.828299	TTTCTACAACAAGACCTTTGTGG	57.172	39.130	0.00	0.00	36.61	4.17
5	6	9.450807	CTAATTTTCTACAACAAGACCTTTGTG	57.549	33.333	0.00	0.00	36.61	3.33
6	7	9.403583	TCTAATTTTCTACAACAAGACCTTTGT	57.596	29.630	0.00	0.00	39.31	2.83
7	8	9.884465	CTCTAATTTTCTACAACAAGACCTTTG	57.116	33.333	0.00	0.00	0.00	2.77
8	9	9.847224	TCTCTAATTTTCTACAACAAGACCTTT	57.153	29.630	0.00	0.00	0.00	3.11
9	10	9.847224	TTCTCTAATTTTCTACAACAAGACCTT	57.153	29.630	0.00	0.00	0.00	3.50
10	11	9.495572	CTTCTCTAATTTTCTACAACAAGACCT	57.504	33.333	0.00	0.00	0.00	3.85
11	12	9.490379	TCTTCTCTAATTTTCTACAACAAGACC	57.510	33.333	0.00	0.00	0.00	3.85
16	17	9.712305	CCTCTTCTTCTCTAATTTTCTACAACA	57.288	33.333	0.00	0.00	0.00	3.33
17	18	9.713713	ACCTCTTCTTCTCTAATTTTCTACAAC	57.286	33.333	0.00	0.00	0.00	3.32
21	22	9.640963	CGAAACCTCTTCTTCTCTAATTTTCTA	57.359	33.333	0.00	0.00	0.00	2.10
22	23	8.151596	ACGAAACCTCTTCTTCTCTAATTTTCT	58.848	33.333	0.00	0.00	0.00	2.52
23	24	8.312896	ACGAAACCTCTTCTTCTCTAATTTTC	57.687	34.615	0.00	0.00	0.00	2.29
24	25	9.774413	TTACGAAACCTCTTCTTCTCTAATTTT	57.226	29.630	0.00	0.00	0.00	1.82
25	26	9.205719	GTTACGAAACCTCTTCTTCTCTAATTT	57.794	33.333	0.00	0.00	0.00	1.82
26	27	8.365647	TGTTACGAAACCTCTTCTTCTCTAATT	58.634	33.333	0.00	0.00	34.49	1.40
27	28	7.893658	TGTTACGAAACCTCTTCTTCTCTAAT	58.106	34.615	0.00	0.00	34.49	1.73
28	29	7.281040	TGTTACGAAACCTCTTCTTCTCTAA	57.719	36.000	0.00	0.00	34.49	2.10
29	30	6.889301	TGTTACGAAACCTCTTCTTCTCTA	57.111	37.500	0.00	0.00	34.49	2.43
30	31	5.786264	TGTTACGAAACCTCTTCTTCTCT	57.214	39.130	0.00	0.00	34.49	3.10
31	32	6.214399	TCTTGTTACGAAACCTCTTCTTCTC	58.786	40.000	0.00	0.00	34.49	2.87
32	33	6.158023	TCTTGTTACGAAACCTCTTCTTCT	57.842	37.500	0.00	0.00	34.49	2.85
33	34	5.984323	ACTCTTGTTACGAAACCTCTTCTTC	59.016	40.000	0.00	0.00	34.49	2.87
34	35	5.915175	ACTCTTGTTACGAAACCTCTTCTT	58.085	37.500	0.00	0.00	34.49	2.52
35	36	5.532664	ACTCTTGTTACGAAACCTCTTCT	57.467	39.130	0.00	0.00	34.49	2.85
36	37	7.384387	ACAATACTCTTGTTACGAAACCTCTTC	59.616	37.037	0.00	0.00	34.49	2.87
37	38	7.215085	ACAATACTCTTGTTACGAAACCTCTT	58.785	34.615	0.00	0.00	34.49	2.85
38	39	6.756221	ACAATACTCTTGTTACGAAACCTCT	58.244	36.000	0.00	0.00	34.49	3.69
39	40	7.288672	CAACAATACTCTTGTTACGAAACCTC	58.711	38.462	3.26	0.00	40.30	3.85
40	41	6.293244	GCAACAATACTCTTGTTACGAAACCT	60.293	38.462	3.26	0.00	40.30	3.50
41	42	5.849604	GCAACAATACTCTTGTTACGAAACC	59.150	40.000	3.26	0.00	40.30	3.27
42	43	6.423862	TGCAACAATACTCTTGTTACGAAAC	58.576	36.000	3.26	0.00	40.30	2.78
43	44	6.480651	TCTGCAACAATACTCTTGTTACGAAA	59.519	34.615	3.26	0.00	40.30	3.46
44	45	5.986741	TCTGCAACAATACTCTTGTTACGAA	59.013	36.000	3.26	0.00	40.30	3.85
45	46	5.534407	TCTGCAACAATACTCTTGTTACGA	58.466	37.500	3.26	0.00	40.30	3.43
46	47	5.839262	TCTGCAACAATACTCTTGTTACG	57.161	39.130	3.26	0.00	40.30	3.18
47	48	9.463443	AATTTTCTGCAACAATACTCTTGTTAC	57.537	29.630	3.26	0.00	40.30	2.50
49	50	9.683069	CTAATTTTCTGCAACAATACTCTTGTT	57.317	29.630	0.00	0.00	42.75	2.83
50	51	9.066892	TCTAATTTTCTGCAACAATACTCTTGT	57.933	29.630	0.00	0.00	0.00	3.16
51	52	9.552114	CTCTAATTTTCTGCAACAATACTCTTG	57.448	33.333	0.00	0.00	0.00	3.02
52	53	8.239998	GCTCTAATTTTCTGCAACAATACTCTT	58.760	33.333	0.00	0.00	0.00	2.85
53	54	7.391554	TGCTCTAATTTTCTGCAACAATACTCT	59.608	33.333	0.00	0.00	0.00	3.24
54	55	7.530010	TGCTCTAATTTTCTGCAACAATACTC	58.470	34.615	0.00	0.00	0.00	2.59
55	56	7.452880	TGCTCTAATTTTCTGCAACAATACT	57.547	32.000	0.00	0.00	0.00	2.12
62	63	4.826733	TGGAGTTGCTCTAATTTTCTGCAA	59.173	37.500	0.00	0.00	40.65	4.08
63	64	4.397420	TGGAGTTGCTCTAATTTTCTGCA	58.603	39.130	0.00	0.00	0.00	4.41
64	65	5.376854	TTGGAGTTGCTCTAATTTTCTGC	57.623	39.130	0.00	0.00	0.00	4.26
65	66	6.327934	CCATTGGAGTTGCTCTAATTTTCTG	58.672	40.000	0.00	0.00	39.14	3.02
66	67	5.420104	CCCATTGGAGTTGCTCTAATTTTCT	59.580	40.000	3.62	0.00	39.14	2.52
67	68	5.394553	CCCCATTGGAGTTGCTCTAATTTTC	60.395	44.000	3.62	0.00	39.14	2.29
68	69	4.467438	CCCCATTGGAGTTGCTCTAATTTT	59.533	41.667	3.62	0.00	39.14	1.82
493	634	0.106918	ACTCCTTTGCCCGTTGTTCA	60.107	50.000	0.00	0.00	0.00	3.18
563	731	1.410050	TTGGTGACCTGCTGCTGAGA	61.410	55.000	2.11	0.00	0.00	3.27
565	736	1.227943	GTTGGTGACCTGCTGCTGA	60.228	57.895	2.11	0.00	0.00	4.26
600	774	0.749454	GTAGACCGCCTCCCTCGTTA	60.749	60.000	0.00	0.00	0.00	3.18
802	982	2.224159	AACCATGCTCACCTCGGGT	61.224	57.895	0.00	0.00	35.62	5.28
1075	1268	3.838244	TCTTTATTGTAGCCAGCGGAT	57.162	42.857	0.00	0.00	0.00	4.18
1091	1284	0.257039	ATGAAGGCGGCCTGATCTTT	59.743	50.000	24.63	5.09	32.13	2.52
1229	1422	2.985847	GGCTTGGTTGGCGAGCTT	60.986	61.111	5.40	0.00	36.66	3.74
1279	1472	2.038269	CGCCGTGTATGCCTTGGTT	61.038	57.895	0.00	0.00	0.00	3.67
1361	1557	5.942826	TCCAAAAGGTTGAATGCTTTTGTTT	59.057	32.000	5.93	0.00	42.09	2.83
1409	1605	4.826600	CGGAAACTTCTTGCGCTG	57.173	55.556	9.73	1.08	0.00	5.18
1525	1726	4.047125	CACGGGGTGGGCCTTGAT	62.047	66.667	4.53	0.00	34.45	2.57
1611	1814	8.661257	CAAAATGATATGCAAATGAACACACAT	58.339	29.630	0.00	0.00	0.00	3.21
1668	1872	2.596346	TGCCTCCAAAGCTTGAAATGA	58.404	42.857	0.00	0.00	0.00	2.57
1768	1973	3.496130	CGACTTGAGGATGGCATATTGTC	59.504	47.826	0.00	3.07	0.00	3.18
1780	1986	2.338620	CACCACGCGACTTGAGGA	59.661	61.111	15.93	0.00	0.00	3.71
1809	2015	1.995626	CGTCCCCAACCTCCTCCAT	60.996	63.158	0.00	0.00	0.00	3.41
1905	2111	0.038166	ATCATGCCCTTCACGGTTGT	59.962	50.000	0.00	0.00	0.00	3.32
2037	2244	0.182061	GCCTCCATCTCAAGCATCCA	59.818	55.000	0.00	0.00	0.00	3.41
2249	2490	1.630126	AAGATGAGGCTCGCCACCAT	61.630	55.000	10.42	12.34	38.92	3.55
2250	2491	1.841302	AAAGATGAGGCTCGCCACCA	61.841	55.000	10.42	8.00	38.92	4.17
2251	2492	0.678048	AAAAGATGAGGCTCGCCACC	60.678	55.000	10.42	2.19	38.92	4.61
2253	2494	1.167851	CAAAAAGATGAGGCTCGCCA	58.832	50.000	10.42	0.00	38.92	5.69
2254	2495	0.453390	CCAAAAAGATGAGGCTCGCC	59.547	55.000	10.42	0.00	0.00	5.54
2256	2497	2.223433	GCATCCAAAAAGATGAGGCTCG	60.223	50.000	10.42	0.00	45.43	5.03
2258	2499	2.105766	GGCATCCAAAAAGATGAGGCT	58.894	47.619	5.73	0.00	45.43	4.58
2264	2506	2.094675	CCTGTCGGCATCCAAAAAGAT	58.905	47.619	0.00	0.00	0.00	2.40
2266	2508	1.068333	CACCTGTCGGCATCCAAAAAG	60.068	52.381	0.00	0.00	0.00	2.27
2317	2563	1.002087	GTGGGACTTGAGTTCGACCAT	59.998	52.381	0.00	0.00	0.00	3.55
2460	2715	3.643978	GACCGATCATGCCAGCGC	61.644	66.667	0.00	0.00	0.00	5.92

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.