AutoCloner

Multiple sequence alignment - TraesCS1D01G253000

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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	TraesCS1D01G253000	chr1D	100.000	3468	0	0	1	3468	345374027	345377494	0.000000e+00	6405.0
1	TraesCS1D01G253000	chr1D	93.601	797	43	6	2677	3468	311688401	311687608	0.000000e+00	1182.0
2	TraesCS1D01G253000	chr1A	96.503	2574	71	9	75	2637	445501615	445504180	0.000000e+00	4237.0
3	TraesCS1D01G253000	chr1A	93.182	792	51	2	2677	3467	391845250	391844461	0.000000e+00	1160.0
4	TraesCS1D01G253000	chr1A	95.951	568	23	0	2901	3468	391794198	391793631	0.000000e+00	922.0
5	TraesCS1D01G253000	chr1A	95.775	568	24	0	2901	3468	391696710	391696143	0.000000e+00	917.0
6	TraesCS1D01G253000	chr1A	95.775	568	24	0	2901	3468	391763737	391763170	0.000000e+00	917.0
7	TraesCS1D01G253000	chr1A	95.599	568	25	0	2901	3468	391678633	391678066	0.000000e+00	911.0
8	TraesCS1D01G253000	chr1B	94.168	2589	89	27	90	2637	465390293	465387726	0.000000e+00	3888.0
9	TraesCS1D01G253000	chr1B	94.207	794	41	4	2677	3467	421534235	421533444	0.000000e+00	1206.0
10	TraesCS1D01G253000	chr1B	88.752	809	70	13	2678	3467	421497219	421496413	0.000000e+00	970.0
11	TraesCS1D01G253000	chr1B	87.763	809	78	13	2678	3467	421454289	421453483	0.000000e+00	926.0
12	TraesCS1D01G253000	chr6A	87.829	797	86	8	1698	2486	15542478	15543271	0.000000e+00	924.0
13	TraesCS1D01G253000	chr6A	86.050	767	94	11	1713	2471	15457423	15456662	0.000000e+00	811.0
14	TraesCS1D01G253000	chr6A	83.526	777	121	5	1699	2470	15491582	15490808	0.000000e+00	719.0
15	TraesCS1D01G253000	chr6A	84.628	631	81	10	1006	1634	15461668	15461052	6.360000e-172	614.0
16	TraesCS1D01G253000	chr6A	84.554	628	85	5	1006	1630	15540721	15541339	2.290000e-171	612.0
17	TraesCS1D01G253000	chr6D	87.242	776	92	5	1698	2468	14241306	14242079	0.000000e+00	878.0
18	TraesCS1D01G253000	chr6D	86.428	781	95	9	1698	2471	14201992	14201216	0.000000e+00	845.0
19	TraesCS1D01G253000	chr6D	84.535	763	109	7	1714	2470	14231354	14230595	0.000000e+00	747.0
20	TraesCS1D01G253000	chr6D	85.443	632	77	9	1006	1634	14203504	14202885	0.000000e+00	643.0
21	TraesCS1D01G253000	chr6D	84.420	629	86	6	1006	1631	14239438	14240057	2.960000e-170	608.0
22	TraesCS1D01G253000	chr6D	82.492	634	89	12	1006	1634	14232267	14231651	1.420000e-148	536.0
23	TraesCS1D01G253000	chr6B	86.615	777	95	7	1698	2468	26004656	26005429	0.000000e+00	850.0
24	TraesCS1D01G253000	chr6B	85.641	780	96	8	1698	2471	26120974	26120205	0.000000e+00	806.0
25	TraesCS1D01G253000	chr6B	84.628	631	84	8	1006	1634	25976120	25975501	1.770000e-172	616.0
26	TraesCS1D01G253000	chr6B	83.148	629	91	4	1006	1631	26001816	26002432	8.410000e-156	560.0
27	TraesCS1D01G253000	chr4B	78.560	611	100	21	1006	1593	629852590	629853192	1.180000e-99	374.0
28	TraesCS1D01G253000	chr7A	94.444	36	2	0	1546	1581	93488862	93488897	4.840000e-04	56.5

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	TraesCS1D01G253000	chr1D	345374027	345377494	3467	False	6405.0	6405	100.0000	1	3468	1	chr1D.!!$F1	3467
1	TraesCS1D01G253000	chr1D	311687608	311688401	793	True	1182.0	1182	93.6010	2677	3468	1	chr1D.!!$R1	791
2	TraesCS1D01G253000	chr1A	445501615	445504180	2565	False	4237.0	4237	96.5030	75	2637	1	chr1A.!!$F1	2562
3	TraesCS1D01G253000	chr1A	391844461	391845250	789	True	1160.0	1160	93.1820	2677	3467	1	chr1A.!!$R5	790
4	TraesCS1D01G253000	chr1A	391793631	391794198	567	True	922.0	922	95.9510	2901	3468	1	chr1A.!!$R4	567
5	TraesCS1D01G253000	chr1A	391696143	391696710	567	True	917.0	917	95.7750	2901	3468	1	chr1A.!!$R2	567
6	TraesCS1D01G253000	chr1A	391763170	391763737	567	True	917.0	917	95.7750	2901	3468	1	chr1A.!!$R3	567
7	TraesCS1D01G253000	chr1A	391678066	391678633	567	True	911.0	911	95.5990	2901	3468	1	chr1A.!!$R1	567
8	TraesCS1D01G253000	chr1B	465387726	465390293	2567	True	3888.0	3888	94.1680	90	2637	1	chr1B.!!$R4	2547
9	TraesCS1D01G253000	chr1B	421533444	421534235	791	True	1206.0	1206	94.2070	2677	3467	1	chr1B.!!$R3	790
10	TraesCS1D01G253000	chr1B	421496413	421497219	806	True	970.0	970	88.7520	2678	3467	1	chr1B.!!$R2	789
11	TraesCS1D01G253000	chr1B	421453483	421454289	806	True	926.0	926	87.7630	2678	3467	1	chr1B.!!$R1	789
12	TraesCS1D01G253000	chr6A	15540721	15543271	2550	False	768.0	924	86.1915	1006	2486	2	chr6A.!!$F1	1480
13	TraesCS1D01G253000	chr6A	15490808	15491582	774	True	719.0	719	83.5260	1699	2470	1	chr6A.!!$R1	771
14	TraesCS1D01G253000	chr6A	15456662	15461668	5006	True	712.5	811	85.3390	1006	2471	2	chr6A.!!$R2	1465
15	TraesCS1D01G253000	chr6D	14201216	14203504	2288	True	744.0	845	85.9355	1006	2471	2	chr6D.!!$R1	1465
16	TraesCS1D01G253000	chr6D	14239438	14242079	2641	False	743.0	878	85.8310	1006	2468	2	chr6D.!!$F1	1462
17	TraesCS1D01G253000	chr6D	14230595	14232267	1672	True	641.5	747	83.5135	1006	2470	2	chr6D.!!$R2	1464
18	TraesCS1D01G253000	chr6B	26120205	26120974	769	True	806.0	806	85.6410	1698	2471	1	chr6B.!!$R2	773
19	TraesCS1D01G253000	chr6B	26001816	26005429	3613	False	705.0	850	84.8815	1006	2468	2	chr6B.!!$F1	1462
20	TraesCS1D01G253000	chr6B	25975501	25976120	619	True	616.0	616	84.6280	1006	1634	1	chr6B.!!$R1	628
21	TraesCS1D01G253000	chr4B	629852590	629853192	602	False	374.0	374	78.5600	1006	1593	1	chr4B.!!$F1	587

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
661	689	0.104304	GAAGCTAGCGGGGATCGAAA	59.896	55.0	9.55	0.0	42.43	3.46	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2642	8377	0.03759	TCCATACACCCAGCCAACAC	59.962	55.0	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
24	25	7.444558	GTTGACACACGTGACAATAAAATTT	57.555	32.000	25.01	0.00	44.20	1.82
25	26	7.326645	GTTGACACACGTGACAATAAAATTTG	58.673	34.615	25.01	7.71	44.20	2.32
26	27	5.457148	TGACACACGTGACAATAAAATTTGC	59.543	36.000	25.01	2.71	32.80	3.68
27	28	5.344066	ACACACGTGACAATAAAATTTGCA	58.656	33.333	25.01	0.00	0.00	4.08
28	29	5.982516	ACACACGTGACAATAAAATTTGCAT	59.017	32.000	25.01	0.00	0.00	3.96
29	30	6.478344	ACACACGTGACAATAAAATTTGCATT	59.522	30.769	25.01	0.00	0.00	3.56
30	31	7.003072	CACACGTGACAATAAAATTTGCATTC	58.997	34.615	25.01	0.00	0.00	2.67
31	32	6.145371	ACACGTGACAATAAAATTTGCATTCC	59.855	34.615	25.01	0.00	0.00	3.01
32	33	6.365789	CACGTGACAATAAAATTTGCATTCCT	59.634	34.615	10.90	0.00	0.00	3.36
33	34	6.586082	ACGTGACAATAAAATTTGCATTCCTC	59.414	34.615	0.00	0.00	0.00	3.71
34	35	6.808212	CGTGACAATAAAATTTGCATTCCTCT	59.192	34.615	0.00	0.00	0.00	3.69
35	36	7.967854	CGTGACAATAAAATTTGCATTCCTCTA	59.032	33.333	0.00	0.00	0.00	2.43
36	37	9.807649	GTGACAATAAAATTTGCATTCCTCTAT	57.192	29.630	0.00	0.00	0.00	1.98
45	46	9.813446	AAATTTGCATTCCTCTATTCAATCTTC	57.187	29.630	0.00	0.00	0.00	2.87
46	47	8.763984	ATTTGCATTCCTCTATTCAATCTTCT	57.236	30.769	0.00	0.00	0.00	2.85
47	48	9.857656	ATTTGCATTCCTCTATTCAATCTTCTA	57.142	29.630	0.00	0.00	0.00	2.10
48	49	9.857656	TTTGCATTCCTCTATTCAATCTTCTAT	57.142	29.630	0.00	0.00	0.00	1.98
49	50	8.843885	TGCATTCCTCTATTCAATCTTCTATG	57.156	34.615	0.00	0.00	0.00	2.23
50	51	8.435187	TGCATTCCTCTATTCAATCTTCTATGT	58.565	33.333	0.00	0.00	0.00	2.29
51	52	9.282569	GCATTCCTCTATTCAATCTTCTATGTT	57.717	33.333	0.00	0.00	0.00	2.71
53	54	8.668510	TTCCTCTATTCAATCTTCTATGTTGC	57.331	34.615	0.00	0.00	0.00	4.17
54	55	7.795047	TCCTCTATTCAATCTTCTATGTTGCA	58.205	34.615	0.00	0.00	0.00	4.08
55	56	7.712639	TCCTCTATTCAATCTTCTATGTTGCAC	59.287	37.037	0.00	0.00	0.00	4.57
56	57	7.496920	CCTCTATTCAATCTTCTATGTTGCACA	59.503	37.037	0.00	0.00	0.00	4.57
57	58	8.969260	TCTATTCAATCTTCTATGTTGCACAT	57.031	30.769	6.93	6.93	42.35	3.21
58	59	9.049523	TCTATTCAATCTTCTATGTTGCACATC	57.950	33.333	5.25	0.00	39.88	3.06
59	60	7.634671	ATTCAATCTTCTATGTTGCACATCA	57.365	32.000	5.25	0.00	39.88	3.07
60	61	7.451501	TTCAATCTTCTATGTTGCACATCAA	57.548	32.000	5.25	1.18	39.88	2.57
61	62	7.451501	TCAATCTTCTATGTTGCACATCAAA	57.548	32.000	5.25	2.25	39.88	2.69
62	63	7.532571	TCAATCTTCTATGTTGCACATCAAAG	58.467	34.615	5.25	9.63	39.88	2.77
63	64	7.175467	TCAATCTTCTATGTTGCACATCAAAGT	59.825	33.333	5.25	0.00	39.88	2.66
64	65	6.882610	TCTTCTATGTTGCACATCAAAGTT	57.117	33.333	5.25	0.00	39.88	2.66
65	66	7.275888	TCTTCTATGTTGCACATCAAAGTTT	57.724	32.000	5.25	0.00	39.88	2.66
66	67	7.715657	TCTTCTATGTTGCACATCAAAGTTTT	58.284	30.769	5.25	0.00	39.88	2.43
67	68	7.862372	TCTTCTATGTTGCACATCAAAGTTTTC	59.138	33.333	5.25	0.00	39.88	2.29
68	69	7.275888	TCTATGTTGCACATCAAAGTTTTCT	57.724	32.000	5.25	0.00	39.88	2.52
69	70	7.362662	TCTATGTTGCACATCAAAGTTTTCTC	58.637	34.615	5.25	0.00	39.88	2.87
70	71	5.321959	TGTTGCACATCAAAGTTTTCTCA	57.678	34.783	0.00	0.00	36.26	3.27
71	72	5.718146	TGTTGCACATCAAAGTTTTCTCAA	58.282	33.333	0.00	0.00	36.26	3.02
72	73	6.162079	TGTTGCACATCAAAGTTTTCTCAAA	58.838	32.000	0.00	0.00	36.26	2.69
73	74	6.817641	TGTTGCACATCAAAGTTTTCTCAAAT	59.182	30.769	0.00	0.00	36.26	2.32
112	113	3.770666	ACACGAATCTCGATGTGGTAAG	58.229	45.455	2.59	0.00	43.74	2.34
191	192	2.628178	GTTTTGTTCCTTCCTTGGAGGG	59.372	50.000	11.15	11.15	37.43	4.30
267	272	4.638865	AGGAAGTGTAAAAAGAAGTGCGTT	59.361	37.500	0.00	0.00	0.00	4.84
661	689	0.104304	GAAGCTAGCGGGGATCGAAA	59.896	55.000	9.55	0.00	42.43	3.46
771	799	2.869801	TCTTTTTGTACGCTCCACACAG	59.130	45.455	0.00	0.00	0.00	3.66
772	800	2.319136	TTTTGTACGCTCCACACAGT	57.681	45.000	0.00	0.00	0.00	3.55
773	801	3.455990	TTTTGTACGCTCCACACAGTA	57.544	42.857	0.00	0.00	0.00	2.74
775	803	1.900245	TGTACGCTCCACACAGTAGA	58.100	50.000	0.00	0.00	0.00	2.59
776	804	1.538512	TGTACGCTCCACACAGTAGAC	59.461	52.381	0.00	0.00	0.00	2.59
777	805	1.538512	GTACGCTCCACACAGTAGACA	59.461	52.381	0.00	0.00	0.00	3.41
1596	1676	2.999485	GCTGCTCGTGCTCCAGAGA	61.999	63.158	11.19	0.00	40.48	3.10
1753	7476	2.191128	ACAGAATGGTGCTCAGGTTC	57.809	50.000	0.00	0.00	43.62	3.62
1918	7641	2.409651	GCGGTGGAGCTCTACGAG	59.590	66.667	22.19	18.96	0.00	4.18
1948	7671	1.795286	CAGTTCAAGACGAGCAAGTCC	59.205	52.381	7.79	0.00	41.83	3.85
2473	8208	0.676184	CATCTCCGATGTGATCCGGT	59.324	55.000	0.00	0.00	45.48	5.28
2602	8337	1.714899	GAGTGGCGTGTTTGTGCTGT	61.715	55.000	0.00	0.00	0.00	4.40
2637	8372	7.927629	TGATTGAATTTCTTTTCAGTTTGGAGG	59.072	33.333	0.00	0.00	36.97	4.30
2638	8373	6.160576	TGAATTTCTTTTCAGTTTGGAGGG	57.839	37.500	0.00	0.00	32.07	4.30
2639	8374	4.607293	ATTTCTTTTCAGTTTGGAGGGC	57.393	40.909	0.00	0.00	0.00	5.19
2640	8375	1.995376	TCTTTTCAGTTTGGAGGGCC	58.005	50.000	0.00	0.00	0.00	5.80
2641	8376	0.598065	CTTTTCAGTTTGGAGGGCCG	59.402	55.000	0.00	0.00	36.79	6.13
2642	8377	0.825840	TTTTCAGTTTGGAGGGCCGG	60.826	55.000	0.00	0.00	36.79	6.13
2643	8378	2.002018	TTTCAGTTTGGAGGGCCGGT	62.002	55.000	1.90	0.00	36.79	5.28
2644	8379	2.672996	CAGTTTGGAGGGCCGGTG	60.673	66.667	1.90	0.00	36.79	4.94
2645	8380	3.175710	AGTTTGGAGGGCCGGTGT	61.176	61.111	1.90	0.00	36.79	4.16
2646	8381	2.203437	GTTTGGAGGGCCGGTGTT	60.203	61.111	1.90	0.00	36.79	3.32
2647	8382	2.203422	TTTGGAGGGCCGGTGTTG	60.203	61.111	1.90	0.00	36.79	3.33
2648	8383	3.801068	TTTGGAGGGCCGGTGTTGG	62.801	63.158	1.90	0.00	36.79	3.77
2656	8391	4.579384	CCGGTGTTGGCTGGGTGT	62.579	66.667	0.00	0.00	0.00	4.16
2657	8392	2.428187	CGGTGTTGGCTGGGTGTA	59.572	61.111	0.00	0.00	0.00	2.90
2658	8393	1.002624	CGGTGTTGGCTGGGTGTAT	60.003	57.895	0.00	0.00	0.00	2.29
2659	8394	1.305219	CGGTGTTGGCTGGGTGTATG	61.305	60.000	0.00	0.00	0.00	2.39
2660	8395	0.965363	GGTGTTGGCTGGGTGTATGG	60.965	60.000	0.00	0.00	0.00	2.74
2661	8396	0.037590	GTGTTGGCTGGGTGTATGGA	59.962	55.000	0.00	0.00	0.00	3.41
2662	8397	0.327924	TGTTGGCTGGGTGTATGGAG	59.672	55.000	0.00	0.00	0.00	3.86
2663	8398	0.618458	GTTGGCTGGGTGTATGGAGA	59.382	55.000	0.00	0.00	0.00	3.71
2664	8399	1.212935	GTTGGCTGGGTGTATGGAGAT	59.787	52.381	0.00	0.00	0.00	2.75
2665	8400	1.131638	TGGCTGGGTGTATGGAGATC	58.868	55.000	0.00	0.00	0.00	2.75
2666	8401	1.131638	GGCTGGGTGTATGGAGATCA	58.868	55.000	0.00	0.00	0.00	2.92
2667	8402	1.701847	GGCTGGGTGTATGGAGATCAT	59.298	52.381	0.00	0.00	39.78	2.45
2668	8403	2.107204	GGCTGGGTGTATGGAGATCATT	59.893	50.000	0.00	0.00	37.30	2.57
2669	8404	3.144506	GCTGGGTGTATGGAGATCATTG	58.855	50.000	0.00	0.00	37.30	2.82
2670	8405	3.434167	GCTGGGTGTATGGAGATCATTGT	60.434	47.826	0.00	0.00	37.30	2.71
2671	8406	4.384056	CTGGGTGTATGGAGATCATTGTC	58.616	47.826	0.00	0.00	37.30	3.18
2672	8407	3.181466	TGGGTGTATGGAGATCATTGTCG	60.181	47.826	0.00	0.00	37.30	4.35
2673	8408	3.393800	GGTGTATGGAGATCATTGTCGG	58.606	50.000	0.00	0.00	37.30	4.79
2674	8409	3.069586	GGTGTATGGAGATCATTGTCGGA	59.930	47.826	0.00	0.00	37.30	4.55
2675	8410	4.302455	GTGTATGGAGATCATTGTCGGAG	58.698	47.826	0.00	0.00	37.30	4.63
2747	8484	0.179018	AATACCCTTGATGCGGCCTC	60.179	55.000	0.00	0.00	0.00	4.70
2770	8511	6.853720	TCTAGAGAACAAGAGAATTGTACCG	58.146	40.000	0.00	0.00	31.50	4.02
3011	8772	1.960040	CTGCCGTGGTAGAGGATGCA	61.960	60.000	0.00	0.00	0.00	3.96
3218	8979	0.462759	CGTCTTCCTCCATGGCTTCC	60.463	60.000	6.96	0.00	35.26	3.46
3404	9165	1.213926	CTAAGGCAGGCCCTGAAGATT	59.786	52.381	16.85	5.21	45.62	2.40
3430	9191	1.522668	CTGGATTCAACGTCAGGCAA	58.477	50.000	0.00	0.00	0.00	4.52

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
0	1	7.326645	CAAATTTTATTGTCACGTGTGTCAAC	58.673	34.615	16.51	6.41	40.30	3.18
1	2	6.020281	GCAAATTTTATTGTCACGTGTGTCAA	60.020	34.615	16.51	18.11	41.32	3.18
2	3	5.457148	GCAAATTTTATTGTCACGTGTGTCA	59.543	36.000	16.51	10.69	32.80	3.58
3	4	5.457148	TGCAAATTTTATTGTCACGTGTGTC	59.543	36.000	16.51	8.18	32.80	3.67
6	7	6.145371	GGAATGCAAATTTTATTGTCACGTGT	59.855	34.615	16.51	0.00	32.80	4.49
7	8	6.365789	AGGAATGCAAATTTTATTGTCACGTG	59.634	34.615	9.94	9.94	32.80	4.49
8	9	6.454795	AGGAATGCAAATTTTATTGTCACGT	58.545	32.000	0.00	0.00	32.80	4.49
9	10	6.808212	AGAGGAATGCAAATTTTATTGTCACG	59.192	34.615	0.00	0.00	32.80	4.35
10	11	9.807649	ATAGAGGAATGCAAATTTTATTGTCAC	57.192	29.630	0.00	0.00	32.80	3.67
19	20	9.813446	GAAGATTGAATAGAGGAATGCAAATTT	57.187	29.630	0.00	0.00	28.13	1.82
20	21	9.198475	AGAAGATTGAATAGAGGAATGCAAATT	57.802	29.630	0.00	0.00	28.13	1.82
21	22	8.763984	AGAAGATTGAATAGAGGAATGCAAAT	57.236	30.769	0.00	0.00	28.13	2.32
22	23	9.857656	ATAGAAGATTGAATAGAGGAATGCAAA	57.142	29.630	0.00	0.00	28.13	3.68
23	24	9.281371	CATAGAAGATTGAATAGAGGAATGCAA	57.719	33.333	0.00	0.00	0.00	4.08
24	25	8.435187	ACATAGAAGATTGAATAGAGGAATGCA	58.565	33.333	0.00	0.00	0.00	3.96
25	26	8.845413	ACATAGAAGATTGAATAGAGGAATGC	57.155	34.615	0.00	0.00	0.00	3.56
27	28	9.282569	GCAACATAGAAGATTGAATAGAGGAAT	57.717	33.333	0.00	0.00	0.00	3.01
28	29	8.267183	TGCAACATAGAAGATTGAATAGAGGAA	58.733	33.333	0.00	0.00	0.00	3.36
29	30	7.712639	GTGCAACATAGAAGATTGAATAGAGGA	59.287	37.037	0.00	0.00	36.32	3.71
30	31	7.496920	TGTGCAACATAGAAGATTGAATAGAGG	59.503	37.037	0.00	0.00	45.67	3.69
31	32	8.429493	TGTGCAACATAGAAGATTGAATAGAG	57.571	34.615	0.00	0.00	45.67	2.43
49	50	6.645700	TTTGAGAAAACTTTGATGTGCAAC	57.354	33.333	0.00	0.00	35.91	4.17
50	51	7.846644	AATTTGAGAAAACTTTGATGTGCAA	57.153	28.000	0.00	0.00	33.88	4.08
92	93	3.116300	CCTTACCACATCGAGATTCGTG	58.884	50.000	0.00	0.00	41.35	4.35
95	96	4.098044	TCACTCCTTACCACATCGAGATTC	59.902	45.833	0.00	0.00	0.00	2.52
112	113	1.653151	GGTAAAGCATCCGTCACTCC	58.347	55.000	0.00	0.00	0.00	3.85
253	254	2.604614	GGCATCGAACGCACTTCTTTTT	60.605	45.455	11.75	0.00	0.00	1.94
258	259	0.095417	GAAGGCATCGAACGCACTTC	59.905	55.000	17.35	17.35	33.02	3.01
267	272	0.759436	GAGGGTAGGGAAGGCATCGA	60.759	60.000	0.00	0.00	0.00	3.59
339	344	3.535561	AGCGAGGAATATGTGAAAGGTG	58.464	45.455	0.00	0.00	0.00	4.00
382	387	2.488836	CTAAACTATGGGGTGGGGAGT	58.511	52.381	0.00	0.00	0.00	3.85
495	500	2.036992	CAGGATGATCAGGAGTAGTGCC	59.963	54.545	0.09	0.00	39.69	5.01
553	558	1.950909	TGGTCAATGGGTCGTTCAAAC	59.049	47.619	0.00	0.00	0.00	2.93
661	689	5.237127	CCATGTAACATGCATTGAGATACGT	59.763	40.000	0.00	0.00	0.00	3.57
746	774	1.071699	TGGAGCGTACAAAAAGAGGCT	59.928	47.619	0.00	0.00	0.00	4.58
776	804	0.392706	TGCTGGACAGGTGTGTACTG	59.607	55.000	1.01	0.00	38.51	2.74
777	805	0.393077	GTGCTGGACAGGTGTGTACT	59.607	55.000	1.01	0.00	38.51	2.73
826	854	2.009051	TGCGGCTATGCATGCATATAC	58.991	47.619	34.35	28.17	40.62	1.47
856	884	1.133262	AGATGATGCTGGGGGAAATGG	60.133	52.381	0.00	0.00	0.00	3.16
862	890	1.493871	AGAAAGAGATGATGCTGGGGG	59.506	52.381	0.00	0.00	0.00	5.40
866	894	9.791820	CTATATGTAGAGAAAGAGATGATGCTG	57.208	37.037	0.00	0.00	0.00	4.41
1747	7470	2.361610	AATGGCGCCAGGAACCTG	60.362	61.111	35.36	13.32	43.26	4.00
1753	7476	3.197790	CGTGAGAATGGCGCCAGG	61.198	66.667	35.36	11.54	0.00	4.45
1918	7641	1.452108	CTTGAACTGGATCCCGGCC	60.452	63.158	9.90	0.00	32.02	6.13
1948	7671	1.211969	GATGTTGTGCAGGCTGCTG	59.788	57.895	36.50	4.23	45.31	4.41
2506	8241	3.308530	GACTCGGAAAGCAAAACCAATG	58.691	45.455	0.00	0.00	0.00	2.82
2602	8337	9.144747	TGAAAAGAAATTCAATCAAAACGAACA	57.855	25.926	0.00	0.00	36.42	3.18
2639	8374	2.478335	ATACACCCAGCCAACACCGG	62.478	60.000	0.00	0.00	0.00	5.28
2640	8375	1.002624	ATACACCCAGCCAACACCG	60.003	57.895	0.00	0.00	0.00	4.94
2641	8376	0.965363	CCATACACCCAGCCAACACC	60.965	60.000	0.00	0.00	0.00	4.16
2642	8377	0.037590	TCCATACACCCAGCCAACAC	59.962	55.000	0.00	0.00	0.00	3.32
2643	8378	0.327924	CTCCATACACCCAGCCAACA	59.672	55.000	0.00	0.00	0.00	3.33
2644	8379	0.618458	TCTCCATACACCCAGCCAAC	59.382	55.000	0.00	0.00	0.00	3.77
2645	8380	1.490490	GATCTCCATACACCCAGCCAA	59.510	52.381	0.00	0.00	0.00	4.52
2646	8381	1.131638	GATCTCCATACACCCAGCCA	58.868	55.000	0.00	0.00	0.00	4.75
2647	8382	1.131638	TGATCTCCATACACCCAGCC	58.868	55.000	0.00	0.00	0.00	4.85
2648	8383	3.144506	CAATGATCTCCATACACCCAGC	58.855	50.000	0.00	0.00	34.45	4.85
2649	8384	4.384056	GACAATGATCTCCATACACCCAG	58.616	47.826	0.00	0.00	34.45	4.45
2650	8385	3.181466	CGACAATGATCTCCATACACCCA	60.181	47.826	0.00	0.00	34.45	4.51
2651	8386	3.393800	CGACAATGATCTCCATACACCC	58.606	50.000	0.00	0.00	34.45	4.61
2652	8387	3.069586	TCCGACAATGATCTCCATACACC	59.930	47.826	0.00	0.00	34.45	4.16
2653	8388	4.302455	CTCCGACAATGATCTCCATACAC	58.698	47.826	0.00	0.00	34.45	2.90
2654	8389	3.243873	GCTCCGACAATGATCTCCATACA	60.244	47.826	0.00	0.00	34.45	2.29
2655	8390	3.006323	AGCTCCGACAATGATCTCCATAC	59.994	47.826	0.00	0.00	34.45	2.39
2656	8391	3.234353	AGCTCCGACAATGATCTCCATA	58.766	45.455	0.00	0.00	34.45	2.74
2657	8392	2.045524	AGCTCCGACAATGATCTCCAT	58.954	47.619	0.00	0.00	36.99	3.41
2658	8393	1.489481	AGCTCCGACAATGATCTCCA	58.511	50.000	0.00	0.00	0.00	3.86
2659	8394	2.625790	ACTAGCTCCGACAATGATCTCC	59.374	50.000	0.00	0.00	0.00	3.71
2660	8395	4.276183	TGTACTAGCTCCGACAATGATCTC	59.724	45.833	0.00	0.00	0.00	2.75
2661	8396	4.207955	TGTACTAGCTCCGACAATGATCT	58.792	43.478	0.00	0.00	0.00	2.75
2662	8397	4.569761	TGTACTAGCTCCGACAATGATC	57.430	45.455	0.00	0.00	0.00	2.92
2663	8398	5.537300	AATGTACTAGCTCCGACAATGAT	57.463	39.130	0.00	0.00	0.00	2.45
2664	8399	5.339008	AAATGTACTAGCTCCGACAATGA	57.661	39.130	0.00	0.00	0.00	2.57
2665	8400	7.534085	TTTAAATGTACTAGCTCCGACAATG	57.466	36.000	0.00	0.00	0.00	2.82
2666	8401	8.038944	TCTTTTAAATGTACTAGCTCCGACAAT	58.961	33.333	0.00	0.00	0.00	2.71
2667	8402	7.380536	TCTTTTAAATGTACTAGCTCCGACAA	58.619	34.615	0.00	0.00	0.00	3.18
2668	8403	6.927416	TCTTTTAAATGTACTAGCTCCGACA	58.073	36.000	0.00	0.00	0.00	4.35
2669	8404	7.758528	TCTTCTTTTAAATGTACTAGCTCCGAC	59.241	37.037	0.00	0.00	0.00	4.79
2670	8405	7.833786	TCTTCTTTTAAATGTACTAGCTCCGA	58.166	34.615	0.00	0.00	0.00	4.55
2671	8406	8.475331	TTCTTCTTTTAAATGTACTAGCTCCG	57.525	34.615	0.00	0.00	0.00	4.63
2747	8484	5.517054	GCGGTACAATTCTCTTGTTCTCTAG	59.483	44.000	0.00	0.00	34.11	2.43
2894	8655	3.322541	TGTAAGACACGGGAAGAACATGA	59.677	43.478	0.00	0.00	0.00	3.07
3011	8772	1.021390	CCGCTGCGACAGATCCTTTT	61.021	55.000	25.45	0.00	32.44	2.27
3218	8979	2.978018	GCGGCTGAAGGAAAACCCG	61.978	63.158	0.00	0.00	40.87	5.28
3404	9165	0.400213	ACGTTGAATCCAGGCTCCAA	59.600	50.000	0.00	0.00	0.00	3.53
3430	9191	7.222872	CCTTGATCAGCTTATCTACATTCCTT	58.777	38.462	9.25	0.00	0.00	3.36

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.