Locus 2860

Sequence ID	3L_DroMel_CAF1
Location	8,176,590 – 8,176,868
Length	278
Max. P	0.998184

overview

Window 7

Location	8,176,590 – 8,176,710
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	93.00
Mean single sequence MFE	-41.14
Consensus MFE	-37.04
Energy contribution	-38.16
Covariance contribution	1.12
Combinations/Pair	1.14
Mean z-score	-2.11
Structure conservation index	0.90
SVM decision value	3.03
SVM RNA-class probability	0.998184
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 8176590 120 - 23771897
ACAACCCACUUGGUCAUCCGGCGAAGGCCGCGCUUACACAUGCAGCUGUCGUCGUCGACAUGGCAGCACAACGUCUUUGACUCCGAUCCAACUUACUGGCCAGUUGAAGACGUUGUUGCU
............(((((.((((((.(((.((((........)).)).))).))))))..)))))(((((((((((((..(((.....(((......)))..)))..))))))))).)))) ( -45.70)
>DroSec_CAF1 4371 120 - 1
ACAAACAACUUGGUCAUCCGGCGAAGGCCGCGCUUACACAUGCAGCUGUCGUCGCCGACAUGGCAGCACAACGUCUUUGACUCCGAUCCAACUUACUGGCCAGUUGAAGAAGUUGUUGCU
............(((((.((((((.(((.((((........)).)).))).))))))..)))))((((((((.((((..(((.....(((......)))..)))..)))).)))).)))) ( -42.70)
>DroSim_CAF1 4346 120 - 1
ACAAACCACUUGGUCAUCCGGCGAAGGCCGCGCUUACACAUGCAGCUGUCGUCGCCGACAUGGCAGCACAACGUCUUUGACUCCGAUCCAACUUACUGGCCAGUUGAAGACGUUGUUGCU
............(((((.((((((.(((.((((........)).)).))).))))))..)))))(((((((((((((..(((.....(((......)))..)))..))))))))).)))) ( -48.40)
>DroEre_CAF1 4574 120 - 1
ACACCUCACUUGGCCAUCUGGAGAAGGCCGCGCUUACACAUGCAGCUGUCGUCGUCGACAUCGCAGCACAAAGUCUUUGACUCCGAUCCGAGUUACUUGCCAAUUGAAGACGUUGUUGCU
...........((((.((....)).))))((((........)).))(((((....)))))..((((((....(((((((((((......)))))...........))))))..)))))). ( -33.60)
>DroYak_CAF1 4455 120 - 1
ACACCUCACUUGGUCAUCCGGCGAAGGCCGCGCUUACACAUGCAGCUGUCGUCGCCGACGUCGCAGCACAAAGUCUUUGACUCCGAUCCAACUUGCUUGCCAAUUGAAGACGUUGUUGCU
..(((......)))....((((((.(((.((((........)).)).))).)))))).....((((((....(((((..(...(((.(......).)))....)..)))))..)))))). ( -35.30)
>consensus
ACAACCCACUUGGUCAUCCGGCGAAGGCCGCGCUUACACAUGCAGCUGUCGUCGCCGACAUGGCAGCACAACGUCUUUGACUCCGAUCCAACUUACUGGCCAGUUGAAGACGUUGUUGCU
............(((((.((((((.(((.((((........)).)).))).))))))..)))))(((((((((((((..(((.....(((......)))..)))..))))))))).)))) (-37.04 = -38.16 +   1.12)

alignment

secondary structure

dotplot

Window 8

Location	8,176,710 – 8,176,828
Length	118
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	86.45
Mean single sequence MFE	-19.82
Consensus MFE	-14.98
Energy contribution	-16.18
Covariance contribution	1.20
Combinations/Pair	1.11
Mean z-score	-1.80
Structure conservation index	0.76
SVM decision value	0.44
SVM RNA-class probability	0.736132
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 8176710 118 + 23771897
AUAUAAGCUGGCCAGCUGGGUUAAUUCAACAUCAAACCUAGCUCACAGCUCCCAGUAGUCACUUCUACCAAACA-AAGCACC-AAUCAACAAUCAACAUGAAAUUCGUAAGUUCAUUGAU
.....(((((...(((((((((............)))))))))..)))))....((((......))))......-.......-......((((.((((((.....)))..))).)))).. ( -24.40)
>DroSec_CAF1 4491 112 + 1
AUAUAAGCUGGCUAGCUGGGUUAACUCGACAUCAAACCAAGCUCACAGCUCCAAGUAGUCACUACAACCAAACACAAAAACC-AAU-------CAACAUGAAAUUCGUAAGUUCAUUGAU
.....(((((...((((.((((............)))).))))..)))))....((((...)))).................-.((-------((..(((((...(....)))))))))) ( -19.20)
>DroSim_CAF1 4466 119 + 1
AUAUAAGCUGGCCAGCUGGGUUAACUCGACAUCAAACCAAGCUUACAGCUCCAAGUAGUCACUACAACCAAACACAAAAACC-AAUCAACAAUCAACAUGAAAUUCGUAAGUUCAUUGAU
.....(((((...((((.((((............)))).))))..)))))....((((...)))).................-......((((.((((((.....)))..))).)))).. ( -19.30)
>DroEre_CAF1 4694 115 + 1
AUAUAAACUGGCCAGCUUGGUUGAGUCAGUAUCAAACCAAGCUCACAGCUCCAAGUAGUCACUGCUACCAAACA-AAACCCC-AUUCAACAAUC---AUGAAAUUCGUAAGUCCAUUGAU
.......(((...(((((((((((.......)).)))))))))..)))......(((((....)))))......-.......-........(((---(.......(....).....)))) ( -20.60)
>DroYak_CAF1 4575 116 + 1
AUAUAAACUGGCCAGCUGGGUUAACUCAAUAUCAAACACAGCUCACAGCUUCAAGUAGUCACUACUACCAAACA-CAACACCAAUUCAACAAUC---AUGAAAUUCGUAAGUUCAUUGAU
.......(((...(((((.(((............))).)))))..)))......(((((....)))))......-................(((---(((((...(....))))).)))) ( -15.60)
>consensus
AUAUAAGCUGGCCAGCUGGGUUAACUCAACAUCAAACCAAGCUCACAGCUCCAAGUAGUCACUACUACCAAACA_AAACACC_AAUCAACAAUCAACAUGAAAUUCGUAAGUUCAUUGAU
.....(((((...(((((((((............)))))))))..)))))....((((......)))).................................................... (-14.98 = -16.18 +   1.20)

alignment

secondary structure

dotplot

Window 9

Location	8,176,750 – 8,176,868
Length	118
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	84.01
Mean single sequence MFE	-18.72
Consensus MFE	-13.24
Energy contribution	-14.44
Covariance contribution	1.20
Combinations/Pair	1.26
Mean z-score	-1.64
Structure conservation index	0.71
SVM decision value	0.06
SVM RNA-class probability	0.562921
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 8176750 118 + 23771897
GCUCACAGCUCCCAGUAGUCACUUCUACCAAACA-AAGCACC-AAUCAACAAUCAACAUGAAAUUCGUAAGUUCAUUGAUUAUCUUAAGGAUUGAUGGGAUCUAUUAAUUAAGGAGUACU
((((..((.(((((((((......))))......-......(-((((...(((((..(((((...(....)))))))))))........))))).))))).))..........))))... ( -20.00)
>DroSec_CAF1 4531 112 + 1
GCUCACAGCUCCAAGUAGUCACUACAACCAAACACAAAAACC-AAU-------CAACAUGAAAUUCGUAAGUUCAUUGAUUAUCUUAAGGAUUUAAAGAACUUACCCAUUAAGGAUUACU
((.....))....(((((((.((...................-..(-------(.....)).....((((((((.((((..(((.....))))))).))))))))......))))))))) ( -18.30)
>DroSim_CAF1 4506 119 + 1
GCUUACAGCUCCAAGUAGUCACUACAACCAAACACAAAAACC-AAUCAACAAUCAACAUGAAAUUCGUAAGUUCAUUGAUUAUCUUAAGGAUUUAAAGGACUUACCCAUUAAGGAUUACU
((.....))....(((((((.((...................-.........((.....)).....((((((((.((((..(((.....))))))).))))))))......))))))))) ( -17.80)
>DroEre_CAF1 4734 115 + 1
GCUCACAGCUCCAAGUAGUCACUGCUACCAAACA-AAACCCC-AUUCAACAAUC---AUGAAAUUCGUAAGUCCAUUGAUCACCUAAAGGAUUUAAAGGACUUAAUUAUUAAGGAGUACU
.......(((((..(((((....)))))......-.......-...........---....(((...(((((((.((((...((....))..)))).)))))))...)))..)))))... ( -23.90)
>DroYak_CAF1 4615 116 + 1
GCUCACAGCUUCAAGUAGUCACUACUACCAAACA-CAACACCAAUUCAACAAUC---AUGAAAUUCGUAAGUUCAUUGAUUACCUUAAGGAUUUAAAGGACUUUCUUAUUAAUUAGCACU
.......(((....(((((....)))))......-.....((........((((---(((((...(....))))).))))).((....)).......))...............)))... ( -13.60)
>consensus
GCUCACAGCUCCAAGUAGUCACUACUACCAAACA_AAACACC_AAUCAACAAUCAACAUGAAAUUCGUAAGUUCAUUGAUUAUCUUAAGGAUUUAAAGGACUUACUCAUUAAGGAGUACU
.......(((((..((((......))))......................................((((((((.((((...((....))..)))).)))))))).......)))))... (-13.24 = -14.44 +   1.20)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:43:35 2006