AutoCloner

Multiple sequence alignment - TraesCS3D01G276300

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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	TraesCS3D01G276300	chr3D	100.000	3469	0	0	1	3469	383173761	383170293	0.000000e+00	6407
1	TraesCS3D01G276300	chr3D	89.286	1764	145	31	695	2441	149758703	149760439	0.000000e+00	2170
2	TraesCS3D01G276300	chr3D	92.205	821	57	4	2649	3469	336050	336863	0.000000e+00	1155
3	TraesCS3D01G276300	chr3D	97.738	619	13	1	1	619	383180723	383180106	0.000000e+00	1064
4	TraesCS3D01G276300	chr7D	93.321	2785	161	11	693	3469	503838184	503835417	0.000000e+00	4089
5	TraesCS3D01G276300	chr7D	94.618	799	36	2	1825	2623	519747677	519748468	0.000000e+00	1230
6	TraesCS3D01G276300	chr7D	92.665	818	53	3	2652	3469	531065818	531065008	0.000000e+00	1171
7	TraesCS3D01G276300	chr7D	97.092	619	16	2	1	619	93073253	93072637	0.000000e+00	1042
8	TraesCS3D01G276300	chr4D	94.433	2425	118	11	695	3111	470184638	470182223	0.000000e+00	3714
9	TraesCS3D01G276300	chr4D	92.326	821	56	4	2649	3469	491383407	491384220	0.000000e+00	1160
10	TraesCS3D01G276300	chr7B	89.802	2775	221	28	694	3463	43570136	43572853	0.000000e+00	3500
11	TraesCS3D01G276300	chr7B	90.406	2439	199	26	695	3121	730310146	730312561	0.000000e+00	3175
12	TraesCS3D01G276300	chr7B	89.363	1946	169	24	695	2621	672859561	672857635	0.000000e+00	2412
13	TraesCS3D01G276300	chr7B	91.897	1703	125	9	1768	3469	156407289	156405599	0.000000e+00	2368
14	TraesCS3D01G276300	chr7B	91.905	803	57	3	2169	2971	610669818	610669024	0.000000e+00	1116
15	TraesCS3D01G276300	chr7B	85.220	318	41	4	695	1011	672845630	672845942	4.320000e-84	322
16	TraesCS3D01G276300	chr1A	94.263	2179	101	13	695	2869	518113446	518115604	0.000000e+00	3310
17	TraesCS3D01G276300	chr6D	89.207	1955	139	34	695	2621	25731321	25733231	0.000000e+00	2375
18	TraesCS3D01G276300	chr6D	92.579	822	53	4	2649	3469	25733228	25734042	0.000000e+00	1173
19	TraesCS3D01G276300	chr6D	97.078	616	16	2	1	616	31283474	31284087	0.000000e+00	1037
20	TraesCS3D01G276300	chr6D	97.078	616	17	1	1	616	97457098	97457712	0.000000e+00	1037
21	TraesCS3D01G276300	chr5A	87.344	1762	165	41	694	2441	396679716	396677999	0.000000e+00	1965
22	TraesCS3D01G276300	chr2D	92.326	821	56	3	2649	3469	617342661	617343474	0.000000e+00	1160
23	TraesCS3D01G276300	chr2D	97.078	616	17	1	1	616	43048620	43049234	0.000000e+00	1037
24	TraesCS3D01G276300	chr5D	97.092	619	17	1	1	619	480903379	480902762	0.000000e+00	1042
25	TraesCS3D01G276300	chr5D	96.774	620	18	2	1	619	300169078	300168460	0.000000e+00	1033
26	TraesCS3D01G276300	chr1D	96.931	619	17	2	1	619	334306079	334305463	0.000000e+00	1037
27	TraesCS3D01G276300	chr1D	96.921	617	17	2	1	616	312892680	312893295	0.000000e+00	1033
28	TraesCS3D01G276300	chr6B	85.173	607	68	18	695	1289	142984893	142984297	1.380000e-168	603

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	TraesCS3D01G276300	chr3D	383170293	383173761	3468	True	6407	6407	100.000	1	3469	1	chr3D.!!$R1	3468
1	TraesCS3D01G276300	chr3D	149758703	149760439	1736	False	2170	2170	89.286	695	2441	1	chr3D.!!$F2	1746
2	TraesCS3D01G276300	chr3D	336050	336863	813	False	1155	1155	92.205	2649	3469	1	chr3D.!!$F1	820
3	TraesCS3D01G276300	chr3D	383180106	383180723	617	True	1064	1064	97.738	1	619	1	chr3D.!!$R2	618
4	TraesCS3D01G276300	chr7D	503835417	503838184	2767	True	4089	4089	93.321	693	3469	1	chr7D.!!$R2	2776
5	TraesCS3D01G276300	chr7D	519747677	519748468	791	False	1230	1230	94.618	1825	2623	1	chr7D.!!$F1	798
6	TraesCS3D01G276300	chr7D	531065008	531065818	810	True	1171	1171	92.665	2652	3469	1	chr7D.!!$R3	817
7	TraesCS3D01G276300	chr7D	93072637	93073253	616	True	1042	1042	97.092	1	619	1	chr7D.!!$R1	618
8	TraesCS3D01G276300	chr4D	470182223	470184638	2415	True	3714	3714	94.433	695	3111	1	chr4D.!!$R1	2416
9	TraesCS3D01G276300	chr4D	491383407	491384220	813	False	1160	1160	92.326	2649	3469	1	chr4D.!!$F1	820
10	TraesCS3D01G276300	chr7B	43570136	43572853	2717	False	3500	3500	89.802	694	3463	1	chr7B.!!$F1	2769
11	TraesCS3D01G276300	chr7B	730310146	730312561	2415	False	3175	3175	90.406	695	3121	1	chr7B.!!$F3	2426
12	TraesCS3D01G276300	chr7B	672857635	672859561	1926	True	2412	2412	89.363	695	2621	1	chr7B.!!$R3	1926
13	TraesCS3D01G276300	chr7B	156405599	156407289	1690	True	2368	2368	91.897	1768	3469	1	chr7B.!!$R1	1701
14	TraesCS3D01G276300	chr7B	610669024	610669818	794	True	1116	1116	91.905	2169	2971	1	chr7B.!!$R2	802
15	TraesCS3D01G276300	chr1A	518113446	518115604	2158	False	3310	3310	94.263	695	2869	1	chr1A.!!$F1	2174
16	TraesCS3D01G276300	chr6D	25731321	25734042	2721	False	1774	2375	90.893	695	3469	2	chr6D.!!$F3	2774
17	TraesCS3D01G276300	chr6D	31283474	31284087	613	False	1037	1037	97.078	1	616	1	chr6D.!!$F1	615
18	TraesCS3D01G276300	chr6D	97457098	97457712	614	False	1037	1037	97.078	1	616	1	chr6D.!!$F2	615
19	TraesCS3D01G276300	chr5A	396677999	396679716	1717	True	1965	1965	87.344	694	2441	1	chr5A.!!$R1	1747
20	TraesCS3D01G276300	chr2D	617342661	617343474	813	False	1160	1160	92.326	2649	3469	1	chr2D.!!$F2	820
21	TraesCS3D01G276300	chr2D	43048620	43049234	614	False	1037	1037	97.078	1	616	1	chr2D.!!$F1	615
22	TraesCS3D01G276300	chr5D	480902762	480903379	617	True	1042	1042	97.092	1	619	1	chr5D.!!$R2	618
23	TraesCS3D01G276300	chr5D	300168460	300169078	618	True	1033	1033	96.774	1	619	1	chr5D.!!$R1	618
24	TraesCS3D01G276300	chr1D	334305463	334306079	616	True	1037	1037	96.931	1	619	1	chr1D.!!$R1	618
25	TraesCS3D01G276300	chr1D	312892680	312893295	615	False	1033	1033	96.921	1	616	1	chr1D.!!$F1	615
26	TraesCS3D01G276300	chr6B	142984297	142984893	596	True	603	603	85.173	695	1289	1	chr6B.!!$R1	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	Hairpin	End Stability	Orientation
624	627	0.034380	TCAGTACTCCCTCTGTCCCG	60.034	60.0	0.00	33.89	5.14	F
662	665	0.175073	GACACGGCGGAGGAGTAATT	59.825	55.0	13.24	0.00	1.40	F
1426	1449	0.546122	TTGAAGGCACTGACACTGGT	59.454	50.0	0.00	40.86	4.00	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2212	2276	0.251354	TCAGGAGCTCAGCAATGACC	59.749	55.0	17.19	0.00	0.00	4.02	R
2346	2414	0.264359	AGGCTGATCAGTCCTAGGCT	59.736	55.0	27.23	16.08	40.68	4.58	R
3359	3444	0.534652	TGGGTTGCCATGCTTTTTGC	60.535	50.0	0.00	0.00	43.25	3.68	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
33	34	2.270352	TTCCGTAATGCATCATCCCC	57.730	50.000	0.00	0.00	0.00	4.81
186	187	2.092592	TCGGAGACACCTGTAGAGCATA	60.093	50.000	0.00	0.00	36.31	3.14
214	215	1.758280	TCACCCAGTTACGTTGTGACT	59.242	47.619	0.00	0.00	32.61	3.41
247	248	5.299279	CACACAAAGTGTTCCTCTGGTATTT	59.701	40.000	0.00	0.00	45.08	1.40
526	528	8.943002	ACTAAGTTTCCGGTTAATACAATTCTG	58.057	33.333	0.00	0.00	0.00	3.02
616	619	4.103311	GGCATATTTCCTTCAGTACTCCCT	59.897	45.833	0.00	0.00	0.00	4.20
617	620	5.301555	GCATATTTCCTTCAGTACTCCCTC	58.698	45.833	0.00	0.00	0.00	4.30
618	621	5.071115	GCATATTTCCTTCAGTACTCCCTCT	59.929	44.000	0.00	0.00	0.00	3.69
619	622	6.520272	CATATTTCCTTCAGTACTCCCTCTG	58.480	44.000	0.00	0.00	0.00	3.35
620	623	3.544698	TTCCTTCAGTACTCCCTCTGT	57.455	47.619	0.00	0.00	33.89	3.41
621	624	3.088789	TCCTTCAGTACTCCCTCTGTC	57.911	52.381	0.00	0.00	33.89	3.51
622	625	2.104170	CCTTCAGTACTCCCTCTGTCC	58.896	57.143	0.00	0.00	33.89	4.02
623	626	2.104170	CTTCAGTACTCCCTCTGTCCC	58.896	57.143	0.00	0.00	33.89	4.46
624	627	0.034380	TCAGTACTCCCTCTGTCCCG	60.034	60.000	0.00	0.00	33.89	5.14
625	628	0.323542	CAGTACTCCCTCTGTCCCGT	60.324	60.000	0.00	0.00	0.00	5.28
626	629	1.064906	CAGTACTCCCTCTGTCCCGTA	60.065	57.143	0.00	0.00	0.00	4.02
627	630	1.637553	AGTACTCCCTCTGTCCCGTAA	59.362	52.381	0.00	0.00	0.00	3.18
628	631	2.244252	AGTACTCCCTCTGTCCCGTAAT	59.756	50.000	0.00	0.00	0.00	1.89
629	632	3.461085	AGTACTCCCTCTGTCCCGTAATA	59.539	47.826	0.00	0.00	0.00	0.98
630	633	3.614568	ACTCCCTCTGTCCCGTAATAT	57.385	47.619	0.00	0.00	0.00	1.28
631	634	4.736611	ACTCCCTCTGTCCCGTAATATA	57.263	45.455	0.00	0.00	0.00	0.86
632	635	5.070823	ACTCCCTCTGTCCCGTAATATAA	57.929	43.478	0.00	0.00	0.00	0.98
633	636	5.461327	ACTCCCTCTGTCCCGTAATATAAA	58.539	41.667	0.00	0.00	0.00	1.40
634	637	6.082707	ACTCCCTCTGTCCCGTAATATAAAT	58.917	40.000	0.00	0.00	0.00	1.40
635	638	7.243824	ACTCCCTCTGTCCCGTAATATAAATA	58.756	38.462	0.00	0.00	0.00	1.40
636	639	7.899709	ACTCCCTCTGTCCCGTAATATAAATAT	59.100	37.037	0.00	0.00	0.00	1.28
637	640	9.417561	CTCCCTCTGTCCCGTAATATAAATATA	57.582	37.037	0.00	0.00	0.00	0.86
638	641	9.947189	TCCCTCTGTCCCGTAATATAAATATAT	57.053	33.333	0.00	0.00	0.00	0.86
652	655	9.834628	AATATAAATATATTTTTGACACGGCGG	57.165	29.630	15.64	2.35	35.86	6.13
653	656	5.821516	AAATATATTTTTGACACGGCGGA	57.178	34.783	13.24	0.00	0.00	5.54
654	657	5.418310	AATATATTTTTGACACGGCGGAG	57.582	39.130	13.24	5.87	0.00	4.63
655	658	1.444836	TATTTTTGACACGGCGGAGG	58.555	50.000	13.24	2.44	0.00	4.30
656	659	0.250553	ATTTTTGACACGGCGGAGGA	60.251	50.000	13.24	0.00	0.00	3.71
657	660	0.882927	TTTTTGACACGGCGGAGGAG	60.883	55.000	13.24	0.00	0.00	3.69
658	661	2.035237	TTTTGACACGGCGGAGGAGT	62.035	55.000	13.24	0.91	0.00	3.85
659	662	1.180456	TTTGACACGGCGGAGGAGTA	61.180	55.000	13.24	0.00	0.00	2.59
660	663	1.180456	TTGACACGGCGGAGGAGTAA	61.180	55.000	13.24	0.00	0.00	2.24
661	664	0.968901	TGACACGGCGGAGGAGTAAT	60.969	55.000	13.24	0.00	0.00	1.89
662	665	0.175073	GACACGGCGGAGGAGTAATT	59.825	55.000	13.24	0.00	0.00	1.40
663	666	1.406539	GACACGGCGGAGGAGTAATTA	59.593	52.381	13.24	0.00	0.00	1.40
664	667	1.407979	ACACGGCGGAGGAGTAATTAG	59.592	52.381	13.24	0.00	0.00	1.73
665	668	1.407979	CACGGCGGAGGAGTAATTAGT	59.592	52.381	13.24	0.00	0.00	2.24
666	669	2.620115	CACGGCGGAGGAGTAATTAGTA	59.380	50.000	13.24	0.00	0.00	1.82
667	670	2.620585	ACGGCGGAGGAGTAATTAGTAC	59.379	50.000	13.24	0.00	0.00	2.73
668	671	2.350197	CGGCGGAGGAGTAATTAGTACG	60.350	54.545	0.00	0.56	37.81	3.67
669	672	2.620585	GGCGGAGGAGTAATTAGTACGT	59.379	50.000	0.00	0.00	37.81	3.57
670	673	3.815401	GGCGGAGGAGTAATTAGTACGTA	59.185	47.826	0.00	0.00	37.81	3.57
671	674	4.083590	GGCGGAGGAGTAATTAGTACGTAG	60.084	50.000	0.00	0.00	37.81	3.51
672	675	4.083590	GCGGAGGAGTAATTAGTACGTAGG	60.084	50.000	0.00	0.00	37.81	3.18
673	676	4.083590	CGGAGGAGTAATTAGTACGTAGGC	60.084	50.000	0.00	0.00	37.81	3.93
674	677	4.083590	GGAGGAGTAATTAGTACGTAGGCG	60.084	50.000	0.00	0.00	44.93	5.52
707	711	2.494059	CTGTCCCGAGTGTTTGACAAT	58.506	47.619	0.00	0.00	37.29	2.71
739	744	4.404098	GGGGTTCGCGTCCCACAT	62.404	66.667	30.86	0.00	46.26	3.21
918	924	1.495509	GCGCATGTGCTGTCGTTAA	59.504	52.632	23.77	0.00	39.32	2.01
991	998	2.997315	CTCGTCCCCACCAGCTCA	60.997	66.667	0.00	0.00	0.00	4.26
1014	1021	1.684049	CTCTCCCCCGAGCTCACTT	60.684	63.158	15.40	0.00	35.94	3.16
1025	1032	1.132262	GAGCTCACTTCACTCCTCTCG	59.868	57.143	9.40	0.00	0.00	4.04
1031	1038	1.181786	CTTCACTCCTCTCGGCTCTT	58.818	55.000	0.00	0.00	0.00	2.85
1426	1449	0.546122	TTGAAGGCACTGACACTGGT	59.454	50.000	0.00	0.00	40.86	4.00
1433	1456	1.203523	GCACTGACACTGGTAGGAGAG	59.796	57.143	0.00	0.00	0.00	3.20
1445	1468	5.144100	CTGGTAGGAGAGTCATAGGATGTT	58.856	45.833	0.00	0.00	0.00	2.71
1451	1474	7.395525	AGGAGAGTCATAGGATGTTCTACTA	57.604	40.000	0.00	0.00	35.78	1.82
1616	1652	8.655092	GCATAGAGCACTAGAAACATATTGATC	58.345	37.037	0.00	0.00	44.79	2.92
1725	1780	7.718272	TGTTAACTATGGTGTTCACTGTAAC	57.282	36.000	7.22	0.00	0.00	2.50
1763	1822	2.030007	GGATGGTGTGAATTGTGGTGTG	60.030	50.000	0.00	0.00	0.00	3.82
1967	2030	7.950512	TGATGTGTCCAAGTTGTTTGATTATT	58.049	30.769	1.45	0.00	39.21	1.40
1974	2037	8.739972	GTCCAAGTTGTTTGATTATTAGGATGT	58.260	33.333	1.45	0.00	39.21	3.06
2042	2105	4.640364	ACTGAAGGAGAAGAAGAAGCAAG	58.360	43.478	0.00	0.00	0.00	4.01
2212	2276	4.806640	AGAGAAGAAGAAGCTGGAGAAG	57.193	45.455	0.00	0.00	0.00	2.85
2277	2341	1.742268	GCTGGACAAGATCAAGGAAGC	59.258	52.381	0.00	0.00	0.00	3.86
2278	2342	2.363683	CTGGACAAGATCAAGGAAGCC	58.636	52.381	0.00	0.00	0.00	4.35
2647	2718	9.994432	CTGCAAGAAAGGTAAACAATATCTAAG	57.006	33.333	0.00	0.00	34.07	2.18
2656	2727	9.515226	AGGTAAACAATATCTAAGCAAGTTCAA	57.485	29.630	0.00	0.00	0.00	2.69
2811	2882	5.211174	ACACCCTACTAAACTGACAGAAC	57.789	43.478	10.08	0.00	0.00	3.01
2869	2954	6.755141	GGCGATAACTGTTGTAACTGAATCTA	59.245	38.462	2.69	0.00	0.00	1.98
2924	3009	1.878522	GCTATGCGACCTGACCGTG	60.879	63.158	0.00	0.00	0.00	4.94
3014	3099	0.760945	GATGGGAGGAGGATGTCGGT	60.761	60.000	0.00	0.00	0.00	4.69
3022	3107	1.608717	GAGGATGTCGGTGAGCCAGT	61.609	60.000	0.00	0.00	34.09	4.00
3046	3131	1.976132	CTGGTGGGGCGATGATCTGT	61.976	60.000	0.00	0.00	0.00	3.41
3116	3201	0.485543	TGGAGGGATATAGCGGTGGA	59.514	55.000	0.00	0.00	0.00	4.02
3196	3281	0.520404	GCATGTCGATGGGCATGATC	59.480	55.000	24.37	5.43	43.60	2.92
3204	3289	1.425066	GATGGGCATGATCCCCTTACA	59.575	52.381	8.20	0.00	45.97	2.41
3243	3328	1.144716	CCATGCGCTGCTTCTCCTA	59.855	57.895	9.73	0.00	0.00	2.94
3296	3381	1.340399	ATCCATGAGCCCTTCTGCGA	61.340	55.000	0.00	0.00	36.02	5.10
3318	3403	5.107182	CGATGTTGTATCTCATGGCAATCTC	60.107	44.000	0.00	0.00	0.00	2.75
3331	3416	2.092968	GGCAATCTCCATGTAGTCCACA	60.093	50.000	0.00	0.00	42.69	4.17
3414	3501	1.739608	AAGGGGTTCAGCCATGGGTT	61.740	55.000	15.37	0.00	39.65	4.11
3459	3546	3.388024	GCCATGGATGTAGGTAGAGTGAA	59.612	47.826	18.40	0.00	0.00	3.18

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
82	83	1.830408	CTCTGGGCCCTCTCGGTAG	60.830	68.421	25.70	10.33	0.00	3.18
186	187	7.825270	TCACAACGTAACTGGGTGATTATAAAT	59.175	33.333	0.00	0.00	33.88	1.40
214	215	5.359576	AGGAACACTTTGTGTGCTATCAAAA	59.640	36.000	8.51	0.00	46.79	2.44
247	248	5.366477	TGACTATGAGATTATGCAACTCCCA	59.634	40.000	0.00	0.00	0.00	4.37
626	629	9.834628	CCGCCGTGTCAAAAATATATTTATATT	57.165	29.630	11.07	0.00	39.79	1.28
627	630	9.221933	TCCGCCGTGTCAAAAATATATTTATAT	57.778	29.630	11.07	0.00	0.00	0.86
628	631	8.604640	TCCGCCGTGTCAAAAATATATTTATA	57.395	30.769	11.07	0.00	0.00	0.98
629	632	7.308348	CCTCCGCCGTGTCAAAAATATATTTAT	60.308	37.037	11.07	0.01	0.00	1.40
630	633	6.017770	CCTCCGCCGTGTCAAAAATATATTTA	60.018	38.462	11.07	0.00	0.00	1.40
631	634	5.220970	CCTCCGCCGTGTCAAAAATATATTT	60.221	40.000	4.81	4.81	0.00	1.40
632	635	4.274950	CCTCCGCCGTGTCAAAAATATATT	59.725	41.667	0.00	0.00	0.00	1.28
633	636	3.813166	CCTCCGCCGTGTCAAAAATATAT	59.187	43.478	0.00	0.00	0.00	0.86
634	637	3.118702	TCCTCCGCCGTGTCAAAAATATA	60.119	43.478	0.00	0.00	0.00	0.86
635	638	2.014128	CCTCCGCCGTGTCAAAAATAT	58.986	47.619	0.00	0.00	0.00	1.28
636	639	1.002201	TCCTCCGCCGTGTCAAAAATA	59.998	47.619	0.00	0.00	0.00	1.40
637	640	0.250553	TCCTCCGCCGTGTCAAAAAT	60.251	50.000	0.00	0.00	0.00	1.82
638	641	0.882927	CTCCTCCGCCGTGTCAAAAA	60.883	55.000	0.00	0.00	0.00	1.94
639	642	1.301401	CTCCTCCGCCGTGTCAAAA	60.301	57.895	0.00	0.00	0.00	2.44
640	643	1.180456	TACTCCTCCGCCGTGTCAAA	61.180	55.000	0.00	0.00	0.00	2.69
641	644	1.180456	TTACTCCTCCGCCGTGTCAA	61.180	55.000	0.00	0.00	0.00	3.18
642	645	0.968901	ATTACTCCTCCGCCGTGTCA	60.969	55.000	0.00	0.00	0.00	3.58
643	646	0.175073	AATTACTCCTCCGCCGTGTC	59.825	55.000	0.00	0.00	0.00	3.67
644	647	1.407979	CTAATTACTCCTCCGCCGTGT	59.592	52.381	0.00	0.00	0.00	4.49
645	648	1.407979	ACTAATTACTCCTCCGCCGTG	59.592	52.381	0.00	0.00	0.00	4.94
646	649	1.772836	ACTAATTACTCCTCCGCCGT	58.227	50.000	0.00	0.00	0.00	5.68
647	650	2.350197	CGTACTAATTACTCCTCCGCCG	60.350	54.545	0.00	0.00	0.00	6.46
648	651	2.620585	ACGTACTAATTACTCCTCCGCC	59.379	50.000	0.00	0.00	0.00	6.13
649	652	3.978718	ACGTACTAATTACTCCTCCGC	57.021	47.619	0.00	0.00	0.00	5.54
650	653	4.083590	GCCTACGTACTAATTACTCCTCCG	60.084	50.000	0.00	0.00	0.00	4.63
651	654	4.083590	CGCCTACGTACTAATTACTCCTCC	60.084	50.000	0.00	0.00	33.53	4.30
652	655	5.028428	CGCCTACGTACTAATTACTCCTC	57.972	47.826	0.00	0.00	33.53	3.71
667	670	1.335689	GGGAGTAATGCTACGCCTACG	60.336	57.143	5.98	0.00	44.91	3.51
668	671	1.962100	AGGGAGTAATGCTACGCCTAC	59.038	52.381	5.98	0.00	44.91	3.18
669	672	1.961394	CAGGGAGTAATGCTACGCCTA	59.039	52.381	5.98	0.00	44.91	3.93
670	673	0.753262	CAGGGAGTAATGCTACGCCT	59.247	55.000	5.98	0.00	44.91	5.52
671	674	0.464452	ACAGGGAGTAATGCTACGCC	59.536	55.000	0.00	0.00	44.84	5.68
672	675	1.538419	GGACAGGGAGTAATGCTACGC	60.538	57.143	0.00	0.00	32.87	4.42
673	676	1.068741	GGGACAGGGAGTAATGCTACG	59.931	57.143	0.00	0.00	32.87	3.51
674	677	1.068741	CGGGACAGGGAGTAATGCTAC	59.931	57.143	0.00	0.00	0.00	3.58
675	678	1.063492	TCGGGACAGGGAGTAATGCTA	60.063	52.381	0.00	0.00	0.00	3.49
676	679	0.325296	TCGGGACAGGGAGTAATGCT	60.325	55.000	0.00	0.00	0.00	3.79
677	680	0.105039	CTCGGGACAGGGAGTAATGC	59.895	60.000	0.00	0.00	0.00	3.56
678	681	1.137086	CACTCGGGACAGGGAGTAATG	59.863	57.143	0.00	0.00	41.37	1.90
679	682	1.273098	ACACTCGGGACAGGGAGTAAT	60.273	52.381	0.00	0.00	41.37	1.89
680	683	0.113776	ACACTCGGGACAGGGAGTAA	59.886	55.000	0.00	0.00	41.37	2.24
681	684	0.113776	AACACTCGGGACAGGGAGTA	59.886	55.000	0.00	0.00	41.37	2.59
682	685	0.763223	AAACACTCGGGACAGGGAGT	60.763	55.000	0.00	0.00	43.99	3.85
683	686	0.320771	CAAACACTCGGGACAGGGAG	60.321	60.000	0.00	0.00	36.36	4.30
684	687	0.761323	TCAAACACTCGGGACAGGGA	60.761	55.000	0.00	0.00	0.00	4.20
685	688	0.602905	GTCAAACACTCGGGACAGGG	60.603	60.000	0.00	0.00	0.00	4.45
686	689	0.105964	TGTCAAACACTCGGGACAGG	59.894	55.000	0.00	0.00	35.51	4.00
687	690	1.948104	TTGTCAAACACTCGGGACAG	58.052	50.000	0.00	0.00	40.90	3.51
688	691	2.631160	ATTGTCAAACACTCGGGACA	57.369	45.000	0.00	0.00	38.41	4.02
689	692	4.514066	AGTTTATTGTCAAACACTCGGGAC	59.486	41.667	0.00	0.00	40.22	4.46
690	693	4.710324	AGTTTATTGTCAAACACTCGGGA	58.290	39.130	0.00	0.00	40.22	5.14
691	694	5.106830	GGTAGTTTATTGTCAAACACTCGGG	60.107	44.000	1.99	0.00	40.22	5.14
707	711	4.563374	GCGAACCCCTAAAGTGGTAGTTTA	60.563	45.833	0.00	0.00	33.52	2.01
904	910	0.796312	CGGCTTTAACGACAGCACAT	59.204	50.000	0.00	0.00	37.81	3.21
905	911	1.837538	GCGGCTTTAACGACAGCACA	61.838	55.000	0.00	0.00	37.81	4.57
991	998	2.363147	GCTCGGGGGAGAGTGAGT	60.363	66.667	0.00	0.00	40.26	3.41
1025	1032	2.470983	AACAGAAGCAGAGAAGAGCC	57.529	50.000	0.00	0.00	0.00	4.70
1031	1038	5.537188	GAGAAGAAGAAACAGAAGCAGAGA	58.463	41.667	0.00	0.00	0.00	3.10
1085	1092	2.031919	TCGTTGCTGTTCGGCCAT	59.968	55.556	2.24	0.00	0.00	4.40
1393	1416	3.386078	TGCCTTCAAATGCCACAAACTTA	59.614	39.130	0.00	0.00	0.00	2.24
1426	1449	7.395525	AGTAGAACATCCTATGACTCTCCTA	57.604	40.000	0.00	0.00	31.69	2.94
1433	1456	9.915629	CATTACCTTAGTAGAACATCCTATGAC	57.084	37.037	0.00	0.00	0.00	3.06
1687	1737	9.423061	ACCATAGTTAACAAGCAAATTCAATTC	57.577	29.630	8.61	0.00	0.00	2.17
1688	1738	9.206870	CACCATAGTTAACAAGCAAATTCAATT	57.793	29.630	8.61	0.00	0.00	2.32
1689	1739	8.367156	ACACCATAGTTAACAAGCAAATTCAAT	58.633	29.630	8.61	0.00	0.00	2.57
1690	1740	7.721402	ACACCATAGTTAACAAGCAAATTCAA	58.279	30.769	8.61	0.00	0.00	2.69
1691	1741	7.283625	ACACCATAGTTAACAAGCAAATTCA	57.716	32.000	8.61	0.00	0.00	2.57
1725	1780	8.928733	CACACCATCCTGAAAATCAATTTAAAG	58.071	33.333	0.00	0.00	0.00	1.85
1763	1822	2.191641	GGCATCTCCCACTCCAGC	59.808	66.667	0.00	0.00	0.00	4.85
1786	1847	5.242795	AGCACCTTTGTAGAATTACAGGT	57.757	39.130	0.00	0.00	40.68	4.00
1988	2051	1.274167	CTGGCTTGTGCAATCCATGTT	59.726	47.619	7.79	0.00	41.91	2.71
2042	2105	3.062042	CAATTTTTGCCTGCTCCTCAAC	58.938	45.455	0.00	0.00	0.00	3.18
2212	2276	0.251354	TCAGGAGCTCAGCAATGACC	59.749	55.000	17.19	0.00	0.00	4.02
2277	2341	0.898320	ACTTCACTCCTCCATCACGG	59.102	55.000	0.00	0.00	0.00	4.94
2278	2342	1.404717	CCACTTCACTCCTCCATCACG	60.405	57.143	0.00	0.00	0.00	4.35
2341	2409	4.528596	GGCTGATCAGTCCTAGGCTAATTA	59.471	45.833	23.38	0.00	33.44	1.40
2342	2410	3.326297	GGCTGATCAGTCCTAGGCTAATT	59.674	47.826	23.38	0.00	33.44	1.40
2346	2414	0.264359	AGGCTGATCAGTCCTAGGCT	59.736	55.000	27.23	16.08	40.68	4.58
2610	2680	2.502142	TTCTTGCAGCCTGTGATGAT	57.498	45.000	0.00	0.00	0.00	2.45
2647	2718	6.753744	ACTTCTCTGAATTTGTTTGAACTTGC	59.246	34.615	0.00	0.00	0.00	4.01
2656	2727	7.122650	TGTCTTCCAAACTTCTCTGAATTTGTT	59.877	33.333	0.00	0.00	31.48	2.83
2811	2882	8.763049	TGTGAGATTCAGTTATGTCTGTTTAG	57.237	34.615	0.00	0.00	36.85	1.85
2882	2967	2.357154	GGCATGGGACCTAACAATCTGT	60.357	50.000	0.00	0.00	0.00	3.41
2895	2980	2.517414	GCATAGCAGGGCATGGGA	59.483	61.111	0.00	0.00	0.00	4.37
2924	3009	2.805099	CTCAAGTCAAGCAAGAGGTGTC	59.195	50.000	0.00	0.00	0.00	3.67
3022	3107	2.687200	ATCGCCCCACCAGCACTA	60.687	61.111	0.00	0.00	0.00	2.74
3046	3131	1.412710	GGCAATGACGATGAGGACCTA	59.587	52.381	0.00	0.00	0.00	3.08
3116	3201	3.637273	GAGGGAACGGTGGGCAGT	61.637	66.667	0.00	0.00	0.00	4.40
3243	3328	1.902508	TGAGGAAGAAGGCGATGACTT	59.097	47.619	0.00	0.00	31.13	3.01
3296	3381	5.068636	GGAGATTGCCATGAGATACAACAT	58.931	41.667	0.00	0.00	0.00	2.71
3318	3403	5.359194	AGACCTATTTGTGGACTACATGG	57.641	43.478	0.00	0.00	39.48	3.66
3359	3444	0.534652	TGGGTTGCCATGCTTTTTGC	60.535	50.000	0.00	0.00	43.25	3.68
3414	3501	1.137086	GTTCTTCCTCATCTGCGCCTA	59.863	52.381	4.18	0.00	0.00	3.93

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.