Locus 3170

Sequence ID 2R_DroMel_CAF1
Location 10,829,252 – 10,829,344
Length 92
Max. P 0.999984
window5217 window5218

overview

Window 7

Location 10,829,252 – 10,829,344
Length 92
Sequences 3
Columns 117
Reading direction forward
Mean pairwise identity 64.69
Mean single sequence MFE -22.53
Consensus MFE -12.14
Energy contribution -13.70
Covariance contribution 1.56
Combinations/Pair 1.12
Mean z-score -2.88
Structure conservation index 0.54
SVM decision value 5.16
SVM RNA-class probability 0.999976
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 10829252 92 + 20766785
CCCGGUUUAUUUUAAUUCAUUUA--CAAAUGUAUUUAAAUUCAAAAUCAUGGAUAUG--AUCAUAUCCAUGGUUCAUAUUGGGAAUCUCAAUUUUC---------------------
((((((....(((((..((((..--..))))...))))).....((((((((((((.--...))))))))))))...)))))).............--------------------- ( -21.50)
>DroSim_CAF1 36838 104 + 1
CCCGAUUUAUUUUAAUUCAUUAA--CAAAUGUUUUUAAAUUGGAAAACAUGGAUAUG--AUCAUAUCCAUGGACCAUAUUGGGAAUCUACAUUUUUGUAAACUUUUU--------U-
((((((...((((((((.(..((--(....)))..).))))))))..(((((((((.--...)))))))))......))))))....((((....))))........--------.- ( -24.10)
>DroEre_CAF1 42138 113 + 1
CC-G--UUUUUUUAAGUCAUUAGAGGAAACGUAUUUUAAUUUGAUAAUGUGGAUAUGUGGAUAUAUCCAAAGAUCAUGUUGUGAAUCGUAAUUCUA-AAAACAAUUUGAAUUCUAUA
..-.--.........((..((((((...(((.((((((((.((((....((((((((....))))))))...)))).)))).)))))))..)))))-)..))............... ( -22.00)
>consensus
CCCG_UUUAUUUUAAUUCAUUAA__CAAAUGUAUUUAAAUUCGAAAACAUGGAUAUG__AUCAUAUCCAUGGAUCAUAUUGGGAAUCUAAAUUUUA__AAAC__UUU________U_
((((((....(((((..((((......))))...)))))........((((((((((....))))))))))......)))))).................................. (-12.14 = -13.70 +   1.56)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 8

Location 10,829,252 – 10,829,344
Length 92
Sequences 3
Columns 117
Reading direction reverse
Mean pairwise identity 64.69
Mean single sequence MFE -19.18
Consensus MFE -11.73
Energy contribution -12.40
Covariance contribution 0.67
Combinations/Pair 1.12
Mean z-score -2.44
Structure conservation index 0.61
SVM decision value 5.34
SVM RNA-class probability 0.999984
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 10829252 92 - 20766785
---------------------GAAAAUUGAGAUUCCCAAUAUGAACCAUGGAUAUGAU--CAUAUCCAUGAUUUUGAAUUUAAAUACAUUUG--UAAAUGAAUUAAAAUAAACCGGG
---------------------.............(((.........(((((((((...--.)))))))))(((((((.((((..(((....)--))..))))))))))).....))) ( -19.70)
>DroSim_CAF1 36838 104 - 1
-A--------AAAAAGUUUACAAAAAUGUAGAUUCCCAAUAUGGUCCAUGGAUAUGAU--CAUAUCCAUGUUUUCCAAUUUAAAAACAUUUG--UUAAUGAAUUAAAAUAAAUCGGG
-.--------....((((((((....))))))))(((.....((..(((((((((...--.)))))))))....))((((((..(((....)--))..))))))..........))) ( -23.20)
>DroEre_CAF1 42138 113 - 1
UAUAGAAUUCAAAUUGUUUU-UAGAAUUACGAUUCACAACAUGAUCUUUGGAUAUAUCCACAUAUCCACAUUAUCAAAUUAAAAUACGUUUCCUCUAAUGACUUAAAAAAA--C-GG
...............(((.(-((((...(((..........((((...(((((((......)))))))....))))..........)))....))))).))).........--.-.. ( -14.65)
>consensus
_A________AAA__GUUU__AAAAAUUAAGAUUCCCAAUAUGAUCCAUGGAUAUGAU__CAUAUCCAUGUUUUCAAAUUUAAAUACAUUUG__UUAAUGAAUUAAAAUAAA_CGGG
..................................(((.........((((((((((....))))))))))................((((......))))..............))) (-11.73 = -12.40 +   0.67)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:49:08 2006