AutoCloner

Multiple sequence alignment - TraesCS5D01G114300

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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	TraesCS5D01G114300	chr5D	100.000	3615	0	0	1	3615	133535649	133539263	0.000000e+00	6676.0
1	TraesCS5D01G114300	chr5D	85.294	748	79	14	2877	3615	9391455	9392180	0.000000e+00	743.0
2	TraesCS5D01G114300	chr5D	87.209	86	7	2	2790	2874	255575122	255575040	1.070000e-15	95.3
3	TraesCS5D01G114300	chr5A	96.073	1986	57	9	668	2638	156224657	156226636	0.000000e+00	3216.0
4	TraesCS5D01G114300	chr5A	92.282	596	37	8	1	591	156209269	156209860	0.000000e+00	837.0
5	TraesCS5D01G114300	chr5A	94.340	53	2	1	628	679	156209874	156209926	2.990000e-11	80.5
6	TraesCS5D01G114300	chr5B	94.794	1844	51	19	808	2632	144815518	144817335	0.000000e+00	2832.0
7	TraesCS5D01G114300	chr5B	90.520	654	54	5	166	816	144813709	144814357	0.000000e+00	857.0
8	TraesCS5D01G114300	chr5B	81.467	750	98	20	2877	3615	594754280	594753561	8.700000e-161	577.0
9	TraesCS5D01G114300	chr5B	96.154	78	3	0	2676	2753	144817441	144817518	1.050000e-25	128.0
10	TraesCS5D01G114300	chr4D	87.534	746	62	14	2877	3615	128909813	128909092	0.000000e+00	833.0
11	TraesCS5D01G114300	chr4D	85.445	742	71	17	2878	3613	343093033	343092323	0.000000e+00	737.0
12	TraesCS5D01G114300	chr2A	85.944	747	72	18	2877	3615	21146930	21147651	0.000000e+00	767.0
13	TraesCS5D01G114300	chr2A	82.258	744	75	24	2877	3615	518338211	518337520	1.120000e-164	590.0
14	TraesCS5D01G114300	chr2A	81.956	593	73	13	2881	3470	37214148	37214709	4.220000e-129	472.0
15	TraesCS5D01G114300	chr2A	87.368	95	12	0	2780	2874	518338254	518338160	3.820000e-20	110.0
16	TraesCS5D01G114300	chr2A	97.561	41	1	0	2807	2847	595385699	595385739	1.800000e-08	71.3
17	TraesCS5D01G114300	chr6D	85.542	747	72	17	2877	3615	458532314	458533032	0.000000e+00	749.0
18	TraesCS5D01G114300	chr6D	83.423	742	87	16	2885	3615	3183525	3182809	0.000000e+00	656.0
19	TraesCS5D01G114300	chr6D	91.753	97	8	0	2780	2876	147688222	147688318	6.300000e-28	135.0
20	TraesCS5D01G114300	chr6D	89.474	95	9	1	2780	2874	458532271	458532364	6.340000e-23	119.0
21	TraesCS5D01G114300	chr1B	85.560	741	72	14	2881	3615	402785934	402785223	0.000000e+00	743.0
22	TraesCS5D01G114300	chr2D	84.005	744	68	22	2877	3615	383561813	383561116	0.000000e+00	667.0
23	TraesCS5D01G114300	chr2D	83.580	743	72	22	2881	3615	34271255	34271955	0.000000e+00	651.0
24	TraesCS5D01G114300	chr2D	89.474	95	7	1	2780	2874	383561853	383561762	2.280000e-22	117.0
25	TraesCS5D01G114300	chr1A	89.414	529	50	3	3092	3615	552458589	552459116	0.000000e+00	662.0
26	TraesCS5D01G114300	chr1A	79.675	738	99	19	2881	3600	496076917	496077621	5.430000e-133	484.0
27	TraesCS5D01G114300	chr4B	78.630	730	127	11	2877	3601	642374235	642374940	1.180000e-124	457.0
28	TraesCS5D01G114300	chr2B	91.176	68	6	0	2807	2874	130011674	130011607	3.840000e-15	93.5
29	TraesCS5D01G114300	chr2B	89.831	59	5	1	580	638	655890068	655890011	1.390000e-09	75.0
30	TraesCS5D01G114300	chr7B	83.516	91	14	1	2785	2874	725187966	725188056	2.310000e-12	84.2
31	TraesCS5D01G114300	chr6A	93.617	47	3	0	580	626	87493044	87493090	1.800000e-08	71.3

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	TraesCS5D01G114300	chr5D	133535649	133539263	3614	False	6676.000000	6676	100.000000	1	3615	1	chr5D.!!$F2	3614
1	TraesCS5D01G114300	chr5D	9391455	9392180	725	False	743.000000	743	85.294000	2877	3615	1	chr5D.!!$F1	738
2	TraesCS5D01G114300	chr5A	156224657	156226636	1979	False	3216.000000	3216	96.073000	668	2638	1	chr5A.!!$F1	1970
3	TraesCS5D01G114300	chr5A	156209269	156209926	657	False	458.750000	837	93.311000	1	679	2	chr5A.!!$F2	678
4	TraesCS5D01G114300	chr5B	144813709	144817518	3809	False	1272.333333	2832	93.822667	166	2753	3	chr5B.!!$F1	2587
5	TraesCS5D01G114300	chr5B	594753561	594754280	719	True	577.000000	577	81.467000	2877	3615	1	chr5B.!!$R1	738
6	TraesCS5D01G114300	chr4D	128909092	128909813	721	True	833.000000	833	87.534000	2877	3615	1	chr4D.!!$R1	738
7	TraesCS5D01G114300	chr4D	343092323	343093033	710	True	737.000000	737	85.445000	2878	3613	1	chr4D.!!$R2	735
8	TraesCS5D01G114300	chr2A	21146930	21147651	721	False	767.000000	767	85.944000	2877	3615	1	chr2A.!!$F1	738
9	TraesCS5D01G114300	chr2A	37214148	37214709	561	False	472.000000	472	81.956000	2881	3470	1	chr2A.!!$F2	589
10	TraesCS5D01G114300	chr2A	518337520	518338254	734	True	350.000000	590	84.813000	2780	3615	2	chr2A.!!$R1	835
11	TraesCS5D01G114300	chr6D	3182809	3183525	716	True	656.000000	656	83.423000	2885	3615	1	chr6D.!!$R1	730
12	TraesCS5D01G114300	chr6D	458532271	458533032	761	False	434.000000	749	87.508000	2780	3615	2	chr6D.!!$F2	835
13	TraesCS5D01G114300	chr1B	402785223	402785934	711	True	743.000000	743	85.560000	2881	3615	1	chr1B.!!$R1	734
14	TraesCS5D01G114300	chr2D	34271255	34271955	700	False	651.000000	651	83.580000	2881	3615	1	chr2D.!!$F1	734
15	TraesCS5D01G114300	chr2D	383561116	383561853	737	True	392.000000	667	86.739500	2780	3615	2	chr2D.!!$R1	835
16	TraesCS5D01G114300	chr1A	552458589	552459116	527	False	662.000000	662	89.414000	3092	3615	1	chr1A.!!$F2	523
17	TraesCS5D01G114300	chr1A	496076917	496077621	704	False	484.000000	484	79.675000	2881	3600	1	chr1A.!!$F1	719
18	TraesCS5D01G114300	chr4B	642374235	642374940	705	False	457.000000	457	78.630000	2877	3601	1	chr4B.!!$F1	724

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	Hairpin	End Stability	Orientation
230	231	0.026285	GAAATTCGTCGATGCCACGG	59.974	55.000	0.00	37.85	4.94	F
1592	2767	0.034896	TGCAGAGTTTCCCCTTCGTC	59.965	55.000	0.00	0.00	4.20	F
1969	3181	1.302431	CACGTGGAATGAGGTGGCA	60.302	57.895	7.95	0.00	4.92	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2014	3226	0.250901	ACGCCTGCTGGAAGAATTGT	60.251	50.000	14.77	0.00	34.07	2.71	R
2575	3787	0.250513	GCTCCATGTCCTCGAGGTTT	59.749	55.000	30.17	13.84	36.34	3.27	R
2879	4153	1.458588	CCAGCTAGAGGAGGGGGAC	60.459	68.421	0.00	0.00	0.00	4.46	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
38	39	7.064728	CACACATCATCTATGCCTAATCTGATG	59.935	40.741	7.80	7.80	42.48	3.07
61	62	5.349270	TGAAACACCGAATCTTTACCATACG	59.651	40.000	0.00	0.00	0.00	3.06
65	66	2.800544	CCGAATCTTTACCATACGCCTG	59.199	50.000	0.00	0.00	0.00	4.85
109	110	4.388773	TCACACTTTCATCTATGTCGTTGC	59.611	41.667	0.00	0.00	0.00	4.17
116	117	1.732941	TCTATGTCGTTGCCGCAAAT	58.267	45.000	7.54	0.10	0.00	2.32
133	134	0.180406	AATACCATCGAGCACACCCC	59.820	55.000	0.00	0.00	0.00	4.95
150	151	0.254747	CCCATCAAAACCCTAGCGGA	59.745	55.000	4.45	0.00	34.64	5.54
154	155	1.886886	TCAAAACCCTAGCGGAACAC	58.113	50.000	4.45	0.00	34.64	3.32
200	201	2.592897	CGGACAACTCGATTTCGTACAG	59.407	50.000	0.00	0.00	40.80	2.74
219	220	5.470047	ACAGTAGTTCAGAGGAAATTCGT	57.530	39.130	0.00	0.00	34.13	3.85
230	231	0.026285	GAAATTCGTCGATGCCACGG	59.974	55.000	0.00	0.00	37.85	4.94
314	315	0.179076	ACGCCGAAGATGATCATGCA	60.179	50.000	14.30	0.00	0.00	3.96
337	338	1.747745	GGTTTGGGGCGCGTTATCT	60.748	57.895	8.43	0.00	0.00	1.98
409	411	3.969976	CTCCCCATTCTCAATCAGGACTA	59.030	47.826	0.00	0.00	0.00	2.59
412	414	3.384789	CCCATTCTCAATCAGGACTACGA	59.615	47.826	0.00	0.00	0.00	3.43
481	483	8.466798	AGACTAATTTGTATGAAAATTTCCCCG	58.533	33.333	3.00	0.00	39.73	5.73
482	484	8.129496	ACTAATTTGTATGAAAATTTCCCCGT	57.871	30.769	3.00	0.00	39.73	5.28
520	522	4.536765	ACCCACTTGTCTCAGTTTTCAAT	58.463	39.130	0.00	0.00	0.00	2.57
521	523	4.956075	ACCCACTTGTCTCAGTTTTCAATT	59.044	37.500	0.00	0.00	0.00	2.32
559	562	2.371841	TCTGGCAGTGAAGTTGGTGTAT	59.628	45.455	15.27	0.00	0.00	2.29
568	571	6.262273	CAGTGAAGTTGGTGTATTTTAGGTGT	59.738	38.462	0.00	0.00	0.00	4.16
627	631	9.461312	TTTCTCATTAACTATTTGCCACATACT	57.539	29.630	0.00	0.00	0.00	2.12
679	684	0.106167	TACTCCCACTATGGCGAGCT	60.106	55.000	11.19	0.00	37.95	4.09
693	698	3.067833	GGCGAGCTTAAGGTGGATTATC	58.932	50.000	19.29	2.38	0.00	1.75
937	2109	9.416794	GTCATCAATATTCCTACATGACTAGTG	57.583	37.037	0.00	0.00	37.97	2.74
988	2160	4.162690	CCAGGGACGGGCAGTAGC	62.163	72.222	0.00	0.00	36.55	3.58
1590	2765	1.301677	GCTGCAGAGTTTCCCCTTCG	61.302	60.000	20.43	0.00	0.00	3.79
1592	2767	0.034896	TGCAGAGTTTCCCCTTCGTC	59.965	55.000	0.00	0.00	0.00	4.20
1617	2811	4.548451	TGATGCTTCAGAGTTGTCTCAT	57.452	40.909	0.00	0.00	42.66	2.90
1969	3181	1.302431	CACGTGGAATGAGGTGGCA	60.302	57.895	7.95	0.00	0.00	4.92
2158	3370	2.276116	GGCGGGCTCGATCCTGATA	61.276	63.158	18.31	0.00	39.00	2.15
2236	3448	4.742201	ATGACGGCGTCGCTGCTT	62.742	61.111	31.90	13.23	38.71	3.91
2335	3547	2.251642	GGCGTTCGTCTGCACCTTT	61.252	57.895	0.00	0.00	0.00	3.11
2617	3829	2.574322	CTTTTCCGCACAAAGTGATCG	58.426	47.619	0.58	0.00	35.23	3.69
2622	3834	0.652592	CGCACAAAGTGATCGATCCC	59.347	55.000	22.31	11.57	35.23	3.85
2641	3853	2.801859	CCAACCCGTGGTCACTTTT	58.198	52.632	0.00	0.00	43.20	2.27
2642	3854	1.107945	CCAACCCGTGGTCACTTTTT	58.892	50.000	0.00	0.00	43.20	1.94
2665	3877	4.473477	TTTTGAAAAATCAACCCGTGGT	57.527	36.364	0.00	0.00	37.65	4.16
2666	3878	3.719173	TTGAAAAATCAACCCGTGGTC	57.281	42.857	0.00	0.00	33.12	4.02
2667	3879	2.656002	TGAAAAATCAACCCGTGGTCA	58.344	42.857	0.00	0.00	33.12	4.02
2668	3880	2.359531	TGAAAAATCAACCCGTGGTCAC	59.640	45.455	0.00	0.00	33.12	3.67
2669	3881	2.060050	AAAATCAACCCGTGGTCACA	57.940	45.000	1.90	0.00	33.12	3.58
2670	3882	2.286365	AAATCAACCCGTGGTCACAT	57.714	45.000	1.90	0.00	33.12	3.21
2671	3883	2.286365	AATCAACCCGTGGTCACATT	57.714	45.000	1.90	0.00	33.12	2.71
2672	3884	1.533625	ATCAACCCGTGGTCACATTG	58.466	50.000	1.90	3.37	33.12	2.82
2673	3885	0.470341	TCAACCCGTGGTCACATTGA	59.530	50.000	1.90	5.42	33.12	2.57
2674	3886	1.073125	TCAACCCGTGGTCACATTGAT	59.927	47.619	1.90	0.00	33.12	2.57
2675	3887	2.303311	TCAACCCGTGGTCACATTGATA	59.697	45.455	1.90	0.00	33.12	2.15
2676	3888	3.054728	TCAACCCGTGGTCACATTGATAT	60.055	43.478	1.90	0.00	33.12	1.63
2677	3889	3.644966	ACCCGTGGTCACATTGATATT	57.355	42.857	1.90	0.00	0.00	1.28
2679	3891	5.105567	ACCCGTGGTCACATTGATATTAA	57.894	39.130	1.90	0.00	0.00	1.40
2680	3892	4.879545	ACCCGTGGTCACATTGATATTAAC	59.120	41.667	1.90	0.00	0.00	2.01
2709	3983	8.066612	TCTCTGGATTTGGATGGTAAATTTTC	57.933	34.615	0.00	0.00	0.00	2.29
2720	3994	6.751888	GGATGGTAAATTTTCTGATCAAACGG	59.248	38.462	0.00	0.00	0.00	4.44
2759	4033	9.020813	TCAAAATGATTCTTTCTATCGTAGTCG	57.979	33.333	0.00	0.00	38.55	4.18
2760	4034	8.808529	CAAAATGATTCTTTCTATCGTAGTCGT	58.191	33.333	0.00	0.00	38.33	4.34
2762	4036	9.666626	AAATGATTCTTTCTATCGTAGTCGTAG	57.333	33.333	0.00	0.00	38.33	3.51
2763	4037	7.783090	TGATTCTTTCTATCGTAGTCGTAGT	57.217	36.000	0.00	0.00	38.33	2.73
2764	4038	7.628235	TGATTCTTTCTATCGTAGTCGTAGTG	58.372	38.462	0.00	0.00	38.33	2.74
2765	4039	7.493645	TGATTCTTTCTATCGTAGTCGTAGTGA	59.506	37.037	0.00	0.00	38.33	3.41
2766	4040	6.825284	TCTTTCTATCGTAGTCGTAGTGAG	57.175	41.667	0.00	0.00	38.33	3.51
2767	4041	5.752472	TCTTTCTATCGTAGTCGTAGTGAGG	59.248	44.000	0.00	0.00	38.33	3.86
2768	4042	4.662468	TCTATCGTAGTCGTAGTGAGGT	57.338	45.455	0.00	0.00	38.33	3.85
2769	4043	5.016051	TCTATCGTAGTCGTAGTGAGGTT	57.984	43.478	0.00	0.00	38.33	3.50
2770	4044	5.423015	TCTATCGTAGTCGTAGTGAGGTTT	58.577	41.667	0.00	0.00	38.33	3.27
2771	4045	6.573434	TCTATCGTAGTCGTAGTGAGGTTTA	58.427	40.000	0.00	0.00	38.33	2.01
2772	4046	5.731599	ATCGTAGTCGTAGTGAGGTTTAG	57.268	43.478	0.00	0.00	38.33	1.85
2773	4047	4.820897	TCGTAGTCGTAGTGAGGTTTAGA	58.179	43.478	0.00	0.00	38.33	2.10
2774	4048	4.867047	TCGTAGTCGTAGTGAGGTTTAGAG	59.133	45.833	0.00	0.00	38.33	2.43
2775	4049	4.493872	CGTAGTCGTAGTGAGGTTTAGAGC	60.494	50.000	0.00	0.00	0.00	4.09
2776	4050	3.688235	AGTCGTAGTGAGGTTTAGAGCT	58.312	45.455	0.00	0.00	36.03	4.09
2829	4103	1.344763	CCTCCACCATAGATCGGTTCC	59.655	57.143	0.00	0.00	33.25	3.62
2830	4104	1.344763	CTCCACCATAGATCGGTTCCC	59.655	57.143	0.00	0.00	33.25	3.97
2831	4105	0.396811	CCACCATAGATCGGTTCCCC	59.603	60.000	0.00	0.00	33.25	4.81
2832	4106	0.396811	CACCATAGATCGGTTCCCCC	59.603	60.000	0.00	0.00	33.25	5.40
2833	4107	0.267960	ACCATAGATCGGTTCCCCCT	59.732	55.000	0.00	0.00	30.53	4.79
2834	4108	0.977395	CCATAGATCGGTTCCCCCTC	59.023	60.000	0.00	0.00	0.00	4.30
2835	4109	0.977395	CATAGATCGGTTCCCCCTCC	59.023	60.000	0.00	0.00	0.00	4.30
2836	4110	0.868186	ATAGATCGGTTCCCCCTCCT	59.132	55.000	0.00	0.00	0.00	3.69
2837	4111	0.640495	TAGATCGGTTCCCCCTCCTT	59.360	55.000	0.00	0.00	0.00	3.36
2838	4112	0.691413	AGATCGGTTCCCCCTCCTTC	60.691	60.000	0.00	0.00	0.00	3.46
2839	4113	2.029307	GATCGGTTCCCCCTCCTTCG	62.029	65.000	0.00	0.00	0.00	3.79
2840	4114	3.782443	CGGTTCCCCCTCCTTCGG	61.782	72.222	0.00	0.00	0.00	4.30
2841	4115	4.111053	GGTTCCCCCTCCTTCGGC	62.111	72.222	0.00	0.00	0.00	5.54
2842	4116	4.111053	GTTCCCCCTCCTTCGGCC	62.111	72.222	0.00	0.00	0.00	6.13
2861	4135	4.077184	GCCATGTCGGTGTCGGGA	62.077	66.667	0.00	0.00	36.97	5.14
2862	4136	2.184322	CCATGTCGGTGTCGGGAG	59.816	66.667	0.00	0.00	36.95	4.30
2863	4137	2.184322	CATGTCGGTGTCGGGAGG	59.816	66.667	0.00	0.00	36.95	4.30
2864	4138	3.075005	ATGTCGGTGTCGGGAGGG	61.075	66.667	0.00	0.00	36.95	4.30
2875	4149	3.015753	GGGAGGGGTGGGGAACTC	61.016	72.222	0.00	0.00	0.00	3.01
2876	4150	2.125225	GGAGGGGTGGGGAACTCT	59.875	66.667	0.00	0.00	0.00	3.24
2877	4151	1.996187	GGAGGGGTGGGGAACTCTC	60.996	68.421	0.00	0.00	0.00	3.20
2878	4152	2.284699	AGGGGTGGGGAACTCTCG	60.285	66.667	0.00	0.00	0.00	4.04
2879	4153	3.400054	GGGGTGGGGAACTCTCGG	61.400	72.222	0.00	0.00	0.00	4.63
3048	4335	2.499693	TGGAGATGGCATCGTCTACAAA	59.500	45.455	21.01	0.90	44.54	2.83
3071	4358	7.761038	AAAAGTAATCTTCGTCCCTTCATTT	57.239	32.000	0.00	0.00	32.90	2.32
3160	4450	2.695147	TCAGATCTTGCTTCGCCAGATA	59.305	45.455	0.00	0.00	40.38	1.98
3171	4465	3.194005	TCGCCAGATAGGTTTTGGATC	57.806	47.619	0.00	0.00	40.61	3.36
3260	4563	5.360999	TCGACAATGGTGATTCATACTCTCT	59.639	40.000	0.00	0.00	0.00	3.10
3391	4695	1.514087	CTTGGCATTGCGGCTCAAT	59.486	52.632	0.00	0.00	45.82	2.57
3437	4755	6.148150	TCGTTGGTATTTACAGGTTTGTGATC	59.852	38.462	0.00	0.00	38.23	2.92
3470	4788	0.392998	ATGTTCCTACGGCTGCCTTG	60.393	55.000	17.92	4.42	0.00	3.61
3509	4831	5.059161	TGTGTCATGGAAGAAGAGTTTGAG	58.941	41.667	0.00	0.00	0.00	3.02
3516	4838	4.840680	TGGAAGAAGAGTTTGAGGATCTCA	59.159	41.667	0.00	0.00	38.87	3.27
3529	4851	2.941720	AGGATCTCAAAGATTTGCTCGC	59.058	45.455	0.30	0.00	34.53	5.03
3563	4886	8.656849	AGACTTTATTTTGTAATCGCTGTAGTG	58.343	33.333	0.00	0.00	0.00	2.74
3588	4911	5.182190	AGCTCATGTATCTCTACCATGTACG	59.818	44.000	0.00	0.00	0.00	3.67

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
38	39	5.725864	GCGTATGGTAAAGATTCGGTGTTTC	60.726	44.000	0.00	0.00	0.00	2.78
61	62	2.997315	GGGGGAGTTTTGGCAGGC	60.997	66.667	0.00	0.00	0.00	4.85
109	110	0.304705	GTGCTCGATGGTATTTGCGG	59.695	55.000	0.00	0.00	0.00	5.69
116	117	0.980754	ATGGGGTGTGCTCGATGGTA	60.981	55.000	0.00	0.00	0.00	3.25
133	134	2.161609	GTGTTCCGCTAGGGTTTTGATG	59.838	50.000	6.02	0.00	38.33	3.07
150	151	0.535102	CTCCCTTGCTTGGTCGTGTT	60.535	55.000	0.00	0.00	0.00	3.32
154	155	2.032528	TGCTCCCTTGCTTGGTCG	59.967	61.111	0.00	0.00	0.00	4.79
200	201	4.730657	TCGACGAATTTCCTCTGAACTAC	58.269	43.478	0.00	0.00	0.00	2.73
230	231	3.391665	CTGGATGGAGCCACGTCCC	62.392	68.421	12.51	0.82	44.32	4.46
261	262	0.109086	CTCTGTTGGAGACGCACGAT	60.109	55.000	0.00	0.00	44.45	3.73
337	338	1.064803	GTGAATTGTCACGTTGGCACA	59.935	47.619	0.00	0.00	44.58	4.57
476	478	0.250553	CTAAACTTGCACCACGGGGA	60.251	55.000	12.96	0.00	38.05	4.81
481	483	1.607148	GGGTCACTAAACTTGCACCAC	59.393	52.381	0.00	0.00	0.00	4.16
482	484	1.213182	TGGGTCACTAAACTTGCACCA	59.787	47.619	0.00	0.00	0.00	4.17
601	605	9.461312	AGTATGTGGCAAATAGTTAATGAGAAA	57.539	29.630	0.00	0.00	0.00	2.52
626	630	9.875675	GATGCATCTGAAGCTAAATTTACTTAG	57.124	33.333	19.70	9.52	32.88	2.18
627	631	9.394767	TGATGCATCTGAAGCTAAATTTACTTA	57.605	29.630	26.32	0.00	0.00	2.24
628	632	8.284945	TGATGCATCTGAAGCTAAATTTACTT	57.715	30.769	26.32	10.77	0.00	2.24
638	642	4.778579	AGTAACATGATGCATCTGAAGCT	58.221	39.130	26.32	14.37	0.00	3.74
639	643	5.757320	AGTAGTAACATGATGCATCTGAAGC	59.243	40.000	26.32	12.55	0.00	3.86
728	734	6.122850	TCAATAGCACAAGTCAACATATGC	57.877	37.500	1.58	0.00	0.00	3.14
937	2109	2.552315	TCTGGCACGGAAATTTCAGTTC	59.448	45.455	19.53	15.34	43.00	3.01
988	2160	2.418471	GCTGCTCCATGGCTATAGCTAG	60.418	54.545	23.53	16.55	41.70	3.42
1175	2350	1.096967	TATGCTCGCGGTCCGAAGTA	61.097	55.000	17.49	11.30	46.81	2.24
1201	2376	3.362986	CCACGTCTACATGCGCATTATTC	60.363	47.826	22.81	9.49	0.00	1.75
1363	2538	4.015406	ACAATGGTGAGGCGGCGA	62.015	61.111	12.98	0.00	0.00	5.54
1590	2765	4.177026	ACAACTCTGAAGCATCATACGAC	58.823	43.478	0.00	0.00	34.37	4.34
1592	2767	4.428209	AGACAACTCTGAAGCATCATACG	58.572	43.478	0.00	0.00	34.37	3.06
1887	3081	0.747852	GACAACCTCCTCGATCTCCC	59.252	60.000	0.00	0.00	0.00	4.30
2014	3226	0.250901	ACGCCTGCTGGAAGAATTGT	60.251	50.000	14.77	0.00	34.07	2.71
2236	3448	3.825160	GAACACGGAGCCCAGCACA	62.825	63.158	0.00	0.00	0.00	4.57
2575	3787	0.250513	GCTCCATGTCCTCGAGGTTT	59.749	55.000	30.17	13.84	36.34	3.27
2644	3856	4.081642	TGACCACGGGTTGATTTTTCAAAA	60.082	37.500	0.00	0.00	35.25	2.44
2648	3860	2.359531	TGTGACCACGGGTTGATTTTTC	59.640	45.455	0.00	0.00	35.25	2.29
2650	3862	2.060050	TGTGACCACGGGTTGATTTT	57.940	45.000	0.00	0.00	35.25	1.82
2652	3864	1.885887	CAATGTGACCACGGGTTGATT	59.114	47.619	0.00	0.00	35.25	2.57
2653	3865	1.073125	TCAATGTGACCACGGGTTGAT	59.927	47.619	9.67	0.00	35.25	2.57
2654	3866	0.470341	TCAATGTGACCACGGGTTGA	59.530	50.000	9.67	9.67	35.25	3.18
2656	3868	3.644966	ATATCAATGTGACCACGGGTT	57.355	42.857	0.00	0.00	35.25	4.11
2658	3870	4.878971	TGTTAATATCAATGTGACCACGGG	59.121	41.667	0.00	0.00	0.00	5.28
2659	3871	6.429791	TTGTTAATATCAATGTGACCACGG	57.570	37.500	0.00	0.00	0.00	4.94
2660	3872	8.397906	AGATTTGTTAATATCAATGTGACCACG	58.602	33.333	0.00	0.00	0.00	4.94
2661	3873	9.722056	GAGATTTGTTAATATCAATGTGACCAC	57.278	33.333	0.00	0.00	33.25	4.16
2662	3874	9.685276	AGAGATTTGTTAATATCAATGTGACCA	57.315	29.630	0.00	0.00	35.03	4.02
2663	3875	9.941664	CAGAGATTTGTTAATATCAATGTGACC	57.058	33.333	0.00	0.00	35.03	4.02
2664	3876	9.941664	CCAGAGATTTGTTAATATCAATGTGAC	57.058	33.333	0.00	0.00	35.03	3.67
2665	3877	9.904198	TCCAGAGATTTGTTAATATCAATGTGA	57.096	29.630	0.00	0.00	35.03	3.58
2709	3983	9.040939	TGATAATGTTGTATACCGTTTGATCAG	57.959	33.333	0.00	0.00	0.00	2.90
2753	4027	4.635324	AGCTCTAAACCTCACTACGACTAC	59.365	45.833	0.00	0.00	0.00	2.73
2754	4028	4.841422	AGCTCTAAACCTCACTACGACTA	58.159	43.478	0.00	0.00	0.00	2.59
2755	4029	3.688235	AGCTCTAAACCTCACTACGACT	58.312	45.455	0.00	0.00	0.00	4.18
2756	4030	3.439476	TGAGCTCTAAACCTCACTACGAC	59.561	47.826	16.19	0.00	33.44	4.34
2757	4031	3.682696	TGAGCTCTAAACCTCACTACGA	58.317	45.455	16.19	0.00	33.44	3.43
2758	4032	4.436242	TTGAGCTCTAAACCTCACTACG	57.564	45.455	16.19	0.00	37.78	3.51
2844	4118	4.077184	TCCCGACACCGACATGGC	62.077	66.667	0.00	0.00	43.94	4.40
2845	4119	2.184322	CTCCCGACACCGACATGG	59.816	66.667	0.00	0.00	46.41	3.66
2846	4120	2.184322	CCTCCCGACACCGACATG	59.816	66.667	0.00	0.00	38.22	3.21
2847	4121	3.075005	CCCTCCCGACACCGACAT	61.075	66.667	0.00	0.00	38.22	3.06
2858	4132	3.015753	GAGTTCCCCACCCCTCCC	61.016	72.222	0.00	0.00	0.00	4.30
2859	4133	1.996187	GAGAGTTCCCCACCCCTCC	60.996	68.421	0.00	0.00	0.00	4.30
2860	4134	2.359967	CGAGAGTTCCCCACCCCTC	61.360	68.421	0.00	0.00	0.00	4.30
2861	4135	2.284699	CGAGAGTTCCCCACCCCT	60.285	66.667	0.00	0.00	0.00	4.79
2862	4136	3.400054	CCGAGAGTTCCCCACCCC	61.400	72.222	0.00	0.00	0.00	4.95
2863	4137	2.606826	ACCGAGAGTTCCCCACCC	60.607	66.667	0.00	0.00	0.00	4.61
2864	4138	2.657066	GGACCGAGAGTTCCCCACC	61.657	68.421	0.00	0.00	0.00	4.61
2865	4139	2.657066	GGGACCGAGAGTTCCCCAC	61.657	68.421	0.00	0.00	38.38	4.61
2866	4140	2.284405	GGGACCGAGAGTTCCCCA	60.284	66.667	0.00	0.00	38.38	4.96
2879	4153	1.458588	CCAGCTAGAGGAGGGGGAC	60.459	68.421	0.00	0.00	0.00	4.46
2996	4275	4.041198	AGACGACTACCAATCCCTCAAAAA	59.959	41.667	0.00	0.00	0.00	1.94
2997	4276	3.581332	AGACGACTACCAATCCCTCAAAA	59.419	43.478	0.00	0.00	0.00	2.44
2998	4277	3.170717	AGACGACTACCAATCCCTCAAA	58.829	45.455	0.00	0.00	0.00	2.69
2999	4278	2.816411	AGACGACTACCAATCCCTCAA	58.184	47.619	0.00	0.00	0.00	3.02
3000	4279	2.526888	AGACGACTACCAATCCCTCA	57.473	50.000	0.00	0.00	0.00	3.86
3001	4280	3.025262	AGAAGACGACTACCAATCCCTC	58.975	50.000	0.00	0.00	0.00	4.30
3002	4281	3.103080	AGAAGACGACTACCAATCCCT	57.897	47.619	0.00	0.00	0.00	4.20
3003	4282	3.889520	AAGAAGACGACTACCAATCCC	57.110	47.619	0.00	0.00	0.00	3.85
3004	4283	4.566987	ACAAAGAAGACGACTACCAATCC	58.433	43.478	0.00	0.00	0.00	3.01
3005	4284	5.107065	CCAACAAAGAAGACGACTACCAATC	60.107	44.000	0.00	0.00	0.00	2.67
3006	4285	4.755123	CCAACAAAGAAGACGACTACCAAT	59.245	41.667	0.00	0.00	0.00	3.16
3048	4335	6.940298	TCAAATGAAGGGACGAAGATTACTTT	59.060	34.615	0.00	0.00	36.39	2.66
3071	4358	2.649331	GGGAAAAGATCTCGTCGTCA	57.351	50.000	0.00	0.00	0.00	4.35
3216	4519	1.582968	GACGTAGCAGTCGGGACAA	59.417	57.895	1.17	0.00	0.00	3.18
3271	4574	1.515521	CCGAACAACCAGGTCAAGGC	61.516	60.000	0.00	0.00	31.63	4.35
3470	4788	7.173218	TCCATGACACAATCTTGTACTTTTCTC	59.827	37.037	0.00	0.00	39.91	2.87
3509	4831	2.941720	AGCGAGCAAATCTTTGAGATCC	59.058	45.455	6.84	0.00	40.55	3.36
3516	4838	6.205658	AGTCTAAAAGAAGCGAGCAAATCTTT	59.794	34.615	13.74	13.74	42.30	2.52
3563	4886	5.720371	ACATGGTAGAGATACATGAGCTC	57.280	43.478	6.82	6.82	43.46	4.09

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.