Locus 3988

Sequence ID 3L_DroMel_CAF1
Location 11,610,991 – 11,611,210
Length 219
Max. P 0.979375
window6212 window6213

overview

Window 2

Location 11,610,991 – 11,611,097
Length 106
Sequences 5
Columns 106
Reading direction reverse
Mean pairwise identity 77.75
Mean single sequence MFE -23.92
Consensus MFE -13.26
Energy contribution -13.26
Covariance contribution -0.00
Combinations/Pair 1.14
Mean z-score -2.43
Structure conservation index 0.55
SVM decision value 1.84
SVM RNA-class probability 0.979375
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 11610991 106 - 23771897
GCUCACAUACCGACUUCUGGCUAUAUAUAUAUUUACUCAAACAGUGGGUUAUGAACCCGCCAUACCCCAAAGAAAACAACAACUUGUUUGCUUAACACACUGCAGA
((...............((((.............(((.....)))((((.....)))))))).......(((.((((((....)))))).)))........))... ( -16.00)
>DroSec_CAF1 104628 102 - 1
GCUCACAUACCGACUUCUGGGUAU----AUAUUCACACAAACAGUGGGUUAUGAAGCCACGAUACCCCAAAUGAAACAACAACUUGUGGGCUUAACCCACUGUAGA
......(((((........)))))----............(((((((((((...((((((((.....................)))).)))))))))))))))... ( -27.40)
>DroSim_CAF1 105070 99 - 1
GCUCACAUACCGACUUCUGGGUAU----AUAUUUACACAAACAGUGGGUUAUGAAGCCGCGAUAUCCCAAAUGAAAC---AAUUUGUGGGCUUAACCCACUGCAGA
......(((((........)))))----.............((((((((((...((((.((......(((((.....---.))))))))))))))))))))).... ( -26.40)
>DroEre_CAF1 95422 86 - 1
GCUCACAUACUGACUUCUGGGUAC----AUAUUUACUCAAACAGUGGGUUAUAAG----------------GGAAACAACAACGUGUUUGCUUAACCCACUGCACA
.................((((((.----.....))))))..((((((((((...(----------------(.(((((......))))).)))))))))))).... ( -24.70)
>DroYak_CAF1 109957 86 - 1
GCUCACAUACUGACUUCUGGGUGA----AUAUUUGCUCAAACAGUGGGUUAUAAA----------------GAAAACAACAACGUGUUUGAUUAACCCACUGCAGA
.........(((.....((((..(----....)..))))..((((((((((....----------------..(((((......)))))...))))))))))))). ( -25.10)
>consensus
GCUCACAUACCGACUUCUGGGUAU____AUAUUUACUCAAACAGUGGGUUAUGAA_CC_C_AUA_CCCAAAGGAAACAACAACUUGUUUGCUUAACCCACUGCAGA
.......((((........))))..................((((((((((.........................................)))))))))).... (-13.26 = -13.26 +  -0.00)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 3

Location 11,611,097 – 11,611,210
Length 113
Sequences 6
Columns 113
Reading direction forward
Mean pairwise identity 83.34
Mean single sequence MFE -23.74
Consensus MFE -17.34
Energy contribution -19.37
Covariance contribution 2.03
Combinations/Pair 1.03
Mean z-score -1.82
Structure conservation index 0.73
SVM decision value 0.18
SVM RNA-class probability 0.623047
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 11611097 113 + 23771897
UUAAUGUUUUGUGUACAUAUUUAUCUCGGCACAUGGAUAAGUACACAUACAUAUUCACAUAUCGCAGCUACAUUGCGACUUCCUCGAUGUGUGUGCCCCGCAUCAAUGGAAAC
...((((..(((((((.(((((((........))))))).))))))).)))).........((((((.....)))))).((((..((((((.......))))))...)))).. ( -30.70)
>DroSec_CAF1 104730 99 + 1
UCAAUGUUUUGUGUACAUAUUUAUCUCGGCACAUGCAUAAGUACACA--------------UCGCAGAUACAUUGCGACUUCCUCGAUGUGUGUGCCCCGCAUCAAUGGAAAC
.........(((((((.(((.(((........))).))).)))))))--------------((((((.....)))))).((((..((((((.......))))))...)))).. ( -24.00)
>DroSim_CAF1 105169 99 + 1
UUAAUGUUUUGUGUACAUAUUUAUCUCGGCACAUGCAUAAGUACACA--------------UCGCAGAUACAUUGCGACUUCCUCGAUGUGUGUGCCCCGCAUCAAUGGAAAC
.........(((((((.(((.(((........))).))).)))))))--------------((((((.....)))))).((((..((((((.......))))))...)))).. ( -24.00)
>DroEre_CAF1 95508 108 + 1
UUAUUGUUUUGUGUACAUAUUUAUCUCGC-ACAUGCAUAAGUACACAU----ACUCACACAUCGCAGAUACAUUGCGACUUCCUCGAUGUGUGUGCCCCGCAUCAAUGGAAAC
((((((...(((((((.(((.(((.....-..))).))).))))))).----.(.((((((((((((.....))))((.....)))))))))).)........)))))).... ( -24.40)
>DroYak_CAF1 110043 109 + 1
CUAAUGUUUUGUGUACAUAUUUAUCUCGCCACAUGCAUAAGUACACAU----AUUCACACAUCGCAGAUACAUUGCGACUUCCUCGAUGUGUGUGCCCCGCAUCAAUGGAAAC
...((((.......))))..........(((.((((....((((((((----(((......((((((.....)))))).......)))))))))))...))))...))).... ( -24.62)
>DroAna_CAF1 114868 88 + 1
UUAAUAUUUUGUGUACACAUUUAUCUCCAAACAC--AU--AUACAUUU-----------------AUGCACAUGGCGACUUCCUCGAUG----UGCCCCGCAUCAAUGGAAAC
.........(((....)))....((.(((....(--((--(......)-----------------)))....))).)).((((..((((----((...))))))...)))).. ( -14.70)
>consensus
UUAAUGUUUUGUGUACAUAUUUAUCUCGGCACAUGCAUAAGUACACAU_____________UCGCAGAUACAUUGCGACUUCCUCGAUGUGUGUGCCCCGCAUCAAUGGAAAC
.........(((((((.(((.(((........))).))).)))))))..............((((((.....)))))).((((..((((((.......))))))...)))).. (-17.34 = -19.37 +   2.03)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:11:46 2006