AutoCloner

Multiple sequence alignment - TraesCS4D01G236700

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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	TraesCS4D01G236700	chr4D	100.000	2273	0	0	1	2273	398866805	398869077	0.000000e+00	4198
1	TraesCS4D01G236700	chr3D	92.150	1465	100	9	1	1465	134639507	134640956	0.000000e+00	2054
2	TraesCS4D01G236700	chr5A	92.908	1396	95	4	1	1395	697889093	697890485	0.000000e+00	2026
3	TraesCS4D01G236700	chr5A	91.126	1465	107	13	1	1465	651581860	651580419	0.000000e+00	1964
4	TraesCS4D01G236700	chr5A	89.191	1471	141	13	1	1467	476064451	476062995	0.000000e+00	1820
5	TraesCS4D01G236700	chr6B	91.491	1469	108	14	1	1465	132658808	132657353	0.000000e+00	2004
6	TraesCS4D01G236700	chr5D	91.058	1465	119	11	1	1465	292727478	292726026	0.000000e+00	1969
7	TraesCS4D01G236700	chr4A	90.550	1492	113	24	1	1467	718008863	718007375	0.000000e+00	1949
8	TraesCS4D01G236700	chr4A	85.761	309	25	5	1157	1465	709875349	709875060	2.190000e-80	309
9	TraesCS4D01G236700	chr4A	91.250	80	7	0	1534	1613	56197644	56197723	2.390000e-20	110
10	TraesCS4D01G236700	chr2B	92.543	1341	94	4	1	1341	138738176	138736842	0.000000e+00	1917
11	TraesCS4D01G236700	chr2D	90.279	1471	130	11	1	1465	573649377	573650840	0.000000e+00	1912
12	TraesCS4D01G236700	chr2D	99.242	660	5	0	1614	2273	619453097	619453756	0.000000e+00	1192
13	TraesCS4D01G236700	chr2D	99.242	660	4	1	1614	2273	449706755	449706097	0.000000e+00	1190
14	TraesCS4D01G236700	chr2D	87.980	391	19	15	1076	1466	6067113	6066751	9.640000e-119	436
15	TraesCS4D01G236700	chr1D	99.242	660	5	0	1614	2273	459821643	459820984	0.000000e+00	1192
16	TraesCS4D01G236700	chr1D	99.094	662	6	0	1612	2273	144278940	144278279	0.000000e+00	1190
17	TraesCS4D01G236700	chr1D	98.361	671	11	0	1603	2273	388972894	388973564	0.000000e+00	1179
18	TraesCS4D01G236700	chr7D	98.651	667	9	0	1607	2273	602429505	602428839	0.000000e+00	1182
19	TraesCS4D01G236700	chr6D	98.227	677	9	3	1600	2273	459653668	459654344	0.000000e+00	1181
20	TraesCS4D01G236700	chr6D	98.361	671	11	0	1603	2273	459664601	459665271	0.000000e+00	1179
21	TraesCS4D01G236700	chrUn	98.361	671	11	0	1603	2273	196265559	196266229	0.000000e+00	1179
22	TraesCS4D01G236700	chr3B	86.443	804	76	19	664	1467	769385940	769385170	0.000000e+00	850
23	TraesCS4D01G236700	chr3B	89.247	93	10	0	1374	1466	559098022	559098114	1.430000e-22	117
24	TraesCS4D01G236700	chr2A	92.157	204	12	1	1263	1466	40955186	40954987	3.700000e-73	285
25	TraesCS4D01G236700	chr4B	91.765	85	7	0	1529	1613	491782712	491782796	3.970000e-23	119

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	TraesCS4D01G236700	chr4D	398866805	398869077	2272	False	4198	4198	100.000	1	2273	1	chr4D.!!$F1	2272
1	TraesCS4D01G236700	chr3D	134639507	134640956	1449	False	2054	2054	92.150	1	1465	1	chr3D.!!$F1	1464
2	TraesCS4D01G236700	chr5A	697889093	697890485	1392	False	2026	2026	92.908	1	1395	1	chr5A.!!$F1	1394
3	TraesCS4D01G236700	chr5A	651580419	651581860	1441	True	1964	1964	91.126	1	1465	1	chr5A.!!$R2	1464
4	TraesCS4D01G236700	chr5A	476062995	476064451	1456	True	1820	1820	89.191	1	1467	1	chr5A.!!$R1	1466
5	TraesCS4D01G236700	chr6B	132657353	132658808	1455	True	2004	2004	91.491	1	1465	1	chr6B.!!$R1	1464
6	TraesCS4D01G236700	chr5D	292726026	292727478	1452	True	1969	1969	91.058	1	1465	1	chr5D.!!$R1	1464
7	TraesCS4D01G236700	chr4A	718007375	718008863	1488	True	1949	1949	90.550	1	1467	1	chr4A.!!$R2	1466
8	TraesCS4D01G236700	chr2B	138736842	138738176	1334	True	1917	1917	92.543	1	1341	1	chr2B.!!$R1	1340
9	TraesCS4D01G236700	chr2D	573649377	573650840	1463	False	1912	1912	90.279	1	1465	1	chr2D.!!$F1	1464
10	TraesCS4D01G236700	chr2D	619453097	619453756	659	False	1192	1192	99.242	1614	2273	1	chr2D.!!$F2	659
11	TraesCS4D01G236700	chr2D	449706097	449706755	658	True	1190	1190	99.242	1614	2273	1	chr2D.!!$R2	659
12	TraesCS4D01G236700	chr1D	459820984	459821643	659	True	1192	1192	99.242	1614	2273	1	chr1D.!!$R2	659
13	TraesCS4D01G236700	chr1D	144278279	144278940	661	True	1190	1190	99.094	1612	2273	1	chr1D.!!$R1	661
14	TraesCS4D01G236700	chr1D	388972894	388973564	670	False	1179	1179	98.361	1603	2273	1	chr1D.!!$F1	670
15	TraesCS4D01G236700	chr7D	602428839	602429505	666	True	1182	1182	98.651	1607	2273	1	chr7D.!!$R1	666
16	TraesCS4D01G236700	chr6D	459653668	459654344	676	False	1181	1181	98.227	1600	2273	1	chr6D.!!$F1	673
17	TraesCS4D01G236700	chr6D	459664601	459665271	670	False	1179	1179	98.361	1603	2273	1	chr6D.!!$F2	670
18	TraesCS4D01G236700	chrUn	196265559	196266229	670	False	1179	1179	98.361	1603	2273	1	chrUn.!!$F1	670
19	TraesCS4D01G236700	chr3B	769385170	769385940	770	True	850	850	86.443	664	1467	1	chr3B.!!$R1	803

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
660	661	2.766313	CCACTGTCTCCAATGAAACGA	58.234	47.619	0.0	0.0	0.0	3.85	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1596	1696	0.034574	ACATTGCCAACGCCTCCATA	60.035	50.0	0.0	0.0	0.0	2.74	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
108	109	6.376299	CCAAGAGCATTATATATGCCATGTGT	59.624	38.462	13.08	0.00	45.59	3.72
263	264	4.081322	ACATGTTCCTAGTTTGACCGTT	57.919	40.909	0.00	0.00	0.00	4.44
273	274	6.027749	CCTAGTTTGACCGTTAAATCATTGC	58.972	40.000	0.00	0.00	0.00	3.56
283	284	5.067153	CCGTTAAATCATTGCCCAATACTCA	59.933	40.000	0.00	0.00	0.00	3.41
335	336	6.261603	CAGCAATAAGATATCAAGCCACTGAA	59.738	38.462	5.32	0.00	0.00	3.02
435	436	3.489355	TGATGCACTTGGTCACTTTGAT	58.511	40.909	0.00	0.00	0.00	2.57
516	517	4.260985	AGATGTTGCAATCGTCAACCATA	58.739	39.130	17.67	0.00	42.17	2.74
525	526	5.209977	CAATCGTCAACCATATGCATTGAG	58.790	41.667	16.70	12.36	33.16	3.02
537	538	6.461092	CCATATGCATTGAGTCTGCTTTGAAT	60.461	38.462	3.54	0.00	40.34	2.57
643	644	3.891049	ACTGAAATGGGAATAGAGCCAC	58.109	45.455	0.00	0.00	0.00	5.01
647	648	3.567478	AATGGGAATAGAGCCACTGTC	57.433	47.619	0.00	0.00	0.00	3.51
660	661	2.766313	CCACTGTCTCCAATGAAACGA	58.234	47.619	0.00	0.00	0.00	3.85
906	907	5.629097	TGCACAAAATTTGCAGAAACTTTG	58.371	33.333	5.52	4.06	45.06	2.77
925	926	8.697507	AACTTTGTCTCTTAATGGTTCATCTT	57.302	30.769	0.00	0.00	0.00	2.40
980	981	8.571461	TTGAAGATTATGAGATTCACTTTGCT	57.429	30.769	0.00	0.00	31.72	3.91
993	994	6.624352	TTCACTTTGCTAGATGGCATAATC	57.376	37.500	0.00	0.00	42.09	1.75
997	998	7.015584	TCACTTTGCTAGATGGCATAATCTCTA	59.984	37.037	0.00	0.00	42.09	2.43
1035	1036	3.427233	GGCATGTGAGAGAAGTTGATTGC	60.427	47.826	0.00	0.00	0.00	3.56
1079	1080	6.348458	GCCTATCGCATCTTATTTATTGTGCA	60.348	38.462	0.00	0.00	37.47	4.57
1084	1085	5.400188	CGCATCTTATTTATTGTGCATGTGG	59.600	40.000	0.00	0.00	33.09	4.17
1174	1175	5.794894	TGACTCAAGAGAGGTTAAATGGTC	58.205	41.667	3.73	0.00	46.44	4.02
1178	1179	4.844085	TCAAGAGAGGTTAAATGGTCTGGA	59.156	41.667	0.00	0.00	0.00	3.86
1181	1182	7.348274	TCAAGAGAGGTTAAATGGTCTGGATAT	59.652	37.037	0.00	0.00	0.00	1.63
1193	1194	6.544928	TGGTCTGGATATATTATGCATCGT	57.455	37.500	0.19	0.00	0.00	3.73
1239	1240	3.648067	ACATCGACCCCATCATAAGTGAT	59.352	43.478	0.00	0.00	45.87	3.06
1321	1322	6.432936	ACGCATACTGATTTTAGATGCATTG	58.567	36.000	0.00	0.00	42.41	2.82
1336	1388	7.783090	AGATGCATTGAAGTGTTACTGATAG	57.217	36.000	0.00	0.00	0.00	2.08
1471	1571	4.864334	GACCGGCCCTGGATGCAG	62.864	72.222	7.35	7.35	0.00	4.41
1473	1573	4.559063	CCGGCCCTGGATGCAGAG	62.559	72.222	16.85	2.98	0.00	3.35
1474	1574	4.559063	CGGCCCTGGATGCAGAGG	62.559	72.222	16.85	15.56	0.00	3.69
1475	1575	4.891037	GGCCCTGGATGCAGAGGC	62.891	72.222	27.38	27.38	37.62	4.70
1476	1576	4.891037	GCCCTGGATGCAGAGGCC	62.891	72.222	25.97	14.10	40.13	5.19
1477	1577	4.559063	CCCTGGATGCAGAGGCCG	62.559	72.222	16.85	0.00	40.13	6.13
1478	1578	3.473647	CCTGGATGCAGAGGCCGA	61.474	66.667	16.85	0.00	40.13	5.54
1479	1579	2.108566	CTGGATGCAGAGGCCGAG	59.891	66.667	8.85	0.00	40.13	4.63
1480	1580	2.364186	TGGATGCAGAGGCCGAGA	60.364	61.111	0.00	0.00	40.13	4.04
1481	1581	1.756408	CTGGATGCAGAGGCCGAGAT	61.756	60.000	8.85	0.00	40.13	2.75
1482	1582	0.469892	TGGATGCAGAGGCCGAGATA	60.470	55.000	0.00	0.00	40.13	1.98
1483	1583	0.901124	GGATGCAGAGGCCGAGATAT	59.099	55.000	0.00	0.00	40.13	1.63
1484	1584	1.134848	GGATGCAGAGGCCGAGATATC	60.135	57.143	0.00	0.00	40.13	1.63
1485	1585	1.824230	GATGCAGAGGCCGAGATATCT	59.176	52.381	4.47	4.47	40.13	1.98
1486	1586	1.709578	TGCAGAGGCCGAGATATCTT	58.290	50.000	6.70	0.00	40.13	2.40
1487	1587	2.876581	TGCAGAGGCCGAGATATCTTA	58.123	47.619	6.70	0.00	40.13	2.10
1488	1588	2.558795	TGCAGAGGCCGAGATATCTTAC	59.441	50.000	6.70	0.00	40.13	2.34
1489	1589	2.094442	GCAGAGGCCGAGATATCTTACC	60.094	54.545	6.70	8.87	0.00	2.85
1490	1590	2.494073	CAGAGGCCGAGATATCTTACCC	59.506	54.545	6.70	7.44	0.00	3.69
1491	1591	2.380590	AGAGGCCGAGATATCTTACCCT	59.619	50.000	6.70	11.93	0.00	4.34
1492	1592	2.756207	GAGGCCGAGATATCTTACCCTC	59.244	54.545	21.01	21.01	0.00	4.30
1493	1593	2.380590	AGGCCGAGATATCTTACCCTCT	59.619	50.000	6.70	0.00	0.00	3.69
1494	1594	3.166679	GGCCGAGATATCTTACCCTCTT	58.833	50.000	6.70	0.00	0.00	2.85
1495	1595	3.579151	GGCCGAGATATCTTACCCTCTTT	59.421	47.826	6.70	0.00	0.00	2.52
1496	1596	4.040584	GGCCGAGATATCTTACCCTCTTTT	59.959	45.833	6.70	0.00	0.00	2.27
1497	1597	5.454897	GGCCGAGATATCTTACCCTCTTTTT	60.455	44.000	6.70	0.00	0.00	1.94
1498	1598	5.467063	GCCGAGATATCTTACCCTCTTTTTG	59.533	44.000	6.70	0.00	0.00	2.44
1499	1599	6.685620	GCCGAGATATCTTACCCTCTTTTTGA	60.686	42.308	6.70	0.00	0.00	2.69
1500	1600	6.926272	CCGAGATATCTTACCCTCTTTTTGAG	59.074	42.308	6.70	0.00	42.30	3.02
1501	1601	7.201920	CCGAGATATCTTACCCTCTTTTTGAGA	60.202	40.741	6.70	0.00	45.39	3.27
1502	1602	8.198109	CGAGATATCTTACCCTCTTTTTGAGAA	58.802	37.037	6.70	0.00	45.39	2.87
1503	1603	9.892130	GAGATATCTTACCCTCTTTTTGAGAAA	57.108	33.333	6.70	0.00	45.39	2.52
1528	1628	8.667076	AAAATTTGGGAAGAAACTCAATCTTG	57.333	30.769	0.00	0.00	37.26	3.02
1529	1629	4.853924	TTGGGAAGAAACTCAATCTTGC	57.146	40.909	0.00	0.00	42.49	4.01
1530	1630	2.813754	TGGGAAGAAACTCAATCTTGCG	59.186	45.455	2.45	0.00	43.67	4.85
1531	1631	3.074412	GGGAAGAAACTCAATCTTGCGA	58.926	45.455	0.00	0.00	43.67	5.10
1532	1632	3.126000	GGGAAGAAACTCAATCTTGCGAG	59.874	47.826	0.00	0.00	43.67	5.03
1533	1633	3.126000	GGAAGAAACTCAATCTTGCGAGG	59.874	47.826	0.00	0.00	37.26	4.63
1534	1634	3.685139	AGAAACTCAATCTTGCGAGGA	57.315	42.857	0.00	0.00	33.36	3.71
1535	1635	4.213564	AGAAACTCAATCTTGCGAGGAT	57.786	40.909	0.00	0.00	33.36	3.24
1536	1636	4.583871	AGAAACTCAATCTTGCGAGGATT	58.416	39.130	0.00	0.00	34.21	3.01
1537	1637	5.734720	AGAAACTCAATCTTGCGAGGATTA	58.265	37.500	0.00	0.00	32.86	1.75
1538	1638	6.173339	AGAAACTCAATCTTGCGAGGATTAA	58.827	36.000	0.00	0.00	32.86	1.40
1539	1639	6.825721	AGAAACTCAATCTTGCGAGGATTAAT	59.174	34.615	0.00	0.00	32.86	1.40
1540	1640	7.337942	AGAAACTCAATCTTGCGAGGATTAATT	59.662	33.333	0.00	0.00	32.86	1.40
1541	1641	8.506168	AAACTCAATCTTGCGAGGATTAATTA	57.494	30.769	0.00	0.00	32.86	1.40
1542	1642	8.682936	AACTCAATCTTGCGAGGATTAATTAT	57.317	30.769	0.00	0.00	32.86	1.28
1543	1643	8.316640	ACTCAATCTTGCGAGGATTAATTATC	57.683	34.615	0.00	0.00	32.86	1.75
1544	1644	7.933577	ACTCAATCTTGCGAGGATTAATTATCA	59.066	33.333	0.00	0.00	34.77	2.15
1545	1645	8.853077	TCAATCTTGCGAGGATTAATTATCAT	57.147	30.769	0.00	0.00	34.77	2.45
1546	1646	9.288576	TCAATCTTGCGAGGATTAATTATCATT	57.711	29.630	0.00	0.00	34.77	2.57
1547	1647	9.552114	CAATCTTGCGAGGATTAATTATCATTC	57.448	33.333	0.00	0.00	34.77	2.67
1548	1648	8.853077	ATCTTGCGAGGATTAATTATCATTCA	57.147	30.769	0.00	0.00	34.77	2.57
1549	1649	8.853077	TCTTGCGAGGATTAATTATCATTCAT	57.147	30.769	0.00	0.00	34.77	2.57
1550	1650	9.288576	TCTTGCGAGGATTAATTATCATTCATT	57.711	29.630	0.00	0.00	34.77	2.57
1551	1651	9.552114	CTTGCGAGGATTAATTATCATTCATTC	57.448	33.333	0.00	0.00	34.77	2.67
1552	1652	8.620116	TGCGAGGATTAATTATCATTCATTCA	57.380	30.769	0.00	0.00	34.77	2.57
1553	1653	8.724229	TGCGAGGATTAATTATCATTCATTCAG	58.276	33.333	0.00	0.00	34.77	3.02
1554	1654	8.939929	GCGAGGATTAATTATCATTCATTCAGA	58.060	33.333	0.00	0.00	34.77	3.27
1604	1704	9.120538	TCTTGTTAATTACTCAATTATGGAGGC	57.879	33.333	1.29	0.00	36.68	4.70
2226	2326	5.047235	ACGAGTAAAGAGACTTGCCAGTAAT	60.047	40.000	0.00	0.00	34.59	1.89
2231	2331	4.464069	AGAGACTTGCCAGTAATGAGAC	57.536	45.455	0.00	0.00	31.22	3.36

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
65	66	6.767902	GCTCTTGGATTCATATCAAGTAACCA	59.232	38.462	0.00	0.00	32.09	3.67
108	109	5.540337	AGAGTGAGGTTGAGACTATGACAAA	59.460	40.000	0.00	0.00	0.00	2.83
222	223	4.058721	GTTTCAGCAAAACATTCCACCT	57.941	40.909	9.19	0.00	45.49	4.00
239	240	4.514066	ACGGTCAAACTAGGAACATGTTTC	59.486	41.667	13.36	11.15	34.84	2.78
283	284	6.784031	ACACTTTTGATTCTACTCTCCCAAT	58.216	36.000	0.00	0.00	0.00	3.16
335	336	4.632153	ACTCAGACAAAGCTGACGTTAAT	58.368	39.130	0.00	0.00	39.84	1.40
340	341	2.405357	CGTAACTCAGACAAAGCTGACG	59.595	50.000	0.00	0.00	39.84	4.35
435	436	8.271458	TGCCAGATAATCATACCAACTAGAAAA	58.729	33.333	0.00	0.00	0.00	2.29
516	517	4.461431	TGATTCAAAGCAGACTCAATGCAT	59.539	37.500	0.00	0.00	46.31	3.96
525	526	9.860898	ATACCTTTTATTTGATTCAAAGCAGAC	57.139	29.630	16.34	0.00	36.76	3.51
643	644	2.155732	CACGTCGTTTCATTGGAGACAG	59.844	50.000	0.00	0.00	44.54	3.51
647	648	1.148310	AGCACGTCGTTTCATTGGAG	58.852	50.000	0.00	0.00	0.00	3.86
660	661	1.338973	TGTTTCTTCCTCGTAGCACGT	59.661	47.619	8.22	0.00	43.14	4.49
853	854	7.874940	TCTTCAAGTTCATTGTCACTTAATGG	58.125	34.615	0.00	0.00	40.05	3.16
906	907	9.383519	TCAACATAAGATGAACCATTAAGAGAC	57.616	33.333	0.00	0.00	0.00	3.36
980	981	8.560903	TCTCCATAGTAGAGATTATGCCATCTA	58.439	37.037	0.00	0.00	35.46	1.98
993	994	5.684704	TGCCCAAAAATCTCCATAGTAGAG	58.315	41.667	0.00	0.00	0.00	2.43
997	998	4.403432	CACATGCCCAAAAATCTCCATAGT	59.597	41.667	0.00	0.00	0.00	2.12
1035	1036	8.303156	CGATAGGCAATGGAGATATTAGGATAG	58.697	40.741	0.00	0.00	0.00	2.08
1098	1099	5.169836	TCAACTTCGAAAAGCTTCTTTCC	57.830	39.130	0.00	0.00	35.81	3.13
1174	1175	8.707938	TTCTTCACGATGCATAATATATCCAG	57.292	34.615	0.00	0.00	0.00	3.86
1193	1194	9.465199	TGTCAATCTCATCCAATAATTTCTTCA	57.535	29.630	0.00	0.00	0.00	3.02
1239	1240	5.937540	TCTTCTAACATTCCTCGATGCAAAA	59.062	36.000	0.00	0.00	0.00	2.44
1312	1313	7.334090	ACTATCAGTAACACTTCAATGCATCT	58.666	34.615	0.00	0.00	0.00	2.90
1411	1511	1.896465	CGAACTAAAAATTGGGGGCCA	59.104	47.619	4.39	0.00	0.00	5.36
1467	1567	1.709578	AAGATATCTCGGCCTCTGCA	58.290	50.000	5.51	0.00	40.13	4.41
1468	1568	2.094442	GGTAAGATATCTCGGCCTCTGC	60.094	54.545	5.51	0.00	0.00	4.26
1469	1569	2.494073	GGGTAAGATATCTCGGCCTCTG	59.506	54.545	5.51	0.00	0.00	3.35
1470	1570	2.380590	AGGGTAAGATATCTCGGCCTCT	59.619	50.000	5.51	5.76	0.00	3.69
1471	1571	2.756207	GAGGGTAAGATATCTCGGCCTC	59.244	54.545	5.51	3.78	0.00	4.70
1472	1572	2.380590	AGAGGGTAAGATATCTCGGCCT	59.619	50.000	5.51	0.00	0.00	5.19
1473	1573	2.810164	AGAGGGTAAGATATCTCGGCC	58.190	52.381	5.51	8.44	0.00	6.13
1474	1574	4.875561	AAAGAGGGTAAGATATCTCGGC	57.124	45.455	5.51	0.00	0.00	5.54
1475	1575	6.817184	TCAAAAAGAGGGTAAGATATCTCGG	58.183	40.000	5.51	0.00	0.00	4.63
1476	1576	7.717568	TCTCAAAAAGAGGGTAAGATATCTCG	58.282	38.462	5.51	0.00	44.81	4.04
1477	1577	9.892130	TTTCTCAAAAAGAGGGTAAGATATCTC	57.108	33.333	5.51	0.00	44.81	2.75
1502	1602	9.112725	CAAGATTGAGTTTCTTCCCAAATTTTT	57.887	29.630	0.00	0.00	31.11	1.94
1503	1603	7.227314	GCAAGATTGAGTTTCTTCCCAAATTTT	59.773	33.333	0.00	0.00	31.11	1.82
1504	1604	6.707608	GCAAGATTGAGTTTCTTCCCAAATTT	59.292	34.615	0.00	0.00	31.11	1.82
1505	1605	6.226052	GCAAGATTGAGTTTCTTCCCAAATT	58.774	36.000	0.00	0.00	31.11	1.82
1506	1606	5.565439	CGCAAGATTGAGTTTCTTCCCAAAT	60.565	40.000	0.00	0.00	43.02	2.32
1507	1607	4.261572	CGCAAGATTGAGTTTCTTCCCAAA	60.262	41.667	0.00	0.00	43.02	3.28
1508	1608	3.253188	CGCAAGATTGAGTTTCTTCCCAA	59.747	43.478	0.00	0.00	43.02	4.12
1509	1609	2.813754	CGCAAGATTGAGTTTCTTCCCA	59.186	45.455	0.00	0.00	43.02	4.37
1510	1610	3.074412	TCGCAAGATTGAGTTTCTTCCC	58.926	45.455	0.00	0.00	45.01	3.97
1518	1618	7.933577	TGATAATTAATCCTCGCAAGATTGAGT	59.066	33.333	0.00	0.00	37.99	3.41
1519	1619	8.315391	TGATAATTAATCCTCGCAAGATTGAG	57.685	34.615	0.00	0.00	37.99	3.02
1520	1620	8.853077	ATGATAATTAATCCTCGCAAGATTGA	57.147	30.769	0.00	0.00	37.99	2.57
1521	1621	9.552114	GAATGATAATTAATCCTCGCAAGATTG	57.448	33.333	3.73	0.00	37.99	2.67
1522	1622	9.288576	TGAATGATAATTAATCCTCGCAAGATT	57.711	29.630	0.00	0.00	37.99	2.40
1523	1623	8.853077	TGAATGATAATTAATCCTCGCAAGAT	57.147	30.769	0.00	0.00	37.99	2.40
1524	1624	8.853077	ATGAATGATAATTAATCCTCGCAAGA	57.147	30.769	0.00	0.00	37.73	3.02
1525	1625	9.552114	GAATGAATGATAATTAATCCTCGCAAG	57.448	33.333	0.00	0.00	33.22	4.01
1526	1626	9.065798	TGAATGAATGATAATTAATCCTCGCAA	57.934	29.630	0.00	0.00	33.22	4.85
1527	1627	8.620116	TGAATGAATGATAATTAATCCTCGCA	57.380	30.769	0.00	0.00	33.22	5.10
1528	1628	8.939929	TCTGAATGAATGATAATTAATCCTCGC	58.060	33.333	0.00	0.00	33.22	5.03
1578	1678	9.120538	GCCTCCATAATTGAGTAATTAACAAGA	57.879	33.333	10.58	4.24	40.91	3.02
1579	1679	8.070171	CGCCTCCATAATTGAGTAATTAACAAG	58.930	37.037	10.58	0.00	40.91	3.16
1580	1680	7.554835	ACGCCTCCATAATTGAGTAATTAACAA	59.445	33.333	8.21	8.21	40.91	2.83
1581	1681	7.051623	ACGCCTCCATAATTGAGTAATTAACA	58.948	34.615	0.00	0.00	40.91	2.41
1582	1682	7.492352	ACGCCTCCATAATTGAGTAATTAAC	57.508	36.000	0.00	0.00	40.91	2.01
1583	1683	7.012894	CCAACGCCTCCATAATTGAGTAATTAA	59.987	37.037	0.00	0.00	40.91	1.40
1584	1684	6.485313	CCAACGCCTCCATAATTGAGTAATTA	59.515	38.462	0.00	0.00	41.56	1.40
1585	1685	5.299279	CCAACGCCTCCATAATTGAGTAATT	59.701	40.000	0.00	0.00	39.69	1.40
1586	1686	4.821805	CCAACGCCTCCATAATTGAGTAAT	59.178	41.667	0.00	0.00	0.00	1.89
1587	1687	4.196193	CCAACGCCTCCATAATTGAGTAA	58.804	43.478	0.00	0.00	0.00	2.24
1588	1688	3.804036	CCAACGCCTCCATAATTGAGTA	58.196	45.455	0.00	0.00	0.00	2.59
1589	1689	2.643551	CCAACGCCTCCATAATTGAGT	58.356	47.619	0.00	0.00	0.00	3.41
1590	1690	1.334869	GCCAACGCCTCCATAATTGAG	59.665	52.381	0.00	0.00	0.00	3.02
1591	1691	1.340502	TGCCAACGCCTCCATAATTGA	60.341	47.619	0.00	0.00	0.00	2.57
1592	1692	1.102154	TGCCAACGCCTCCATAATTG	58.898	50.000	0.00	0.00	0.00	2.32
1593	1693	1.846007	TTGCCAACGCCTCCATAATT	58.154	45.000	0.00	0.00	0.00	1.40
1594	1694	1.682854	CATTGCCAACGCCTCCATAAT	59.317	47.619	0.00	0.00	0.00	1.28
1595	1695	1.102154	CATTGCCAACGCCTCCATAA	58.898	50.000	0.00	0.00	0.00	1.90
1596	1696	0.034574	ACATTGCCAACGCCTCCATA	60.035	50.000	0.00	0.00	0.00	2.74
1597	1697	0.899717	AACATTGCCAACGCCTCCAT	60.900	50.000	0.00	0.00	0.00	3.41
1598	1698	1.530419	AACATTGCCAACGCCTCCA	60.530	52.632	0.00	0.00	0.00	3.86
1599	1699	1.080569	CAACATTGCCAACGCCTCC	60.081	57.895	0.00	0.00	0.00	4.30
1600	1700	1.080569	CCAACATTGCCAACGCCTC	60.081	57.895	0.00	0.00	0.00	4.70
1601	1701	1.112315	TTCCAACATTGCCAACGCCT	61.112	50.000	0.00	0.00	0.00	5.52
1604	1704	3.306703	GCATATTTCCAACATTGCCAACG	59.693	43.478	0.00	0.00	0.00	4.10
1710	1810	9.594478	TGTATTCACACATGTATTACGATTTCT	57.406	29.630	0.00	0.00	0.00	2.52
2226	2326	4.942944	TCCCAATACCTAGTTCAGTCTCA	58.057	43.478	0.00	0.00	0.00	3.27

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.