Locus 2249

Sequence ID 3L_DroMel_CAF1
Location 6,241,299 – 6,241,397
Length 98
Max. P 0.959675
window3476 window3477

overview

Window 6

Location 6,241,299 – 6,241,397
Length 98
Sequences 5
Columns 105
Reading direction forward
Mean pairwise identity 78.02
Mean single sequence MFE -21.10
Consensus MFE -13.99
Energy contribution -17.20
Covariance contribution 3.21
Combinations/Pair 1.07
Mean z-score -2.14
Structure conservation index 0.66
SVM decision value 1.50
SVM RNA-class probability 0.959675
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 6241299 98 + 23771897
AAAAA--CAUCU----GACAAUAUGAGGUGGGA-AUUUUAAUUAACACAGUGAGUGUUAUUUGUUCAUGGAAAUAGCAUUCGAAUGUCAAUUAAAAUUGACACAU
.....--.....----...........(((..(-(((((((((.(((...((((((((((((.(....).))))))))))))..))).))))))))))..))).. ( -26.20)
>DroSec_CAF1 7260 100 + 1
AAAAA-CCAUGU----GGCGAUAUCAGGUGGGAAAUUUUAAUUAACACAGUGAGUGUUAUUUGUUCAUUGAAAUAGCAUUCGAAUGUCAAUUAAAAUUGACACAU
.....-((((.(----((.....))).))))..((((((((((.(((...((((((((((((........))))))))))))..))).))))))))))....... ( -26.80)
>DroSim_CAF1 7263 100 + 1
AAAAA-CCAUGU----GGGGAUAUCAGGUGGGAAAUUUUAAUUAACACAGUGAGUGUUAUUUGUUCAUUGAAAUAGCAUUCGAAUGUCAAUUAAAAUUGACACAU
.....-((((.(----((.....))).))))..((((((((((.(((...((((((((((((........))))))))))))..))).))))))))))....... ( -27.60)
>DroEre_CAF1 7443 81 + 1
GAAAAUACAUGU---------------GUGGGAAAUUUUAAUUAACACAGC----GUUCUUUGUUUAUUGAAUCAACAUU----CGUCAAUUA-AAUUGGCACAU
........((((---------------((.((....(((((((.((..(((----(.....))))....((((....)))----))).)))))-)))).)))))) ( -10.50)
>DroYak_CAF1 7740 101 + 1
GAAAAUAUAUAUAUCAGGCUUUAUCAGGUGGGAAAAUGUAAUUAACACAGC----GGUGUUUGUUCAACGAAAUAGCAUUGAAAUGUCAAUUAAAAUUGGCACAU
.............(((((((...((...((((...........(((((...----.)))))..))))..))...))).))))..(((((((....)))))))... ( -14.42)
>consensus
AAAAA_ACAUGU____GGCGAUAUCAGGUGGGAAAUUUUAAUUAACACAGUGAGUGUUAUUUGUUCAUUGAAAUAGCAUUCGAAUGUCAAUUAAAAUUGACACAU
...........................(((...((((((((((.(((...((((((((((((........))))))))))))..))).))))))))))..))).. (-13.99 = -17.20 +   3.21)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 7

Location 6,241,299 – 6,241,397
Length 98
Sequences 5
Columns 105
Reading direction reverse
Mean pairwise identity 78.02
Mean single sequence MFE -15.67
Consensus MFE -9.21
Energy contribution -11.70
Covariance contribution 2.49
Combinations/Pair 1.04
Mean z-score -1.68
Structure conservation index 0.59
SVM decision value 0.02
SVM RNA-class probability 0.543681
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 6241299 98 - 23771897
AUGUGUCAAUUUUAAUUGACAUUCGAAUGCUAUUUCCAUGAACAAAUAACACUCACUGUGUUAAUUAAAAU-UCCCACCUCAUAUUGUC----AGAUG--UUUUU
..(((..(((((((((((((((..((.((.(((((........))))).)).))...))))))))))))))-)..)))...........----.....--..... ( -19.20)
>DroSec_CAF1 7260 100 - 1
AUGUGUCAAUUUUAAUUGACAUUCGAAUGCUAUUUCAAUGAACAAAUAACACUCACUGUGUUAAUUAAAAUUUCCCACCUGAUAUCGCC----ACAUGG-UUUUU
..(((..(((((((((((((((..((.((.(((((........))))).)).))...)))))))))))))))...)))........(((----....))-).... ( -19.00)
>DroSim_CAF1 7263 100 - 1
AUGUGUCAAUUUUAAUUGACAUUCGAAUGCUAUUUCAAUGAACAAAUAACACUCACUGUGUUAAUUAAAAUUUCCCACCUGAUAUCCCC----ACAUGG-UUUUU
..(((..(((((((((((((((..((.((.(((((........))))).)).))...)))))))))))))))...))).........((----....))-..... ( -17.50)
>DroEre_CAF1 7443 81 - 1
AUGUGCCAAUU-UAAUUGACG----AAUGUUGAUUCAAUAAACAAAGAAC----GCUGUGUUAAUUAAAAUUUCCCAC---------------ACAUGUAUUUUC
.((((....((-(((((((((----(((....)))).....(((......----..)))))))))))))......)))---------------)........... ( -11.30)
>DroYak_CAF1 7740 101 - 1
AUGUGCCAAUUUUAAUUGACAUUUCAAUGCUAUUUCGUUGAACAAACACC----GCUGUGUUAAUUACAUUUUCCCACCUGAUAAAGCCUGAUAUAUAUAUUUUC
..(((.......(((((((((((((((((......)))))))........----...))))))))))........)))........................... ( -11.36)
>consensus
AUGUGUCAAUUUUAAUUGACAUUCGAAUGCUAUUUCAAUGAACAAAUAACACUCACUGUGUUAAUUAAAAUUUCCCACCUGAUAUCGCC____ACAUGG_UUUUU
..(((..(((((((((((((((..((.((.(((((........))))).)).))...)))))))))))))))...)))........................... ( -9.21 = -11.70 +   2.49)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:27:46 2006