AutoCloner

Multiple sequence alignment - TraesCS2B01G266100

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	TraesCS2B01G266100	chr2B	100.000	3432	0	0	1	3432	358531707	358528276	0.000000e+00	6338.0
1	TraesCS2B01G266100	chr2B	90.852	634	56	2	14	647	694490992	694490361	0.000000e+00	848.0
2	TraesCS2B01G266100	chr2A	96.273	1878	40	9	648	2496	374592609	374594485	0.000000e+00	3053.0
3	TraesCS2B01G266100	chr2A	85.463	227	14	4	2569	2776	374594581	374594807	5.770000e-53	219.0
4	TraesCS2B01G266100	chr2D	94.737	1900	47	14	648	2494	299529387	299531286	0.000000e+00	2905.0
5	TraesCS2B01G266100	chr2D	91.496	635	52	2	17	651	638865280	638864648	0.000000e+00	872.0
6	TraesCS2B01G266100	chr2D	91.038	636	47	9	19	651	589512830	589512202	0.000000e+00	850.0
7	TraesCS2B01G266100	chr2D	87.419	620	49	14	2778	3389	521536418	521537016	0.000000e+00	686.0
8	TraesCS2B01G266100	chr2D	87.562	201	10	3	2596	2781	299531325	299531525	5.770000e-53	219.0
9	TraesCS2B01G266100	chr2D	88.571	70	6	2	2516	2584	233429851	233429919	2.190000e-12	84.2
10	TraesCS2B01G266100	chr2D	90.323	62	6	0	2517	2578	389889320	389889381	7.890000e-12	82.4
11	TraesCS2B01G266100	chr2D	91.228	57	5	0	2520	2576	236134107	236134051	1.020000e-10	78.7
12	TraesCS2B01G266100	chr1B	94.198	655	27	3	2778	3429	684863818	684864464	0.000000e+00	989.0
13	TraesCS2B01G266100	chr1B	92.553	658	36	4	2778	3432	30732075	30732722	0.000000e+00	931.0
14	TraesCS2B01G266100	chr1B	93.019	616	32	4	2778	3390	574274782	574274175	0.000000e+00	889.0
15	TraesCS2B01G266100	chr5D	92.030	665	33	10	2778	3432	423275491	423274837	0.000000e+00	917.0
16	TraesCS2B01G266100	chr5D	91.994	662	34	10	2778	3432	407317353	407316704	0.000000e+00	911.0
17	TraesCS2B01G266100	chr5D	91.223	638	48	8	17	651	430918595	430917963	0.000000e+00	861.0
18	TraesCS2B01G266100	chr5D	90.979	654	36	13	2782	3432	551893406	551894039	0.000000e+00	859.0
19	TraesCS2B01G266100	chr3B	91.541	662	42	6	2774	3430	28149517	28150169	0.000000e+00	900.0
20	TraesCS2B01G266100	chr3B	91.228	57	5	0	2520	2576	704159308	704159364	1.020000e-10	78.7
21	TraesCS2B01G266100	chr3B	88.889	63	5	2	2520	2582	558501822	558501762	3.670000e-10	76.8
22	TraesCS2B01G266100	chr3D	91.207	671	41	11	2778	3432	500888568	500887900	0.000000e+00	896.0
23	TraesCS2B01G266100	chr3D	91.038	636	53	4	17	651	542834520	542833888	0.000000e+00	856.0
24	TraesCS2B01G266100	chr3D	90.866	635	56	2	17	651	547514882	547514250	0.000000e+00	850.0
25	TraesCS2B01G266100	chr3D	90.625	640	55	5	14	651	574245198	574245834	0.000000e+00	845.0
26	TraesCS2B01G266100	chr3D	90.625	64	6	0	2520	2583	540967515	540967452	6.100000e-13	86.1
27	TraesCS2B01G266100	chr3D	90.164	61	6	0	2517	2577	5601026	5601086	2.840000e-11	80.5
28	TraesCS2B01G266100	chr6B	91.066	638	56	1	14	651	57451774	57452410	0.000000e+00	861.0
29	TraesCS2B01G266100	chr6B	90.868	657	31	9	2778	3432	29417794	29417165	0.000000e+00	854.0
30	TraesCS2B01G266100	chr4D	91.038	636	53	4	17	651	39302848	39302216	0.000000e+00	856.0
31	TraesCS2B01G266100	chr1D	90.015	661	30	8	2778	3432	470209446	470208816	0.000000e+00	822.0
32	TraesCS2B01G266100	chr5B	87.941	680	37	16	2778	3432	478600198	478600857	0.000000e+00	760.0
33	TraesCS2B01G266100	chr5B	88.012	659	45	6	2778	3432	687694073	687693445	0.000000e+00	749.0
34	TraesCS2B01G266100	chr5B	92.153	497	28	5	2947	3432	660788177	660788673	0.000000e+00	691.0
35	TraesCS2B01G266100	chr4B	86.838	661	38	11	2774	3431	465750979	465750365	0.000000e+00	693.0
36	TraesCS2B01G266100	chr4B	88.406	69	7	1	2512	2580	625981823	625981756	7.890000e-12	82.4
37	TraesCS2B01G266100	chr7B	91.822	428	23	3	2778	3201	596984914	596985333	1.370000e-163	586.0
38	TraesCS2B01G266100	chr7B	90.244	41	3	1	2485	2525	725637554	725637515	6.000000e-03	52.8
39	TraesCS2B01G266100	chr4A	90.000	60	6	0	2520	2579	215247596	215247537	1.020000e-10	78.7
40	TraesCS2B01G266100	chrUn	90.244	41	3	1	2485	2525	380047220	380047181	6.000000e-03	52.8

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	TraesCS2B01G266100	chr2B	358528276	358531707	3431	True	6338	6338	100.0000	1	3432	1	chr2B.!!$R1	3431
1	TraesCS2B01G266100	chr2B	694490361	694490992	631	True	848	848	90.8520	14	647	1	chr2B.!!$R2	633
2	TraesCS2B01G266100	chr2A	374592609	374594807	2198	False	1636	3053	90.8680	648	2776	2	chr2A.!!$F1	2128
3	TraesCS2B01G266100	chr2D	299529387	299531525	2138	False	1562	2905	91.1495	648	2781	2	chr2D.!!$F4	2133
4	TraesCS2B01G266100	chr2D	638864648	638865280	632	True	872	872	91.4960	17	651	1	chr2D.!!$R3	634
5	TraesCS2B01G266100	chr2D	589512202	589512830	628	True	850	850	91.0380	19	651	1	chr2D.!!$R2	632
6	TraesCS2B01G266100	chr2D	521536418	521537016	598	False	686	686	87.4190	2778	3389	1	chr2D.!!$F3	611
7	TraesCS2B01G266100	chr1B	684863818	684864464	646	False	989	989	94.1980	2778	3429	1	chr1B.!!$F2	651
8	TraesCS2B01G266100	chr1B	30732075	30732722	647	False	931	931	92.5530	2778	3432	1	chr1B.!!$F1	654
9	TraesCS2B01G266100	chr1B	574274175	574274782	607	True	889	889	93.0190	2778	3390	1	chr1B.!!$R1	612
10	TraesCS2B01G266100	chr5D	423274837	423275491	654	True	917	917	92.0300	2778	3432	1	chr5D.!!$R2	654
11	TraesCS2B01G266100	chr5D	407316704	407317353	649	True	911	911	91.9940	2778	3432	1	chr5D.!!$R1	654
12	TraesCS2B01G266100	chr5D	430917963	430918595	632	True	861	861	91.2230	17	651	1	chr5D.!!$R3	634
13	TraesCS2B01G266100	chr5D	551893406	551894039	633	False	859	859	90.9790	2782	3432	1	chr5D.!!$F1	650
14	TraesCS2B01G266100	chr3B	28149517	28150169	652	False	900	900	91.5410	2774	3430	1	chr3B.!!$F1	656
15	TraesCS2B01G266100	chr3D	500887900	500888568	668	True	896	896	91.2070	2778	3432	1	chr3D.!!$R1	654
16	TraesCS2B01G266100	chr3D	542833888	542834520	632	True	856	856	91.0380	17	651	1	chr3D.!!$R3	634
17	TraesCS2B01G266100	chr3D	547514250	547514882	632	True	850	850	90.8660	17	651	1	chr3D.!!$R4	634
18	TraesCS2B01G266100	chr3D	574245198	574245834	636	False	845	845	90.6250	14	651	1	chr3D.!!$F2	637
19	TraesCS2B01G266100	chr6B	57451774	57452410	636	False	861	861	91.0660	14	651	1	chr6B.!!$F1	637
20	TraesCS2B01G266100	chr6B	29417165	29417794	629	True	854	854	90.8680	2778	3432	1	chr6B.!!$R1	654
21	TraesCS2B01G266100	chr4D	39302216	39302848	632	True	856	856	91.0380	17	651	1	chr4D.!!$R1	634
22	TraesCS2B01G266100	chr1D	470208816	470209446	630	True	822	822	90.0150	2778	3432	1	chr1D.!!$R1	654
23	TraesCS2B01G266100	chr5B	478600198	478600857	659	False	760	760	87.9410	2778	3432	1	chr5B.!!$F1	654
24	TraesCS2B01G266100	chr5B	687693445	687694073	628	True	749	749	88.0120	2778	3432	1	chr5B.!!$R1	654
25	TraesCS2B01G266100	chr4B	465750365	465750979	614	True	693	693	86.8380	2774	3431	1	chr4B.!!$R1	657

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
400	404	0.035458	GCCGAAATCCTCCCATCGAT	59.965	55.000	0.0	0.0	37.48	3.59	F
1069	1101	1.219393	CCCTTCTCCGAGCTTCACC	59.781	63.158	0.0	0.0	0.00	4.02	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1850	1908	1.739466	CCATCATCACGTTGTTGGAGG	59.261	52.381	10.58	0.0	38.3	4.30	R
2450	2518	1.007387	CCCGCAAGCAAAGGACAAC	60.007	57.895	0.00	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
57	58	6.004574	AGCAATCAATCATATCAGCTCACAT	58.995	36.000	0.00	0.00	0.00	3.21
303	306	2.737376	GCGTCGACGGGAAAGCTT	60.737	61.111	36.13	0.00	40.23	3.74
329	332	2.757124	GGGAGAATGGTGGCGGGAT	61.757	63.158	0.00	0.00	0.00	3.85
395	399	1.602237	GTGAGCCGAAATCCTCCCA	59.398	57.895	0.00	0.00	0.00	4.37
396	400	0.181350	GTGAGCCGAAATCCTCCCAT	59.819	55.000	0.00	0.00	0.00	4.00
400	404	0.035458	GCCGAAATCCTCCCATCGAT	59.965	55.000	0.00	0.00	37.48	3.59
548	553	2.381911	CTGGCCTGGACATGCTTTAAT	58.618	47.619	0.75	0.00	0.00	1.40
591	596	4.981674	CACAATAAACGCAGACAACCAAAT	59.018	37.500	0.00	0.00	0.00	2.32
594	599	1.686355	AACGCAGACAACCAAATGGA	58.314	45.000	6.42	0.00	38.94	3.41
605	610	4.469586	ACAACCAAATGGACCAAGTTCTTT	59.530	37.500	6.42	0.00	38.94	2.52
612	617	1.305201	GACCAAGTTCTTTCCACGCA	58.695	50.000	0.00	0.00	0.00	5.24
651	656	3.532155	GGCAACCAAACACGCCCA	61.532	61.111	0.00	0.00	38.67	5.36
652	657	2.279186	GCAACCAAACACGCCCAC	60.279	61.111	0.00	0.00	0.00	4.61
762	767	2.215196	GGACCGACACAAAAGCAAGTA	58.785	47.619	0.00	0.00	0.00	2.24
773	778	2.355717	AAGCAAGTAGACTCGAGCAC	57.644	50.000	13.61	8.32	0.00	4.40
808	813	1.467342	GGGCAGCACGGTTTTAACTAG	59.533	52.381	0.00	0.00	0.00	2.57
836	841	2.431023	GGCAGAAGAGGATAGGCGA	58.569	57.895	0.00	0.00	0.00	5.54
1010	1042	2.745308	CCAGACGGATGGGCATGGA	61.745	63.158	0.00	0.00	36.64	3.41
1069	1101	1.219393	CCCTTCTCCGAGCTTCACC	59.781	63.158	0.00	0.00	0.00	4.02
1079	1123	1.671850	CGAGCTTCACCGCCTTCTTTA	60.672	52.381	0.00	0.00	0.00	1.85
1376	1422	1.227438	CCTCAACCACCGACACGTT	60.227	57.895	0.00	0.00	0.00	3.99
1480	1533	6.688813	CCTAACTAATTTTCTGATTTGCGCTC	59.311	38.462	9.73	0.00	0.00	5.03
1569	1624	6.062095	CCACGGTAATAAATTCTTGAGGGAT	58.938	40.000	0.00	0.00	0.00	3.85
1744	1801	3.243839	GCCACATCCACAACACTTCAAAT	60.244	43.478	0.00	0.00	0.00	2.32
1782	1839	8.871686	AAGACAACACCATTTATTTTCTTGAC	57.128	30.769	0.00	0.00	0.00	3.18
1850	1908	1.227031	TGTTCCACGTGACGGTGAC	60.227	57.895	19.30	6.55	40.38	3.67
1854	1912	2.049433	CACGTGACGGTGACCTCC	60.049	66.667	10.90	0.00	40.38	4.30
1856	1914	2.129146	ACGTGACGGTGACCTCCAA	61.129	57.895	10.66	0.00	0.00	3.53
2109	2167	0.605083	CACTGACACTAGAGCCTGCA	59.395	55.000	0.00	0.00	0.00	4.41
2450	2518	4.421033	TGACAGTACGTAGCTCTTCTTG	57.579	45.455	0.00	0.00	0.00	3.02
2501	2569	5.768333	GCAAATTGCAATGTACTTCTTCC	57.232	39.130	13.82	0.00	44.26	3.46
2502	2570	5.229423	GCAAATTGCAATGTACTTCTTCCA	58.771	37.500	13.82	0.00	44.26	3.53
2505	2573	7.412237	GCAAATTGCAATGTACTTCTTCCATTC	60.412	37.037	13.82	0.00	44.26	2.67
2506	2574	5.643379	TTGCAATGTACTTCTTCCATTCC	57.357	39.130	0.00	0.00	0.00	3.01
2510	2578	6.041409	TGCAATGTACTTCTTCCATTCCAAAA	59.959	34.615	0.00	0.00	0.00	2.44
2512	2580	7.603784	GCAATGTACTTCTTCCATTCCAAAATT	59.396	33.333	0.00	0.00	0.00	1.82
2515	2583	8.477419	TGTACTTCTTCCATTCCAAAATTCTT	57.523	30.769	0.00	0.00	0.00	2.52
2519	2587	7.288621	ACTTCTTCCATTCCAAAATTCTTGTCT	59.711	33.333	0.00	0.00	0.00	3.41
2520	2588	7.601705	TCTTCCATTCCAAAATTCTTGTCTT	57.398	32.000	0.00	0.00	0.00	3.01
2524	2592	8.884124	TCCATTCCAAAATTCTTGTCTTAGAT	57.116	30.769	0.00	0.00	0.00	1.98
2529	2597	8.561738	TCCAAAATTCTTGTCTTAGATACACC	57.438	34.615	0.00	0.00	0.00	4.16
2530	2598	7.610305	TCCAAAATTCTTGTCTTAGATACACCC	59.390	37.037	0.00	0.00	0.00	4.61
2533	2601	4.713824	TCTTGTCTTAGATACACCCGTG	57.286	45.455	0.00	0.00	0.00	4.94
2538	2606	4.880120	TGTCTTAGATACACCCGTGTCTAG	59.120	45.833	3.23	0.00	43.94	2.43
2540	2608	5.007528	GTCTTAGATACACCCGTGTCTAGAC	59.992	48.000	16.32	16.32	43.94	2.59
2541	2609	2.286872	AGATACACCCGTGTCTAGACG	58.713	52.381	17.85	7.66	41.37	4.18
2542	2610	2.093288	AGATACACCCGTGTCTAGACGA	60.093	50.000	17.85	4.78	41.37	4.20
2544	2612	1.542492	ACACCCGTGTCTAGACGAAT	58.458	50.000	17.85	0.00	40.24	3.34
2545	2613	1.471684	ACACCCGTGTCTAGACGAATC	59.528	52.381	17.85	7.57	40.24	2.52
2546	2614	1.743958	CACCCGTGTCTAGACGAATCT	59.256	52.381	17.85	0.00	42.10	2.40
2547	2615	2.941064	CACCCGTGTCTAGACGAATCTA	59.059	50.000	17.85	0.00	42.10	1.98
2549	2617	3.626670	ACCCGTGTCTAGACGAATCTAAG	59.373	47.826	17.85	1.91	42.10	2.18
2551	2619	4.260702	CCCGTGTCTAGACGAATCTAAGAC	60.261	50.000	17.85	6.30	42.10	3.01
2552	2620	4.331992	CCGTGTCTAGACGAATCTAAGACA	59.668	45.833	17.85	0.00	42.10	3.41
2553	2621	5.163784	CCGTGTCTAGACGAATCTAAGACAA	60.164	44.000	17.85	0.00	41.73	3.18
2554	2622	5.960683	CGTGTCTAGACGAATCTAAGACAAG	59.039	44.000	17.85	4.05	41.73	3.16
2555	2623	6.183360	CGTGTCTAGACGAATCTAAGACAAGA	60.183	42.308	17.85	0.00	41.73	3.02
2558	2626	8.740906	TGTCTAGACGAATCTAAGACAAGAATT	58.259	33.333	17.85	0.00	39.72	2.17
2559	2627	9.575783	GTCTAGACGAATCTAAGACAAGAATTT	57.424	33.333	7.22	0.00	36.98	1.82
2563	2631	9.372369	AGACGAATCTAAGACAAGAATTTTAGG	57.628	33.333	0.00	0.00	31.46	2.69
2565	2633	9.720769	ACGAATCTAAGACAAGAATTTTAGGAA	57.279	29.630	0.00	0.00	0.00	3.36
2590	2681	6.787170	TGAGGGAGTATGTATTATACGTCCT	58.213	40.000	0.00	1.77	35.85	3.85
2613	2723	5.714047	TCGCAGAGATATTGTATGACATCC	58.286	41.667	0.00	0.00	0.00	3.51
2634	2744	0.976641	TGGCGAAGAAGTCTCCACAT	59.023	50.000	0.00	0.00	36.14	3.21
2635	2745	1.347707	TGGCGAAGAAGTCTCCACATT	59.652	47.619	0.00	0.00	36.14	2.71
2636	2746	2.224523	TGGCGAAGAAGTCTCCACATTT	60.225	45.455	0.00	0.00	36.14	2.32
2637	2747	2.416893	GGCGAAGAAGTCTCCACATTTC	59.583	50.000	0.00	0.00	30.77	2.17
2638	2748	2.416893	GCGAAGAAGTCTCCACATTTCC	59.583	50.000	0.00	0.00	0.00	3.13
2706	2835	4.014406	ACAGAAACTCCAAAACTCGGTTT	58.986	39.130	0.00	0.00	37.34	3.27
2833	2963	0.382515	AAAAACTAGTTTGCCGCGCA	59.617	45.000	21.22	0.00	36.47	6.09
2836	2966	3.411351	CTAGTTTGCCGCGCACGT	61.411	61.111	8.75	0.00	38.71	4.49
2923	3057	0.166814	GCTCCAGCAGCGTGTAAAAG	59.833	55.000	0.00	0.00	38.76	2.27
2928	3064	1.021202	AGCAGCGTGTAAAAGTGCAA	58.979	45.000	0.00	0.00	36.57	4.08
3076	3256	4.021544	TGCCCACAAGTTCAAAATCATACC	60.022	41.667	0.00	0.00	0.00	2.73
3077	3257	4.620567	GCCCACAAGTTCAAAATCATACCC	60.621	45.833	0.00	0.00	0.00	3.69
3079	3259	5.187576	CCCACAAGTTCAAAATCATACCCAT	59.812	40.000	0.00	0.00	0.00	4.00
3083	3263	7.975616	CACAAGTTCAAAATCATACCCATAAGG	59.024	37.037	0.00	0.00	43.78	2.69
3174	3381	3.506455	TCTTTCTCGTCTTCGTCCTCATT	59.494	43.478	0.00	0.00	38.33	2.57
3254	3476	2.456119	GCATCACGTGAAGCTCCGG	61.456	63.158	32.16	13.51	36.02	5.14
3279	3501	1.880027	GTTGGCAAGATCTTCAACGGT	59.120	47.619	18.78	0.00	31.77	4.83

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
2	3	6.509677	GCGGTTGCAATTAGTACTAGATGTTC	60.510	42.308	0.59	8.21	42.15	3.18
4	5	4.809426	GCGGTTGCAATTAGTACTAGATGT	59.191	41.667	0.59	0.00	42.15	3.06
5	6	5.330271	GCGGTTGCAATTAGTACTAGATG	57.670	43.478	0.59	7.54	42.15	2.90
29	30	7.119407	GTGAGCTGATATGATTGATTGCTATGT	59.881	37.037	0.00	0.00	0.00	2.29
57	58	5.104569	TGCATGGTTGATTAGTGGTCTGATA	60.105	40.000	0.00	0.00	0.00	2.15
109	110	8.887264	TTCTCTCTGTTCCTTCTAGTTAGATT	57.113	34.615	0.00	0.00	31.40	2.40
115	116	4.775253	CCCTTTCTCTCTGTTCCTTCTAGT	59.225	45.833	0.00	0.00	0.00	2.57
180	181	2.284039	TTCCACGATCGTCCCCCA	60.284	61.111	19.84	0.00	0.00	4.96
238	241	2.974698	CATCTTCATCGGCCGGCC	60.975	66.667	36.69	36.69	0.00	6.13
292	295	0.602905	CTCCGTTCAAGCTTTCCCGT	60.603	55.000	0.00	0.00	0.00	5.28
303	306	0.613260	CACCATTCTCCCTCCGTTCA	59.387	55.000	0.00	0.00	0.00	3.18
329	332	3.646715	CTCCCTCACCGCCCCAAA	61.647	66.667	0.00	0.00	0.00	3.28
513	518	0.679960	GCCAGGCCCATAGAAAACGT	60.680	55.000	0.00	0.00	0.00	3.99
572	577	3.823873	TCCATTTGGTTGTCTGCGTTTAT	59.176	39.130	0.00	0.00	36.34	1.40
591	596	1.961793	CGTGGAAAGAACTTGGTCCA	58.038	50.000	4.47	4.47	37.83	4.02
594	599	1.308998	CTGCGTGGAAAGAACTTGGT	58.691	50.000	0.00	0.00	0.00	3.67
626	631	2.352617	CGTGTTTGGTTGCCTGCATATT	60.353	45.455	0.00	0.00	0.00	1.28
651	656	0.617820	AACTAGGGAGGCATCACCGT	60.618	55.000	0.00	0.00	46.52	4.83
652	657	0.105039	GAACTAGGGAGGCATCACCG	59.895	60.000	0.00	0.00	46.52	4.94
762	767	3.386237	GCAGGGGTGCTCGAGTCT	61.386	66.667	15.13	1.74	0.00	3.24
808	813	1.079503	CTCTTCTGCCGCTGGTAAAC	58.920	55.000	0.00	0.00	0.00	2.01
836	841	3.446161	TCTTCAGGTACGACGAAATGGAT	59.554	43.478	0.00	0.00	0.00	3.41
1069	1101	0.248289	TTCCCGAGGTAAAGAAGGCG	59.752	55.000	0.00	0.00	0.00	5.52
1079	1123	2.818274	GCGCGAAATTCCCGAGGT	60.818	61.111	12.10	0.00	0.00	3.85
1465	1518	2.479566	AGAGGAGCGCAAATCAGAAA	57.520	45.000	11.47	0.00	0.00	2.52
1480	1533	5.239525	CCAGAAACCTGTAACAAGAAAGAGG	59.760	44.000	0.00	0.00	32.50	3.69
1569	1624	4.713814	ACTGAAGAGCACAAGAGATATCCA	59.286	41.667	0.00	0.00	0.00	3.41
1744	1801	4.162812	GTGTTGTCTTTCTTGCGTCAAAA	58.837	39.130	0.00	0.00	0.00	2.44
1782	1839	4.008330	ACTCCTGCATCACTCAAAATCAG	58.992	43.478	0.00	0.00	0.00	2.90
1850	1908	1.739466	CCATCATCACGTTGTTGGAGG	59.261	52.381	10.58	0.00	38.30	4.30
1854	1912	2.421073	AGCATCCATCATCACGTTGTTG	59.579	45.455	0.00	0.00	0.00	3.33
1856	1914	2.011947	CAGCATCCATCATCACGTTGT	58.988	47.619	0.00	0.00	0.00	3.32
2109	2167	5.702670	TGAATTCGCTCTGAAGAAAGAACAT	59.297	36.000	0.04	0.00	40.65	2.71
2450	2518	1.007387	CCCGCAAGCAAAGGACAAC	60.007	57.895	0.00	0.00	0.00	3.32
2491	2559	8.360390	ACAAGAATTTTGGAATGGAAGAAGTAC	58.640	33.333	5.68	0.00	0.00	2.73
2496	2564	7.601705	AAGACAAGAATTTTGGAATGGAAGA	57.398	32.000	5.68	0.00	0.00	2.87
2498	2566	8.704849	TCTAAGACAAGAATTTTGGAATGGAA	57.295	30.769	5.68	0.00	0.00	3.53
2505	2573	7.414098	CGGGTGTATCTAAGACAAGAATTTTGG	60.414	40.741	5.68	0.00	0.00	3.28
2506	2574	7.119262	ACGGGTGTATCTAAGACAAGAATTTTG	59.881	37.037	0.00	0.00	0.00	2.44
2510	2578	5.187186	ACACGGGTGTATCTAAGACAAGAAT	59.813	40.000	1.96	0.00	42.90	2.40
2512	2580	4.084287	ACACGGGTGTATCTAAGACAAGA	58.916	43.478	1.96	0.00	42.90	3.02
2515	2583	3.693807	AGACACGGGTGTATCTAAGACA	58.306	45.455	0.00	0.00	45.05	3.41
2519	2587	3.873361	CGTCTAGACACGGGTGTATCTAA	59.127	47.826	22.37	0.00	45.05	2.10
2520	2588	3.132824	TCGTCTAGACACGGGTGTATCTA	59.867	47.826	22.37	2.76	45.05	1.98
2524	2592	2.183478	TTCGTCTAGACACGGGTGTA	57.817	50.000	22.37	0.00	45.05	2.90
2526	2594	1.743958	AGATTCGTCTAGACACGGGTG	59.256	52.381	22.37	5.35	40.35	4.61
2527	2595	2.125773	AGATTCGTCTAGACACGGGT	57.874	50.000	22.37	0.00	40.35	5.28
2528	2596	3.875727	TCTTAGATTCGTCTAGACACGGG	59.124	47.826	22.37	6.44	40.35	5.28
2529	2597	4.331992	TGTCTTAGATTCGTCTAGACACGG	59.668	45.833	22.37	6.80	40.35	4.94
2530	2598	5.466432	TGTCTTAGATTCGTCTAGACACG	57.534	43.478	22.37	10.49	41.36	4.49
2533	2601	9.575783	AAATTCTTGTCTTAGATTCGTCTAGAC	57.424	33.333	13.18	13.18	0.00	2.59
2538	2606	9.367444	TCCTAAAATTCTTGTCTTAGATTCGTC	57.633	33.333	0.00	0.00	0.00	4.20
2544	2612	9.672673	CCTCATTCCTAAAATTCTTGTCTTAGA	57.327	33.333	0.00	0.00	0.00	2.10
2545	2613	8.897752	CCCTCATTCCTAAAATTCTTGTCTTAG	58.102	37.037	0.00	0.00	0.00	2.18
2546	2614	8.611257	TCCCTCATTCCTAAAATTCTTGTCTTA	58.389	33.333	0.00	0.00	0.00	2.10
2547	2615	7.470192	TCCCTCATTCCTAAAATTCTTGTCTT	58.530	34.615	0.00	0.00	0.00	3.01
2549	2617	6.887002	ACTCCCTCATTCCTAAAATTCTTGTC	59.113	38.462	0.00	0.00	0.00	3.18
2551	2619	8.844244	CATACTCCCTCATTCCTAAAATTCTTG	58.156	37.037	0.00	0.00	0.00	3.02
2552	2620	8.560903	ACATACTCCCTCATTCCTAAAATTCTT	58.439	33.333	0.00	0.00	0.00	2.52
2553	2621	8.107196	ACATACTCCCTCATTCCTAAAATTCT	57.893	34.615	0.00	0.00	0.00	2.40
2560	2628	9.404848	CGTATAATACATACTCCCTCATTCCTA	57.595	37.037	0.00	0.00	0.00	2.94
2561	2629	7.894364	ACGTATAATACATACTCCCTCATTCCT	59.106	37.037	0.00	0.00	0.00	3.36
2562	2630	8.064336	ACGTATAATACATACTCCCTCATTCC	57.936	38.462	0.00	0.00	0.00	3.01
2563	2631	8.189460	GGACGTATAATACATACTCCCTCATTC	58.811	40.741	0.00	0.00	0.00	2.67
2565	2633	7.411808	AGGACGTATAATACATACTCCCTCAT	58.588	38.462	0.00	0.00	0.00	2.90
2566	2634	6.787170	AGGACGTATAATACATACTCCCTCA	58.213	40.000	0.00	0.00	0.00	3.86
2567	2635	6.036953	CGAGGACGTATAATACATACTCCCTC	59.963	46.154	15.00	15.00	37.38	4.30
2582	2673	3.821600	ACAATATCTCTGCGAGGACGTAT	59.178	43.478	0.00	0.00	41.98	3.06
2590	2681	5.619981	CGGATGTCATACAATATCTCTGCGA	60.620	44.000	0.00	0.00	0.00	5.10
2613	2723	1.289066	TGGAGACTTCTTCGCCACG	59.711	57.895	0.00	0.00	46.45	4.94
2776	2905	1.338200	ACGGCTGTTGGAGATGTTCTC	60.338	52.381	0.00	0.00	42.66	2.87
2833	2963	1.134226	CGCTAAACCAGACGAAACGT	58.866	50.000	0.00	0.00	45.10	3.99
2836	2966	1.286354	CCGCGCTAAACCAGACGAAA	61.286	55.000	5.56	0.00	0.00	3.46
2918	3050	2.426098	GCGCGCGTTGCACTTTTA	60.426	55.556	32.35	0.00	46.97	1.52
2951	3090	6.788598	TTGTGTCCAAAATGCCATATATGT	57.211	33.333	11.73	0.00	0.00	2.29
3076	3256	2.689983	GGATGAACTTGTGGCCTTATGG	59.310	50.000	3.32	0.00	0.00	2.74
3077	3257	3.355378	TGGATGAACTTGTGGCCTTATG	58.645	45.455	3.32	0.00	0.00	1.90
3079	3259	3.153919	GTTGGATGAACTTGTGGCCTTA	58.846	45.455	3.32	0.00	0.00	2.69
3083	3263	1.327303	TGGTTGGATGAACTTGTGGC	58.673	50.000	0.00	0.00	34.66	5.01
3254	3476	0.169009	GAAGATCTTGCCAACACCGC	59.831	55.000	14.00	0.00	0.00	5.68
3279	3501	5.882000	CCTCACACACATTTCCATGAAGATA	59.118	40.000	0.00	0.00	34.11	1.98
3345	3574	1.150081	CTCATGGGAGGCATGGGTC	59.850	63.158	0.00	0.00	37.51	4.46

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.