Locus 1381

Sequence ID 3R_DroMel_CAF1
Location 4,031,016 – 4,031,139
Length 123
Max. P 0.925936
window2276 window2277 window2278

overview

Window 6

Location 4,031,016 – 4,031,107
Length 91
Sequences 6
Columns 102
Reading direction forward
Mean pairwise identity 80.71
Mean single sequence MFE -27.03
Consensus MFE -18.76
Energy contribution -19.90
Covariance contribution 1.14
Combinations/Pair 1.11
Mean z-score -2.53
Structure conservation index 0.69
SVM decision value 1.17
SVM RNA-class probability 0.925936
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 4031016 91 + 27905053
UAUUUGUUCGCCUCGAACGUCGAUACUAUGUAC-----------AUAUAUAUAUACUACAUGGGCAAUAAAAAUAUUGGCCUGCCUUCGCCGGCAGGACAAA
..((((((.((((((.....)))...((((((.-----------.(((....))).)))))))))))))))....(((.((((((......)))))).))). ( -23.90)
>DroSec_CAF1 36534 89 + 1
UAUUUGUUCGCCUCGAACAUCGAUACUAUGUAC-----------AUAUA--UUUGGUACAUGGGCAAUAAAAAUAUUGGCCUGCCUUCGCCGGCAUGACAAA
..((((((.((((((.....)))..((((((((-----------.....--....))))))))..............))).((((......)))).)))))) ( -22.10)
>DroSim_CAF1 37075 89 + 1
UAUUUGUUCGCCUCGAACAUCGAUACUAUGUAC-----------AUAUA--UAUGGUACAUGGGCAAUAAAAAUAUUGGCCUGCCUUCGCCGGCAGGACAAA
..((((((.((((((.....)))(((((((((.-----------...))--)))))))....)))))))))....(((.((((((......)))))).))). ( -28.40)
>DroEre_CAF1 19653 100 + 1
UAUUUGUUCGCCCCGAACGCCGAUACUAUGUGCGGGUAUAUGGCGUAUA--UAUGGUACAUGGGCAAUAAAAAUAUUGGCCUGCCUUCGCCGGCAGGACAAA
..((((((.((((.....(((((((((.......))))).))))((((.--....))))..))))))))))....(((.((((((......)))))).))). ( -34.50)
>DroYak_CAF1 37579 93 + 1
UAUUUGUUCGCCUCGAACGUCGAUACUAUAGGC---UGUAUGCUG------UAUGGUACAUGGGCAAUAAAAAUAUUGGCCUGCCUUCGCCGGCAGGACAAA
..((((((.((((((.....)))((((((((((---.....))).------)))))))....)))))))))....(((.((((((......)))))).))). ( -30.20)
>DroAna_CAF1 20313 82 + 1
UAUUUGUUAGUAGUGG----CCCUGCUACAUGC----------UA------CAUACAACAUGGGCAAUAAAAAUAUUGGCCUGCCUUCGCCGGCAGGACAAA
..((((((.(((((..----....)))))..((----------(.------(((.....))))))))))))....(((.((((((......)))))).))). ( -23.10)
>consensus
UAUUUGUUCGCCUCGAACGUCGAUACUAUGUAC___________AUAUA__UAUGGUACAUGGGCAAUAAAAAUAUUGGCCUGCCUUCGCCGGCAGGACAAA
..((((((.((.(((.....)))..((((((((......................))))))))))))))))....(((.((((((......)))))).))). (-18.76 = -19.90 +   1.14)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 7

Location 4,031,016 – 4,031,107
Length 91
Sequences 6
Columns 102
Reading direction reverse
Mean pairwise identity 80.71
Mean single sequence MFE -26.02
Consensus MFE -15.53
Energy contribution -15.79
Covariance contribution 0.25
Combinations/Pair 1.19
Mean z-score -2.16
Structure conservation index 0.60
SVM decision value 0.56
SVM RNA-class probability 0.781015
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 4031016 91 - 27905053
UUUGUCCUGCCGGCGAAGGCAGGCCAAUAUUUUUAUUGCCCAUGUAGUAUAUAUAUAU-----------GUACAUAGUAUCGACGUUCGAGGCGAACAAAUA
.(((.((((((......)))))).)))........(((((......((((((....))-----------))))......(((.....))))))))....... ( -26.00)
>DroSec_CAF1 36534 89 - 1
UUUGUCAUGCCGGCGAAGGCAGGCCAAUAUUUUUAUUGCCCAUGUACCAAA--UAUAU-----------GUACAUAGUAUCGAUGUUCGAGGCGAACAAAUA
(((((...(((.((....)).)))...........(((((.((((((....--.....-----------))))))....(((.....))))))))))))).. ( -22.60)
>DroSim_CAF1 37075 89 - 1
UUUGUCCUGCCGGCGAAGGCAGGCCAAUAUUUUUAUUGCCCAUGUACCAUA--UAUAU-----------GUACAUAGUAUCGAUGUUCGAGGCGAACAAAUA
.(((.((((((......)))))).)))........(((((.((((((....--.....-----------))))))....(((.....))))))))....... ( -26.00)
>DroEre_CAF1 19653 100 - 1
UUUGUCCUGCCGGCGAAGGCAGGCCAAUAUUUUUAUUGCCCAUGUACCAUA--UAUACGCCAUAUACCCGCACAUAGUAUCGGCGUUCGGGGCGAACAAAUA
.(((.((((((......)))))).)))........(((((((((((...))--)))(((((..((((.........)))).)))))...))))))....... ( -30.70)
>DroYak_CAF1 37579 93 - 1
UUUGUCCUGCCGGCGAAGGCAGGCCAAUAUUUUUAUUGCCCAUGUACCAUA------CAGCAUACA---GCCUAUAGUAUCGACGUUCGAGGCGAACAAAUA
(((((..((((.((..((((.((.(((((....))))).))((((......------..))))...---))))...)).(((.....))))))).))))).. ( -24.40)
>DroAna_CAF1 20313 82 - 1
UUUGUCCUGCCGGCGAAGGCAGGCCAAUAUUUUUAUUGCCCAUGUUGUAUG------UA----------GCAUGUAGCAGGG----CCACUACUAACAAAUA
.(((.((((((......)))))).)))..........((((.(((((((((------..----------.))))))))))))----)............... ( -26.40)
>consensus
UUUGUCCUGCCGGCGAAGGCAGGCCAAUAUUUUUAUUGCCCAUGUACCAUA__UAUAU___________GCACAUAGUAUCGACGUUCGAGGCGAACAAAUA
.(((.((((((......)))))).)))........(((((.((((..........................))))....(((.....))))))))....... (-15.53 = -15.79 +   0.25)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 8

Location 4,031,049 – 4,031,139
Length 90
Sequences 6
Columns 106
Reading direction reverse
Mean pairwise identity 77.91
Mean single sequence MFE -24.45
Consensus MFE -13.88
Energy contribution -14.52
Covariance contribution 0.64
Combinations/Pair 1.19
Mean z-score -2.03
Structure conservation index 0.57
SVM decision value 0.85
SVM RNA-class probability 0.866127
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 4031049 90 - 27905053
-GAAAUUGUGCAUGC--AUUUUAUGGUGCAAUUCCUUUGUCCUGCC------GGCGAAGGCAGGCCAAUAUUUUUAUUGCCCAU--GUAGUA-----UAUAUAUAU
-.....((((.((((--....(((((.(((((....(((.((((((------......)))))).))).......)))))))))--)..)))-----).))))... ( -27.60)
>DroPse_CAF1 17929 100 - 1
-CAUAUUGUGUAUAC--AUUUUAUGGUGCAAUUCCUUUGUCCUCGC--AG-CGCCGAAGGCAGGCCAAUAUUUUUAUUGCUCGCUUCUGCCAGAGCAACUAUCCAU
-((((..(((....)--))..))))...........(((..((.((--((-......((((..((.((((....))))))..)))))))).))..)))........ ( -21.40)
>DroSec_CAF1 36567 88 - 1
-GAAAUUGUGCAUGC--AUUUUAUGGUGCAAUUCCUUUGUCAUGCC------GGCGAAGGCAGGCCAAUAUUUUUAUUGCCCAU--GUACCA-----AA--UAUAU
-.(((.(((....))--).))).(((((((...((((((((.....------))))))))..((.(((((....))))).)).)--))))))-----..--..... ( -25.80)
>DroSim_CAF1 37108 88 - 1
-GAAAUUGUGCAUGC--AUUUUAUGGUGCAAUUCCUUUGUCCUGCC------GGCGAAGGCAGGCCAAUAUUUUUAUUGCCCAU--GUACCA-----UA--UAUAU
-......(((....)--))..(((((((((...((((((((.....------))))))))..((.(((((....))))).)).)--))))))-----))--..... ( -26.50)
>DroWil_CAF1 46295 98 - 1
UCAGAUUGUGUAUGCACAUUUUAUGGUGCAAUUCUUUUGUGCUCUCGCACUUGGCGAAGGCAGGCCAAUAUUUUUAUUACCCGCUUGUACAAGA----A--UUU--
............(((((........)))))....((((((((..((((.....))))((((.((..((((....)))).)).))))))))))))----.--...-- ( -24.00)
>DroPer_CAF1 18235 100 - 1
-CAUAUUGUGUAUAC--AUUUUAUGGUGCAAUUCCUUUGUCCUCGC--AG-CGCCGAAGGCAGGCCAAUAUUUUUAUUGCUCGCUUCUGCCAGAGCAACUAUCCAU
-((((..(((....)--))..))))...........(((..((.((--((-......((((..((.((((....))))))..)))))))).))..)))........ ( -21.40)
>consensus
_CAAAUUGUGCAUGC__AUUUUAUGGUGCAAUUCCUUUGUCCUCCC______GGCGAAGGCAGGCCAAUAUUUUUAUUGCCCAC__GUACCA_____AA__UAUAU
.......................((((((....((((((((...........))))))))..((.(((((....))))).))....)))))).............. (-13.88 = -14.52 +   0.64)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:08:39 2006