AutoCloner

Multiple sequence alignment - TraesCS1D01G299200

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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	TraesCS1D01G299200	chr1D	100.000	4043	0	0	1	4043	397181682	397177640	0.000000e+00	7467.0
1	TraesCS1D01G299200	chr1D	84.202	652	75	11	33	662	439108965	439108320	3.460000e-170	608.0
2	TraesCS1D01G299200	chr1A	91.626	4096	233	43	1	4043	494720512	494716474	0.000000e+00	5563.0
3	TraesCS1D01G299200	chr1B	93.399	3348	136	34	743	4043	532405409	532402100	0.000000e+00	4879.0
4	TraesCS1D01G299200	chr1B	81.090	587	79	16	104	666	48734842	48734264	1.330000e-119	440.0
5	TraesCS1D01G299200	chr7D	84.580	655	68	19	33	664	91749066	91748422	1.600000e-173	619.0
6	TraesCS1D01G299200	chr7D	82.563	671	80	21	30	671	483286697	483287359	1.270000e-154	556.0
7	TraesCS1D01G299200	chr7D	80.288	624	89	14	70	671	454676250	454676861	1.330000e-119	440.0
8	TraesCS1D01G299200	chr7D	87.500	256	21	5	3791	4043	637025458	637025211	6.610000e-73	285.0
9	TraesCS1D01G299200	chrUn	84.290	662	72	19	33	669	92406758	92407412	5.740000e-173	617.0
10	TraesCS1D01G299200	chrUn	84.290	662	72	19	33	669	380756812	380756158	5.740000e-173	617.0
11	TraesCS1D01G299200	chrUn	83.258	663	85	10	27	668	223002381	223001724	1.620000e-163	586.0
12	TraesCS1D01G299200	chrUn	82.256	665	90	12	33	674	97466165	97466824	2.120000e-152	549.0
13	TraesCS1D01G299200	chrUn	77.586	290	54	9	1071	1359	213327110	213327389	8.990000e-37	165.0
14	TraesCS1D01G299200	chr3D	83.358	673	66	25	20	666	93254342	93254994	7.530000e-162	580.0
15	TraesCS1D01G299200	chr3D	82.956	663	86	14	27	668	29494033	29493377	1.260000e-159	573.0
16	TraesCS1D01G299200	chr3D	80.711	591	81	11	91	657	520712003	520711422	2.890000e-116	429.0
17	TraesCS1D01G299200	chr3D	87.308	260	21	6	3787	4043	500873619	500873869	1.840000e-73	287.0
18	TraesCS1D01G299200	chr3D	100.000	33	0	0	1	33	542996306	542996274	1.210000e-05	62.1
19	TraesCS1D01G299200	chr3D	96.875	32	1	0	1	32	426000605	426000574	2.000000e-03	54.7
20	TraesCS1D01G299200	chr5D	84.720	589	62	15	44	611	395694334	395693753	7.590000e-157	564.0
21	TraesCS1D01G299200	chr2B	82.663	646	79	22	42	663	799545079	799545715	3.550000e-150	542.0
22	TraesCS1D01G299200	chr2A	82.389	653	81	15	42	669	69301445	69300802	4.600000e-149	538.0
23	TraesCS1D01G299200	chr2A	88.710	62	2	4	1	60	772096081	772096139	2.020000e-08	71.3
24	TraesCS1D01G299200	chr2A	88.710	62	2	4	1	60	772136482	772136540	2.020000e-08	71.3
25	TraesCS1D01G299200	chr2A	88.710	62	2	4	1	60	772179207	772179265	2.020000e-08	71.3
26	TraesCS1D01G299200	chr3A	79.026	801	122	25	1030	1810	707384199	707384973	1.300000e-139	507.0
27	TraesCS1D01G299200	chr3A	86.739	460	48	4	33	483	19767941	19767486	2.170000e-137	499.0
28	TraesCS1D01G299200	chr2D	80.787	635	81	23	48	658	160328560	160327943	3.680000e-125	459.0
29	TraesCS1D01G299200	chr2D	86.617	269	24	6	3778	4043	473951760	473952019	1.840000e-73	287.0
30	TraesCS1D01G299200	chr2D	85.769	260	26	5	3787	4043	66186504	66186253	8.620000e-67	265.0
31	TraesCS1D01G299200	chr4D	87.739	261	19	7	3787	4043	484990157	484989906	3.950000e-75	292.0
32	TraesCS1D01G299200	chr4D	100.000	33	0	0	1	33	469913098	469913130	1.210000e-05	62.1
33	TraesCS1D01G299200	chr5B	87.356	261	19	9	3787	4043	155250402	155250152	1.840000e-73	287.0
34	TraesCS1D01G299200	chr7A	84.375	256	30	4	3791	4043	98519952	98519704	4.040000e-60	243.0
35	TraesCS1D01G299200	chr7B	100.000	33	0	0	1	33	554757584	554757552	1.210000e-05	62.1

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	TraesCS1D01G299200	chr1D	397177640	397181682	4042	True	7467	7467	100.000	1	4043	1	chr1D.!!$R1	4042
1	TraesCS1D01G299200	chr1D	439108320	439108965	645	True	608	608	84.202	33	662	1	chr1D.!!$R2	629
2	TraesCS1D01G299200	chr1A	494716474	494720512	4038	True	5563	5563	91.626	1	4043	1	chr1A.!!$R1	4042
3	TraesCS1D01G299200	chr1B	532402100	532405409	3309	True	4879	4879	93.399	743	4043	1	chr1B.!!$R2	3300
4	TraesCS1D01G299200	chr1B	48734264	48734842	578	True	440	440	81.090	104	666	1	chr1B.!!$R1	562
5	TraesCS1D01G299200	chr7D	91748422	91749066	644	True	619	619	84.580	33	664	1	chr7D.!!$R1	631
6	TraesCS1D01G299200	chr7D	483286697	483287359	662	False	556	556	82.563	30	671	1	chr7D.!!$F2	641
7	TraesCS1D01G299200	chr7D	454676250	454676861	611	False	440	440	80.288	70	671	1	chr7D.!!$F1	601
8	TraesCS1D01G299200	chrUn	92406758	92407412	654	False	617	617	84.290	33	669	1	chrUn.!!$F1	636
9	TraesCS1D01G299200	chrUn	380756158	380756812	654	True	617	617	84.290	33	669	1	chrUn.!!$R2	636
10	TraesCS1D01G299200	chrUn	223001724	223002381	657	True	586	586	83.258	27	668	1	chrUn.!!$R1	641
11	TraesCS1D01G299200	chrUn	97466165	97466824	659	False	549	549	82.256	33	674	1	chrUn.!!$F2	641
12	TraesCS1D01G299200	chr3D	93254342	93254994	652	False	580	580	83.358	20	666	1	chr3D.!!$F1	646
13	TraesCS1D01G299200	chr3D	29493377	29494033	656	True	573	573	82.956	27	668	1	chr3D.!!$R1	641
14	TraesCS1D01G299200	chr3D	520711422	520712003	581	True	429	429	80.711	91	657	1	chr3D.!!$R3	566
15	TraesCS1D01G299200	chr5D	395693753	395694334	581	True	564	564	84.720	44	611	1	chr5D.!!$R1	567
16	TraesCS1D01G299200	chr2B	799545079	799545715	636	False	542	542	82.663	42	663	1	chr2B.!!$F1	621
17	TraesCS1D01G299200	chr2A	69300802	69301445	643	True	538	538	82.389	42	669	1	chr2A.!!$R1	627
18	TraesCS1D01G299200	chr3A	707384199	707384973	774	False	507	507	79.026	1030	1810	1	chr3A.!!$F1	780
19	TraesCS1D01G299200	chr2D	160327943	160328560	617	True	459	459	80.787	48	658	1	chr2D.!!$R2	610

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
846	903	0.035439	ATTAGTGCCTTGGTCCCACG	60.035	55.000	0.00	0.00	34.79	4.94	F
852	909	1.301716	CCTTGGTCCCACGTGTCAG	60.302	63.158	15.65	2.83	0.00	3.51	F
1034	1096	1.690985	CCTCCACCCTCTTCCTCCC	60.691	68.421	0.00	0.00	0.00	4.30	F
2278	2394	0.457166	CATGCTTGATTGCCCACACG	60.457	55.000	0.00	0.00	0.00	4.49	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1716	1823	1.475403	ACATGTACGTGAGGAGGAGG	58.525	55.000	21.82	0.0	0.00	4.30	R
2278	2394	1.745489	GTGGCACGAGATTGGGGTC	60.745	63.158	0.00	0.0	0.00	4.46	R
3033	3149	1.200484	TGTATGCACGTCTAGCGACAA	59.800	47.619	12.46	0.0	44.77	3.18	R
3695	3819	0.809385	CTTCTGACATGCAAGCAGGG	59.191	55.000	11.58	3.5	31.33	4.45	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
170	176	9.671279	AAAATCTCTTGAAAACACCTTTTTCAT	57.329	25.926	11.80	0.00	44.72	2.57
251	258	2.079158	CTGGAGCAACGATGTTGTCAT	58.921	47.619	10.96	0.00	36.95	3.06
265	275	2.198827	TGTCATTCTTTCACCCGCAT	57.801	45.000	0.00	0.00	0.00	4.73
266	276	2.513753	TGTCATTCTTTCACCCGCATT	58.486	42.857	0.00	0.00	0.00	3.56
341	355	3.525537	TGAGAAGCCTTGATCGATGAAC	58.474	45.455	0.54	0.00	0.00	3.18
342	356	3.055891	TGAGAAGCCTTGATCGATGAACA	60.056	43.478	0.54	0.00	0.00	3.18
343	357	4.125703	GAGAAGCCTTGATCGATGAACAT	58.874	43.478	0.54	0.00	0.00	2.71
344	358	5.163416	TGAGAAGCCTTGATCGATGAACATA	60.163	40.000	0.54	0.00	0.00	2.29
366	380	0.991355	TACTTGGGCCGGGGATGATT	60.991	55.000	2.18	0.00	0.00	2.57
519	560	1.667236	TTAATCTCATGGCACCGCTG	58.333	50.000	0.00	0.00	0.00	5.18
531	572	2.423538	GGCACCGCTGAAATAACAAGAT	59.576	45.455	0.00	0.00	0.00	2.40
620	665	3.916184	GGTCCCCCACCTCTCAAA	58.084	61.111	0.00	0.00	42.84	2.69
674	719	3.599730	ATTTCTCAGATGACGACAGCA	57.400	42.857	5.85	0.00	34.60	4.41
675	720	3.385193	TTTCTCAGATGACGACAGCAA	57.615	42.857	5.85	0.00	34.60	3.91
676	721	2.643933	TCTCAGATGACGACAGCAAG	57.356	50.000	5.85	2.84	34.60	4.01
677	722	1.889170	TCTCAGATGACGACAGCAAGT	59.111	47.619	5.85	0.00	34.60	3.16
678	723	3.081804	TCTCAGATGACGACAGCAAGTA	58.918	45.455	5.85	0.00	34.60	2.24
679	724	3.119814	TCTCAGATGACGACAGCAAGTAC	60.120	47.826	5.85	0.00	34.60	2.73
680	725	2.556622	TCAGATGACGACAGCAAGTACA	59.443	45.455	5.85	0.00	34.60	2.90
682	727	3.928992	CAGATGACGACAGCAAGTACATT	59.071	43.478	5.85	0.00	34.60	2.71
689	738	6.259167	TGACGACAGCAAGTACATTTTTAGTT	59.741	34.615	0.00	0.00	0.00	2.24
696	745	9.820229	CAGCAAGTACATTTTTAGTTATTTCGA	57.180	29.630	0.00	0.00	0.00	3.71
724	773	1.863267	CTTGTCTCCGATGGATCAGC	58.137	55.000	0.00	0.00	0.00	4.26
726	775	0.397675	TGTCTCCGATGGATCAGCCT	60.398	55.000	0.00	0.00	37.63	4.58
727	776	0.755686	GTCTCCGATGGATCAGCCTT	59.244	55.000	0.00	0.00	37.63	4.35
729	778	1.839994	TCTCCGATGGATCAGCCTTTT	59.160	47.619	0.00	0.00	37.63	2.27
794	851	2.514013	GGCATCGCGTTACTGGACG	61.514	63.158	5.77	2.12	45.40	4.79
820	877	3.127030	CGTTTAAGGCCCAGAGAATGTTC	59.873	47.826	0.00	0.00	0.00	3.18
846	903	0.035439	ATTAGTGCCTTGGTCCCACG	60.035	55.000	0.00	0.00	34.79	4.94
852	909	1.301716	CCTTGGTCCCACGTGTCAG	60.302	63.158	15.65	2.83	0.00	3.51
994	1056	4.893601	GGAGAACCTAGCCGCGCC	62.894	72.222	0.00	0.00	0.00	6.53
1034	1096	1.690985	CCTCCACCCTCTTCCTCCC	60.691	68.421	0.00	0.00	0.00	4.30
1626	1733	3.825833	CTGGATCGAGTACCGCGCC	62.826	68.421	0.00	0.00	38.37	6.53
1716	1823	4.176851	GACGTCGACCTCTCCGGC	62.177	72.222	10.58	0.00	35.61	6.13
1899	2012	4.711949	AAGAGCCCACTGCCGCTG	62.712	66.667	0.00	0.00	42.71	5.18
1932	2048	2.806945	ATCACCACCACCATAACCTG	57.193	50.000	0.00	0.00	0.00	4.00
2278	2394	0.457166	CATGCTTGATTGCCCACACG	60.457	55.000	0.00	0.00	0.00	4.49
2289	2405	1.078426	CCCACACGACCCCAATCTC	60.078	63.158	0.00	0.00	0.00	2.75
2805	2921	2.669569	GCAGACCAGCGGCTTCAA	60.670	61.111	0.00	0.00	34.66	2.69
2808	2924	3.435186	GACCAGCGGCTTCAAGGC	61.435	66.667	0.00	0.00	37.44	4.35
2820	2936	4.383602	CAAGGCCGGTTTGTCGCG	62.384	66.667	1.90	0.00	0.00	5.87
3012	3128	3.270877	GTCAGTGAACACCATGGATACC	58.729	50.000	21.47	5.39	0.00	2.73
3096	3212	8.438676	ACTTTCTTATCCATATGTAGTTGTGC	57.561	34.615	1.24	0.00	0.00	4.57
3107	3223	2.831526	TGTAGTTGTGCTCTATCTGCCA	59.168	45.455	0.00	0.00	0.00	4.92
3108	3224	3.452264	TGTAGTTGTGCTCTATCTGCCAT	59.548	43.478	0.00	0.00	0.00	4.40
3157	3273	9.017669	GTATTGCTTTCTGAATTCTTAGCATTG	57.982	33.333	18.19	1.62	38.30	2.82
3159	3275	7.686438	TGCTTTCTGAATTCTTAGCATTGTA	57.314	32.000	15.42	0.35	34.05	2.41
3160	3276	7.530010	TGCTTTCTGAATTCTTAGCATTGTAC	58.470	34.615	15.42	0.00	34.05	2.90
3161	3277	7.174772	TGCTTTCTGAATTCTTAGCATTGTACA	59.825	33.333	15.42	0.00	34.05	2.90
3162	3278	8.023128	GCTTTCTGAATTCTTAGCATTGTACAA	58.977	33.333	11.41	11.41	0.00	2.41
3231	3347	5.104444	TGTTTGGAAAGGTTACTACTGGTGA	60.104	40.000	0.00	0.00	0.00	4.02
3240	3356	6.932947	AGGTTACTACTGGTGAACTATCAAC	58.067	40.000	0.00	0.00	43.94	3.18
3245	3361	4.537135	ACTGGTGAACTATCAACGACAT	57.463	40.909	0.00	0.00	46.79	3.06
3301	3417	5.466393	AGTGTTATTTTCTGGTGCAAATTGC	59.534	36.000	11.58	11.58	45.29	3.56
3354	3476	6.820152	TCAGATTCAGGTGTCATTTATGTGAG	59.180	38.462	0.00	0.00	0.00	3.51
3357	3479	5.089970	TCAGGTGTCATTTATGTGAGGAG	57.910	43.478	0.00	0.00	0.00	3.69
3364	3486	7.040409	GGTGTCATTTATGTGAGGAGAGTTTTT	60.040	37.037	0.00	0.00	0.00	1.94
3365	3487	7.805071	GTGTCATTTATGTGAGGAGAGTTTTTG	59.195	37.037	0.00	0.00	0.00	2.44
3377	3499	7.112452	AGGAGAGTTTTTGTAAATGTTTGCT	57.888	32.000	0.00	0.00	0.00	3.91
3413	3537	2.419673	CTGGCAAATGCGAACTGTCATA	59.580	45.455	0.00	0.00	43.26	2.15
3467	3591	4.491676	TCCTATTGTAAGCAGTCGTGTTC	58.508	43.478	0.00	0.00	0.00	3.18
3468	3592	4.021807	TCCTATTGTAAGCAGTCGTGTTCA	60.022	41.667	0.00	0.00	0.00	3.18
3514	3638	2.009774	GGGCACAGTAGCTGTATTGTG	58.990	52.381	7.56	7.56	43.43	3.33
3560	3684	4.704457	TCGCTGCGTTTATTTTACACTTC	58.296	39.130	22.48	0.00	0.00	3.01
3568	3692	8.569641	TGCGTTTATTTTACACTTCTGGTATTT	58.430	29.630	0.00	0.00	0.00	1.40
3584	3708	8.542497	TCTGGTATTTGATGTACACTGTTTAC	57.458	34.615	0.00	0.00	0.00	2.01
3588	3712	5.564213	TTTGATGTACACTGTTTACGTCG	57.436	39.130	17.02	0.00	38.01	5.12
3611	3735	7.481798	GTCGATTGATACATGGAAGACAAAAAC	59.518	37.037	0.00	0.00	0.00	2.43
3695	3819	5.734855	AATCTGGAATATACACAACGTGC	57.265	39.130	0.00	0.00	36.98	5.34
3701	3825	0.611200	TATACACAACGTGCCCTGCT	59.389	50.000	0.00	0.00	36.98	4.24
3702	3826	0.250727	ATACACAACGTGCCCTGCTT	60.251	50.000	0.00	0.00	36.98	3.91
3703	3827	1.163420	TACACAACGTGCCCTGCTTG	61.163	55.000	0.00	0.00	36.98	4.01
3704	3828	3.595758	ACAACGTGCCCTGCTTGC	61.596	61.111	0.00	0.00	0.00	4.01
3705	3829	3.594775	CAACGTGCCCTGCTTGCA	61.595	61.111	0.00	0.00	36.12	4.08
3711	3835	1.974875	TGCCCTGCTTGCATGTCAG	60.975	57.895	13.47	13.47	32.85	3.51
3742	3866	4.288626	TGATTACCCTAGACAGTTTTGGCT	59.711	41.667	0.00	0.00	46.96	4.75
3748	3872	4.505039	CCCTAGACAGTTTTGGCTTGTACT	60.505	45.833	0.00	0.00	40.86	2.73
3753	3877	4.134563	ACAGTTTTGGCTTGTACTGTAGG	58.865	43.478	11.57	0.00	46.72	3.18
3778	3902	5.807011	GCTTGTACAGAAAATAGCATTTGGG	59.193	40.000	9.55	0.00	0.00	4.12
3785	3909	3.473113	AAATAGCATTTGGGGAGTGGT	57.527	42.857	0.00	0.00	0.00	4.16
3804	3928	2.755103	GGTAGCACCCATTTTCTCTTGG	59.245	50.000	0.00	0.00	30.04	3.61
3811	3935	5.869344	GCACCCATTTTCTCTTGGTTAATTC	59.131	40.000	0.00	0.00	0.00	2.17
3812	3936	6.518200	GCACCCATTTTCTCTTGGTTAATTCA	60.518	38.462	0.00	0.00	0.00	2.57
3813	3937	7.614494	CACCCATTTTCTCTTGGTTAATTCAT	58.386	34.615	0.00	0.00	0.00	2.57
3815	3939	7.454380	ACCCATTTTCTCTTGGTTAATTCATGA	59.546	33.333	0.00	0.00	0.00	3.07
3816	3940	8.313292	CCCATTTTCTCTTGGTTAATTCATGAA	58.687	33.333	11.26	11.26	0.00	2.57
3931	4055	8.879342	AAAGACTATTAGCTGCATAGTACTTG	57.121	34.615	16.50	0.52	37.54	3.16
3932	4056	7.589958	AGACTATTAGCTGCATAGTACTTGT	57.410	36.000	16.50	0.00	37.54	3.16
3936	4060	6.978674	ATTAGCTGCATAGTACTTGTCCTA	57.021	37.500	0.00	0.51	0.00	2.94
3957	4081	2.694628	AGCCTGATTGTTGTTTTGAGCA	59.305	40.909	0.00	0.00	0.00	4.26
4008	4132	9.566432	AATTTCCAGGTATCAATTAGATCAGAC	57.434	33.333	0.00	0.00	38.19	3.51
4016	4140	9.039870	GGTATCAATTAGATCAGACTGTTCTTG	57.960	37.037	18.77	12.42	38.19	3.02
4026	4153	4.753610	TCAGACTGTTCTTGAGCATTTCAG	59.246	41.667	1.59	0.00	37.07	3.02

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
170	176	0.826062	TCGAGCAGAGATTGATGCCA	59.174	50.000	0.00	0.00	43.60	4.92
251	258	6.829298	TGGTAATATTAATGCGGGTGAAAGAA	59.171	34.615	0.00	0.00	0.00	2.52
341	355	2.193127	TCCCCGGCCCAAGTATATATG	58.807	52.381	0.00	0.00	0.00	1.78
342	356	2.653543	TCCCCGGCCCAAGTATATAT	57.346	50.000	0.00	0.00	0.00	0.86
343	357	2.193127	CATCCCCGGCCCAAGTATATA	58.807	52.381	0.00	0.00	0.00	0.86
344	358	0.991920	CATCCCCGGCCCAAGTATAT	59.008	55.000	0.00	0.00	0.00	0.86
366	380	2.359169	CGGCCTGCACTTCTAGGGA	61.359	63.158	0.00	0.00	34.58	4.20
566	608	5.003804	ACTTCTATGTTCTTCGCCATTGTT	58.996	37.500	0.00	0.00	0.00	2.83
635	680	0.326238	TTTATGTCCCCTCGCCTCCT	60.326	55.000	0.00	0.00	0.00	3.69
650	695	6.108687	TGCTGTCGTCATCTGAGAAATTTAT	58.891	36.000	0.00	0.00	0.00	1.40
689	738	6.035650	CGGAGACAAGCAAAAGTATCGAAATA	59.964	38.462	0.00	0.00	0.00	1.40
696	745	3.941483	CCATCGGAGACAAGCAAAAGTAT	59.059	43.478	0.00	0.00	42.51	2.12
794	851	1.017387	CTCTGGGCCTTAAACGCATC	58.983	55.000	4.53	0.00	0.00	3.91
846	903	1.226435	CGAGTAGAGCGGCTGACAC	60.226	63.158	7.50	3.08	0.00	3.67
852	909	0.870735	GGTTTAGCGAGTAGAGCGGC	60.871	60.000	0.00	0.00	40.04	6.53
917	978	2.200955	GAAGAAGGGGATGGGAGAGTT	58.799	52.381	0.00	0.00	0.00	3.01
926	987	0.123266	TTGGGGAGGAAGAAGGGGAT	59.877	55.000	0.00	0.00	0.00	3.85
927	988	0.103608	TTTGGGGAGGAAGAAGGGGA	60.104	55.000	0.00	0.00	0.00	4.81
928	989	1.010795	ATTTGGGGAGGAAGAAGGGG	58.989	55.000	0.00	0.00	0.00	4.79
929	990	1.063642	GGATTTGGGGAGGAAGAAGGG	60.064	57.143	0.00	0.00	0.00	3.95
930	991	1.063642	GGGATTTGGGGAGGAAGAAGG	60.064	57.143	0.00	0.00	0.00	3.46
1034	1096	2.018086	AGGAGGAGGAGGAGGAGGG	61.018	68.421	0.00	0.00	0.00	4.30
1716	1823	1.475403	ACATGTACGTGAGGAGGAGG	58.525	55.000	21.82	0.00	0.00	4.30
1770	1877	3.930376	CTCGACGACGTGAAGCGCT	62.930	63.158	2.64	2.64	46.11	5.92
1932	2048	2.033194	GCCCAGCACCGTGTAGAAC	61.033	63.158	0.00	0.00	0.00	3.01
2278	2394	1.745489	GTGGCACGAGATTGGGGTC	60.745	63.158	0.00	0.00	0.00	4.46
2289	2405	1.746615	CCATCCCAAGAGTGGCACG	60.747	63.158	12.71	0.00	44.46	5.34
2808	2924	4.367023	TCCTCCGCGACAAACCGG	62.367	66.667	8.23	0.00	45.64	5.28
2839	2955	2.598394	GCAGAGGCCCACAAGCAA	60.598	61.111	0.00	0.00	0.00	3.91
3012	3128	7.216881	CGACAACTGTAAAATGCAGTATTCATG	59.783	37.037	1.54	0.00	45.36	3.07
3033	3149	1.200484	TGTATGCACGTCTAGCGACAA	59.800	47.619	12.46	0.00	44.77	3.18
3092	3208	4.406972	AGAACTAATGGCAGATAGAGCACA	59.593	41.667	14.83	0.00	0.00	4.57
3096	3212	6.757237	ACATCAGAACTAATGGCAGATAGAG	58.243	40.000	14.83	0.79	0.00	2.43
3189	3305	8.065473	TCCAAACAATAGTATGCAACATTCAT	57.935	30.769	0.00	0.00	0.00	2.57
3205	3321	6.264518	CACCAGTAGTAACCTTTCCAAACAAT	59.735	38.462	0.00	0.00	0.00	2.71
3231	3347	7.808381	CCTAATATGTCGATGTCGTTGATAGTT	59.192	37.037	2.04	0.00	40.80	2.24
3240	3356	7.535997	TCCTAATTCCTAATATGTCGATGTCG	58.464	38.462	0.00	0.00	41.45	4.35
3245	3361	7.963532	AGCTTTCCTAATTCCTAATATGTCGA	58.036	34.615	0.00	0.00	0.00	4.20
3301	3417	9.941664	CAAAGCTAATTATGAAATACCTCACTG	57.058	33.333	0.00	0.00	0.00	3.66
3354	3476	7.770801	AAGCAAACATTTACAAAAACTCTCC	57.229	32.000	0.00	0.00	0.00	3.71
3364	3486	9.352784	GCAATGTAAGATAAGCAAACATTTACA	57.647	29.630	0.00	0.00	38.39	2.41
3365	3487	8.807581	GGCAATGTAAGATAAGCAAACATTTAC	58.192	33.333	0.00	0.00	38.39	2.01
3413	3537	9.507329	GTCCAAATACCATATGAATATGTGACT	57.493	33.333	3.65	0.00	38.73	3.41
3467	3591	6.560251	GCGAAAACAAAATCAGCTACTGTTTG	60.560	38.462	9.96	9.41	39.48	2.93
3468	3592	5.458779	GCGAAAACAAAATCAGCTACTGTTT	59.541	36.000	0.00	0.00	40.87	2.83
3527	3651	1.016130	ACGCAGCGAGACAATTCTGG	61.016	55.000	24.65	0.00	29.47	3.86
3560	3684	7.117236	ACGTAAACAGTGTACATCAAATACCAG	59.883	37.037	0.00	0.00	0.00	4.00
3568	3692	4.486574	TCGACGTAAACAGTGTACATCA	57.513	40.909	0.00	0.00	0.00	3.07
3570	3694	5.463286	TCAATCGACGTAAACAGTGTACAT	58.537	37.500	0.00	0.00	0.00	2.29
3584	3708	4.359706	TGTCTTCCATGTATCAATCGACG	58.640	43.478	0.00	0.00	0.00	5.12
3588	3712	9.774742	GTAGTTTTTGTCTTCCATGTATCAATC	57.225	33.333	0.00	0.00	0.00	2.67
3611	3735	6.253946	ACAGGAATAGGAAAGGGATTGTAG	57.746	41.667	0.00	0.00	0.00	2.74
3681	3805	1.209504	AGCAGGGCACGTTGTGTATAT	59.790	47.619	0.00	0.00	35.75	0.86
3695	3819	0.809385	CTTCTGACATGCAAGCAGGG	59.191	55.000	11.58	3.50	31.33	4.45
3701	3825	3.421919	TCATGGACTTCTGACATGCAA	57.578	42.857	0.00	0.00	41.22	4.08
3702	3826	3.639672	ATCATGGACTTCTGACATGCA	57.360	42.857	0.00	0.00	41.22	3.96
3703	3827	4.274459	GGTAATCATGGACTTCTGACATGC	59.726	45.833	0.00	0.00	41.22	4.06
3704	3828	4.818546	GGGTAATCATGGACTTCTGACATG	59.181	45.833	0.00	0.00	42.44	3.21
3705	3829	4.723789	AGGGTAATCATGGACTTCTGACAT	59.276	41.667	0.00	0.00	0.00	3.06
3711	3835	5.364157	ACTGTCTAGGGTAATCATGGACTTC	59.636	44.000	0.00	0.00	0.00	3.01
3742	3866	4.154176	TCTGTACAAGCCCTACAGTACAA	58.846	43.478	0.00	0.00	44.14	2.41
3748	3872	5.183228	GCTATTTTCTGTACAAGCCCTACA	58.817	41.667	3.99	0.00	0.00	2.74
3753	3877	5.807011	CCAAATGCTATTTTCTGTACAAGCC	59.193	40.000	11.43	0.00	0.00	4.35
3763	3887	3.769300	ACCACTCCCCAAATGCTATTTTC	59.231	43.478	0.00	0.00	0.00	2.29
3778	3902	2.092323	GAAAATGGGTGCTACCACTCC	58.908	52.381	1.97	0.00	44.72	3.85
3785	3909	3.806949	ACCAAGAGAAAATGGGTGCTA	57.193	42.857	0.00	0.00	41.17	3.49
3804	3928	8.572828	TGTCACACACAATTTCATGAATTAAC	57.427	30.769	9.40	0.00	35.79	2.01
3840	3964	9.369672	TGGTTTACATTTTCTAATAAACAGGGT	57.630	29.630	7.73	0.00	29.61	4.34
3857	3981	4.657814	ACCCAGAAGTGATGGTTTACAT	57.342	40.909	0.00	0.00	44.18	2.29
3861	3985	3.312736	ACAACCCAGAAGTGATGGTTT	57.687	42.857	0.00	0.00	39.01	3.27
3931	4055	4.518970	TCAAAACAACAATCAGGCTAGGAC	59.481	41.667	0.00	0.00	0.00	3.85
3932	4056	4.724399	TCAAAACAACAATCAGGCTAGGA	58.276	39.130	0.00	0.00	0.00	2.94
3936	4060	2.694628	TGCTCAAAACAACAATCAGGCT	59.305	40.909	0.00	0.00	0.00	4.58
4003	4127	4.707105	TGAAATGCTCAAGAACAGTCTGA	58.293	39.130	6.91	0.00	33.05	3.27
4008	4132	3.909776	TGCTGAAATGCTCAAGAACAG	57.090	42.857	0.00	0.00	32.17	3.16

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.