Locus 5616

Sequence ID 2R_DroMel_CAF1
Location 17,880,726 – 17,880,910
Length 184
Max. P 0.956053
window9003 window9004 window9005

overview

Window 3

Location 17,880,726 – 17,880,830
Length 104
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 76.06
Mean single sequence MFE -30.02
Consensus MFE -15.08
Energy contribution -15.33
Covariance contribution 0.26
Combinations/Pair 1.30
Mean z-score -2.36
Structure conservation index 0.50
SVM decision value 1.46
SVM RNA-class probability 0.956053
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 17880726 104 - 20766785
AAAGUGGUAAGAAAGAGUGAGAGGGAGCGGAAA----AAAACCAUUCUCUCGAGAGAGCGAGAGCGGCCAUUAAAGCUCGGCUCAUC-----------UAGCUGUUAAAACU-AGCAAAG
..((..((.(((........(((((((.((...----....)).)))))))....((((..((((..........)))).)))).))-----------).))..))......-....... ( -28.50)
>DroSec_CAF1 45703 103 - 1
AAAGUGGUAAGAAAGAGUGAGAGGGAGUGGAAA-----ACACCAUUCUCUCGAGAGAGCGAGAGCGGCCAUUAAAGCUCGGCUCACC-----------UAGCUGUAAAACCU-AGCAAAG
.....(((............((((((((((...-----...))))))))))....((((..((((..........)))).)))))))-----------..((((.......)-))).... ( -33.50)
>DroSim_CAF1 46066 103 - 1
AAAGUGGUAAGAAAGAGUGAGAGGGAGUGGAAG-----AAACCAUUUUCUCGAGAGAGCGAGAGCGGCCAUUAAAGCUCGGCUCACC-----------UAGCUGUAAAAACU-AGCAAAG
.....(((............(((..(((((...-----...)))))..)))....((((..((((..........)))).)))))))-----------..((((.......)-))).... ( -31.00)
>DroEre_CAF1 48084 108 - 1
AAAGUGGUAAGAAAGAGUGAGAGGGAGCGGCAAAGAAAAAACAAUUCACUCGCGAGCGCGAGAGCGGCCAUUAAAGCUCGGCUCACC-----------UAGCUGUAAAAACU-AGCAAAG
.....(((.((...((((......(.((.((...(((.......))).(((((....))))).)).)))......))))..)).)))-----------..((((.......)-))).... ( -28.50)
>DroWil_CAF1 63155 103 - 1
AC----GUAGAGAC------GGGGGUGUUGUUU-----GAGUGAUGUGCCAGAGAGAGCGAGAGAGUG-AG-CGAGCUUUUGCCACCUUUUGUUGCUGUCGCUGUAACAACUAAGCAAAG
.(----((....))------)......((((((-----.(((..(((..(((.((.(((((.((((((-.(-(((....)))))))..))).))))).)).)))..)))))))))))).. ( -28.70)
>DroYak_CAF1 45351 105 - 1
AAAGUGGUAAGAAAGAGUGAGAGGGAGCGGAAGAGA---AACCCUUCUCUCGAGAGAGCGAGAGCGGCCAGUAAAGCUCGGCUCACC-----------UAGCUGUAAAAACU-AGCAAAG
.....(((......(((.((.((((..(....)...---..)))))).)))....((((..((((..........)))).)))))))-----------..((((.......)-))).... ( -29.90)
>consensus
AAAGUGGUAAGAAAGAGUGAGAGGGAGCGGAAA_____AAACCAUUCUCUCGAGAGAGCGAGAGCGGCCAUUAAAGCUCGGCUCACC___________UAGCUGUAAAAACU_AGCAAAG
.....(((............(((((((.((...........)).)))))))....((((..((((..........)))).))))))).............(((..........))).... (-15.08 = -15.33 +   0.26)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 4

Location 17,880,754 – 17,880,870
Length 116
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 79.11
Mean single sequence MFE -39.83
Consensus MFE -30.11
Energy contribution -30.12
Covariance contribution 0.01
Combinations/Pair 1.29
Mean z-score -2.12
Structure conservation index 0.76
SVM decision value 1.35
SVM RNA-class probability 0.945245
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 17880754 116 - 20766785
GCGUUGGCGUUGCGUUUUUGUUGCGCCGGCUGUUUUGCCAAAAGUGGUAAGAAAGAGUGAGAGGGAGCGGAAA----AAAACCAUUCUCUCGAGAGAGCGAGAGCGGCCAUUAAAGCUCG
..((((((((.(((....))).))))))))..((((((((....))))))))..((((..(((((((.((...----....)).)))))))......((....))..........)))). ( -41.20)
>DroSec_CAF1 45731 115 - 1
GCGUUGGCGUUGCGUUUUUGUUGCGCCGGCUGUUUUGCCAAAAGUGGUAAGAAAGAGUGAGAGGGAGUGGAAA-----ACACCAUUCUCUCGAGAGAGCGAGAGCGGCCAUUAAAGCUCG
..((((((((.(((....))).))))))))..((((((((....))))))))..((((..((((((((((...-----...))))))))))......((....))..........)))). ( -46.30)
>DroSim_CAF1 46094 115 - 1
GCGUUGGCGUUGCGUUUUUGUUGCGCCGGCUGUUUUGCCAAAAGUGGUAAGAAAGAGUGAGAGGGAGUGGAAG-----AAACCAUUUUCUCGAGAGAGCGAGAGCGGCCAUUAAAGCUCG
..((((((((.(((....))).))))))))..((((((((....))))))))..((((..(((..(((((...-----...)))))..)))......((....))..........)))). ( -43.80)
>DroEre_CAF1 48112 120 - 1
GCGUUGGCGUUGCGUUUUUGUUGCGCCGGCUGUUUUGCCAAAAGUGGUAAGAAAGAGUGAGAGGGAGCGGCAAAGAAAAAACAAUUCACUCGCGAGCGCGAGAGCGGCCAUUAAAGCUCG
..((((((((.(((....))).))))))))..((((((((....))))))))..((((......(.((.((...(((.......))).(((((....))))).)).)))......)))). ( -42.70)
>DroWil_CAF1 63195 99 - 1
GCGUUGGCGUUGGAC----AUUGCGCCGGUGAAUUUAGCGAC----GUAGAGAC------GGGGGUGUUGUUU-----GAGUGAUGUGCCAGAGAGAGCGAGAGAGUG-AG-CGAGCUUU
.((..(((((.....----...)))))..))......((..(----((....))------)((.(..(..(..-----..)..)..).)).......))...(((((.-..-...))))) ( -22.50)
>DroYak_CAF1 45379 117 - 1
GCGUUGGCGUUGCGUUUUUGUUGCGCCGGCUGUUUUGCCAAAAGUGGUAAGAAAGAGUGAGAGGGAGCGGAAGAGA---AACCCUUCUCUCGAGAGAGCGAGAGCGGCCAGUAAAGCUCG
((...(((((.(((....))).)))))(((((((((((((....))))))))........(((((..(....)...---..)))))((((((......)))))))))))......))... ( -42.50)
>consensus
GCGUUGGCGUUGCGUUUUUGUUGCGCCGGCUGUUUUGCCAAAAGUGGUAAGAAAGAGUGAGAGGGAGCGGAAA_____AAACCAUUCUCUCGAGAGAGCGAGAGCGGCCAUUAAAGCUCG
((((((((((.(((....))).))))))))..((((((((....))))))))........(((((((.((...........)).)))))))......))..((((..........)))). (-30.11 = -30.12 +   0.01)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 5

Location 17,880,794 – 17,880,910
Length 116
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 82.16
Mean single sequence MFE -39.06
Consensus MFE -30.33
Energy contribution -31.67
Covariance contribution 1.34
Combinations/Pair 1.18
Mean z-score -1.85
Structure conservation index 0.78
SVM decision value 0.57
SVM RNA-class probability 0.785779
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 17880794 116 - 20766785
GCCAUUUUUGGGUUGAAAGCUCUUGUCCGGCGGCGCUGUUGCGUUGGCGUUGCGUUUUUGUUGCGCCGGCUGUUUUGCCAAAAGUGGUAAGAAAGAGUGAGAGGGAGCGGAAA----AAA
.(((....))).......((((((.(((((((((((....)))))(((((.(((....))).))))).))))((((((((....))))))))......))..)))))).....----... ( -39.60)
>DroSec_CAF1 45771 115 - 1
GCCAUUUUUGGGUUGAAAGCUCUUGUCCGGCGGCGCUGUUGCGUUGGCGUUGCGUUUUUGUUGCGCCGGCUGUUUUGCCAAAAGUGGUAAGAAAGAGUGAGAGGGAGUGGAAA-----AC
.((((((((.........((((((...(((((((((....)))))(((((.(((....))).))))).))))((((((((....))))))))))))))....))))))))...-----.. ( -40.92)
>DroSim_CAF1 46134 115 - 1
GCCAUUUUUGGGUUGAAAGCUCUUGUCCGGCGGCGCUGUUGCGUUGGCGUUGCGUUUUUGUUGCGCCGGCUGUUUUGCCAAAAGUGGUAAGAAAGAGUGAGAGGGAGUGGAAG-----AA
.((((((((.........((((((...(((((((((....)))))(((((.(((....))).))))).))))((((((((....))))))))))))))....))))))))...-----.. ( -40.92)
>DroEre_CAF1 48152 120 - 1
GCCAUUUUUGGGUUGAAAGCUCUUGUCCGGCGGCGCUGUUGCGUUGGCGUUGCGUUUUUGUUGCGCCGGCUGUUUUGCCAAAAGUGGUAAGAAAGAGUGAGAGGGAGCGGCAAAGAAAAA
(((.((((......))))((((((.(((((((((((....)))))(((((.(((....))).))))).))))((((((((....))))))))......))..)))))))))......... ( -42.10)
>DroWil_CAF1 63233 93 - 1
GCCAUUUUUGGGUGGAAACUU--------ACGGCUCUGUUGCGUUGGCGUUGGAC----AUUGCGCCGGUGAAUUUAGCGAC----GUAGAGAC------GGGGGUGUUGUUU-----GA
.(((((....)))))((((..--------(((.(((((((((((((((((.....----...))))).((.......)))))----))...)))------)))).))).))))-----.. ( -29.10)
>DroYak_CAF1 45419 117 - 1
GCCAUUUUUGGGUUGAAAGCUCUUGUCCGGCGGCGCUGUUGCGUUGGCGUUGCGUUUUUGUUGCGCCGGCUGUUUUGCCAAAAGUGGUAAGAAAGAGUGAGAGGGAGCGGAAGAGA---A
.(((....))).........((((.((((.(..(.((.(..(((((((((.(((....))).))))))))..((((((((....))))))))....)..).)).).))))).))))---. ( -41.70)
>consensus
GCCAUUUUUGGGUUGAAAGCUCUUGUCCGGCGGCGCUGUUGCGUUGGCGUUGCGUUUUUGUUGCGCCGGCUGUUUUGCCAAAAGUGGUAAGAAAGAGUGAGAGGGAGCGGAAA_____AA
.(((....))).......((((((...(((((((((....)))))(((((.(((....))).))))).))))((((((((....))))))))..........))))))............ (-30.33 = -31.67 +   1.34)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:50:10 2006