Locus 7607

Sequence ID	3L_DroMel_CAF1
Location	20,474,645 – 20,474,862
Length	217
Max. P	0.975020

overview

Window 9

Location	20,474,645 – 20,474,757
Length	112
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	85.92
Mean single sequence MFE	-22.60
Consensus MFE	-17.85
Energy contribution	-18.60
Covariance contribution	0.75
Combinations/Pair	1.05
Mean z-score	-2.57
Structure conservation index	0.79
SVM decision value	1.74
SVM RNA-class probability	0.975020
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 20474645 112 - 23771897
CAACGAACGUAUAAGCAUUAUCGCGUAUACGCACUAUAAACAAACAAUUUUACCUUUAUUAAGCAUACGAACAGUGGUACAAGGAUUCAAAAUUCUGAGUGCAAAUAA--------AAUA
........(((((.((......)).)))))(((((...............((((.....................))))..(((((.....))))).)))))......--------.... ( -17.00)
>DroSec_CAF1 17466 112 - 1
CAACGAACGUAUACGCAUUAUCGCGUAUACGCACUAUAAACAAACCGUUUCAAUUUUAUAAAGCAUACGAACAGUGGUACAACGAUUCAAAAUUCGGAGUGCAAAUAA--------AAUA
.......(((((((((......))))))))).....................(((((((......(((.....)))((((..(((........)))..))))..))))--------))). ( -24.30)
>DroSim_CAF1 17342 112 - 1
CAACGAACGUAUACGCAUUAUCGCGUAUACGCACUAUAAACAAACCGUUUCAAUUUUAUAAAGCAUACGAACAGUGGUACAACGAUUCAAAAUUCGGAGUGCAAAUAA--------AAUA
.......(((((((((......))))))))).....................(((((((......(((.....)))((((..(((........)))..))))..))))--------))). ( -24.30)
>DroEre_CAF1 17265 114 - 1
CAAUGAGCGUAUACGCUUUAUCGCGUAUACGCACUAUAAACAAACCAUUUCACAAUUUU------UACGAACAGUGGUACAAAGAUUCGAAAUCAGGAGUGCAAAUAAUCCUUAAAAAUA
...((((.((((((((......))))))))(((((........((((((((........------...)))..))))).....(((.....)))...)))))........))))...... ( -24.80)
>consensus
CAACGAACGUAUACGCAUUAUCGCGUAUACGCACUAUAAACAAACCAUUUCAAUUUUAUAAAGCAUACGAACAGUGGUACAACGAUUCAAAAUUCGGAGUGCAAAUAA________AAUA
........((((((((......))))))))(((((..............................(((.....)))......(((........))).))))).................. (-17.85 = -18.60 +   0.75)

alignment

secondary structure

dotplot

Window 0

Location	20,474,717 – 20,474,822
Length	105
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	81.87
Mean single sequence MFE	-31.47
Consensus MFE	-20.58
Energy contribution	-20.89
Covariance contribution	0.31
Combinations/Pair	1.14
Mean z-score	-1.87
Structure conservation index	0.65
SVM decision value	0.42
SVM RNA-class probability	0.730183
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 20474717 105 + 23771897
UUUAUAGUGCGUAUACGCGAUAAUGCUUAUACGUUCGUUGUGACCUAUCGAUUAUUUCGUGCGAUGUUAUAUCGAUUAACGACUUAUA---------------GCUGUAAAAUGCUGAUA
(((((((((((((((.((......)).)))))))..(((((.....((((((.((.((....)).))...))))))..))))).....---------------))))))))......... ( -25.40)
>DroSec_CAF1 17538 119 + 1
UUUAUAGUGCGUAUACGCGAUAAUGCGUAUACGUUCGUUGUGACCUAUCGUUUAUUUCAUGCAGCCUUAUAUCGAUUAAC-ACUGUCAGCCGUGGCGUUCUGUGCUGAAAAAUGCUGAUA
.((((((.((((((((((......))))))))))...))))))..((((((...((((((((((.........(((....-...))).((....))...))))).)))))...)).)))) ( -28.90)
>DroSim_CAF1 17414 119 + 1
UUUAUAGUGCGUAUACGCGAUAAUGCGUAUACGUUCGUUGUGACCUAUCGAUUAUUUUAUGCGACCUUAAAUCGAUUAAC-ACUGUCAGCUGUGGCGUUCGGUGCUGUAAUAUGCUAAUA
.((((((..(((((((((......))))))))(..(((..((((..(((((((................)))))))....-...)))....)..)))..).)..)))))).......... ( -29.89)
>DroEre_CAF1 17339 119 + 1
UUUAUAGUGCGUAUACGCGAUAAAGCGUAUACGCUCAUUGUGACCUAUCGAUUAUUUCACGCGACGUUAUAUCGAUUAGC-AUCCACAGCUGUGACGUUCUGUGGUGUGAAAUGCUGAUA
.(((((((((((((((((......))))))))))..)))))))..(((((..((((((((((.(((..(..(((..((((-.......)))))))..)..))).)))))))))).))))) ( -41.70)
>consensus
UUUAUAGUGCGUAUACGCGAUAAUGCGUAUACGUUCGUUGUGACCUAUCGAUUAUUUCAUGCGACCUUAUAUCGAUUAAC_ACUGACAGCUGUGGCGUUCUGUGCUGUAAAAUGCUGAUA
((((((((((((((((((......))))))))))..((.((.....((((((..................))))))..)).))....................))))))))......... (-20.58 = -20.89 +   0.31)

alignment

secondary structure

dotplot

Window 1

Location	20,474,717 – 20,474,822
Length	105
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	81.87
Mean single sequence MFE	-26.08
Consensus MFE	-16.28
Energy contribution	-17.34
Covariance contribution	1.06
Combinations/Pair	1.29
Mean z-score	-1.75
Structure conservation index	0.62
SVM decision value	0.06
SVM RNA-class probability	0.562144
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 20474717 105 - 23771897
UAUCAGCAUUUUACAGC---------------UAUAAGUCGUUAAUCGAUAUAACAUCGCACGAAAUAAUCGAUAGGUCACAACGAACGUAUAAGCAUUAUCGCGUAUACGCACUAUAAA
....(((........))---------------).....(((((.((((((......((....))....)))))).(....)))))).((((((.((......)).))))))......... ( -16.30)
>DroSec_CAF1 17538 119 - 1
UAUCAGCAUUUUUCAGCACAGAACGCCACGGCUGACAGU-GUUAAUCGAUAUAAGGCUGCAUGAAAUAAACGAUAGGUCACAACGAACGUAUACGCAUUAUCGCGUAUACGCACUAUAAA
((((((((((..(((((...(.....)...))))).)))-)))....))))...((.(((.(((..((.....))..)))........((((((((......)))))))))))))..... ( -25.70)
>DroSim_CAF1 17414 119 - 1
UAUUAGCAUAUUACAGCACCGAACGCCACAGCUGACAGU-GUUAAUCGAUUUAAGGUCGCAUAAAAUAAUCGAUAGGUCACAACGAACGUAUACGCAUUAUCGCGUAUACGCACUAUAAA
.....((......((((.............))))...((-((..(((((((................)))))))..).))).......((((((((......))))))))))........ ( -26.21)
>DroEre_CAF1 17339 119 - 1
UAUCAGCAUUUCACACCACAGAACGUCACAGCUGUGGAU-GCUAAUCGAUAUAACGUCGCGUGAAAUAAUCGAUAGGUCACAAUGAGCGUAUACGCUUUAUCGCGUAUACGCACUAUAAA
(((((..(((((((.((((((..........))))))..-......((((.....)))).)))))))..).))))...........((((((((((......))))))))))........ ( -36.10)
>consensus
UAUCAGCAUUUUACAGCACAGAACGCCACAGCUGACAGU_GUUAAUCGAUAUAACGUCGCAUGAAAUAAUCGAUAGGUCACAACGAACGUAUACGCAUUAUCGCGUAUACGCACUAUAAA
(((((((..((((((((.............))))))))..)))...((((.....))))............))))............(((((((((......)))))))))......... (-16.28 = -17.34 +   1.06)

alignment

secondary structure

dotplot

Window 2

Location	20,474,757 – 20,474,862
Length	105
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	77.41
Mean single sequence MFE	-29.53
Consensus MFE	-18.43
Energy contribution	-18.25
Covariance contribution	-0.19
Combinations/Pair	1.42
Mean z-score	-1.86
Structure conservation index	0.62
SVM decision value	0.53
SVM RNA-class probability	0.770736
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 20474757 105 - 23771897
AUCCGGUUGCUUAGCAGCUCUGUUAAUUAACAGUGCAGCUUAUCAGCAUUUUACAGC---------------UAUAAGUCGUUAAUCGAUAUAACAUCGCACGAAAUAAUCGAUAGGUCA
....((((((...))))))((((..((((...((((.((((((.(((........))---------------))))))).((((.......))))...))))....))))..)))).... ( -24.90)
>DroSec_CAF1 17578 119 - 1
AUUUGGUUGCCUAACUGCUCUGUUAAAUAACAGUGCAGCCUAUCAGCAUUUUUCAGCACAGAACGCCACGGCUGACAGU-GUUAAUCGAUAUAAGGCUGCAUGAAAUAAACGAUAGGUCA
........(((((......(((((....)))))(((((((((((((((((..(((((...(.....)...))))).)))-)))....)))...))))))))............))))).. ( -30.40)
>DroSim_CAF1 17454 119 - 1
AUUUGGUUGCCCAACUGCUCUGUUAAAUAACAGUGCAGCCUAUUAGCAUAUUACAGCACCGAACGCCACAGCUGACAGU-GUUAAUCGAUUUAAGGUCGCAUAAAAUAAUCGAUAGGUCA
..((((....))))((((.(((((....))))).))))(((((((((((....((((.............))))...))-)))))((((((................))))))))))... ( -27.71)
>DroEre_CAF1 17379 119 - 1
UUUUAGUUUUCUAGCGGCACUGUUAAUUAACAGUGCAGCUUAUCAGCAUUUCACACCACAGAACGUCACAGCUGUGGAU-GCUAAUCGAUAUAACGUCGCGUGAAAUAAUCGAUAGGUCA
.....(((....))).((((((((....)))))))).((((((((..(((((((.((((((..........))))))..-......((((.....)))).)))))))..).))))))).. ( -35.10)
>consensus
AUUUGGUUGCCUAACUGCUCUGUUAAAUAACAGUGCAGCCUAUCAGCAUUUUACAGCACAGAACGCCACAGCUGACAGU_GUUAAUCGAUAUAACGUCGCAUGAAAUAAUCGAUAGGUCA
..((((....))))..((.(((((....))))).)).((((((((((..((((((((.............))))))))..)))...((((.....))))............))))))).. (-18.43 = -18.25 +  -0.19)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:51:32 2006