Locus 5150

Sequence ID 2R_DroMel_CAF1
Location 16,764,650 – 16,764,774
Length 124
Max. P 0.997862
window8236 window8237 window8238

overview

Window 6

Location 16,764,650 – 16,764,755
Length 105
Sequences 5
Columns 110
Reading direction reverse
Mean pairwise identity 74.34
Mean single sequence MFE -17.82
Consensus MFE -2.14
Energy contribution -1.74
Covariance contribution -0.40
Combinations/Pair 1.25
Mean z-score -1.57
Structure conservation index 0.12
SVM decision value 0.39
SVM RNA-class probability 0.719013
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 16764650 105 - 20766785
GAGCUGCAGAAACAUGAAACUGCAUACGAG----UAAAGUUGCAUGUAUAUGAAAAACAAACAUGCCACAUAAUUCCAGGAAAAUGUAAUUACU-GUAACCAAAAGUUCA
(((((((((..........)))).(((.((----(((.((.((((((.............)))))).)).......((......))...)))))-)))......))))). ( -20.32)
>DroSec_CAF1 76797 84 - 1
GAGCUGCACAAA--------------CGAG----UAUAUUUGCA------UGAAAAACAAACAUGCAACAUAAUUCCAGGGAAAUGUAAUUACU-GUGACCG-AAGUUCU
(((((......(--------------(.((----((....((((------((.........))))))((((..(((....)))))))...))))-)).....-.))))). ( -17.40)
>DroSim_CAF1 75004 98 - 1
GAGCUGCACAAACAUGAAACAGCACACGAG----UAUAUUUGCA------UGAAAAACAAACAUGCAACAUAAUUCCAGGGAAAUGUAAUUACU-GUGACCG-AAGUUCA
(((((((..............)).(((.((----((....((((------((.........))))))((((..(((....)))))))...))))-)))....-.))))). ( -19.14)
>DroEre_CAF1 74165 98 - 1
GAGUUUCCCAAACAUGAAACUGCAUACUAUACGGGU---AUGUA------UGA-AAAGAAACAUGCAACAUAAUUCCUGGAAAAUGUAAUUGCU-AUGAGCA-AAGUUCU
.((((((........))))))(((((((.....)))---)))).------...-..((((((((....((.......))....))))..((((.-....)))-)..)))) ( -16.80)
>DroYak_CAF1 80147 96 - 1
GAGUUUCACAAACGUGAAACUGCAUAUAGU----UA---AUACA------UGAGAAACAAACAUGCAACAUAAUUCUUGAGAAAUGUAAUUACUAAUGACCA-AAGUUCA
.((((((((....)))))))).(((.((((----..---.((((------((((((.................))))).....)))))...)))))))....-....... ( -15.43)
>consensus
GAGCUGCACAAACAUGAAACUGCAUACGAG____UA_A_UUGCA______UGAAAAACAAACAUGCAACAUAAUUCCAGGGAAAUGUAAUUACU_GUGACCA_AAGUUCA
(((((...................................((((......(....).......))))((((..((....))..)))).................))))). ( -2.14 =  -1.74 +  -0.40)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 7

Location 16,764,679 – 16,764,774
Length 95
Sequences 3
Columns 99
Reading direction forward
Mean pairwise identity 70.71
Mean single sequence MFE -19.23
Consensus MFE -10.49
Energy contribution -11.28
Covariance contribution 0.78
Combinations/Pair 1.14
Mean z-score -2.49
Structure conservation index 0.55
SVM decision value 2.95
SVM RNA-class probability 0.997862
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 16764679 95 + 20766785
CCUGGAAUUAUGUGGCAUGUUUGUUUUUCAUAUACAUGCAACUUUA----CUCGUAUGCAGUUUCAUGUUUCUGCAGCUCAUCAUUCCGUUCUUUUUUU
...(((((.(((.(((((((.(((.....))).)))))).......----......(((((..........))))).).))).)))))........... ( -21.40)
>DroEre_CAF1 74193 85 + 1
CCAGGAAUUAUGUUGCAUGUUUCUUU-UCA------UACAU---ACCCGUAUAGUAUGCAGUUUCAUGUUUGGGAAACUCAUCAUUCCGUUUUUG----
...(((((.(((..(((((...((..-.((------(((((---(....))).))))).))...)))))..((....))))).))))).......---- ( -17.90)
>DroYak_CAF1 80176 82 + 1
UCAAGAAUUAUGUUGCAUGUUUGUUUCUCA------UGUAU---UA----ACUAUAUGCAGUUUCACGUUUGUGAAACUCAUCAUUCGGUUUUUG----
....((((.(((.(((((((..(((.....------.....---.)----)).)))))))(((((((....))))))).))).))))........---- ( -18.40)
>consensus
CCAGGAAUUAUGUUGCAUGUUUGUUU_UCA______UGCAU___UA____AUAGUAUGCAGUUUCAUGUUUGUGAAACUCAUCAUUCCGUUUUUG____
...(((((.(((..((((((.................................))))))((((((((....))))))))))).)))))........... (-10.49 = -11.28 +   0.78)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 8

Location 16,764,679 – 16,764,774
Length 95
Sequences 3
Columns 99
Reading direction reverse
Mean pairwise identity 70.71
Mean single sequence MFE -17.47
Consensus MFE -8.99
Energy contribution -10.32
Covariance contribution 1.33
Combinations/Pair 1.00
Mean z-score -2.58
Structure conservation index 0.51
SVM decision value 2.48
SVM RNA-class probability 0.994400
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 16764679 95 - 20766785
AAAAAAAGAACGGAAUGAUGAGCUGCAGAAACAUGAAACUGCAUACGAG----UAAAGUUGCAUGUAUAUGAAAAACAAACAUGCCACAUAAUUCCAGG
...........(((((.(((...(((((..........)))))......----.......((((((.............))))))..))).)))))... ( -18.12)
>DroEre_CAF1 74193 85 - 1
----CAAAAACGGAAUGAUGAGUUUCCCAAACAUGAAACUGCAUACUAUACGGGU---AUGUA------UGA-AAAGAAACAUGCAACAUAAUUCCUGG
----.......(((((.(((((((((........))))))(((((((.....)))---)))).------...-..............))).)))))... ( -18.70)
>DroYak_CAF1 80176 82 - 1
----CAAAAACCGAAUGAUGAGUUUCACAAACGUGAAACUGCAUAUAGU----UA---AUACA------UGAGAAACAAACAUGCAACAUAAUUCUUGA
----........((((.(((((((((((....))))))))((((...((----(.---.....------.....)))....))))..))).)))).... ( -15.60)
>consensus
____CAAAAACGGAAUGAUGAGUUUCACAAACAUGAAACUGCAUACAAU____UA___AUGCA______UGA_AAACAAACAUGCAACAUAAUUCCUGG
...........(((((.((((((((((......)))))))((((.....................................))))..))).)))))... ( -8.99 = -10.32 +   1.33)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:37:50 2006