Locus 1446

Sequence ID 2R_DroMel_CAF1
Location 5,525,230 – 5,525,365
Length 135
Max. P 0.994873
window2471 window2472

overview

Window 1

Location 5,525,230 – 5,525,343
Length 113
Sequences 5
Columns 118
Reading direction reverse
Mean pairwise identity 78.62
Mean single sequence MFE -29.90
Consensus MFE -18.98
Energy contribution -20.26
Covariance contribution 1.28
Combinations/Pair 1.09
Mean z-score -1.92
Structure conservation index 0.63
SVM decision value 0.77
SVM RNA-class probability 0.847247
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 5525230 113 - 20766785
UCCCAGAU--ACAGAUACAAGCACAUCCGUUUACUGUACUCACACCGAAGGGUGGAUGGCACAGUGAACACUCCAUAUGGCACAAUUAUCCACUAG---UCUGUGACAUUUUUGGUCA
..((((((--((((((............(((((((((.((..((((....))))...)).)))))))))...((....))...............)---)))))).....)))))... ( -31.50)
>DroSec_CAF1 48523 104 - 1
-CCCAGAU--ACAGAUACAAGCACAUCCGUUUACUGUACUCACACCGAAGGGUGGAUGGCACAGUGAACACUCUAUAUG--------AUCCACUAG---UCUGUGACAUUUUCAGACA
-....(.(--((((((............(((((((((.((..((((....))))...)).)))))))))..((.....)--------).......)---)))))).)........... ( -28.10)
>DroSim_CAF1 25823 104 - 1
-UCCAGAU--ACAGAUACAAGCACAUCCGUUUACUGUACUCACACCGAAGGGUGGAUGGCACAGUGAACACUCAAUAUG--------AUCCACUAG---UCUGUGACAUUUUCAGACA
-....(.(--((((((............(((((((((.((..((((....))))...)).)))))))))..((.....)--------).......)---)))))).)........... ( -27.90)
>DroEre_CAF1 25711 113 - 1
-U-CAGAUAUACAGAUGCCAGCACAUCCGUUCACU---CAAACACCGAAGGGUGGCAGGCACAGUGAACACUCUGUAUGGGACAAUUGUCUACUAAUCAUCGCCGACAUUUACUGGCA
-.-..((((((((((((((.((.(((((.(((...---........)))))))))).))))..(....)..))))))).((((....))))....)))...((((........)))). ( -32.40)
>DroYak_CAF1 26960 111 - 1
-U-CAGAU--ACAGAUACAAGCACAUCCGUUUACU---CACACACCGAAGGGUGGAAGGCACAGUGAGCACUCUGUAUGGCGCAACUGGGUAGUAAUCUUCUGCGAUAUUUUCGUGCU
-.-...((--(((((...((((......)))).((---(((.((((....))))(....)...)))))...)))))))(((((......((((.......))))((.....))))))) ( -29.60)
>consensus
_UCCAGAU__ACAGAUACAAGCACAUCCGUUUACUGUACUCACACCGAAGGGUGGAUGGCACAGUGAACACUCUAUAUGG__CAA_UAUCCACUAG___UCUGUGACAUUUUCAGACA
...((((......(((........))).(((((((((.((..((((....))))...)).)))))))))..............................))))............... (-18.98 = -20.26 +   1.28)

alignment

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secondary structure

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dotplot

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Window 2

Location 5,525,267 – 5,525,365
Length 98
Sequences 5
Columns 100
Reading direction reverse
Mean pairwise identity 89.81
Mean single sequence MFE -29.10
Consensus MFE -25.53
Energy contribution -26.41
Covariance contribution 0.88
Combinations/Pair 1.09
Mean z-score -2.16
Structure conservation index 0.88
SVM decision value 2.52
SVM RNA-class probability 0.994873
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 5525267 98 - 20766785
AUCGCUUUUCCUAGGGUGGCUCUCCCAGAU--ACAGAUACAAGCACAUCCGUUUACUGUACUCACACCGAAGGGUGGAUGGCACAGUGAACACUCCAUAU
.............((((((((.........--.........))).)))))(((((((((.((..((((....))))...)).)))))))))......... ( -29.47)
>DroSec_CAF1 48552 96 - 1
AUCGCUUUUCCUAGGGUGGCU--CCCAGAU--ACAGAUACAAGCACAUCCGUUUACUGUACUCACACCGAAGGGUGGAUGGCACAGUGAACACUCUAUAU
.............((((((((--.......--.........))).)))))(((((((((.((..((((....))))...)).)))))))))......... ( -29.59)
>DroSim_CAF1 25852 96 - 1
AUCGCUUUUCCUAGGGUGGCU--UCCAGAU--ACAGAUACAAGCACAUCCGUUUACUGUACUCACACCGAAGGGUGGAUGGCACAGUGAACACUCAAUAU
.............((((((((--(......--........)))).)))))(((((((((.((..((((....))))...)).)))))))))......... ( -30.54)
>DroEre_CAF1 25751 94 - 1
AUCGCUUUUCCUAGGGUGGCA--U-CAGAUAUACAGAUGCCAGCACAUCCGUUCACU---CAAACACCGAAGGGUGGCAGGCACAGUGAACACUCUGUAU
...........((((((((((--(-(.........)))))).........(((((((---(...((((....))))....)...)))))))))))))... ( -29.90)
>DroYak_CAF1 27000 92 - 1
AUCGCUUUUCCUAGGGUGGCU--U-CAGAU--ACAGAUACAAGCACAUCCGUUUACU---CACACACCGAAGGGUGGAAGGCACAGUGAGCACUCUGUAU
...((((((....((((((((--(-...((--....))..)))).))))).......---....((((....))))))))))((((........)))).. ( -26.00)
>consensus
AUCGCUUUUCCUAGGGUGGCU__UCCAGAU__ACAGAUACAAGCACAUCCGUUUACUGUACUCACACCGAAGGGUGGAUGGCACAGUGAACACUCUAUAU
.............(((((((......................)).)))))(((((((((.((..((((....))))...)).)))))))))......... (-25.53 = -26.41 +   0.88)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:05:05 2006