Locus 294

Sequence ID 2R_DroMel_CAF1
Location 1,730,053 – 1,730,205
Length 152
Max. P 0.990091
window609 window610 window611 window612

overview

Window 9

Location 1,730,053 – 1,730,169
Length 116
Sequences 3
Columns 116
Reading direction forward
Mean pairwise identity 85.07
Mean single sequence MFE -23.53
Consensus MFE -18.09
Energy contribution -18.87
Covariance contribution 0.78
Combinations/Pair 1.03
Mean z-score -1.82
Structure conservation index 0.77
SVM decision value 0.13
SVM RNA-class probability 0.597594
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 1730053 116 + 20766785
UAAUAAGAAUGUGUGCUGCAUGAAUGUAUAUGUUUCGUCUUUUUAAGAAUUAUCGUUGCUCAAUUUAUUUACAGUUGAACUGUACAGUUGAACUGUAAAUAAAUACAGUCUUUCGU
....((((.((((.((.(((((((.........)))))........((....)))).)).).((((((((((((((.((((....)))).))))))))))))))))).)))).... ( -27.10)
>DroSec_CAF1 14686 103 + 1
UAAUAAGAAGUUGUGGUGCAUGAAUGUAUGUGUUUCCUCUUUUUAAGAAUUGUCGUUGCUCAAUUUAUUUACAGUUG-------------AACUGUAAAUAAAUACAGUCUUUUGG
...(((((((..(..(..((((....))))..)..)..)))))))(((.((((.........((((((((((((...-------------..)))))))))))))))))))..... ( -22.00)
>DroSim_CAF1 15441 101 + 1
UAAUAAGAAGUUGUGGUGCAUGAAUGUAUGUGUUUCCUCUUUUUAAGAAUUGUAGCUGCUCAAUUUAUUUACAGUUG-------------AACUGUAAAUAAAU--AGUCUUUUGU
...(((((((..(..(..((((....))))..)..)..)))))))............(((..((((((((((((...-------------..))))))))))))--)))....... ( -21.50)
>consensus
UAAUAAGAAGUUGUGGUGCAUGAAUGUAUGUGUUUCCUCUUUUUAAGAAUUGUCGUUGCUCAAUUUAUUUACAGUUG_____________AACUGUAAAUAAAUACAGUCUUUUGU
...(((((((....(..((((........))))..)..)))))))............(((..((((((((((((((.((((....)))).))))))))))))))..)))....... (-18.09 = -18.87 +   0.78)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 0

Location 1,730,053 – 1,730,169
Length 116
Sequences 3
Columns 116
Reading direction reverse
Mean pairwise identity 85.07
Mean single sequence MFE -19.60
Consensus MFE -15.30
Energy contribution -15.97
Covariance contribution 0.67
Combinations/Pair 1.00
Mean z-score -3.32
Structure conservation index 0.78
SVM decision value 1.75
SVM RNA-class probability 0.975691
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 1730053 116 - 20766785
ACGAAAGACUGUAUUUAUUUACAGUUCAACUGUACAGUUCAACUGUAAAUAAAUUGAGCAACGAUAAUUCUUAAAAAGACGAAACAUAUACAUUCAUGCAGCACACAUUCUUAUUA
....((((.(((((((((((((((((.((((....)))).))))))))))))))...(((..((....))..........(((.........))).))).....))).)))).... ( -23.20)
>DroSec_CAF1 14686 103 - 1
CCAAAAGACUGUAUUUAUUUACAGUU-------------CAACUGUAAAUAAAUUGAGCAACGACAAUUCUUAAAAAGAGGAAACACAUACAUUCAUGCACCACAACUUCUUAUUA
....((((.(((((((((((((((..-------------...))))))))))))...(((........(((.....)))(....)...........)))...)))...)))).... ( -17.70)
>DroSim_CAF1 15441 101 - 1
ACAAAAGACU--AUUUAUUUACAGUU-------------CAACUGUAAAUAAAUUGAGCAGCUACAAUUCUUAAAAAGAGGAAACACAUACAUUCAUGCACCACAACUUCUUAUUA
....(((((.--((((((((((((..-------------...)))))))))))).).(((........(((.....)))(....)...........))).........)))).... ( -17.90)
>consensus
ACAAAAGACUGUAUUUAUUUACAGUU_____________CAACUGUAAAUAAAUUGAGCAACGACAAUUCUUAAAAAGAGGAAACACAUACAUUCAUGCACCACAACUUCUUAUUA
....((((....((((((((((((((.((((....)))).))))))))))))))...(((........(((.....))).(((.........))).))).........)))).... (-15.30 = -15.97 +   0.67)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 1

Location 1,730,089 – 1,730,205
Length 116
Sequences 3
Columns 117
Reading direction forward
Mean pairwise identity 82.14
Mean single sequence MFE -24.67
Consensus MFE -17.90
Energy contribution -18.57
Covariance contribution 0.67
Combinations/Pair 1.06
Mean z-score -2.62
Structure conservation index 0.73
SVM decision value 1.58
SVM RNA-class probability 0.965164
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 1730089 116 + 20766785
GUCUUUUUAAGAAUUAUCGUUGCUCAAUUUAUUUACAGUUGAACUGUACAGUUGAACUGUAAAUAAAUACAGUCUUUCGUUGAA-UGGGUUUUUUUUAAUCGGUUUAUGUAGCUAAA
..................(((((...((((((((((((((.((((....)))).))))))))))))))............((((-(.((((......)))).))))).))))).... ( -29.40)
>DroSec_CAF1 14722 102 + 1
CUCUUUUUAAGAAUUGUCGUUGCUCAAUUUAUUUACAGUUG-------------AACUGUAAAUAAAUACAGUCUUUUGGUGAAAUAGG--UUUUUUAUUGGGUUUGUGUAGCUAAA
..................(((((...((((((((((((...-------------..))))))))))))((((...((..((((((....--..))))))..)).))))))))).... ( -23.50)
>DroSim_CAF1 15477 100 + 1
CUCUUUUUAAGAAUUGUAGCUGCUCAAUUUAUUUACAGUUG-------------AACUGUAAAUAAAU--AGUCUUUUGUUGAA-UAGU-UUUUUUUAAUGGGUUUGUGAAGCUAAA
................(((((.(.((((((((((((((...-------------..))))))))))))--.....((..(((((-....-....)))))..))..)).).))))).. ( -21.10)
>consensus
CUCUUUUUAAGAAUUGUCGUUGCUCAAUUUAUUUACAGUUG_____________AACUGUAAAUAAAUACAGUCUUUUGUUGAA_UAGG_UUUUUUUAAUGGGUUUGUGUAGCUAAA
..................(((((.((((((((((((((((.((((....)))).)))))))))))))).......((..(((((..........)))))..))..)).))))).... (-17.90 = -18.57 +   0.67)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 2

Location 1,730,089 – 1,730,205
Length 116
Sequences 3
Columns 117
Reading direction reverse
Mean pairwise identity 82.14
Mean single sequence MFE -16.60
Consensus MFE -14.20
Energy contribution -14.87
Covariance contribution 0.67
Combinations/Pair 1.00
Mean z-score -2.74
Structure conservation index 0.86
SVM decision value 2.20
SVM RNA-class probability 0.990091
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 1730089 116 - 20766785
UUUAGCUACAUAAACCGAUUAAAAAAAACCCA-UUCAACGAAAGACUGUAUUUAUUUACAGUUCAACUGUACAGUUCAACUGUAAAUAAAUUGAGCAACGAUAAUUCUUAAAAAGAC
....(((.((......................-.....(....).....((((((((((((((.((((....)))).)))))))))))))))))))..................... ( -21.80)
>DroSec_CAF1 14722 102 - 1
UUUAGCUACACAAACCCAAUAAAAAA--CCUAUUUCACCAAAAGACUGUAUUUAUUUACAGUU-------------CAACUGUAAAUAAAUUGAGCAACGACAAUUCUUAAAAAGAG
....(((.((................--......((.......))....((((((((((((..-------------...)))))))))))))))))..................... ( -12.80)
>DroSim_CAF1 15477 100 - 1
UUUAGCUUCACAAACCCAUUAAAAAAA-ACUA-UUCAACAAAAGACU--AUUUAUUUACAGUU-------------CAACUGUAAAUAAAUUGAGCAGCUACAAUUCUUAAAAAGAG
..(((((.(.(((..............-....-.((.......))..--.(((((((((((..-------------...)))))))))))))).).)))))................ ( -15.20)
>consensus
UUUAGCUACACAAACCCAUUAAAAAAA_CCUA_UUCAACAAAAGACUGUAUUUAUUUACAGUU_____________CAACUGUAAAUAAAUUGAGCAACGACAAUUCUUAAAAAGAG
....(((.((............................(....).....((((((((((((((.((((....)))).)))))))))))))))))))..................... (-14.20 = -14.87 +   0.67)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:34:47 2006