AutoCloner

Multiple sequence alignment - TraesCS1D01G404100

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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	TraesCS1D01G404100	chr1D	100.000	3359	0	0	1	3359	469021122	469024480	0.000000e+00	6204
1	TraesCS1D01G404100	chr6D	96.669	3302	67	12	90	3359	214545038	214548328	0.000000e+00	5448
2	TraesCS1D01G404100	chr6D	95.833	3264	97	10	127	3359	338806098	338802843	0.000000e+00	5238
3	TraesCS1D01G404100	chr6D	95.655	3268	104	9	124	3359	4300783	4304044	0.000000e+00	5214
4	TraesCS1D01G404100	chr5D	96.573	3268	68	6	124	3359	334926886	334930141	0.000000e+00	5374
5	TraesCS1D01G404100	chr2D	96.082	3267	96	4	124	3359	377138683	377141948	0.000000e+00	5295
6	TraesCS1D01G404100	chr2D	95.493	1531	47	10	192	1701	286991176	286989647	0.000000e+00	2425
7	TraesCS1D01G404100	chr2D	92.173	856	27	8	124	961	218023911	218024744	0.000000e+00	1173
8	TraesCS1D01G404100	chr2D	93.506	154	6	4	88	239	286991330	286991179	3.370000e-55	226
9	TraesCS1D01G404100	chr7D	95.386	3251	119	5	127	3359	5555738	5552501	0.000000e+00	5144
10	TraesCS1D01G404100	chr7D	93.039	3304	163	30	88	3359	126657568	126654300	0.000000e+00	4765
11	TraesCS1D01G404100	chr7D	92.498	3306	186	33	90	3359	26441829	26438550	0.000000e+00	4674
12	TraesCS1D01G404100	chr7D	96.161	2553	49	13	124	2645	394369758	394372292	0.000000e+00	4126
13	TraesCS1D01G404100	chr7D	93.856	944	30	4	186	1111	184174464	184175397	0.000000e+00	1397
14	TraesCS1D01G404100	chr7D	89.297	327	9	6	90	390	394374920	394375246	1.460000e-103	387
15	TraesCS1D01G404100	chr7D	93.421	152	6	4	90	239	184174318	184174467	4.360000e-54	222
16	TraesCS1D01G404100	chr6A	94.526	3215	125	11	166	3359	387978010	387981194	0.000000e+00	4915
17	TraesCS1D01G404100	chr3B	94.446	3223	125	14	166	3359	355442717	355445914	0.000000e+00	4911
18	TraesCS1D01G404100	chr4B	94.244	3249	128	15	145	3359	253697318	253700541	0.000000e+00	4909
19	TraesCS1D01G404100	chr4B	96.198	2762	102	3	600	3359	322661828	322664588	0.000000e+00	4516
20	TraesCS1D01G404100	chr3A	94.384	3223	127	12	166	3359	298167742	298164545	0.000000e+00	4900
21	TraesCS1D01G404100	chr5B	94.355	3224	127	13	166	3359	710631582	710634780	0.000000e+00	4894
22	TraesCS1D01G404100	chr2B	92.443	3295	188	29	90	3359	227852673	227849415	0.000000e+00	4649
23	TraesCS1D01G404100	chr2B	89.809	314	17	5	90	390	227847493	227847182	4.060000e-104	388
24	TraesCS1D01G404100	chr1B	96.703	91	3	0	1	91	648454424	648454514	5.800000e-33	152
25	TraesCS1D01G404100	chr1A	96.703	91	3	0	1	91	561976734	561976824	5.800000e-33	152

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	TraesCS1D01G404100	chr1D	469021122	469024480	3358	False	6204.0	6204	100.0000	1	3359	1	chr1D.!!$F1	3358
1	TraesCS1D01G404100	chr6D	214545038	214548328	3290	False	5448.0	5448	96.6690	90	3359	1	chr6D.!!$F2	3269
2	TraesCS1D01G404100	chr6D	338802843	338806098	3255	True	5238.0	5238	95.8330	127	3359	1	chr6D.!!$R1	3232
3	TraesCS1D01G404100	chr6D	4300783	4304044	3261	False	5214.0	5214	95.6550	124	3359	1	chr6D.!!$F1	3235
4	TraesCS1D01G404100	chr5D	334926886	334930141	3255	False	5374.0	5374	96.5730	124	3359	1	chr5D.!!$F1	3235
5	TraesCS1D01G404100	chr2D	377138683	377141948	3265	False	5295.0	5295	96.0820	124	3359	1	chr2D.!!$F2	3235
6	TraesCS1D01G404100	chr2D	286989647	286991330	1683	True	1325.5	2425	94.4995	88	1701	2	chr2D.!!$R1	1613
7	TraesCS1D01G404100	chr2D	218023911	218024744	833	False	1173.0	1173	92.1730	124	961	1	chr2D.!!$F1	837
8	TraesCS1D01G404100	chr7D	5552501	5555738	3237	True	5144.0	5144	95.3860	127	3359	1	chr7D.!!$R1	3232
9	TraesCS1D01G404100	chr7D	126654300	126657568	3268	True	4765.0	4765	93.0390	88	3359	1	chr7D.!!$R3	3271
10	TraesCS1D01G404100	chr7D	26438550	26441829	3279	True	4674.0	4674	92.4980	90	3359	1	chr7D.!!$R2	3269
11	TraesCS1D01G404100	chr7D	394369758	394375246	5488	False	2256.5	4126	92.7290	90	2645	2	chr7D.!!$F2	2555
12	TraesCS1D01G404100	chr7D	184174318	184175397	1079	False	809.5	1397	93.6385	90	1111	2	chr7D.!!$F1	1021
13	TraesCS1D01G404100	chr6A	387978010	387981194	3184	False	4915.0	4915	94.5260	166	3359	1	chr6A.!!$F1	3193
14	TraesCS1D01G404100	chr3B	355442717	355445914	3197	False	4911.0	4911	94.4460	166	3359	1	chr3B.!!$F1	3193
15	TraesCS1D01G404100	chr4B	253697318	253700541	3223	False	4909.0	4909	94.2440	145	3359	1	chr4B.!!$F1	3214
16	TraesCS1D01G404100	chr4B	322661828	322664588	2760	False	4516.0	4516	96.1980	600	3359	1	chr4B.!!$F2	2759
17	TraesCS1D01G404100	chr3A	298164545	298167742	3197	True	4900.0	4900	94.3840	166	3359	1	chr3A.!!$R1	3193
18	TraesCS1D01G404100	chr5B	710631582	710634780	3198	False	4894.0	4894	94.3550	166	3359	1	chr5B.!!$F1	3193
19	TraesCS1D01G404100	chr2B	227847182	227852673	5491	True	2518.5	4649	91.1260	90	3359	2	chr2B.!!$R1	3269

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
77	78	0.035630	GAAGTCACAGGGCTGAGCAT	60.036	55.0	6.82	0.00	0.00	3.79	F
78	79	0.322277	AAGTCACAGGGCTGAGCATG	60.322	55.0	6.82	7.08	0.00	4.06	F
1000	1177	0.467384	CCTCTACGAGGTCCGGACTA	59.533	60.0	32.52	16.77	44.25	2.59	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1298	1475	2.482494	CCAGGTTCTCCCACTCCTTAT	58.518	52.381	0.00	0.00	34.66	1.73	R
2270	2454	1.690283	CTCAATCAGCACGCGTGAGG	61.690	60.000	41.19	29.78	33.57	3.86	R
3183	3406	1.025812	CGTAGCCGATGAAGACTCCT	58.974	55.000	0.00	0.00	35.63	3.69	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
18	19	3.196040	TTCAGCAATGCATCTCCCC	57.804	52.632	8.35	0.00	0.00	4.81
19	20	0.749091	TTCAGCAATGCATCTCCCCG	60.749	55.000	8.35	0.00	0.00	5.73
20	21	1.452651	CAGCAATGCATCTCCCCGT	60.453	57.895	8.35	0.00	0.00	5.28
21	22	1.033746	CAGCAATGCATCTCCCCGTT	61.034	55.000	8.35	0.00	0.00	4.44
22	23	0.546122	AGCAATGCATCTCCCCGTTA	59.454	50.000	8.35	0.00	0.00	3.18
23	24	1.143684	AGCAATGCATCTCCCCGTTAT	59.856	47.619	8.35	0.00	0.00	1.89
24	25	1.537202	GCAATGCATCTCCCCGTTATC	59.463	52.381	0.00	0.00	0.00	1.75
25	26	2.154462	CAATGCATCTCCCCGTTATCC	58.846	52.381	0.00	0.00	0.00	2.59
26	27	1.434188	ATGCATCTCCCCGTTATCCA	58.566	50.000	0.00	0.00	0.00	3.41
27	28	1.208706	TGCATCTCCCCGTTATCCAA	58.791	50.000	0.00	0.00	0.00	3.53
28	29	1.774254	TGCATCTCCCCGTTATCCAAT	59.226	47.619	0.00	0.00	0.00	3.16
29	30	2.174639	TGCATCTCCCCGTTATCCAATT	59.825	45.455	0.00	0.00	0.00	2.32
30	31	2.554032	GCATCTCCCCGTTATCCAATTG	59.446	50.000	0.00	0.00	0.00	2.32
31	32	3.820557	CATCTCCCCGTTATCCAATTGT	58.179	45.455	4.43	0.00	0.00	2.71
32	33	4.745478	GCATCTCCCCGTTATCCAATTGTA	60.745	45.833	4.43	0.00	0.00	2.41
33	34	5.560724	CATCTCCCCGTTATCCAATTGTAT	58.439	41.667	4.43	0.00	0.00	2.29
34	35	5.223449	TCTCCCCGTTATCCAATTGTATC	57.777	43.478	4.43	0.00	0.00	2.24
35	36	4.905456	TCTCCCCGTTATCCAATTGTATCT	59.095	41.667	4.43	0.00	0.00	1.98
36	37	5.368523	TCTCCCCGTTATCCAATTGTATCTT	59.631	40.000	4.43	0.00	0.00	2.40
37	38	5.373222	TCCCCGTTATCCAATTGTATCTTG	58.627	41.667	4.43	0.00	0.00	3.02
38	39	5.131308	TCCCCGTTATCCAATTGTATCTTGA	59.869	40.000	4.43	0.00	0.00	3.02
39	40	5.470098	CCCCGTTATCCAATTGTATCTTGAG	59.530	44.000	4.43	0.00	0.00	3.02
40	41	6.288294	CCCGTTATCCAATTGTATCTTGAGA	58.712	40.000	4.43	0.00	0.00	3.27
41	42	6.936900	CCCGTTATCCAATTGTATCTTGAGAT	59.063	38.462	4.43	0.00	38.51	2.75
42	43	7.445402	CCCGTTATCCAATTGTATCTTGAGATT	59.555	37.037	4.43	0.00	36.05	2.40
43	44	8.285394	CCGTTATCCAATTGTATCTTGAGATTG	58.715	37.037	4.43	0.00	36.05	2.67
44	45	9.045223	CGTTATCCAATTGTATCTTGAGATTGA	57.955	33.333	4.43	0.00	36.05	2.57
48	49	8.672823	TCCAATTGTATCTTGAGATTGATCTG	57.327	34.615	4.43	0.00	37.25	2.90
49	50	7.718314	TCCAATTGTATCTTGAGATTGATCTGG	59.282	37.037	4.43	2.72	37.25	3.86
50	51	7.501559	CCAATTGTATCTTGAGATTGATCTGGT	59.498	37.037	4.43	0.00	37.25	4.00
51	52	8.343366	CAATTGTATCTTGAGATTGATCTGGTG	58.657	37.037	0.00	0.00	37.25	4.17
52	53	6.796785	TGTATCTTGAGATTGATCTGGTGA	57.203	37.500	0.00	0.00	37.25	4.02
53	54	7.370905	TGTATCTTGAGATTGATCTGGTGAT	57.629	36.000	0.00	2.39	37.25	3.06
54	55	7.440198	TGTATCTTGAGATTGATCTGGTGATC	58.560	38.462	0.00	0.00	41.05	2.92
66	67	6.154203	GATCTGGTGATCATAGAAGTCACA	57.846	41.667	14.27	0.00	46.20	3.58
67	68	5.588958	TCTGGTGATCATAGAAGTCACAG	57.411	43.478	0.00	0.00	43.01	3.66
68	69	4.403752	TCTGGTGATCATAGAAGTCACAGG	59.596	45.833	0.00	0.14	43.01	4.00
69	70	3.452264	TGGTGATCATAGAAGTCACAGGG	59.548	47.826	0.00	0.00	43.01	4.45
70	71	3.462021	GTGATCATAGAAGTCACAGGGC	58.538	50.000	0.00	0.00	41.35	5.19
71	72	3.133721	GTGATCATAGAAGTCACAGGGCT	59.866	47.826	0.00	0.00	41.35	5.19
72	73	3.133542	TGATCATAGAAGTCACAGGGCTG	59.866	47.826	0.00	0.00	0.00	4.85
73	74	2.820178	TCATAGAAGTCACAGGGCTGA	58.180	47.619	0.00	0.00	0.00	4.26
74	75	2.762887	TCATAGAAGTCACAGGGCTGAG	59.237	50.000	0.00	0.00	0.00	3.35
75	76	0.898320	TAGAAGTCACAGGGCTGAGC	59.102	55.000	0.00	0.00	0.00	4.26
76	77	1.123861	AGAAGTCACAGGGCTGAGCA	61.124	55.000	6.82	0.00	0.00	4.26
77	78	0.035630	GAAGTCACAGGGCTGAGCAT	60.036	55.000	6.82	0.00	0.00	3.79
78	79	0.322277	AAGTCACAGGGCTGAGCATG	60.322	55.000	6.82	7.08	0.00	4.06
79	80	2.045634	TCACAGGGCTGAGCATGC	60.046	61.111	10.51	10.51	0.00	4.06
80	81	3.506096	CACAGGGCTGAGCATGCG	61.506	66.667	13.01	0.00	0.00	4.73
81	82	3.709633	ACAGGGCTGAGCATGCGA	61.710	61.111	13.01	1.76	0.00	5.10
82	83	3.200593	CAGGGCTGAGCATGCGAC	61.201	66.667	13.01	11.35	0.00	5.19
83	84	3.709633	AGGGCTGAGCATGCGACA	61.710	61.111	13.01	15.37	0.00	4.35
84	85	2.747460	GGGCTGAGCATGCGACAA	60.747	61.111	13.01	0.00	0.00	3.18
85	86	2.482374	GGCTGAGCATGCGACAAC	59.518	61.111	13.01	11.79	0.00	3.32
86	87	2.482374	GCTGAGCATGCGACAACC	59.518	61.111	13.01	7.17	0.00	3.77
125	126	7.289549	GTCTATGTACTAAGGTCTTTATGGGGT	59.710	40.741	0.00	0.00	0.00	4.95
210	261	4.596643	AGGATAGCATCTTAGACTGGCATT	59.403	41.667	5.42	0.00	0.00	3.56
256	371	1.362717	GCATATGCTTGGCTGGCTG	59.637	57.895	20.64	0.00	38.21	4.85
356	474	3.708631	CCAACTCTCCTAGTGTCATCCAT	59.291	47.826	0.00	0.00	38.88	3.41
418	536	6.014156	GGTATCAGAGCCAGGTTATCTTGTAT	60.014	42.308	0.00	0.00	0.00	2.29
497	615	2.817396	GCTGCTTCGTCTGCCTCC	60.817	66.667	0.00	0.00	0.00	4.30
546	665	1.823470	AGCAGCTCGGCAACAACAA	60.823	52.632	0.00	0.00	35.83	2.83
585	705	3.865383	CCCCTGCAGCGAGCCATA	61.865	66.667	8.66	0.00	44.83	2.74
805	981	2.740055	GAGGCTATGGCGGATGCG	60.740	66.667	0.65	0.65	44.10	4.73
1000	1177	0.467384	CCTCTACGAGGTCCGGACTA	59.533	60.000	32.52	16.77	44.25	2.59
1056	1233	5.338953	GCCTACCCTCACTAAAACCAACTAT	60.339	44.000	0.00	0.00	0.00	2.12
1298	1475	2.113774	CACCCTGCAGGCACTTCA	59.886	61.111	28.39	0.00	40.58	3.02
1975	2159	2.037367	CTCCCCTCCACCTCGACA	59.963	66.667	0.00	0.00	0.00	4.35
2270	2454	1.079503	GGACAACTGGATGAGAACGC	58.920	55.000	0.00	0.00	0.00	4.84
2402	2586	0.108992	GCACAACCGGTATGTCTCGA	60.109	55.000	8.00	0.00	0.00	4.04
2440	2624	2.703798	GCGTGGCAATGGCATGAGT	61.704	57.895	29.49	0.00	46.06	3.41
2718	2938	2.432874	CTCCCGTTACATGTGGGTGATA	59.567	50.000	17.08	0.32	43.75	2.15
3129	3352	2.747855	CGGGTCTTTGGCTGCCTC	60.748	66.667	21.03	5.20	0.00	4.70
3245	3468	0.246635	ATCCTCGACCCAAAGACACG	59.753	55.000	0.00	0.00	0.00	4.49

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
0	1	0.749091	CGGGGAGATGCATTGCTGAA	60.749	55.000	10.49	0.00	0.00	3.02
3	4	0.546122	TAACGGGGAGATGCATTGCT	59.454	50.000	10.49	0.00	0.00	3.91
5	6	2.154462	GGATAACGGGGAGATGCATTG	58.846	52.381	0.00	0.00	0.00	2.82
6	7	1.774254	TGGATAACGGGGAGATGCATT	59.226	47.619	0.00	0.00	0.00	3.56
7	8	1.434188	TGGATAACGGGGAGATGCAT	58.566	50.000	0.00	0.00	0.00	3.96
8	9	1.208706	TTGGATAACGGGGAGATGCA	58.791	50.000	0.00	0.00	0.00	3.96
9	10	2.554032	CAATTGGATAACGGGGAGATGC	59.446	50.000	0.00	0.00	0.00	3.91
10	11	3.820557	ACAATTGGATAACGGGGAGATG	58.179	45.455	10.83	0.00	0.00	2.90
11	12	5.548056	AGATACAATTGGATAACGGGGAGAT	59.452	40.000	10.83	0.00	0.00	2.75
12	13	4.905456	AGATACAATTGGATAACGGGGAGA	59.095	41.667	10.83	0.00	0.00	3.71
13	14	5.228945	AGATACAATTGGATAACGGGGAG	57.771	43.478	10.83	0.00	0.00	4.30
14	15	5.131308	TCAAGATACAATTGGATAACGGGGA	59.869	40.000	10.83	0.00	0.00	4.81
15	16	5.373222	TCAAGATACAATTGGATAACGGGG	58.627	41.667	10.83	0.00	0.00	5.73
16	17	6.288294	TCTCAAGATACAATTGGATAACGGG	58.712	40.000	10.83	0.00	0.00	5.28
17	18	7.969536	ATCTCAAGATACAATTGGATAACGG	57.030	36.000	10.83	0.00	32.01	4.44
18	19	9.045223	TCAATCTCAAGATACAATTGGATAACG	57.955	33.333	10.83	0.00	33.73	3.18
22	23	9.286170	CAGATCAATCTCAAGATACAATTGGAT	57.714	33.333	1.71	1.71	34.22	3.41
23	24	7.718314	CCAGATCAATCTCAAGATACAATTGGA	59.282	37.037	10.83	0.10	34.22	3.53
24	25	7.501559	ACCAGATCAATCTCAAGATACAATTGG	59.498	37.037	10.83	2.94	34.22	3.16
25	26	8.343366	CACCAGATCAATCTCAAGATACAATTG	58.657	37.037	3.24	3.24	34.22	2.32
26	27	8.270030	TCACCAGATCAATCTCAAGATACAATT	58.730	33.333	0.00	0.00	34.22	2.32
27	28	7.799081	TCACCAGATCAATCTCAAGATACAAT	58.201	34.615	0.00	0.00	34.22	2.71
28	29	7.186570	TCACCAGATCAATCTCAAGATACAA	57.813	36.000	0.00	0.00	34.22	2.41
29	30	6.796785	TCACCAGATCAATCTCAAGATACA	57.203	37.500	0.00	0.00	34.22	2.29
44	45	5.070180	CCTGTGACTTCTATGATCACCAGAT	59.930	44.000	0.00	0.00	41.71	2.90
45	46	4.403752	CCTGTGACTTCTATGATCACCAGA	59.596	45.833	0.00	0.53	41.71	3.86
46	47	4.442612	CCCTGTGACTTCTATGATCACCAG	60.443	50.000	0.00	0.00	41.71	4.00
47	48	3.452264	CCCTGTGACTTCTATGATCACCA	59.548	47.826	0.00	0.00	41.71	4.17
48	49	3.742640	GCCCTGTGACTTCTATGATCACC	60.743	52.174	0.00	0.00	41.71	4.02
49	50	3.133721	AGCCCTGTGACTTCTATGATCAC	59.866	47.826	0.00	0.00	42.54	3.06
50	51	3.133542	CAGCCCTGTGACTTCTATGATCA	59.866	47.826	0.00	0.00	0.00	2.92
51	52	3.386078	TCAGCCCTGTGACTTCTATGATC	59.614	47.826	0.00	0.00	0.00	2.92
52	53	3.378512	TCAGCCCTGTGACTTCTATGAT	58.621	45.455	0.00	0.00	0.00	2.45
53	54	2.762887	CTCAGCCCTGTGACTTCTATGA	59.237	50.000	0.00	0.00	0.00	2.15
54	55	2.741228	GCTCAGCCCTGTGACTTCTATG	60.741	54.545	1.84	0.00	0.00	2.23
55	56	1.484240	GCTCAGCCCTGTGACTTCTAT	59.516	52.381	1.84	0.00	0.00	1.98
56	57	0.898320	GCTCAGCCCTGTGACTTCTA	59.102	55.000	1.84	0.00	0.00	2.10
57	58	1.123861	TGCTCAGCCCTGTGACTTCT	61.124	55.000	0.00	0.00	0.00	2.85
58	59	0.035630	ATGCTCAGCCCTGTGACTTC	60.036	55.000	0.00	0.00	0.00	3.01
59	60	0.322277	CATGCTCAGCCCTGTGACTT	60.322	55.000	0.00	0.00	0.00	3.01
60	61	1.298993	CATGCTCAGCCCTGTGACT	59.701	57.895	0.00	0.00	0.00	3.41
61	62	2.404995	GCATGCTCAGCCCTGTGAC	61.405	63.158	11.37	0.00	0.00	3.67
62	63	2.045634	GCATGCTCAGCCCTGTGA	60.046	61.111	11.37	0.00	0.00	3.58
63	64	3.506096	CGCATGCTCAGCCCTGTG	61.506	66.667	17.13	0.00	0.00	3.66
64	65	3.709633	TCGCATGCTCAGCCCTGT	61.710	61.111	17.13	0.00	0.00	4.00
65	66	3.200593	GTCGCATGCTCAGCCCTG	61.201	66.667	17.13	0.00	0.00	4.45
66	67	3.258228	TTGTCGCATGCTCAGCCCT	62.258	57.895	17.13	0.00	0.00	5.19
67	68	2.747460	TTGTCGCATGCTCAGCCC	60.747	61.111	17.13	0.00	0.00	5.19
68	69	2.482374	GTTGTCGCATGCTCAGCC	59.518	61.111	17.13	6.04	0.00	4.85
69	70	1.975363	GAGGTTGTCGCATGCTCAGC	61.975	60.000	17.13	15.54	0.00	4.26
70	71	0.390866	AGAGGTTGTCGCATGCTCAG	60.391	55.000	17.13	0.00	0.00	3.35
71	72	0.671472	CAGAGGTTGTCGCATGCTCA	60.671	55.000	17.13	11.99	0.00	4.26
72	73	0.390340	TCAGAGGTTGTCGCATGCTC	60.390	55.000	17.13	9.37	0.00	4.26
73	74	0.251354	ATCAGAGGTTGTCGCATGCT	59.749	50.000	17.13	0.00	0.00	3.79
74	75	0.376152	CATCAGAGGTTGTCGCATGC	59.624	55.000	7.91	7.91	0.00	4.06
75	76	1.012086	CCATCAGAGGTTGTCGCATG	58.988	55.000	0.00	0.00	0.00	4.06
76	77	0.904649	TCCATCAGAGGTTGTCGCAT	59.095	50.000	0.00	0.00	0.00	4.73
77	78	0.904649	ATCCATCAGAGGTTGTCGCA	59.095	50.000	0.00	0.00	0.00	5.10
78	79	2.890808	TATCCATCAGAGGTTGTCGC	57.109	50.000	0.00	0.00	0.00	5.19
79	80	4.098654	AGACTTATCCATCAGAGGTTGTCG	59.901	45.833	0.00	0.00	0.00	4.35
80	81	5.606348	AGACTTATCCATCAGAGGTTGTC	57.394	43.478	0.00	0.00	0.00	3.18
81	82	6.613271	ACATAGACTTATCCATCAGAGGTTGT	59.387	38.462	0.00	0.00	0.00	3.32
82	83	7.060383	ACATAGACTTATCCATCAGAGGTTG	57.940	40.000	0.00	0.00	0.00	3.77
83	84	8.007742	AGTACATAGACTTATCCATCAGAGGTT	58.992	37.037	0.00	0.00	0.00	3.50
84	85	7.531317	AGTACATAGACTTATCCATCAGAGGT	58.469	38.462	0.00	0.00	0.00	3.85
85	86	9.521841	TTAGTACATAGACTTATCCATCAGAGG	57.478	37.037	0.00	0.00	0.00	3.69
119	120	1.985662	CCATGTGCTGCAACCCCAT	60.986	57.895	2.77	0.06	0.00	4.00
125	126	0.467844	ACAAGGACCATGTGCTGCAA	60.468	50.000	2.77	0.00	33.74	4.08
210	261	5.598416	TGCTAGTCTAAGATGCTGCTAAA	57.402	39.130	0.00	0.00	0.00	1.85
256	371	4.141688	GGGGATACATACTTATAGGCTGCC	60.142	50.000	11.65	11.65	39.74	4.85
356	474	5.357742	TCAGCCTGAGCATTTCATAGTTA	57.642	39.130	0.00	0.00	43.56	2.24
497	615	1.043673	CAGAGGGAGGGAGGTAACCG	61.044	65.000	0.00	0.00	37.17	4.44
546	665	0.034059	CTGTTGCGTGAAGAGGAGGT	59.966	55.000	0.00	0.00	0.00	3.85
1000	1177	0.625849	GGACCAACATCCCTGACCAT	59.374	55.000	0.00	0.00	31.94	3.55
1298	1475	2.482494	CCAGGTTCTCCCACTCCTTAT	58.518	52.381	0.00	0.00	34.66	1.73
2270	2454	1.690283	CTCAATCAGCACGCGTGAGG	61.690	60.000	41.19	29.78	33.57	3.86
2394	2578	1.725557	CCCGACGGACATCGAGACAT	61.726	60.000	17.49	0.00	45.13	3.06
2718	2938	1.123928	CTCCCTTACTGCCGAGGATT	58.876	55.000	0.00	0.00	34.91	3.01
2839	3059	1.614385	CAGTACGACGCGAATTCAGT	58.386	50.000	15.93	4.75	0.00	3.41
3183	3406	1.025812	CGTAGCCGATGAAGACTCCT	58.974	55.000	0.00	0.00	35.63	3.69
3287	3510	0.542702	CTTGTCCCATTGCCACCCTT	60.543	55.000	0.00	0.00	0.00	3.95

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.