Locus 1018

Sequence ID	3R_DroMel_CAF1
Location	3,208,109 – 3,208,297
Length	188
Max. P	0.840892

overview

Window 4

Location	3,208,109 – 3,208,218
Length	109
Sequences	4
Columns	109
Reading direction	reverse
Mean pairwise identity	91.51
Mean single sequence MFE	-34.42
Consensus MFE	-27.06
Energy contribution	-27.75
Covariance contribution	0.69
Combinations/Pair	1.08
Mean z-score	-1.90
Structure conservation index	0.79
SVM decision value	0.46
SVM RNA-class probability	0.746626
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 3208109 109 - 27905053
GUUUCGUGGACUGCCAAUUUGCAUUGGCCUGGCCAUUAGGAUCGGGUCAGUCAGUAUAAGUUGGAGUUCUUUAUUGUUGUGUGAUAGUCUGAUAGUCGGACCACAGGCA
.......(((((.((((((((.((((((.(((((..........))))))))))).))))))))))))).....((((.((((...(((((.....))))))))))))) ( -35.50)
>DroSec_CAF1 27499 107 - 1
GUUUCGUGGACUACCAAUUUGCAUUGGCCUGGCCAUUAGGAUCGGGUCAGUCAGU--UAGUUGGAGUUCUUUAUUGUUGUGUGAUAGUCUGAUAGUCGGGACACAGGCA
.....(((((((.((((((.((((((((((((((....)).))))))))))..))--.))))))))))).......((((((.....((((.....)))))))))))). ( -33.70)
>DroSim_CAF1 34318 107 - 1
GUUUCGUUGACUGCCAAUUUGCAUUGGCCUGGCCAUUAGGAUCGGGUCAGUCAGU--AAGUUGGAGUUCUUUAUUGUUGUGUGAUAGUCUGAUAGUCGGGACACAGGCA
((.((.((((((((((((((((((((((((((((....)).))))))))))..))--)))))))...((...((((((....))))))..))))))))))).))..... ( -34.40)
>DroEre_CAF1 27000 99 - 1
GUUUCGUGGACUGCCAAUUUGCAUUGGCCUGGCCAUUAGCAUCGGGUCAGUCAGU--AAGUUGGAGUUCUUUAUUGUUGUGUGAU--------AGUUGGGCCACAGACA
((((.(((((((.((((((((((((((((((((.....))..)))))))))..))--)))))))))).((..((((((....)))--------)))..)))))))))). ( -34.10)
>consensus
GUUUCGUGGACUGCCAAUUUGCAUUGGCCUGGCCAUUAGGAUCGGGUCAGUCAGU__AAGUUGGAGUUCUUUAUUGUUGUGUGAUAGUCUGAUAGUCGGGACACAGGCA
.....(((((((.(((((((((((((((((((((....)).))))))))))..))..))))))))))))....((((.((.((((.........)))).)).)))))). (-27.06 = -27.75 +   0.69)

alignment

secondary structure

dotplot

Window 5

Location	3,208,149 – 3,208,257
Length	108
Sequences	4
Columns	108
Reading direction	reverse
Mean pairwise identity	87.54
Mean single sequence MFE	-28.42
Consensus MFE	-21.67
Energy contribution	-22.43
Covariance contribution	0.75
Combinations/Pair	1.00
Mean z-score	-1.98
Structure conservation index	0.76
SVM decision value	0.75
SVM RNA-class probability	0.840892
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 3208149 108 - 27905053
AGGUUCAACUUUUUUUGCUUUCAUUGAUUCUGCUUUUUAGUUUCGUGGACUGCCAAUUUGCAUUGGCCUGGCCAUUAGGAUCGGGUCAGUCAGUAUAAGUUGGAGUUC
((.((((((((....((((..(((.((..(((.....)))..)))))((((((......))).((((((((((....)).))))))))))))))).)))))))).)). ( -28.80)
>DroSec_CAF1 27539 106 - 1
AGGUUUAUCUAUUUUUGCUUCCAUUGAUUCUGCUUUUUAGUUUCGUGGACUACCAAUUUGCAUUGGCCUGGCCAUUAGGAUCGGGUCAGUCAGU--UAGUUGGAGUUC
...................(((((.((..(((.....)))..)))))))((.((((((.((((((((((((((....)).))))))))))..))--.))))))))... ( -29.00)
>DroSim_CAF1 34358 106 - 1
AGGUUUAACUUUUUUUGCUUCCAUUGAUUCUGCUUUUUAGUUUCGUUGACUGCCAAUUUGCAUUGGCCUGGCCAUUAGGAUCGGGUCAGUCAGU--AAGUUGGAGUUC
.....................((.(((..(((.....)))..))).))(((.(((((((((((((((((((((....)).))))))))))..))--)))))))))).. ( -29.90)
>DroEre_CAF1 27032 89 - 1
AGGUUUAACUUUUU-UGCU----------------UUUAGUUUCGUGGACUGCCAAUUUGCAUUGGCCUGGCCAUUAGCAUCGGGUCAGUCAGU--AAGUUGGAGUUC
..............-....----------------...........(((((.((((((((((((((((((((.....))..)))))))))..))--)))))))))))) ( -26.00)
>consensus
AGGUUUAACUUUUUUUGCUUCCAUUGAUUCUGCUUUUUAGUUUCGUGGACUGCCAAUUUGCAUUGGCCUGGCCAUUAGGAUCGGGUCAGUCAGU__AAGUUGGAGUUC
..............................................(((((.(((((((((((((((((((((....)).))))))))))..))..)))))))))))) (-21.67 = -22.43 +   0.75)

alignment

secondary structure

dotplot

Window 6

Location	3,208,184 – 3,208,297
Length	113
Sequences	4
Columns	113
Reading direction	forward
Mean pairwise identity	87.17
Mean single sequence MFE	-24.40
Consensus MFE	-17.00
Energy contribution	-17.62
Covariance contribution	0.62
Combinations/Pair	1.09
Mean z-score	-2.14
Structure conservation index	0.70
SVM decision value	0.63
SVM RNA-class probability	0.805746
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 3208184 113 + 27905053
GGCCAGGCCAAUGCAAAUUGGCAGUCCACGAAACUAAAAAGCAGAAUCAAUGAAAGCAAAAAAAGUUGAACCUAAUCGUUGUGGGUCAAUAAGCUUAGCGUUGCACAAAAAAA
((....((((((....))))))...))....................(((((.((((.......(((((.((((.......)))))))))..))))..))))).......... ( -20.70)
>DroSec_CAF1 27572 113 + 1
GGCCAGGCCAAUGCAAAUUGGUAGUCCACGAAACUAAAAAGCAGAAUCAAUGGAAGCAAAAAUAGAUAAACCUAAUCGUUGUGGGUCAAUAUGCUUGGCGUUGCACAAAAAAA
.((.(.(((((.(((.(((((...(((((((.........((.............)).....(((......)))....)))))))))))).)))))))).).))......... ( -26.02)
>DroSim_CAF1 34391 113 + 1
GGCCAGGCCAAUGCAAAUUGGCAGUCAACGAAACUAAAAAGCAGAAUCAAUGGAAGCAAAAAAAGUUAAACCUAAUCGUUGUGGGUCAAUAUGCUUGGCGUUGCACAAAAAAA
.((.(.(((((.(((.((((((...((((((.........((.............))......((......))..))))))...)))))).)))))))).).))......... ( -28.92)
>DroEre_CAF1 27065 94 + 1
GGCCAGGCCAAUGCAAAUUGGCAGUCCACGAAACUAAA----------------AGCA-AAAAAGUUAAACCUAAUCGUUGUGGGUCAAUAAGCU-GGUAUUGCACAAA-AAA
.(((((((((((....)))))).((((((((.......----------------(((.-.....)))...........))))))).)......))-)))..........-... ( -21.97)
>consensus
GGCCAGGCCAAUGCAAAUUGGCAGUCCACGAAACUAAAAAGCAGAAUCAAUGGAAGCAAAAAAAGUUAAACCUAAUCGUUGUGGGUCAAUAAGCUUGGCGUUGCACAAAAAAA
.((.(.(((((.(((.((((((...(.((((............................................)))).)...)))))).)))))))).).))......... (-17.00 = -17.62 +   0.62)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:58:27 2006