Locus 7917

Sequence ID	3L_DroMel_CAF1
Location	21,056,072 – 21,056,347
Length	275
Max. P	0.925607

overview

Window 9

Location	21,056,072 – 21,056,192
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	98.67
Mean single sequence MFE	-27.26
Consensus MFE	-24.94
Energy contribution	-24.66
Covariance contribution	-0.28
Combinations/Pair	1.09
Mean z-score	-1.47
Structure conservation index	0.91
SVM decision value	0.57
SVM RNA-class probability	0.784509
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 21056072 120 - 23771897
AAGACCGUUGCGAAAUGCAAAUAUCAACAAAUGAGCAAAUCGUUUCGUUAUUUGUUUGACAGCAACACAAACGUUGCAUCAAAGUGGGUAAACAAAGGCCAGAUAUGCCAAUGGAGAUGA
....(((((((((((((......(((.....)))......))))))))((((..(((....(((((......)))))....)))..))))......(((.......))))))))...... ( -26.70)
>DroSec_CAF1 111075 120 - 1
AAGACCGUUGCGAAAUGCAAAUAUCAACAAAUGAGCAAAUCGUUUCGUUAUUUGUUUGACAGCAACACAAACGUUGCAUCAAAGUGGGUAAACAAAGGCCAGAUAUGCCGAUGGAGAUGA
....(((((((((((((......(((.....)))......))))))))((((..(((....(((((......)))))....)))..))))......(((.......))))))))...... ( -27.10)
>DroSim_CAF1 17343 120 - 1
AAGACCGUUGCGAAAUGCAAAUAUCAACAAAUGAGCAAAUCGUUUCGUUAUUUGUUUGACAGCAACACAAACGUUGCAUCAAAGUGGGUAAACAAAGACCAGAUAUGCCGAUGGAGAUGA
....(((((((((..((((((((..(((((((((.....)))))).)))...)))))).))(((((......))))).))......(((........)))......).))))))...... ( -25.80)
>DroEre_CAF1 33634 120 - 1
AAGACCGUUGCAAAAUGCAAAUAUCAACAAAUGAGCAAAUCGUUUCGUUAUUUGUUUGACAGCAACACAAACGUUGCAUCAAAGUGGGUAAACAAAGGCCAGAUAUGCCGAUGGAGAUGA
..((...((((.....))))...))..............(((((((.(((((..(((....(((((......)))))....)))..))))).((..(((.......)))..))))))))) ( -26.90)
>DroYak_CAF1 4532 120 - 1
AAGACCGUUGCGAAAUGCAAAUAUCAACAAAUGAGCAAAUCGUUUCGUUAUUUGUUUGACAGCAACACAAACGUUGCAUCAAAGUGGGUAAACAAAGGCCAGAUAUGCCGAUGCAGAUGA
......(((((.....(((((((...((((((((.....)))))).)))))))))......))))).....(((((((((...((......))...(((.......))))))))).))). ( -29.80)
>consensus
AAGACCGUUGCGAAAUGCAAAUAUCAACAAAUGAGCAAAUCGUUUCGUUAUUUGUUUGACAGCAACACAAACGUUGCAUCAAAGUGGGUAAACAAAGGCCAGAUAUGCCGAUGGAGAUGA
....((((((((...((((((((..(((((((((.....)))))).)))...)))))).))(((((......))))).........(((........))).....)).))))))...... (-24.94 = -24.66 +  -0.28)

alignment

secondary structure

dotplot

Window 0

Location	21,056,112 – 21,056,232
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	97.00
Mean single sequence MFE	-34.48
Consensus MFE	-29.40
Energy contribution	-30.20
Covariance contribution	0.80
Combinations/Pair	1.00
Mean z-score	-1.71
Structure conservation index	0.85
SVM decision value	0.84
SVM RNA-class probability	0.863594
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 21056112 120 - 23771897
UGGGGAGUAGAGGCAUCCGCAGACUUCUUCUGCUGCCCCGAAGACCGUUGCGAAAUGCAAAUAUCAACAAAUGAGCAAAUCGUUUCGUUAUUUGUUUGACAGCAACACAAACGUUGCAUC
.((((((((((((..((....))...)))))))).))))..((((....((((((((......(((.....)))......)))))))).....))))....(((((......)))))... ( -34.90)
>DroSec_CAF1 111115 120 - 1
UGGGGAGUAGAGGCAUCCGCAGACUUCUUCUGCUGCCCCGAAGACCGUUGCGAAAUGCAAAUAUCAACAAAUGAGCAAAUCGUUUCGUUAUUUGUUUGACAGCAACACAAACGUUGCAUC
.((((((((((((..((....))...)))))))).))))..((((....((((((((......(((.....)))......)))))))).....))))....(((((......)))))... ( -34.90)
>DroSim_CAF1 17383 120 - 1
UGGGGAGUAGAGGCAUCCGCAGACUUCUUCUGCUGCCCCGAAGACCGUUGCGAAAUGCAAAUAUCAACAAAUGAGCAAAUCGUUUCGUUAUUUGUUUGACAGCAACACAAACGUUGCAUC
.((((((((((((..((....))...)))))))).))))..((((....((((((((......(((.....)))......)))))))).....))))....(((((......)))))... ( -34.90)
>DroEre_CAF1 33674 120 - 1
UGGGGCGGAGAGGCAUCCAUUGACUUCUUCUGCUGCCGCGAAGACCGUUGCAAAAUGCAAAUAUCAACAAAUGAGCAAAUCGUUUCGUUAUUUGUUUGACAGCAACACAAACGUUGCAUC
.((((((((((((((.....)).)))).)))))).))((((......))))....((((((((..(((((((((.....)))))).)))...)))))).))(((((......)))))... ( -33.80)
>DroYak_CAF1 4572 120 - 1
UGGGGAGGAGAGGCAUCCAUUGACUUCUUCUGCUGCCCCGAAGACCGUUGCGAAAUGCAAAUAUCAACAAAUGAGCAAAUCGUUUCGUUAUUUGUUUGACAGCAACACAAACGUUGCAUC
.((((((((((((((.....)).))))))))....))))..((((....((((((((......(((.....)))......)))))))).....))))....(((((......)))))... ( -33.90)
>consensus
UGGGGAGUAGAGGCAUCCGCAGACUUCUUCUGCUGCCCCGAAGACCGUUGCGAAAUGCAAAUAUCAACAAAUGAGCAAAUCGUUUCGUUAUUUGUUUGACAGCAACACAAACGUUGCAUC
.((((((((((((..((....))...)))))))).))))................((((((((..(((((((((.....)))))).)))...)))))).))(((((......)))))... (-29.40 = -30.20 +   0.80)

alignment

secondary structure

dotplot

Window 1

Location	21,056,192 – 21,056,312
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	93.42
Mean single sequence MFE	-41.70
Consensus MFE	-33.26
Energy contribution	-34.54
Covariance contribution	1.28
Combinations/Pair	1.12
Mean z-score	-1.85
Structure conservation index	0.80
SVM decision value	0.84
SVM RNA-class probability	0.863021
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 21056192 120 - 23771897
UGGAGUUUAAGUCCCAAGAGGUCGUAGAAAUCGCAAAGUCCAUUGCGAAAUCUUUAGCACACUCGAGAUUUGCAUUCUUAUGGGGAGUAGAGGCAUCCGCAGACUUCUUCUGCUGCCCCG
.(((((.((((((....((((((..(((..((((((......))))))..)))...).)).)))..)))))).)))))...((((((((((((..((....))...)))))))).)))). ( -38.20)
>DroSec_CAF1 111195 120 - 1
UGGAGUUCAAGUCCCGAGAGGUCGUAGAAAUCGCAGAGUCCAUUGCGAAAUCUUUAGCACACUCGAGAUUUGCAUUCUUAUGGGGAGUAGAGGCAUCCGCAGACUUCUUCUGCUGCCCCG
.(((((.((((((.((((.(((...(((..((((((......))))))..)))...)).).)))).)))))).)))))...((((((((((((..((....))...)))))))).)))). ( -42.90)
>DroSim_CAF1 17463 120 - 1
UGGAGUUCAAGUCCCGAGAGGUCGUAGAAAUCGCAGAGUCCAUUGCGAAAUCUUUAGCACACUCGAGAUUUGCAUUCUUAUGGGGAGUAGAGGCAUCCGCAGACUUCUUCUGCUGCCCCG
.(((((.((((((.((((.(((...(((..((((((......))))))..)))...)).).)))).)))))).)))))...((((((((((((..((....))...)))))))).)))). ( -42.90)
>DroEre_CAF1 33754 120 - 1
UGGAGUUCAAGCCCCGAGAGGUCGUAGAAAUCGCAGAGUCCAUUGCGAAAUCUUUAGCGCACUUGAGAUCUGCGUUCUUAUGGGGCGGAGAGGCAUCCAUUGACUUCUUCUGCUGCCGCG
.(((((....((((((.(((..((((((..((((((......))))))..((((.((....)).))))))))))..))).))))))(((((((((.....)).))))))).))).))... ( -45.30)
>DroYak_CAF1 4652 120 - 1
UGGAGUUCAAGCCCCAAGAGGUCGUAGAAAUCGCACAGUCCAUUGCGAAAUCUUUAGCACACUUGAGAUCUGCAUUCUUGUGGGGAGGAGAGGCAUCCAUUGACUUCUUCUGCUGCCCCG
.(((((.....(((((.((((..(((((..(((((........)))))..((((.((....)).)))))))))..)))).)))))((((((((((.....)).))))))))))).))... ( -39.20)
>consensus
UGGAGUUCAAGUCCCGAGAGGUCGUAGAAAUCGCAGAGUCCAUUGCGAAAUCUUUAGCACACUCGAGAUUUGCAUUCUUAUGGGGAGUAGAGGCAUCCGCAGACUUCUUCUGCUGCCCCG
.(((((.((((((.((((.(((...(((..((((((......))))))..)))...)).).)))).)))))).)))))...((((((((((((..((....))...)))))))).)))). (-33.26 = -34.54 +   1.28)

alignment

secondary structure

dotplot

Window 2

Location	21,056,232 – 21,056,347
Length	115
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	92.39
Mean single sequence MFE	-36.12
Consensus MFE	-31.22
Energy contribution	-31.50
Covariance contribution	0.28
Combinations/Pair	1.18
Mean z-score	-1.60
Structure conservation index	0.86
SVM decision value	1.17
SVM RNA-class probability	0.925607
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 21056232 115 - 23771897
GCGGGGAAUUUGCUCACAUA-----UGUGGUUUCCUCGUGUGGAGUUUAAGUCCCAAGAGGUCGUAGAAAUCGCAAAGUCCAUUGCGAAAUCUUUAGCACACUCGAGAUUUGCAUUCUUA
(((((((....((((.((((-----((.((...)).)))))))))).....))))..((((((..(((..((((((......))))))..)))...).)).)))......)))....... ( -35.60)
>DroSec_CAF1 111235 115 - 1
GCGGGGAAUAUGCUCACAUA-----UGUGGUUUCCUCGUGUGGAGUUCAAGUCCCGAGAGGUCGUAGAAAUCGCAGAGUCCAUUGCGAAAUCUUUAGCACACUCGAGAUUUGCAUUCUUA
((((((((...((.(((...-----.)))))))))))))..(((((.((((((.((((.(((...(((..((((((......))))))..)))...)).).)))).)))))).))))).. ( -38.70)
>DroSim_CAF1 17503 115 - 1
GCGGGGAAUAUGCUCACAUA-----UGUGGUUUCCUCGUGUGGAGUUCAAGUCCCGAGAGGUCGUAGAAAUCGCAGAGUCCAUUGCGAAAUCUUUAGCACACUCGAGAUUUGCAUUCUUA
((((((((...((.(((...-----.)))))))))))))..(((((.((((((.((((.(((...(((..((((((......))))))..)))...)).).)))).)))))).))))).. ( -38.70)
>DroEre_CAF1 33794 120 - 1
GCGGGGAAAAUGCUUACAUACUCGAUGUGGUUUCCUCGUGUGGAGUUCAAGCCCCGAGAGGUCGUAGAAAUCGCAGAGUCCAUUGCGAAAUCUUUAGCGCACUUGAGAUCUGCGUUCUUA
.(((((.....((((.(((((..((.......))...))))))))).....))))).(((..((((((..((((((......))))))..((((.((....)).))))))))))..))). ( -36.60)
>DroYak_CAF1 4692 115 - 1
GCAGGGAAUAUGCUUACAUA-----UGUGAUUUCCUCGUGUGGAGUUCAAGCCCCAAGAGGUCGUAGAAAUCGCACAGUCCAUUGCGAAAUCUUUAGCACACUUGAGAUCUGCAUUCUUG
...(((.....((((.((((-----((.(.....).)))))))))).....)))((((((...(((((..(((((........)))))..((((.((....)).))))))))).)))))) ( -31.00)
>consensus
GCGGGGAAUAUGCUCACAUA_____UGUGGUUUCCUCGUGUGGAGUUCAAGUCCCGAGAGGUCGUAGAAAUCGCAGAGUCCAUUGCGAAAUCUUUAGCACACUCGAGAUUUGCAUUCUUA
((((((((.....(((((.......))))).))))))))..(((((.((((((.((((.(((...(((..((((((......))))))..)))...)).).)))).)))))).))))).. (-31.22 = -31.50 +   0.28)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:00:50 2006