AutoCloner

Multiple sequence alignment - TraesCS4A01G003200

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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	TraesCS4A01G003200	chr4A	100.000	3426	0	0	1	3426	2644953	2641528	0.000000e+00	6327
1	TraesCS4A01G003200	chr4A	93.412	1017	43	7	1669	2678	692365677	692366676	0.000000e+00	1485
2	TraesCS4A01G003200	chr4A	81.717	361	60	6	3035	3393	589339345	589338989	2.590000e-76	296
3	TraesCS4A01G003200	chr7A	95.204	2231	74	15	636	2852	100756027	100753816	0.000000e+00	3496
4	TraesCS4A01G003200	chr7A	94.504	2256	69	15	631	2852	732102926	732100692	0.000000e+00	3428
5	TraesCS4A01G003200	chr7A	94.467	2241	67	16	635	2852	2773073	2775279	0.000000e+00	3398
6	TraesCS4A01G003200	chr5B	96.037	2044	62	11	636	2665	74638685	74640723	0.000000e+00	3308
7	TraesCS4A01G003200	chr3D	93.286	2264	85	22	636	2852	595953694	595951451	0.000000e+00	3277
8	TraesCS4A01G003200	chr4D	92.166	2285	84	30	636	2852	414636101	414633844	0.000000e+00	3140
9	TraesCS4A01G003200	chr4D	92.279	1062	39	11	636	1662	469101972	469103025	0.000000e+00	1467
10	TraesCS4A01G003200	chr4D	87.847	576	37	17	75	632	469071915	469072475	0.000000e+00	645
11	TraesCS4A01G003200	chr4D	85.684	475	62	5	2852	3324	469076377	469075907	2.370000e-136	496
12	TraesCS4A01G003200	chr4D	96.774	62	2	0	31	92	469071838	469071899	1.680000e-18	104
13	TraesCS4A01G003200	chr1A	96.235	1514	39	3	1329	2842	534527439	534525944	0.000000e+00	2464
14	TraesCS4A01G003200	chr1A	95.932	1524	44	2	1329	2852	1316423	1317928	0.000000e+00	2455
15	TraesCS4A01G003200	chr2D	95.241	1534	45	3	1329	2852	459831577	459833092	0.000000e+00	2403
16	TraesCS4A01G003200	chr2D	89.452	1204	81	20	1669	2850	25088106	25089285	0.000000e+00	1478
17	TraesCS4A01G003200	chr2D	78.804	552	90	12	2876	3424	633398561	633399088	2.530000e-91	346
18	TraesCS4A01G003200	chr7D	96.246	1039	39	0	1814	2852	510433884	510432846	0.000000e+00	1703
19	TraesCS4A01G003200	chr7D	78.728	456	84	13	2977	3424	426499341	426499791	3.340000e-75	292
20	TraesCS4A01G003200	chr1D	92.703	1069	37	10	630	1662	276513487	276512424	0.000000e+00	1504
21	TraesCS4A01G003200	chr1D	91.345	1063	51	15	634	1662	414481959	414480904	0.000000e+00	1415
22	TraesCS4A01G003200	chr1D	92.711	343	20	4	2515	2852	414457407	414457065	1.100000e-134	490
23	TraesCS4A01G003200	chr6D	90.323	496	19	12	1329	1813	469310733	469311210	1.040000e-174	623
24	TraesCS4A01G003200	chr4B	83.218	578	85	11	2852	3424	588790306	588789736	1.410000e-143	520
25	TraesCS4A01G003200	chr4B	78.220	427	79	12	2995	3414	601932647	601932228	9.430000e-66	261
26	TraesCS4A01G003200	chr2B	81.797	423	73	4	3004	3424	776500718	776501138	5.440000e-93	351
27	TraesCS4A01G003200	chr3A	80.787	432	70	11	2995	3419	750258615	750258190	3.300000e-85	326
28	TraesCS4A01G003200	chr3B	80.220	455	71	14	2977	3424	790644095	790644537	1.190000e-84	324
29	TraesCS4A01G003200	chrUn	80.323	371	63	9	3032	3398	93031641	93031277	4.360000e-69	272
30	TraesCS4A01G003200	chr5A	78.211	436	81	12	2997	3424	321168368	321167939	2.030000e-67	267
31	TraesCS4A01G003200	chr5A	78.554	415	79	8	2994	3401	645418540	645418129	7.290000e-67	265
32	TraesCS4A01G003200	chr5A	76.840	462	89	12	2941	3397	534814496	534814944	9.500000e-61	244

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	TraesCS4A01G003200	chr4A	2641528	2644953	3425	True	6327.0	6327	100.0000	1	3426	1	chr4A.!!$R1	3425
1	TraesCS4A01G003200	chr4A	692365677	692366676	999	False	1485.0	1485	93.4120	1669	2678	1	chr4A.!!$F1	1009
2	TraesCS4A01G003200	chr7A	100753816	100756027	2211	True	3496.0	3496	95.2040	636	2852	1	chr7A.!!$R1	2216
3	TraesCS4A01G003200	chr7A	732100692	732102926	2234	True	3428.0	3428	94.5040	631	2852	1	chr7A.!!$R2	2221
4	TraesCS4A01G003200	chr7A	2773073	2775279	2206	False	3398.0	3398	94.4670	635	2852	1	chr7A.!!$F1	2217
5	TraesCS4A01G003200	chr5B	74638685	74640723	2038	False	3308.0	3308	96.0370	636	2665	1	chr5B.!!$F1	2029
6	TraesCS4A01G003200	chr3D	595951451	595953694	2243	True	3277.0	3277	93.2860	636	2852	1	chr3D.!!$R1	2216
7	TraesCS4A01G003200	chr4D	414633844	414636101	2257	True	3140.0	3140	92.1660	636	2852	1	chr4D.!!$R1	2216
8	TraesCS4A01G003200	chr4D	469101972	469103025	1053	False	1467.0	1467	92.2790	636	1662	1	chr4D.!!$F1	1026
9	TraesCS4A01G003200	chr4D	469071838	469072475	637	False	374.5	645	92.3105	31	632	2	chr4D.!!$F2	601
10	TraesCS4A01G003200	chr1A	534525944	534527439	1495	True	2464.0	2464	96.2350	1329	2842	1	chr1A.!!$R1	1513
11	TraesCS4A01G003200	chr1A	1316423	1317928	1505	False	2455.0	2455	95.9320	1329	2852	1	chr1A.!!$F1	1523
12	TraesCS4A01G003200	chr2D	459831577	459833092	1515	False	2403.0	2403	95.2410	1329	2852	1	chr2D.!!$F2	1523
13	TraesCS4A01G003200	chr2D	25088106	25089285	1179	False	1478.0	1478	89.4520	1669	2850	1	chr2D.!!$F1	1181
14	TraesCS4A01G003200	chr2D	633398561	633399088	527	False	346.0	346	78.8040	2876	3424	1	chr2D.!!$F3	548
15	TraesCS4A01G003200	chr7D	510432846	510433884	1038	True	1703.0	1703	96.2460	1814	2852	1	chr7D.!!$R1	1038
16	TraesCS4A01G003200	chr1D	276512424	276513487	1063	True	1504.0	1504	92.7030	630	1662	1	chr1D.!!$R1	1032
17	TraesCS4A01G003200	chr1D	414480904	414481959	1055	True	1415.0	1415	91.3450	634	1662	1	chr1D.!!$R3	1028
18	TraesCS4A01G003200	chr4B	588789736	588790306	570	True	520.0	520	83.2180	2852	3424	1	chr4B.!!$R1	572

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
426	470	0.391966	GAGTACTATTCCCCCGTGGC	59.608	60.0	0.00	0.0	0.0	5.01	F
1264	1326	0.251253	TGATGTGTGAGCATGGCCAA	60.251	50.0	10.96	0.0	0.0	4.52	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2182	2345	1.180456	CCATTGCACCCAGCTGTTCA	61.180	55.0	13.81	1.68	45.94	3.18	R
3140	3365	0.243907	ACCACCATCGAAGTCACTCG	59.756	55.0	0.00	0.00	40.25	4.18	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
92	126	6.571150	GCCCCACAAAAGATATCATATGCTTC	60.571	42.308	5.32	0.00	0.00	3.86
130	164	2.223618	CCTTAGTCGAGTGAGGCTTAGC	60.224	54.545	17.29	0.00	0.00	3.09
147	181	1.523938	GCCGCCACCTCCAAGATAC	60.524	63.158	0.00	0.00	0.00	2.24
151	185	1.691976	CGCCACCTCCAAGATACCATA	59.308	52.381	0.00	0.00	0.00	2.74
153	187	3.513912	CGCCACCTCCAAGATACCATATA	59.486	47.826	0.00	0.00	0.00	0.86
156	190	6.485171	GCCACCTCCAAGATACCATATATTT	58.515	40.000	0.00	0.00	0.00	1.40
158	192	7.094205	GCCACCTCCAAGATACCATATATTTTG	60.094	40.741	0.00	0.00	0.00	2.44
159	193	7.944554	CCACCTCCAAGATACCATATATTTTGT	59.055	37.037	0.00	0.00	0.00	2.83
216	250	1.003331	TGCATCGTTGGTTTTCGTGAC	60.003	47.619	0.00	0.00	0.00	3.67
246	280	5.184711	AGTTTACCAACTTTGACCACGTTA	58.815	37.500	0.00	0.00	40.66	3.18
250	284	3.375922	ACCAACTTTGACCACGTTAACAG	59.624	43.478	6.39	1.29	0.00	3.16
252	286	4.495184	CCAACTTTGACCACGTTAACAGAC	60.495	45.833	6.39	0.00	0.00	3.51
253	287	3.864243	ACTTTGACCACGTTAACAGACA	58.136	40.909	6.39	0.00	0.00	3.41
258	292	7.874016	ACTTTGACCACGTTAACAGACAATATA	59.126	33.333	6.39	0.00	0.00	0.86
264	298	9.095065	ACCACGTTAACAGACAATATATTTCTC	57.905	33.333	6.39	0.00	0.00	2.87
426	470	0.391966	GAGTACTATTCCCCCGTGGC	59.608	60.000	0.00	0.00	0.00	5.01
451	495	4.098055	GTGAGCTCACGAGTAGAATTGA	57.902	45.455	29.84	0.00	37.10	2.57
499	551	1.941209	GCACTGAAAGATCTCCGTGCA	60.941	52.381	22.76	4.18	40.87	4.57
509	561	1.446792	CTCCGTGCAGCTCGTCAAT	60.447	57.895	15.31	0.00	0.00	2.57
535	587	4.094442	CCTTTAGGACGGTCTTATTTGTGC	59.906	45.833	8.23	0.00	37.39	4.57
536	588	1.722011	AGGACGGTCTTATTTGTGCG	58.278	50.000	8.23	0.00	0.00	5.34
556	608	3.300009	CGACCAAAGTCATGCTCAAAAC	58.700	45.455	0.00	0.00	43.73	2.43
557	609	3.642705	GACCAAAGTCATGCTCAAAACC	58.357	45.455	0.00	0.00	42.99	3.27
558	610	3.030291	ACCAAAGTCATGCTCAAAACCA	58.970	40.909	0.00	0.00	0.00	3.67
559	611	3.450457	ACCAAAGTCATGCTCAAAACCAA	59.550	39.130	0.00	0.00	0.00	3.67
560	612	4.053295	CCAAAGTCATGCTCAAAACCAAG	58.947	43.478	0.00	0.00	0.00	3.61
561	613	4.053295	CAAAGTCATGCTCAAAACCAAGG	58.947	43.478	0.00	0.00	0.00	3.61
562	614	2.949447	AGTCATGCTCAAAACCAAGGT	58.051	42.857	0.00	0.00	0.00	3.50
563	615	4.098914	AGTCATGCTCAAAACCAAGGTA	57.901	40.909	0.00	0.00	0.00	3.08
564	616	3.821033	AGTCATGCTCAAAACCAAGGTAC	59.179	43.478	0.00	0.00	0.00	3.34
565	617	3.568007	GTCATGCTCAAAACCAAGGTACA	59.432	43.478	0.00	0.00	0.00	2.90
566	618	4.218417	GTCATGCTCAAAACCAAGGTACAT	59.782	41.667	0.00	0.00	0.00	2.29
567	619	4.832266	TCATGCTCAAAACCAAGGTACATT	59.168	37.500	0.00	0.00	0.00	2.71
568	620	5.304101	TCATGCTCAAAACCAAGGTACATTT	59.696	36.000	0.00	0.00	0.00	2.32
569	621	5.606348	TGCTCAAAACCAAGGTACATTTT	57.394	34.783	0.00	0.00	0.00	1.82
570	622	5.983540	TGCTCAAAACCAAGGTACATTTTT	58.016	33.333	0.00	0.00	0.00	1.94
571	623	7.113658	TGCTCAAAACCAAGGTACATTTTTA	57.886	32.000	0.00	0.00	0.00	1.52
572	624	7.206687	TGCTCAAAACCAAGGTACATTTTTAG	58.793	34.615	0.00	0.00	0.00	1.85
573	625	7.147811	TGCTCAAAACCAAGGTACATTTTTAGT	60.148	33.333	0.00	0.00	0.00	2.24
574	626	8.354426	GCTCAAAACCAAGGTACATTTTTAGTA	58.646	33.333	0.00	0.00	0.00	1.82
626	678	6.385649	AATCAACTAAATCGGTTTGTGTGT	57.614	33.333	3.29	0.00	0.00	3.72
627	679	5.163302	TCAACTAAATCGGTTTGTGTGTG	57.837	39.130	3.29	4.94	0.00	3.82
628	680	3.619233	ACTAAATCGGTTTGTGTGTGC	57.381	42.857	3.29	0.00	0.00	4.57
629	681	2.946329	ACTAAATCGGTTTGTGTGTGCA	59.054	40.909	3.29	0.00	0.00	4.57
630	682	2.949451	AAATCGGTTTGTGTGTGCAA	57.051	40.000	0.00	0.00	0.00	4.08
631	683	2.949451	AATCGGTTTGTGTGTGCAAA	57.051	40.000	0.00	0.00	36.17	3.68
705	757	5.850614	ACTACCAAGTCGTTAATCTGTTGT	58.149	37.500	0.00	0.00	0.00	3.32
903	956	3.083349	CGCCAGACAGATCCCCCA	61.083	66.667	0.00	0.00	0.00	4.96
1264	1326	0.251253	TGATGTGTGAGCATGGCCAA	60.251	50.000	10.96	0.00	0.00	4.52
1351	1447	9.665264	GGACTTATTTTGTGAAGAAACTACAAG	57.335	33.333	0.00	0.00	35.91	3.16
1472	1608	7.907214	ACCATAGTGAGTGAGTGAAATAAAC	57.093	36.000	0.00	0.00	0.00	2.01
1478	1614	8.827177	AGTGAGTGAGTGAAATAAACGAATTA	57.173	30.769	0.00	0.00	0.00	1.40
1859	2013	9.073475	AGGAAGTAAATGCATTTGTACTTGTTA	57.927	29.630	31.04	11.77	31.98	2.41
1913	2067	1.646447	AGTGGGTAGATGAGGAGTGGA	59.354	52.381	0.00	0.00	0.00	4.02
1969	2123	4.088634	AGCTTTTGTATGAGGATTGCCAA	58.911	39.130	0.00	0.00	36.29	4.52
1970	2124	4.713321	AGCTTTTGTATGAGGATTGCCAAT	59.287	37.500	0.00	0.00	36.29	3.16
2172	2335	6.782494	ACTCCTCCTTTGGACAACAATATTTT	59.218	34.615	0.00	0.00	39.21	1.82
2179	2342	9.921637	CCTTTGGACAACAATATTTTAGCTTTA	57.078	29.630	0.00	0.00	39.21	1.85
2488	2651	7.880160	AAGCATTGAACTATGGCTTGTAATA	57.120	32.000	0.00	0.00	0.00	0.98
2854	3078	9.678260	GAGGCACCTTAGATGATCAAATTATAT	57.322	33.333	0.00	0.00	0.00	0.86
2863	3087	6.769822	AGATGATCAAATTATATGGATCCGGC	59.230	38.462	7.39	0.00	36.24	6.13
2867	3091	3.713826	AATTATATGGATCCGGCGGTT	57.286	42.857	27.32	18.90	0.00	4.44
2881	3105	2.892425	GGTTCGCTGCATCGGGAG	60.892	66.667	10.42	0.00	35.23	4.30
2883	3107	3.074369	TTCGCTGCATCGGGAGGA	61.074	61.111	10.42	0.00	32.28	3.71
2884	3108	2.434843	TTCGCTGCATCGGGAGGAT	61.435	57.895	10.42	0.00	35.09	3.24
2936	3160	0.828022	TTTGTGTCGTGACCACTCCT	59.172	50.000	0.00	0.00	0.00	3.69
2939	3163	2.131067	TGTCGTGACCACTCCTGCA	61.131	57.895	0.00	0.00	0.00	4.41
2956	3180	0.577269	GCATATGGTGACGACTTCGC	59.423	55.000	4.56	0.00	44.43	4.70
2959	3183	0.885879	TATGGTGACGACTTCGCTGT	59.114	50.000	0.00	0.00	44.43	4.40
2960	3184	0.388649	ATGGTGACGACTTCGCTGTC	60.389	55.000	0.00	0.00	44.43	3.51
2973	3197	1.738099	GCTGTCGATTGCGGTGACT	60.738	57.895	0.00	0.00	38.28	3.41
2974	3198	0.457853	GCTGTCGATTGCGGTGACTA	60.458	55.000	0.00	0.00	38.28	2.59
2983	3207	5.813157	TCGATTGCGGTGACTATATTGAAAA	59.187	36.000	0.00	0.00	38.28	2.29
2992	3216	7.360861	CGGTGACTATATTGAAAAGTCTTTGCA	60.361	37.037	1.45	1.45	40.25	4.08
3049	3274	5.948162	ACACCAAGAGCAATCTATGAACAAT	59.052	36.000	0.00	0.00	0.00	2.71
3057	3282	7.774157	AGAGCAATCTATGAACAATGACTTGAT	59.226	33.333	0.00	0.00	36.20	2.57
3083	3308	1.003959	TATGGTTGTGCAGCTGCGA	60.004	52.632	32.11	19.52	45.83	5.10
3110	3335	0.107993	ACATCGCATGTAGCTGCTGT	60.108	50.000	13.43	0.00	42.78	4.40
3114	3339	2.204237	TCGCATGTAGCTGCTGTAATG	58.796	47.619	13.43	13.46	42.61	1.90
3122	3347	3.659183	AGCTGCTGTAATGGAGGAAAT	57.341	42.857	0.00	0.00	0.00	2.17
3125	3350	4.080356	AGCTGCTGTAATGGAGGAAATGTA	60.080	41.667	0.00	0.00	0.00	2.29
3129	3354	6.186957	TGCTGTAATGGAGGAAATGTAATGT	58.813	36.000	0.00	0.00	0.00	2.71
3135	3360	7.865706	AATGGAGGAAATGTAATGTAGACAC	57.134	36.000	0.00	0.00	0.00	3.67
3140	3365	6.335777	AGGAAATGTAATGTAGACACCGTAC	58.664	40.000	0.00	0.00	0.00	3.67
3187	3412	2.752238	CACCCGGTCTCGAGCTCT	60.752	66.667	12.85	0.00	39.00	4.09
3189	3414	2.438614	CCCGGTCTCGAGCTCTGA	60.439	66.667	12.85	9.89	39.00	3.27
3190	3415	2.477176	CCCGGTCTCGAGCTCTGAG	61.477	68.421	21.94	21.94	39.00	3.35
3218	3443	6.672266	AAATCTAGTTCTGACCTGAGTTGA	57.328	37.500	0.00	0.00	0.00	3.18
3226	3451	8.824756	AGTTCTGACCTGAGTTGATTATACTA	57.175	34.615	0.00	0.00	0.00	1.82
3234	3459	6.148480	CCTGAGTTGATTATACTAGCAATGGC	59.852	42.308	0.00	0.00	41.61	4.40
3284	3509	1.875514	GCATTGCTCGGATATGCTCAA	59.124	47.619	0.16	0.00	41.04	3.02
3287	3512	1.953559	TGCTCGGATATGCTCAAACC	58.046	50.000	0.00	0.00	0.00	3.27
3296	3524	5.335583	CGGATATGCTCAAACCAGTTTTCAA	60.336	40.000	0.00	0.00	0.00	2.69
3331	3559	0.960364	TCTGGCCTTTCGTGATTGGC	60.960	55.000	3.32	0.00	44.22	4.52
3393	3622	2.747446	GGCTTTGCCGTTGAAGAATCTA	59.253	45.455	0.00	0.00	39.62	1.98
3398	3627	1.588861	GCCGTTGAAGAATCTAGTCGC	59.411	52.381	0.00	0.00	0.00	5.19
3405	3634	3.260884	TGAAGAATCTAGTCGCCCTTGTT	59.739	43.478	0.00	0.00	0.00	2.83
3424	3653	7.871973	CCCTTGTTTGTGTCATGAAATATTTGA	59.128	33.333	5.17	0.00	0.00	2.69
3425	3654	9.426837	CCTTGTTTGTGTCATGAAATATTTGAT	57.573	29.630	5.17	0.00	0.00	2.57

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
36	37	6.098266	AGGCCAAGTAGACAAACAAAGAAAAT	59.902	34.615	5.01	0.00	0.00	1.82
68	69	6.718454	AGAAGCATATGATATCTTTTGTGGGG	59.282	38.462	6.97	0.00	0.00	4.96
101	135	5.452077	GCCTCACTCGACTAAGGAATACAAT	60.452	44.000	6.44	0.00	0.00	2.71
104	138	3.633065	AGCCTCACTCGACTAAGGAATAC	59.367	47.826	6.44	0.00	0.00	1.89
109	143	2.223618	GCTAAGCCTCACTCGACTAAGG	60.224	54.545	0.00	0.00	0.00	2.69
113	147	2.194460	GGCTAAGCCTCACTCGACT	58.806	57.895	0.00	0.00	46.69	4.18
130	164	1.146263	GGTATCTTGGAGGTGGCGG	59.854	63.158	0.00	0.00	0.00	6.13
184	218	9.462174	AAAACCAACGATGCACATTATATTATG	57.538	29.630	0.17	0.17	0.00	1.90
201	235	0.316689	GGCTGTCACGAAAACCAACG	60.317	55.000	0.00	0.00	0.00	4.10
264	298	8.917415	ACGTATATGTGTGCTATCAATGATAG	57.083	34.615	22.37	22.37	43.31	2.08
304	338	9.823647	ACATCTAGAATACCAACTCAATTAGTG	57.176	33.333	0.00	0.00	38.88	2.74
382	425	3.056393	TCCGTCCCTAAATACAGTGTGTG	60.056	47.826	5.88	0.00	0.00	3.82
383	426	3.167485	TCCGTCCCTAAATACAGTGTGT	58.833	45.455	5.88	0.00	0.00	3.72
422	466	2.393768	CGTGAGCTCACATGGCCAC	61.394	63.158	38.31	16.26	46.75	5.01
426	470	1.745653	TCTACTCGTGAGCTCACATGG	59.254	52.381	38.31	29.12	46.75	3.66
477	529	0.603569	ACGGAGATCTTTCAGTGCGT	59.396	50.000	0.00	0.00	0.00	5.24
535	587	3.300009	GTTTTGAGCATGACTTTGGTCG	58.700	45.455	0.00	0.00	44.98	4.79
536	588	3.068024	TGGTTTTGAGCATGACTTTGGTC	59.932	43.478	0.00	0.00	42.93	4.02
600	652	9.221933	ACACACAAACCGATTTAGTTGATTATA	57.778	29.630	0.00	0.00	0.00	0.98
601	653	8.020819	CACACACAAACCGATTTAGTTGATTAT	58.979	33.333	0.00	0.00	0.00	1.28
602	654	7.356540	CACACACAAACCGATTTAGTTGATTA	58.643	34.615	0.00	0.00	0.00	1.75
603	655	6.205784	CACACACAAACCGATTTAGTTGATT	58.794	36.000	0.00	0.00	0.00	2.57
604	656	5.757886	CACACACAAACCGATTTAGTTGAT	58.242	37.500	0.00	0.00	0.00	2.57
605	657	4.496673	GCACACACAAACCGATTTAGTTGA	60.497	41.667	0.00	0.00	0.00	3.18
606	658	3.728718	GCACACACAAACCGATTTAGTTG	59.271	43.478	0.00	0.00	0.00	3.16
607	659	3.378742	TGCACACACAAACCGATTTAGTT	59.621	39.130	0.00	0.00	0.00	2.24
608	660	2.946329	TGCACACACAAACCGATTTAGT	59.054	40.909	0.00	0.00	0.00	2.24
609	661	3.617540	TGCACACACAAACCGATTTAG	57.382	42.857	0.00	0.00	0.00	1.85
610	662	4.371855	TTTGCACACACAAACCGATTTA	57.628	36.364	0.00	0.00	34.68	1.40
611	663	2.949451	TTGCACACACAAACCGATTT	57.051	40.000	0.00	0.00	0.00	2.17
612	664	2.949451	TTTGCACACACAAACCGATT	57.051	40.000	0.00	0.00	34.68	3.34
618	670	2.163412	GACTCTGGTTTGCACACACAAA	59.837	45.455	5.20	0.00	37.20	2.83
619	671	1.742831	GACTCTGGTTTGCACACACAA	59.257	47.619	5.20	0.00	0.00	3.33
620	672	1.339535	TGACTCTGGTTTGCACACACA	60.340	47.619	5.20	0.04	0.00	3.72
621	673	1.378531	TGACTCTGGTTTGCACACAC	58.621	50.000	5.20	0.00	0.00	3.82
622	674	2.121291	TTGACTCTGGTTTGCACACA	57.879	45.000	5.20	0.00	0.00	3.72
623	675	3.374745	CAATTGACTCTGGTTTGCACAC	58.625	45.455	0.00	0.00	0.00	3.82
624	676	2.223782	GCAATTGACTCTGGTTTGCACA	60.224	45.455	10.34	0.00	41.67	4.57
625	677	2.223782	TGCAATTGACTCTGGTTTGCAC	60.224	45.455	10.34	0.00	45.42	4.57
626	678	2.798976	GCAATTGACTCTGGTTTGCA	57.201	45.000	10.34	0.00	41.67	4.08
627	679	2.798976	TGCAATTGACTCTGGTTTGC	57.201	45.000	10.34	0.00	42.23	3.68
628	680	4.572985	TCTTGCAATTGACTCTGGTTTG	57.427	40.909	10.34	0.00	0.00	2.93
629	681	5.351458	GTTTCTTGCAATTGACTCTGGTTT	58.649	37.500	10.34	0.00	0.00	3.27
630	682	4.202151	GGTTTCTTGCAATTGACTCTGGTT	60.202	41.667	10.34	0.00	0.00	3.67
631	683	3.319122	GGTTTCTTGCAATTGACTCTGGT	59.681	43.478	10.34	0.00	0.00	4.00
632	684	3.318839	TGGTTTCTTGCAATTGACTCTGG	59.681	43.478	10.34	0.00	0.00	3.86
910	963	0.108585	CGAGAGAGAGAGAGAGGGGG	59.891	65.000	0.00	0.00	0.00	5.40
911	964	0.535102	GCGAGAGAGAGAGAGAGGGG	60.535	65.000	0.00	0.00	0.00	4.79
1264	1326	1.342174	CAAACATGCCTCTTTGCTGGT	59.658	47.619	0.00	0.00	0.00	4.00
1351	1447	6.151691	ACAATGAACAGTGCATATGAACAAC	58.848	36.000	16.42	4.91	0.00	3.32
1913	2067	1.380524	GCATTCTGCAGATGCTCTGT	58.619	50.000	28.74	7.78	45.94	3.41
1969	2123	4.042560	AGACATGCCATCCTATTAGCACAT	59.957	41.667	0.00	0.00	38.21	3.21
1970	2124	3.392285	AGACATGCCATCCTATTAGCACA	59.608	43.478	0.00	0.00	38.21	4.57
2172	2335	4.458989	CACCCAGCTGTTCATTTAAAGCTA	59.541	41.667	13.81	0.00	44.00	3.32
2179	2342	1.412079	TTGCACCCAGCTGTTCATTT	58.588	45.000	13.81	0.00	45.94	2.32
2182	2345	1.180456	CCATTGCACCCAGCTGTTCA	61.180	55.000	13.81	1.68	45.94	3.18
2488	2651	2.554032	GCAAACTGCCACTAGTTCACAT	59.446	45.455	0.00	0.00	39.86	3.21
2836	3060	9.836864	CCGGATCCATATAATTTGATCATCTAA	57.163	33.333	13.41	0.00	36.24	2.10
2863	3087	4.812476	TCCCGATGCAGCGAACCG	62.812	66.667	28.29	8.82	0.00	4.44
2867	3091	2.369257	GAATCCTCCCGATGCAGCGA	62.369	60.000	28.29	5.34	0.00	4.93
2881	3105	1.677637	AACCTCGCCGGAGAGAATCC	61.678	60.000	33.72	0.00	43.27	3.01
2883	3107	0.684805	AGAACCTCGCCGGAGAGAAT	60.685	55.000	33.72	22.06	43.27	2.40
2884	3108	1.304217	AGAACCTCGCCGGAGAGAA	60.304	57.895	33.72	0.17	43.27	2.87
2924	3148	1.575244	CATATGCAGGAGTGGTCACG	58.425	55.000	0.00	0.00	36.20	4.35
2936	3160	1.921243	CGAAGTCGTCACCATATGCA	58.079	50.000	0.00	0.00	34.11	3.96
2939	3163	1.476891	ACAGCGAAGTCGTCACCATAT	59.523	47.619	2.25	0.00	42.22	1.78
2956	3180	2.209838	ATAGTCACCGCAATCGACAG	57.790	50.000	0.00	0.00	38.10	3.51
2959	3183	4.577834	TCAATATAGTCACCGCAATCGA	57.422	40.909	0.00	0.00	38.10	3.59
2960	3184	5.651172	TTTCAATATAGTCACCGCAATCG	57.349	39.130	0.00	0.00	0.00	3.34
3029	3253	7.317842	AGTCATTGTTCATAGATTGCTCTTG	57.682	36.000	0.00	0.00	32.66	3.02
3030	3254	7.609146	TCAAGTCATTGTTCATAGATTGCTCTT	59.391	33.333	0.00	0.00	37.68	2.85
3049	3274	2.840038	ACCATACCTCTGCATCAAGTCA	59.160	45.455	0.00	0.00	0.00	3.41
3057	3282	0.399833	TGCACAACCATACCTCTGCA	59.600	50.000	0.00	0.00	32.35	4.41
3110	3335	7.990886	GGTGTCTACATTACATTTCCTCCATTA	59.009	37.037	0.00	0.00	0.00	1.90
3114	3339	4.809426	CGGTGTCTACATTACATTTCCTCC	59.191	45.833	0.00	0.00	0.00	4.30
3122	3347	4.002982	ACTCGTACGGTGTCTACATTACA	58.997	43.478	16.52	0.00	0.00	2.41
3125	3350	3.076621	TCACTCGTACGGTGTCTACATT	58.923	45.455	25.67	0.00	36.25	2.71
3129	3354	2.462456	AGTCACTCGTACGGTGTCTA	57.538	50.000	25.67	12.14	33.02	2.59
3135	3360	1.531264	CCATCGAAGTCACTCGTACGG	60.531	57.143	16.52	8.79	39.84	4.02
3140	3365	0.243907	ACCACCATCGAAGTCACTCG	59.756	55.000	0.00	0.00	40.25	4.18
3187	3412	5.544176	AGGTCAGAACTAGATTTTCACCTCA	59.456	40.000	0.00	0.00	28.01	3.86
3189	3414	5.544176	TCAGGTCAGAACTAGATTTTCACCT	59.456	40.000	0.00	0.00	32.29	4.00
3190	3415	5.794894	TCAGGTCAGAACTAGATTTTCACC	58.205	41.667	0.00	0.00	0.00	4.02
3258	3483	2.708216	TATCCGAGCAATGCCTTCAA	57.292	45.000	0.00	0.00	0.00	2.69
3296	3524	2.290960	GCCAGATTGTAGGGTTTCACCT	60.291	50.000	0.00	0.00	44.75	4.00
3309	3537	2.159338	CCAATCACGAAAGGCCAGATTG	60.159	50.000	5.01	13.53	43.04	2.67
3375	3604	3.678072	CGACTAGATTCTTCAACGGCAAA	59.322	43.478	0.00	0.00	0.00	3.68
3379	3608	2.194271	GGCGACTAGATTCTTCAACGG	58.806	52.381	0.00	0.00	0.00	4.44
3380	3609	2.159226	AGGGCGACTAGATTCTTCAACG	60.159	50.000	0.00	0.00	0.00	4.10
3393	3622	0.107410	TGACACAAACAAGGGCGACT	60.107	50.000	0.00	0.00	0.00	4.18
3398	3627	7.871973	TCAAATATTTCATGACACAAACAAGGG	59.128	33.333	0.00	0.00	0.00	3.95

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.