Locus 8687

Sequence ID	3L_DroMel_CAF1
Location	22,530,490 – 22,530,678
Length	188
Max. P	0.865936

overview

Window 6

Location	22,530,490 – 22,530,604
Length	114
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	89.89
Mean single sequence MFE	-27.48
Consensus MFE	-22.23
Energy contribution	-23.35
Covariance contribution	1.12
Combinations/Pair	1.07
Mean z-score	-1.78
Structure conservation index	0.81
SVM decision value	0.56
SVM RNA-class probability	0.780956
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 22530490 114 + 23771897
GAAAGU------AAAGACCAAAAGCAAAUAUAUUAACGUAGAACUCCAACGGAAGGGUAUCUUAGCCAAAUGCUGAUGUGCUCCUUUAAAUAAUUCGCUGGACAAAAUUGCAGUCUUAUG
......------.(((((.....((((.(((......)))....((((.(((((((((((.(((((.....))))).)))).)))........)))).)))).....)))).)))))... ( -22.10)
>DroSec_CAF1 13923 114 + 1
AAAAGU------AAAGACCAAAAAGCAAUAUAUUAACGUGGAUCUCCCACGGAAGGGUAUCUUAGCCAAAUGCUGAUGUGCUCCUUUAAAUAAUUCGCUGGACAAAAUUGCAGUCUUAUG
......------.(((((......(((((.......(((((.....)))))(((((((((.(((((.....))))).)))).)))))...................))))).)))))... ( -28.40)
>DroSim_CAF1 14814 114 + 1
AAAAGU------AAAGACCAAGAAGCAAUAUAUUAACGUGGAUCUCCCACGGAAGGGUAUCUUAGCCAAAUGCUGAUGUGCUCCUUUAAAUAAUUCGCUGGACAAAAUUGCAGUCUUAUG
......------.......((((.(((((.......(((((.....)))))(((((((((.(((((.....))))).)))).)))))...................)))))..))))... ( -28.50)
>DroEre_CAF1 12915 120 + 1
UAAAGUUGAGCUUAAGAGCAAAAAGCGAUGUAUUUACAAGGAUCUACCACGGAAGGGUAUCUCAGCCAAAUGCUGAUGUGCUCCUUUAAAUAAUUCGCUGGACAAAAUUGCAGUCUUAUG
.........(((....)))....(((((..((((((.(((((..((((.(....)))))..(((((.....))))).....)))))))))))..)))))((((.........)))).... ( -30.90)
>consensus
AAAAGU______AAAGACCAAAAAGCAAUAUAUUAACGUGGAUCUCCCACGGAAGGGUAUCUUAGCCAAAUGCUGAUGUGCUCCUUUAAAUAAUUCGCUGGACAAAAUUGCAGUCUUAUG
.............(((((......(((((.......(((((.....)))))(((((((((.(((((.....))))).)))).)))))...................))))).)))))... (-22.23 = -23.35 +   1.12)

alignment

secondary structure

dotplot

Window 7

Location	22,530,524 – 22,530,644
Length	120
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	97.92
Mean single sequence MFE	-36.38
Consensus MFE	-35.25
Energy contribution	-35.38
Covariance contribution	0.12
Combinations/Pair	1.06
Mean z-score	-2.04
Structure conservation index	0.97
SVM decision value	0.85
SVM RNA-class probability	0.865936
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 22530524 120 + 23771897
GAACUCCAACGGAAGGGUAUCUUAGCCAAAUGCUGAUGUGCUCCUUUAAAUAAUUCGCUGGACAAAAUUGCAGUCUUAUGGGAAAAUUCCCCACAUGCCGCAGACUUUGCGGUAUUGGUC
....(((....(((((((((.(((((.....))))).)))).)))))........((..((((.........))))..))))).......(((.(((((((((...)))))))))))).. ( -33.60)
>DroSec_CAF1 13957 120 + 1
GAUCUCCCACGGAAGGGUAUCUUAGCCAAAUGCUGAUGUGCUCCUUUAAAUAAUUCGCUGGACAAAAUUGCAGUCUUAUGGGAAAAUUCCCCACAUGCCGCAGACUUUGCGGUAUUGGUC
....(((((..(((((((((.(((((.....))))).)))).))))).........((((.(......).))))....))))).......(((.(((((((((...)))))))))))).. ( -37.10)
>DroSim_CAF1 14848 120 + 1
GAUCUCCCACGGAAGGGUAUCUUAGCCAAAUGCUGAUGUGCUCCUUUAAAUAAUUCGCUGGACAAAAUUGCAGUCUUAUGGGAAAAUUCCCCACAUGCCGCAGACUUUGCGGUAUUGGUC
....(((((..(((((((((.(((((.....))))).)))).))))).........((((.(......).))))....))))).......(((.(((((((((...)))))))))))).. ( -37.10)
>DroEre_CAF1 12955 120 + 1
GAUCUACCACGGAAGGGUAUCUCAGCCAAAUGCUGAUGUGCUCCUUUAAAUAAUUCGCUGGACAAAAUUGCAGUCUUAUGGGAAAAUUCCCCACAUGCCGCAGACUCUGCGGUAUUGGUC
..........((((((((((.(((((.....))))).))))))..........(((.(.((((.........))))...).)))..))))(((.(((((((((...)))))))))))).. ( -37.70)
>consensus
GAUCUCCCACGGAAGGGUAUCUUAGCCAAAUGCUGAUGUGCUCCUUUAAAUAAUUCGCUGGACAAAAUUGCAGUCUUAUGGGAAAAUUCCCCACAUGCCGCAGACUUUGCGGUAUUGGUC
....(((((..(((((((((.(((((.....))))).)))).))))).........((((.(......).))))....))))).......(((.(((((((((...)))))))))))).. (-35.25 = -35.38 +   0.12)

alignment

secondary structure

dotplot

Window 8

Location	22,530,564 – 22,530,678
Length	114
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	85.65
Mean single sequence MFE	-32.18
Consensus MFE	-23.06
Energy contribution	-25.50
Covariance contribution	2.44
Combinations/Pair	1.03
Mean z-score	-1.96
Structure conservation index	0.72
SVM decision value	0.49
SVM RNA-class probability	0.757203
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 22530564 114 - 23771897
C-AACAGC-----CCCAUUACAAGUUUUUCGCUUUCGGUCGACCAAUACCGCAAAGUCUGCGGCAUGUGGGGAAUUUUCCCAUAAGACUGCAAUUUUGUCCAGCGAAUUAUUUAAAGGAG
.-......-----.((.(((..(((..((((((...(((........)))(((((((.((((((.((((((((...)))))))).).))))))))))))..))))))..)))))).)).. ( -32.20)
>DroPse_CAF1 37012 103 - 1
CGAGCAGCUACUGCUCAUCAGAAGUGCUCUGUUUUUGGGCUACCAAUACCGCAAUGUCUGCGGCAUGUGGAGAAUUUUCCCAUAAGACUGCAAUUUUAUCCUU-----------------
.((((((...))))))...((((.(((...(((((((((((.(((...(((((.....)))))....)))))......)))).))))).))).))))......----------------- ( -30.50)
>DroSec_CAF1 13997 114 - 1
C-AACAGC-----CCCAUUACAAGUUUUUCGCUUUCGGUCGACCAAUACCGCAAAGUCUGCGGCAUGUGGGGAAUUUUCCCAUAAGACUGCAAUUUUGUCCAGCGAAUUAUUUAAAGGAG
.-......-----.((.(((..(((..((((((...(((........)))(((((((.((((((.((((((((...)))))))).).))))))))))))..))))))..)))))).)).. ( -32.20)
>DroSim_CAF1 14888 114 - 1
C-AACAGC-----CCCAUUACAAGUUUUUCGCUUUCGGUCGACCAAUACCGCAAAGUCUGCGGCAUGUGGGGAAUUUUCCCAUAAGACUGCAAUUUUGUCCAGCGAAUUAUUUAAAGGAG
.-......-----.((.(((..(((..((((((...(((........)))(((((((.((((((.((((((((...)))))))).).))))))))))))..))))))..)))))).)).. ( -32.20)
>DroEre_CAF1 12995 114 - 1
C-AACAGC-----CCCAUUACAAGUUUUUCGCUUUGGGUCGACCAAUACCGCAGAGUCUGCGGCAUGUGGGGAAUUUUCCCAUAAGACUGCAAUUUUGUCCAGCGAAUUAUUUAAAGGAG
.-......-----.((.(((..(((..((((((((((.....))))....(((((((.((((((.((((((((...)))))))).).))))))))))))..))))))..)))))).)).. ( -33.80)
>consensus
C_AACAGC_____CCCAUUACAAGUUUUUCGCUUUCGGUCGACCAAUACCGCAAAGUCUGCGGCAUGUGGGGAAUUUUCCCAUAAGACUGCAAUUUUGUCCAGCGAAUUAUUUAAAGGAG
.....................((((..((((((...((....))......(((((((.((((((.((((((((...)))))))).).))))))))))))..))))))..))))....... (-23.06 = -25.50 +   2.44)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:22:20 2006