AutoCloner

Multiple sequence alignment - TraesCS5A01G255400

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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	TraesCS5A01G255400	chr5A	100.000	2985	0	0	965	3949	471299450	471296466	0.000000e+00	5513
1	TraesCS5A01G255400	chr5A	100.000	501	0	0	1	501	471300414	471299914	0.000000e+00	926
2	TraesCS5A01G255400	chr5D	95.056	3014	98	19	966	3949	369140095	369143087	0.000000e+00	4693
3	TraesCS5A01G255400	chr5D	95.609	501	20	1	1	501	369139462	369139960	0.000000e+00	802
4	TraesCS5A01G255400	chr5D	82.514	732	94	22	3070	3782	353295123	353294407	2.610000e-171	612
5	TraesCS5A01G255400	chr5D	80.732	410	62	11	3039	3435	495552969	495553374	1.780000e-78	303
6	TraesCS5A01G255400	chr4A	83.357	709	86	18	3044	3733	513294623	513293928	9.320000e-176	627
7	TraesCS5A01G255400	chr3A	82.503	743	97	22	3064	3790	96000935	96000210	4.330000e-174	621
8	TraesCS5A01G255400	chr7D	81.865	772	96	26	3044	3790	529605341	529604589	9.380000e-171	610
9	TraesCS5A01G255400	chr2B	82.585	735	87	21	3077	3790	11266939	11266225	9.380000e-171	610
10	TraesCS5A01G255400	chr2B	82.292	576	80	10	3221	3790	200474686	200474127	2.760000e-131	479
11	TraesCS5A01G255400	chr1A	81.344	729	106	11	3078	3790	5174854	5174140	2.060000e-157	566
12	TraesCS5A01G255400	chr1A	80.685	730	110	18	3078	3790	5244336	5243621	4.490000e-149	538
13	TraesCS5A01G255400	chr1A	82.578	574	83	10	3221	3790	5365440	5364880	1.280000e-134	490
14	TraesCS5A01G255400	chr1A	77.325	785	120	25	3046	3790	572220741	572219975	1.020000e-110	411
15	TraesCS5A01G255400	chr4B	82.216	686	83	22	3046	3709	100575330	100574662	4.460000e-154	555
16	TraesCS5A01G255400	chrUn	80.585	752	112	19	3057	3790	281345796	281346531	2.070000e-152	549
17	TraesCS5A01G255400	chrUn	80.585	752	112	19	3057	3790	348581344	348580609	2.070000e-152	549
18	TraesCS5A01G255400	chrUn	80.186	752	114	20	3057	3790	88013	88747	7.510000e-147	531
19	TraesCS5A01G255400	chr6A	80.026	776	107	24	3046	3790	2937894	2938652	7.510000e-147	531
20	TraesCS5A01G255400	chr3D	80.716	726	96	23	3092	3790	120895040	120894332	3.500000e-145	525
21	TraesCS5A01G255400	chr3D	83.835	266	25	5	3047	3294	516183645	516183910	1.830000e-58	237
22	TraesCS5A01G255400	chr7B	79.832	714	109	25	3089	3786	66883779	66884473	4.590000e-134	488
23	TraesCS5A01G255400	chr7B	82.465	576	72	18	3227	3790	748714707	748714149	9.930000e-131	477
24	TraesCS5A01G255400	chr7B	83.824	340	33	10	3044	3361	733488000	733487661	1.780000e-78	303
25	TraesCS5A01G255400	chr7A	78.553	774	123	19	3046	3790	56979927	56980686	1.660000e-128	470
26	TraesCS5A01G255400	chr1D	80.178	676	88	26	3039	3686	97910798	97911455	7.730000e-127	464
27	TraesCS5A01G255400	chr5B	81.845	336	41	11	3046	3361	672889143	672889478	8.410000e-67	265

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	TraesCS5A01G255400	chr5A	471296466	471300414	3948	True	3219.5	5513	100.0000	1	3949	2	chr5A.!!$R1	3948
1	TraesCS5A01G255400	chr5D	369139462	369143087	3625	False	2747.5	4693	95.3325	1	3949	2	chr5D.!!$F2	3948
2	TraesCS5A01G255400	chr5D	353294407	353295123	716	True	612.0	612	82.5140	3070	3782	1	chr5D.!!$R1	712
3	TraesCS5A01G255400	chr4A	513293928	513294623	695	True	627.0	627	83.3570	3044	3733	1	chr4A.!!$R1	689
4	TraesCS5A01G255400	chr3A	96000210	96000935	725	True	621.0	621	82.5030	3064	3790	1	chr3A.!!$R1	726
5	TraesCS5A01G255400	chr7D	529604589	529605341	752	True	610.0	610	81.8650	3044	3790	1	chr7D.!!$R1	746
6	TraesCS5A01G255400	chr2B	11266225	11266939	714	True	610.0	610	82.5850	3077	3790	1	chr2B.!!$R1	713
7	TraesCS5A01G255400	chr2B	200474127	200474686	559	True	479.0	479	82.2920	3221	3790	1	chr2B.!!$R2	569
8	TraesCS5A01G255400	chr1A	5174140	5174854	714	True	566.0	566	81.3440	3078	3790	1	chr1A.!!$R1	712
9	TraesCS5A01G255400	chr1A	5243621	5244336	715	True	538.0	538	80.6850	3078	3790	1	chr1A.!!$R2	712
10	TraesCS5A01G255400	chr1A	5364880	5365440	560	True	490.0	490	82.5780	3221	3790	1	chr1A.!!$R3	569
11	TraesCS5A01G255400	chr1A	572219975	572220741	766	True	411.0	411	77.3250	3046	3790	1	chr1A.!!$R4	744
12	TraesCS5A01G255400	chr4B	100574662	100575330	668	True	555.0	555	82.2160	3046	3709	1	chr4B.!!$R1	663
13	TraesCS5A01G255400	chrUn	281345796	281346531	735	False	549.0	549	80.5850	3057	3790	1	chrUn.!!$F2	733
14	TraesCS5A01G255400	chrUn	348580609	348581344	735	True	549.0	549	80.5850	3057	3790	1	chrUn.!!$R1	733
15	TraesCS5A01G255400	chrUn	88013	88747	734	False	531.0	531	80.1860	3057	3790	1	chrUn.!!$F1	733
16	TraesCS5A01G255400	chr6A	2937894	2938652	758	False	531.0	531	80.0260	3046	3790	1	chr6A.!!$F1	744
17	TraesCS5A01G255400	chr3D	120894332	120895040	708	True	525.0	525	80.7160	3092	3790	1	chr3D.!!$R1	698
18	TraesCS5A01G255400	chr7B	66883779	66884473	694	False	488.0	488	79.8320	3089	3786	1	chr7B.!!$F1	697
19	TraesCS5A01G255400	chr7B	748714149	748714707	558	True	477.0	477	82.4650	3227	3790	1	chr7B.!!$R2	563
20	TraesCS5A01G255400	chr7A	56979927	56980686	759	False	470.0	470	78.5530	3046	3790	1	chr7A.!!$F1	744
21	TraesCS5A01G255400	chr1D	97910798	97911455	657	False	464.0	464	80.1780	3039	3686	1	chr1D.!!$F1	647

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
318	319	0.391130	TTTCCTTGGCCGTCAGATCG	60.391	55.0	0.00	0.00	3.69	F
1001	1002	0.176219	CCGCCAACAGGTAATCGGTA	59.824	55.0	0.00	32.93	4.02	F
1588	1590	0.975887	TTACGTTGGTACCACTCCCC	59.024	55.0	16.04	0.00	4.81	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2049	2053	0.522180	AGCATCGTCGTCTTCTTCGT	59.478	50.000	0.00	0.00	0.00	3.85	R
2377	2381	0.320374	TGTAGCCCTCGAGGTTGTTG	59.680	55.000	29.25	14.98	38.26	3.33	R
3437	3495	1.405105	ACATGCAACCACAGACACAAC	59.595	47.619	0.00	0.00	0.00	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
41	42	2.877691	GGGGCAACACGCATCTTC	59.122	61.111	0.00	0.00	45.17	2.87
65	66	9.817809	TTCTCCATAGTAGTACATGTGAAATTC	57.182	33.333	9.11	0.00	0.00	2.17
73	74	4.702131	AGTACATGTGAAATTCAGGGAAGC	59.298	41.667	9.11	0.00	0.00	3.86
114	115	0.534203	AAGAAACGTGACGGCCACAT	60.534	50.000	10.66	0.00	45.98	3.21
239	240	2.673258	TCGGGATAAGCAGATACCACA	58.327	47.619	0.44	0.00	28.97	4.17
283	284	5.751028	TGGAAAGTTTAGAAAAACATTGGCG	59.249	36.000	4.04	0.00	46.18	5.69
284	285	5.333035	GGAAAGTTTAGAAAAACATTGGCGC	60.333	40.000	0.00	0.00	46.18	6.53
301	302	1.668628	GCGCACGATTTTGATGGGTTT	60.669	47.619	0.30	0.00	0.00	3.27
318	319	0.391130	TTTCCTTGGCCGTCAGATCG	60.391	55.000	0.00	0.00	0.00	3.69
353	354	1.443828	GGAGGATCGGGCTGAAGAC	59.556	63.158	0.00	0.00	34.37	3.01
377	378	4.678742	CGCTACACATCAGACATCTGTATG	59.321	45.833	8.70	12.29	44.12	2.39
415	416	9.990360	GTTTCCCATTGTTTTTCTATTTCCTTA	57.010	29.630	0.00	0.00	0.00	2.69
457	458	3.444034	ACTCTCAATCGTCGGATCTCAAA	59.556	43.478	0.00	0.00	30.81	2.69
471	472	5.463392	CGGATCTCAAATGTACATCGACAAT	59.537	40.000	9.23	0.98	31.83	2.71
998	999	2.808958	CGCCGCCAACAGGTAATCG	61.809	63.158	0.00	0.00	0.00	3.34
999	1000	2.469516	GCCGCCAACAGGTAATCGG	61.470	63.158	0.00	0.00	39.81	4.18
1000	1001	1.078708	CCGCCAACAGGTAATCGGT	60.079	57.895	0.00	0.00	32.93	4.69
1001	1002	0.176219	CCGCCAACAGGTAATCGGTA	59.824	55.000	0.00	0.00	32.93	4.02
1002	1003	1.405797	CCGCCAACAGGTAATCGGTAA	60.406	52.381	0.00	0.00	32.93	2.85
1003	1004	2.557317	CGCCAACAGGTAATCGGTAAT	58.443	47.619	0.00	0.00	0.00	1.89
1004	1005	2.542595	CGCCAACAGGTAATCGGTAATC	59.457	50.000	0.00	0.00	0.00	1.75
1030	1031	2.482142	CCTAACTCACAGATCCGCCTTC	60.482	54.545	0.00	0.00	0.00	3.46
1033	1034	1.066573	ACTCACAGATCCGCCTTCAAG	60.067	52.381	0.00	0.00	0.00	3.02
1038	1039	3.077359	ACAGATCCGCCTTCAAGAAAAG	58.923	45.455	0.00	0.00	0.00	2.27
1041	1042	4.216257	CAGATCCGCCTTCAAGAAAAGAAA	59.784	41.667	0.00	0.00	0.00	2.52
1200	1202	3.070590	ACTTACACGGGTTACTGCTTCTT	59.929	43.478	0.00	0.00	0.00	2.52
1586	1588	4.081476	ACCTAATTACGTTGGTACCACTCC	60.081	45.833	16.04	4.65	0.00	3.85
1588	1590	0.975887	TTACGTTGGTACCACTCCCC	59.024	55.000	16.04	0.00	0.00	4.81
1589	1591	1.250154	TACGTTGGTACCACTCCCCG	61.250	60.000	16.04	13.91	0.00	5.73
1590	1592	2.277591	CGTTGGTACCACTCCCCGA	61.278	63.158	16.04	0.00	0.00	5.14
1592	1594	1.611261	TTGGTACCACTCCCCGAGG	60.611	63.158	16.04	0.00	33.35	4.63
1593	1595	2.096707	TTGGTACCACTCCCCGAGGA	62.097	60.000	16.04	0.00	41.08	3.71
1594	1596	1.075450	GGTACCACTCCCCGAGGAT	60.075	63.158	7.15	0.00	42.93	3.24
1636	1640	4.627035	TCAGAAACACATTACGAGCATGAG	59.373	41.667	0.00	0.00	0.00	2.90
1688	1692	2.428491	CATACTTGTACCCCGTGCAAA	58.572	47.619	0.00	0.00	37.65	3.68
1702	1706	3.242518	CGTGCAAATCTACTCGTCAAGA	58.757	45.455	0.00	0.00	0.00	3.02
1716	1720	4.660938	AAGAACCGGGCAGTGGGC	62.661	66.667	6.32	0.00	43.74	5.36
1725	1729	2.359230	GCAGTGGGCTGACAGGAC	60.359	66.667	4.26	0.00	45.28	3.85
1858	1862	1.514443	GCTCTACGTCCACTGTCGC	60.514	63.158	0.00	0.00	0.00	5.19
1931	1935	2.542020	TTTGTCTCGTCCTTGATGCA	57.458	45.000	0.00	0.00	0.00	3.96
1959	1963	9.061610	CGTTCAATCTAACCAACATGTTTAATC	57.938	33.333	8.77	0.00	0.00	1.75
2010	2014	6.749139	TGTCATTAGTGGAGGAGATTTATCG	58.251	40.000	0.00	0.00	0.00	2.92
2049	2053	4.267536	AGACTACATGTAGCCGAGTACAA	58.732	43.478	28.88	0.00	36.51	2.41
2053	2057	2.229543	ACATGTAGCCGAGTACAACGAA	59.770	45.455	12.69	0.00	36.51	3.85
2377	2381	5.245751	TGCTGATATGGAAGAAGAGGAGATC	59.754	44.000	0.00	0.00	0.00	2.75
2509	2513	5.541101	TGCCTACTACCTAGACAACTCAAAA	59.459	40.000	0.00	0.00	0.00	2.44
2647	2651	9.260002	CACAATGATATTTAGGGTTTATTTGGC	57.740	33.333	0.00	0.00	0.00	4.52
2798	2802	2.505819	TGGGACCATTTCTTAGGCTCTC	59.494	50.000	0.00	0.00	0.00	3.20
2828	2832	2.851195	AGGCTCATCAACGTTGTTCTT	58.149	42.857	26.47	8.77	0.00	2.52
2844	2848	8.617809	ACGTTGTTCTTTACTTTTGACATACAT	58.382	29.630	0.00	0.00	0.00	2.29
2929	2933	3.486383	TGGCCAAAGAAGAAGGTAACAG	58.514	45.455	0.61	0.00	41.41	3.16
3009	3022	2.099921	GACATCTGACGGTGATGCTAGT	59.900	50.000	12.33	0.00	43.53	2.57
3020	3033	0.826715	GATGCTAGTGTCCTGCTCCA	59.173	55.000	0.00	0.00	0.00	3.86
3408	3466	5.234329	GTGGTGTCATTCCGTGTTATCTATG	59.766	44.000	0.00	0.00	0.00	2.23
3437	3495	9.762933	CCAACCTATATTTATGTGGGAAAATTG	57.237	33.333	0.00	0.00	0.00	2.32
3556	3625	5.011227	TGTTTTTATAGGTTGGTTTCTGCCC	59.989	40.000	0.00	0.00	0.00	5.36
3558	3627	2.990740	ATAGGTTGGTTTCTGCCCAA	57.009	45.000	0.00	0.00	39.62	4.12
3561	3630	1.970640	AGGTTGGTTTCTGCCCAATTC	59.029	47.619	0.00	0.00	43.50	2.17
3567	3636	6.172630	GTTGGTTTCTGCCCAATTCATTTAT	58.827	36.000	0.00	0.00	43.50	1.40
3568	3637	7.327214	GTTGGTTTCTGCCCAATTCATTTATA	58.673	34.615	0.00	0.00	43.50	0.98
3569	3638	7.673641	TGGTTTCTGCCCAATTCATTTATAT	57.326	32.000	0.00	0.00	0.00	0.86
3570	3639	7.499292	TGGTTTCTGCCCAATTCATTTATATG	58.501	34.615	0.00	0.00	0.00	1.78
3571	3640	7.125507	TGGTTTCTGCCCAATTCATTTATATGT	59.874	33.333	0.00	0.00	33.34	2.29
3572	3641	7.986889	GGTTTCTGCCCAATTCATTTATATGTT	59.013	33.333	0.00	0.00	33.34	2.71
3573	3642	9.382275	GTTTCTGCCCAATTCATTTATATGTTT	57.618	29.630	0.00	0.00	33.34	2.83
3574	3643	9.956640	TTTCTGCCCAATTCATTTATATGTTTT	57.043	25.926	0.00	0.00	33.34	2.43
3575	3644	8.945481	TCTGCCCAATTCATTTATATGTTTTG	57.055	30.769	0.00	0.22	33.34	2.44
3576	3645	8.756927	TCTGCCCAATTCATTTATATGTTTTGA	58.243	29.630	10.17	0.00	31.94	2.69
3577	3646	9.550406	CTGCCCAATTCATTTATATGTTTTGAT	57.450	29.630	10.17	0.00	31.94	2.57
3578	3647	9.545105	TGCCCAATTCATTTATATGTTTTGATC	57.455	29.630	10.17	0.00	31.94	2.92
3800	3908	6.443934	AAGCACAGTGTATCTCTACTACTG	57.556	41.667	1.61	0.00	39.83	2.74
3806	3914	9.557338	CACAGTGTATCTCTACTACTGTTAAAC	57.443	37.037	5.66	0.00	42.15	2.01
3842	3950	2.580276	CTAAACGCACCCCGCCTA	59.420	61.111	0.00	0.00	41.76	3.93
3845	3953	2.109517	TAAACGCACCCCGCCTAACA	62.110	55.000	0.00	0.00	41.76	2.41
3857	3965	2.417651	CCGCCTAACATACACGGAAAGA	60.418	50.000	0.00	0.00	46.71	2.52
3862	3970	5.049267	GCCTAACATACACGGAAAGAAACAA	60.049	40.000	0.00	0.00	0.00	2.83
3879	3987	8.887036	AAGAAACAAATGAATTAAAGGGTCAC	57.113	30.769	0.00	0.00	0.00	3.67
3892	4000	0.824759	GGGTCACGATCAGCCTACTT	59.175	55.000	0.00	0.00	0.00	2.24
3923	4031	9.182214	AGATCTAACCGTCTACATAACAACTAA	57.818	33.333	0.00	0.00	0.00	2.24
3928	4036	5.032863	CCGTCTACATAACAACTAACCTCG	58.967	45.833	0.00	0.00	0.00	4.63

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
23	24	1.675641	GAAGATGCGTGTTGCCCCT	60.676	57.895	0.00	0.00	45.60	4.79
41	42	9.254133	CTGAATTTCACATGTACTACTATGGAG	57.746	37.037	0.00	0.00	0.00	3.86
88	89	3.002553	GGCCGTCACGTTTCTTTTTAAGA	59.997	43.478	0.00	0.00	35.26	2.10
89	90	3.242804	TGGCCGTCACGTTTCTTTTTAAG	60.243	43.478	0.00	0.00	0.00	1.85
125	126	1.651240	TTCTACCGCCTTCGTCTCCG	61.651	60.000	0.00	0.00	0.00	4.63
184	185	0.463833	CCAAACCGACCCCATCTAGC	60.464	60.000	0.00	0.00	0.00	3.42
239	240	0.461961	GTCTTCACGCCTATGCTCCT	59.538	55.000	0.00	0.00	34.43	3.69
258	259	6.074356	CGCCAATGTTTTTCTAAACTTTCCAG	60.074	38.462	0.00	0.00	43.25	3.86
283	284	2.231235	AGGAAACCCATCAAAATCGTGC	59.769	45.455	0.00	0.00	0.00	5.34
284	285	4.236935	CAAGGAAACCCATCAAAATCGTG	58.763	43.478	0.00	0.00	0.00	4.35
301	302	1.254975	TTCGATCTGACGGCCAAGGA	61.255	55.000	2.24	0.00	0.00	3.36
318	319	1.594862	CTCCGCCGTTGATTCATCTTC	59.405	52.381	0.00	0.00	0.00	2.87
353	354	2.159184	ACAGATGTCTGATGTGTAGCGG	60.159	50.000	16.41	0.00	46.59	5.52
457	458	5.451937	CCAGTCCTACATTGTCGATGTACAT	60.452	44.000	8.43	8.43	47.00	2.29
471	472	2.646175	GCGCCAGACCAGTCCTACA	61.646	63.158	0.00	0.00	0.00	2.74
998	999	7.927092	GGATCTGTGAGTTAGGTTTAGATTACC	59.073	40.741	0.00	0.00	35.85	2.85
999	1000	7.648510	CGGATCTGTGAGTTAGGTTTAGATTAC	59.351	40.741	0.00	0.00	0.00	1.89
1000	1001	7.683704	GCGGATCTGTGAGTTAGGTTTAGATTA	60.684	40.741	2.89	0.00	0.00	1.75
1001	1002	6.574350	CGGATCTGTGAGTTAGGTTTAGATT	58.426	40.000	0.00	0.00	0.00	2.40
1002	1003	5.452077	GCGGATCTGTGAGTTAGGTTTAGAT	60.452	44.000	2.89	0.00	0.00	1.98
1003	1004	4.142227	GCGGATCTGTGAGTTAGGTTTAGA	60.142	45.833	2.89	0.00	0.00	2.10
1004	1005	4.113354	GCGGATCTGTGAGTTAGGTTTAG	58.887	47.826	2.89	0.00	0.00	1.85
1030	1031	4.584325	TGGATCTGTGGGTTTCTTTTCTTG	59.416	41.667	0.00	0.00	0.00	3.02
1033	1034	4.022849	CAGTGGATCTGTGGGTTTCTTTTC	60.023	45.833	0.00	0.00	39.17	2.29
1038	1039	2.859165	TCAGTGGATCTGTGGGTTTC	57.141	50.000	0.00	0.00	43.97	2.78
1041	1042	3.593442	TTTTTCAGTGGATCTGTGGGT	57.407	42.857	0.00	0.00	43.97	4.51
1066	1067	1.348036	GGGAAGATCCATCGGGTTAGG	59.652	57.143	0.00	0.00	38.64	2.69
1218	1220	5.470047	AAATGTAGTTGACGAAGAGACCT	57.530	39.130	0.00	0.00	0.00	3.85
1471	1473	1.525535	GACGGCGGTAGAGAGGCTA	60.526	63.158	13.24	0.00	0.00	3.93
1588	1590	3.917760	GACCCCGGCTGATCCTCG	61.918	72.222	0.00	0.00	0.00	4.63
1589	1591	3.917760	CGACCCCGGCTGATCCTC	61.918	72.222	0.00	0.00	0.00	3.71
1590	1592	4.779733	ACGACCCCGGCTGATCCT	62.780	66.667	0.00	0.00	40.78	3.24
1592	1594	4.570663	CGACGACCCCGGCTGATC	62.571	72.222	0.00	0.00	42.92	2.92
1636	1640	2.953466	TCGAGCTGGTGGTGTTATAC	57.047	50.000	0.00	0.00	0.00	1.47
1688	1692	1.749634	CCCGGTTCTTGACGAGTAGAT	59.250	52.381	0.00	0.00	0.00	1.98
1716	1720	2.104792	TCTGGGACAAAAGTCCTGTCAG	59.895	50.000	13.76	12.21	44.16	3.51
1725	1729	2.629617	ACATTGCCTTCTGGGACAAAAG	59.370	45.455	0.00	0.00	38.70	2.27
1734	1738	0.606401	ACCCGTCACATTGCCTTCTG	60.606	55.000	0.00	0.00	0.00	3.02
1760	1764	1.628340	TGGATCTGACCAAACGTCCAT	59.372	47.619	0.00	0.00	41.18	3.41
1768	1772	0.605319	GTGGCGTTGGATCTGACCAA	60.605	55.000	7.37	7.37	46.02	3.67
1858	1862	4.353737	CATGCCTCATAACAAAATCACCG	58.646	43.478	0.00	0.00	0.00	4.94
1909	1913	4.574892	TGCATCAAGGACGAGACAAAATA	58.425	39.130	0.00	0.00	0.00	1.40
1931	1935	4.072131	ACATGTTGGTTAGATTGAACGCT	58.928	39.130	0.00	0.00	0.00	5.07
1964	1968	7.717436	TGACAACCTAGTGTATGACATGAAAAA	59.283	33.333	0.00	0.00	0.00	1.94
2010	2014	3.756117	AGTCTTGGGGTTTTGATCACTC	58.244	45.455	0.00	0.00	0.00	3.51
2049	2053	0.522180	AGCATCGTCGTCTTCTTCGT	59.478	50.000	0.00	0.00	0.00	3.85
2053	2057	3.056749	AGGTTTTAGCATCGTCGTCTTCT	60.057	43.478	0.00	0.00	0.00	2.85
2377	2381	0.320374	TGTAGCCCTCGAGGTTGTTG	59.680	55.000	29.25	14.98	38.26	3.33
2509	2513	8.753497	GGAAAAGTGATCCCAAATACTCTAAT	57.247	34.615	0.00	0.00	0.00	1.73
2647	2651	5.392811	GGAGTGCAGATGAATTTCCTTTGAG	60.393	44.000	0.00	0.00	0.00	3.02
2798	2802	4.083110	ACGTTGATGAGCCTTGAGAAATTG	60.083	41.667	0.00	0.00	0.00	2.32
2828	2832	6.878923	CAGGGACTCATGTATGTCAAAAGTAA	59.121	38.462	14.45	0.00	34.60	2.24
2844	2848	4.968719	TCTGCTAATTAATCCAGGGACTCA	59.031	41.667	9.50	0.00	34.60	3.41
2929	2933	4.508662	CCAATAGAGAAACTGACAGGACC	58.491	47.826	7.51	0.00	0.00	4.46
2936	2940	4.908601	TGGAAGCCAATAGAGAAACTGA	57.091	40.909	0.00	0.00	0.00	3.41
2965	2969	6.952548	GTCCAGCAAAAAGCACATGGATATAC	60.953	42.308	0.00	0.00	44.12	1.47
3009	3022	1.419381	TGTAACACTGGAGCAGGACA	58.581	50.000	0.00	0.00	35.51	4.02
3020	3033	6.561519	AGCAACCCTTCTATATGTAACACT	57.438	37.500	0.00	0.00	0.00	3.55
3408	3466	8.528044	TTTCCCACATAAATATAGGTTGGTTC	57.472	34.615	0.00	0.00	32.19	3.62
3437	3495	1.405105	ACATGCAACCACAGACACAAC	59.595	47.619	0.00	0.00	0.00	3.32
3550	3619	8.756927	TCAAAACATATAAATGAATTGGGCAGA	58.243	29.630	0.00	0.00	36.54	4.26
3567	3636	7.392418	TGGGCAAATGATTTGATCAAAACATA	58.608	30.769	31.92	19.09	41.09	2.29
3568	3637	6.239396	TGGGCAAATGATTTGATCAAAACAT	58.761	32.000	28.52	28.52	42.89	2.71
3569	3638	5.618236	TGGGCAAATGATTTGATCAAAACA	58.382	33.333	26.99	26.99	43.50	2.83
3570	3639	6.557291	TTGGGCAAATGATTTGATCAAAAC	57.443	33.333	23.91	21.08	43.50	2.43
3571	3640	6.940867	TGATTGGGCAAATGATTTGATCAAAA	59.059	30.769	23.91	9.87	43.50	2.44
3572	3641	6.473758	TGATTGGGCAAATGATTTGATCAAA	58.526	32.000	22.52	22.52	43.50	2.69
3573	3642	6.051179	TGATTGGGCAAATGATTTGATCAA	57.949	33.333	21.14	20.52	43.50	2.57
3574	3643	5.678955	TGATTGGGCAAATGATTTGATCA	57.321	34.783	21.14	16.42	43.26	2.92
3575	3644	6.988622	TTTGATTGGGCAAATGATTTGATC	57.011	33.333	21.14	14.30	43.26	2.92
3576	3645	7.612244	TGATTTTGATTGGGCAAATGATTTGAT	59.388	29.630	21.14	5.86	43.26	2.57
3577	3646	6.940867	TGATTTTGATTGGGCAAATGATTTGA	59.059	30.769	21.14	0.84	43.26	2.69
3578	3647	7.147143	TGATTTTGATTGGGCAAATGATTTG	57.853	32.000	13.32	13.32	43.44	2.32
3806	3914	8.856247	GCGTTTAGGGTAATTAATGTTTTCTTG	58.144	33.333	0.00	0.00	0.00	3.02
3809	3917	7.274033	GGTGCGTTTAGGGTAATTAATGTTTTC	59.726	37.037	0.00	0.00	0.00	2.29
3822	3930	4.710167	GCGGGGTGCGTTTAGGGT	62.710	66.667	0.00	0.00	0.00	4.34
3842	3950	7.033530	TCATTTGTTTCTTTCCGTGTATGTT	57.966	32.000	0.00	0.00	0.00	2.71
3857	3965	7.045126	TCGTGACCCTTTAATTCATTTGTTT	57.955	32.000	0.00	0.00	0.00	2.83
3862	3970	5.066505	GCTGATCGTGACCCTTTAATTCATT	59.933	40.000	0.00	0.00	0.00	2.57
3917	4025	5.295152	AGGTACTTTTCACGAGGTTAGTTG	58.705	41.667	0.00	0.00	27.25	3.16
3923	4031	3.802675	GCTTGAGGTACTTTTCACGAGGT	60.803	47.826	0.00	0.00	41.55	3.85

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.