Locus 1024

Sequence ID	2R_DroMel_CAF1
Location	4,226,210 – 4,226,518
Length	308
Max. P	0.996881

overview

Window 7

Location	4,226,210 – 4,226,324
Length	114
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	94.50
Mean single sequence MFE	-27.46
Consensus MFE	-23.36
Energy contribution	-23.76
Covariance contribution	0.40
Combinations/Pair	1.00
Mean z-score	-1.97
Structure conservation index	0.85
SVM decision value	1.85
SVM RNA-class probability	0.979837
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 4226210 114 + 20766785
GACUGGGAUAUU------AAAUACCGCCAAAACCAGCGGUCAACUUCACAAUCGGUAGCAGACCAGAGCCAACUAUUUGCCACUUGAACCGCAGUCUCAUUAACGACAUCCUCGUUAACA
(((((((.....------....(((((........)))))...........(((((.(((((..((......)).))))).)).))).)).)))))...(((((((.....))))))).. ( -27.10)
>DroSec_CAF1 38077 114 + 1
GACUGGGAUAUU------AAAUACCGCCAAAAGCAGCGGUCAACUUCACAAUCGGUCGCAGACCAGAGCCAACUAUUUGCCACUUGAACCGCAGUCUCAUUAACGACAUCCUCGUUAACA
(((((((.....------....(((((........)))))...........(((((.(((((..((......)).))))).)).))).)).)))))...(((((((.....))))))).. ( -27.10)
>DroSim_CAF1 67479 114 + 1
GACUGGGAUAUU------AAAUACCGCCAAAAGCAGCGGUCAACUUCACAAUCGGUCGCAGACCAGAGCCAACUAUUUGCCACUUGAACCGCAGUCUCAUUAACGACAUCCUCGUUAACA
(((((((.....------....(((((........)))))...........(((((.(((((..((......)).))))).)).))).)).)))))...(((((((.....))))))).. ( -27.10)
>DroEre_CAF1 39588 114 + 1
GACUGAGAUAUU------AAAUACCGCCAAAAGCAGCGGUCAACUUCACAAUCGGUCGCAGAGCAGAGCAAACUAUUUGCCACUUGAACCGCAGUCUCAUUAACGACAUCCUCGUUAACA
(((((.......------....(((((........)))))............((((((.((.(((((........)))))..)))).)))))))))...(((((((.....))))))).. ( -27.00)
>DroYak_CAF1 40721 120 + 1
CACUGAGAUAUUACUCGUAAAUACCGCCAAAAGCAGCGGUCAGCUUUACAAUCGGUCACAGACCAGAGCAAACUAUUUGCCACUUGAACCGCAGUCUCAUUAACGACAUCCUCGUUAACA
...((((((................((.....)).((((((((..........((((...)))).(.((((.....)))))..))).))))).))))))(((((((.....))))))).. ( -29.00)
>consensus
GACUGGGAUAUU______AAAUACCGCCAAAAGCAGCGGUCAACUUCACAAUCGGUCGCAGACCAGAGCCAACUAUUUGCCACUUGAACCGCAGUCUCAUUAACGACAUCCUCGUUAACA
(((((.(...............(((((........)))))...........(((((.(((((..((......)).))))).)).)))..).)))))...(((((((.....))))))).. (-23.36 = -23.76 +   0.40)

alignment

secondary structure

dotplot

Window 8

Location	4,226,284 – 4,226,404
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	96.15
Mean single sequence MFE	-24.86
Consensus MFE	-24.60
Energy contribution	-24.60
Covariance contribution	-0.00
Combinations/Pair	1.00
Mean z-score	-1.59
Structure conservation index	0.99
SVM decision value	2.25
SVM RNA-class probability	0.991216
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 4226284 120 + 20766785
CACUUGAACCGCAGUCUCAUUAACGACAUCCUCGUUAACAAAGUUGCUCUGAAUGGGUUUCAGUUGUUUUUGUGCUUAAUAACUUGCUUAAGCUUUCAGUUUUUAAGUUCAACUCCGUCC
...((((((.((((..(..(((((((.....)))))))..)..)))).(((((..(((((.(((.(((.(((....))).)))..))).)))))))))).......))))))........ ( -25.40)
>DroSec_CAF1 38151 120 + 1
CACUUGAACCGCAGUCUCAUUAACGACAUCCUCGUUAACAAAGUUGCUCUGAAUGGGUUUCAGUUGUUUUUGUGCUUAAUAACUUGCUUAAGCUUUCAGUUUUUAAGUUCACCUCCGUCC
(((..((((.((((..(..(((((((.....)))))))..)..)))).(((((.....)))))..))))..)))(((((.((((.((....))....)))).)))))............. ( -24.60)
>DroSim_CAF1 67553 120 + 1
CACUUGAACCGCAGUCUCAUUAACGACAUCCUCGUUAACAAAGUUGCUCUGAAUGGGUUUCAGUUGUUUUUGUGCUUAAUAACUUGCUUAAGCUUUCAGUUUUUAAGUUCACCUCCGUCC
(((..((((.((((..(..(((((((.....)))))))..)..)))).(((((.....)))))..))))..)))(((((.((((.((....))....)))).)))))............. ( -24.60)
>DroEre_CAF1 39662 116 + 1
CACUUGAACCGCAGUCUCAUUAACGACAUCCUCGUUAACAAAGUUGCUCUGAAUGAGUUUCAGUUGUUUUUGUGCUUAAUAACUUGCUUAAGCUUUCAGUUUUUAAGUUCACU----CCC
....(((((.((((..(..(((((((.....)))))))..)..)))).((((..((((((.(((.(((.(((....))).)))..))).)))))))))).......)))))..----... ( -25.00)
>DroYak_CAF1 40801 116 + 1
CACUUGAACCGCAGUCUCAUUAACGACAUCCUCGUUAACAAAGUUGCUCUGAAUGAGUUUCAGUUGUUUUUGUGCUUAAUAACUUGCUUAAGCUUUCAGUUUUUAAGUUCCCC----UCC
.(((((((..((((..(..(((((((.....)))))))..)..)))).((((..((((((.(((.(((.(((....))).)))..))).))))))))))..))))))).....----... ( -24.70)
>consensus
CACUUGAACCGCAGUCUCAUUAACGACAUCCUCGUUAACAAAGUUGCUCUGAAUGGGUUUCAGUUGUUUUUGUGCUUAAUAACUUGCUUAAGCUUUCAGUUUUUAAGUUCACCUCCGUCC
(((..((((.((((..(..(((((((.....)))))))..)..)))).(((((.....)))))..))))..)))(((((.((((.((....))....)))).)))))............. (-24.60 = -24.60 +  -0.00)

alignment

secondary structure

dotplot

Window 9

Location	4,226,284 – 4,226,404
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	96.15
Mean single sequence MFE	-28.28
Consensus MFE	-27.08
Energy contribution	-27.28
Covariance contribution	0.20
Combinations/Pair	1.00
Mean z-score	-1.83
Structure conservation index	0.96
SVM decision value	2.76
SVM RNA-class probability	0.996881
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 4226284 120 - 20766785
GGACGGAGUUGAACUUAAAAACUGAAAGCUUAAGCAAGUUAUUAAGCACAAAAACAACUGAAACCCAUUCAGAGCAACUUUGUUAACGAGGAUGUCGUUAAUGAGACUGCGGUUCAAGUG
......(.(((((((......(((((.((((((........)))))).((........)).......))))).(((..((..(((((((.....)))))))..))..)))))))))).). ( -29.30)
>DroSec_CAF1 38151 120 - 1
GGACGGAGGUGAACUUAAAAACUGAAAGCUUAAGCAAGUUAUUAAGCACAAAAACAACUGAAACCCAUUCAGAGCAACUUUGUUAACGAGGAUGUCGUUAAUGAGACUGCGGUUCAAGUG
((((....(((..(((((.((((....((....)).)))).))))))))........(((((.....))))).(((..((..(((((((.....)))))))..))..))).))))..... ( -28.40)
>DroSim_CAF1 67553 120 - 1
GGACGGAGGUGAACUUAAAAACUGAAAGCUUAAGCAAGUUAUUAAGCACAAAAACAACUGAAACCCAUUCAGAGCAACUUUGUUAACGAGGAUGUCGUUAAUGAGACUGCGGUUCAAGUG
((((....(((..(((((.((((....((....)).)))).))))))))........(((((.....))))).(((..((..(((((((.....)))))))..))..))).))))..... ( -28.40)
>DroEre_CAF1 39662 116 - 1
GGG----AGUGAACUUAAAAACUGAAAGCUUAAGCAAGUUAUUAAGCACAAAAACAACUGAAACUCAUUCAGAGCAACUUUGUUAACGAGGAUGUCGUUAAUGAGACUGCGGUUCAAGUG
...----..((((((......(((((.((((((........))))))...........((.....))))))).(((..((..(((((((.....)))))))..))..))))))))).... ( -28.10)
>DroYak_CAF1 40801 116 - 1
GGA----GGGGAACUUAAAAACUGAAAGCUUAAGCAAGUUAUUAAGCACAAAAACAACUGAAACUCAUUCAGAGCAACUUUGUUAACGAGGAUGUCGUUAAUGAGACUGCGGUUCAAGUG
...----...(((((......(((((.((((((........))))))...........((.....))))))).(((..((..(((((((.....)))))))..))..))))))))..... ( -27.20)
>consensus
GGACGGAGGUGAACUUAAAAACUGAAAGCUUAAGCAAGUUAUUAAGCACAAAAACAACUGAAACCCAUUCAGAGCAACUUUGUUAACGAGGAUGUCGUUAAUGAGACUGCGGUUCAAGUG
.........((((((......(((((.((((((........)))))).((........)).......))))).(((..((..(((((((.....)))))))..))..))))))))).... (-27.08 = -27.28 +   0.20)

alignment

secondary structure

dotplot

Window 0

Location	4,226,404 – 4,226,518
Length	114
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	93.50
Mean single sequence MFE	-38.39
Consensus MFE	-35.26
Energy contribution	-35.74
Covariance contribution	0.48
Combinations/Pair	1.08
Mean z-score	-1.13
Structure conservation index	0.92
SVM decision value	0.17
SVM RNA-class probability	0.615066
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 4226404 114 - 20766785
------UGCAGCUCGAAAGACCUGCAGAGGGACAGCAAGGUGAGUGCGUUGGGCUGUAACCACUUUGUCAAUCCACUUUGUCCAACCAACCGAGUGCCACCAAGUGCUUUCCUUAUGGCA
------(((((.((....)).))))).(((((.((((.((((.(..((((((((.........................)))))))(....).)..)))))...)))).)))))...... ( -38.21)
>DroSec_CAF1 38271 120 - 1
AUAAUCUGCAGCUCGAAGGACCUGCAGAGGGACAGCAAGGUGAGUGCGUUGGGCUGGAACCACUUUGUCAAUCCACUUUGUCCAACCAACCGAGUGCCACCAAGUGCUUUCCUUGUGGCA
....(((((((.((....)).)))))))((((.((((.((((.(..((((((((((((.............))))....)))))))(....).)..)))))...)))).))))....... ( -43.32)
>DroSim_CAF1 67673 120 - 1
AUAAUCUGCAGCUCGAAGGACCUGCAGAGGGACAGCAAGGUGAGUGCGUUGGGCUGGAACCACUUUGUCAAUCCACUUUGUCCAACCAACCGAGUGUUACCAAGUGCUUUCCUUGUGGCA
....(((((((.((....)).)))))))..(...((((((.(((..((((((((((((.............))))....))))))).(((.....))).....)..))).))))))..). ( -40.52)
>DroEre_CAF1 39778 119 - 1
AUCAUCUGAAGCUCGAAGGACCUGCAGAAGGAUAGCA-GGUGAGUGCGUUGGGCUGGAACCACUUUGUCAAUCUACUUUGUCCAACCAACCGAGUGCCACCAAGUGCUUUCCUUGUGGCA
.(((((((.((.((....)).)).)))(((((.((((-((((.(..((((((..((((........(.....).......)))).)))))...)..)))))...)))).))))))))).. ( -35.66)
>DroYak_CAF1 40917 120 - 1
AUAAUCUGAAGCUCGAAGGACCUGCAGAAGGAUAGCAAGGUGAGUGCGUUGGGCUGGAACCACUUUGUCAAUCUACUUUGUCCAACCAACCGAGUGGCACCAAGUGCUUUCCUUGUGGCA
....((((.((.((....)).)).))))((((.((((.((((..((.(((((..((((........(.....).......)))).))))))).....))))...)))).))))....... ( -34.26)
>consensus
AUAAUCUGCAGCUCGAAGGACCUGCAGAGGGACAGCAAGGUGAGUGCGUUGGGCUGGAACCACUUUGUCAAUCCACUUUGUCCAACCAACCGAGUGCCACCAAGUGCUUUCCUUGUGGCA
.....((((((.((....)).))))))(((((.((((.((((.(((((((((..((((..........(((......))))))).)))))...))))))))...)))).)))))...... (-35.26 = -35.74 +   0.48)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:54:33 2006