Locus 3514

Sequence ID 2R_DroMel_CAF1
Location 11,769,224 – 11,769,354
Length 130
Max. P 0.870957
window5723 window5724 window5725

overview

Window 3

Location 11,769,224 – 11,769,332
Length 108
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 81.43
Mean single sequence MFE -26.09
Consensus MFE -15.74
Energy contribution -16.62
Covariance contribution 0.88
Combinations/Pair 1.05
Mean z-score -1.82
Structure conservation index 0.60
SVM decision value 0.09
SVM RNA-class probability 0.578085
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 11769224 108 + 20766785
-----------CGCUGAACUAAAUGAACUCAUCUGCUGAUAAGUUUAGCUGGCCACCGUUUAGCAA-CUCACCUGUAUCAGCUUCCUGCCAUUUUCCACAUAACUGGAAUCGCUGGCAUU
-----------.(((((......((((((.(((....))).))))))(((((.......)))))..-..........)))))....(((((..(((((......)))))....))))).. ( -27.90)
>DroSec_CAF1 13963 109 + 1
-----------ACCUGGUCCAAAUGAACUCAUCUGCUGAAAAGUUUAGCUGGCCACCGUUUAGCAAUCUCACCUGUAUCAGCUUCCUGCCAUUUUCCACAUAACUGGAAUCGCUGGCAUU
-----------...(((.(((..((((((..((....))..))))))..))))))..(((..(((........)))...)))....(((((..(((((......)))))....))))).. ( -24.40)
>DroSim_CAF1 13290 109 + 1
-----------CCCUGCUCUAAAUGAACUCAUCUGCUGAUAAGUCUAGUUGGCCACCGUUUAGCAAACUCACCUGUAUCAGCUUCCUGCCAUUUUCCACAUAACUGGAAUCGCUGGCAUU
-----------.......................(((((((.....((((.((.........)).))))......)))))))....(((((..(((((......)))))....))))).. ( -23.20)
>DroEre_CAF1 13599 118 + 1
AGGUGCAGUCACCCUUGACUAAAUGAACUCAUCUGCUGAUAAGU-AAGGUAGUUAUAGUUUAGCAA-CUCACCUGUAUCAGCUUCCUGCCAUUUUCCACAUAACUGGAAUCGCUGGCACU
.(((((((......(((.((((((.((((.(((((((....)))-.))))))))...)))))))))-.....))))))).......(((((..(((((......)))))....))))).. ( -32.10)
>DroYak_CAF1 14749 104 + 1
AGGUGCAGACACCCUUGACUAAAUGGACUCAUCUGCUGAUAA---------------GUUUAGCAA-CUCACCUGUAUCAGCUUCCUGCCAUUUUCCACACAACUGCCAUCGCUGGCAUU
.((((....))))..((...((((((........((((((((---------------(((....))-))......)))))))......))))))..))......(((((....))))).. ( -22.84)
>consensus
___________CCCUGGACUAAAUGAACUCAUCUGCUGAUAAGU_UAGCUGGCCACCGUUUAGCAA_CUCACCUGUAUCAGCUUCCUGCCAUUUUCCACAUAACUGGAAUCGCUGGCAUU
..................................(((((((..........((.........))...........)))))))....(((((..(((((......)))))....))))).. (-15.74 = -16.62 +   0.88)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 4

Location 11,769,224 – 11,769,332
Length 108
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 81.43
Mean single sequence MFE -32.92
Consensus MFE -19.96
Energy contribution -22.04
Covariance contribution 2.08
Combinations/Pair 1.03
Mean z-score -1.87
Structure conservation index 0.61
SVM decision value 0.21
SVM RNA-class probability 0.633450
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 11769224 108 - 20766785
AAUGCCAGCGAUUCCAGUUAUGUGGAAAAUGGCAGGAAGCUGAUACAGGUGAG-UUGCUAAACGGUGGCCAGCUAAACUUAUCAGCAGAUGAGUUCAUUUAGUUCAGCG-----------
..(((((....(((((......)))))..)))))....(((((.((((.((.(-(..((....))..)))).)).((((((((....))))))))......))))))).----------- ( -35.40)
>DroSec_CAF1 13963 109 - 1
AAUGCCAGCGAUUCCAGUUAUGUGGAAAAUGGCAGGAAGCUGAUACAGGUGAGAUUGCUAAACGGUGGCCAGCUAAACUUUUCAGCAGAUGAGUUCAUUUGGACCAGGU-----------
..(((((....(((((......)))))..)))))((..(((((...((...((...((((.....))))...))...))..)))))(((((....)))))...))....----------- ( -28.90)
>DroSim_CAF1 13290 109 - 1
AAUGCCAGCGAUUCCAGUUAUGUGGAAAAUGGCAGGAAGCUGAUACAGGUGAGUUUGCUAAACGGUGGCCAACUAGACUUAUCAGCAGAUGAGUUCAUUUAGAGCAGGG-----------
..(((((....(((((......)))))..)))))....(((((((.((...((((.((((.....)))).))))...)))))))))......((((.....))))....----------- ( -33.30)
>DroEre_CAF1 13599 118 - 1
AGUGCCAGCGAUUCCAGUUAUGUGGAAAAUGGCAGGAAGCUGAUACAGGUGAG-UUGCUAAACUAUAACUACCUU-ACUUAUCAGCAGAUGAGUUCAUUUAGUCAAGGGUGACUGCACCU
.(((.((((...(((.(((((.......))))).))).)))).)))(((((((-(..((........((((....-(((((((....))))))).....))))....))..))).))))) ( -35.90)
>DroYak_CAF1 14749 104 - 1
AAUGCCAGCGAUGGCAGUUGUGUGGAAAAUGGCAGGAAGCUGAUACAGGUGAG-UUGCUAAAC---------------UUAUCAGCAGAUGAGUCCAUUUAGUCAAGGGUGUCUGCACCU
..(((((....)))))((((.(((((...((((((...(((......)))...-))))))..(---------------(((((....))))))))))).))).)..(((((....))))) ( -31.10)
>consensus
AAUGCCAGCGAUUCCAGUUAUGUGGAAAAUGGCAGGAAGCUGAUACAGGUGAG_UUGCUAAACGGUGGCCAGCUA_ACUUAUCAGCAGAUGAGUUCAUUUAGUCCAGGG___________
..(((((....(((((......)))))..)))))....(((((((.((...((...((((.....))))...))...)))))))))(((((....))))).................... (-19.96 = -22.04 +   2.08)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 5

Location 11,769,253 – 11,769,354
Length 101
Sequences 5
Columns 111
Reading direction forward
Mean pairwise identity 85.74
Mean single sequence MFE -27.57
Consensus MFE -23.21
Energy contribution -23.45
Covariance contribution 0.24
Combinations/Pair 1.05
Mean z-score -1.82
Structure conservation index 0.84
SVM decision value 0.87
SVM RNA-class probability 0.870957
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 11769253 101 + 20766785
AAGUUUAGCUGGCCACCGUUUAGCAA-CUCACCUGUAUCAGCUUCCUGCCAUUUUCCACAUAACUGGAAUCGCUGGCAUUUGGCUGAUAGU---------GCUGUUUUUGC
.......(((((.......)))))((-(.(((...((((((((...(((((..(((((......)))))....)))))...))))))))))---------)..)))..... ( -27.80)
>DroSec_CAF1 13992 102 + 1
AAGUUUAGCUGGCCACCGUUUAGCAAUCUCACCUGUAUCAGCUUCCUGCCAUUUUCCACAUAACUGGAAUCGCUGGCAUUUGGCUGGUAGU---------GCUGUUUUUGC
......................((((...((.(..((((((((...(((((..(((((......)))))....)))))...))))))))..---------).))...)))) ( -26.70)
>DroSim_CAF1 13319 102 + 1
AAGUCUAGUUGGCCACCGUUUAGCAAACUCACCUGUAUCAGCUUCCUGCCAUUUUCCACAUAACUGGAAUCGCUGGCAUUUGGCUGGUAGU---------GCUGUUUUUGC
..(((.....))).........(((((..((.(..((((((((...(((((..(((((......)))))....)))))...))))))))..---------).))..))))) ( -29.50)
>DroEre_CAF1 13639 100 + 1
AAGU-AAGGUAGUUAUAGUUUAGCAA-CUCACCUGUAUCAGCUUCCUGCCAUUUUCCACAUAACUGGAAUCGCUGGCACUUGGCUGGUAGU---------GCUGUUUUUGC
.(((-(((((((((..........))-)).)))).((((((((...(((((..(((((......)))))....)))))...)))))))).)---------)))........ ( -29.00)
>DroYak_CAF1 14789 95 + 1
AA---------------GUUUAGCAA-CUCACCUGUAUCAGCUUCCUGCCAUUUUCCACACAACUGCCAUCGCUGGCAUUUGGCUGGUAGUGAUGCUUCUGCUGUUUUUGC
.(---------------((..((((.-.((((...((((((((...(((((.......((....)).......)))))...))))))))))))))))...)))........ ( -24.84)
>consensus
AAGU_UAGCUGGCCACCGUUUAGCAA_CUCACCUGUAUCAGCUUCCUGCCAUUUUCCACAUAACUGGAAUCGCUGGCAUUUGGCUGGUAGU_________GCUGUUUUUGC
....................((((...........((((((((...(((((..(((((......)))))....)))))...))))))))...........))))....... (-23.21 = -23.45 +   0.24)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:57:23 2006