Locus 4338

Sequence ID	3R_DroMel_CAF1
Location	11,458,604 – 11,458,918
Length	314
Max. P	0.992572

overview

Window 9

Location	11,458,604 – 11,458,718
Length	114
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	93.56
Mean single sequence MFE	-32.75
Consensus MFE	-29.50
Energy contribution	-29.70
Covariance contribution	0.20
Combinations/Pair	1.07
Mean z-score	-1.46
Structure conservation index	0.90
SVM decision value	1.18
SVM RNA-class probability	0.926351
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11458604 114 - 27905053
ACGCAUGGCAACAAUUGCAGCCAGUUUAAUGAGCUCAAAAAUGCGCGCAACAAUGAAGAGCUGGCCCGGCUCCAAACCAACGCCAAUUCC------CCGAUGGCCAACCCUACUCGGCAU
..(((((....))..))).((((((((.....((.((....)).)).((....))..))))))))..(((...........)))......------(((((((......))).))))... ( -25.50)
>DroSec_CAF1 191121 114 - 1
ACGCAUGGCAACAAUUGCAGCCGGUUUAAUGAGCUCAAAAAUGCGCGCAACAAUGAAGAGCUGGCCCGGCUCCAAACCAAGGCCAAUUCC------CCGUUGGCCAACCCGACUCGGCAU
..(((((....))..))).((((((((..((.((.((....)).)).))........((((((...)))))).)))))..(((((((...------..)))))))..........))).. ( -36.80)
>DroSim_CAF1 186239 114 - 1
ACGCAUGGCAACAAUUGCAGCCGGUUUAAUGAGCUCAAAAAUGCGCGCAACAAUGAAGAGCUGGCCCGGCUCCAAACCAAGGCCAAUUCC------CCGAUGGCCAACCCCACUCGGCAU
..(((((....))..))).((((((((..((.((.((....)).)).))........((((((...)))))).)))))..(((((.....------....)))))..........))).. ( -33.90)
>DroEre_CAF1 180347 120 - 1
ACGCAUGGCAACAAUUGCAGCCGGUUUAAUGAGCUCAAAAAUGCGCGCAACAAUGAAGAGCUGGCCGAGCUCCAAGCCAAGGCCAAUUCCCAGUCCCAAAUGGCCAACCCCACGCGGCAU
..(((((....))..))).((((((((...((((((......((...((....))....)).....)))))).)))))..(((((...............)))))..........))).. ( -34.06)
>DroYak_CAF1 184364 114 - 1
ACGCAUGGCAACAAUUGCAGCCAGUUUAAUGAGCUCAAAAAUGCGCGCAACAAUGAAGAGCUGGCCCGGCUCCAAGCCAAGGCCAAUUCC------CCAAUGGCCAACCCCACGCGGCAU
..(((((....))..))).(((..........((........))(((......((..(((.(((((.(((.....)))..))))).))).------.)).(((......))))))))).. ( -33.50)
>consensus
ACGCAUGGCAACAAUUGCAGCCGGUUUAAUGAGCUCAAAAAUGCGCGCAACAAUGAAGAGCUGGCCCGGCUCCAAACCAAGGCCAAUUCC______CCGAUGGCCAACCCCACUCGGCAU
..(((((....))..))).((((((((..((.((.((....)).)).))........(((((.....))))).)))))..(((((...............)))))..........))).. (-29.50 = -29.70 +   0.20)

alignment

secondary structure

dotplot

Window 0

Location	11,458,678 – 11,458,798
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	90.29
Mean single sequence MFE	-32.34
Consensus MFE	-27.84
Energy contribution	-27.80
Covariance contribution	-0.04
Combinations/Pair	1.03
Mean z-score	-1.31
Structure conservation index	0.86
SVM decision value	0.17
SVM RNA-class probability	0.616888
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11458678 120 - 27905053
GACUGUCGACUGCUGACUGCUGACUGCAAAUUGAUUGCCGGCCAACAAAAGGGCAGAAACUGCAGCAGAGUACUCACGCAACGCAUGGCAACAAUUGCAGCCAGUUUAAUGAGCUCAAAA
...........(((.(..((((.((((((.(((.((((((((..........((((...)))).((.((....))..))...)).))))))))))))))).))))....).)))...... ( -33.00)
>DroSec_CAF1 191195 113 - 1
GACUGUCGA-------CUGCUGACUGCAAAUUGAUUGCCGGCAAACAAAAGGGCAGAAUCUGCAGCAGAGUACUCACGCAACGCAUGGCAACAAUUGCAGCCGGUUUAAUGAGCUCAAAA
.....(((.-------..((((.((((((.(((.((((((((..........((((...)))).((.((....))..))...)).))))))))))))))).))))....)))........ ( -30.70)
>DroSim_CAF1 186313 120 - 1
GACUGUCGACUCCUGACUGCUGACUGCAAAUUGAUUGCCGGCCAACAAAAGGGCAGAAUCUGCAGCAGAGUACUCACGCAACGCAUGGCAACAAUUGCAGCCGGUUUAAUGAGCUCAAAA
.......(((((......((((.((((((.(((.((((((((..........((((...)))).((.((....))..))...)).))))))))))))))).)))).....))).)).... ( -33.10)
>DroEre_CAF1 180427 106 - 1
--------------GUCUGCUGACUGCAAAUUGAUUGCCGGCCAACAAAAGGGCAGAAACUGCAGCGGAGUACUCACGCAACGCAUGGCAACAAUUGCAGCCGGUUUAAUGAGCUCAAAA
--------------....((((.((((((.(((.((((((((..........((((...)))).(((((....)).)))...)).))))))))))))))).))))............... ( -32.80)
>DroYak_CAF1 184438 120 - 1
AACUGCAGACUGUCGACUGCUGACUGCAAAUUGAUUGCCGGGCAACAAAAGGGCAGAAACUGCAGCAGAGUACUCACGCAACGCAUGGCAACAAUUGCAGCCAGUUUAAUGAGCUCAAAA
.......((...(((...((((.((((((.(((.((((((.((.........((((...)))).((.((....))..))...)).))))))))))))))).))))....)))..)).... ( -32.10)
>consensus
GACUGUCGACU___GACUGCUGACUGCAAAUUGAUUGCCGGCCAACAAAAGGGCAGAAACUGCAGCAGAGUACUCACGCAACGCAUGGCAACAAUUGCAGCCGGUUUAAUGAGCUCAAAA
..................((((.((((((.(((.((((((((..........((((...)))).((.((....))..))...)).))))))))))))))).))))............... (-27.84 = -27.80 +  -0.04)

alignment

secondary structure

dotplot

Window 1

Location	11,458,718 – 11,458,838
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	90.79
Mean single sequence MFE	-37.16
Consensus MFE	-28.94
Energy contribution	-29.46
Covariance contribution	0.52
Combinations/Pair	1.06
Mean z-score	-2.46
Structure conservation index	0.78
SVM decision value	1.67
SVM RNA-class probability	0.970899
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11458718 120 + 27905053
UGCGUGAGUACUCUGCUGCAGUUUCUGCCCUUUUGUUGGCCGGCAAUCAAUUUGCAGUCAGCAGUCAGCAGUCGACAGUCUGCAGUUUGCAAAAGUUGCAGAAAUGCAAAAACGAAAUUA
(((((..((...(((((((((...))))....((((((((..((((.....)))).))))))))..)))))...))..((((((..((....))..)))))).)))))............ ( -37.90)
>DroSec_CAF1 191235 113 + 1
UGCGUGAGUACUCUGCUGCAGAUUCUGCCCUUUUGUUUGCCGGCAAUCAAUUUGCAGUCAGCAG-------UCGACAGUCUGCAGUUUGCAAAAGUUGCAGAAAUGCAAAAACGAAAUUA
(((....)))......((((..((((((.(((((((..((..((((.....)))).....((((-------.(....).)))).))..)))))))..)))))).))))............ ( -34.90)
>DroSim_CAF1 186353 120 + 1
UGCGUGAGUACUCUGCUGCAGAUUCUGCCCUUUUGUUGGCCGGCAAUCAAUUUGCAGUCAGCAGUCAGGAGUCGACAGUCUGCAGUUUGCAAAAGUUGCAGAAAUGCAAAAACGAAAUUA
..(((..(((....(((((((((((.(((((.((((((((..((((.....)))).))))))))..))).)).))..))))))))).))).....(((((....)))))..)))...... ( -41.70)
>DroEre_CAF1 180467 106 + 1
UGCGUGAGUACUCCGCUGCAGUUUCUGCCCUUUUGUUGGCCGGCAAUCAAUUUGCAGUCAGCAGAC--------------UGCAGUUUGCAAAAGUUGCAGAAAUGCAAAAACGAAAUUA
.(((.((....)))))(((((...((((...(((((((((..((((.....)))).))))))))).--------------.)))).)))))....(((((....)))))........... ( -35.70)
>DroYak_CAF1 184478 120 + 1
UGCGUGAGUACUCUGCUGCAGUUUCUGCCCUUUUGUUGCCCGGCAAUCAAUUUGCAGUCAGCAGUCGACAGUCUGCAGUUUGCAGUUUGCAAAAGUUGCAGAAAUGCAAAAACGAAAUUA
(((....)))......((((.(((((((.((((((((((...)))).(((.((((((...((((.(....).))))...)))))).)))))))))..)))))))))))............ ( -35.60)
>consensus
UGCGUGAGUACUCUGCUGCAGUUUCUGCCCUUUUGUUGGCCGGCAAUCAAUUUGCAGUCAGCAGUC___AGUCGACAGUCUGCAGUUUGCAAAAGUUGCAGAAAUGCAAAAACGAAAUUA
.(((.((....)))))((((.(((((((.(((((((..((..((((.....)))).....((((...............)))).))..)))))))..)))))))))))............ (-28.94 = -29.46 +   0.52)

alignment

secondary structure

dotplot

Window 2

Location	11,458,798 – 11,458,918
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	98.17
Mean single sequence MFE	-31.50
Consensus MFE	-27.60
Energy contribution	-29.80
Covariance contribution	2.20
Combinations/Pair	1.00
Mean z-score	-2.43
Structure conservation index	0.88
SVM decision value	2.34
SVM RNA-class probability	0.992572
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11458798 120 + 27905053
UGCAGUUUGCAAAAGUUGCAGAAAUGCAAAAACGAAAUUAUAUUUGCGGGGCCCAGGCACAUCAUUAAAAUGCAUCGACCUGCAGAACAAACGAGUCGAACACCUCUCGGCAAAAAGCUU
.((..(((((.....(((((....))))).............((((((((......(((...........))).....)))))))).....((((..(....)..)))))))))..)).. ( -31.50)
>DroSec_CAF1 191308 120 + 1
UGCAGUUUGCAAAAGUUGCAGAAAUGCAAAAACGAAAUUAUAUUUGCGGGGCCCAGGCACAUCAUUAAAAUGCAUCGACCUGCAGAACAAACGAGUCGAACACCUCUCGGCAAAAAGCUU
.((..(((((.....(((((....))))).............((((((((......(((...........))).....)))))))).....((((..(....)..)))))))))..)).. ( -31.50)
>DroSim_CAF1 186433 120 + 1
UGCAGUUUGCAAAAGUUGCAGAAAUGCAAAAACGAAAUUAUAUUUGCGGGGCCCAGGCACAUCAUUAAAAUGCAUCGACCUGCAGAACAAACGAGUCGAACACCUCUCGGCAAAAAGCUU
.((..(((((.....(((((....))))).............((((((((......(((...........))).....)))))))).....((((..(....)..)))))))))..)).. ( -31.50)
>DroEre_CAF1 180533 120 + 1
UGCAGUUUGCAAAAGUUGCAGAAAUGCAAAAACGAAAUUAUAUUUGCGGGGCCCAGGCACAUCAUUAAAAUGCAUCGACCUGCAGAGCAAACAAGUCGAACACCUCUCGGCAUAAAGCCU
.((.((((((.....(((((....))))).............((((((((......(((...........))).....))))))))))))))..(((((.......))))).....)).. ( -34.90)
>DroYak_CAF1 184558 120 + 1
UGCAGUUUGCAAAAGUUGCAGAAAUGCAAAAACGAAAUUAUAUUUGCGGGGCCCAGGCACAUCAUUAAAAUGCAUCGACCUGCAGAACAAACGAGUCAAACACCUCUCGGCAUAAAGCUU
.((..(.(((.....(((((....)))))...(((.......((((((((......(((...........))).....))))))))......(((........))))))))).)..)).. ( -28.10)
>consensus
UGCAGUUUGCAAAAGUUGCAGAAAUGCAAAAACGAAAUUAUAUUUGCGGGGCCCAGGCACAUCAUUAAAAUGCAUCGACCUGCAGAACAAACGAGUCGAACACCUCUCGGCAAAAAGCUU
.((.(((((......(((((....))))).............((((((((......(((...........))).....)))))))).)))))..(((((.......))))).....)).. (-27.60 = -29.80 +   2.20)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:26:39 2006