Locus 156

Sequence ID 3R_DroMel_CAF1
Location 799,476 – 799,796
Length 320
Max. P 0.964799
window253 window254 window255 window256 window257

overview

Window 3

Location 799,476 – 799,596
Length 120
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 89.89
Mean single sequence MFE -28.40
Consensus MFE -21.17
Energy contribution -22.05
Covariance contribution 0.88
Combinations/Pair 1.07
Mean z-score -1.94
Structure conservation index 0.75
SVM decision value 0.44
SVM RNA-class probability 0.737770
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 799476 120 - 27905053
UACAAGCGGGCAAAUGUUUAAAUACUUGAGUGCCGUACACGAGCAUAUUAACUUUUACUCAGCGCUCAGGGUUCGAAAUUGUCAACAAGACAAUUCACUUAUAUACAUAGAUCUGCACUU
.....(((((...((((.((....(((((((((.(.....(((........))).....).)))))))))....(((.(((((.....)))))))).....)).))))...))))).... ( -28.60)
>DroSec_CAF1 37497 120 - 1
UACAAGCGGGCAAAUGUUUAAAUACUUGAGUGCCGUACACGAGCAUAUUAACUUUUACUCAGCGCUCAGGGUUCGAAAUUGUCAACACGACAAUUCACUUACAUACAUAGAUCUGCACUU
.....(((((...((((.......(((((((((.(.....(((........))).....).)))))))))....(((.(((((.....))))))))........))))...))))).... ( -28.00)
>DroEre_CAF1 21190 110 - 1
UACGAGCGGGCAAAUGUUUAAAUACUUGAGUGCCGUACACGAGCAUAUUAACUUUUACUCAGCGCUCAGUGUUCGA--UUGUCAACACGACAAUUCACUU--------AGAUCUGCACUU
.....((((((.........((((((.((((((.(.....(((........))).....).)))))))))))).((--(((((.....))))))).....--------.).))))).... ( -25.70)
>DroYak_CAF1 27214 112 - 1
UACUAGCAGGCAAAUGUUUAAAUACUUGAGUGCCGUACACGAGCAUAUUAACUUUUGCUCAGCGCUCAGUGUUUGAAAGUGUCAACACGAAAAUUCACUU--------AGAUCUGUGCUU
....((((((((....((((((((((.((((((.(....)(((((..........))))).))))))))))))))))..)))).....((....))....--------.......)))). ( -31.30)
>consensus
UACAAGCGGGCAAAUGUUUAAAUACUUGAGUGCCGUACACGAGCAUAUUAACUUUUACUCAGCGCUCAGGGUUCGAAAUUGUCAACACGACAAUUCACUU________AGAUCUGCACUU
.....((((((.............(((((((((.(.....(((........))).....).)))))))))....(((.(((((.....)))))))).............).))))).... (-21.17 = -22.05 +   0.88)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 4

Location 799,596 – 799,716
Length 120
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 97.78
Mean single sequence MFE -46.48
Consensus MFE -44.80
Energy contribution -44.67
Covariance contribution -0.12
Combinations/Pair 1.06
Mean z-score -2.69
Structure conservation index 0.96
SVM decision value 1.57
SVM RNA-class probability 0.964799
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 799596 120 + 27905053
AUUCGAGCCGAAUGCAAGUGCAGAUACGCGCAUCUGAGAGAAUGCCUUUGAAUUUCCGUAUCUGGGCGAUGCACAACGUCCUGGGAGAUGGCAUGUUCGGCAUGCGUGCUUGUUUGUAUC
(((((...)))))....(((((((((((((((((((((...(((((.....((((((......(((((........)))))..))))))))))).))))).)))))))..))))))))). ( -41.00)
>DroSec_CAF1 37617 120 + 1
AUUCGAGCCGCAUGCAAGUGCAGAUACGCGCAUCUGAGAGAAUGCCUUUGAAUCUCCGUAUCUGGGCGAUGCACAACGUCCUGGGAGAUGGCAUGUUCGGCAUGCGUGCUUGUUUGUAUC
...((((((((((((..((((......))))......(((.(((((.....((((((......(((((........)))))..))))))))))).))).))))))).)))))........ ( -46.80)
>DroEre_CAF1 21300 120 + 1
AUUCGAGCCGCAUGCAAGUGCAGAUACGCGCAUCUGAGAGAAUGCCUUUGAAUCUCCGUAUCAGGGCGAUGUACAACGUCCUGGGAGAUGGCAUGUUCGGCAUGCGUGCUUGUUUGUAUC
...((((((((((((..((((......))))......(((.(((((.....((((((....(((((((........)))))))))))))))))).))).))))))).)))))........ ( -51.00)
>DroYak_CAF1 27326 120 + 1
AUUCGAGCCGCAUGCAAGUGCAGAUACGCGCAUCUGAGAAAAUGCCUUUGAAUCUCCGUAUCUGGGCGAUGUACAACGUCCUGGGAGAUGGCAUGUUCGGCAUGCGUGCUUGUUUGUAUC
...((((((((((((..((((......))))......(((.(((((.....((((((......(((((........)))))..))))))))))).))).))))))).)))))........ ( -47.10)
>consensus
AUUCGAGCCGCAUGCAAGUGCAGAUACGCGCAUCUGAGAGAAUGCCUUUGAAUCUCCGUAUCUGGGCGAUGCACAACGUCCUGGGAGAUGGCAUGUUCGGCAUGCGUGCUUGUUUGUAUC
...((((((((((((..((((......))))......(((.(((((.....((((((......(((((........)))))..))))))))))).))).))))))).)))))........ (-44.80 = -44.67 +  -0.12)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 5

Location 799,596 – 799,716
Length 120
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 97.78
Mean single sequence MFE -36.30
Consensus MFE -33.35
Energy contribution -33.85
Covariance contribution 0.50
Combinations/Pair 1.00
Mean z-score -1.67
Structure conservation index 0.92
SVM decision value 0.02
SVM RNA-class probability 0.542925
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 799596 120 - 27905053
GAUACAAACAAGCACGCAUGCCGAACAUGCCAUCUCCCAGGACGUUGUGCAUCGCCCAGAUACGGAAAUUCAAAGGCAUUCUCUCAGAUGCGCGUAUCUGCACUUGCAUUCGGCUCGAAU
..............((...(((((..(((((........)).))).(((((.....(((((((((.....)....(((((......))))).))))))))....)))))))))).))... ( -29.90)
>DroSec_CAF1 37617 120 - 1
GAUACAAACAAGCACGCAUGCCGAACAUGCCAUCUCCCAGGACGUUGUGCAUCGCCCAGAUACGGAGAUUCAAAGGCAUUCUCUCAGAUGCGCGUAUCUGCACUUGCAUGCGGCUCGAAU
........(.(((.(((((((.((..(((((((((((..((.((........)).))......)))))).....)))))..)).((((((....)))))).....)))))))))).)... ( -36.20)
>DroEre_CAF1 21300 120 - 1
GAUACAAACAAGCACGCAUGCCGAACAUGCCAUCUCCCAGGACGUUGUACAUCGCCCUGAUACGGAGAUUCAAAGGCAUUCUCUCAGAUGCGCGUAUCUGCACUUGCAUGCGGCUCGAAU
........(.(((.(((((((.((..(((((((((((((((.((........)).))))....)))))).....)))))..)).((((((....)))))).....)))))))))).)... ( -41.10)
>DroYak_CAF1 27326 120 - 1
GAUACAAACAAGCACGCAUGCCGAACAUGCCAUCUCCCAGGACGUUGUACAUCGCCCAGAUACGGAGAUUCAAAGGCAUUUUCUCAGAUGCGCGUAUCUGCACUUGCAUGCGGCUCGAAU
........(.(((.(((((((.(((.(((((((((((..((.((........)).))......)))))).....))))).))).((((((....)))))).....)))))))))).)... ( -38.00)
>consensus
GAUACAAACAAGCACGCAUGCCGAACAUGCCAUCUCCCAGGACGUUGUACAUCGCCCAGAUACGGAGAUUCAAAGGCAUUCUCUCAGAUGCGCGUAUCUGCACUUGCAUGCGGCUCGAAU
........(.(((.(((((((.((..(((((((((((..((.((........)).))......)))))).....)))))..)).((((((....)))))).....)))))))))).)... (-33.35 = -33.85 +   0.50)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 6

Location 799,636 – 799,756
Length 120
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 97.36
Mean single sequence MFE -35.02
Consensus MFE -31.30
Energy contribution -31.80
Covariance contribution 0.50
Combinations/Pair 1.00
Mean z-score -2.08
Structure conservation index 0.89
SVM decision value 0.56
SVM RNA-class probability 0.782471
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 799636 120 - 27905053
GAGCGCAGCGUCUGCGAAUGAACAGCAAAAGUAUCUUAAAGAUACAAACAAGCACGCAUGCCGAACAUGCCAUCUCCCAGGACGUUGUGCAUCGCCCAGAUACGGAAAUUCAAAGGCAUU
(((((((((((((..(((((..........(((((.....)))))..........(((((.....)))))))).))...))))))))))).))(((..((.........))...)))... ( -35.40)
>DroSec_CAF1 37657 120 - 1
GAGCGCAGCGUCUGCGAGCGAACAGCAAAAGUAUCUUAAAGAUACAAACAAGCACGCAUGCCGAACAUGCCAUCUCCCAGGACGUUGUGCAUCGCCCAGAUACGGAGAUUCAAAGGCAUU
(((((((((((((((..((.....))....(((((.....)))))......))..(((((.....))))).........))))))))))).))(((..((.........))...)))... ( -38.00)
>DroEre_CAF1 21340 120 - 1
GAGCGCAGCGUCUGCGAACGAACAGCAAAAGUAUCUUAAAGAUACAAACAAGCACGCAUGCCGAACAUGCCAUCUCCCAGGACGUUGUACAUCGCCCUGAUACGGAGAUUCAAAGGCAUU
..(.(((((((((((.........))....(((((.....))))).....)).)))).))))....(((((((((((((((.((........)).))))....)))))).....))))). ( -34.10)
>DroYak_CAF1 27366 120 - 1
GAGCGCAGCGUCUGCGGACGAACAGCAAAAGUAUCUUAAAGAUACAAACAAGCACGCAUGCCGAACAUGCCAUCUCCCAGGACGUUGUACAUCGCCCAGAUACGGAGAUUCAAAGGCAUU
(((..((((((((..(((.((.........(((((.....)))))..........(((((.....)))))..)))))..))))))))..).))(((..((.........))...)))... ( -32.60)
>consensus
GAGCGCAGCGUCUGCGAACGAACAGCAAAAGUAUCUUAAAGAUACAAACAAGCACGCAUGCCGAACAUGCCAUCUCCCAGGACGUUGUACAUCGCCCAGAUACGGAGAUUCAAAGGCAUU
(((((((((((((((.........))....(((((.....)))))..........(((((.....))))).........))))))))))).))(((..((.........))...)))... (-31.30 = -31.80 +   0.50)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 7

Location 799,676 – 799,796
Length 120
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 95.39
Mean single sequence MFE -29.43
Consensus MFE -25.31
Energy contribution -25.38
Covariance contribution 0.06
Combinations/Pair 1.07
Mean z-score -1.81
Structure conservation index 0.86
SVM decision value 0.33
SVM RNA-class probability 0.691608
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 799676 120 - 27905053
CACGAACGAAAUGGUUUAUACAAUAAAUAAAGUGUGUGUGGAGCGCAGCGUCUGCGAAUGAACAGCAAAAGUAUCUUAAAGAUACAAACAAGCACGCAUGCCGAACAUGCCAUCUCCCAG
.......((.(((((((((.......)))).(((((((((...(((((...)))))..............(((((.....))))).......))))))))).......))))).)).... ( -26.80)
>DroSec_CAF1 37697 120 - 1
CACGAACGAAAUGGUUUAUACAAUAAAUAAAGUGUGUGUGGAGCGCAGCGUCUGCGAGCGAACAGCAAAAGUAUCUUAAAGAUACAAACAAGCACGCAUGCCGAACAUGCCAUCUCCCAG
.......((.(((((((((.......)))).((((((((((..(((((...)))))..)...........(((((.....))))).......))))))))).......))))).)).... ( -28.50)
>DroEre_CAF1 21380 116 - 1
CACG----AAAUGGUAUAUACAAUAAAUAAAGUGUGUGCGGAGCGCAGCGUCUGCGAACGAACAGCAAAAGUAUCUUAAAGAUACAAACAAGCACGCAUGCCGAACAUGCCAUCUCCCAG
...(----(.(((((((..............(((((((((...(((((...)))))..)...........(((((.....)))))......))))))))(.....)))))))).)).... ( -30.10)
>DroYak_CAF1 27406 116 - 1
CACG----AAAUGGUAUAUACAAUAAAUAAAGUGUGUGCGGAGCGCAGCGUCUGCGGACGAACAGCAAAAGUAUCUUAAAGAUACAAACAAGCACGCAUGCCGAACAUGCCAUCUCCCAG
...(----(.(((((((..............((((((((...((....((((....))))....))....(((((.....)))))......))))))))(.....)))))))).)).... ( -32.30)
>consensus
CACG____AAAUGGUAUAUACAAUAAAUAAAGUGUGUGCGGAGCGCAGCGUCUGCGAACGAACAGCAAAAGUAUCUUAAAGAUACAAACAAGCACGCAUGCCGAACAUGCCAUCUCCCAG
..........(((((((..............((((((((.(..(((((...)))))..)...........(((((.....)))))......))))))))(.....))))))))....... (-25.31 = -25.38 +   0.06)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:35:11 2006