AutoCloner

Multiple sequence alignment - TraesCS1D01G076400

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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	TraesCS1D01G076400	chr1D	100.000	3092	0	0	1	3092	58623468	58620377	0.000000e+00	5710
1	TraesCS1D01G076400	chr1D	92.927	2050	118	13	418	2448	58444163	58446204	0.000000e+00	2957
2	TraesCS1D01G076400	chr1D	78.612	1066	200	17	475	1518	49426354	49425295	0.000000e+00	680
3	TraesCS1D01G076400	chr1D	78.895	1014	194	17	512	1512	38368018	38367012	0.000000e+00	669
4	TraesCS1D01G076400	chr1D	82.664	548	91	4	1525	2070	36622736	36622191	1.670000e-132	483
5	TraesCS1D01G076400	chr1D	88.889	360	23	4	2607	2964	58447994	58448338	7.920000e-116	427
6	TraesCS1D01G076400	chr1D	91.447	152	13	0	2460	2611	58446930	58447081	3.120000e-50	209
7	TraesCS1D01G076400	chr1D	91.398	93	3	4	3002	3090	58448457	58448548	4.190000e-24	122
8	TraesCS1D01G076400	chr1A	90.525	2438	172	31	49	2448	57400526	57398110	0.000000e+00	3168
9	TraesCS1D01G076400	chr1A	92.821	1755	121	5	438	2188	57185013	57186766	0.000000e+00	2538
10	TraesCS1D01G076400	chr1A	91.512	648	42	4	2455	3092	57397425	57396781	0.000000e+00	880
11	TraesCS1D01G076400	chr1A	90.947	486	40	3	2608	3092	57311038	57310556	0.000000e+00	651
12	TraesCS1D01G076400	chr1A	80.747	857	140	18	685	1522	36174643	36173793	0.000000e+00	645
13	TraesCS1D01G076400	chr1A	78.274	1031	186	32	510	1513	36613184	36614203	2.020000e-176	628
14	TraesCS1D01G076400	chr1A	91.601	381	26	5	2714	3092	57189030	57189406	3.530000e-144	521
15	TraesCS1D01G076400	chr1A	82.545	550	92	4	1525	2072	36606715	36607262	6.000000e-132	481
16	TraesCS1D01G076400	chr1A	82.396	551	91	6	1525	2072	36637416	36637963	2.790000e-130	475
17	TraesCS1D01G076400	chr1A	82.084	547	94	4	1526	2070	36757469	36758013	6.040000e-127	464
18	TraesCS1D01G076400	chr1A	88.258	264	20	7	2187	2448	57187538	57187792	3.870000e-79	305
19	TraesCS1D01G076400	chr1B	91.952	671	42	10	1783	2448	94211311	94210648	0.000000e+00	929
20	TraesCS1D01G076400	chr1B	92.251	542	37	4	2553	3092	94210093	94209555	0.000000e+00	763
21	TraesCS1D01G076400	chr1B	80.519	1001	178	14	529	1518	56501772	56500778	0.000000e+00	752
22	TraesCS1D01G076400	chr1B	79.045	1026	180	27	510	1513	57015901	57016913	0.000000e+00	671
23	TraesCS1D01G076400	chr1B	78.829	1025	192	21	512	1518	58328673	58327656	0.000000e+00	667
24	TraesCS1D01G076400	chr1B	79.103	914	172	15	610	1513	69260373	69259469	2.040000e-171	612
25	TraesCS1D01G076400	chr1B	82.299	548	91	5	1525	2070	56499930	56499387	1.300000e-128	470
26	TraesCS1D01G076400	chr1B	86.040	351	34	10	3	347	16995166	16995507	2.270000e-96	363
27	TraesCS1D01G076400	chr6A	84.007	544	83	4	1530	2071	547817038	547817579	1.270000e-143	520
28	TraesCS1D01G076400	chr6B	83.273	556	84	7	1530	2079	601867740	601868292	1.280000e-138	503
29	TraesCS1D01G076400	chr6B	85.678	391	40	14	1	377	498671276	498670888	6.210000e-107	398
30	TraesCS1D01G076400	chr2B	85.646	418	46	12	12	416	233164043	233164459	7.920000e-116	427
31	TraesCS1D01G076400	chr2D	85.539	408	45	12	12	406	176099792	176100198	6.170000e-112	414
32	TraesCS1D01G076400	chr7D	87.332	371	30	15	1	358	403542836	403542470	2.870000e-110	409
33	TraesCS1D01G076400	chr7D	88.571	315	31	5	1	312	633234278	633233966	8.090000e-101	377
34	TraesCS1D01G076400	chr6D	85.530	387	41	12	4	377	455773978	455773594	1.040000e-104	390
35	TraesCS1D01G076400	chr6D	84.456	386	40	12	1	377	107769488	107769114	2.270000e-96	363
36	TraesCS1D01G076400	chr5D	89.439	303	31	1	1	303	263162277	263161976	6.260000e-102	381
37	TraesCS1D01G076400	chr5D	81.944	216	24	8	175	377	311618078	311617865	5.300000e-38	169

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	TraesCS1D01G076400	chr1D	58620377	58623468	3091	True	5710.000000	5710	100.000000	1	3092	1	chr1D.!!$R4	3091
1	TraesCS1D01G076400	chr1D	58444163	58448548	4385	False	928.750000	2957	91.165250	418	3090	4	chr1D.!!$F1	2672
2	TraesCS1D01G076400	chr1D	49425295	49426354	1059	True	680.000000	680	78.612000	475	1518	1	chr1D.!!$R3	1043
3	TraesCS1D01G076400	chr1D	38367012	38368018	1006	True	669.000000	669	78.895000	512	1512	1	chr1D.!!$R2	1000
4	TraesCS1D01G076400	chr1D	36622191	36622736	545	True	483.000000	483	82.664000	1525	2070	1	chr1D.!!$R1	545
5	TraesCS1D01G076400	chr1A	57396781	57400526	3745	True	2024.000000	3168	91.018500	49	3092	2	chr1A.!!$R3	3043
6	TraesCS1D01G076400	chr1A	57185013	57189406	4393	False	1121.333333	2538	90.893333	438	3092	3	chr1A.!!$F5	2654
7	TraesCS1D01G076400	chr1A	36173793	36174643	850	True	645.000000	645	80.747000	685	1522	1	chr1A.!!$R1	837
8	TraesCS1D01G076400	chr1A	36613184	36614203	1019	False	628.000000	628	78.274000	510	1513	1	chr1A.!!$F2	1003
9	TraesCS1D01G076400	chr1A	36606715	36607262	547	False	481.000000	481	82.545000	1525	2072	1	chr1A.!!$F1	547
10	TraesCS1D01G076400	chr1A	36637416	36637963	547	False	475.000000	475	82.396000	1525	2072	1	chr1A.!!$F3	547
11	TraesCS1D01G076400	chr1A	36757469	36758013	544	False	464.000000	464	82.084000	1526	2070	1	chr1A.!!$F4	544
12	TraesCS1D01G076400	chr1B	94209555	94211311	1756	True	846.000000	929	92.101500	1783	3092	2	chr1B.!!$R4	1309
13	TraesCS1D01G076400	chr1B	57015901	57016913	1012	False	671.000000	671	79.045000	510	1513	1	chr1B.!!$F2	1003
14	TraesCS1D01G076400	chr1B	58327656	58328673	1017	True	667.000000	667	78.829000	512	1518	1	chr1B.!!$R1	1006
15	TraesCS1D01G076400	chr1B	69259469	69260373	904	True	612.000000	612	79.103000	610	1513	1	chr1B.!!$R2	903
16	TraesCS1D01G076400	chr1B	56499387	56501772	2385	True	611.000000	752	81.409000	529	2070	2	chr1B.!!$R3	1541
17	TraesCS1D01G076400	chr6A	547817038	547817579	541	False	520.000000	520	84.007000	1530	2071	1	chr6A.!!$F1	541
18	TraesCS1D01G076400	chr6B	601867740	601868292	552	False	503.000000	503	83.273000	1530	2079	1	chr6B.!!$F1	549

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
376	397	0.179084	ATTATCTGTGGACGTGCCCG	60.179	55.0	4.04	0.0	40.83	6.13	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2144	3076	0.106819	GCAAGAGACCCAGATGGCAT	60.107	55.0	0.0	0.0	37.83	4.4	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
17	18	2.362503	AGTCCGACGAGATGGCCA	60.363	61.111	8.56	8.56	0.00	5.36
18	19	1.982395	AGTCCGACGAGATGGCCAA	60.982	57.895	10.96	0.00	0.00	4.52
19	20	1.519455	GTCCGACGAGATGGCCAAG	60.519	63.158	10.96	4.20	0.00	3.61
20	21	2.892425	CCGACGAGATGGCCAAGC	60.892	66.667	10.96	4.92	0.00	4.01
21	22	2.125552	CGACGAGATGGCCAAGCA	60.126	61.111	10.96	0.00	0.00	3.91
22	23	2.169789	CGACGAGATGGCCAAGCAG	61.170	63.158	10.96	4.62	0.00	4.24
23	24	2.437359	ACGAGATGGCCAAGCAGC	60.437	61.111	10.96	0.58	0.00	5.25
24	25	2.437180	CGAGATGGCCAAGCAGCA	60.437	61.111	10.96	0.00	0.00	4.41
25	26	2.470362	CGAGATGGCCAAGCAGCAG	61.470	63.158	10.96	0.00	0.00	4.24
26	27	2.044252	AGATGGCCAAGCAGCAGG	60.044	61.111	10.96	0.00	0.00	4.85
31	32	3.834799	GCCAAGCAGCAGGCCATC	61.835	66.667	16.10	0.00	45.18	3.51
32	33	3.145551	CCAAGCAGCAGGCCATCC	61.146	66.667	5.01	0.00	46.50	3.51
33	34	2.044252	CAAGCAGCAGGCCATCCT	60.044	61.111	5.01	0.00	46.50	3.24
41	42	2.456364	AGGCCATCCTGGAGTCCA	59.544	61.111	12.40	12.40	40.96	4.02
42	43	1.005289	AGGCCATCCTGGAGTCCAT	59.995	57.895	13.56	0.00	40.96	3.41
43	44	1.059006	AGGCCATCCTGGAGTCCATC	61.059	60.000	13.56	0.00	40.96	3.51
74	75	2.608970	CTATGTGGAGGCCAACCGGG	62.609	65.000	6.32	0.00	42.76	5.73
113	114	3.943034	CGGAGATCGACGCGCTCT	61.943	66.667	5.73	3.00	42.43	4.09
133	134	4.872485	GACGAGCTCGACGCGGAG	62.872	72.222	40.58	11.30	46.87	4.63
135	136	3.943034	CGAGCTCGACGCGGAGAT	61.943	66.667	32.06	7.01	45.59	2.75
136	137	2.595878	CGAGCTCGACGCGGAGATA	61.596	63.158	32.06	0.00	45.59	1.98
137	138	1.205568	GAGCTCGACGCGGAGATAG	59.794	63.158	12.47	1.14	45.59	2.08
138	139	1.222766	GAGCTCGACGCGGAGATAGA	61.223	60.000	12.47	0.00	45.59	1.98
139	140	1.205568	GCTCGACGCGGAGATAGAG	59.794	63.158	12.47	10.40	36.08	2.43
232	233	2.105128	CCGGGCACAGAGATCGTC	59.895	66.667	0.00	0.00	0.00	4.20
241	242	1.944024	ACAGAGATCGTCGACATCTCC	59.056	52.381	31.90	22.43	45.23	3.71
293	312	9.958285	GTAGTACGTAGGTTTATTTTAGTTTGC	57.042	33.333	0.00	0.00	0.00	3.68
297	316	7.878036	ACGTAGGTTTATTTTAGTTTGCATGT	58.122	30.769	0.00	0.00	0.00	3.21
298	317	8.019094	ACGTAGGTTTATTTTAGTTTGCATGTC	58.981	33.333	0.00	0.00	0.00	3.06
302	321	9.260002	AGGTTTATTTTAGTTTGCATGTCTTTG	57.740	29.630	0.00	0.00	0.00	2.77
335	356	4.681074	TGATATGGTCGGATGCAAAGTA	57.319	40.909	0.00	0.00	0.00	2.24
342	363	5.226396	TGGTCGGATGCAAAGTAAAATTTG	58.774	37.500	0.00	0.00	42.00	2.32
347	368	4.327087	GGATGCAAAGTAAAATTTGAGGCG	59.673	41.667	7.05	0.00	41.71	5.52
349	370	4.047822	TGCAAAGTAAAATTTGAGGCGTG	58.952	39.130	7.05	0.00	41.71	5.34
350	371	3.121025	GCAAAGTAAAATTTGAGGCGTGC	60.121	43.478	7.05	0.00	41.71	5.34
354	375	2.153547	AAAATTTGAGGCGTGCCCGG	62.154	55.000	7.39	0.00	39.21	5.73
360	381	3.379865	GAGGCGTGCCCGGTCATTA	62.380	63.158	7.39	0.00	39.21	1.90
361	382	2.203153	GGCGTGCCCGGTCATTAT	60.203	61.111	0.00	0.00	33.68	1.28
363	384	1.227556	GCGTGCCCGGTCATTATCT	60.228	57.895	0.00	0.00	33.68	1.98
368	389	0.468226	GCCCGGTCATTATCTGTGGA	59.532	55.000	0.00	0.00	0.00	4.02
369	390	1.810412	GCCCGGTCATTATCTGTGGAC	60.810	57.143	0.00	0.00	0.00	4.02
372	393	2.193447	CGGTCATTATCTGTGGACGTG	58.807	52.381	0.00	0.00	0.00	4.49
373	394	1.933853	GGTCATTATCTGTGGACGTGC	59.066	52.381	0.00	0.00	0.00	5.34
374	395	1.933853	GTCATTATCTGTGGACGTGCC	59.066	52.381	4.04	0.43	37.10	5.01
375	396	1.134521	TCATTATCTGTGGACGTGCCC	60.135	52.381	4.04	0.00	34.97	5.36
376	397	0.179084	ATTATCTGTGGACGTGCCCG	60.179	55.000	4.04	0.00	40.83	6.13
377	398	2.845752	TTATCTGTGGACGTGCCCGC	62.846	60.000	4.04	1.76	37.70	6.13
403	424	3.763057	GTTTGAGGGGGTGTATTTGTCT	58.237	45.455	0.00	0.00	0.00	3.41
404	425	3.433306	TTGAGGGGGTGTATTTGTCTG	57.567	47.619	0.00	0.00	0.00	3.51
405	426	2.344592	TGAGGGGGTGTATTTGTCTGT	58.655	47.619	0.00	0.00	0.00	3.41
406	427	3.522759	TGAGGGGGTGTATTTGTCTGTA	58.477	45.455	0.00	0.00	0.00	2.74
408	429	2.844348	AGGGGGTGTATTTGTCTGTAGG	59.156	50.000	0.00	0.00	0.00	3.18
413	443	3.684788	GGTGTATTTGTCTGTAGGTGCTG	59.315	47.826	0.00	0.00	0.00	4.41
494	526	1.965754	GATGCCTCGCTTCCACTCCT	61.966	60.000	0.00	0.00	0.00	3.69
788	855	3.254024	AACCGCCTGTGCCGAGAAT	62.254	57.895	0.00	0.00	0.00	2.40
921	994	2.997897	GGCCTGAGGACAGACGGT	60.998	66.667	0.65	0.00	46.03	4.83
936	1009	2.202570	GGTGTCGACGCATACGCT	60.203	61.111	28.67	0.00	45.53	5.07
1035	1108	1.672030	TGTGCCTGATGCCTTGTCG	60.672	57.895	0.00	0.00	40.16	4.35
1080	1153	0.175760	GTGACGATAGCAGGAGCCAA	59.824	55.000	0.00	0.00	43.56	4.52
1125	1198	0.685097	TGTCGAAAGAAGGAGGTGGG	59.315	55.000	0.00	0.00	45.01	4.61
1330	1406	3.126001	TCCTTCGGCATATGGTCAATC	57.874	47.619	4.56	0.00	0.00	2.67
1356	1432	0.810823	TTCGACCCAACAACGTGACC	60.811	55.000	0.00	0.00	0.00	4.02
1364	1440	4.527816	ACCCAACAACGTGACCTATAAGTA	59.472	41.667	0.00	0.00	0.00	2.24
1377	1453	7.620094	GTGACCTATAAGTATATGATCCAGGGT	59.380	40.741	0.00	0.00	0.00	4.34
1452	1528	6.204495	CGACAAGTAGGGGTCTTATACTAGAC	59.796	46.154	0.00	0.00	43.05	2.59
1631	2556	3.535561	AGGAAGCAATCATACTGTTCCG	58.464	45.455	0.00	0.00	38.80	4.30
1963	2888	8.934023	TTATTTGTCTAAAGTTGATGGGAAGT	57.066	30.769	0.00	0.00	0.00	3.01
2144	3076	7.235079	TGGAAGGTACAGTTGATTTATTCCAA	58.765	34.615	0.00	0.00	40.37	3.53
2256	3963	6.151144	TCTGGGTATCTTTTAAGCTTCTTTGC	59.849	38.462	0.00	0.00	0.00	3.68
2290	3997	5.395768	GGTGAACCACATAGTCTAGCAGAAT	60.396	44.000	0.00	0.00	35.86	2.40
2326	4037	5.103771	AGGGATAATGGCTTCTGATTGAACT	60.104	40.000	0.00	0.00	0.00	3.01
2342	4053	8.742125	TGATTGAACTGGGAAGGTATAGATAT	57.258	34.615	0.00	0.00	0.00	1.63
2453	4893	7.406916	TCTCTAGAACAGTCACTTTCTCCTAT	58.593	38.462	5.75	0.00	33.96	2.57
2473	4923	0.666577	GCACGTGTACAGTCCTGTCC	60.667	60.000	18.38	0.00	43.74	4.02
2493	4943	1.616374	CGGTTTTGGTGCCCTAAATGT	59.384	47.619	4.70	0.00	31.82	2.71
2502	4952	1.663379	GCCCTAAATGTTCCACCGCC	61.663	60.000	0.00	0.00	0.00	6.13
2513	4963	2.104331	CACCGCCGCGACTTCTAT	59.896	61.111	15.93	0.00	0.00	1.98
2678	6046	4.963318	AGTTGATCCACACTGAGAAGAA	57.037	40.909	0.00	0.00	0.00	2.52
2679	6047	5.296151	AGTTGATCCACACTGAGAAGAAA	57.704	39.130	0.00	0.00	0.00	2.52
2680	6048	5.684704	AGTTGATCCACACTGAGAAGAAAA	58.315	37.500	0.00	0.00	0.00	2.29
2686	6054	6.867662	TCCACACTGAGAAGAAAAATCTTC	57.132	37.500	9.93	9.93	44.67	2.87
2689	6057	7.173907	TCCACACTGAGAAGAAAAATCTTCATC	59.826	37.037	17.94	13.06	46.22	2.92
2722	6385	1.404391	CTTGCTGGACTGGCATCAATC	59.596	52.381	0.00	0.00	39.54	2.67
2726	6389	2.189499	GGACTGGCATCAATCGGGC	61.189	63.158	0.00	0.00	0.00	6.13
2743	6406	1.578423	GCTGGCAACACTCTGCTTC	59.422	57.895	0.00	0.00	46.17	3.86
2840	6511	5.443185	TCTGAGAATTGTTTCAGGCTTTG	57.557	39.130	9.91	0.00	40.89	2.77
2864	6535	1.608283	GGTACCAACTGGAGTGACTGC	60.608	57.143	7.15	0.00	38.94	4.40
2953	6626	5.815581	TGTTATACTCCACCAAGAATGCTT	58.184	37.500	0.00	0.00	33.74	3.91
2954	6627	5.880332	TGTTATACTCCACCAAGAATGCTTC	59.120	40.000	0.00	0.00	30.14	3.86
2990	6663	3.624777	GGCTTTTCTCAATCATCTGGGA	58.375	45.455	0.00	0.00	0.00	4.37
2997	6670	3.118992	TCTCAATCATCTGGGAACGTGAG	60.119	47.826	0.00	0.00	34.01	3.51
3000	6755	0.247460	TCATCTGGGAACGTGAGCTG	59.753	55.000	0.00	0.00	0.00	4.24
3070	6828	7.093289	ACACAATCCCTACATATATGGTAGCTC	60.093	40.741	16.96	0.00	37.49	4.09

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
5	6	2.467826	GCTGCTTGGCCATCTCGTC	61.468	63.158	6.09	0.00	0.00	4.20
6	7	2.437359	GCTGCTTGGCCATCTCGT	60.437	61.111	6.09	0.00	0.00	4.18
9	10	2.044252	CCTGCTGCTTGGCCATCT	60.044	61.111	6.09	0.00	0.00	2.90
10	11	3.834799	GCCTGCTGCTTGGCCATC	61.835	66.667	20.81	1.67	43.11	3.51
15	16	3.145551	GGATGGCCTGCTGCTTGG	61.146	66.667	3.32	4.52	40.92	3.61
16	17	2.044252	AGGATGGCCTGCTGCTTG	60.044	61.111	3.32	0.00	44.90	4.01
39	40	1.281287	CATAGGCCTCATCCTGGATGG	59.719	57.143	30.88	22.12	40.15	3.51
40	41	1.983691	ACATAGGCCTCATCCTGGATG	59.016	52.381	27.23	27.23	41.00	3.51
41	42	1.983691	CACATAGGCCTCATCCTGGAT	59.016	52.381	9.68	2.57	37.01	3.41
42	43	1.427809	CACATAGGCCTCATCCTGGA	58.572	55.000	9.68	0.00	37.01	3.86
43	44	0.399454	CCACATAGGCCTCATCCTGG	59.601	60.000	9.68	4.33	37.01	4.45
44	45	1.347050	CTCCACATAGGCCTCATCCTG	59.653	57.143	9.68	2.86	37.01	3.86
45	46	1.727062	CTCCACATAGGCCTCATCCT	58.273	55.000	9.68	0.00	40.21	3.24
46	47	0.689623	CCTCCACATAGGCCTCATCC	59.310	60.000	9.68	0.00	37.29	3.51
128	129	2.631580	CCTCCGCCTCTATCTCCGC	61.632	68.421	0.00	0.00	0.00	5.54
129	130	0.958382	CTCCTCCGCCTCTATCTCCG	60.958	65.000	0.00	0.00	0.00	4.63
130	131	0.610785	CCTCCTCCGCCTCTATCTCC	60.611	65.000	0.00	0.00	0.00	3.71
131	132	1.248101	GCCTCCTCCGCCTCTATCTC	61.248	65.000	0.00	0.00	0.00	2.75
132	133	1.228737	GCCTCCTCCGCCTCTATCT	60.229	63.158	0.00	0.00	0.00	1.98
133	134	2.279810	GGCCTCCTCCGCCTCTATC	61.280	68.421	0.00	0.00	43.48	2.08
134	135	2.203714	GGCCTCCTCCGCCTCTAT	60.204	66.667	0.00	0.00	43.48	1.98
135	136	4.896829	CGGCCTCCTCCGCCTCTA	62.897	72.222	0.00	0.00	44.73	2.43
153	154	2.726351	GCCTCCAGCTACTCCGCTT	61.726	63.158	0.00	0.00	38.41	4.68
220	221	2.286713	GGAGATGTCGACGATCTCTGTG	60.287	54.545	32.80	0.00	43.70	3.66
222	223	1.070242	CGGAGATGTCGACGATCTCTG	60.070	57.143	32.80	31.69	43.70	3.35
223	224	1.202545	TCGGAGATGTCGACGATCTCT	60.203	52.381	32.80	23.30	43.70	3.10
241	242	1.657594	TCAACTAGCTACTCGTCGTCG	59.342	52.381	0.00	0.00	38.55	5.12
304	323	9.898152	TGCATCCGACCATATCATATTAAATTA	57.102	29.630	0.00	0.00	0.00	1.40
308	327	7.882791	ACTTTGCATCCGACCATATCATATTAA	59.117	33.333	0.00	0.00	0.00	1.40
311	330	5.809001	ACTTTGCATCCGACCATATCATAT	58.191	37.500	0.00	0.00	0.00	1.78
317	336	6.767524	AATTTTACTTTGCATCCGACCATA	57.232	33.333	0.00	0.00	0.00	2.74
321	340	5.572896	CCTCAAATTTTACTTTGCATCCGAC	59.427	40.000	0.00	0.00	36.32	4.79
322	341	5.708948	CCTCAAATTTTACTTTGCATCCGA	58.291	37.500	0.00	0.00	36.32	4.55
335	356	1.288752	CGGGCACGCCTCAAATTTT	59.711	52.632	8.20	0.00	36.10	1.82
342	363	2.660258	ATAATGACCGGGCACGCCTC	62.660	60.000	15.41	0.00	39.22	4.70
347	368	1.299541	CACAGATAATGACCGGGCAC	58.700	55.000	15.41	0.00	0.00	5.01
349	370	0.468226	TCCACAGATAATGACCGGGC	59.532	55.000	6.32	1.57	0.00	6.13
350	371	1.538204	CGTCCACAGATAATGACCGGG	60.538	57.143	6.32	0.00	0.00	5.73
354	375	1.933853	GGCACGTCCACAGATAATGAC	59.066	52.381	0.00	0.00	34.01	3.06
360	381	4.760047	GCGGGCACGTCCACAGAT	62.760	66.667	11.45	0.00	43.45	2.90
378	399	2.206182	ATACACCCCCTCAAACGCCC	62.206	60.000	0.00	0.00	0.00	6.13
379	400	0.323087	AATACACCCCCTCAAACGCC	60.323	55.000	0.00	0.00	0.00	5.68
380	401	1.201414	CAAATACACCCCCTCAAACGC	59.799	52.381	0.00	0.00	0.00	4.84
381	402	2.486592	GACAAATACACCCCCTCAAACG	59.513	50.000	0.00	0.00	0.00	3.60
382	403	3.506067	CAGACAAATACACCCCCTCAAAC	59.494	47.826	0.00	0.00	0.00	2.93
383	404	3.139397	ACAGACAAATACACCCCCTCAAA	59.861	43.478	0.00	0.00	0.00	2.69
384	405	2.714250	ACAGACAAATACACCCCCTCAA	59.286	45.455	0.00	0.00	0.00	3.02
385	406	2.344592	ACAGACAAATACACCCCCTCA	58.655	47.619	0.00	0.00	0.00	3.86
386	407	3.118371	CCTACAGACAAATACACCCCCTC	60.118	52.174	0.00	0.00	0.00	4.30
387	408	2.844348	CCTACAGACAAATACACCCCCT	59.156	50.000	0.00	0.00	0.00	4.79
388	409	2.574824	ACCTACAGACAAATACACCCCC	59.425	50.000	0.00	0.00	0.00	5.40
392	413	4.315803	ACAGCACCTACAGACAAATACAC	58.684	43.478	0.00	0.00	0.00	2.90
393	414	4.617253	ACAGCACCTACAGACAAATACA	57.383	40.909	0.00	0.00	0.00	2.29
403	424	4.425180	TTTTGGACTTACAGCACCTACA	57.575	40.909	0.00	0.00	0.00	2.74
404	425	4.215613	CCTTTTTGGACTTACAGCACCTAC	59.784	45.833	0.00	0.00	38.35	3.18
405	426	4.103469	TCCTTTTTGGACTTACAGCACCTA	59.897	41.667	0.00	0.00	40.56	3.08
406	427	3.117663	TCCTTTTTGGACTTACAGCACCT	60.118	43.478	0.00	0.00	40.56	4.00
408	429	4.911514	TTCCTTTTTGGACTTACAGCAC	57.088	40.909	0.00	0.00	46.14	4.40
413	443	4.928601	AGCGTTTTCCTTTTTGGACTTAC	58.071	39.130	0.00	0.00	46.14	2.34
632	687	0.953960	AATTCGTCGAACAGGTGGCC	60.954	55.000	10.39	0.00	0.00	5.36
788	855	4.758251	CGACGCATGTGGGCTGGA	62.758	66.667	11.65	0.00	0.00	3.86
936	1009	1.627329	AGGCAGAAGCACTTGATGAGA	59.373	47.619	0.00	0.00	44.61	3.27
1134	1207	1.597663	GTGCTATATGCCACCACGTTC	59.402	52.381	0.00	0.00	42.00	3.95
1156	1229	3.523157	TCCTTACAGAAGCCATGGATGAA	59.477	43.478	18.40	0.00	0.00	2.57
1192	1266	1.640069	CGAACAGATCGCATGCCTG	59.360	57.895	17.65	17.65	45.89	4.85
1364	1440	6.786843	AAGTGGAATAACCCTGGATCATAT	57.213	37.500	0.00	0.00	38.00	1.78
1377	1453	2.896685	CAACCAGCCCAAAGTGGAATAA	59.103	45.455	0.00	0.00	40.96	1.40
1434	1510	6.445451	ACATCGTCTAGTATAAGACCCCTA	57.555	41.667	0.03	0.00	42.46	3.53
1435	1511	5.321934	ACATCGTCTAGTATAAGACCCCT	57.678	43.478	0.03	0.00	42.46	4.79
1452	1528	3.718036	CGAACAAGTTGCGAGTAACATCG	60.718	47.826	1.81	6.90	45.48	3.84
1515	1591	3.657398	ATCATCTGATGGGCAAACTCA	57.343	42.857	17.06	0.00	32.68	3.41
1631	2556	3.922240	CACATTCACTGCACCTAATTTGC	59.078	43.478	0.00	0.00	40.63	3.68
1798	2723	8.884124	TCTTCCATTGATCCTTCTTTTACAAT	57.116	30.769	0.00	0.00	0.00	2.71
1801	2726	7.121907	AGCTTCTTCCATTGATCCTTCTTTTAC	59.878	37.037	0.00	0.00	0.00	2.01
1963	2888	4.098349	AGTTGAAGCTTCAAGTGAAATGCA	59.902	37.500	37.02	15.65	46.80	3.96
2062	2987	3.251004	ACTGTGCTGACTCCGAAAAATTC	59.749	43.478	0.00	0.00	0.00	2.17
2144	3076	0.106819	GCAAGAGACCCAGATGGCAT	60.107	55.000	0.00	0.00	37.83	4.40
2217	3924	8.503428	AAGATACCCAGATATGAACTGAATCT	57.497	34.615	0.00	0.00	37.54	2.40
2218	3925	9.566432	AAAAGATACCCAGATATGAACTGAATC	57.434	33.333	0.00	0.00	37.54	2.52
2235	3942	4.793731	GCGCAAAGAAGCTTAAAAGATACC	59.206	41.667	0.30	0.00	0.00	2.73
2256	3963	1.890041	TGGTTCACCTTTCCACGCG	60.890	57.895	3.53	3.53	36.82	6.01
2290	3997	4.100808	GCCATTATCCCTAAATGCAACCAA	59.899	41.667	0.00	0.00	33.80	3.67
2326	4037	4.763355	AGCACCATATCTATACCTTCCCA	58.237	43.478	0.00	0.00	0.00	4.37
2342	4053	3.244875	TGCTTCTTATGGAAAGAGCACCA	60.245	43.478	0.00	0.00	40.57	4.17
2434	4145	4.390297	GTGCATAGGAGAAAGTGACTGTTC	59.610	45.833	0.00	0.00	0.00	3.18
2453	4893	0.031585	GACAGGACTGTACACGTGCA	59.968	55.000	17.22	5.50	45.05	4.57
2502	4952	7.045725	TGTAAAAGAGAAAATAGAAGTCGCG	57.954	36.000	0.00	0.00	0.00	5.87
2513	4963	7.607250	TGCCTTTCAAGTTGTAAAAGAGAAAA	58.393	30.769	15.25	1.02	32.89	2.29
2678	6046	9.908747	AAGATCTGAAGAGATGATGAAGATTTT	57.091	29.630	0.00	0.00	39.19	1.82
2679	6047	9.332502	CAAGATCTGAAGAGATGATGAAGATTT	57.667	33.333	0.00	0.00	39.19	2.17
2680	6048	7.442969	GCAAGATCTGAAGAGATGATGAAGATT	59.557	37.037	0.00	0.00	39.19	2.40
2686	6054	4.752604	CCAGCAAGATCTGAAGAGATGATG	59.247	45.833	0.00	0.00	39.19	3.07
2689	6057	4.121317	GTCCAGCAAGATCTGAAGAGATG	58.879	47.826	0.00	0.00	39.19	2.90
2722	6385	3.052082	CAGAGTGTTGCCAGCCCG	61.052	66.667	0.00	0.00	0.00	6.13
2726	6389	1.572085	CCGAAGCAGAGTGTTGCCAG	61.572	60.000	0.00	0.00	45.18	4.85
2743	6406	2.095567	CCAAAACATCTTCACAGAGCCG	60.096	50.000	0.00	0.00	30.36	5.52
2840	6511	2.876550	GTCACTCCAGTTGGTACCAAAC	59.123	50.000	28.67	20.92	37.70	2.93
2953	6626	1.302511	GCCCAAGCAAAGACTCGGA	60.303	57.895	0.00	0.00	39.53	4.55
2954	6627	0.890996	AAGCCCAAGCAAAGACTCGG	60.891	55.000	0.00	0.00	43.56	4.63
2990	6663	1.523758	GAATGGTTCCAGCTCACGTT	58.476	50.000	0.00	0.00	0.00	3.99

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.