Locus 2580

Sequence ID	X_DroMel_CAF1
Location	6,913,096 – 6,913,236
Length	140
Max. P	0.933748

overview

Window 5

Location	6,913,096 – 6,913,201
Length	105
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	85.93
Mean single sequence MFE	-23.18
Consensus MFE	-16.90
Energy contribution	-18.15
Covariance contribution	1.25
Combinations/Pair	1.00
Mean z-score	-1.95
Structure conservation index	0.73
SVM decision value	0.67
SVM RNA-class probability	0.817451
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 6913096 105 + 22224390
GAAAUUUGCCUACAGCCACCAUAAAUCAGAUUCAAUUUAAAUUAUCUGGCCACUGGUUGCCGGCCAUAAAUUACU-UAUCGUUUCAUUUGACCAGACAAGG--------------UUUUU
(((((..(((..((((((.......((((((............))))))....))))))..))).((((.....)-))).)))))....((((......))--------------))... ( -18.10)
>DroSec_CAF1 37454 105 + 1
GAAAUUUGCCUACAGCCACCAUAAAUCAGAUUCAAUUUAAAUUAUCUGGACACUGGUUGCCGGCCAUAAAUAACU-UAUCGUUUCACUUGGCCAGACAACG--------------UUUUU
((((((((.((...((.((((....((((((............))))))....)))).)).(((((.....(((.-....))).....))))))).))).)--------------)))). ( -22.50)
>DroSim_CAF1 21604 105 + 1
GAAAUUUGCCUACAGCCACCAUAAAUCAGAUUCAAUUUAAAUUAUCUGGACACUGGUUGCCGGCCAUAAAUAACU-UAUCGUUUCACUUGGCCAGACAACG--------------UUUUU
((((((((.((...((.((((....((((((............))))))....)))).)).(((((.....(((.-....))).....))))))).))).)--------------)))). ( -22.50)
>DroYak_CAF1 41389 120 + 1
GAAAUUUGCCUACGGCCAUCAUAAAUCAGAUUUAAUUUAAAUUAUCUGCUCACUGCCUGCCGGCCAUAAAUAACCAAAUCGUUUCACUUGGCCAGGCAACAGUCAACAGGCAACAGUUUU
.....((((((...............(((((............)))))...((((..(((((((((.....(((......))).....))))).)))).))))....))))))....... ( -29.60)
>consensus
GAAAUUUGCCUACAGCCACCAUAAAUCAGAUUCAAUUUAAAUUAUCUGGACACUGGUUGCCGGCCAUAAAUAACU_UAUCGUUUCACUUGGCCAGACAACG______________UUUUU
.....(((.((...((.((((....((((((............))))))....)))).)).(((((.....(((......))).....))))))).)))..................... (-16.90 = -18.15 +   1.25)

alignment

secondary structure

dotplot

Window 6

Location	6,913,096 – 6,913,201
Length	105
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	85.93
Mean single sequence MFE	-28.30
Consensus MFE	-26.48
Energy contribution	-26.22
Covariance contribution	-0.25
Combinations/Pair	1.15
Mean z-score	-1.69
Structure conservation index	0.94
SVM decision value	0.95
SVM RNA-class probability	0.887463
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 6913096 105 - 22224390
AAAAA--------------CCUUGUCUGGUCAAAUGAAACGAUA-AGUAAUUUAUGGCCGGCAACCAGUGGCCAGAUAAUUUAAAUUGAAUCUGAUUUAUGGUGGCUGUAGGCAAAUUUC
.....--------------.((((((...((....))...))))-)).........((((....)((((.((((...((((............))))..)))).))))..)))....... ( -23.20)
>DroSec_CAF1 37454 105 - 1
AAAAA--------------CGUUGUCUGGCCAAGUGAAACGAUA-AGUUAUUUAUGGCCGGCAACCAGUGUCCAGAUAAUUUAAAUUGAAUCUGAUUUAUGGUGGCUGUAGGCAAAUUUC
.....--------------..(((((((((((.....(((....-.))).....)))))(((.((((..(((.((((............)))))))...)))).)))..))))))..... ( -27.10)
>DroSim_CAF1 21604 105 - 1
AAAAA--------------CGUUGUCUGGCCAAGUGAAACGAUA-AGUUAUUUAUGGCCGGCAACCAGUGUCCAGAUAAUUUAAAUUGAAUCUGAUUUAUGGUGGCUGUAGGCAAAUUUC
.....--------------..(((((((((((.....(((....-.))).....)))))(((.((((..(((.((((............)))))))...)))).)))..))))))..... ( -27.10)
>DroYak_CAF1 41389 120 - 1
AAAACUGUUGCCUGUUGACUGUUGCCUGGCCAAGUGAAACGAUUUGGUUAUUUAUGGCCGGCAGGCAGUGAGCAGAUAAUUUAAAUUAAAUCUGAUUUAUGAUGGCCGUAGGCAAAUUUC
....(((..(((((((.(((((((((.(((((.....(((......))).....))))))))).))))).)))).......(((((((....)))))))....)))..)))......... ( -35.80)
>consensus
AAAAA______________CGUUGUCUGGCCAAGUGAAACGAUA_AGUUAUUUAUGGCCGGCAACCAGUGUCCAGAUAAUUUAAAUUGAAUCUGAUUUAUGGUGGCUGUAGGCAAAUUUC
.....................(((((((((((.....(((......))).....)))))(((.((((.....(((((............))))).....)))).)))..))))))..... (-26.48 = -26.22 +  -0.25)

alignment

secondary structure

dotplot

Window 7

Location	6,913,136 – 6,913,236
Length	100
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	75.61
Mean single sequence MFE	-27.28
Consensus MFE	-15.09
Energy contribution	-15.53
Covariance contribution	0.44
Combinations/Pair	1.16
Mean z-score	-2.24
Structure conservation index	0.55
SVM decision value	1.23
SVM RNA-class probability	0.933748
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 6913136 100 - 22224390
UAACAAAAGCCCUGGGACUACAAAAACAC-----AUAAAAAAAAA--------------CCUUGUCUGGUCAAAUGAAACGAUA-AGUAAUUUAUGGCCGGCAACCAGUGGCCAGAUAAU
........((((((((....)........-----...........--------------..(((.(((((((......((....-.))......)))))))))))))).)))........ ( -19.40)
>DroSec_CAF1 37494 94 - 1
AGGCAAAGGCCCUGGGACUACAAA-ACAC----------AAAAAA--------------CGUUGUCUGGCCAAGUGAAACGAUA-AGUUAUUUAUGGCCGGCAACCAGUGUCCAGAUAAU
.(((....)))((((((((.....-....----------......--------------.((((.(((((((.....(((....-.))).....))))))))))).))).)))))..... ( -25.13)
>DroSim_CAF1 21644 94 - 1
AGGCAAAGGCCCUGGGACUACAAA-ACGC----------AAAAAA--------------CGUUGUCUGGCCAAGUGAAACGAUA-AGUUAUUUAUGGCCGGCAACCAGUGUCCAGAUAAU
.(((....)))((((((((.....-..(.----------......--------------)((((.(((((((.....(((....-.))).....))))))))))).))).)))))..... ( -26.10)
>DroYak_CAF1 41429 119 - 1
AGCCAAAGGCCCUGGGUUUUGGGA-ACACAAACAAUAAAAAAAACUGUUGCCUGUUGACUGUUGCCUGGCCAAGUGAAACGAUUUGGUUAUUUAUGGCCGGCAGGCAGUGAGCAGAUAAU
..((((((.(....).))))))..-.......(((((........))))).(((((.(((((((((.(((((.....(((......))).....))))))))).))))).)))))..... ( -38.50)
>consensus
AGGCAAAGGCCCUGGGACUACAAA_ACAC__________AAAAAA______________CGUUGUCUGGCCAAGUGAAACGAUA_AGUUAUUUAUGGCCGGCAACCAGUGUCCAGAUAAU
...........(((((..........).................................((((((.(((((.....(((......))).....)))))))))))......))))..... (-15.09 = -15.53 +   0.44)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:38:15 2006