Locus 4266

Sequence ID	3R_DroMel_CAF1
Location	11,397,651 – 11,397,791
Length	140
Max. P	0.965644

overview

Window 3

Location	11,397,651 – 11,397,751
Length	100
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	89.72
Mean single sequence MFE	-31.82
Consensus MFE	-27.38
Energy contribution	-27.98
Covariance contribution	0.60
Combinations/Pair	1.00
Mean z-score	-1.42
Structure conservation index	0.86
SVM decision value	0.42
SVM RNA-class probability	0.728891
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11397651 100 + 27905053
----G----------------GAAUCUGCCGGGCGGCAGUCAUAAAGCCCAGGAAACAUGGCCAUGGUCUUCAUACCGGCUCAACACUGACAGGUGUAAAUUGCCGAGGCUUAACAAAAG
----.----------------......(((...(((((((.....((((..(....)..(((....)))........))))..(((((....)))))..))))))).))).......... ( -29.60)
>DroSec_CAF1 145350 100 + 1
----G----------------GAAUCUGCCGGUCGGCAGUCAUAAAGCCCAGGAAACAUGGCCAUGGUCUUCAUGCCGGCUCAACACUGACAGGUGUAAAUUGCCGAGGCUUAACAAAAG
----.----------------......(((..((((((((.....((((..(....)..(((.(((.....))))))))))..(((((....)))))..))))))))))).......... ( -32.20)
>DroSim_CAF1 136432 100 + 1
----G----------------GAAUCUGCCGGUCGGCAGUCAUAAAGCCCAGGAAACAUGGCCAUGGUCUUCAUGCCGGCUCAACACUGACAGGUGUAAAUUGCCGAGGCUUAACAAAAG
----.----------------......(((..((((((((.....((((..(....)..(((.(((.....))))))))))..(((((....)))))..))))))))))).......... ( -32.20)
>DroEre_CAF1 133520 101 + 1
UUUCG----------------GAAUCUGCCGG---GCAGUCAUAAAGCCCAGGAAACAUGGCCAUGGUCUUCAUGCCGGCUCAACACUGACAGGUGUAAAUUGCCGAGGCUUAACAAAAG
.....----------------......(((.(---(((((.....((((..(....)..(((.(((.....))))))))))..(((((....)))))..))))))..))).......... ( -29.90)
>DroYak_CAF1 136308 117 + 1
UUUCGGCAUUUCAACAUUUUGGAAUCUGCCGG---GCAGUCAUAAAGCCCAGGAAACAUGGCCAUGGUCUUCAUGCCGGCUCAACACUGACAGGUGUAAAUUGCCGAGGCUUAACAAAAG
.(((((((((((((....))))))...(((((---((.........)))).(....)..(((.(((.....)))))))))...(((((....)))))....)))))))............ ( -35.20)
>consensus
____G________________GAAUCUGCCGG_CGGCAGUCAUAAAGCCCAGGAAACAUGGCCAUGGUCUUCAUGCCGGCUCAACACUGACAGGUGUAAAUUGCCGAGGCUUAACAAAAG
.....................((..(((((....)))))))...((((((.(....)..(((.(((.....))))))(((...(((((....))))).....)))).)))))........ (-27.38 = -27.98 +   0.60)

alignment

secondary structure

dotplot

Window 4

Location	11,397,671 – 11,397,791
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	97.08
Mean single sequence MFE	-36.22
Consensus MFE	-33.32
Energy contribution	-33.32
Covariance contribution	0.00
Combinations/Pair	1.00
Mean z-score	-1.64
Structure conservation index	0.92
SVM decision value	1.58
SVM RNA-class probability	0.965644
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11397671 120 + 27905053
CAUAAAGCCCAGGAAACAUGGCCAUGGUCUUCAUACCGGCUCAACACUGACAGGUGUAAAUUGCCGAGGCUUAACAAAAGCCACUGCAGAGCUUCGAGUAAACAGGAGGAGCAGGAUGUG
((((....((((....).)))((.((.(((((.(((((((((.(((((....)))))....(((.(.(((((.....))))).).)))))))..)).))).....))))).)))).)))) ( -36.50)
>DroSec_CAF1 145370 120 + 1
CAUAAAGCCCAGGAAACAUGGCCAUGGUCUUCAUGCCGGCUCAACACUGACAGGUGUAAAUUGCCGAGGCUUAACAAAAGCCACUGCAGAGCUUUGAGUAAACAGGAGGAGCAGGAUGUG
((((....((((....).)))((.((.(((((.((...((((((((((....)))))...((((.(.(((((.....))))).).)))).....)))))...)).))))).)))).)))) ( -37.40)
>DroSim_CAF1 136452 120 + 1
CAUAAAGCCCAGGAAACAUGGCCAUGGUCUUCAUGCCGGCUCAACACUGACAGGUGUAAAUUGCCGAGGCUUAACAAAAGCCACUGCAGAGCUUUGAGUAAACAGGAGGAGCAGGAUGUG
((((....((((....).)))((.((.(((((.((...((((((((((....)))))...((((.(.(((((.....))))).).)))).....)))))...)).))))).)))).)))) ( -37.40)
>DroEre_CAF1 133541 119 + 1
CAUAAAGCCCAGGAAACAUGGCCAUGGUCUUCAUGCCGGCUCAACACUGACAGGUGUAAAUUGCCGAGGCUUAACAAAAGCCACUGGG-AGCUUUGAGUAAACAGGAGGAGCAGGAUGUA
........((((....).)))((.((.(((((.((...((((((..((..((((((.....))))..(((((.....)))))..))..-))..))))))...)).))))).))))..... ( -35.40)
>DroYak_CAF1 136345 120 + 1
CAUAAAGCCCAGGAAACAUGGCCAUGGUCUUCAUGCCGGCUCAACACUGACAGGUGUAAAUUGCCGAGGCUUAACAAAAGCCACUGCGAAGCUUUCAGUAAACAGGAGGAGCAGGAUGUA
......(((..(....)..)))((((.....)))).((((...(((((....))))).....)))).(((((.....))))).((((....(((((........))))).))))...... ( -34.40)
>consensus
CAUAAAGCCCAGGAAACAUGGCCAUGGUCUUCAUGCCGGCUCAACACUGACAGGUGUAAAUUGCCGAGGCUUAACAAAAGCCACUGCAGAGCUUUGAGUAAACAGGAGGAGCAGGAUGUG
........((((....).)))((.((.(((((....((((...(((((....))))).....)))).(((((.....))))).(((....((.....))...)))))))).))))..... (-33.32 = -33.32 +   0.00)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:23:57 2006