AutoCloner

Multiple sequence alignment - TraesCS3D01G542700

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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	TraesCS3D01G542700	chr3D	100.000	2381	0	0	1	2381	613593053	613595433	0.000000e+00	4397.0
1	TraesCS3D01G542700	chr3D	92.308	104	6	2	361	462	16320402	16320505	1.910000e-31	147.0
2	TraesCS3D01G542700	chr3D	96.429	84	2	1	6	89	186291360	186291442	1.150000e-28	137.0
3	TraesCS3D01G542700	chr2D	95.547	1078	34	7	700	1777	25222456	25221393	0.000000e+00	1712.0
4	TraesCS3D01G542700	chr3B	89.469	1130	81	20	585	1701	822816763	822817867	0.000000e+00	1393.0
5	TraesCS3D01G542700	chr3B	95.146	103	3	2	84	186	822813345	822813445	6.810000e-36	161.0
6	TraesCS3D01G542700	chr3B	91.892	74	4	1	508	581	822815749	822815820	4.190000e-18	102.0
7	TraesCS3D01G542700	chr3B	95.122	41	1	1	1778	1818	753509112	753509073	1.980000e-06	63.9
8	TraesCS3D01G542700	chr3A	92.086	935	58	7	585	1518	749189675	749190594	0.000000e+00	1303.0
9	TraesCS3D01G542700	chr3A	87.943	423	37	10	1956	2378	677866556	677866964	9.890000e-134	486.0
10	TraesCS3D01G542700	chr3A	92.377	223	15	2	361	581	749189113	749189335	1.370000e-82	316.0
11	TraesCS3D01G542700	chr3A	91.228	114	7	1	255	368	749188636	749188746	4.100000e-33	152.0
12	TraesCS3D01G542700	chr3A	97.619	42	1	0	219	260	749188582	749188623	3.280000e-09	73.1
13	TraesCS3D01G542700	chr5A	89.256	605	47	9	1779	2378	552586347	552586938	0.000000e+00	741.0
14	TraesCS3D01G542700	chr5A	91.589	107	6	3	361	464	272142811	272142917	6.860000e-31	145.0
15	TraesCS3D01G542700	chr7A	88.944	606	48	10	1778	2378	726745843	726746434	0.000000e+00	730.0
16	TraesCS3D01G542700	chr7A	89.425	539	47	9	1843	2378	31992514	31991983	0.000000e+00	671.0
17	TraesCS3D01G542700	chr7A	89.054	539	49	9	1843	2378	32001366	32001897	0.000000e+00	660.0
18	TraesCS3D01G542700	chr7D	88.099	605	54	11	1778	2378	566955694	566955104	0.000000e+00	702.0
19	TraesCS3D01G542700	chr6A	89.591	538	47	8	1843	2378	212034503	212033973	0.000000e+00	675.0
20	TraesCS3D01G542700	chr6A	94.186	86	5	0	1	86	593828806	593828721	5.340000e-27	132.0
21	TraesCS3D01G542700	chr2A	86.545	602	61	12	1784	2378	649961946	649962534	0.000000e+00	645.0
22	TraesCS3D01G542700	chr4A	88.652	423	35	8	1956	2378	619968189	619967780	9.820000e-139	503.0
23	TraesCS3D01G542700	chr1A	85.570	298	23	11	1771	2058	516013539	516013252	6.440000e-76	294.0
24	TraesCS3D01G542700	chr7B	92.308	104	6	2	361	462	560533640	560533537	1.910000e-31	147.0
25	TraesCS3D01G542700	chr7B	94.186	86	5	0	1	86	576928235	576928320	5.340000e-27	132.0
26	TraesCS3D01G542700	chr5D	92.308	104	6	2	361	462	39039028	39039131	1.910000e-31	147.0
27	TraesCS3D01G542700	chr5D	96.512	86	3	0	1	86	456088005	456088090	2.470000e-30	143.0
28	TraesCS3D01G542700	chr1D	92.381	105	5	3	361	462	426644013	426644117	1.910000e-31	147.0
29	TraesCS3D01G542700	chr6D	90.179	112	7	4	361	468	359520212	359520323	2.470000e-30	143.0
30	TraesCS3D01G542700	chr5B	91.346	104	7	2	361	462	681661939	681662042	8.870000e-30	141.0
31	TraesCS3D01G542700	chr5B	94.318	88	4	1	1	88	629275152	629275238	1.480000e-27	134.0
32	TraesCS3D01G542700	chr5B	91.304	92	8	0	1	92	478495136	478495045	2.480000e-25	126.0
33	TraesCS3D01G542700	chr5B	91.954	87	7	0	1	87	403545752	403545838	3.210000e-24	122.0
34	TraesCS3D01G542700	chr1B	88.596	114	10	3	361	471	556821731	556821844	4.130000e-28	135.0
35	TraesCS3D01G542700	chr6B	95.238	84	4	0	1	84	672946758	672946841	1.480000e-27	134.0
36	TraesCS3D01G542700	chrUn	97.333	75	2	0	1778	1852	94129424	94129350	6.910000e-26	128.0
37	TraesCS3D01G542700	chrUn	95.455	44	2	0	1775	1818	30966151	30966108	1.180000e-08	71.3
38	TraesCS3D01G542700	chr2B	91.398	93	8	0	1	93	511150795	511150703	6.910000e-26	128.0
39	TraesCS3D01G542700	chr2B	85.271	129	13	3	2254	2378	787483487	787483361	6.910000e-26	128.0
40	TraesCS3D01G542700	chr2B	95.122	41	2	0	1778	1818	438463891	438463851	5.490000e-07	65.8

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	TraesCS3D01G542700	chr3D	613593053	613595433	2380	False	4397.000	4397	100.0000	1	2381	1	chr3D.!!$F3	2380
1	TraesCS3D01G542700	chr2D	25221393	25222456	1063	True	1712.000	1712	95.5470	700	1777	1	chr2D.!!$R1	1077
2	TraesCS3D01G542700	chr3B	822813345	822817867	4522	False	552.000	1393	92.1690	84	1701	3	chr3B.!!$F1	1617
3	TraesCS3D01G542700	chr3A	749188582	749190594	2012	False	461.025	1303	93.3275	219	1518	4	chr3A.!!$F2	1299
4	TraesCS3D01G542700	chr5A	552586347	552586938	591	False	741.000	741	89.2560	1779	2378	1	chr5A.!!$F2	599
5	TraesCS3D01G542700	chr7A	726745843	726746434	591	False	730.000	730	88.9440	1778	2378	1	chr7A.!!$F2	600
6	TraesCS3D01G542700	chr7A	31991983	31992514	531	True	671.000	671	89.4250	1843	2378	1	chr7A.!!$R1	535
7	TraesCS3D01G542700	chr7A	32001366	32001897	531	False	660.000	660	89.0540	1843	2378	1	chr7A.!!$F1	535
8	TraesCS3D01G542700	chr7D	566955104	566955694	590	True	702.000	702	88.0990	1778	2378	1	chr7D.!!$R1	600
9	TraesCS3D01G542700	chr6A	212033973	212034503	530	True	675.000	675	89.5910	1843	2378	1	chr6A.!!$R1	535
10	TraesCS3D01G542700	chr2A	649961946	649962534	588	False	645.000	645	86.5450	1784	2378	1	chr2A.!!$F1	594

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
188	204	0.026803	GATCAAACGCGAGGTGCATC	59.973	55.0	15.93	8.66	46.97	3.91	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1678	4849	0.252197	GGACCGACCTTTACCATGCT	59.748	55.0	0.0	0.0	35.41	3.79	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
57	58	8.335532	ACATTCATTTTTAGACATTTCTCCGA	57.664	30.769	0.00	0.00	32.75	4.55
58	59	8.237267	ACATTCATTTTTAGACATTTCTCCGAC	58.763	33.333	0.00	0.00	32.75	4.79
59	60	7.737972	TTCATTTTTAGACATTTCTCCGACA	57.262	32.000	0.00	0.00	32.75	4.35
60	61	7.737972	TCATTTTTAGACATTTCTCCGACAA	57.262	32.000	0.00	0.00	32.75	3.18
61	62	7.806690	TCATTTTTAGACATTTCTCCGACAAG	58.193	34.615	0.00	0.00	32.75	3.16
62	63	7.444183	TCATTTTTAGACATTTCTCCGACAAGT	59.556	33.333	0.00	0.00	32.75	3.16
63	64	8.717821	CATTTTTAGACATTTCTCCGACAAGTA	58.282	33.333	0.00	0.00	32.75	2.24
64	65	8.842358	TTTTTAGACATTTCTCCGACAAGTAT	57.158	30.769	0.00	0.00	32.75	2.12
65	66	8.842358	TTTTAGACATTTCTCCGACAAGTATT	57.158	30.769	0.00	0.00	32.75	1.89
66	67	8.842358	TTTAGACATTTCTCCGACAAGTATTT	57.158	30.769	0.00	0.00	32.75	1.40
67	68	6.969828	AGACATTTCTCCGACAAGTATTTC	57.030	37.500	0.00	0.00	0.00	2.17
68	69	5.875359	AGACATTTCTCCGACAAGTATTTCC	59.125	40.000	0.00	0.00	0.00	3.13
69	70	4.630069	ACATTTCTCCGACAAGTATTTCCG	59.370	41.667	0.00	0.00	0.00	4.30
70	71	2.953466	TCTCCGACAAGTATTTCCGG	57.047	50.000	0.00	0.00	41.36	5.14
71	72	2.449464	TCTCCGACAAGTATTTCCGGA	58.551	47.619	0.00	0.00	45.74	5.14
72	73	2.165030	TCTCCGACAAGTATTTCCGGAC	59.835	50.000	1.83	0.00	43.47	4.79
73	74	1.135315	TCCGACAAGTATTTCCGGACG	60.135	52.381	1.83	0.00	43.47	4.79
74	75	1.274596	CGACAAGTATTTCCGGACGG	58.725	55.000	1.83	3.96	0.00	4.79
75	76	1.135315	CGACAAGTATTTCCGGACGGA	60.135	52.381	1.83	9.76	43.52	4.69
76	77	2.537401	GACAAGTATTTCCGGACGGAG	58.463	52.381	13.64	3.15	46.06	4.63
77	78	1.206371	ACAAGTATTTCCGGACGGAGG	59.794	52.381	13.64	0.00	46.06	4.30
78	79	0.828677	AAGTATTTCCGGACGGAGGG	59.171	55.000	13.64	0.00	46.06	4.30
79	80	0.032813	AGTATTTCCGGACGGAGGGA	60.033	55.000	13.64	4.95	46.06	4.20
80	81	0.388294	GTATTTCCGGACGGAGGGAG	59.612	60.000	13.64	0.00	46.06	4.30
81	82	0.032813	TATTTCCGGACGGAGGGAGT	60.033	55.000	13.64	0.00	46.06	3.85
82	83	0.032813	ATTTCCGGACGGAGGGAGTA	60.033	55.000	13.64	0.00	46.06	2.59
83	84	0.967380	TTTCCGGACGGAGGGAGTAC	60.967	60.000	13.64	0.00	46.06	2.73
84	85	1.856539	TTCCGGACGGAGGGAGTACT	61.857	60.000	13.64	0.00	46.06	2.73
85	86	0.982852	TCCGGACGGAGGGAGTACTA	60.983	60.000	9.76	0.00	39.76	1.82
86	87	0.110104	CCGGACGGAGGGAGTACTAT	59.890	60.000	4.40	0.00	37.50	2.12
87	88	1.349026	CCGGACGGAGGGAGTACTATA	59.651	57.143	4.40	0.00	37.50	1.31
88	89	2.026449	CCGGACGGAGGGAGTACTATAT	60.026	54.545	4.40	0.00	37.50	0.86
89	90	3.198635	CCGGACGGAGGGAGTACTATATA	59.801	52.174	4.40	0.00	37.50	0.86
90	91	4.141528	CCGGACGGAGGGAGTACTATATAT	60.142	50.000	4.40	0.00	37.50	0.86
97	98	7.054751	CGGAGGGAGTACTATATATGTGATCA	58.945	42.308	0.00	0.00	0.00	2.92
173	174	2.662596	GTGACACGGGCAGGATCA	59.337	61.111	0.00	0.00	0.00	2.92
188	204	0.026803	GATCAAACGCGAGGTGCATC	59.973	55.000	15.93	8.66	46.97	3.91
193	209	0.447801	AACGCGAGGTGCATCAATTC	59.552	50.000	15.93	0.00	46.97	2.17
195	211	0.302890	CGCGAGGTGCATCAATTCTC	59.697	55.000	0.00	0.00	46.97	2.87
204	220	3.943381	GTGCATCAATTCTCCATCAGTGA	59.057	43.478	0.00	0.00	0.00	3.41
332	584	6.404712	GTTCGATCTAGAACCGTTCAATTT	57.595	37.500	13.69	0.00	43.33	1.82
368	621	6.627395	AAATAGTACGGAGAGTCAGAGATG	57.373	41.667	0.00	0.00	0.00	2.90
369	622	3.637911	AGTACGGAGAGTCAGAGATGT	57.362	47.619	0.00	0.00	0.00	3.06
370	623	3.958018	AGTACGGAGAGTCAGAGATGTT	58.042	45.455	0.00	0.00	0.00	2.71
371	624	3.942748	AGTACGGAGAGTCAGAGATGTTC	59.057	47.826	0.00	0.00	0.00	3.18
372	625	3.080300	ACGGAGAGTCAGAGATGTTCT	57.920	47.619	0.00	0.00	36.25	3.01
373	626	4.223556	ACGGAGAGTCAGAGATGTTCTA	57.776	45.455	0.00	0.00	33.83	2.10
374	627	3.942748	ACGGAGAGTCAGAGATGTTCTAC	59.057	47.826	0.00	0.00	33.83	2.59
376	629	5.104859	ACGGAGAGTCAGAGATGTTCTACTA	60.105	44.000	0.00	0.00	33.83	1.82
401	2324	6.205784	TCTTTTCAATTTTGTCATGTCGGTC	58.794	36.000	0.00	0.00	0.00	4.79
410	2333	2.293955	TGTCATGTCGGTCTTTACGTGA	59.706	45.455	0.00	0.00	38.87	4.35
421	2344	7.114811	GTCGGTCTTTACGTGACTTGTATTTTA	59.885	37.037	0.00	0.00	35.04	1.52
491	2580	1.226603	CTTGGATCGACCGACGGAC	60.227	63.158	23.38	14.37	42.61	4.79
581	2670	0.822164	GTACGTATGGCCTGTCAGGT	59.178	55.000	20.24	3.21	37.80	4.00
582	2671	2.026641	GTACGTATGGCCTGTCAGGTA	58.973	52.381	20.24	10.27	37.80	3.08
607	3767	4.888326	AGATATCCTCATCTCCAGCAAC	57.112	45.455	0.00	0.00	28.83	4.17
640	3800	9.139734	AGGTCGTTATTTACTTCCATGTATAGA	57.860	33.333	0.00	0.00	0.00	1.98
684	3844	8.484214	AGTAAAAGATATCCTCATCTACAGCA	57.516	34.615	0.00	0.00	34.08	4.41
743	3903	8.560903	AGAATACCAAACAATATCCTCCTCTTT	58.439	33.333	0.00	0.00	0.00	2.52
874	4035	3.768757	CACCATCCTTGTTCTCTCTCTCT	59.231	47.826	0.00	0.00	0.00	3.10
957	4118	0.392863	TCCACAACATCCATGCCGAG	60.393	55.000	0.00	0.00	0.00	4.63
1063	4224	2.805671	GTGTTTGACGATGTGATCACCA	59.194	45.455	22.85	10.29	0.00	4.17
1080	4241	2.285368	AAGGGGCCCTCGATCACA	60.285	61.111	28.97	0.00	30.89	3.58
1101	4262	0.734889	CTAAGGTGCTTGGGAATGCG	59.265	55.000	0.00	0.00	0.00	4.73
1151	4312	3.426787	TGGGTACACGATTTTGATGGT	57.573	42.857	0.00	0.00	0.00	3.55
1386	4547	2.012673	CTCTGGCACCATTAGTTGAGC	58.987	52.381	0.00	0.00	0.00	4.26
1483	4654	5.744345	TGTTGTGCTTTGTAAAAATACCACG	59.256	36.000	0.00	0.00	0.00	4.94
1484	4655	4.291783	TGTGCTTTGTAAAAATACCACGC	58.708	39.130	0.00	0.00	0.00	5.34
1678	4849	9.541143	GAAGAAGAAGAAGAAGAAGAAGAAGAA	57.459	33.333	0.00	0.00	0.00	2.52
1693	4864	3.600388	AGAAGAAGCATGGTAAAGGTCG	58.400	45.455	0.00	0.00	0.00	4.79
1738	4909	3.374402	CCCTGCTCCGTGACGACT	61.374	66.667	6.54	0.00	0.00	4.18
1756	4927	3.318539	TAGTGCGACCACGAGCGTC	62.319	63.158	0.00	0.00	46.62	5.19
1761	4932	2.081212	CGACCACGAGCGTCAAGAC	61.081	63.158	0.00	0.00	42.66	3.01
1929	5102	6.823497	TCATCATGTATTGATCTCTCTTGCA	58.177	36.000	0.00	0.00	43.40	4.08
1950	5123	9.654417	CTTGCATTTTTAGAAAATGTTTCCTTG	57.346	29.630	20.77	2.77	39.25	3.61
2007	5184	7.283625	TGCGCTTGATAATTTATATTTGGGT	57.716	32.000	9.73	0.00	0.00	4.51
2030	5207	7.283354	GGGTAGAGAAGATTAAACCATGAAAGG	59.717	40.741	0.00	0.00	0.00	3.11
2084	5263	4.400884	TGCGGGTTAATACTTGAATTGCAT	59.599	37.500	0.00	0.00	0.00	3.96
2132	5311	3.954258	TGCATCTAGTCTTCCGAGAATCA	59.046	43.478	0.00	0.00	32.66	2.57
2268	5448	1.003839	CAGTTACGAGCCCTTGCCA	60.004	57.895	0.00	0.00	38.69	4.92
2272	5452	1.669265	GTTACGAGCCCTTGCCATAAC	59.331	52.381	0.00	0.00	38.69	1.89
2279	5459	1.689258	GCCCTTGCCATAACCCTCAAT	60.689	52.381	0.00	0.00	0.00	2.57
2285	5465	3.515562	TGCCATAACCCTCAATGGTTTT	58.484	40.909	0.15	0.00	46.45	2.43
2287	5467	5.276440	TGCCATAACCCTCAATGGTTTTAT	58.724	37.500	0.15	0.00	46.45	1.40
2338	5518	1.366111	CGCATTGGGGTCCGTACTTG	61.366	60.000	0.00	0.00	0.00	3.16
2370	5550	5.112129	ACCTTATATTTTTCCTCCGCTGT	57.888	39.130	0.00	0.00	0.00	4.40

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
31	32	9.443323	TCGGAGAAATGTCTAAAAATGAATGTA	57.557	29.630	0.00	0.00	32.80	2.29
32	33	8.237267	GTCGGAGAAATGTCTAAAAATGAATGT	58.763	33.333	0.00	0.00	39.69	2.71
33	34	8.236586	TGTCGGAGAAATGTCTAAAAATGAATG	58.763	33.333	0.00	0.00	39.69	2.67
34	35	8.335532	TGTCGGAGAAATGTCTAAAAATGAAT	57.664	30.769	0.00	0.00	39.69	2.57
35	36	7.737972	TGTCGGAGAAATGTCTAAAAATGAA	57.262	32.000	0.00	0.00	39.69	2.57
36	37	7.444183	ACTTGTCGGAGAAATGTCTAAAAATGA	59.556	33.333	0.00	0.00	39.69	2.57
37	38	7.584987	ACTTGTCGGAGAAATGTCTAAAAATG	58.415	34.615	0.00	0.00	39.69	2.32
38	39	7.745620	ACTTGTCGGAGAAATGTCTAAAAAT	57.254	32.000	0.00	0.00	39.69	1.82
39	40	8.842358	ATACTTGTCGGAGAAATGTCTAAAAA	57.158	30.769	0.00	0.00	39.69	1.94
40	41	8.842358	AATACTTGTCGGAGAAATGTCTAAAA	57.158	30.769	0.00	0.00	39.69	1.52
41	42	8.842358	AAATACTTGTCGGAGAAATGTCTAAA	57.158	30.769	0.00	0.00	39.69	1.85
42	43	7.548075	GGAAATACTTGTCGGAGAAATGTCTAA	59.452	37.037	0.00	0.00	39.69	2.10
43	44	7.039882	GGAAATACTTGTCGGAGAAATGTCTA	58.960	38.462	0.00	0.00	39.69	2.59
44	45	5.875359	GGAAATACTTGTCGGAGAAATGTCT	59.125	40.000	0.00	0.00	39.69	3.41
45	46	5.220416	CGGAAATACTTGTCGGAGAAATGTC	60.220	44.000	0.00	0.00	39.69	3.06
46	47	4.630069	CGGAAATACTTGTCGGAGAAATGT	59.370	41.667	0.00	0.00	39.69	2.71
47	48	4.034048	CCGGAAATACTTGTCGGAGAAATG	59.966	45.833	0.00	0.00	42.94	2.32
48	49	4.081309	TCCGGAAATACTTGTCGGAGAAAT	60.081	41.667	0.00	0.00	43.84	2.17
49	50	3.258872	TCCGGAAATACTTGTCGGAGAAA	59.741	43.478	0.00	0.00	43.84	2.52
50	51	2.827322	TCCGGAAATACTTGTCGGAGAA	59.173	45.455	0.00	0.00	43.84	2.87
51	52	2.449464	TCCGGAAATACTTGTCGGAGA	58.551	47.619	0.00	0.00	43.84	3.71
52	53	2.953466	TCCGGAAATACTTGTCGGAG	57.047	50.000	0.00	0.00	43.84	4.63
53	54	1.135315	CGTCCGGAAATACTTGTCGGA	60.135	52.381	5.23	0.00	46.06	4.55
54	55	1.274596	CGTCCGGAAATACTTGTCGG	58.725	55.000	5.23	0.00	41.80	4.79
55	56	1.135315	TCCGTCCGGAAATACTTGTCG	60.135	52.381	5.23	1.25	42.05	4.35
56	57	2.537401	CTCCGTCCGGAAATACTTGTC	58.463	52.381	5.23	0.00	44.66	3.18
57	58	1.206371	CCTCCGTCCGGAAATACTTGT	59.794	52.381	5.23	0.00	44.66	3.16
58	59	1.472728	CCCTCCGTCCGGAAATACTTG	60.473	57.143	5.23	0.00	44.66	3.16
59	60	0.828677	CCCTCCGTCCGGAAATACTT	59.171	55.000	5.23	0.00	44.66	2.24
60	61	0.032813	TCCCTCCGTCCGGAAATACT	60.033	55.000	5.23	0.00	44.66	2.12
61	62	0.388294	CTCCCTCCGTCCGGAAATAC	59.612	60.000	5.23	0.00	44.66	1.89
62	63	0.032813	ACTCCCTCCGTCCGGAAATA	60.033	55.000	5.23	0.00	44.66	1.40
63	64	0.032813	TACTCCCTCCGTCCGGAAAT	60.033	55.000	5.23	0.00	44.66	2.17
64	65	0.967380	GTACTCCCTCCGTCCGGAAA	60.967	60.000	5.23	0.00	44.66	3.13
65	66	1.379044	GTACTCCCTCCGTCCGGAA	60.379	63.158	5.23	0.00	44.66	4.30
66	67	0.982852	TAGTACTCCCTCCGTCCGGA	60.983	60.000	0.00	0.00	42.90	5.14
67	68	0.110104	ATAGTACTCCCTCCGTCCGG	59.890	60.000	0.00	0.00	0.00	5.14
68	69	2.847327	TATAGTACTCCCTCCGTCCG	57.153	55.000	0.00	0.00	0.00	4.79
69	70	5.589452	CACATATATAGTACTCCCTCCGTCC	59.411	48.000	0.00	0.00	0.00	4.79
70	71	6.413052	TCACATATATAGTACTCCCTCCGTC	58.587	44.000	0.00	0.00	0.00	4.79
71	72	6.384342	TCACATATATAGTACTCCCTCCGT	57.616	41.667	0.00	0.00	0.00	4.69
72	73	7.054751	TGATCACATATATAGTACTCCCTCCG	58.945	42.308	0.00	0.00	0.00	4.63
73	74	9.073475	GATGATCACATATATAGTACTCCCTCC	57.927	40.741	0.00	0.00	36.82	4.30
74	75	9.073475	GGATGATCACATATATAGTACTCCCTC	57.927	40.741	0.00	0.00	36.82	4.30
75	76	8.569596	TGGATGATCACATATATAGTACTCCCT	58.430	37.037	0.00	0.00	36.82	4.20
76	77	8.768501	TGGATGATCACATATATAGTACTCCC	57.231	38.462	0.00	0.00	36.82	4.30
86	87	7.989170	GCCTGATTACATGGATGATCACATATA	59.011	37.037	0.00	0.00	36.82	0.86
87	88	6.827251	GCCTGATTACATGGATGATCACATAT	59.173	38.462	0.00	0.00	36.82	1.78
88	89	6.175471	GCCTGATTACATGGATGATCACATA	58.825	40.000	0.00	0.00	36.82	2.29
89	90	5.008331	GCCTGATTACATGGATGATCACAT	58.992	41.667	0.00	0.00	39.67	3.21
90	91	4.392047	GCCTGATTACATGGATGATCACA	58.608	43.478	0.00	0.00	0.00	3.58
97	98	2.779430	TCTGTGGCCTGATTACATGGAT	59.221	45.455	3.32	0.00	0.00	3.41
165	166	1.741770	ACCTCGCGTTTGATCCTGC	60.742	57.895	5.77	0.00	0.00	4.85
173	174	0.881118	AATTGATGCACCTCGCGTTT	59.119	45.000	5.77	0.00	46.97	3.60
188	204	4.248859	ACGTCTTCACTGATGGAGAATTG	58.751	43.478	0.00	0.00	42.46	2.32
193	209	1.821753	AGGACGTCTTCACTGATGGAG	59.178	52.381	16.46	0.00	31.81	3.86
195	211	1.134965	GGAGGACGTCTTCACTGATGG	60.135	57.143	26.50	0.00	0.00	3.51
204	220	2.125512	GCGCATGGAGGACGTCTT	60.126	61.111	16.46	7.97	0.00	3.01
342	595	8.788806	CATCTCTGACTCTCCGTACTATTTATT	58.211	37.037	0.00	0.00	0.00	1.40
373	626	8.023128	CCGACATGACAAAATTGAAAAGATAGT	58.977	33.333	0.00	0.00	0.00	2.12
374	627	8.023128	ACCGACATGACAAAATTGAAAAGATAG	58.977	33.333	0.00	0.00	0.00	2.08
376	629	6.748132	ACCGACATGACAAAATTGAAAAGAT	58.252	32.000	0.00	0.00	0.00	2.40
581	2670	5.840693	TGCTGGAGATGAGGATATCTTTGTA	59.159	40.000	2.05	0.00	37.53	2.41
582	2671	4.657504	TGCTGGAGATGAGGATATCTTTGT	59.342	41.667	2.05	0.00	37.53	2.83
607	3767	5.390567	GGAAGTAAATAACGACCTGCACTTG	60.391	44.000	0.00	0.00	0.00	3.16
649	3809	9.624373	TGAGGATATCTTTTACTAGTACTTCGT	57.376	33.333	0.00	1.45	0.00	3.85
660	3820	9.717942	ATTGCTGTAGATGAGGATATCTTTTAC	57.282	33.333	2.05	0.00	38.35	2.01
684	3844	9.744468	GGAAATAAATAAGGACGTGCATTTATT	57.256	29.630	21.79	21.79	41.70	1.40
743	3903	6.043854	TGGTGTGTGTATTTGTAGCTGATA	57.956	37.500	0.00	0.00	0.00	2.15
874	4035	2.230892	CAACGGAAGCGTTGCACTA	58.769	52.632	0.00	0.00	41.85	2.74
1063	4224	1.694169	ATGTGATCGAGGGCCCCTT	60.694	57.895	21.43	0.00	31.76	3.95
1080	4241	2.659428	GCATTCCCAAGCACCTTAGAT	58.341	47.619	0.00	0.00	0.00	1.98
1101	4262	2.890474	CCGACGTACATGCCCTGC	60.890	66.667	0.00	0.00	0.00	4.85
1151	4312	4.866486	CAGTTGTGATCTCAACATCGATGA	59.134	41.667	31.44	9.80	46.78	2.92
1386	4547	6.964934	GCTACAAACGACCCAAAATACATAAG	59.035	38.462	0.00	0.00	0.00	1.73
1442	4613	8.396272	AGCACAACAAGTCAATAACTAGAAAT	57.604	30.769	0.00	0.00	37.17	2.17
1483	4654	8.305317	AGTATATATAAGTCGAGGGAGTTTTGC	58.695	37.037	0.00	0.00	37.09	3.68
1484	4655	9.843334	GAGTATATATAAGTCGAGGGAGTTTTG	57.157	37.037	0.00	0.00	37.09	2.44
1545	4716	6.983906	ATCATCCCATCCTAATTTTGGAAC	57.016	37.500	3.67	0.00	37.13	3.62
1548	4719	9.768662	CTAAAAATCATCCCATCCTAATTTTGG	57.231	33.333	0.00	0.00	0.00	3.28
1616	4787	9.778993	ATGATGACATATTTTGTTCTTCTTTCG	57.221	29.630	0.00	0.00	39.18	3.46
1678	4849	0.252197	GGACCGACCTTTACCATGCT	59.748	55.000	0.00	0.00	35.41	3.79
1693	4864	3.400054	CCTTCCCCTCCACGGACC	61.400	72.222	0.00	0.00	33.16	4.46
1738	4909	3.318539	GACGCTCGTGGTCGCACTA	62.319	63.158	0.00	0.00	36.96	2.74
1921	5092	9.260002	GGAAACATTTTCTAAAAATGCAAGAGA	57.740	29.630	19.76	0.00	40.35	3.10
2132	5311	1.027357	GATCGGCATTTGTGCTGGAT	58.973	50.000	9.15	7.96	41.28	3.41
2256	5436	1.823899	GGGTTATGGCAAGGGCTCG	60.824	63.158	0.00	0.00	40.87	5.03
2272	5452	6.588719	TCTTGTTCATAAAACCATTGAGGG	57.411	37.500	0.00	0.00	43.89	4.30

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.