Locus 7900

Sequence ID 3R_DroMel_CAF1
Location 21,180,218 – 21,180,343
Length 125
Max. P 0.556841
window12720 window12721

overview

Window 0

Location 21,180,218 – 21,180,317
Length 99
Sequences 5
Columns 103
Reading direction reverse
Mean pairwise identity 83.92
Mean single sequence MFE -24.94
Consensus MFE -18.48
Energy contribution -18.52
Covariance contribution 0.04
Combinations/Pair 1.25
Mean z-score -1.54
Structure conservation index 0.74
SVM decision value -0.02
SVM RNA-class probability 0.522684
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 21180218 99 - 27905053
U-UGUCGAAUUGUGAUGAAAGUUGCGAUUAGCUUUCGGCACUUGAUCUGCGCCAUGUAC-AUGUACAUAUAGUACGUAUUUCGUUCAUAUGGUAGAUU--UAU
.-((((((((((..((....))..))))......))))))...(((((..(((((((((-((((((.....)))))).....))..))))))))))))--... ( -24.60)
>DroSec_CAF1 6956 89 - 1
U-UGCCGGAUUGUGAUGAAAGUUGCGAUUAGCUUUCGGCACUUGAUCUGCGCCAU-----------AUAUAGUACGUAUUUCGUUCAUAUGGUAGAUU--UAU
.-((((((((((..((....))..)))))......)))))...(((((..(((((-----------((.....(((.....)))..))))))))))))--... ( -24.50)
>DroSim_CAF1 6998 89 - 1
U-UGCCGGAUUGUGAUGAAAGUUGCGAUUAGCUUUCGGCACUUGAUCUGCGCCAU-----------AUAUAGUACGUAUUUCGUUCAUAUGGUAGAUU--UAU
.-((((((((((..((....))..)))))......)))))...(((((..(((((-----------((.....(((.....)))..))))))))))))--... ( -24.50)
>DroEre_CAF1 6826 97 - 1
U-UGCCGAACUGCGAUGAAAGUUGCGAUUAGCUUUCGGCACUUGAUCUGCGCUGUAUAAC--CCUAGUAC-GUAGAUAUAUCGUUCAUAUGGUAGAUU--UAU
.-((((((((((((((....)))))....))..)))))))...(((((((((((......--..)))).(-(((((........)).)))))))))))--... ( -24.30)
>DroYak_CAF1 6959 103 - 1
UCUGCCGGAUUGUGAUGGAAGUUGCGAUUAGCUUUUGGCACUUGAUCUGCGCCAUAUAGUGCGCUCGUAUAGUACGUAUAUCGUUCAUAUGGUAGAUAUAUAU
((((((((((((((..((((((((....))))))))..)))..)))))(((((.....).))))..((((.(.(((.....))).)))))))))))....... ( -26.80)
>consensus
U_UGCCGGAUUGUGAUGAAAGUUGCGAUUAGCUUUCGGCACUUGAUCUGCGCCAU_UA________AUAUAGUACGUAUUUCGUUCAUAUGGUAGAUU__UAU
..((((((((((((((....)))))))......)))))))...(((((((((.((((.........)))).)).(((((.......))))))))))))..... (-18.48 = -18.52 +   0.04)

alignment

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secondary structure

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dotplot

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Window 1

Location 21,180,248 – 21,180,343
Length 95
Sequences 6
Columns 98
Reading direction forward
Mean pairwise identity 77.18
Mean single sequence MFE -16.27
Consensus MFE -11.07
Energy contribution -12.02
Covariance contribution 0.95
Combinations/Pair 1.25
Mean z-score -1.08
Structure conservation index 0.68
SVM decision value 0.05
SVM RNA-class probability 0.556841
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 21180248 95 + 27905053
UAUAUGUACAU-GUACAUGGCGCAGAUCAAGUGCCGAAAGCUAAUCGCAACUUUCAUCACAAUUCGACA-AA-AAGGAUAAAAAUGAAAAAUUGCUCC
...(((((...-.)))))(((((.......)))))...........((((.((((((....((((....-..-..))))....))))))..))))... ( -19.20)
>DroSec_CAF1 6986 85 + 1
UAUAU-----------AUGGCGCAGAUCAAGUGCCGAAAGCUAAUCGCAACUUUCAUCACAAUCCGGCA-AA-AAGGAUAAAAAUGAAAAAUUGCUCC
.....-----------.((((((.......))))))..........((((.((((((....((((....-..-..))))....))))))..))))... ( -19.40)
>DroSim_CAF1 7028 85 + 1
UAUAU-----------AUGGCGCAGAUCAAGUGCCGAAAGCUAAUCGCAACUUUCAUCACAAUCCGGCA-AA-AAGGAUAAAAAUGAAAAAUUGCUCC
.....-----------.((((((.......))))))..........((((.((((((....((((....-..-..))))....))))))..))))... ( -19.40)
>DroEre_CAF1 6856 94 + 1
-GUACUAGG--GUUAUACAGCGCAGAUCAAGUGCCGAAAGCUAAUCGCAACUUUCAUCGCAGUUCGGCA-AAAAUGGAUAAAAAUGAAAAAUUGCUAC
-.......(--((((....((((.......))))(....).)))))((((.((((((....(((((...-....)))))....))))))..))))... ( -15.00)
>DroYak_CAF1 6991 98 + 1
UAUACGAGCGCACUAUAUGGCGCAGAUCAAGUGCCAAAAGCUAAUCGCAACUUCCAUCACAAUCCGGCAGAAAAGGGAUAAAAAUGAAAAAUUGCCAA
.......(((.......((((((.......)))))).........))).................(((((.....................))))).. ( -15.19)
>DroAna_CAF1 6690 73 + 1
----------------------GAUAUCAAGUGCCGAAAGCUAAUCGCAACUUUCAUCAGCAUCGGGCA-G--GAGGAUAAAAAUGAAAAAUAGUGUU
----------------------..((((...(((((((((..........)))))..(......)))))-.--...)))).................. (  -9.40)
>consensus
UAUAU___________AUGGCGCAGAUCAAGUGCCGAAAGCUAAUCGCAACUUUCAUCACAAUCCGGCA_AA_AAGGAUAAAAAUGAAAAAUUGCUCC
.................((((((.......))))))..........((((.((((((....((((..........))))....))))))..))))... (-11.07 = -12.02 +   0.95)

alignment

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secondary structure

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dotplot

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Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:57:32 2006