Locus 5420

Sequence ID	3L_DroMel_CAF1
Location	14,853,916 – 14,854,066
Length	150
Max. P	0.864861

overview

Window 7

Location	14,853,916 – 14,854,028
Length	112
Sequences	5
Columns	112
Reading direction	forward
Mean pairwise identity	74.46
Mean single sequence MFE	-22.95
Consensus MFE	-10.57
Energy contribution	-11.53
Covariance contribution	0.96
Combinations/Pair	1.33
Mean z-score	-1.98
Structure conservation index	0.46
SVM decision value	0.84
SVM RNA-class probability	0.864861
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 14853916 112 + 23771897
UUUGACUUUAAGCUUAGCAUAUAGACUGUCAUCUAAAAUAUCGAUGUUUGUUAGGCUUUGUUUAUGCAGUCAUUAAAAUAUCAUUAAUUUCAUAAAUAUUGUGCUGCAAAAG
...(((...((((((((((..........((((.........))))..)))))))))).)))..(((((.(((...(((((..............))))))))))))).... ( -19.44)
>DroSec_CAF1 30504 97 + 1
UUUGACUUUUAGCUAAGCACAUAGACUGUCAUCUAAAAUAAUGAUGUUUGU---------------CAGUCAUUAAAAUAUCAUUCAUUUGAUAAAUAUUGUGCUGCAAAAG
.....(((((.((..((((((..(((((.((((.........)))).....---------------))))).......(((((......))))).....))))))))))))) ( -23.80)
>DroSim_CAF1 31101 112 + 1
UUUGACUUUUAGCUAAGCACAUGGACUGUCAUCUAAAAUAAUGAUGUUUGUUUGGCUUUCUUUAUGCAGUCAUUAAAAUAUCAUUUAUUUGAUAAAUAUUGUGCUGCAAAAG
.....(((((.((..((((((.....(((((..(((....(((((((((...(((((..........)))))...))))))))))))..))))).....))))))))))))) ( -26.60)
>DroEre_CAF1 32619 91 + 1
--UGACUUUUAGCUAAGCAUAUAGACCGACUUCUAAAAUAAUCAUGUUUGCCUGACU--------GCAAGCUG-CAAGUCU-------CUUAAGAAUUUUGUUUUUCAA---
--.(((((.(((((..(((..((((......))))......(((.(....).))).)--------)).)))))-.))))).-------.....(((........)))..--- ( -15.80)
>DroYak_CAF1 27103 112 + 1
UUUGACUUUGAGCUAAGCAUAUAGACUGACAUCUGAAAUAAUGAUGUUUGCUUGGUUUGGUUUAUGCAGUCAUUAAAAUGUCAUGCAAUUGAUAAAUGUUGUGCUGCAAAUG
.......(..(((((((((........((((((.........)))))))))))))))..)....(((((.(((.....(((((......)))))......)))))))).... ( -29.10)
>consensus
UUUGACUUUUAGCUAAGCAUAUAGACUGUCAUCUAAAAUAAUGAUGUUUGUUUGGCUU__UUUAUGCAGUCAUUAAAAUAUCAUUCAUUUGAUAAAUAUUGUGCUGCAAAAG
..........((((((((...((((......))))(((((....)))))))))))))........(((((........(((((......)))))........)))))..... (-10.57 = -11.53 +   0.96)

alignment

secondary structure

dotplot

Window 8

Location	14,853,916 – 14,854,028
Length	112
Sequences	5
Columns	112
Reading direction	reverse
Mean pairwise identity	74.46
Mean single sequence MFE	-17.98
Consensus MFE	-3.28
Energy contribution	-4.16
Covariance contribution	0.88
Combinations/Pair	1.14
Mean z-score	-1.55
Structure conservation index	0.18
SVM decision value	0.12
SVM RNA-class probability	0.593544
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 14853916 112 - 23771897
CUUUUGCAGCACAAUAUUUAUGAAAUUAAUGAUAUUUUAAUGACUGCAUAAACAAAGCCUAACAAACAUCGAUAUUUUAGAUGACAGUCUAUAUGCUAAGCUUAAAGUCAAA
((((.((((((.........((((((.......))))))..(((((..........(.....)...((((.........)))).)))))....))))..))..))))..... ( -13.30)
>DroSec_CAF1 30504 97 - 1
CUUUUGCAGCACAAUAUUUAUCAAAUGAAUGAUAUUUUAAUGACUG---------------ACAAACAUCAUUAUUUUAGAUGACAGUCUAUGUGCUUAGCUAAAAGUCAAA
(((((((((((((.....(((((......))))).......(((((---------------.......(((((......))))))))))..))))))..)).)))))..... ( -20.71)
>DroSim_CAF1 31101 112 - 1
CUUUUGCAGCACAAUAUUUAUCAAAUAAAUGAUAUUUUAAUGACUGCAUAAAGAAAGCCAAACAAACAUCAUUAUUUUAGAUGACAGUCCAUGUGCUUAGCUAAAAGUCAAA
(((((((((((((.....(((((......))))).......((((((((...((((..................))))..))).)))))..))))))..)).)))))..... ( -20.67)
>DroEre_CAF1 32619 91 - 1
---UUGAAAAACAAAAUUCUUAAG-------AGACUUG-CAGCUUGC--------AGUCAGGCAAACAUGAUUAUUUUAGAAGUCGGUCUAUAUGCUUAGCUAAAAGUCA--
---.....................-------.(((((.-.((((.((--------(...((((..((.(((.....)))...))..))))...)))..))))..))))).-- ( -19.80)
>DroYak_CAF1 27103 112 - 1
CAUUUGCAGCACAACAUUUAUCAAUUGCAUGACAUUUUAAUGACUGCAUAAACCAAACCAAGCAAACAUCAUUAUUUCAGAUGUCAGUCUAUAUGCUUAGCUCAAAGUCAAA
..((((.(((...................((((((((((((((.(((..............)))....))))))....))))))))((......))...)))))))...... ( -15.44)
>consensus
CUUUUGCAGCACAAUAUUUAUCAAAUGAAUGAUAUUUUAAUGACUGCAUAAA__AAGCCAAACAAACAUCAUUAUUUUAGAUGACAGUCUAUAUGCUUAGCUAAAAGUCAAA
........................................(((((.....................((((.........))))..((.(((......)))))...))))).. ( -3.28 =  -4.16 +   0.88)

alignment

secondary structure

dotplot

Window 9

Location	14,853,956 – 14,854,066
Length	110
Sequences	4
Columns	112
Reading direction	forward
Mean pairwise identity	79.79
Mean single sequence MFE	-21.23
Consensus MFE	-13.68
Energy contribution	-15.49
Covariance contribution	1.81
Combinations/Pair	1.12
Mean z-score	-1.74
Structure conservation index	0.64
SVM decision value	0.19
SVM RNA-class probability	0.624975
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 14853956 110 + 23771897
UCGAUGUUUGUUAGGCUUUGUUUAUGCAGUCAUUAAAAUAUCAUUAAUUUCAUAAAUAUUGUGCUGCAAAAGU--UAAGCCUCUUAAGCAUUCUGUUUUUCAAUUUAUAUGA
..((((((((..((((((..(((.(((((.(((...(((((..............))))))))))))).))).--.))))))..)))))))).................... ( -24.64)
>DroSec_CAF1 30544 95 + 1
AUGAUGUUUGU---------------CAGUCAUUAAAAUAUCAUUCAUUUGAUAAAUAUUGUGCUGCAAAAGUC-UAAGCCUCUUAAGCAUUCUGUU-UUCAACAUAUAUGA
(((((((((..---------------.........)))))))))((((((((.(((((..(((((......((.-...))......)))))..))))-))))).....)))) ( -14.50)
>DroSim_CAF1 31141 111 + 1
AUGAUGUUUGUUUGGCUUUCUUUAUGCAGUCAUUAAAAUAUCAUUUAUUUGAUAAAUAUUGUGCUGCAAAAGUCCUAAGCCUCUUAAGCAUUCUGUU-UUCAACAUAUAUGA
..((((((((...(((((.((((.(((((.(((.....(((((......)))))......))))))))))))....)))))...)))))))).....-.............. ( -27.70)
>DroYak_CAF1 27143 104 + 1
AUGAUGUUUGCUUGGUUUGGUUUAUGCAGUCAUUAAAAUGUCAUGCAAUUGAUAAAUGUUGUGCUGCAAAUGUAUUAAGUCUCUUAAGAAUUUUG--------UAUAUAUGA
...((((.(((..(((((......(((((.(((.....(((((......)))))......))))))))......(((((...))))))))))..)--------)).)))).. ( -18.10)
>consensus
AUGAUGUUUGUUUGGCUUUGUUUAUGCAGUCAUUAAAAUAUCAUUCAUUUGAUAAAUAUUGUGCUGCAAAAGUC_UAAGCCUCUUAAGCAUUCUGUU_UUCAACAUAUAUGA
..((((((((...(((((......(((((.(((.....(((((......)))))......))))))))........)))))...)))))))).................... (-13.68 = -15.49 +   1.81)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:49:56 2006