AutoCloner

Multiple sequence alignment - TraesCS2D01G338600

Loading Multiple Alignment...

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	TraesCS2D01G338600	chr2D	100.000	2507	0	0	1	2507	431999325	432001831	0.000000e+00	4630.0
1	TraesCS2D01G338600	chr2D	84.106	755	92	6	975	1728	432029811	432030538	0.000000e+00	704.0
2	TraesCS2D01G338600	chr2D	80.874	183	26	5	2283	2459	82897801	82897980	4.350000e-28	135.0
3	TraesCS2D01G338600	chr2B	90.490	1346	99	16	755	2084	510787638	510788970	0.000000e+00	1749.0
4	TraesCS2D01G338600	chr2B	84.230	799	97	15	975	1772	510792751	510793521	0.000000e+00	750.0
5	TraesCS2D01G338600	chr2B	85.202	446	42	16	2078	2505	510789018	510789457	1.060000e-118	436.0
6	TraesCS2D01G338600	chr2B	97.727	44	1	0	1591	1634	510793386	510793429	2.670000e-10	76.8
7	TraesCS2D01G338600	chr2B	85.714	63	8	1	1986	2047	150676582	150676644	5.790000e-07	65.8
8	TraesCS2D01G338600	chr2A	93.385	1028	49	10	755	1768	554519773	554518751	0.000000e+00	1504.0
9	TraesCS2D01G338600	chr2A	85.556	720	78	11	975	1693	554512320	554511626	0.000000e+00	730.0
10	TraesCS2D01G338600	chr2A	90.826	109	9	1	2396	2503	554517563	554517455	7.230000e-31	145.0
11	TraesCS2D01G338600	chr2A	84.286	140	19	3	2211	2348	72518843	72518705	1.560000e-27	134.0
12	TraesCS2D01G338600	chr2A	100.000	45	0	0	1590	1634	554511686	554511642	1.600000e-12	84.2
13	TraesCS2D01G338600	chr3B	94.161	685	37	3	1	684	66195018	66194336	0.000000e+00	1040.0
14	TraesCS2D01G338600	chr3B	88.889	81	3	4	681	759	572465928	572465852	7.380000e-16	95.3
15	TraesCS2D01G338600	chr7A	93.294	686	42	4	1	684	85658015	85658698	0.000000e+00	1009.0
16	TraesCS2D01G338600	chr7A	95.312	64	1	2	695	757	38226521	38226459	1.590000e-17	100.0
17	TraesCS2D01G338600	chr7B	91.108	686	58	3	1	684	730202742	730202058	0.000000e+00	926.0
18	TraesCS2D01G338600	chr6A	89.213	686	71	3	1	684	190585449	190586133	0.000000e+00	854.0
19	TraesCS2D01G338600	chr6A	76.151	239	44	13	2219	2455	556739228	556739001	2.040000e-21	113.0
20	TraesCS2D01G338600	chr4B	88.192	686	78	3	1	684	627154980	627155664	0.000000e+00	815.0
21	TraesCS2D01G338600	chr7D	88.548	489	53	3	197	684	209827548	209828034	7.720000e-165	590.0
22	TraesCS2D01G338600	chr7D	88.710	62	6	1	1985	2045	159440355	159440416	9.620000e-10	75.0
23	TraesCS2D01G338600	chr4A	82.465	576	94	7	100	671	729000164	729000736	4.820000e-137	497.0
24	TraesCS2D01G338600	chr4A	88.312	77	5	4	681	756	620742230	620742303	3.430000e-14	89.8
25	TraesCS2D01G338600	chr6D	83.193	238	33	6	2220	2455	23434072	23434304	7.030000e-51	211.0
26	TraesCS2D01G338600	chr6D	82.773	238	34	6	2220	2455	31764188	31764420	3.270000e-49	206.0
27	TraesCS2D01G338600	chr3D	82.609	161	22	4	2219	2378	11452690	11452535	1.210000e-28	137.0
28	TraesCS2D01G338600	chr3D	78.531	177	26	5	2283	2456	26810859	26810692	3.410000e-19	106.0
29	TraesCS2D01G338600	chr6B	81.921	177	17	9	2285	2455	619524372	619524205	4.350000e-28	135.0
30	TraesCS2D01G338600	chr5D	84.397	141	18	4	2219	2356	481641859	481641720	4.350000e-28	135.0
31	TraesCS2D01G338600	chr5D	82.143	140	21	4	2219	2356	557142176	557142313	1.580000e-22	117.0
32	TraesCS2D01G338600	chr3A	79.602	201	31	7	2255	2453	657302359	657302551	4.350000e-28	135.0
33	TraesCS2D01G338600	chrUn	77.686	242	29	12	2218	2456	38657415	38657196	9.420000e-25	124.0
34	TraesCS2D01G338600	chrUn	90.000	60	3	2	1984	2041	27564611	27564669	9.620000e-10	75.0
35	TraesCS2D01G338600	chr5A	84.416	77	7	5	681	755	636303643	636303716	1.240000e-08	71.3
36	TraesCS2D01G338600	chr1B	78.333	120	17	6	1933	2045	478591451	478591334	4.470000e-08	69.4

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	TraesCS2D01G338600	chr2D	431999325	432001831	2506	False	4630.00	4630	100.00000	1	2507	1	chr2D.!!$F2	2506
1	TraesCS2D01G338600	chr2D	432029811	432030538	727	False	704.00	704	84.10600	975	1728	1	chr2D.!!$F3	753
2	TraesCS2D01G338600	chr2B	510787638	510793521	5883	False	752.95	1749	89.41225	755	2505	4	chr2B.!!$F2	1750
3	TraesCS2D01G338600	chr2A	554517455	554519773	2318	True	824.50	1504	92.10550	755	2503	2	chr2A.!!$R3	1748
4	TraesCS2D01G338600	chr2A	554511626	554512320	694	True	407.10	730	92.77800	975	1693	2	chr2A.!!$R2	718
5	TraesCS2D01G338600	chr3B	66194336	66195018	682	True	1040.00	1040	94.16100	1	684	1	chr3B.!!$R1	683
6	TraesCS2D01G338600	chr7A	85658015	85658698	683	False	1009.00	1009	93.29400	1	684	1	chr7A.!!$F1	683
7	TraesCS2D01G338600	chr7B	730202058	730202742	684	True	926.00	926	91.10800	1	684	1	chr7B.!!$R1	683
8	TraesCS2D01G338600	chr6A	190585449	190586133	684	False	854.00	854	89.21300	1	684	1	chr6A.!!$F1	683
9	TraesCS2D01G338600	chr4B	627154980	627155664	684	False	815.00	815	88.19200	1	684	1	chr4B.!!$F1	683
10	TraesCS2D01G338600	chr4A	729000164	729000736	572	False	497.00	497	82.46500	100	671	1	chr4A.!!$F2	571

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
710	713	0.179048	GCTTTGGTTTGCCTTGGCTT	60.179	50.0	13.18	0.0	35.27	4.35	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2117	2732	0.110238	GATCGCTTTGCTTGCAACGA	60.11	50.0	18.36	18.36	0.0	3.85	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
73	74	1.768077	CTGTCCCCCATCTCCTCCC	60.768	68.421	0.00	0.00	0.00	4.30
246	247	5.163447	CCAAGTGATAACATCTCCCTCGTAA	60.163	44.000	0.00	0.00	0.00	3.18
376	377	6.865834	TTAAAATCACCCAAACATAGCCAT	57.134	33.333	0.00	0.00	0.00	4.40
478	479	5.423610	CCCATATACTCCAGTAATCCTCCAG	59.576	48.000	0.00	0.00	33.76	3.86
492	493	2.196595	CCTCCAGGTTGAACCATCCTA	58.803	52.381	17.83	0.00	41.95	2.94
497	498	2.571653	CAGGTTGAACCATCCTACTCCA	59.428	50.000	17.83	0.00	41.95	3.86
550	551	4.038042	ACCGATCGCAAAGAGAGATTGATA	59.962	41.667	10.32	0.00	39.53	2.15
602	605	0.243907	TTCCTTCTGAGTCCTTCGCG	59.756	55.000	0.00	0.00	0.00	5.87
640	643	1.059913	AGCTTCCACCTGTACTGCTT	58.940	50.000	0.00	0.00	0.00	3.91
684	687	3.354397	GTCTCGCACAAAAACAGAACAG	58.646	45.455	0.00	0.00	0.00	3.16
685	688	3.006940	TCTCGCACAAAAACAGAACAGT	58.993	40.909	0.00	0.00	0.00	3.55
686	689	3.063452	TCTCGCACAAAAACAGAACAGTC	59.937	43.478	0.00	0.00	0.00	3.51
687	690	3.006940	TCGCACAAAAACAGAACAGTCT	58.993	40.909	0.00	0.00	32.85	3.24
688	691	3.438781	TCGCACAAAAACAGAACAGTCTT	59.561	39.130	0.00	0.00	28.78	3.01
689	692	4.083003	TCGCACAAAAACAGAACAGTCTTT	60.083	37.500	0.00	0.00	28.78	2.52
690	693	4.621034	CGCACAAAAACAGAACAGTCTTTT	59.379	37.500	0.00	0.00	28.78	2.27
691	694	5.443170	CGCACAAAAACAGAACAGTCTTTTG	60.443	40.000	4.50	4.50	36.11	2.44
692	695	5.668621	GCACAAAAACAGAACAGTCTTTTGC	60.669	40.000	5.69	0.00	34.51	3.68
693	696	5.634859	CACAAAAACAGAACAGTCTTTTGCT	59.365	36.000	5.69	0.00	34.51	3.91
694	697	6.146021	CACAAAAACAGAACAGTCTTTTGCTT	59.854	34.615	5.69	0.00	34.51	3.91
695	698	6.705825	ACAAAAACAGAACAGTCTTTTGCTTT	59.294	30.769	5.69	0.00	34.51	3.51
696	699	6.710692	AAAACAGAACAGTCTTTTGCTTTG	57.289	33.333	0.00	0.00	28.78	2.77
697	700	4.376340	ACAGAACAGTCTTTTGCTTTGG	57.624	40.909	0.00	0.00	28.78	3.28
698	701	3.763897	ACAGAACAGTCTTTTGCTTTGGT	59.236	39.130	0.00	0.00	28.78	3.67
699	702	4.220602	ACAGAACAGTCTTTTGCTTTGGTT	59.779	37.500	0.00	0.00	28.78	3.67
700	703	5.170748	CAGAACAGTCTTTTGCTTTGGTTT	58.829	37.500	0.00	0.00	28.78	3.27
701	704	5.062558	CAGAACAGTCTTTTGCTTTGGTTTG	59.937	40.000	0.00	0.00	28.78	2.93
702	705	3.261580	ACAGTCTTTTGCTTTGGTTTGC	58.738	40.909	0.00	0.00	0.00	3.68
703	706	2.609002	CAGTCTTTTGCTTTGGTTTGCC	59.391	45.455	0.00	0.00	0.00	4.52
704	707	2.501316	AGTCTTTTGCTTTGGTTTGCCT	59.499	40.909	0.00	0.00	35.27	4.75
705	708	3.055167	AGTCTTTTGCTTTGGTTTGCCTT	60.055	39.130	0.00	0.00	35.27	4.35
706	709	3.063861	GTCTTTTGCTTTGGTTTGCCTTG	59.936	43.478	0.00	0.00	35.27	3.61
707	710	2.035530	TTTGCTTTGGTTTGCCTTGG	57.964	45.000	0.00	0.00	35.27	3.61
708	711	0.463474	TTGCTTTGGTTTGCCTTGGC	60.463	50.000	4.43	4.43	35.27	4.52
709	712	1.336632	TGCTTTGGTTTGCCTTGGCT	61.337	50.000	13.18	0.00	35.27	4.75
710	713	0.179048	GCTTTGGTTTGCCTTGGCTT	60.179	50.000	13.18	0.00	35.27	4.35
711	714	1.746861	GCTTTGGTTTGCCTTGGCTTT	60.747	47.619	13.18	0.00	35.27	3.51
712	715	2.484594	GCTTTGGTTTGCCTTGGCTTTA	60.485	45.455	13.18	0.00	35.27	1.85
713	716	3.802866	CTTTGGTTTGCCTTGGCTTTAA	58.197	40.909	13.18	2.27	35.27	1.52
714	717	4.388485	CTTTGGTTTGCCTTGGCTTTAAT	58.612	39.130	13.18	0.00	35.27	1.40
715	718	5.546526	CTTTGGTTTGCCTTGGCTTTAATA	58.453	37.500	13.18	0.00	35.27	0.98
716	719	5.552870	TTGGTTTGCCTTGGCTTTAATAA	57.447	34.783	13.18	0.00	35.27	1.40
717	720	5.552870	TGGTTTGCCTTGGCTTTAATAAA	57.447	34.783	13.18	1.20	35.27	1.40
718	721	5.930135	TGGTTTGCCTTGGCTTTAATAAAA	58.070	33.333	13.18	0.51	35.27	1.52
719	722	6.357367	TGGTTTGCCTTGGCTTTAATAAAAA	58.643	32.000	13.18	0.00	35.27	1.94
733	736	2.525629	AAAAAGTTGGGGCGGGGG	60.526	61.111	0.00	0.00	0.00	5.40
734	737	3.089419	AAAAAGTTGGGGCGGGGGA	62.089	57.895	0.00	0.00	0.00	4.81
735	738	2.607139	AAAAAGTTGGGGCGGGGGAA	62.607	55.000	0.00	0.00	0.00	3.97
736	739	2.607139	AAAAGTTGGGGCGGGGGAAA	62.607	55.000	0.00	0.00	0.00	3.13
737	740	3.820825	AAGTTGGGGCGGGGGAAAC	62.821	63.158	0.00	0.00	0.00	2.78
775	778	1.738099	CAGTACTGTCACGCTGCCC	60.738	63.158	15.06	0.00	0.00	5.36
824	830	4.104261	TCTGGAGATGGTAATCCGAGACTA	59.896	45.833	0.00	0.00	38.52	2.59
898	905	0.401738	GCCATATAAGCCAGCAGGGA	59.598	55.000	0.00	0.00	40.01	4.20
914	922	3.465753	GACGCGCGTCCAATGTAA	58.534	55.556	44.30	0.00	39.08	2.41
937	945	1.795170	AAGTTCACGCCGCTGCATTT	61.795	50.000	0.00	0.00	37.32	2.32
1351	1359	1.495951	GAATTCGCCGCTTTCACGT	59.504	52.632	0.00	0.00	0.00	4.49
1359	1367	2.357760	GCTTTCACGTGCCGGGTA	60.358	61.111	11.67	0.00	0.00	3.69
1542	1550	2.946762	GAACGCTCCAACACTGCC	59.053	61.111	0.00	0.00	0.00	4.85
1641	1658	7.982371	AACTAGATTATCGGTCGTTTGTTAG	57.018	36.000	0.00	0.00	0.00	2.34
1747	1765	6.646267	TGTTGAACATATAAGACCTACCCAC	58.354	40.000	0.00	0.00	0.00	4.61
1773	1791	4.260784	CGGGCAGTCAAATTCTAATGCTAC	60.261	45.833	10.88	5.50	34.19	3.58
1776	1794	5.522460	GGCAGTCAAATTCTAATGCTACGTA	59.478	40.000	10.88	0.00	34.19	3.57
1777	1795	6.411652	GCAGTCAAATTCTAATGCTACGTAC	58.588	40.000	0.00	0.00	0.00	3.67
1778	1796	6.255887	GCAGTCAAATTCTAATGCTACGTACT	59.744	38.462	0.00	0.00	0.00	2.73
1780	1798	8.959058	CAGTCAAATTCTAATGCTACGTACTAG	58.041	37.037	0.00	0.00	0.00	2.57
1800	1818	9.526713	GTACTAGTACTAGGGTTAAAAATGCTC	57.473	37.037	29.05	0.69	37.49	4.26
1836	2383	6.697641	ACAAAAGGGAAGGAGTACATCTTA	57.302	37.500	0.00	0.00	0.00	2.10
1859	2407	4.389664	TCTCGAAGTTTGAGAAATTGCG	57.610	40.909	18.82	0.00	39.44	4.85
1912	2460	3.934457	CCGTAAAAAGGCCAGACAAAT	57.066	42.857	5.01	0.00	0.00	2.32
1920	2468	1.117150	GGCCAGACAAATGCCATGAT	58.883	50.000	0.00	0.00	44.70	2.45
1957	2506	1.829523	AACGCGGTTACTTAGGGCCA	61.830	55.000	12.47	0.00	0.00	5.36
1958	2507	1.520787	CGCGGTTACTTAGGGCCAG	60.521	63.158	6.18	0.00	0.00	4.85
1966	2515	6.527423	CGGTTACTTAGGGCCAGATTTATTA	58.473	40.000	6.18	0.00	0.00	0.98
1972	2521	8.753497	ACTTAGGGCCAGATTTATTAAAAGAG	57.247	34.615	6.18	0.00	0.00	2.85
1973	2522	8.557450	ACTTAGGGCCAGATTTATTAAAAGAGA	58.443	33.333	6.18	0.00	0.00	3.10
1976	2525	8.844865	AGGGCCAGATTTATTAAAAGAGAATT	57.155	30.769	6.18	0.00	0.00	2.17
1977	2526	9.271921	AGGGCCAGATTTATTAAAAGAGAATTT	57.728	29.630	6.18	0.00	0.00	1.82
1978	2527	9.317936	GGGCCAGATTTATTAAAAGAGAATTTG	57.682	33.333	4.39	0.00	0.00	2.32
1979	2528	8.820933	GGCCAGATTTATTAAAAGAGAATTTGC	58.179	33.333	0.00	0.00	0.00	3.68
1980	2529	9.591792	GCCAGATTTATTAAAAGAGAATTTGCT	57.408	29.630	0.00	0.00	0.00	3.91
2028	2585	1.922135	AATCGTCACAACATGCCCGC	61.922	55.000	0.00	0.00	0.00	6.13
2034	2591	1.069823	TCACAACATGCCCGCAAAAAT	59.930	42.857	0.00	0.00	0.00	1.82
2043	2600	1.708822	CCCGCAAAAATAAGGCACAC	58.291	50.000	0.00	0.00	0.00	3.82
2108	2723	3.245016	ACACATTTCCAGAATCCAGAGCA	60.245	43.478	0.00	0.00	0.00	4.26
2117	2732	4.525024	CAGAATCCAGAGCAAAGGATCTT	58.475	43.478	4.57	0.00	43.67	2.40
2129	2744	1.896220	AGGATCTTCGTTGCAAGCAA	58.104	45.000	0.00	2.89	0.00	3.91
2136	2751	0.110238	TCGTTGCAAGCAAAGCGATC	60.110	50.000	14.47	0.00	37.70	3.69
2142	2757	0.729116	CAAGCAAAGCGATCGGTCAT	59.271	50.000	21.51	10.01	0.00	3.06
2187	2818	4.794439	CCGTCGGCGCTCATGTCA	62.794	66.667	2.51	0.00	36.67	3.58
2195	2826	1.438651	GCGCTCATGTCAAACACCTA	58.561	50.000	0.00	0.00	0.00	3.08
2200	2831	2.684881	CTCATGTCAAACACCTATGGGC	59.315	50.000	0.00	0.00	35.63	5.36
2212	2843	2.041081	ACCTATGGGCTTGTTGCTTACA	59.959	45.455	0.00	0.00	42.39	2.41
2234	2865	7.297229	ACAACCAAGGTTAAAAATTTCAACG	57.703	32.000	3.82	0.00	36.46	4.10
2279	2910	7.399765	TGAAATTTCACATATTCTGATGGGGTT	59.600	33.333	16.91	0.00	30.63	4.11
2280	2911	7.738437	AATTTCACATATTCTGATGGGGTTT	57.262	32.000	0.00	0.00	30.63	3.27
2326	2957	6.817765	TCGAGCCAGATTCAAACTAATTTT	57.182	33.333	0.00	0.00	0.00	1.82
2404	3035	8.442384	CCTATGATTTTGTTTTGGAAATTTCGG	58.558	33.333	11.95	0.00	0.00	4.30
2409	3040	9.971744	GATTTTGTTTTGGAAATTTCGGATATG	57.028	29.630	11.95	0.00	0.00	1.78
2421	3052	1.043816	CGGATATGTCAGTGAGGCCT	58.956	55.000	3.86	3.86	0.00	5.19
2505	3137	1.068885	GCCTAGACATCATCTCCGACG	60.069	57.143	0.00	0.00	39.04	5.12

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
40	41	2.124996	CAGGGGGAGGAAGGGACA	59.875	66.667	0.00	0.00	0.00	4.02
246	247	3.580458	AGTGCAAGTTGAGTGATCTAGGT	59.420	43.478	7.16	0.00	0.00	3.08
313	314	1.273886	GAGAAGAGAGGTGGTGTGGAC	59.726	57.143	0.00	0.00	0.00	4.02
376	377	0.253160	AACATCAGGAGGGTAGGCCA	60.253	55.000	5.01	0.00	36.17	5.36
478	479	3.933861	ATGGAGTAGGATGGTTCAACC	57.066	47.619	0.00	0.00	39.22	3.77
492	493	3.206150	GTTGATGCGGACATAATGGAGT	58.794	45.455	0.00	0.00	36.35	3.85
497	498	1.330521	GCACGTTGATGCGGACATAAT	59.669	47.619	0.00	0.00	36.35	1.28
550	551	1.512735	GCTATTTCTGGAGGAGGGGT	58.487	55.000	0.00	0.00	0.00	4.95
602	605	2.223805	GCTAGGGTTGGCAAATATGTGC	60.224	50.000	9.58	9.58	44.14	4.57
640	643	0.322975	GCTGTTGGAGAAGGAGCTGA	59.677	55.000	0.00	0.00	0.00	4.26
684	687	2.905075	AGGCAAACCAAAGCAAAAGAC	58.095	42.857	0.00	0.00	39.06	3.01
685	688	3.269178	CAAGGCAAACCAAAGCAAAAGA	58.731	40.909	0.00	0.00	39.06	2.52
686	689	2.355444	CCAAGGCAAACCAAAGCAAAAG	59.645	45.455	0.00	0.00	39.06	2.27
687	690	2.363683	CCAAGGCAAACCAAAGCAAAA	58.636	42.857	0.00	0.00	39.06	2.44
688	691	2.016096	GCCAAGGCAAACCAAAGCAAA	61.016	47.619	6.14	0.00	41.49	3.68
689	692	0.463474	GCCAAGGCAAACCAAAGCAA	60.463	50.000	6.14	0.00	41.49	3.91
690	693	1.145819	GCCAAGGCAAACCAAAGCA	59.854	52.632	6.14	0.00	41.49	3.91
691	694	0.179048	AAGCCAAGGCAAACCAAAGC	60.179	50.000	14.40	0.00	44.88	3.51
692	695	2.330440	AAAGCCAAGGCAAACCAAAG	57.670	45.000	14.40	0.00	44.88	2.77
693	696	3.914426	TTAAAGCCAAGGCAAACCAAA	57.086	38.095	14.40	0.00	44.88	3.28
694	697	5.552870	TTATTAAAGCCAAGGCAAACCAA	57.447	34.783	14.40	0.38	44.88	3.67
695	698	5.552870	TTTATTAAAGCCAAGGCAAACCA	57.447	34.783	14.40	0.00	44.88	3.67
696	699	6.869315	TTTTTATTAAAGCCAAGGCAAACC	57.131	33.333	14.40	0.00	44.88	3.27
716	719	2.525629	CCCCCGCCCCAACTTTTT	60.526	61.111	0.00	0.00	0.00	1.94
717	720	2.607139	TTTCCCCCGCCCCAACTTTT	62.607	55.000	0.00	0.00	0.00	2.27
718	721	3.089419	TTTCCCCCGCCCCAACTTT	62.089	57.895	0.00	0.00	0.00	2.66
719	722	3.513566	TTTCCCCCGCCCCAACTT	61.514	61.111	0.00	0.00	0.00	2.66
720	723	4.295199	GTTTCCCCCGCCCCAACT	62.295	66.667	0.00	0.00	0.00	3.16
752	755	2.031683	GCAGCGTGACAGTACTGTTTTT	59.968	45.455	28.49	6.70	45.05	1.94
753	756	1.597663	GCAGCGTGACAGTACTGTTTT	59.402	47.619	28.49	7.10	45.05	2.43
775	778	1.585214	GCGGGTCTGAAATACGTTACG	59.415	52.381	2.19	2.19	0.00	3.18
861	868	2.265904	CCGACCACTCCGACTGTCA	61.266	63.158	8.73	0.00	0.00	3.58
898	905	2.385091	GGTTACATTGGACGCGCGT	61.385	57.895	38.52	38.52	0.00	6.01
911	919	1.864176	CGGCGTGAACTTGGGTTAC	59.136	57.895	0.00	0.00	35.58	2.50
912	920	1.962306	GCGGCGTGAACTTGGGTTA	60.962	57.895	9.37	0.00	35.58	2.85
913	921	3.284449	GCGGCGTGAACTTGGGTT	61.284	61.111	9.37	0.00	38.52	4.11
914	922	4.250305	AGCGGCGTGAACTTGGGT	62.250	61.111	9.37	0.00	0.00	4.51
1203	1211	4.761058	TTCGCCTCCTCCTCCGCT	62.761	66.667	0.00	0.00	0.00	5.52
1219	1227	3.036084	CGTGTGCTCGGCGTTCTT	61.036	61.111	6.85	0.00	0.00	2.52
1335	1343	2.860293	CACGTGAAAGCGGCGAAT	59.140	55.556	12.98	0.00	35.98	3.34
1357	1365	4.874977	GACCGGCAGCGAGGCTAC	62.875	72.222	0.00	0.00	36.40	3.58
1526	1534	2.186826	GTGGCAGTGTTGGAGCGTT	61.187	57.895	0.00	0.00	0.00	4.84
1671	1689	5.363580	TGTATACATCATCTGAAGCTGACCA	59.636	40.000	0.08	0.00	0.00	4.02
1728	1746	4.100498	CGTGGTGGGTAGGTCTTATATGTT	59.900	45.833	0.00	0.00	0.00	2.71
1733	1751	1.492764	CCGTGGTGGGTAGGTCTTAT	58.507	55.000	0.00	0.00	0.00	1.73
1747	1765	2.107950	TAGAATTTGACTGCCCGTGG	57.892	50.000	0.00	0.00	0.00	4.94
1773	1791	8.193438	AGCATTTTTAACCCTAGTACTAGTACG	58.807	37.037	24.84	15.46	40.80	3.67
1776	1794	8.376803	AGAGCATTTTTAACCCTAGTACTAGT	57.623	34.615	24.84	11.90	0.00	2.57
1815	1833	8.164057	AGATTAAGATGTACTCCTTCCCTTTT	57.836	34.615	0.00	0.00	0.00	2.27
1817	1835	6.041069	CGAGATTAAGATGTACTCCTTCCCTT	59.959	42.308	0.00	0.00	0.00	3.95
1821	1839	7.708998	ACTTCGAGATTAAGATGTACTCCTTC	58.291	38.462	0.00	0.00	0.00	3.46
1836	2383	5.385617	CGCAATTTCTCAAACTTCGAGATT	58.614	37.500	0.00	0.00	39.22	2.40
1859	2407	1.876156	CAGTTCAAGTCCAGTTCAGGC	59.124	52.381	0.00	0.00	0.00	4.85
1906	2454	3.891422	TTGGGAATCATGGCATTTGTC	57.109	42.857	0.00	0.00	0.00	3.18
1912	2460	6.013898	TCAAAATAAGTTTGGGAATCATGGCA	60.014	34.615	0.00	0.00	45.73	4.92
1917	2465	6.422400	GCGTTTCAAAATAAGTTTGGGAATCA	59.578	34.615	0.90	0.00	45.73	2.57
1920	2468	4.740695	CGCGTTTCAAAATAAGTTTGGGAA	59.259	37.500	0.00	0.00	45.73	3.97
2002	2559	3.425193	GCATGTTGTGACGATTTTTGTCC	59.575	43.478	0.00	0.00	35.46	4.02
2028	2585	4.744631	GTCCACTTGTGTGCCTTATTTTTG	59.255	41.667	0.00	0.00	42.54	2.44
2034	2591	2.171659	TCTTGTCCACTTGTGTGCCTTA	59.828	45.455	0.00	0.00	42.54	2.69
2043	2600	5.089970	TGGTCTATGATCTTGTCCACTTG	57.910	43.478	0.00	0.00	0.00	3.16
2079	2636	7.286546	TCTGGATTCTGGAAATGTGTGTTTTTA	59.713	33.333	0.00	0.00	0.00	1.52
2108	2723	2.229792	TGCTTGCAACGAAGATCCTTT	58.770	42.857	0.00	0.00	0.00	3.11
2117	2732	0.110238	GATCGCTTTGCTTGCAACGA	60.110	50.000	18.36	18.36	0.00	3.85
2129	2744	0.674534	GTCCCTATGACCGATCGCTT	59.325	55.000	10.32	0.00	38.09	4.68
2136	2751	1.162181	TCGCTACGTCCCTATGACCG	61.162	60.000	0.00	0.00	41.18	4.79
2142	2757	2.775890	CCTCTATTCGCTACGTCCCTA	58.224	52.381	0.00	0.00	0.00	3.53
2187	2818	1.618343	GCAACAAGCCCATAGGTGTTT	59.382	47.619	0.00	0.00	31.67	2.83
2212	2843	8.725405	ATTCGTTGAAATTTTTAACCTTGGTT	57.275	26.923	10.11	10.11	0.00	3.67
2262	2893	9.438163	AATATTTCAAACCCCATCAGAATATGT	57.562	29.630	0.00	0.00	0.00	2.29
2295	2926	5.703978	TTGAATCTGGCTCGAAATTTTGA	57.296	34.783	7.89	7.89	0.00	2.69
2389	3020	7.273381	CACTGACATATCCGAAATTTCCAAAAC	59.727	37.037	12.54	0.00	0.00	2.43
2390	3021	7.175816	TCACTGACATATCCGAAATTTCCAAAA	59.824	33.333	12.54	0.00	0.00	2.44
2394	3025	5.237344	CCTCACTGACATATCCGAAATTTCC	59.763	44.000	12.54	0.00	0.00	3.13
2404	3035	3.827008	TTCAGGCCTCACTGACATATC	57.173	47.619	0.00	0.00	46.44	1.63
2409	3040	2.508526	ACAATTTCAGGCCTCACTGAC	58.491	47.619	0.00	0.00	46.44	3.51

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.