Locus 2030

Sequence ID	3R_DroMel_CAF1
Location	5,751,944 – 5,752,108
Length	164
Max. P	0.999941

overview

Window 8

Location	5,751,944 – 5,752,043
Length	99
Sequences	6
Columns	118
Reading direction	forward
Mean pairwise identity	81.55
Mean single sequence MFE	-31.31
Consensus MFE	-15.73
Energy contribution	-16.51
Covariance contribution	0.78
Combinations/Pair	1.04
Mean z-score	-2.50
Structure conservation index	0.50
SVM decision value	0.11
SVM RNA-class probability	0.587662
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 5751944 99 + 27905053
AUUUGAAAGUCUUUGACUUGCUGCAGUUAGCUCAAACAAAAUAAAAACUGCCU----CGGCCCAAGGUAAUGGGCAAUUAGCUGCAG---------------CAACCUUCUGGGCCAA
........((((..((.((((((((((((((..................))..----..(((((......)))))...)))))))))---------------)))...)).))))... ( -29.87)
>DroPse_CAF1 49179 110 + 1
AUUUGAAAGUCUUUGAGUU---GCAGUUAGCUCGA----AAUAA-AAUUGCCGGUACCGAGGCAGGGUAAUGGGCAAUUAGCUGCAGCAGCAGCAACAACAGCAACCUUUUGGGCCUG
........((((..(((((---((.(((.......----.....-(((((((.(((((.......))).)).))))))).(((((....)))))...))).)))).)))..))))... ( -34.20)
>DroSim_CAF1 44319 99 + 1
AUUUGAAAGUCUUUGACUUGCUGCAGUUAGCUCAAACAAAAUAAAAACUGCCU----CGGCCCAAGGUAAUGGGCAAUUAGCUGCAG---------------CAACCUUCUGGGCCAA
........((((..((.((((((((((((((..................))..----..(((((......)))))...)))))))))---------------)))...)).))))... ( -29.87)
>DroEre_CAF1 39188 99 + 1
AUUUGAAAGUCUUUGACUUGCUGCAGUUAGCUCAAACAAAAUAAAAACUGCCU----CGGCCCAAGGUAAUGGGCAAUUAGCUGCAG---------------CAACCUUCUGGGCCAA
........((((..((.((((((((((((((..................))..----..(((((......)))))...)))))))))---------------)))...)).))))... ( -29.87)
>DroYak_CAF1 27654 99 + 1
AUUUGAAAGUCUUUGACUUGCUGCAGUUAGCUCAAACAAAAUAAAAACUGCCU----CGGCCCAAGGUAAUGGGCAAUUAGCUGCAG---------------CAACCUUCUGGGCCAA
........((((..((.((((((((((((((..................))..----..(((((......)))))...)))))))))---------------)))...)).))))... ( -29.87)
>DroPer_CAF1 48826 110 + 1
AUUUGAAAGUCUUUGAGUU---GCAGUUAGCUCGA----AAUAA-AAUUGCCGGUACCGAGGCAGGGUAAUGGGCAAUUAGCUGCAGCAGCAGCAACAACAGCAACCUUUUGGGCCUG
........((((..(((((---((.(((.......----.....-(((((((.(((((.......))).)).))))))).(((((....)))))...))).)))).)))..))))... ( -34.20)
>consensus
AUUUGAAAGUCUUUGACUUGCUGCAGUUAGCUCAAACAAAAUAAAAACUGCCU____CGGCCCAAGGUAAUGGGCAAUUAGCUGCAG_______________CAACCUUCUGGGCCAA
......(((((...))))).((((((((((((((..............((((.............)))).)))))...)))))))))..................((....))..... (-15.73 = -16.51 +   0.78)

alignment

secondary structure

dotplot

Window 9

Location	5,751,982 – 5,752,072
Length	90
Sequences	5
Columns	100
Reading direction	forward
Mean pairwise identity	95.74
Mean single sequence MFE	-25.30
Consensus MFE	-23.53
Energy contribution	-23.53
Covariance contribution	-0.00
Combinations/Pair	1.00
Mean z-score	-2.96
Structure conservation index	0.93
SVM decision value	4.71
SVM RNA-class probability	0.999941
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 5751982 90 + 27905053
AAAUAAAAACUGCCUCGGCCCAAGGUAAUGGGCAAUUAGCUGCAGCAACCUUCUGGGCCAAAAACCAACAGCCA----------ACAUGGGCUAGUCAAA
................((((((((((..(((((.....))).))...))))..))))))..........((((.----------.....))))....... ( -25.10)
>DroSec_CAF1 43243 90 + 1
AAAUAAAAACUGCCUCGGCCCAAGGUAAUGGGCAAUUAGCUGCAGCAACCUUCUGGGCCAAAAACCAACAGCCA----------ACAUGGGCUAGUCAAA
................((((((((((..(((((.....))).))...))))..))))))..........((((.----------.....))))....... ( -25.10)
>DroSim_CAF1 44357 90 + 1
AAAUAAAAACUGCCUCGGCCCAAGGUAAUGGGCAAUUAGCUGCAGCAACCUUCUGGGCCAAAAACCAACAGCCA----------ACAUGGGCUAGUCAAA
................((((((((((..(((((.....))).))...))))..))))))..........((((.----------.....))))....... ( -25.10)
>DroEre_CAF1 39226 90 + 1
AAAUAAAAACUGCCUCGGCCCAAGGUAAUGGGCAAUUAGCUGCAGCAACCUUCUGGGCCAAAAACCAACAGCCA----------ACAUGGGCUAGUCAAA
................((((((((((..(((((.....))).))...))))..))))))..........((((.----------.....))))....... ( -25.10)
>DroYak_CAF1 27692 100 + 1
AAAUAAAAACUGCCUCGGCCCAAGGUAAUGGGCAAUUAGCUGCAGCAACCUUCUGGGCCAAAAACCAACAGCCAACAGCCAACAACAUGGGCUAGUCAAA
........(((((((.((((((((((..(((((.....))).))...))))..))))))...........((.....)).........)))).))).... ( -26.10)
>consensus
AAAUAAAAACUGCCUCGGCCCAAGGUAAUGGGCAAUUAGCUGCAGCAACCUUCUGGGCCAAAAACCAACAGCCA__________ACAUGGGCUAGUCAAA
........((((((..((((((((((..(((((.....))).))...))))..)))))).........((.................))))).))).... (-23.53 = -23.53 +  -0.00)

alignment

secondary structure

dotplot

Window 0

Location	5,751,982 – 5,752,072
Length	90
Sequences	5
Columns	100
Reading direction	reverse
Mean pairwise identity	95.74
Mean single sequence MFE	-29.40
Consensus MFE	-27.19
Energy contribution	-27.19
Covariance contribution	-0.00
Combinations/Pair	1.00
Mean z-score	-2.09
Structure conservation index	0.92
SVM decision value	3.14
SVM RNA-class probability	0.998568
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 5751982 90 - 27905053
UUUGACUAGCCCAUGU----------UGGCUGUUGGUUUUUGGCCCAGAAGGUUGCUGCAGCUAAUUGCCCAUUACCUUGGGCCGAGGCAGUUUUUAUUU
.(..((.((((.....----------.))))))..).((((((((((..((((....((((....)))).....))))))))))))))............ ( -28.80)
>DroSec_CAF1 43243 90 - 1
UUUGACUAGCCCAUGU----------UGGCUGUUGGUUUUUGGCCCAGAAGGUUGCUGCAGCUAAUUGCCCAUUACCUUGGGCCGAGGCAGUUUUUAUUU
.(..((.((((.....----------.))))))..).((((((((((..((((....((((....)))).....))))))))))))))............ ( -28.80)
>DroSim_CAF1 44357 90 - 1
UUUGACUAGCCCAUGU----------UGGCUGUUGGUUUUUGGCCCAGAAGGUUGCUGCAGCUAAUUGCCCAUUACCUUGGGCCGAGGCAGUUUUUAUUU
.(..((.((((.....----------.))))))..).((((((((((..((((....((((....)))).....))))))))))))))............ ( -28.80)
>DroEre_CAF1 39226 90 - 1
UUUGACUAGCCCAUGU----------UGGCUGUUGGUUUUUGGCCCAGAAGGUUGCUGCAGCUAAUUGCCCAUUACCUUGGGCCGAGGCAGUUUUUAUUU
.(..((.((((.....----------.))))))..).((((((((((..((((....((((....)))).....))))))))))))))............ ( -28.80)
>DroYak_CAF1 27692 100 - 1
UUUGACUAGCCCAUGUUGUUGGCUGUUGGCUGUUGGUUUUUGGCCCAGAAGGUUGCUGCAGCUAAUUGCCCAUUACCUUGGGCCGAGGCAGUUUUUAUUU
.(((.((.(((((.((.((.(((.(((((((((.(((....((((.....)))))))))))))))).))).)).))..)))))..)).)))......... ( -31.80)
>consensus
UUUGACUAGCCCAUGU__________UGGCUGUUGGUUUUUGGCCCAGAAGGUUGCUGCAGCUAAUUGCCCAUUACCUUGGGCCGAGGCAGUUUUUAUUU
.(..((.((((................))))))..).((((((((((..((((....((((....)))).....))))))))))))))............ (-27.19 = -27.19 +  -0.00)

alignment

secondary structure

dotplot

Window 1

Location	5,752,018 – 5,752,108
Length	90
Sequences	3
Columns	90
Reading direction	forward
Mean pairwise identity	91.85
Mean single sequence MFE	-21.00
Consensus MFE	-20.85
Energy contribution	-20.63
Covariance contribution	-0.22
Combinations/Pair	1.06
Mean z-score	-1.39
Structure conservation index	0.99
SVM decision value	0.46
SVM RNA-class probability	0.746051
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 5752018 90 + 27905053
UAGCUGCAGCAACCUUCUGGGCCAAAAACCAACAGCCAACAUGGGCUAGUCAAACAAAUGAGGCAAGCGGACAGCAAACUCCGGACCUGG
..(((((.((..((....))(((..........((((......))))..(((......))))))..)).).)))).....(((....))) ( -22.10)
>DroSec_CAF1 43279 90 + 1
UAGCUGCAGCAACCUUCUGGGCCAAAAACCAACAGCCAACAUGGGCUAGUCAAACAAAUGAGGCAAGCGUACAGUAAACUCCGGACCAGC
..((((..((..((....))(((..........((((......))))..(((......))))))..))...))))............... ( -19.10)
>DroEre_CAF1 39262 82 + 1
UAGCUGCAGCAACCUUCUGGGCCAAAAACCAACAGCCAACAUGGGCUAGUCAAACAAAUGAGGCAAGCGGACAGCAAACUCC--------
..(((((.((..((....))(((..........((((......))))..(((......))))))..)).).)))).......-------- ( -21.80)
>consensus
UAGCUGCAGCAACCUUCUGGGCCAAAAACCAACAGCCAACAUGGGCUAGUCAAACAAAUGAGGCAAGCGGACAGCAAACUCCGGACC_G_
..((((..((..((....))(((..........((((......))))..(((......))))))..))...))))............... (-20.85 = -20.63 +  -0.22)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:25:43 2006