AutoCloner

Multiple sequence alignment - TraesCS2A01G306700

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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	TraesCS2A01G306700	chr2A	100.000	4229	0	0	1	4229	527470346	527466118	0.000000e+00	7810
1	TraesCS2A01G306700	chr2A	81.803	599	77	23	426	1001	116004665	116005254	1.380000e-129	473
2	TraesCS2A01G306700	chr2D	96.499	2685	60	16	981	3652	390899812	390897149	0.000000e+00	4407
3	TraesCS2A01G306700	chr2D	86.987	999	111	14	1	991	343541533	343540546	0.000000e+00	1107
4	TraesCS2A01G306700	chr2D	85.957	883	95	19	1	868	296535377	296536245	0.000000e+00	917
5	TraesCS2A01G306700	chr2D	90.618	469	35	8	3766	4229	390896134	390895670	7.770000e-172	614
6	TraesCS2A01G306700	chr2D	87.879	330	36	4	1	327	407907398	407907070	6.630000e-103	385
7	TraesCS2A01G306700	chr2D	79.317	556	87	22	440	982	526251522	526252062	8.640000e-97	364
8	TraesCS2A01G306700	chr2B	95.285	2757	103	12	980	3718	462013536	462010789	0.000000e+00	4346
9	TraesCS2A01G306700	chr2B	81.086	571	87	12	416	977	407991966	407992524	1.810000e-118	436
10	TraesCS2A01G306700	chr2B	86.217	341	22	10	3730	4069	462008620	462008304	3.130000e-91	346
11	TraesCS2A01G306700	chr1D	87.516	761	74	14	1	756	61383715	61382971	0.000000e+00	859
12	TraesCS2A01G306700	chr1D	82.897	573	74	17	423	977	77346808	77346242	1.060000e-135	494
13	TraesCS2A01G306700	chr5A	82.975	652	87	17	335	977	693362755	693362119	6.140000e-158	568
14	TraesCS2A01G306700	chr5A	90.407	344	28	4	30	370	693363131	693362790	8.340000e-122	448
15	TraesCS2A01G306700	chr5A	91.860	86	7	0	3625	3710	341688274	341688359	2.070000e-23	121
16	TraesCS2A01G306700	chr3A	82.547	636	91	17	335	959	167876049	167876675	3.720000e-150	542
17	TraesCS2A01G306700	chr3A	90.860	372	26	6	1	370	167875649	167876014	3.800000e-135	492
18	TraesCS2A01G306700	chr3A	87.736	106	7	3	3640	3744	416307029	416307129	7.430000e-23	119
19	TraesCS2A01G306700	chr3B	90.244	369	32	3	5	370	237215334	237215701	2.960000e-131	479
20	TraesCS2A01G306700	chr3B	79.358	654	89	21	335	984	237215736	237216347	6.540000e-113	418
21	TraesCS2A01G306700	chr3B	79.842	253	36	10	605	846	739020199	739020447	2.020000e-38	171
22	TraesCS2A01G306700	chr3D	82.487	571	74	19	423	977	263229449	263228889	1.060000e-130	477
23	TraesCS2A01G306700	chr4D	89.702	369	33	3	1	365	497396890	497397257	2.300000e-127	466
24	TraesCS2A01G306700	chr4D	82.878	403	55	8	571	971	497399225	497399615	2.420000e-92	350
25	TraesCS2A01G306700	chr6B	87.273	330	33	4	1	328	592965548	592965226	6.680000e-98	368
26	TraesCS2A01G306700	chr6B	89.247	93	10	0	3626	3718	203686100	203686192	2.670000e-22	117
27	TraesCS2A01G306700	chr6D	76.541	665	103	32	143	790	431923188	431923816	8.830000e-82	315
28	TraesCS2A01G306700	chr4A	79.320	353	54	12	439	787	538219335	538218998	3.290000e-56	230
29	TraesCS2A01G306700	chr4A	89.623	106	9	1	3617	3720	660788014	660788119	2.650000e-27	134
30	TraesCS2A01G306700	chr4A	88.182	110	10	2	3637	3744	84537373	84537481	1.230000e-25	128
31	TraesCS2A01G306700	chr7D	82.895	152	16	7	3622	3763	481183121	481182970	1.230000e-25	128
32	TraesCS2A01G306700	chr7B	82.993	147	15	7	3627	3763	506761605	506761459	1.600000e-24	124
33	TraesCS2A01G306700	chr7A	86.869	99	13	0	3618	3716	546634080	546634178	1.240000e-20	111

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	TraesCS2A01G306700	chr2A	527466118	527470346	4228	True	7810.0	7810	100.0000	1	4229	1	chr2A.!!$R1	4228
1	TraesCS2A01G306700	chr2A	116004665	116005254	589	False	473.0	473	81.8030	426	1001	1	chr2A.!!$F1	575
2	TraesCS2A01G306700	chr2D	390895670	390899812	4142	True	2510.5	4407	93.5585	981	4229	2	chr2D.!!$R3	3248
3	TraesCS2A01G306700	chr2D	343540546	343541533	987	True	1107.0	1107	86.9870	1	991	1	chr2D.!!$R1	990
4	TraesCS2A01G306700	chr2D	296535377	296536245	868	False	917.0	917	85.9570	1	868	1	chr2D.!!$F1	867
5	TraesCS2A01G306700	chr2D	526251522	526252062	540	False	364.0	364	79.3170	440	982	1	chr2D.!!$F2	542
6	TraesCS2A01G306700	chr2B	462008304	462013536	5232	True	2346.0	4346	90.7510	980	4069	2	chr2B.!!$R1	3089
7	TraesCS2A01G306700	chr2B	407991966	407992524	558	False	436.0	436	81.0860	416	977	1	chr2B.!!$F1	561
8	TraesCS2A01G306700	chr1D	61382971	61383715	744	True	859.0	859	87.5160	1	756	1	chr1D.!!$R1	755
9	TraesCS2A01G306700	chr1D	77346242	77346808	566	True	494.0	494	82.8970	423	977	1	chr1D.!!$R2	554
10	TraesCS2A01G306700	chr5A	693362119	693363131	1012	True	508.0	568	86.6910	30	977	2	chr5A.!!$R1	947
11	TraesCS2A01G306700	chr3A	167875649	167876675	1026	False	517.0	542	86.7035	1	959	2	chr3A.!!$F2	958
12	TraesCS2A01G306700	chr3B	237215334	237216347	1013	False	448.5	479	84.8010	5	984	2	chr3B.!!$F2	979
13	TraesCS2A01G306700	chr3D	263228889	263229449	560	True	477.0	477	82.4870	423	977	1	chr3D.!!$R1	554
14	TraesCS2A01G306700	chr4D	497396890	497399615	2725	False	408.0	466	86.2900	1	971	2	chr4D.!!$F1	970
15	TraesCS2A01G306700	chr6D	431923188	431923816	628	False	315.0	315	76.5410	143	790	1	chr6D.!!$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	Self end TH	Hairpin	End Stability	Orientation
686	2531	0.034186	CTACTTTGGGGCTGCCATGA	60.034	55.0	22.05	1.68	0.00	3.07	F
1038	2924	0.035458	CACAACACCCTGTCCCTCTC	59.965	60.0	0.00	0.00	0.00	3.20	F
2183	4071	1.139163	GGTGCTTTGCATTTGTTCCG	58.861	50.0	0.00	0.00	41.91	4.30	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Hairpin	End Stability	Orientation
1635	3523	0.378257	CATACACATCAACCAGCGCC	59.622	55.0	2.29	0.00	6.53	R
2266	4154	0.840722	TGGACCTCCTCACCTTTCCC	60.841	60.0	0.00	36.82	3.97	R
3962	8952	0.107897	TGCGTTACCTGCATACTGGG	60.108	55.0	0.00	39.16	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
24	25	3.941483	GCCTAGTATGCATGTTGAGTTGT	59.059	43.478	10.16	0.00	0.00	3.32
66	69	3.382546	GCTGGGATGTATTTCAGTTGCAT	59.617	43.478	0.00	0.00	0.00	3.96
185	190	4.082245	GGCTACATTGCATGTTTAGTTGGT	60.082	41.667	7.02	0.00	41.63	3.67
237	242	2.028112	TGCCTTAGTCGACTTGCTGAAT	60.028	45.455	25.44	0.00	0.00	2.57
259	268	1.162329	TCCAGGGGGAACTTGGCTA	59.838	57.895	0.00	0.00	41.32	3.93
275	284	3.824133	TGGCTAGCATGCATGTTAGAAT	58.176	40.909	39.10	18.51	42.12	2.40
332	341	9.553064	AACCATGTTTATTGTGCAAATAGAAAA	57.447	25.926	0.00	0.00	0.00	2.29
333	412	8.987890	ACCATGTTTATTGTGCAAATAGAAAAC	58.012	29.630	0.00	0.62	0.00	2.43
387	466	7.759489	AGTTGCATGAACCAGAAAATAGTAA	57.241	32.000	0.00	0.00	34.80	2.24
388	467	8.353423	AGTTGCATGAACCAGAAAATAGTAAT	57.647	30.769	0.00	0.00	34.80	1.89
392	472	9.023962	TGCATGAACCAGAAAATAGTAATCTTT	57.976	29.630	0.00	0.00	0.00	2.52
431	534	3.187022	TCAATTTGCAGACATGACACTCG	59.813	43.478	0.00	0.00	0.00	4.18
435	538	0.038251	GCAGACATGACACTCGTGGA	60.038	55.000	0.00	0.00	37.70	4.02
438	542	0.888619	GACATGACACTCGTGGAGGA	59.111	55.000	0.00	0.00	37.70	3.71
442	546	0.251608	TGACACTCGTGGAGGATGGA	60.252	55.000	1.77	0.00	33.35	3.41
504	625	3.317430	CACTCCTTTCTTGAAGCAGCTTT	59.683	43.478	9.62	0.00	33.84	3.51
522	644	5.063438	CAGCTTTTTCATGGATTTGCTGATG	59.937	40.000	18.85	0.00	46.40	3.07
527	649	4.173290	TCATGGATTTGCTGATGGATCA	57.827	40.909	0.00	0.00	35.16	2.92
537	659	3.457012	TGCTGATGGATCAATGGAGAAGA	59.543	43.478	0.00	0.00	36.18	2.87
538	660	3.814283	GCTGATGGATCAATGGAGAAGAC	59.186	47.826	0.00	0.00	36.18	3.01
556	678	4.207891	AGACGGTTTACAGATGCAGAAT	57.792	40.909	0.00	0.00	0.00	2.40
566	688	3.782523	ACAGATGCAGAATAAGAAGGGGA	59.217	43.478	0.00	0.00	0.00	4.81
568	690	4.102210	CAGATGCAGAATAAGAAGGGGAGA	59.898	45.833	0.00	0.00	0.00	3.71
601	2442	2.644676	GCAGAGGGGAATTACTTGTCC	58.355	52.381	0.00	0.00	0.00	4.02
603	2444	3.878778	CAGAGGGGAATTACTTGTCCAG	58.121	50.000	0.00	0.00	35.44	3.86
605	2446	4.469945	CAGAGGGGAATTACTTGTCCAGTA	59.530	45.833	0.00	0.00	36.88	2.74
629	2470	2.806019	GCTGTCTGGTATGGCTCTGATG	60.806	54.545	0.00	0.00	0.00	3.07
635	2476	2.090775	TGGTATGGCTCTGATGACCCTA	60.091	50.000	0.00	0.00	0.00	3.53
686	2531	0.034186	CTACTTTGGGGCTGCCATGA	60.034	55.000	22.05	1.68	0.00	3.07
708	2553	6.285224	TGACGATTGTACAAAAGGAGAAAGA	58.715	36.000	13.23	0.00	0.00	2.52
712	2557	7.282450	ACGATTGTACAAAAGGAGAAAGAAAGT	59.718	33.333	13.23	0.00	0.00	2.66
724	2570	3.075134	AGAAAGAAAGTGCCTTGGATCCT	59.925	43.478	14.23	0.00	0.00	3.24
738	2585	2.903784	TGGATCCTCTTCTTTCGTGGAA	59.096	45.455	14.23	0.00	0.00	3.53
848	2716	3.181500	GCGCTTTTCTGTTCGGGATTAAT	60.181	43.478	0.00	0.00	0.00	1.40
851	2719	4.094442	GCTTTTCTGTTCGGGATTAATCGT	59.906	41.667	9.32	0.00	0.00	3.73
855	2723	2.538449	CTGTTCGGGATTAATCGTTCGG	59.462	50.000	17.91	7.60	0.00	4.30
886	2757	1.131638	TGGTGGCTGTCTGTCTCTTT	58.868	50.000	0.00	0.00	0.00	2.52
902	2773	5.163488	TGTCTCTTTCTTTTCTGTACCACGA	60.163	40.000	0.00	0.00	0.00	4.35
905	2776	4.342951	TCTTTCTTTTCTGTACCACGAGGA	59.657	41.667	5.68	0.00	38.69	3.71
936	2815	0.035739	TCTTTTTAGGTCGGCCGCTT	59.964	50.000	23.51	14.85	40.50	4.68
1038	2924	0.035458	CACAACACCCTGTCCCTCTC	59.965	60.000	0.00	0.00	0.00	3.20
1100	2988	4.570663	CGGCGCCTCTACTTCCGG	62.571	72.222	26.68	0.00	36.73	5.14
1251	3139	2.363147	GACCACGGCTCCCTCTCT	60.363	66.667	0.00	0.00	0.00	3.10
1450	3338	1.455959	ATCTACGCTTCCTCCCGCT	60.456	57.895	0.00	0.00	0.00	5.52
1611	3499	2.158755	CCATATCTCCAAGCGGGACTTT	60.159	50.000	0.00	0.00	42.15	2.66
1635	3523	1.811965	TCCAATGTGATTCTTGGCACG	59.188	47.619	0.00	0.00	41.41	5.34
1857	3745	1.600916	ACTTCTTGCTTGCCGGGAC	60.601	57.895	2.18	0.00	0.00	4.46
1905	3793	2.177394	TGCATACTTTTGTGCTCCGA	57.823	45.000	0.00	0.00	40.41	4.55
1925	3813	1.980232	ATGGGTACGAGCACCACGA	60.980	57.895	0.00	0.00	40.65	4.35
1926	3814	1.945354	ATGGGTACGAGCACCACGAG	61.945	60.000	0.00	0.00	40.65	4.18
2015	3903	2.669569	CGTGGCACCAGTGAAGGG	60.670	66.667	12.86	0.00	0.00	3.95
2106	3994	3.567797	GACGGGATGCAAGAGCGC	61.568	66.667	0.00	0.00	46.23	5.92
2183	4071	1.139163	GGTGCTTTGCATTTGTTCCG	58.861	50.000	0.00	0.00	41.91	4.30
2232	4120	5.619981	GCTTGATGATGTTACACTTGGTTCC	60.620	44.000	0.00	0.00	0.00	3.62
2266	4154	5.278169	GCTTGTACTGGGATGCTTGATATTG	60.278	44.000	0.00	0.00	0.00	1.90
2335	4223	6.503560	TGAGTTACCCTTTCCTAAAGAACA	57.496	37.500	0.99	0.00	41.02	3.18
3275	5169	6.095440	GGTGGCTGAGCTGAAATTCTTAATTA	59.905	38.462	3.72	0.00	0.00	1.40
3324	5218	2.957402	TTTCAGGTGCTTGTGATCCT	57.043	45.000	0.00	0.00	0.00	3.24
3336	5230	5.539955	TGCTTGTGATCCTATAGCATCAGTA	59.460	40.000	6.60	0.00	36.96	2.74
3386	5290	1.000163	GTTGGTCGAGCTGAAGACAGA	60.000	52.381	16.64	0.00	46.03	3.41
3389	5293	1.271102	GGTCGAGCTGAAGACAGAGTT	59.729	52.381	7.51	0.00	46.03	3.01
3408	5312	1.488705	TTCTGGGCCGAACATGGAGT	61.489	55.000	0.00	0.00	0.00	3.85
3459	5363	2.399916	AGCTTTCATCTCAGCTGACC	57.600	50.000	13.74	0.00	44.98	4.02
3550	5457	5.571285	TCTAGTCTGTCTATGTTGAGTGGT	58.429	41.667	0.00	0.00	0.00	4.16
3565	5480	1.076014	TGGTCAGGTGCCGAGACTA	59.924	57.895	13.54	7.49	32.98	2.59
3571	5486	2.128507	GGTGCCGAGACTAGGGGAG	61.129	68.421	3.58	0.00	0.00	4.30
3634	5549	8.747538	AAGTTGTAAAGTATCACCTTTGTTCT	57.252	30.769	0.00	0.00	36.18	3.01
3635	5550	8.154649	AGTTGTAAAGTATCACCTTTGTTCTG	57.845	34.615	0.00	0.00	36.18	3.02
3667	5582	8.980143	AAAACGTTTTGGATATTTCAGTATGG	57.020	30.769	24.68	0.00	36.16	2.74
3699	5614	4.035091	TGGACTGAAATGAGTGAACAAACG	59.965	41.667	0.00	0.00	0.00	3.60
3700	5615	4.035208	GGACTGAAATGAGTGAACAAACGT	59.965	41.667	0.00	0.00	0.00	3.99
3762	7834	7.114754	TCTTATAACTCGAAACAGAGGGAGTA	58.885	38.462	0.00	0.00	42.31	2.59
3794	8779	7.556844	TGTAAAAGGAAGTTGTAAATTGCCAA	58.443	30.769	0.00	0.00	0.00	4.52
3861	8848	7.087639	TGACCTCAAAACAAAAACTAACACTG	58.912	34.615	0.00	0.00	0.00	3.66
3863	8850	6.099341	CCTCAAAACAAAAACTAACACTGCT	58.901	36.000	0.00	0.00	0.00	4.24
3962	8952	2.726821	TGGAGATCATGAACAAAGGGC	58.273	47.619	0.00	0.00	0.00	5.19
4017	9007	2.223548	TGATTGTTATCGCTTGGCATGC	60.224	45.455	9.90	9.90	33.23	4.06
4100	9091	0.230769	GCGCGTGCTGCTAGAATTAG	59.769	55.000	15.02	0.00	43.27	1.73
4140	9131	2.036346	AGGTGTTGCTCCAAATGCTTTC	59.964	45.455	0.00	0.00	0.00	2.62
4158	9149	7.016153	TGCTTTCCTTCCTCTGATACTAAAA	57.984	36.000	0.00	0.00	0.00	1.52
4165	9156	9.137459	TCCTTCCTCTGATACTAAAAGATGTAG	57.863	37.037	0.00	0.00	0.00	2.74
4171	9162	9.307121	CTCTGATACTAAAAGATGTAGGTGTTG	57.693	37.037	0.00	0.00	0.00	3.33
4183	9174	3.874543	TGTAGGTGTTGTCACATGTGAAC	59.125	43.478	29.42	23.80	45.45	3.18
4193	9184	4.576053	TGTCACATGTGAACAAAGAGGAAG	59.424	41.667	29.42	0.00	41.85	3.46
4202	9193	9.793259	ATGTGAACAAAGAGGAAGATTTAGTTA	57.207	29.630	0.00	0.00	0.00	2.24

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
8	9	6.878389	TGTATTCTGACAACTCAACATGCATA	59.122	34.615	0.00	0.00	0.00	3.14
24	25	4.973168	AGCCAACTGAACTTGTATTCTGA	58.027	39.130	0.00	0.00	33.20	3.27
94	97	5.651387	TGAACACATTGACTGTCCAAAAA	57.349	34.783	5.17	0.00	35.29	1.94
95	98	5.850557	ATGAACACATTGACTGTCCAAAA	57.149	34.783	5.17	0.00	35.29	2.44
140	143	8.404107	AGCCAAAACTAAACATGTATTGTACT	57.596	30.769	0.00	0.00	37.68	2.73
148	151	5.925969	GCAATGTAGCCAAAACTAAACATGT	59.074	36.000	0.00	0.00	0.00	3.21
185	190	6.945435	TCTGGCCAACTAAAACATGATTCTAA	59.055	34.615	7.01	0.00	0.00	2.10
237	242	1.295020	CCAAGTTCCCCCTGGATGTA	58.705	55.000	0.00	0.00	41.40	2.29
332	341	7.067008	ACAAGTCATTAAGTTTAGTTGCACAGT	59.933	33.333	0.00	0.00	0.00	3.55
333	412	7.376866	CACAAGTCATTAAGTTTAGTTGCACAG	59.623	37.037	0.00	0.00	0.00	3.66
387	466	6.648192	TGAAAACCAACCATGAACAAAAGAT	58.352	32.000	0.00	0.00	0.00	2.40
388	467	6.042638	TGAAAACCAACCATGAACAAAAGA	57.957	33.333	0.00	0.00	0.00	2.52
392	472	6.404074	GCAAATTGAAAACCAACCATGAACAA	60.404	34.615	0.00	0.00	37.63	2.83
396	476	4.774124	TGCAAATTGAAAACCAACCATGA	58.226	34.783	0.00	0.00	37.63	3.07
431	534	1.616628	ACCACCCTCCATCCTCCAC	60.617	63.158	0.00	0.00	0.00	4.02
435	538	0.253347	ATCACACCACCCTCCATCCT	60.253	55.000	0.00	0.00	0.00	3.24
438	542	1.075601	AACATCACACCACCCTCCAT	58.924	50.000	0.00	0.00	0.00	3.41
442	546	0.843309	TGTCAACATCACACCACCCT	59.157	50.000	0.00	0.00	0.00	4.34
504	625	4.957327	TGATCCATCAGCAAATCCATGAAA	59.043	37.500	0.00	0.00	32.11	2.69
522	644	2.990066	ACCGTCTTCTCCATTGATCC	57.010	50.000	0.00	0.00	0.00	3.36
527	649	4.884668	TCTGTAAACCGTCTTCTCCATT	57.115	40.909	0.00	0.00	0.00	3.16
537	659	5.730550	TCTTATTCTGCATCTGTAAACCGT	58.269	37.500	0.00	0.00	0.00	4.83
538	660	6.238211	CCTTCTTATTCTGCATCTGTAAACCG	60.238	42.308	0.00	0.00	0.00	4.44
556	678	6.465894	CCTTTCTTCAGTTTCTCCCCTTCTTA	60.466	42.308	0.00	0.00	0.00	2.10
566	688	3.497584	CCCTCTGCCTTTCTTCAGTTTCT	60.498	47.826	0.00	0.00	0.00	2.52
568	690	2.489802	CCCCTCTGCCTTTCTTCAGTTT	60.490	50.000	0.00	0.00	0.00	2.66
603	2444	3.134458	GAGCCATACCAGACAGCAATAC	58.866	50.000	0.00	0.00	0.00	1.89
605	2446	1.842562	AGAGCCATACCAGACAGCAAT	59.157	47.619	0.00	0.00	0.00	3.56
686	2531	7.282450	ACTTTCTTTCTCCTTTTGTACAATCGT	59.718	33.333	9.56	0.00	0.00	3.73
712	2557	2.355108	CGAAAGAAGAGGATCCAAGGCA	60.355	50.000	15.82	0.00	33.66	4.75
738	2585	1.845809	CGCACGCTGCCTTCTTCTTT	61.846	55.000	0.00	0.00	41.12	2.52
800	2667	1.544093	CCATATGGCCAGCTGTACCTG	60.544	57.143	20.31	12.18	0.00	4.00
848	2716	0.039256	AAACCGAATCGACCGAACGA	60.039	50.000	3.36	6.40	46.04	3.85
851	2719	0.033781	ACCAAACCGAATCGACCGAA	59.966	50.000	3.36	0.00	0.00	4.30
855	2723	0.953960	AGCCACCAAACCGAATCGAC	60.954	55.000	3.36	0.00	0.00	4.20
886	2757	4.141892	TGTTTCCTCGTGGTACAGAAAAGA	60.142	41.667	2.99	0.00	41.80	2.52
902	2773	7.462590	ACCTAAAAAGATAAGCTCTGTTTCCT	58.537	34.615	0.00	0.00	40.06	3.36
905	2776	6.371825	CCGACCTAAAAAGATAAGCTCTGTTT	59.628	38.462	0.00	0.00	42.82	2.83
911	2789	3.542648	GGCCGACCTAAAAAGATAAGCT	58.457	45.455	0.00	0.00	0.00	3.74
1019	2898	0.035458	GAGAGGGACAGGGTGTTGTG	59.965	60.000	0.00	0.00	0.00	3.33
1020	2899	0.104934	AGAGAGGGACAGGGTGTTGT	60.105	55.000	0.00	0.00	0.00	3.32
1021	2900	0.610687	GAGAGAGGGACAGGGTGTTG	59.389	60.000	0.00	0.00	0.00	3.33
1026	2912	2.038659	GAGAATGAGAGAGGGACAGGG	58.961	57.143	0.00	0.00	0.00	4.45
1038	2924	1.045350	TCTGGCGGGAGGAGAATGAG	61.045	60.000	0.00	0.00	0.00	2.90
1100	2988	3.254014	ATTGCGGACACAGTTGCGC	62.254	57.895	0.00	0.00	35.49	6.09
1450	3338	1.683365	CCTCGGTAGGTTTCCCGGA	60.683	63.158	0.73	0.00	44.32	5.14
1461	3349	2.682494	AGGGAAAGCGCCTCGGTA	60.682	61.111	2.29	0.00	36.27	4.02
1464	3352	1.376037	AAAGAGGGAAAGCGCCTCG	60.376	57.895	2.29	0.00	36.89	4.63
1635	3523	0.378257	CATACACATCAACCAGCGCC	59.622	55.000	2.29	0.00	0.00	6.53
1857	3745	2.030893	TCCTTCTTCAAGCGCATTGTTG	60.031	45.455	11.47	5.32	40.05	3.33
1905	3793	1.295423	GTGGTGCTCGTACCCATGT	59.705	57.895	1.69	0.00	40.09	3.21
1925	3813	2.125229	CTGAGCTCCGCACATGCT	60.125	61.111	12.15	0.00	40.02	3.79
1926	3814	2.435586	ACTGAGCTCCGCACATGC	60.436	61.111	12.15	0.00	37.78	4.06
2015	3903	5.652744	AATTGAGGTCGACATTATTACGC	57.347	39.130	18.91	0.04	0.00	4.42
2092	3980	1.589716	AAGTTGCGCTCTTGCATCCC	61.590	55.000	9.73	0.00	45.78	3.85
2106	3994	3.679389	AGCATTCCAGGACACTAAGTTG	58.321	45.455	0.00	0.00	0.00	3.16
2183	4071	1.198713	TGTCTCCTTCCTCATCTGCC	58.801	55.000	0.00	0.00	0.00	4.85
2266	4154	0.840722	TGGACCTCCTCACCTTTCCC	60.841	60.000	0.00	0.00	36.82	3.97
3275	5169	3.152341	CAAGTCTGCTCCTTGATTTGGT	58.848	45.455	5.08	0.00	41.44	3.67
3324	5218	7.781056	TGTCAAGTGTCAATACTGATGCTATA	58.219	34.615	0.00	0.00	33.05	1.31
3336	5230	3.008049	GGGTAGTCCTGTCAAGTGTCAAT	59.992	47.826	0.00	0.00	0.00	2.57
3386	5290	0.609131	CCATGTTCGGCCCAGAAACT	60.609	55.000	0.00	0.00	0.00	2.66
3389	5293	1.299648	CTCCATGTTCGGCCCAGAA	59.700	57.895	0.00	0.00	0.00	3.02
3459	5363	0.181114	TGGGCTCCAATTCATCCTCG	59.819	55.000	0.00	0.00	0.00	4.63
3550	5457	1.379977	CCCTAGTCTCGGCACCTGA	60.380	63.158	0.00	0.00	0.00	3.86
3565	5480	1.204113	GGCCTGCTATATGCTCCCCT	61.204	60.000	0.00	0.00	43.37	4.79
3571	5486	1.649664	CGATGAGGCCTGCTATATGC	58.350	55.000	12.00	0.00	43.25	3.14
3644	5559	7.610305	AGTCCATACTGAAATATCCAAAACGTT	59.390	33.333	0.00	0.00	33.57	3.99
3662	5577	8.367911	TCATTTCAGTCCATATGTAGTCCATAC	58.632	37.037	1.24	0.00	38.83	2.39
3667	5582	7.492524	TCACTCATTTCAGTCCATATGTAGTC	58.507	38.462	1.24	0.00	0.00	2.59
3676	5591	4.035091	CGTTTGTTCACTCATTTCAGTCCA	59.965	41.667	0.00	0.00	0.00	4.02
3745	7817	2.448453	AGGTACTCCCTCTGTTTCGAG	58.552	52.381	0.00	0.00	40.71	4.04
3777	8762	8.821894	TGTGTTAAATTGGCAATTTACAACTTC	58.178	29.630	33.70	26.66	41.61	3.01
3815	8800	9.962783	AGGTCATTGTTACGAATATACTTAGAC	57.037	33.333	0.00	0.00	0.00	2.59
3833	8818	8.379902	GTGTTAGTTTTTGTTTTGAGGTCATTG	58.620	33.333	0.00	0.00	0.00	2.82
3834	8819	8.311109	AGTGTTAGTTTTTGTTTTGAGGTCATT	58.689	29.630	0.00	0.00	0.00	2.57
3836	8821	7.087639	CAGTGTTAGTTTTTGTTTTGAGGTCA	58.912	34.615	0.00	0.00	0.00	4.02
3837	8822	6.034577	GCAGTGTTAGTTTTTGTTTTGAGGTC	59.965	38.462	0.00	0.00	0.00	3.85
3861	8848	5.405571	TCGTTCTTGTCTCTTAACATGAAGC	59.594	40.000	0.00	0.00	41.31	3.86
3863	8850	6.423905	CCTTCGTTCTTGTCTCTTAACATGAA	59.576	38.462	0.00	2.37	39.56	2.57
3962	8952	0.107897	TGCGTTACCTGCATACTGGG	60.108	55.000	0.00	0.00	39.16	4.45
4017	9007	3.505464	AACCGGATAGAACTGAACTCG	57.495	47.619	9.46	0.00	0.00	4.18
4097	9088	7.174253	CACCTAACCACTCATTACAAAAGCTAA	59.826	37.037	0.00	0.00	0.00	3.09
4100	9091	5.240844	ACACCTAACCACTCATTACAAAAGC	59.759	40.000	0.00	0.00	0.00	3.51
4101	9092	6.877611	ACACCTAACCACTCATTACAAAAG	57.122	37.500	0.00	0.00	0.00	2.27
4140	9131	8.364142	CCTACATCTTTTAGTATCAGAGGAAGG	58.636	40.741	0.00	0.00	0.00	3.46
4158	9149	4.040339	TCACATGTGACAACACCTACATCT	59.960	41.667	24.56	0.00	45.40	2.90
4165	9156	3.773860	TTGTTCACATGTGACAACACC	57.226	42.857	27.88	11.83	45.40	4.16
4171	9162	4.816385	TCTTCCTCTTTGTTCACATGTGAC	59.184	41.667	27.88	21.24	39.66	3.67

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.