Locus 7749

Sequence ID 3R_DroMel_CAF1
Location 20,788,230 – 20,788,444
Length 214
Max. P 0.980176
window12497 window12498 window12499 window12500 window12501

overview

Window 7

Location 20,788,230 – 20,788,326
Length 96
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 85.65
Mean single sequence MFE -22.62
Consensus MFE -13.89
Energy contribution -14.95
Covariance contribution 1.06
Combinations/Pair 1.05
Mean z-score -1.91
Structure conservation index 0.61
SVM decision value 0.01
SVM RNA-class probability 0.541135
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 20788230 96 + 27905053
AAUUGGCCACCUAAACAAGCCGAAAACAUAUUCACAACAUUGCCCACAUUGAUAAGGGUCACAAAUUAAAUGACCCGUCGUGAGCACUGAGAGAAA------------------------
..(((((...........)))))..............((.(((.(((...(((..((((((.........)))))))))))).))).)).......------------------------ ( -20.20)
>DroSec_CAF1 4042 96 + 1
AAUUGGCCACCUAAACAAGCCGAAAACAUAUUCACAACAUUGCCCACAUUGAUAAGGGUCACAAAUUAAAUGACCCGUCGAGAGCACUGAGAGAAA------------------------
..(((((...........)))))..............((.(((.....(((((..((((((.........)))))))))))..))).)).......------------------------ ( -18.80)
>DroSim_CAF1 3997 96 + 1
AAUUGGCCACCUAAACAAGCCGAAAACAUAUUCACAACAUUGCCCACAUUGAUAAGGGUCACAAAUUAAAUGACCCGACGUGAGCACUGAGAGAAA------------------------
..(((((...........)))))..............((.(((.(((........((((((.........))))))...))).))).)).......------------------------ ( -18.90)
>DroEre_CAF1 661 120 + 1
AAUUGGGCACCUAAACAAGCCCAAAACAUAUUCACAACAUUGCCCACAUUGAUAAGGGUCACAAAUUAAGUGAGCUGUCGUGAGCACUGAGAGAAAAUGGGGCAGCAAACUGCGUGUUUG
...(((((..........)))))((((((...........(((((.((((.....((.((((.......)))).))(((....).))........)))))))))((.....)))))))). ( -32.60)
>consensus
AAUUGGCCACCUAAACAAGCCGAAAACAUAUUCACAACAUUGCCCACAUUGAUAAGGGUCACAAAUUAAAUGACCCGUCGUGAGCACUGAGAGAAA________________________
..(((((...........)))))..............((.(((.(((...(((..((((((.........)))))))))))).))).))............................... (-13.89 = -14.95 +   1.06)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 8

Location 20,788,230 – 20,788,326
Length 96
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 85.65
Mean single sequence MFE -27.75
Consensus MFE -21.84
Energy contribution -22.65
Covariance contribution 0.81
Combinations/Pair 1.04
Mean z-score -1.83
Structure conservation index 0.79
SVM decision value 0.65
SVM RNA-class probability 0.813063
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 20788230 96 - 27905053
------------------------UUUCUCUCAGUGCUCACGACGGGUCAUUUAAUUUGUGACCCUUAUCAAUGUGGGCAAUGUUGUGAAUAUGUUUUCGGCUUGUUUAGGUGGCCAAUU
------------------------.(((.(.((.((((((((..(((((((.......))))))).......)))))))).))..).))).........((((.........)))).... ( -27.10)
>DroSec_CAF1 4042 96 - 1
------------------------UUUCUCUCAGUGCUCUCGACGGGUCAUUUAAUUUGUGACCCUUAUCAAUGUGGGCAAUGUUGUGAAUAUGUUUUCGGCUUGUUUAGGUGGCCAAUU
------------------------.(((.(.((.(((((.((..(((((((.......))))))).......)).))))).))..).))).........((((.........)))).... ( -23.10)
>DroSim_CAF1 3997 96 - 1
------------------------UUUCUCUCAGUGCUCACGUCGGGUCAUUUAAUUUGUGACCCUUAUCAAUGUGGGCAAUGUUGUGAAUAUGUUUUCGGCUUGUUUAGGUGGCCAAUU
------------------------.(((.(.((.(((((((((.(((((((.......)))))))......))))))))).))..).))).........((((.........)))).... ( -28.70)
>DroEre_CAF1 661 120 - 1
CAAACACGCAGUUUGCUGCCCCAUUUUCUCUCAGUGCUCACGACAGCUCACUUAAUUUGUGACCCUUAUCAAUGUGGGCAAUGUUGUGAAUAUGUUUUGGGCUUGUUUAGGUGCCCAAUU
.((((..((((....))))..............(((.((((((((((((((........(((......)))..))))))..)))))))).)))))))(((((..........)))))... ( -32.10)
>consensus
________________________UUUCUCUCAGUGCUCACGACGGGUCAUUUAAUUUGUGACCCUUAUCAAUGUGGGCAAUGUUGUGAAUAUGUUUUCGGCUUGUUUAGGUGGCCAAUU
.........................(((.(.((.((((((((..(((((((.......))))))).......)))))))).))..).))).........((((.........)))).... (-21.84 = -22.65 +   0.81)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 9

Location 20,788,270 – 20,788,364
Length 94
Sequences 3
Columns 94
Reading direction forward
Mean pairwise identity 96.45
Mean single sequence MFE -28.20
Consensus MFE -26.30
Energy contribution -26.30
Covariance contribution 0.00
Combinations/Pair 1.00
Mean z-score -3.05
Structure conservation index 0.93
SVM decision value 1.78
SVM RNA-class probability 0.976675
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 20788270 94 + 27905053
UGCCCACAUUGAUAAGGGUCACAAAUUAAAUGACCCGUCGUGAGCACUGAGAGAAAUUUCGAGUGUCUGGCAGUGCAUAUUAAGGCAAACAUUU
((((....((((((.((((((.........))))))...((.((((((((((....)))).)))).)).))......))))))))))....... ( -28.60)
>DroSec_CAF1 4082 94 + 1
UGCCCACAUUGAUAAGGGUCACAAAUUAAAUGACCCGUCGAGAGCACUGAGAGAAAUUUCAAGUGACUGGCAGUGCAUAUUAAGGCAAACAUUC
((((....(((((..((((((.........)))))))))))..((((((..((..((.....))..))..)))))).......))))....... ( -27.40)
>DroSim_CAF1 4037 94 + 1
UGCCCACAUUGAUAAGGGUCACAAAUUAAAUGACCCGACGUGAGCACUGAGAGAAAUUUCAAGUGACUGGCAGUGCAUAUUAAGGCAAACAUUU
((((....((((((.((((((.........))))))...((.((((((((((....)))).)))).)).))......))))))))))....... ( -28.60)
>consensus
UGCCCACAUUGAUAAGGGUCACAAAUUAAAUGACCCGUCGUGAGCACUGAGAGAAAUUUCAAGUGACUGGCAGUGCAUAUUAAGGCAAACAUUU
((((....((((((.((((((.........)))))).......((((((..((..((.....))..))..)))))).))))))))))....... (-26.30 = -26.30 +   0.00)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 0

Location 20,788,270 – 20,788,364
Length 94
Sequences 3
Columns 94
Reading direction reverse
Mean pairwise identity 96.45
Mean single sequence MFE -25.91
Consensus MFE -25.52
Energy contribution -25.52
Covariance contribution -0.00
Combinations/Pair 1.00
Mean z-score -2.56
Structure conservation index 0.98
SVM decision value 1.86
SVM RNA-class probability 0.980176
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 20788270 94 - 27905053
AAAUGUUUGCCUUAAUAUGCACUGCCAGACACUCGAAAUUUCUCUCAGUGCUCACGACGGGUCAUUUAAUUUGUGACCCUUAUCAAUGUGGGCA
.......(((((..((((((((((..(((...........)))..)))))).......(((((((.......)))))))......))))))))) ( -26.60)
>DroSec_CAF1 4082 94 - 1
GAAUGUUUGCCUUAAUAUGCACUGCCAGUCACUUGAAAUUUCUCUCAGUGCUCUCGACGGGUCAUUUAAUUUGUGACCCUUAUCAAUGUGGGCA
.......(((((..((((((((((..((.............))..)))))).......(((((((.......)))))))......))))))))) ( -25.32)
>DroSim_CAF1 4037 94 - 1
AAAUGUUUGCCUUAAUAUGCACUGCCAGUCACUUGAAAUUUCUCUCAGUGCUCACGUCGGGUCAUUUAAUUUGUGACCCUUAUCAAUGUGGGCA
.......((((.......((((((..((.............))..)))))).(((((.(((((((.......)))))))......))))))))) ( -25.82)
>consensus
AAAUGUUUGCCUUAAUAUGCACUGCCAGUCACUUGAAAUUUCUCUCAGUGCUCACGACGGGUCAUUUAAUUUGUGACCCUUAUCAAUGUGGGCA
.......(((((..((((((((((..((.............))..)))))).......(((((((.......)))))))......))))))))) (-25.52 = -25.52 +  -0.00)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 1

Location 20,788,326 – 20,788,444
Length 118
Sequences 3
Columns 118
Reading direction forward
Mean pairwise identity 93.22
Mean single sequence MFE -28.00
Consensus MFE -21.76
Energy contribution -22.43
Covariance contribution 0.67
Combinations/Pair 1.09
Mean z-score -2.27
Structure conservation index 0.78
SVM decision value -0.04
SVM RNA-class probability 0.512517
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 20788326 118 + 27905053
UUUCGAGUGUCUGGCAGUGCAUAUUAAGGCAAACAUUUGUAUUAAAUGCUUAUCAUUUGUUAUUAAGUGUCAAGUCGGACAGUUAAGUGCUAUUAUUAAGGCACUAAAUGAUCUAAAA
....((.((((((((...((((.((((.((((....)))).))))))))....((((((....))))))....)))))))).)).((((((........))))))............. ( -29.70)
>DroSec_CAF1 4138 118 + 1
UUUCAAGUGACUGGCAGUGCAUAUUAAGGCAAACAUUCGUUUUAAAUGCUAAUCAUUUGUUAUUAACUGUCAUGUCUGACAGUUAAGAGCUAUUAUUAAGGUACUAAAUGAUCUAAAA
...(((((((.(((((.......(((((((........))))))).))))).)))))))...((((((((((....))))))))))............((((........)))).... ( -26.10)
>DroSim_CAF1 4093 118 + 1
UUUCAAGUGACUGGCAGUGCAUAUUAAGGCAAACAUUUGUUUUAAAUGCUAAUCAAUUGUUAUUAACUGUCAAGUCUGACAGUUAAGAGCUAUUAUUAGGGUACUAAAUGAUCUAAAA
...............(((((...(((((((((....)))))))))...(((((.(((.(((.((((((((((....)))))))))).))).)))))))).)))))............. ( -28.20)
>consensus
UUUCAAGUGACUGGCAGUGCAUAUUAAGGCAAACAUUUGUUUUAAAUGCUAAUCAUUUGUUAUUAACUGUCAAGUCUGACAGUUAAGAGCUAUUAUUAAGGUACUAAAUGAUCUAAAA
..(((((((.((......((((.(((((((((....))))))))))))).........(((.(((((((((......))))))))).)))........)).))))...)))....... (-21.76 = -22.43 +   0.67)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:53:47 2006