Locus 6872

Sequence ID 2L_DroMel_CAF1
Location 19,229,293 – 19,229,383
Length 90
Max. P 0.993146
window10952 window10953

overview

Window 2

Location 19,229,293 – 19,229,383
Length 90
Sequences 5
Columns 113
Reading direction forward
Mean pairwise identity 64.54
Mean single sequence MFE -23.51
Consensus MFE -13.66
Energy contribution -13.90
Covariance contribution 0.24
Combinations/Pair 1.10
Mean z-score -1.79
Structure conservation index 0.58
SVM decision value 1.35
SVM RNA-class probability 0.944795
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 19229293 90 + 22407834
GGAGCAGGCCCUUUUUAUUGAAGGACCUGCGGAGAUACACAGUAAGAAAUAAC--UUUAUUU------------UAUUUAAAGAGAG---------UCUGGUAAAGAUUUGGU
...(((((.(((((.....))))).))))).((((((...(((.(....).))--).)))))------------).........(((---------(((.....))))))... ( -21.50)
>DroSec_CAF1 49152 90 + 1
AGAGCAGGCCCUUUUUAUUGAAGGACCUGUGGAGAUAUACAGUGAGAAAUAAA--AUGAAGU------------GGCUGAAAGAGAG---------UCUGGCAAAGAUUUGGU
...(((((.(((((.....))))).))))).........((((.(........--......)------------.)))).....(((---------(((.....))))))... ( -19.04)
>DroSim_CAF1 50909 76 + 1
GGAGCAGGCCCUUUUUAUUGAAGGACCUGCGGAGAUACACAGUGAGAAAUAAA--AUAAAGU------------GGCUUAA-----------------------AGAUGUGGU
...(((((.(((((.....))))).))))).......((((.((((..((...--.....))------------..)))).-----------------------...)))).. ( -21.90)
>DroEre_CAF1 48591 88 + 1
AGAGCAGGCCCUU-UUAUUGAAGGACCUGCGGAGUUACACAGUGAGAAAUGCACGCUAAGAA------------------------GGCAGUAAGGACUGGUCAUGUUUUGUC
.(((((((.((((-(....))))).)))))..((((..((.((((....).)))(((.....------------------------))).))...))))..)).......... ( -23.20)
>DroYak_CAF1 50775 111 + 1
AGAGCAGGCCCUU-UUAUUGAAGGACCUGCGGAGUUACACGGUAAGAAAUGCACAGUAAGAAGGACCUUAAUUUGUCUGCAAGUAAGGCAGUUAGGG-UGGUAAUGAUUUGUC
...(((((.((((-(....))))).)))))...(((((((.(((.....)))...)).......(((((((((.((((.......))))))))))))-).)))))........ ( -31.90)
>consensus
AGAGCAGGCCCUUUUUAUUGAAGGACCUGCGGAGAUACACAGUGAGAAAUAAA__AUAAAAU____________GGCUGAAAG__AG_________UCUGGUAAAGAUUUGGU
...(((((.(((((.....))))).)))))................................................................................... (-13.66 = -13.90 +   0.24)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 3

Location 19,229,293 – 19,229,383
Length 90
Sequences 5
Columns 113
Reading direction reverse
Mean pairwise identity 64.54
Mean single sequence MFE -19.55
Consensus MFE -15.64
Energy contribution -15.84
Covariance contribution 0.20
Combinations/Pair 1.00
Mean z-score -2.92
Structure conservation index 0.80
SVM decision value 2.38
SVM RNA-class probability 0.993146
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 19229293 90 - 22407834
ACCAAAUCUUUACCAGA---------CUCUCUUUAAAUA------------AAAUAAA--GUUAUUUCUUACUGUGUAUCUCCGCAGGUCCUUCAAUAAAAAGGGCCUGCUCC
..........((((((.---------....(((((....------------...))))--)..........))).))).....((((((((((.......))))))))))... ( -19.36)
>DroSec_CAF1 49152 90 - 1
ACCAAAUCUUUGCCAGA---------CUCUCUUUCAGCC------------ACUUCAU--UUUAUUUCUCACUGUAUAUCUCCACAGGUCCUUCAAUAAAAAGGGCCUGCUCU
.................---------.............------------.......--........................(((((((((.......))))))))).... ( -13.00)
>DroSim_CAF1 50909 76 - 1
ACCACAUCU-----------------------UUAAGCC------------ACUUUAU--UUUAUUUCUCACUGUGUAUCUCCGCAGGUCCUUCAAUAAAAAGGGCCUGCUCC
.........-----------------------......(------------((.....--.............))).......((((((((((.......))))))))))... ( -17.07)
>DroEre_CAF1 48591 88 - 1
GACAAAACAUGACCAGUCCUUACUGCC------------------------UUCUUAGCGUGCAUUUCUCACUGUGUAACUCCGCAGGUCCUUCAAUAA-AAGGGCCUGCUCU
...........((((((......((((------------------------........).)))......)))).))......((((((((((......-))))))))))... ( -22.90)
>DroYak_CAF1 50775 111 - 1
GACAAAUCAUUACCA-CCCUAACUGCCUUACUUGCAGACAAAUUAAGGUCCUUCUUACUGUGCAUUUCUUACCGUGUAACUCCGCAGGUCCUUCAAUAA-AAGGGCCUGCUCU
.............((-(.....((((.......))))(((...(((((....))))).)))............))).......((((((((((......-))))))))))... ( -25.40)
>consensus
ACCAAAUCUUUACCAGA_________CU__CUUUAAGCC____________ACCUUAU__UUUAUUUCUCACUGUGUAUCUCCGCAGGUCCUUCAAUAAAAAGGGCCUGCUCU
...................................................................................((((((((((.......))))))))))... (-15.64 = -15.84 +   0.20)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:21:44 2006