Locus 3123

Sequence ID 2R_DroMel_CAF1
Location 10,670,739 – 10,670,853
Length 114
Max. P 0.682308
window5152 window5153

overview

Window 2

Location 10,670,739 – 10,670,853
Length 114
Sequences 6
Columns 114
Reading direction forward
Mean pairwise identity 79.19
Mean single sequence MFE -32.54
Consensus MFE -21.73
Energy contribution -22.57
Covariance contribution 0.83
Combinations/Pair 1.00
Mean z-score -1.41
Structure conservation index 0.67
SVM decision value 0.31
SVM RNA-class probability 0.682308
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 10670739 114 + 20766785
AAAAGCCGCGGACUAAAUUGCCAAAUCCUCGAUCCAAUAAGAUGGGCUGCAACACCAGCCAGGAGCUAAAGACGAAGGAUGGCGCAGCCAUGGAUGCGGUCAGCAACGGCGAAC
....((((..((((.....((((..((((((.((..........(((((......)))))..........)))).))))))))(((.(....).))))))).....)))).... ( -35.05)
>DroPse_CAF1 9982 105 + 1
AAUACAAGUGACUUAAAAU--CAAA-------UCAAAUAUAAUGGGCUGCAACACCAGCCAGGAGCUGAAGACGAAGGAUGGCGCCGCCAUCGACGCGGUCAGCAACGGGGAGC
.......((..(((.....--....-------............(((((......))))).(..(((((...((...((((((...))))))....)).)))))..))))..)) ( -28.40)
>DroEre_CAF1 7583 114 + 1
AAAAGCAGCGCACUAAAUUGCCAAAUCCUCGAGCCAGCAAGAUGGGCUGCAACACCAGCCAGGAGCUGAAGACGAAGGAUGGCGCCGCCAUCGAUGCGGUGAGCAAUGGCGAAC
........(((.....(((((...(((((((...((((......(((((......)))))....))))....)).)))))..((((((.......)))))).))))).)))... ( -36.80)
>DroYak_CAF1 7918 97 + 1
-----------------UUGCCAAAUCCUCGAUCCAGUAAGAUGGGCUGCAACACCAGCCAGGAGCUGAAGACGAAGGAUGGCGCCGCCAUCGAUGCGGUCAGCAAUGGCGAAC
-----------------((((((..((((..(((......))).(((((......)))))))))(((((...((...((((((...))))))....)).)))))..)))))).. ( -37.20)
>DroAna_CAF1 7585 107 + 1
AAAAGCCGCGGACUAAAUUGUCAAA-------UCCAGGAUAAUGGGCUGCAACACCAGCCAGGAGCUGAAAACAAAGGAUGGGGCCGCCAUCGAUGCGGUCAGCAAUGGGGAUG
.....((...(((......)))...-------.(((........(((((......)))))....(((((...((...(((((.....)))))..))...)))))..)))))... ( -29.40)
>DroPer_CAF1 10050 105 + 1
AAUACAAGUGACUUAAAAU--CAAA-------UCAAAUAUAAUGGGCUGCAACACCAGCCAGGAGCUGAAGACGAAGGAUGGCGCCGCCAUCGACGCGGUCAGCAACGGGGAGC
.......((..(((.....--....-------............(((((......))))).(..(((((...((...((((((...))))))....)).)))))..))))..)) ( -28.40)
>consensus
AAAAGCAGCGAACUAAAUUGCCAAA_______UCCAAUAAAAUGGGCUGCAACACCAGCCAGGAGCUGAAGACGAAGGAUGGCGCCGCCAUCGAUGCGGUCAGCAACGGCGAAC
............................................(((((......)))))....(((((...((...((((((...))))))....)).))))).......... (-21.73 = -22.57 +   0.83)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 3

Location 10,670,739 – 10,670,853
Length 114
Sequences 6
Columns 114
Reading direction reverse
Mean pairwise identity 79.19
Mean single sequence MFE -34.76
Consensus MFE -20.38
Energy contribution -20.85
Covariance contribution 0.47
Combinations/Pair 1.10
Mean z-score -1.61
Structure conservation index 0.59
SVM decision value 0.06
SVM RNA-class probability 0.562468
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 10670739 114 - 20766785
GUUCGCCGUUGCUGACCGCAUCCAUGGCUGCGCCAUCCUUCGUCUUUAGCUCCUGGCUGGUGUUGCAGCCCAUCUUAUUGGAUCGAGGAUUUGGCAAUUUAGUCCGCGGCUUUU
....(((((.(((((..(((.(....).)))(((((((((.((((.........(((((......))))).........)))).)))))..))))...)))))..))))).... ( -39.67)
>DroPse_CAF1 9982 105 - 1
GCUCCCCGUUGCUGACCGCGUCGAUGGCGGCGCCAUCCUUCGUCUUCAGCUCCUGGCUGGUGUUGCAGCCCAUUAUAUUUGA-------UUUG--AUUUUAAGUCACUUGUAUU
.......(..(((((..(((..((((((...))))))...)))..)))))..).(((((......)))))...((((..(((-------((((--....)))))))..)))).. ( -32.20)
>DroEre_CAF1 7583 114 - 1
GUUCGCCAUUGCUCACCGCAUCGAUGGCGGCGCCAUCCUUCGUCUUCAGCUCCUGGCUGGUGUUGCAGCCCAUCUUGCUGGCUCGAGGAUUUGGCAAUUUAGUGCGCUGCUUUU
...(((((((((.....)))...))))))((((((..(((((...(((((....(((((......)))))......)))))..)))))...)))).....((....)))).... ( -38.50)
>DroYak_CAF1 7918 97 - 1
GUUCGCCAUUGCUGACCGCAUCGAUGGCGGCGCCAUCCUUCGUCUUCAGCUCCUGGCUGGUGUUGCAGCCCAUCUUACUGGAUCGAGGAUUUGGCAA-----------------
((.((((((((.((....)).))))))))))(((((((((.((((.........(((((......))))).........)))).)))))..))))..----------------- ( -37.67)
>DroAna_CAF1 7585 107 - 1
CAUCCCCAUUGCUGACCGCAUCGAUGGCGGCCCCAUCCUUUGUUUUCAGCUCCUGGCUGGUGUUGCAGCCCAUUAUCCUGGA-------UUUGACAAUUUAGUCCGCGGCUUUU
..........(((((..(((..(((((.....)))))...)))..)))))....(((((......)))))......((((((-------((.........)))))).))..... ( -28.30)
>DroPer_CAF1 10050 105 - 1
GCUCCCCGUUGCUGACCGCGUCGAUGGCGGCGCCAUCCUUCGUCUUCAGCUCCUGGCUGGUGUUGCAGCCCAUUAUAUUUGA-------UUUG--AUUUUAAGUCACUUGUAUU
.......(..(((((..(((..((((((...))))))...)))..)))))..).(((((......)))))...((((..(((-------((((--....)))))))..)))).. ( -32.20)
>consensus
GUUCCCCAUUGCUGACCGCAUCGAUGGCGGCGCCAUCCUUCGUCUUCAGCUCCUGGCUGGUGUUGCAGCCCAUCAUACUGGA_______UUUGGCAAUUUAGUCCGCUGCUUUU
.....(((..(((((..((...((((((...))))))....))..)))))....(((((......)))))........)))................................. (-20.38 = -20.85 +   0.47)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:48:06 2006