AutoCloner

Multiple sequence alignment - TraesCS2A01G564600

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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	TraesCS2A01G564600	chr2A	100.000	3188	0	0	1	3188	764729499	764726312	0.000000e+00	5888.0
1	TraesCS2A01G564600	chr2A	100.000	1561	0	0	3430	4990	764726070	764724510	0.000000e+00	2883.0
2	TraesCS2A01G564600	chr2A	92.523	214	16	0	1935	2148	23755085	23754872	1.740000e-79	307.0
3	TraesCS2A01G564600	chr2A	92.523	214	15	1	1935	2148	95604633	95604421	6.280000e-79	305.0
4	TraesCS2A01G564600	chr2B	97.304	2485	54	6	651	3135	798159538	798157067	0.000000e+00	4205.0
5	TraesCS2A01G564600	chr2B	97.950	1561	31	1	3430	4990	798157065	798155506	0.000000e+00	2704.0
6	TraesCS2A01G564600	chr2B	86.628	1376	150	17	3622	4990	798331021	798329673	0.000000e+00	1491.0
7	TraesCS2A01G564600	chr2B	86.245	1374	158	17	3621	4988	798193076	798191728	0.000000e+00	1461.0
8	TraesCS2A01G564600	chr2B	85.911	1377	163	17	3621	4990	798226513	798225161	0.000000e+00	1439.0
9	TraesCS2A01G564600	chr2B	83.608	1275	160	23	585	1829	798195756	798194501	0.000000e+00	1151.0
10	TraesCS2A01G564600	chr2B	78.422	862	143	21	1068	1905	798334231	798333389	5.720000e-144	521.0
11	TraesCS2A01G564600	chr2B	92.113	355	21	6	272	622	798159885	798159534	1.250000e-135	494.0
12	TraesCS2A01G564600	chr2B	90.034	291	29	0	905	1195	798256646	798256356	1.310000e-100	377.0
13	TraesCS2A01G564600	chr2B	90.034	291	29	0	905	1195	798266424	798266134	1.310000e-100	377.0
14	TraesCS2A01G564600	chr2B	92.607	257	13	4	1	256	798160127	798159876	1.020000e-96	364.0
15	TraesCS2A01G564600	chr2B	84.768	302	26	7	557	846	798256931	798256638	8.180000e-73	285.0
16	TraesCS2A01G564600	chr2B	84.768	302	26	7	557	846	798266709	798266416	8.180000e-73	285.0
17	TraesCS2A01G564600	chr2B	75.705	638	93	29	2547	3164	798194050	798193455	3.830000e-66	263.0
18	TraesCS2A01G564600	chr2B	75.385	260	38	15	2147	2402	798194300	798194063	8.840000e-18	102.0
19	TraesCS2A01G564600	chr2B	97.436	39	1	0	864	902	610020598	610020636	3.220000e-07	67.6
20	TraesCS2A01G564600	chr2D	90.601	1564	118	7	3430	4989	639090285	639088747	0.000000e+00	2047.0
21	TraesCS2A01G564600	chr2D	90.672	1190	55	12	2003	3188	639091431	639090294	0.000000e+00	1531.0
22	TraesCS2A01G564600	chr2D	85.177	1383	164	27	3621	4989	639362125	639360770	0.000000e+00	1380.0
23	TraesCS2A01G564600	chr2D	85.040	1377	174	17	3621	4990	638864166	638862815	0.000000e+00	1373.0
24	TraesCS2A01G564600	chr2D	91.246	971	83	2	968	1938	639092543	639091575	0.000000e+00	1321.0
25	TraesCS2A01G564600	chr2D	84.386	1377	164	29	3621	4989	639137010	639135677	0.000000e+00	1304.0
26	TraesCS2A01G564600	chr2D	84.365	1260	156	22	598	1829	639364481	639363235	0.000000e+00	1197.0
27	TraesCS2A01G564600	chr2D	82.905	1363	188	22	3621	4973	639278610	639277283	0.000000e+00	1184.0
28	TraesCS2A01G564600	chr2D	82.406	881	134	14	960	1828	638876115	638875244	0.000000e+00	749.0
29	TraesCS2A01G564600	chr2D	80.904	885	140	16	961	1826	639148131	639147257	0.000000e+00	671.0
30	TraesCS2A01G564600	chr2D	81.303	829	136	11	1010	1827	639279723	639278903	0.000000e+00	654.0
31	TraesCS2A01G564600	chr2D	80.843	261	37	8	2147	2402	639138408	639138156	5.100000e-45	193.0
32	TraesCS2A01G564600	chr2D	81.421	183	23	8	545	721	639148394	639148217	6.740000e-29	139.0
33	TraesCS2A01G564600	chr2D	92.857	42	3	0	802	843	639092646	639092605	1.500000e-05	62.1
34	TraesCS2A01G564600	chr3A	94.811	212	11	0	1937	2148	198839191	198839402	1.040000e-86	331.0
35	TraesCS2A01G564600	chr3A	100.000	30	0	0	1935	1964	77660841	77660870	6.980000e-04	56.5
36	TraesCS2A01G564600	chr3A	100.000	30	0	0	1935	1964	77686238	77686267	6.980000e-04	56.5
37	TraesCS2A01G564600	chr1A	93.925	214	13	0	1935	2148	62247296	62247509	1.730000e-84	324.0
38	TraesCS2A01G564600	chr1A	91.589	214	18	0	1935	2148	62247858	62248071	3.780000e-76	296.0
39	TraesCS2A01G564600	chr3B	94.416	197	11	0	1952	2148	243808991	243808795	2.260000e-78	303.0
40	TraesCS2A01G564600	chr4D	92.788	208	14	1	1935	2142	304361951	304362157	2.920000e-77	300.0
41	TraesCS2A01G564600	chr1D	78.261	184	36	4	4677	4858	12535056	12535237	1.140000e-21	115.0
42	TraesCS2A01G564600	chr7B	93.151	73	5	0	1566	1638	734078041	734077969	1.900000e-19	108.0
43	TraesCS2A01G564600	chr6A	78.182	165	34	2	1573	1736	4596935	4596772	2.460000e-18	104.0
44	TraesCS2A01G564600	chr7A	97.500	40	1	0	864	903	705502268	705502307	8.960000e-08	69.4
45	TraesCS2A01G564600	chr7A	95.000	40	2	0	864	903	67682635	67682674	4.170000e-06	63.9
46	TraesCS2A01G564600	chr6D	97.500	40	1	0	864	903	320198090	320198051	8.960000e-08	69.4
47	TraesCS2A01G564600	chr7D	95.000	40	2	0	864	903	613714901	613714940	4.170000e-06	63.9

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	TraesCS2A01G564600	chr2A	764724510	764729499	4989	True	4385.500	5888	100.00000	1	4990	2	chr2A.!!$R3	4989
1	TraesCS2A01G564600	chr2B	798155506	798160127	4621	True	1941.750	4205	94.99350	1	4990	4	chr2B.!!$R2	4989
2	TraesCS2A01G564600	chr2B	798225161	798226513	1352	True	1439.000	1439	85.91100	3621	4990	1	chr2B.!!$R1	1369
3	TraesCS2A01G564600	chr2B	798329673	798334231	4558	True	1006.000	1491	82.52500	1068	4990	2	chr2B.!!$R6	3922
4	TraesCS2A01G564600	chr2B	798191728	798195756	4028	True	744.250	1461	80.23575	585	4988	4	chr2B.!!$R3	4403
5	TraesCS2A01G564600	chr2B	798256356	798256931	575	True	331.000	377	87.40100	557	1195	2	chr2B.!!$R4	638
6	TraesCS2A01G564600	chr2B	798266134	798266709	575	True	331.000	377	87.40100	557	1195	2	chr2B.!!$R5	638
7	TraesCS2A01G564600	chr2D	638862815	638864166	1351	True	1373.000	1373	85.04000	3621	4990	1	chr2D.!!$R1	1369
8	TraesCS2A01G564600	chr2D	639360770	639364481	3711	True	1288.500	1380	84.77100	598	4989	2	chr2D.!!$R7	4391
9	TraesCS2A01G564600	chr2D	639088747	639092646	3899	True	1240.275	2047	91.34400	802	4989	4	chr2D.!!$R3	4187
10	TraesCS2A01G564600	chr2D	639277283	639279723	2440	True	919.000	1184	82.10400	1010	4973	2	chr2D.!!$R6	3963
11	TraesCS2A01G564600	chr2D	638875244	638876115	871	True	749.000	749	82.40600	960	1828	1	chr2D.!!$R2	868
12	TraesCS2A01G564600	chr2D	639135677	639138408	2731	True	748.500	1304	82.61450	2147	4989	2	chr2D.!!$R4	2842
13	TraesCS2A01G564600	chr2D	639147257	639148394	1137	True	405.000	671	81.16250	545	1826	2	chr2D.!!$R5	1281
14	TraesCS2A01G564600	chr1A	62247296	62248071	775	False	310.000	324	92.75700	1935	2148	2	chr1A.!!$F1	213

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
912	930	0.249120	TCCATGCGGTCCTTGTACTG	59.751	55.000	0.00	0.00	2.74	F
1632	1695	1.873591	ACTACGCTTGCCAAAGAAGTG	59.126	47.619	0.00	35.19	3.16	F
3182	5281	0.456995	GGTGTGCTCACTCTAGTCGC	60.457	60.000	17.68	43.41	5.19	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Hairpin	End Stability	Orientation
2438	3174	5.013704	TGTCTGTATGGCTTAGGGAAAGAAA	59.986	40.000	0.00	37.38	2.52	R
3522	5629	0.903454	AAGGGGGTCGGTACTGACTG	60.903	60.000	29.21	38.91	3.51	R
4713	6924	1.133884	GTGCCCCTTAACCCCAGATAC	60.134	57.143	0.00	0.00	2.24	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
36	37	2.710096	TGGTTATTCCTAGCAGTGGC	57.290	50.000	0.00	0.00	37.43	5.01
37	38	1.134521	TGGTTATTCCTAGCAGTGGCG	60.135	52.381	0.00	0.00	40.36	5.69
49	50	1.140804	AGTGGCGGTGTTTTTGCAC	59.859	52.632	0.00	0.00	38.56	4.57
82	83	3.420893	TGAAGGCATTACTTGGAGGTTG	58.579	45.455	0.00	0.00	0.00	3.77
83	84	3.181434	TGAAGGCATTACTTGGAGGTTGT	60.181	43.478	0.00	0.00	0.00	3.32
84	85	3.525800	AGGCATTACTTGGAGGTTGTT	57.474	42.857	0.00	0.00	0.00	2.83
85	86	3.421844	AGGCATTACTTGGAGGTTGTTC	58.578	45.455	0.00	0.00	0.00	3.18
128	129	6.706716	TGAAAACACATGATACGACCTTTACA	59.293	34.615	0.00	0.00	0.00	2.41
142	143	4.419522	CCTTTACAGGTTGGATTTGACG	57.580	45.455	0.00	0.00	35.06	4.35
145	146	1.508632	ACAGGTTGGATTTGACGACG	58.491	50.000	0.00	0.00	0.00	5.12
160	161	1.853319	GACGAAGACACAAGGTGCG	59.147	57.895	0.00	0.00	36.98	5.34
186	187	1.479389	CCTTTCCTGGAGGTGTTGCTT	60.479	52.381	0.00	0.00	36.34	3.91
218	219	0.463295	TCTCTCGTAGTAGGGTGGCG	60.463	60.000	0.00	0.00	0.00	5.69
226	228	3.454573	TAGGGTGGCGGTGTAGCG	61.455	66.667	0.00	0.00	38.18	4.26
254	256	5.954335	GATGTGGATCATCGGTTTTTCTTT	58.046	37.500	0.00	0.00	42.57	2.52
255	257	5.782893	TGTGGATCATCGGTTTTTCTTTT	57.217	34.783	0.00	0.00	0.00	2.27
256	258	6.155475	TGTGGATCATCGGTTTTTCTTTTT	57.845	33.333	0.00	0.00	0.00	1.94
304	306	0.896479	ATGGCTGTGTGCATGCTTGA	60.896	50.000	20.33	0.00	45.15	3.02
323	325	7.939782	TGCTTGATGTCTTGAATAACTTTTGA	58.060	30.769	0.00	0.00	0.00	2.69
324	326	8.579006	TGCTTGATGTCTTGAATAACTTTTGAT	58.421	29.630	0.00	0.00	0.00	2.57
350	354	5.296035	GTGTGTTATTATTGAGGCCAGGTAC	59.704	44.000	5.01	0.00	0.00	3.34
355	359	8.275758	TGTTATTATTGAGGCCAGGTACAATTA	58.724	33.333	5.01	3.45	35.19	1.40
360	364	9.515226	TTATTGAGGCCAGGTACAATTAATATC	57.485	33.333	5.01	0.00	35.19	1.63
419	423	3.838244	AAACTAGTGAACAGGAGTGCA	57.162	42.857	0.00	0.00	0.00	4.57
434	438	1.087501	GTGCATCCGGTTTCCTCTTC	58.912	55.000	0.00	0.00	0.00	2.87
440	444	3.110293	TCCGGTTTCCTCTTCTCCATA	57.890	47.619	0.00	0.00	0.00	2.74
441	445	3.031736	TCCGGTTTCCTCTTCTCCATAG	58.968	50.000	0.00	0.00	0.00	2.23
466	471	8.979534	AGGTCTTCGGTCTTAGTATATTTTCTT	58.020	33.333	0.00	0.00	0.00	2.52
522	527	2.471255	GGATGAACCTTGAGCCACG	58.529	57.895	0.00	0.00	35.41	4.94
580	585	1.901650	GCAACGAACCAAGAGAGCCG	61.902	60.000	0.00	0.00	0.00	5.52
588	593	1.674057	CAAGAGAGCCGGTGTTCCT	59.326	57.895	1.90	0.00	0.00	3.36
636	648	4.247380	CCTGCCGAGGCCCTCATC	62.247	72.222	12.13	1.78	41.09	2.92
637	649	4.247380	CTGCCGAGGCCCTCATCC	62.247	72.222	12.13	0.00	41.09	3.51
722	739	1.694696	CCCCTCACTACTCATTAGCCC	59.305	57.143	0.00	0.00	0.00	5.19
912	930	0.249120	TCCATGCGGTCCTTGTACTG	59.751	55.000	0.00	0.00	0.00	2.74
1283	1324	2.436109	CTGTGACCCCAACCCCAG	59.564	66.667	0.00	0.00	0.00	4.45
1632	1695	1.873591	ACTACGCTTGCCAAAGAAGTG	59.126	47.619	0.00	0.00	35.19	3.16
1719	1782	8.359060	ACATGAAGAAAGTATTAAGCGATCTC	57.641	34.615	0.00	0.00	0.00	2.75
1901	2046	4.648651	CATCCATAGCATCAATCCTGACA	58.351	43.478	0.00	0.00	33.30	3.58
2352	3088	4.689612	TCCTTGACTGCTCTAAACAACT	57.310	40.909	0.00	0.00	0.00	3.16
3173	5272	1.002366	GATCGACATGGTGTGCTCAC	58.998	55.000	10.44	10.44	43.19	3.51
3182	5281	0.456995	GGTGTGCTCACTCTAGTCGC	60.457	60.000	17.68	0.00	43.41	5.19
3184	5283	1.870016	GTGCTCACTCTAGTCGCGC	60.870	63.158	0.00	0.00	0.00	6.86
3456	5555	0.606096	ATGTGGTAGCGTGCACACTA	59.394	50.000	18.64	14.42	35.02	2.74
3522	5629	1.388547	TTCAAAGTGTGGGCTGTGAC	58.611	50.000	0.00	0.00	32.86	3.67
3754	5925	7.816640	TGGAAAGAAATCAGTTATGCACTTAC	58.183	34.615	0.00	0.00	30.92	2.34
3949	6120	5.649831	GGTTTGAGCAAGTATCCAAAGAGAT	59.350	40.000	0.00	0.00	0.00	2.75
3957	6128	7.667219	AGCAAGTATCCAAAGAGATTCTTGAAA	59.333	33.333	19.00	0.00	46.44	2.69
3982	6153	1.227853	GCAGGGGTACCATTAGCCG	60.228	63.158	15.35	3.33	44.85	5.52
3991	6162	4.056050	GGTACCATTAGCCGTCATTAGTG	58.944	47.826	7.15	0.00	0.00	2.74
4067	6238	2.128771	TTGCTCACTTCTATTGGCCC	57.871	50.000	0.00	0.00	0.00	5.80
4214	6386	2.674796	ATTAGCAGAGACCGGTTGAC	57.325	50.000	9.42	3.25	0.00	3.18
4261	6436	7.899648	TTTATCCAAGTAAAAGGTCAAACCA	57.100	32.000	0.00	0.00	41.95	3.67
4262	6437	7.519032	TTATCCAAGTAAAAGGTCAAACCAG	57.481	36.000	0.00	0.00	41.95	4.00
4263	6438	3.634910	TCCAAGTAAAAGGTCAAACCAGC	59.365	43.478	0.00	0.00	41.95	4.85
4264	6439	3.243737	CCAAGTAAAAGGTCAAACCAGCC	60.244	47.826	0.00	0.00	41.95	4.85
4265	6440	2.594131	AGTAAAAGGTCAAACCAGCCC	58.406	47.619	0.00	0.00	41.95	5.19
4266	6441	2.091555	AGTAAAAGGTCAAACCAGCCCA	60.092	45.455	0.00	0.00	41.95	5.36
4267	6442	1.119684	AAAAGGTCAAACCAGCCCAC	58.880	50.000	0.00	0.00	41.95	4.61
4268	6443	0.261696	AAAGGTCAAACCAGCCCACT	59.738	50.000	0.00	0.00	41.95	4.00
4269	6444	0.261696	AAGGTCAAACCAGCCCACTT	59.738	50.000	0.00	0.00	41.95	3.16
4270	6445	0.468029	AGGTCAAACCAGCCCACTTG	60.468	55.000	0.00	0.00	41.95	3.16
4271	6446	1.363807	GTCAAACCAGCCCACTTGC	59.636	57.895	0.00	0.00	0.00	4.01
4272	6447	1.076412	TCAAACCAGCCCACTTGCA	60.076	52.632	0.00	0.00	0.00	4.08
4273	6448	1.108727	TCAAACCAGCCCACTTGCAG	61.109	55.000	0.00	0.00	0.00	4.41
4274	6449	1.108727	CAAACCAGCCCACTTGCAGA	61.109	55.000	0.00	0.00	0.00	4.26
4275	6450	0.396974	AAACCAGCCCACTTGCAGAA	60.397	50.000	0.00	0.00	0.00	3.02
4276	6451	0.396974	AACCAGCCCACTTGCAGAAA	60.397	50.000	0.00	0.00	0.00	2.52
4277	6452	0.396974	ACCAGCCCACTTGCAGAAAA	60.397	50.000	0.00	0.00	0.00	2.29
4278	6453	0.971386	CCAGCCCACTTGCAGAAAAT	59.029	50.000	0.00	0.00	0.00	1.82
4279	6454	1.067354	CCAGCCCACTTGCAGAAAATC	60.067	52.381	0.00	0.00	0.00	2.17
4280	6455	1.614903	CAGCCCACTTGCAGAAAATCA	59.385	47.619	0.00	0.00	0.00	2.57
4281	6456	2.036217	CAGCCCACTTGCAGAAAATCAA	59.964	45.455	0.00	0.00	0.00	2.57
4282	6457	2.036346	AGCCCACTTGCAGAAAATCAAC	59.964	45.455	0.00	0.00	0.00	3.18
4299	6498	4.317530	TCAACCTAGTCTCCTTGAGCTA	57.682	45.455	0.00	0.00	0.00	3.32
4373	6578	5.367945	AACATACATAGTGGTAGGGTTGG	57.632	43.478	0.00	0.00	29.75	3.77
4609	6820	5.450453	CCTCTGTCAGTAAGATTCCCTCTA	58.550	45.833	0.00	0.00	32.41	2.43
4647	6858	2.602257	TGCGTGTATTGGATCTGGAG	57.398	50.000	0.00	0.00	0.00	3.86
4713	6924	5.991606	TGTTGAGAAGTTGTTACATCTGAGG	59.008	40.000	0.00	0.00	32.77	3.86
4794	7005	4.748102	CGGTTTTTGCAGACACTAGACTTA	59.252	41.667	0.00	0.00	0.00	2.24

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
26	27	0.951558	AAAAACACCGCCACTGCTAG	59.048	50.000	0.00	0.00	34.43	3.42
36	37	3.249917	AGAAAACAGTGCAAAAACACCG	58.750	40.909	0.00	0.00	41.67	4.94
37	38	4.450757	ACAAGAAAACAGTGCAAAAACACC	59.549	37.500	0.00	0.00	41.67	4.16
49	50	6.507023	AGTAATGCCTTCAACAAGAAAACAG	58.493	36.000	0.00	0.00	35.40	3.16
128	129	2.036733	TCTTCGTCGTCAAATCCAACCT	59.963	45.455	0.00	0.00	0.00	3.50
142	143	0.874607	ACGCACCTTGTGTCTTCGTC	60.875	55.000	0.00	0.00	36.11	4.20
145	146	1.014352	ACAACGCACCTTGTGTCTTC	58.986	50.000	0.00	0.00	40.68	2.87
160	161	2.230660	CACCTCCAGGAAAGGAACAAC	58.769	52.381	0.00	0.00	37.20	3.32
218	219	1.369091	CCACATCAAGCCGCTACACC	61.369	60.000	0.00	0.00	0.00	4.16
268	270	9.988815	ACACAGCCATATTACAAAAATAACAAA	57.011	25.926	0.00	0.00	0.00	2.83
269	271	9.416794	CACACAGCCATATTACAAAAATAACAA	57.583	29.630	0.00	0.00	0.00	2.83
270	272	7.543868	GCACACAGCCATATTACAAAAATAACA	59.456	33.333	0.00	0.00	37.23	2.41
271	273	7.543868	TGCACACAGCCATATTACAAAAATAAC	59.456	33.333	0.00	0.00	44.83	1.89
272	274	7.606349	TGCACACAGCCATATTACAAAAATAA	58.394	30.769	0.00	0.00	44.83	1.40
273	275	7.163001	TGCACACAGCCATATTACAAAAATA	57.837	32.000	0.00	0.00	44.83	1.40
274	276	6.035368	TGCACACAGCCATATTACAAAAAT	57.965	33.333	0.00	0.00	44.83	1.82
275	277	5.459536	TGCACACAGCCATATTACAAAAA	57.540	34.783	0.00	0.00	44.83	1.94
276	278	5.409211	CATGCACACAGCCATATTACAAAA	58.591	37.500	0.00	0.00	44.83	2.44
277	279	4.677514	GCATGCACACAGCCATATTACAAA	60.678	41.667	14.21	0.00	44.83	2.83
278	280	3.181488	GCATGCACACAGCCATATTACAA	60.181	43.478	14.21	0.00	44.83	2.41
279	281	2.358582	GCATGCACACAGCCATATTACA	59.641	45.455	14.21	0.00	44.83	2.41
280	282	2.620115	AGCATGCACACAGCCATATTAC	59.380	45.455	21.98	0.00	44.83	1.89
281	283	2.934887	AGCATGCACACAGCCATATTA	58.065	42.857	21.98	0.00	44.83	0.98
323	325	6.126478	ACCTGGCCTCAATAATAACACACTAT	60.126	38.462	3.32	0.00	0.00	2.12
324	326	5.190925	ACCTGGCCTCAATAATAACACACTA	59.809	40.000	3.32	0.00	0.00	2.74
403	407	1.204704	CGGATGCACTCCTGTTCACTA	59.795	52.381	11.74	0.00	42.47	2.74
419	423	1.952621	TGGAGAAGAGGAAACCGGAT	58.047	50.000	9.46	0.00	0.00	4.18
434	438	4.208746	ACTAAGACCGAAGACCTATGGAG	58.791	47.826	0.00	0.00	0.00	3.86
440	444	8.536340	AGAAAATATACTAAGACCGAAGACCT	57.464	34.615	0.00	0.00	0.00	3.85
441	445	9.247126	GAAGAAAATATACTAAGACCGAAGACC	57.753	37.037	0.00	0.00	0.00	3.85
464	469	8.950210	AGCCGATCAATTGTTATATATTGGAAG	58.050	33.333	5.13	0.00	33.58	3.46
466	471	7.277760	CGAGCCGATCAATTGTTATATATTGGA	59.722	37.037	5.13	0.00	33.58	3.53
476	481	1.066143	ACTCCGAGCCGATCAATTGTT	60.066	47.619	5.13	0.00	0.00	2.83
580	585	5.978814	TCTCTTGCTTTCTATAGGAACACC	58.021	41.667	0.00	0.00	33.13	4.16
588	593	7.559486	TCAATCTTGCTCTCTTGCTTTCTATA	58.441	34.615	0.00	0.00	0.00	1.31
644	656	2.202395	GCTTCCAAAGGTGCCAGCA	61.202	57.895	0.00	0.00	31.58	4.41
645	657	2.202395	TGCTTCCAAAGGTGCCAGC	61.202	57.895	0.00	0.00	0.00	4.85
722	739	2.029200	AGAGCTGTATCATCCTGATGCG	60.029	50.000	0.00	0.00	41.50	4.73
912	930	4.142381	GCCCAAATGTTACATCAAGAGACC	60.142	45.833	0.00	0.00	0.00	3.85
1283	1324	3.547567	AGCCTGTTCTGCTCATCAC	57.452	52.632	0.00	0.00	32.41	3.06
1335	1376	1.308047	GTTTTGCCTTGCCCCTTTTG	58.692	50.000	0.00	0.00	0.00	2.44
2155	2884	9.691362	TTCCTTATGAAATGAACTAAAACAAGC	57.309	29.630	0.00	0.00	0.00	4.01
2438	3174	5.013704	TGTCTGTATGGCTTAGGGAAAGAAA	59.986	40.000	0.00	0.00	37.38	2.52
2651	3611	7.999679	TGGTGGAGATTTGATATAGCAAAAAG	58.000	34.615	19.15	0.00	40.72	2.27
3456	5555	1.281925	AAATCGAGGCCCCATGGAGT	61.282	55.000	15.22	0.00	0.00	3.85
3522	5629	0.903454	AAGGGGGTCGGTACTGACTG	60.903	60.000	29.21	0.00	38.91	3.51
3754	5925	2.649331	ACTTCCACACTTATCGTCGG	57.351	50.000	0.00	0.00	0.00	4.79
3957	6128	2.621556	ATGGTACCCCTGCACATTTT	57.378	45.000	10.07	0.00	0.00	1.82
3982	6153	6.458342	GCCAAATAACTAGCCACACTAATGAC	60.458	42.308	0.00	0.00	0.00	3.06
3991	6162	5.890424	TTGTTAGCCAAATAACTAGCCAC	57.110	39.130	0.00	0.00	36.73	5.01
4067	6238	7.395190	TGATCATCACCATTTTTAAGTCCAG	57.605	36.000	0.00	0.00	0.00	3.86
4214	6386	4.338879	ACCTTCACAAATCCATCTCCTTG	58.661	43.478	0.00	0.00	0.00	3.61
4261	6436	1.999648	TGATTTTCTGCAAGTGGGCT	58.000	45.000	0.00	0.00	33.76	5.19
4262	6437	2.407090	GTTGATTTTCTGCAAGTGGGC	58.593	47.619	0.00	0.00	33.76	5.36
4263	6438	2.629617	AGGTTGATTTTCTGCAAGTGGG	59.370	45.455	0.00	0.00	33.76	4.61
4264	6439	4.520492	ACTAGGTTGATTTTCTGCAAGTGG	59.480	41.667	0.00	0.00	33.76	4.00
4265	6440	5.471456	AGACTAGGTTGATTTTCTGCAAGTG	59.529	40.000	0.00	0.00	33.76	3.16
4266	6441	5.625150	AGACTAGGTTGATTTTCTGCAAGT	58.375	37.500	0.00	0.00	33.76	3.16
4267	6442	5.123027	GGAGACTAGGTTGATTTTCTGCAAG	59.877	44.000	0.00	0.00	0.00	4.01
4268	6443	5.003804	GGAGACTAGGTTGATTTTCTGCAA	58.996	41.667	0.00	0.00	0.00	4.08
4269	6444	4.287067	AGGAGACTAGGTTGATTTTCTGCA	59.713	41.667	0.00	0.00	40.61	4.41
4270	6445	4.837972	AGGAGACTAGGTTGATTTTCTGC	58.162	43.478	0.00	0.00	40.61	4.26
4271	6446	6.467677	TCAAGGAGACTAGGTTGATTTTCTG	58.532	40.000	0.00	0.00	42.68	3.02
4272	6447	6.688073	TCAAGGAGACTAGGTTGATTTTCT	57.312	37.500	0.00	0.00	42.68	2.52
4273	6448	5.352846	GCTCAAGGAGACTAGGTTGATTTTC	59.647	44.000	0.00	0.00	42.68	2.29
4274	6449	5.013599	AGCTCAAGGAGACTAGGTTGATTTT	59.986	40.000	0.00	0.00	42.68	1.82
4275	6450	4.534103	AGCTCAAGGAGACTAGGTTGATTT	59.466	41.667	0.00	0.00	42.68	2.17
4276	6451	4.100373	AGCTCAAGGAGACTAGGTTGATT	58.900	43.478	0.00	0.00	42.68	2.57
4277	6452	3.718723	AGCTCAAGGAGACTAGGTTGAT	58.281	45.455	0.00	0.00	42.68	2.57
4278	6453	3.176924	AGCTCAAGGAGACTAGGTTGA	57.823	47.619	0.00	0.00	42.68	3.18
4279	6454	3.383185	CCTAGCTCAAGGAGACTAGGTTG	59.617	52.174	22.20	8.72	43.36	3.77
4280	6455	3.269906	TCCTAGCTCAAGGAGACTAGGTT	59.730	47.826	25.59	0.00	45.53	3.50
4281	6456	2.853707	TCCTAGCTCAAGGAGACTAGGT	59.146	50.000	25.59	5.11	45.53	3.08
4282	6457	3.586470	TCCTAGCTCAAGGAGACTAGG	57.414	52.381	23.35	23.35	46.03	3.02
4373	6578	7.800380	GCATTATATCATGTACACAACAAGCTC	59.200	37.037	0.00	0.00	42.70	4.09
4609	6820	7.425606	ACACGCAAAACTTGAAATCTAGAAAT	58.574	30.769	0.00	0.00	0.00	2.17
4713	6924	1.133884	GTGCCCCTTAACCCCAGATAC	60.134	57.143	0.00	0.00	0.00	2.24

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.