Locus 5640

Sequence ID 2R_DroMel_CAF1
Location 17,944,194 – 17,944,292
Length 98
Max. P 0.829718
window9041 window9042

overview

Window 1

Location 17,944,194 – 17,944,292
Length 98
Sequences 4
Columns 105
Reading direction forward
Mean pairwise identity 93.56
Mean single sequence MFE -27.68
Consensus MFE -23.67
Energy contribution -23.48
Covariance contribution -0.19
Combinations/Pair 1.04
Mean z-score -1.90
Structure conservation index 0.86
SVM decision value 0.71
SVM RNA-class probability 0.829718
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 17944194 98 + 20766785
GUCCGGCCAAAUGAUAGAUGGCAUCUGUAGGCAUCGCA-------AAAAAAUUGCCCCAGACAGCCGACAGAUGUGGAUAAGCAAUUGAUUGAUAUACGGACAGU
(((((.............(.((((((((.(((.(((((-------(.....))))....))..))).)))))))).).(((....))).........)))))... ( -26.80)
>DroSec_CAF1 1569 97 + 1
GUCCGGCCAAAUGAUAGAUGGCAUCUGUAGGCAUCGCA-------AA-AAAUUGCUCCAGACAGCCGACAGAUGUGGAUAAGCAAUUGAUUGAUACACGGACAUU
(((((.............(.((((((((.(((.(((((-------(.-...))))....))..))).)))))))).).(((....))).........)))))... ( -26.80)
>DroEre_CAF1 6325 97 + 1
GUCCGGCCAAAUGAUAGAUGGCUUCUGUAGGCAUCGCA-------AA-AAAUUGCCCCAGACAGCCGACAGAUGUGGAUAAGCAAUUGAUUGAUAUACGGACAUU
(((((.............(((((((((..((((.....-------..-....)))).)))).))))).(((.(((......))).))).........)))))... ( -27.10)
>DroYak_CAF1 6113 104 + 1
GUCCGGCCAAAUGAUAGAUGGCAUCUGAAGGCAUCGCAAAAGGCAAA-AAAUUGCCCCAGACAGCCGACAGAUGUGGAUAAGCAAUUGAUUGAUAUACGGACAUU
(((((.............(.(((((((..(((.((......(((((.-...)))))...))..)))..))))))).).(((....))).........)))))... ( -30.00)
>consensus
GUCCGGCCAAAUGAUAGAUGGCAUCUGUAGGCAUCGCA_______AA_AAAUUGCCCCAGACAGCCGACAGAUGUGGAUAAGCAAUUGAUUGAUAUACGGACAUU
(((((.............((((.((((..((((...................)))).))))..)))).(((.(((......))).))).........)))))... (-23.67 = -23.48 +  -0.19)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 2

Location 17,944,194 – 17,944,292
Length 98
Sequences 4
Columns 105
Reading direction reverse
Mean pairwise identity 93.56
Mean single sequence MFE -27.80
Consensus MFE -21.89
Energy contribution -22.39
Covariance contribution 0.50
Combinations/Pair 1.00
Mean z-score -2.25
Structure conservation index 0.79
SVM decision value 0.52
SVM RNA-class probability 0.766236
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 17944194 98 - 20766785
ACUGUCCGUAUAUCAAUCAAUUGCUUAUCCACAUCUGUCGGCUGUCUGGGGCAAUUUUUU-------UGCGAUGCCUACAGAUGCCAUCUAUCAUUUGGCCGGAC
...(((((........................((((((.(((.(((....((((.....)-------))))))))).))))))((((.........))))))))) ( -26.60)
>DroSec_CAF1 1569 97 - 1
AAUGUCCGUGUAUCAAUCAAUUGCUUAUCCACAUCUGUCGGCUGUCUGGAGCAAUUU-UU-------UGCGAUGCCUACAGAUGCCAUCUAUCAUUUGGCCGGAC
...(((((........................((((((.(((.(((....((((...-.)-------))))))))).))))))((((.........))))))))) ( -26.60)
>DroEre_CAF1 6325 97 - 1
AAUGUCCGUAUAUCAAUCAAUUGCUUAUCCACAUCUGUCGGCUGUCUGGGGCAAUUU-UU-------UGCGAUGCCUACAGAAGCCAUCUAUCAUUUGGCCGGAC
...(((((.........................(((((.(((.(((....((((...-.)-------))))))))).))))).((((.........))))))))) ( -25.80)
>DroYak_CAF1 6113 104 - 1
AAUGUCCGUAUAUCAAUCAAUUGCUUAUCCACAUCUGUCGGCUGUCUGGGGCAAUUU-UUUGCCUUUUGCGAUGCCUUCAGAUGCCAUCUAUCAUUUGGCCGGAC
...(((((........................(((((..((((((..(((((((...-.)))))))..)))..)))..)))))((((.........))))))))) ( -32.20)
>consensus
AAUGUCCGUAUAUCAAUCAAUUGCUUAUCCACAUCUGUCGGCUGUCUGGGGCAAUUU_UU_______UGCGAUGCCUACAGAUGCCAUCUAUCAUUUGGCCGGAC
...(((((........................((((((.(((.(((....(((..............))))))))).))))))((((.........))))))))) (-21.89 = -22.39 +   0.50)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:50:45 2006