AutoCloner

Multiple sequence alignment - TraesCS1D01G443200

Loading Multiple Alignment...

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	TraesCS1D01G443200	chr1D	100.000	3743	0	0	1	3743	487225235	487221493	0.000000e+00	6913.0
1	TraesCS1D01G443200	chr1D	96.828	1734	39	6	1020	2753	427704710	427706427	0.000000e+00	2883.0
2	TraesCS1D01G443200	chr1D	92.451	1722	107	9	1025	2737	482993627	482991920	0.000000e+00	2438.0
3	TraesCS1D01G443200	chr1D	95.701	535	10	6	187	715	427703731	427704258	0.000000e+00	848.0
4	TraesCS1D01G443200	chr1D	92.647	272	14	3	759	1028	427704269	427704536	1.630000e-103	387.0
5	TraesCS1D01G443200	chr1D	90.204	245	18	3	3227	3470	482991703	482991464	7.800000e-82	315.0
6	TraesCS1D01G443200	chr1D	99.306	144	1	0	1	144	427703367	427703510	1.030000e-65	261.0
7	TraesCS1D01G443200	chr1D	85.496	262	19	9	384	627	482994374	482994114	4.800000e-64	255.0
8	TraesCS1D01G443200	chr1D	96.689	151	5	0	889	1039	482993791	482993641	6.210000e-63	252.0
9	TraesCS1D01G443200	chr1D	90.984	122	6	3	331	451	482994958	482994841	3.870000e-35	159.0
10	TraesCS1D01G443200	chr1D	85.600	125	18	0	759	883	415400371	415400247	8.440000e-27	132.0
11	TraesCS1D01G443200	chr1D	79.851	134	6	9	2785	2908	427706420	427706542	1.110000e-10	78.7
12	TraesCS1D01G443200	chr1B	93.183	2215	91	25	895	3089	678469693	678471867	0.000000e+00	3199.0
13	TraesCS1D01G443200	chr1B	93.317	1661	89	12	1080	2737	671258805	671260446	0.000000e+00	2433.0
14	TraesCS1D01G443200	chr1B	86.725	806	62	22	2952	3742	678472181	678472956	0.000000e+00	854.0
15	TraesCS1D01G443200	chr1B	84.396	455	25	18	331	751	671258183	671258625	4.500000e-109	405.0
16	TraesCS1D01G443200	chr1B	84.186	430	25	9	332	751	678469292	678469688	9.810000e-101	377.0
17	TraesCS1D01G443200	chr1B	91.892	111	3	4	2970	3080	671260710	671260814	2.330000e-32	150.0
18	TraesCS1D01G443200	chr1A	95.169	1801	65	8	967	2759	584809288	584807502	0.000000e+00	2824.0
19	TraesCS1D01G443200	chr1A	90.106	1890	120	28	902	2754	579171744	579173603	0.000000e+00	2392.0
20	TraesCS1D01G443200	chr1A	90.722	679	25	14	3093	3742	584807096	584806427	0.000000e+00	870.0
21	TraesCS1D01G443200	chr1A	86.490	681	48	27	82	742	584810096	584809440	0.000000e+00	708.0
22	TraesCS1D01G443200	chr1A	90.204	245	18	3	3227	3470	579173810	579174049	7.800000e-82	315.0
23	TraesCS1D01G443200	chr1A	84.559	272	21	9	2818	3089	584807402	584807152	2.230000e-62	250.0
24	TraesCS1D01G443200	chr1A	94.495	109	5	1	875	983	584809411	584809304	2.310000e-37	167.0
25	TraesCS1D01G443200	chr2D	90.476	1974	100	33	1080	3021	94868451	94870368	0.000000e+00	2523.0
26	TraesCS1D01G443200	chr2D	85.484	124	6	3	632	751	94868164	94868279	6.570000e-23	119.0
27	TraesCS1D01G443200	chr2D	84.034	119	17	1	760	876	204046991	204046873	3.060000e-21	113.0
28	TraesCS1D01G443200	chr2D	80.357	112	20	1	767	876	44460297	44460186	2.400000e-12	84.2
29	TraesCS1D01G443200	chr2B	91.362	1806	91	24	1034	2825	146716119	146717873	0.000000e+00	2410.0
30	TraesCS1D01G443200	chr2B	83.333	198	9	6	550	742	146715766	146715944	1.080000e-35	161.0
31	TraesCS1D01G443200	chr2B	94.286	35	2	0	847	881	718308619	718308585	2.000000e-03	54.7
32	TraesCS1D01G443200	chr7A	76.954	1497	318	21	1241	2731	517582000	517580525	0.000000e+00	828.0
33	TraesCS1D01G443200	chr6D	83.721	430	30	19	350	751	56206169	56206586	1.640000e-98	370.0
34	TraesCS1D01G443200	chr6D	82.121	330	25	17	350	665	56194745	56195054	6.210000e-63	252.0
35	TraesCS1D01G443200	chr6D	82.692	104	16	1	775	876	103525023	103524920	1.430000e-14	91.6
36	TraesCS1D01G443200	chrUn	84.426	122	15	2	759	877	58727926	58727806	2.360000e-22	117.0
37	TraesCS1D01G443200	chr6B	80.870	115	21	1	763	876	222582575	222582461	5.150000e-14	89.8
38	TraesCS1D01G443200	chr7D	82.828	99	15	1	767	863	215903480	215903382	1.850000e-13	87.9
39	TraesCS1D01G443200	chr7D	100.000	28	0	0	851	878	14878318	14878291	7.000000e-03	52.8
40	TraesCS1D01G443200	chr5B	85.915	71	10	0	760	830	106058919	106058989	4.010000e-10	76.8

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	TraesCS1D01G443200	chr1D	487221493	487225235	3742	True	6913.000000	6913	100.000000	1	3743	1	chr1D.!!$R2	3742
1	TraesCS1D01G443200	chr1D	427703367	427706542	3175	False	891.540000	2883	92.866600	1	2908	5	chr1D.!!$F1	2907
2	TraesCS1D01G443200	chr1D	482991464	482994958	3494	True	683.800000	2438	91.164800	331	3470	5	chr1D.!!$R3	3139
3	TraesCS1D01G443200	chr1B	678469292	678472956	3664	False	1476.666667	3199	88.031333	332	3742	3	chr1B.!!$F2	3410
4	TraesCS1D01G443200	chr1B	671258183	671260814	2631	False	996.000000	2433	89.868333	331	3080	3	chr1B.!!$F1	2749
5	TraesCS1D01G443200	chr1A	579171744	579174049	2305	False	1353.500000	2392	90.155000	902	3470	2	chr1A.!!$F1	2568
6	TraesCS1D01G443200	chr1A	584806427	584810096	3669	True	963.800000	2824	90.287000	82	3742	5	chr1A.!!$R1	3660
7	TraesCS1D01G443200	chr2D	94868164	94870368	2204	False	1321.000000	2523	87.980000	632	3021	2	chr2D.!!$F1	2389
8	TraesCS1D01G443200	chr2B	146715766	146717873	2107	False	1285.500000	2410	87.347500	550	2825	2	chr2B.!!$F1	2275
9	TraesCS1D01G443200	chr7A	517580525	517582000	1475	True	828.000000	828	76.954000	1241	2731	1	chr7A.!!$R1	1490

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
168	169	1.053424	AGGTCACGGGTGTATGTGTT	58.947	50.0	0.0	0.0	37.38	3.32	F
1208	2513	0.041576	GGTCAAAACACGCCGTCTTC	60.042	55.0	0.0	0.0	0.00	2.87	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2100	3415	0.107945	GCTCCGTCATTCCAAGCTCT	60.108	55.0	0.0	0.0	0.00	4.09	R
2983	4494	0.807667	GGACACACCTATCGCAGCAG	60.808	60.0	0.0	0.0	35.41	4.24	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
154	155	1.604308	TGAACGTCGGGCTAGGTCA	60.604	57.895	0.00	0.00	0.00	4.02
155	156	1.153881	GAACGTCGGGCTAGGTCAC	60.154	63.158	0.00	0.00	0.00	3.67
156	157	2.862347	GAACGTCGGGCTAGGTCACG	62.862	65.000	0.00	0.00	36.54	4.35
162	163	1.683365	GGGCTAGGTCACGGGTGTA	60.683	63.158	0.00	0.00	0.00	2.90
166	167	1.470979	GCTAGGTCACGGGTGTATGTG	60.471	57.143	0.00	0.00	37.44	3.21
168	169	1.053424	AGGTCACGGGTGTATGTGTT	58.947	50.000	0.00	0.00	37.38	3.32
295	474	1.265095	GCACCATATGACCAGAATGCG	59.735	52.381	3.65	0.00	31.97	4.73
303	482	4.689612	ATGACCAGAATGCGGTTATACT	57.310	40.909	0.00	0.00	36.69	2.12
358	539	3.786213	ATTGGGGCCCCTACAAATTTA	57.214	42.857	40.66	15.63	36.94	1.40
468	655	8.506168	TGTTGAGTGAGTTAACAAAAAGATCT	57.494	30.769	8.61	0.00	31.95	2.75
469	656	8.612619	TGTTGAGTGAGTTAACAAAAAGATCTC	58.387	33.333	8.61	4.91	31.95	2.75
470	657	7.730364	TGAGTGAGTTAACAAAAAGATCTCC	57.270	36.000	8.61	0.00	0.00	3.71
471	658	6.710744	TGAGTGAGTTAACAAAAAGATCTCCC	59.289	38.462	8.61	0.00	0.00	4.30
472	659	6.842676	AGTGAGTTAACAAAAAGATCTCCCT	58.157	36.000	8.61	0.00	0.00	4.20
473	660	6.937465	AGTGAGTTAACAAAAAGATCTCCCTC	59.063	38.462	8.61	0.00	0.00	4.30
486	678	4.956075	AGATCTCCCTCTCTCTCTGTTTTC	59.044	45.833	0.00	0.00	0.00	2.29
600	816	1.064952	ACGAGAAAACCAAAACAGCCG	59.935	47.619	0.00	0.00	0.00	5.52
769	1014	4.519730	ACTCTCGGCTATTATGGACTACAC	59.480	45.833	0.00	0.00	0.00	2.90
790	1035	5.817296	ACACACGAATGTATGTAGATGCATT	59.183	36.000	14.65	14.65	44.75	3.56
791	1036	6.316140	ACACACGAATGTATGTAGATGCATTT	59.684	34.615	15.62	0.00	42.85	2.32
819	1064	6.313905	AGTGTAGATTAACTGATTTTGCTCCG	59.686	38.462	0.00	0.00	0.00	4.63
826	1071	3.009723	ACTGATTTTGCTCCGTATGTGG	58.990	45.455	0.00	0.00	0.00	4.17
828	1073	3.417101	TGATTTTGCTCCGTATGTGGTT	58.583	40.909	0.00	0.00	0.00	3.67
830	1075	1.434555	TTTGCTCCGTATGTGGTTCG	58.565	50.000	0.00	0.00	0.00	3.95
838	1083	4.732784	TCCGTATGTGGTTCGTAGTAAAC	58.267	43.478	0.00	0.00	0.00	2.01
849	1094	7.637519	GTGGTTCGTAGTAAACTTTCTTCAAAC	59.362	37.037	0.00	0.00	0.00	2.93
851	1096	7.637519	GGTTCGTAGTAAACTTTCTTCAAACAC	59.362	37.037	0.00	0.00	0.00	3.32
876	1121	3.712091	ATTTAGGAACGGAGCGAGTAG	57.288	47.619	0.00	0.00	0.00	2.57
1082	2368	1.664965	CCGCCTTCTACATAGCGCC	60.665	63.158	2.29	0.00	46.90	6.53
1123	2422	2.960384	TGTGGATCAATCAATCATGGCC	59.040	45.455	0.00	0.00	0.00	5.36
1124	2423	2.960384	GTGGATCAATCAATCATGGCCA	59.040	45.455	8.56	8.56	0.00	5.36
1125	2424	3.005472	GTGGATCAATCAATCATGGCCAG	59.995	47.826	13.05	3.43	0.00	4.85
1126	2425	2.561419	GGATCAATCAATCATGGCCAGG	59.439	50.000	12.23	12.23	0.00	4.45
1127	2426	3.493334	GATCAATCAATCATGGCCAGGA	58.507	45.455	24.33	24.33	0.00	3.86
1128	2427	2.940158	TCAATCAATCATGGCCAGGAG	58.060	47.619	26.03	13.20	0.00	3.69
1129	2428	1.340248	CAATCAATCATGGCCAGGAGC	59.660	52.381	26.03	0.00	42.60	4.70
1208	2513	0.041576	GGTCAAAACACGCCGTCTTC	60.042	55.000	0.00	0.00	0.00	2.87
1209	2514	0.935196	GTCAAAACACGCCGTCTTCT	59.065	50.000	0.00	0.00	0.00	2.85
1210	2515	1.329599	GTCAAAACACGCCGTCTTCTT	59.670	47.619	0.00	0.00	0.00	2.52
1218	2523	0.640768	CGCCGTCTTCTTTAGCTTCG	59.359	55.000	0.00	0.00	0.00	3.79
1220	2525	1.921230	GCCGTCTTCTTTAGCTTCGAG	59.079	52.381	0.00	0.00	0.00	4.04
1292	2597	2.365635	CCTCATCCAGACCCCGGT	60.366	66.667	0.00	0.00	0.00	5.28
1342	2650	4.918201	CCGCCTGGAATCTCCGCC	62.918	72.222	0.00	0.00	40.17	6.13
1416	2724	3.036084	CACGTGCAGACCACCGTC	61.036	66.667	0.82	0.00	41.53	4.79
1419	2727	4.295119	GTGCAGACCACCGTCCGT	62.295	66.667	0.00	0.00	40.12	4.69
2100	3415	0.252761	TCATGCAAGATCGCTTCCCA	59.747	50.000	0.00	0.00	30.14	4.37
2759	4083	6.179906	ACCGTAGATTCCATTTGATCTGAT	57.820	37.500	0.00	0.00	0.00	2.90
2760	4084	6.226787	ACCGTAGATTCCATTTGATCTGATC	58.773	40.000	10.72	10.72	0.00	2.92
2761	4085	6.042552	ACCGTAGATTCCATTTGATCTGATCT	59.957	38.462	17.82	0.00	0.00	2.75
2762	4086	6.368243	CCGTAGATTCCATTTGATCTGATCTG	59.632	42.308	17.82	8.49	0.00	2.90
2763	4087	7.150640	CGTAGATTCCATTTGATCTGATCTGA	58.849	38.462	17.82	4.63	0.00	3.27
2778	4102	2.936919	TCTGATATGGGCGCTTTCAT	57.063	45.000	7.64	11.67	0.00	2.57
2779	4103	3.213206	TCTGATATGGGCGCTTTCATT	57.787	42.857	7.64	1.12	0.00	2.57
2780	4104	3.554934	TCTGATATGGGCGCTTTCATTT	58.445	40.909	7.64	4.56	0.00	2.32
2781	4105	3.565482	TCTGATATGGGCGCTTTCATTTC	59.435	43.478	7.64	13.38	0.00	2.17
2782	4106	3.554934	TGATATGGGCGCTTTCATTTCT	58.445	40.909	7.64	0.00	0.00	2.52
2783	4107	3.953612	TGATATGGGCGCTTTCATTTCTT	59.046	39.130	7.64	0.00	0.00	2.52
2791	4115	5.333339	GGGCGCTTTCATTTCTTTTTCTTTC	60.333	40.000	7.64	0.00	0.00	2.62
2829	4221	3.307674	TGATTGTCTTTGCATGTTTCGC	58.692	40.909	0.00	0.00	0.00	4.70
2835	4227	2.226437	TCTTTGCATGTTTCGCCTCTTC	59.774	45.455	0.00	0.00	0.00	2.87
2853	4247	2.910688	TCATTTCGGTCTCTATGGCC	57.089	50.000	0.00	0.00	37.00	5.36
2877	4274	2.535012	TGTTGTGCGTCTTGGTGATA	57.465	45.000	0.00	0.00	0.00	2.15
2981	4492	0.250640	AAGCTGTGACTGGGCTCTTG	60.251	55.000	0.00	0.00	35.06	3.02
2982	4493	1.673665	GCTGTGACTGGGCTCTTGG	60.674	63.158	0.00	0.00	0.00	3.61
2983	4494	1.673665	CTGTGACTGGGCTCTTGGC	60.674	63.158	0.00	0.00	40.90	4.52
3014	4525	0.317020	GTGTGTCCTTGCACGAAAGC	60.317	55.000	0.00	0.00	41.94	3.51
3016	4527	1.153066	TGTCCTTGCACGAAAGCCA	60.153	52.632	0.00	0.00	0.00	4.75
3017	4528	1.282875	GTCCTTGCACGAAAGCCAC	59.717	57.895	0.00	0.00	0.00	5.01
3018	4529	1.148273	TCCTTGCACGAAAGCCACT	59.852	52.632	0.00	0.00	0.00	4.00
3066	4577	2.354188	TCGAACACAGCACGGACG	60.354	61.111	0.00	0.00	0.00	4.79
3090	4601	6.996562	CGCAATCAAATGTGCATATTACAT	57.003	33.333	9.27	1.94	40.94	2.29
3124	5073	5.407084	AGCAAATTAAAAATACCAACGGTGC	59.593	36.000	0.00	0.00	36.19	5.01
3176	5134	3.250744	TGTGCTATTCTGCGTCAAGTAC	58.749	45.455	0.00	0.00	35.36	2.73
3217	5175	5.801380	AGGATAAAACGGTACATGTGAACT	58.199	37.500	9.11	0.00	0.00	3.01
3218	5176	6.938507	AGGATAAAACGGTACATGTGAACTA	58.061	36.000	9.11	0.00	0.00	2.24
3219	5177	6.815142	AGGATAAAACGGTACATGTGAACTAC	59.185	38.462	9.11	0.00	0.00	2.73
3256	5214	4.141287	ACTGAAGGAGATGACTAGATCCG	58.859	47.826	0.00	0.00	36.91	4.18
3257	5215	4.141367	ACTGAAGGAGATGACTAGATCCGA	60.141	45.833	0.00	0.00	36.91	4.55
3258	5216	4.138290	TGAAGGAGATGACTAGATCCGAC	58.862	47.826	0.00	0.00	36.91	4.79
3259	5217	3.149005	AGGAGATGACTAGATCCGACC	57.851	52.381	0.00	0.00	36.91	4.79
3260	5218	2.443632	AGGAGATGACTAGATCCGACCA	59.556	50.000	0.00	0.00	36.91	4.02
3261	5219	3.117474	AGGAGATGACTAGATCCGACCAA	60.117	47.826	0.00	0.00	36.91	3.67
3262	5220	3.254657	GGAGATGACTAGATCCGACCAAG	59.745	52.174	0.00	0.00	0.00	3.61
3270	5230	4.717280	ACTAGATCCGACCAAGAAGGAAAT	59.283	41.667	0.00	0.00	41.22	2.17
3358	5319	4.464008	TCATTACCATGATTCAGAAGGGC	58.536	43.478	0.00	0.00	34.22	5.19
3457	5418	3.509967	AGACCGACATCAATGTGACTACA	59.490	43.478	0.00	0.00	41.95	2.74
3545	5526	2.568696	AGATCCACATTGACGTCGAG	57.431	50.000	11.90	5.92	0.00	4.04
3630	5612	0.681733	GCTAGGCCCTCGATCATTCA	59.318	55.000	0.00	0.00	0.00	2.57
3658	5640	2.100631	GGCATCCCTTCACGACGTG	61.101	63.158	21.88	21.88	34.45	4.49

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
8	9	0.254178	CCCACTTGTCAGGATGGAGG	59.746	60.000	5.51	0.00	36.16	4.30
172	173	3.988525	AGCCGGCGCATGCAAAAA	61.989	55.556	23.20	0.00	45.35	1.94
316	496	7.414540	CCAATTTCTAATTGAGGTCTGCTGTAC	60.415	40.741	12.43	0.00	0.00	2.90
358	539	3.322466	CGACAGAACAGGGCCCCT	61.322	66.667	21.43	5.02	0.00	4.79
439	622	8.735315	TCTTTTTGTTAACTCACTCAACATTCA	58.265	29.630	7.22	0.00	32.57	2.57
468	655	3.260269	TGGAAAACAGAGAGAGAGGGA	57.740	47.619	0.00	0.00	0.00	4.20
469	656	4.357918	TTTGGAAAACAGAGAGAGAGGG	57.642	45.455	0.00	0.00	0.00	4.30
513	728	6.655062	TGAGTAACTTTTGTTCGCAACATAG	58.345	36.000	3.15	6.42	42.45	2.23
600	816	0.966179	AAAACGGAACCATTGGGCTC	59.034	50.000	7.78	3.16	37.90	4.70
634	854	3.010420	GCCTACCTTCAGTGAACCATTC	58.990	50.000	0.08	0.00	0.00	2.67
635	855	2.615493	CGCCTACCTTCAGTGAACCATT	60.615	50.000	0.08	0.00	0.00	3.16
636	856	1.066143	CGCCTACCTTCAGTGAACCAT	60.066	52.381	0.08	0.00	0.00	3.55
645	865	1.200519	ATTGCCTACGCCTACCTTCA	58.799	50.000	0.00	0.00	0.00	3.02
736	972	9.823647	CCATAATAGCCGAGAGTTCAATATATT	57.176	33.333	0.00	0.00	0.00	1.28
751	996	3.004002	TCGTGTGTAGTCCATAATAGCCG	59.996	47.826	0.00	0.00	0.00	5.52
754	999	9.129209	CATACATTCGTGTGTAGTCCATAATAG	57.871	37.037	8.23	0.00	37.93	1.73
755	1000	8.635328	ACATACATTCGTGTGTAGTCCATAATA	58.365	33.333	8.23	0.00	44.68	0.98
757	1002	6.869695	ACATACATTCGTGTGTAGTCCATAA	58.130	36.000	8.23	0.00	44.68	1.90
769	1014	9.373750	CTTAAAATGCATCTACATACATTCGTG	57.626	33.333	0.00	0.00	31.75	4.35
804	1049	3.440173	CCACATACGGAGCAAAATCAGTT	59.560	43.478	0.00	0.00	0.00	3.16
805	1050	3.009723	CCACATACGGAGCAAAATCAGT	58.990	45.455	0.00	0.00	0.00	3.41
806	1051	3.009723	ACCACATACGGAGCAAAATCAG	58.990	45.455	0.00	0.00	0.00	2.90
807	1052	3.066291	ACCACATACGGAGCAAAATCA	57.934	42.857	0.00	0.00	0.00	2.57
808	1053	3.485216	CGAACCACATACGGAGCAAAATC	60.485	47.826	0.00	0.00	0.00	2.17
817	1062	4.737054	AGTTTACTACGAACCACATACGG	58.263	43.478	0.00	0.00	0.00	4.02
819	1064	7.880059	AGAAAGTTTACTACGAACCACATAC	57.120	36.000	0.00	0.00	0.00	2.39
826	1071	8.385858	AGTGTTTGAAGAAAGTTTACTACGAAC	58.614	33.333	0.00	0.00	0.00	3.95
828	1073	8.483307	AAGTGTTTGAAGAAAGTTTACTACGA	57.517	30.769	0.00	0.00	0.00	3.43
849	1094	5.526115	TCGCTCCGTTCCTAAATATAAGTG	58.474	41.667	0.00	0.00	0.00	3.16
851	1096	5.770417	ACTCGCTCCGTTCCTAAATATAAG	58.230	41.667	0.00	0.00	0.00	1.73
1061	2328	0.941463	CGCTATGTAGAAGGCGGCAG	60.941	60.000	13.08	0.00	43.25	4.85
1123	2422	4.087892	CGGTGTCCTGGGCTCCTG	62.088	72.222	16.60	7.23	0.00	3.86
1124	2423	4.316823	TCGGTGTCCTGGGCTCCT	62.317	66.667	16.60	0.00	0.00	3.69
1125	2424	3.775654	CTCGGTGTCCTGGGCTCC	61.776	72.222	9.34	9.34	0.00	4.70
1126	2425	3.775654	CCTCGGTGTCCTGGGCTC	61.776	72.222	0.00	0.00	0.00	4.70
1127	2426	4.316823	TCCTCGGTGTCCTGGGCT	62.317	66.667	0.00	0.00	0.00	5.19
1128	2427	4.083862	GTCCTCGGTGTCCTGGGC	62.084	72.222	0.00	0.00	0.00	5.36
1129	2428	3.760035	CGTCCTCGGTGTCCTGGG	61.760	72.222	0.00	0.00	0.00	4.45
1130	2429	2.675423	TCGTCCTCGGTGTCCTGG	60.675	66.667	0.00	0.00	37.69	4.45
1203	2508	3.318017	TGCACTCGAAGCTAAAGAAGAC	58.682	45.455	10.42	0.00	0.00	3.01
1208	2513	2.412065	GCAGTTGCACTCGAAGCTAAAG	60.412	50.000	10.42	0.00	41.59	1.85
1209	2514	1.531149	GCAGTTGCACTCGAAGCTAAA	59.469	47.619	10.42	0.00	41.59	1.85
1210	2515	1.148310	GCAGTTGCACTCGAAGCTAA	58.852	50.000	10.42	1.94	41.59	3.09
1239	2544	1.380302	GGAGAGGCAGCCAAGGAAA	59.620	57.895	15.80	0.00	0.00	3.13
1292	2597	0.685458	GGCAGAGTAGGACGGGGTTA	60.685	60.000	0.00	0.00	0.00	2.85
1335	2643	3.785859	GGCAGGATGTGGCGGAGA	61.786	66.667	0.00	0.00	42.77	3.71
2100	3415	0.107945	GCTCCGTCATTCCAAGCTCT	60.108	55.000	0.00	0.00	0.00	4.09
2759	4083	2.936919	ATGAAAGCGCCCATATCAGA	57.063	45.000	2.29	0.00	0.00	3.27
2760	4084	3.567164	AGAAATGAAAGCGCCCATATCAG	59.433	43.478	2.29	0.00	0.00	2.90
2761	4085	3.554934	AGAAATGAAAGCGCCCATATCA	58.445	40.909	2.29	1.82	0.00	2.15
2762	4086	4.574599	AAGAAATGAAAGCGCCCATATC	57.425	40.909	2.29	0.00	0.00	1.63
2763	4087	5.343307	AAAAGAAATGAAAGCGCCCATAT	57.657	34.783	2.29	0.00	0.00	1.78
2778	4102	5.106317	ACTGCACACTCGAAAGAAAAAGAAA	60.106	36.000	0.00	0.00	41.32	2.52
2779	4103	4.394920	ACTGCACACTCGAAAGAAAAAGAA	59.605	37.500	0.00	0.00	41.32	2.52
2780	4104	3.938963	ACTGCACACTCGAAAGAAAAAGA	59.061	39.130	0.00	0.00	41.32	2.52
2781	4105	4.031028	CACTGCACACTCGAAAGAAAAAG	58.969	43.478	0.00	0.00	41.32	2.27
2782	4106	3.730662	GCACTGCACACTCGAAAGAAAAA	60.731	43.478	0.00	0.00	41.32	1.94
2783	4107	2.223249	GCACTGCACACTCGAAAGAAAA	60.223	45.455	0.00	0.00	41.32	2.29
2791	4115	2.025969	CAGGAGCACTGCACACTCG	61.026	63.158	3.30	0.00	40.97	4.18
2829	4221	4.626042	CCATAGAGACCGAAATGAAGAGG	58.374	47.826	0.00	0.00	0.00	3.69
2835	4227	2.620251	TGGCCATAGAGACCGAAATG	57.380	50.000	0.00	0.00	0.00	2.32
2853	4247	2.535166	CACCAAGACGCACAACATTTTG	59.465	45.455	0.00	0.00	38.83	2.44
2877	4274	5.530915	CCACCCATGATTATAAACACGTCAT	59.469	40.000	0.00	0.00	0.00	3.06
2929	4341	8.426489	AGGGACAATATCATTCCATTTCATTTG	58.574	33.333	0.00	0.00	0.00	2.32
2934	4346	7.785033	ACAAAGGGACAATATCATTCCATTTC	58.215	34.615	6.80	0.00	40.51	2.17
2981	4492	2.176273	CACACCTATCGCAGCAGCC	61.176	63.158	0.00	0.00	37.52	4.85
2982	4493	1.424493	GACACACCTATCGCAGCAGC	61.424	60.000	0.00	0.00	37.42	5.25
2983	4494	0.807667	GGACACACCTATCGCAGCAG	60.808	60.000	0.00	0.00	35.41	4.24
3014	4525	6.480320	GCCATCTTTGATTGTAGTAGTAGTGG	59.520	42.308	0.00	0.00	0.00	4.00
3016	4527	7.343316	AGAGCCATCTTTGATTGTAGTAGTAGT	59.657	37.037	0.00	0.00	28.57	2.73
3017	4528	7.721402	AGAGCCATCTTTGATTGTAGTAGTAG	58.279	38.462	0.00	0.00	28.57	2.57
3018	4529	7.661536	AGAGCCATCTTTGATTGTAGTAGTA	57.338	36.000	0.00	0.00	28.57	1.82
3066	4577	4.739228	TGTAATATGCACATTTGATTGCGC	59.261	37.500	0.00	0.00	41.96	6.09
3124	5073	1.135315	CGCATTCCAATGACCAACCAG	60.135	52.381	3.35	0.00	38.70	4.00
3176	5134	1.607148	CCTCATGCATGCACACTATGG	59.393	52.381	25.37	15.06	0.00	2.74
3250	5208	4.443598	GCTATTTCCTTCTTGGTCGGATCT	60.444	45.833	0.00	0.00	37.07	2.75
3251	5209	3.810386	GCTATTTCCTTCTTGGTCGGATC	59.190	47.826	0.00	0.00	37.07	3.36
3253	5211	2.093128	GGCTATTTCCTTCTTGGTCGGA	60.093	50.000	0.00	0.00	37.07	4.55
3256	5214	3.017442	GGTGGCTATTTCCTTCTTGGTC	58.983	50.000	0.00	0.00	37.07	4.02
3257	5215	2.378547	TGGTGGCTATTTCCTTCTTGGT	59.621	45.455	0.00	0.00	37.07	3.67
3258	5216	3.019564	CTGGTGGCTATTTCCTTCTTGG	58.980	50.000	0.00	0.00	37.10	3.61
3259	5217	3.019564	CCTGGTGGCTATTTCCTTCTTG	58.980	50.000	0.00	0.00	0.00	3.02
3260	5218	2.649816	ACCTGGTGGCTATTTCCTTCTT	59.350	45.455	0.00	0.00	36.63	2.52
3261	5219	2.025887	CACCTGGTGGCTATTTCCTTCT	60.026	50.000	19.23	0.00	36.63	2.85
3262	5220	2.290960	ACACCTGGTGGCTATTTCCTTC	60.291	50.000	29.05	0.00	37.94	3.46
3270	5230	3.799432	ATGTTTAACACCTGGTGGCTA	57.201	42.857	29.05	17.35	37.94	3.93
3352	5313	1.534163	GTTGTTCACCGTAAGCCCTTC	59.466	52.381	0.00	0.00	0.00	3.46
3457	5418	1.837439	TCACCATCGCCCTAAGACATT	59.163	47.619	0.00	0.00	0.00	2.71
3531	5512	2.444624	CGCCCTCGACGTCAATGTG	61.445	63.158	17.16	3.56	38.10	3.21
3576	5558	0.670546	CTCGTTGTTGTGGAGGCGAT	60.671	55.000	0.00	0.00	0.00	4.58
3658	5640	0.668535	GGCTTGTGGTGTTGAAGACC	59.331	55.000	4.29	4.29	0.00	3.85

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.