AutoCloner

Multiple sequence alignment - TraesCS7D01G145100

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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	TraesCS7D01G145100	chr7D	100.000	5437	0	0	1	5437	92593854	92588418	0.000000e+00	10041
1	TraesCS7D01G145100	chr7D	80.896	937	143	23	3413	4341	92418757	92417849	0.000000e+00	706
2	TraesCS7D01G145100	chr7D	99.338	151	1	0	768	918	92598228	92598078	1.930000e-69	274
3	TraesCS7D01G145100	chr7A	96.120	3067	107	5	1656	4719	94776370	94773313	0.000000e+00	4994
4	TraesCS7D01G145100	chr7A	82.387	2447	359	44	1920	4338	94490217	94487815	0.000000e+00	2065
5	TraesCS7D01G145100	chr7A	93.600	750	42	1	930	1673	94777179	94776430	0.000000e+00	1114
6	TraesCS7D01G145100	chr7B	93.471	2282	130	9	1844	4120	44562042	44559775	0.000000e+00	3371
7	TraesCS7D01G145100	chr7B	88.191	398	39	5	1425	1819	44562429	44562037	8.250000e-128	468
8	TraesCS7D01G145100	chr2D	99.019	917	9	0	1	917	426934004	426933088	0.000000e+00	1644
9	TraesCS7D01G145100	chr2D	97.500	160	1	2	766	925	426938380	426938224	2.500000e-68	270
10	TraesCS7D01G145100	chr6D	98.806	921	11	0	1	921	6500685	6499765	0.000000e+00	1640
11	TraesCS7D01G145100	chr6D	97.500	720	18	0	4718	5437	21962514	21961795	0.000000e+00	1230
12	TraesCS7D01G145100	chr6D	99.333	150	1	0	769	918	6505055	6504906	6.940000e-69	272
13	TraesCS7D01G145100	chr2A	98.370	920	14	1	1	920	739696620	739695702	0.000000e+00	1615
14	TraesCS7D01G145100	chr2A	98.667	150	2	0	769	918	739700992	739700843	3.230000e-67	267
15	TraesCS7D01G145100	chr3A	96.510	917	32	0	1	917	644824360	644823444	0.000000e+00	1517
16	TraesCS7D01G145100	chr1D	97.765	716	16	0	4722	5437	473010990	473010275	0.000000e+00	1234
17	TraesCS7D01G145100	chr5D	97.500	720	18	0	4718	5437	58216614	58215895	0.000000e+00	1230
18	TraesCS7D01G145100	chr5D	97.629	717	17	0	4718	5434	369902083	369902799	0.000000e+00	1230
19	TraesCS7D01G145100	chr5D	97.629	717	17	0	4718	5434	428560828	428561544	0.000000e+00	1230
20	TraesCS7D01G145100	chr5D	97.629	717	17	0	4718	5434	493516037	493516753	0.000000e+00	1230
21	TraesCS7D01G145100	chr5D	97.493	718	18	0	4717	5434	514471410	514472127	0.000000e+00	1227
22	TraesCS7D01G145100	chr4D	97.490	717	18	0	4718	5434	395695437	395696153	0.000000e+00	1225
23	TraesCS7D01G145100	chr4D	97.361	720	19	0	4718	5437	435918282	435917563	0.000000e+00	1225
24	TraesCS7D01G145100	chr1B	93.555	512	33	0	1	512	34593806	34594317	0.000000e+00	763
25	TraesCS7D01G145100	chr1B	94.737	399	21	0	507	905	34603815	34604213	5.980000e-174	621
26	TraesCS7D01G145100	chr1B	76.992	778	167	10	3	773	120999265	121000037	8.360000e-118	435
27	TraesCS7D01G145100	chr1B	78.469	418	86	3	358	773	624024467	624024052	2.500000e-68	270
28	TraesCS7D01G145100	chr6B	76.774	775	172	6	3	773	46942929	46942159	1.400000e-115	427
29	TraesCS7D01G145100	chr6B	97.015	67	2	0	4650	4716	652314671	652314737	4.450000e-21	113
30	TraesCS7D01G145100	chr3B	83.333	360	53	6	4359	4717	708052178	708052531	5.250000e-85	326
31	TraesCS7D01G145100	chr1A	78.469	418	86	3	358	773	11723570	11723155	2.500000e-68	270
32	TraesCS7D01G145100	chr3D	82.085	307	45	7	4377	4676	358194079	358194382	2.510000e-63	254
33	TraesCS7D01G145100	chr4B	85.484	186	20	6	4533	4717	667562901	667562722	2.590000e-43	187

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	TraesCS7D01G145100	chr7D	92588418	92593854	5436	True	10041.0	10041	100.000	1	5437	1	chr7D.!!$R2	5436
1	TraesCS7D01G145100	chr7D	92417849	92418757	908	True	706.0	706	80.896	3413	4341	1	chr7D.!!$R1	928
2	TraesCS7D01G145100	chr7A	94773313	94777179	3866	True	3054.0	4994	94.860	930	4719	2	chr7A.!!$R2	3789
3	TraesCS7D01G145100	chr7A	94487815	94490217	2402	True	2065.0	2065	82.387	1920	4338	1	chr7A.!!$R1	2418
4	TraesCS7D01G145100	chr7B	44559775	44562429	2654	True	1919.5	3371	90.831	1425	4120	2	chr7B.!!$R1	2695
5	TraesCS7D01G145100	chr2D	426933088	426934004	916	True	1644.0	1644	99.019	1	917	1	chr2D.!!$R1	916
6	TraesCS7D01G145100	chr6D	6499765	6500685	920	True	1640.0	1640	98.806	1	921	1	chr6D.!!$R1	920
7	TraesCS7D01G145100	chr6D	21961795	21962514	719	True	1230.0	1230	97.500	4718	5437	1	chr6D.!!$R3	719
8	TraesCS7D01G145100	chr2A	739695702	739696620	918	True	1615.0	1615	98.370	1	920	1	chr2A.!!$R1	919
9	TraesCS7D01G145100	chr3A	644823444	644824360	916	True	1517.0	1517	96.510	1	917	1	chr3A.!!$R1	916
10	TraesCS7D01G145100	chr1D	473010275	473010990	715	True	1234.0	1234	97.765	4722	5437	1	chr1D.!!$R1	715
11	TraesCS7D01G145100	chr5D	58215895	58216614	719	True	1230.0	1230	97.500	4718	5437	1	chr5D.!!$R1	719
12	TraesCS7D01G145100	chr5D	369902083	369902799	716	False	1230.0	1230	97.629	4718	5434	1	chr5D.!!$F1	716
13	TraesCS7D01G145100	chr5D	428560828	428561544	716	False	1230.0	1230	97.629	4718	5434	1	chr5D.!!$F2	716
14	TraesCS7D01G145100	chr5D	493516037	493516753	716	False	1230.0	1230	97.629	4718	5434	1	chr5D.!!$F3	716
15	TraesCS7D01G145100	chr5D	514471410	514472127	717	False	1227.0	1227	97.493	4717	5434	1	chr5D.!!$F4	717
16	TraesCS7D01G145100	chr4D	395695437	395696153	716	False	1225.0	1225	97.490	4718	5434	1	chr4D.!!$F1	716
17	TraesCS7D01G145100	chr4D	435917563	435918282	719	True	1225.0	1225	97.361	4718	5437	1	chr4D.!!$R1	719
18	TraesCS7D01G145100	chr1B	34593806	34594317	511	False	763.0	763	93.555	1	512	1	chr1B.!!$F1	511
19	TraesCS7D01G145100	chr1B	120999265	121000037	772	False	435.0	435	76.992	3	773	1	chr1B.!!$F3	770
20	TraesCS7D01G145100	chr6B	46942159	46942929	770	True	427.0	427	76.774	3	773	1	chr6B.!!$R1	770

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
955	959	0.984995	TCAGTCAGTCCTCTCCGAGA	59.015	55.0	0.00	0.00	0.00	4.04	F
1054	1058	0.104855	CCTGCTACTATGCTTGGCGA	59.895	55.0	0.00	0.00	0.00	5.54	F
1065	1069	0.533755	GCTTGGCGATGCTATCCAGT	60.534	55.0	0.00	0.00	0.00	4.00	F
2975	3071	0.742505	ATTCCGTCGGAAGTATGCGA	59.257	50.0	29.12	6.67	45.48	5.10	F
3408	3504	0.040058	TCAATGTCATTGGGCTGCCT	59.960	50.0	22.44	0.00	40.61	4.75	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Hairpin	End Stability	Orientation
2447	2543	1.081174	TGGATGGAGGAAGAGGACCTT	59.919	52.381	0.00	37.93	3.50	R
2459	2555	3.244561	ACTGGTGTGTACTTTGGATGGAG	60.245	47.826	0.00	0.00	3.86	R
2981	3077	5.723295	ACACATCAAGAAACACAAGCTTTT	58.277	33.333	0.00	0.00	2.27	R
4393	4515	1.450531	GCATGCATAGGCTCCACCAC	61.451	60.000	14.21	43.14	4.16	R
5282	5404	0.457035	ATGCATCATCCCGCAACAAC	59.543	50.000	0.00	42.37	3.32	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
72	73	6.460103	AATTAAGGCAGATATGGGTGATCT	57.540	37.500	0.00	0.00	33.82	2.75
194	195	4.719026	ATGCATGACCCAAGATCTACAT	57.281	40.909	0.00	0.00	0.00	2.29
303	304	8.026026	CAGTATAGAGTGTTATACAGATGCTGG	58.974	40.741	0.00	0.00	38.43	4.85
482	485	8.983307	ATTAATATGGCTACGCTTACTACTTC	57.017	34.615	0.00	0.00	0.00	3.01
895	899	4.594920	TCCTCAATGTTCCAGACTTCTCTT	59.405	41.667	0.00	0.00	0.00	2.85
917	921	5.441718	TCCCTTCTTGAGCTAATCAACAT	57.558	39.130	0.00	0.00	43.09	2.71
921	925	6.327934	CCTTCTTGAGCTAATCAACATTTGG	58.672	40.000	0.00	0.00	43.09	3.28
922	926	6.071728	CCTTCTTGAGCTAATCAACATTTGGT	60.072	38.462	0.00	0.00	43.09	3.67
923	927	7.121168	CCTTCTTGAGCTAATCAACATTTGGTA	59.879	37.037	0.00	0.00	43.09	3.25
924	928	8.579850	TTCTTGAGCTAATCAACATTTGGTAT	57.420	30.769	0.00	0.00	43.09	2.73
925	929	7.988737	TCTTGAGCTAATCAACATTTGGTATG	58.011	34.615	0.00	0.00	43.09	2.39
926	930	7.611467	TCTTGAGCTAATCAACATTTGGTATGT	59.389	33.333	0.00	0.00	43.09	2.29
927	931	7.087409	TGAGCTAATCAACATTTGGTATGTG	57.913	36.000	0.00	0.00	34.02	3.21
928	932	6.658816	TGAGCTAATCAACATTTGGTATGTGT	59.341	34.615	0.00	0.00	34.02	3.72
945	949	2.035961	TGTGTACTTGGCTCAGTCAGTC	59.964	50.000	0.00	0.00	0.00	3.51
955	959	0.984995	TCAGTCAGTCCTCTCCGAGA	59.015	55.000	0.00	0.00	0.00	4.04
1054	1058	0.104855	CCTGCTACTATGCTTGGCGA	59.895	55.000	0.00	0.00	0.00	5.54
1065	1069	0.533755	GCTTGGCGATGCTATCCAGT	60.534	55.000	0.00	0.00	0.00	4.00
1072	1076	2.388890	GATGCTATCCAGTGGCGGCT	62.389	60.000	11.43	0.00	37.07	5.52
1144	1148	1.194772	GCCAGTTCAACTACAACTCGC	59.805	52.381	0.00	0.00	32.03	5.03
1218	1228	2.357517	CCCACAGCTCGTGTCACC	60.358	66.667	13.06	0.00	44.78	4.02
1230	1240	4.131088	GTCACCGGCCTCGACCTC	62.131	72.222	0.00	0.00	39.00	3.85
1236	1246	2.490148	CGGCCTCGACCTCAGCATA	61.490	63.158	0.00	0.00	39.00	3.14
1363	1373	2.469516	CCCGGTGCAGGTAATTCGC	61.470	63.158	0.00	0.00	0.00	4.70
1383	1393	3.057596	CGCCCAGACTCTCTAGATTCATC	60.058	52.174	0.00	0.00	0.00	2.92
1384	1394	3.258123	GCCCAGACTCTCTAGATTCATCC	59.742	52.174	0.00	0.00	0.00	3.51
1387	1397	5.139727	CCAGACTCTCTAGATTCATCCAGT	58.860	45.833	0.00	0.00	0.00	4.00
1390	1400	4.285020	ACTCTCTAGATTCATCCAGTGCA	58.715	43.478	0.00	0.00	0.00	4.57
1401	1411	3.698539	TCATCCAGTGCAGTTTTCAAACA	59.301	39.130	5.26	0.00	41.30	2.83
1418	1428	5.698832	TCAAACAAATTATGCTGTTCTCCG	58.301	37.500	0.00	0.00	34.71	4.63
1556	1568	2.376109	GAGAGTGACGTCCCATCCTTA	58.624	52.381	14.12	0.00	0.00	2.69
1710	1800	3.128242	GCCAGTCACATCTTCCAAATCAG	59.872	47.826	0.00	0.00	0.00	2.90
1723	1813	5.710513	TCCAAATCAGTTCTCATGGTTTG	57.289	39.130	4.99	4.99	44.65	2.93
1998	2088	9.183368	GACAATCTTTTATTTGGAGAGATTCCT	57.817	33.333	0.00	0.00	46.92	3.36
2051	2141	3.777465	TCTCGGTCTGTCGGAAAATAG	57.223	47.619	0.00	0.00	0.00	1.73
2099	2189	8.169977	TCTCTTATCTTTGCAAAACTCACATT	57.830	30.769	13.84	0.00	0.00	2.71
2202	2298	1.767759	AACTGGAACTTGCAAGCAGT	58.232	45.000	26.27	25.03	31.19	4.40
2209	2305	0.944386	ACTTGCAAGCAGTGGTAACG	59.056	50.000	26.27	0.00	42.51	3.18
2447	2543	5.152934	AGTTCTGGGTAGTAACTCCTTTGA	58.847	41.667	0.00	0.00	0.00	2.69
2718	2814	7.648142	TGTCAAACATCATTGGTCTAAAACTC	58.352	34.615	0.00	0.00	0.00	3.01
2831	2927	6.127619	GGGAAAATTCCTGAGAAGTTATGTGG	60.128	42.308	11.75	0.00	46.72	4.17
2975	3071	0.742505	ATTCCGTCGGAAGTATGCGA	59.257	50.000	29.12	6.67	45.48	5.10
3186	3282	4.195416	CAAAGCTGATAGGGAAGTCCTTC	58.805	47.826	0.00	0.00	45.47	3.46
3408	3504	0.040058	TCAATGTCATTGGGCTGCCT	59.960	50.000	22.44	0.00	40.61	4.75
3447	3543	1.531365	CAAGGGCAGGCAGGACAAA	60.531	57.895	0.00	0.00	0.00	2.83
3707	3806	2.191354	CTTGCGGTGTCAGTGGCATG	62.191	60.000	0.00	0.00	35.03	4.06
3717	3816	0.390124	CAGTGGCATGCAACAACCTT	59.610	50.000	26.79	2.79	0.00	3.50
3763	3862	3.196254	GGGGCAGTTCATCACATTTGATT	59.804	43.478	0.00	0.00	40.79	2.57
3764	3863	4.322953	GGGGCAGTTCATCACATTTGATTT	60.323	41.667	0.00	0.00	40.79	2.17
3821	3929	4.443315	CCCACCATTGAAAAAGAGTTGCTT	60.443	41.667	0.00	0.00	38.88	3.91
3824	3932	4.571984	ACCATTGAAAAAGAGTTGCTTTGC	59.428	37.500	0.00	0.00	45.85	3.68
3828	3936	2.105323	AAAAGAGTTGCTTTGCGACG	57.895	45.000	4.52	0.00	45.85	5.12
3862	3970	3.997021	TGAGCTCGAAGAAAATGGAGAAC	59.003	43.478	9.64	0.00	34.09	3.01
3864	3972	3.999663	AGCTCGAAGAAAATGGAGAACAG	59.000	43.478	0.00	0.00	34.09	3.16
3880	3991	5.586643	GGAGAACAGGATGATAAAGTTGGTC	59.413	44.000	0.00	0.00	39.69	4.02
3970	4081	2.143925	ACTTTAAGACAAGCTGGCGAC	58.856	47.619	0.00	0.00	0.00	5.19
4128	4239	8.803235	TGTGTGATACTAGTAGAACAACTCAAT	58.197	33.333	17.53	0.00	0.00	2.57
4139	4250	3.078594	ACAACTCAATTCAACGGTTGC	57.921	42.857	15.89	0.00	40.29	4.17
4140	4251	2.425312	ACAACTCAATTCAACGGTTGCA	59.575	40.909	15.89	5.78	40.29	4.08
4352	4474	9.515226	TTAAGCCACTTTCTTAGTCATTGTTAT	57.485	29.630	0.00	0.00	33.85	1.89
4361	4483	9.719355	TTTCTTAGTCATTGTTATCTGCAACTA	57.281	29.630	0.00	0.00	0.00	2.24
4368	4490	5.414789	TTGTTATCTGCAACTAGTAGGCA	57.585	39.130	18.01	18.01	35.96	4.75
4371	4493	6.749139	TGTTATCTGCAACTAGTAGGCATAG	58.251	40.000	19.00	10.95	36.87	2.23
4378	4500	0.528470	CTAGTAGGCATAGGAGCGGC	59.472	60.000	0.00	0.00	34.64	6.53
4423	4545	3.133691	CCTATGCATGCATCTACGTTGT	58.866	45.455	35.35	13.09	37.82	3.32
4424	4546	3.561310	CCTATGCATGCATCTACGTTGTT	59.439	43.478	35.35	12.31	37.82	2.83
4487	4609	1.003839	CCAGCTGGCCACGTAGAAA	60.004	57.895	22.33	0.00	0.00	2.52
4528	4650	8.873215	ATCATTGTACGATCAAGGTAGTTTAG	57.127	34.615	0.00	0.00	32.13	1.85
4529	4651	8.058667	TCATTGTACGATCAAGGTAGTTTAGA	57.941	34.615	0.00	0.00	32.13	2.10
4586	4708	7.176515	ACATGAAAACTCAATACCTGCATTACA	59.823	33.333	0.00	0.00	0.00	2.41
4711	4833	5.568482	TGTCTTTTGAAATTCGGCATATCG	58.432	37.500	0.00	0.00	0.00	2.92
4720	4842	0.668535	TCGGCATATCGTGTCTCTGG	59.331	55.000	0.00	0.00	0.00	3.86
4906	5028	7.881142	TCGTTGATCAAAGATGGTTATGTTTT	58.119	30.769	18.50	0.00	28.23	2.43
4979	5101	5.879223	GGAGAATGATGTGATTGACTTGACT	59.121	40.000	0.00	0.00	0.00	3.41
5299	5421	1.139520	GGTTGTTGCGGGATGATGC	59.860	57.895	0.00	0.00	0.00	3.91
5319	5441	6.821160	TGATGCATTACGGAATGAGTAAAGAA	59.179	34.615	24.73	0.00	44.59	2.52
5332	5454	5.310451	TGAGTAAAGAAACTTGCCGGTAAT	58.690	37.500	5.11	0.00	0.00	1.89
5350	5472	6.868864	CCGGTAATGAGATTGAACTAGGTATG	59.131	42.308	0.00	0.00	0.00	2.39
5352	5474	7.471539	CGGTAATGAGATTGAACTAGGTATGGT	60.472	40.741	0.00	0.00	0.00	3.55
5434	5556	5.645929	TGTTGTTATGCTGTTTGACCGATAT	59.354	36.000	0.00	0.00	0.00	1.63

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
303	304	1.341156	ATCTAGACACCCAGCCCAGC	61.341	60.000	0.00	0.00	0.00	4.85
482	485	5.183140	CCCCTTTGTACAATTGTAGTTCAGG	59.817	44.000	18.56	18.37	0.00	3.86
895	899	4.908601	TGTTGATTAGCTCAAGAAGGGA	57.091	40.909	0.00	0.00	44.44	4.20
917	921	4.202419	ACTGAGCCAAGTACACATACCAAA	60.202	41.667	0.00	0.00	30.88	3.28
921	925	4.177026	CTGACTGAGCCAAGTACACATAC	58.823	47.826	0.00	0.00	0.00	2.39
922	926	3.832490	ACTGACTGAGCCAAGTACACATA	59.168	43.478	0.00	0.00	0.00	2.29
923	927	2.634940	ACTGACTGAGCCAAGTACACAT	59.365	45.455	0.00	0.00	0.00	3.21
924	928	2.035961	GACTGACTGAGCCAAGTACACA	59.964	50.000	0.00	0.00	0.00	3.72
925	929	2.610727	GGACTGACTGAGCCAAGTACAC	60.611	54.545	0.00	0.00	0.00	2.90
926	930	1.618837	GGACTGACTGAGCCAAGTACA	59.381	52.381	0.00	0.00	0.00	2.90
927	931	1.896465	AGGACTGACTGAGCCAAGTAC	59.104	52.381	0.00	0.00	0.00	2.73
928	932	2.171840	GAGGACTGACTGAGCCAAGTA	58.828	52.381	0.00	0.00	0.00	2.24
955	959	1.075374	TGCTAACTGGCCAGGTCAAAT	59.925	47.619	35.42	11.84	0.00	2.32
984	988	1.421410	GCATGGTCCTTGCTCGTACG	61.421	60.000	19.91	9.53	37.14	3.67
986	990	1.220749	GGCATGGTCCTTGCTCGTA	59.779	57.895	24.56	0.00	40.03	3.43
987	991	2.045926	GGCATGGTCCTTGCTCGT	60.046	61.111	24.56	0.00	40.03	4.18
988	992	3.197790	CGGCATGGTCCTTGCTCG	61.198	66.667	24.56	21.48	40.03	5.03
1029	1033	1.143813	AGCATAGTAGCAGGGCCATT	58.856	50.000	6.18	0.00	36.85	3.16
1054	1058	2.111878	GCCGCCACTGGATAGCAT	59.888	61.111	0.00	0.00	0.00	3.79
1079	1083	4.489771	CATCGTCCCTGCACCCCC	62.490	72.222	0.00	0.00	0.00	5.40
1084	1088	2.060383	CCCTCTCATCGTCCCTGCA	61.060	63.158	0.00	0.00	0.00	4.41
1095	1099	2.676822	AGAAGCGTCGCCCTCTCA	60.677	61.111	14.86	0.00	0.00	3.27
1144	1148	0.811616	GTGCTATTCCAGTCCAGCGG	60.812	60.000	0.00	0.00	36.81	5.52
1218	1228	2.490148	TATGCTGAGGTCGAGGCCG	61.490	63.158	0.00	0.00	37.07	6.13
1236	1246	0.692476	TGGAGGCAATACTGTGCAGT	59.308	50.000	9.90	9.90	46.81	4.40
1259	1269	0.036294	GGTGGTGTTGAGTAGGCCTC	60.036	60.000	9.68	0.21	40.89	4.70
1363	1373	4.478203	TGGATGAATCTAGAGAGTCTGGG	58.522	47.826	0.00	0.00	39.62	4.45
1383	1393	5.799681	AATTTGTTTGAAAACTGCACTGG	57.200	34.783	7.39	0.00	39.59	4.00
1384	1394	6.847289	GCATAATTTGTTTGAAAACTGCACTG	59.153	34.615	7.39	0.85	39.59	3.66
1387	1397	6.538021	ACAGCATAATTTGTTTGAAAACTGCA	59.462	30.769	14.24	0.00	39.59	4.41
1390	1400	8.947055	AGAACAGCATAATTTGTTTGAAAACT	57.053	26.923	7.39	0.00	37.63	2.66
1401	1411	2.722094	TGCCGGAGAACAGCATAATTT	58.278	42.857	5.05	0.00	0.00	1.82
1418	1428	4.335400	TGAGGAAAAAGGAACATTTGCC	57.665	40.909	0.00	0.00	44.60	4.52
1526	1538	4.941873	GGGACGTCACTCTCCATTAATTTT	59.058	41.667	18.91	0.00	0.00	1.82
1556	1568	2.538449	CCGTAGCGATAAAATTGCGACT	59.462	45.455	9.68	0.00	44.54	4.18
1636	1648	7.444703	AATACTCCTCAGGCTAAGAGAAATT	57.555	36.000	12.88	9.42	35.09	1.82
1638	1650	6.875972	AAATACTCCTCAGGCTAAGAGAAA	57.124	37.500	12.88	3.41	35.09	2.52
1647	1659	7.021790	CGAAAAAGTTTAAATACTCCTCAGGC	58.978	38.462	0.00	0.00	0.00	4.85
1710	1800	1.547372	AGCATGCCAAACCATGAGAAC	59.453	47.619	15.66	0.00	44.12	3.01
1723	1813	4.963276	TCTGTACAATAAACAGCATGCC	57.037	40.909	15.66	0.00	43.30	4.40
1724	1814	5.796935	CAGTTCTGTACAATAAACAGCATGC	59.203	40.000	10.51	10.51	43.30	4.06
1839	1929	7.761409	ACACATACGATGCATCATTTACTTTT	58.239	30.769	25.70	0.00	0.00	2.27
1840	1930	7.320443	ACACATACGATGCATCATTTACTTT	57.680	32.000	25.70	1.26	0.00	2.66
1998	2088	4.794278	AGTCAGATTTTGCATGCATGAA	57.206	36.364	30.64	18.49	0.00	2.57
2062	2152	6.884836	GCAAAGATAAGAGAGGGGAACTTTAA	59.115	38.462	0.00	0.00	0.00	1.52
2099	2189	3.869065	ACGAGTGAAAGTTTCTCCAACA	58.131	40.909	16.33	0.00	37.93	3.33
2202	2298	2.839975	TGCACATGAAAGTCGTTACCA	58.160	42.857	0.00	0.00	0.00	3.25
2209	2305	4.818534	TCTCAGTTTGCACATGAAAGTC	57.181	40.909	0.00	0.00	0.00	3.01
2329	2425	6.932356	ATCGACCGACTCTAGTTTATGTTA	57.068	37.500	0.00	0.00	0.00	2.41
2447	2543	1.081174	TGGATGGAGGAAGAGGACCTT	59.919	52.381	0.00	0.00	37.93	3.50
2459	2555	3.244561	ACTGGTGTGTACTTTGGATGGAG	60.245	47.826	0.00	0.00	0.00	3.86
2831	2927	7.776933	TCAAATGTCATAAGTATCAGACTGC	57.223	36.000	0.00	0.00	38.87	4.40
2981	3077	5.723295	ACACATCAAGAAACACAAGCTTTT	58.277	33.333	0.00	0.00	0.00	2.27
3300	3396	0.183731	GGCATAAAGGTAGCTGCCCT	59.816	55.000	18.24	9.17	46.76	5.19
3319	3415	4.692625	GTCATCGGATCCCATAATGTTCAG	59.307	45.833	6.06	0.00	0.00	3.02
3384	3480	4.365723	GCAGCCCAATGACATTGAATAAG	58.634	43.478	26.36	13.99	42.83	1.73
3408	3504	5.440207	TGGTCATGAATTCCTCTTGATCA	57.560	39.130	2.27	5.03	43.52	2.92
3447	3543	6.442564	TGTAGTTGAGTATGTTTCCCCTGTAT	59.557	38.462	0.00	0.00	0.00	2.29
3717	3816	0.178926	TTCCCGGTGTAGGACCAGAA	60.179	55.000	0.00	0.00	46.55	3.02
3763	3862	0.034756	TTGCCTTCGTAGCTGCTCAA	59.965	50.000	4.91	0.00	0.00	3.02
3764	3863	0.250234	ATTGCCTTCGTAGCTGCTCA	59.750	50.000	4.91	0.00	0.00	4.26
3828	3936	1.590259	GAGCTCAGGAATCGACGGC	60.590	63.158	9.40	0.00	0.00	5.68
3862	3970	8.859236	ATGATATGACCAACTTTATCATCCTG	57.141	34.615	0.00	0.00	34.86	3.86
3864	3972	9.950496	AGTATGATATGACCAACTTTATCATCC	57.050	33.333	7.37	0.00	36.45	3.51
3880	3991	6.486248	CCGAACAACCAAACAGTATGATATG	58.514	40.000	0.00	0.00	39.69	1.78
3970	4081	2.287547	CCACAACAGAAAACCATGACCG	60.288	50.000	0.00	0.00	0.00	4.79
4123	4234	3.003689	AGTTCTGCAACCGTTGAATTGAG	59.996	43.478	15.63	2.61	32.22	3.02
4128	4239	5.508200	AAATAAGTTCTGCAACCGTTGAA	57.492	34.783	15.63	3.29	32.22	2.69
4225	4344	3.949842	TCACATCTTGAGAGTCCACTG	57.050	47.619	0.00	0.00	0.00	3.66
4227	4346	3.993081	CACTTCACATCTTGAGAGTCCAC	59.007	47.826	0.00	0.00	34.94	4.02
4289	4411	2.827921	AGATTTGGAAAAGCATCGCCTT	59.172	40.909	0.00	0.00	0.00	4.35
4290	4412	2.450476	AGATTTGGAAAAGCATCGCCT	58.550	42.857	0.00	0.00	0.00	5.52
4291	4413	2.925563	CAAGATTTGGAAAAGCATCGCC	59.074	45.455	0.00	0.00	0.00	5.54
4352	4474	3.891977	CTCCTATGCCTACTAGTTGCAGA	59.108	47.826	20.20	16.24	38.58	4.26
4361	4483	2.565645	CGCCGCTCCTATGCCTACT	61.566	63.158	0.00	0.00	0.00	2.57
4393	4515	1.450531	GCATGCATAGGCTCCACCAC	61.451	60.000	14.21	0.00	43.14	4.16
4405	4527	4.439305	AAAACAACGTAGATGCATGCAT	57.561	36.364	32.66	32.66	39.69	3.96
4455	4577	1.603739	GCTGGACCTCAAACCCACC	60.604	63.158	0.00	0.00	0.00	4.61
4487	4609	8.873830	CGTACAATGATCAAAGAGTACAAAGAT	58.126	33.333	20.44	0.00	33.35	2.40
4528	4650	7.730364	TTGAGGATGTTTCTTACTCTGTTTC	57.270	36.000	0.00	0.00	0.00	2.78
4529	4651	8.697507	AATTGAGGATGTTTCTTACTCTGTTT	57.302	30.769	0.00	0.00	0.00	2.83
4586	4708	7.773690	TGCTTCTGTTCTTAGGTTCTTAAAACT	59.226	33.333	0.00	0.00	36.14	2.66
4646	4768	8.844865	TGCATGATTACATACCTCCTATATCT	57.155	34.615	0.00	0.00	35.09	1.98
4650	4772	9.017509	CAAAATGCATGATTACATACCTCCTAT	57.982	33.333	0.00	0.00	35.09	2.57
4711	4833	3.471680	GGCATATTTCCTCCAGAGACAC	58.528	50.000	0.00	0.00	0.00	3.67
4811	4933	5.478233	TCACACATGTATTATGTTTCCGC	57.522	39.130	0.00	0.00	0.00	5.54
4979	5101	3.733988	CGAGTGCTAAGCTAACGGAATGA	60.734	47.826	0.00	0.00	0.00	2.57
5279	5401	1.176527	CATCATCCCGCAACAACCTT	58.823	50.000	0.00	0.00	0.00	3.50
5282	5404	0.457035	ATGCATCATCCCGCAACAAC	59.543	50.000	0.00	0.00	42.37	3.32
5299	5421	7.481798	GCAAGTTTCTTTACTCATTCCGTAATG	59.518	37.037	0.00	0.00	43.32	1.90
5319	5441	3.950397	TCAATCTCATTACCGGCAAGTT	58.050	40.909	0.00	0.00	0.00	2.66
5332	5454	7.952671	GTATCACCATACCTAGTTCAATCTCA	58.047	38.462	0.00	0.00	30.07	3.27
5350	5472	2.225963	AGATTCGATCGTCGGTATCACC	59.774	50.000	15.94	0.00	40.88	4.02
5352	5474	2.157085	CGAGATTCGATCGTCGGTATCA	59.843	50.000	15.94	0.00	43.74	2.15

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.