Locus 1071

Sequence ID	3L_DroMel_CAF1
Location	3,141,145 – 3,141,255
Length	110
Max. P	0.854058

overview

Window 5

Location	3,141,145 – 3,141,255
Length	110
Sequences	6
Columns	114
Reading direction	forward
Mean pairwise identity	77.53
Mean single sequence MFE	-35.38
Consensus MFE	-19.08
Energy contribution	-19.58
Covariance contribution	0.51
Combinations/Pair	1.32
Mean z-score	-1.93
Structure conservation index	0.54
SVM decision value	0.53
SVM RNA-class probability	0.772706
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 3141145 110 + 23771897
UAUUUGUAUUUGUGACAGGACGGCCGCCGAAAGGUUGACCUCCAUCAG---ACUAGAAGCCACGCAUUGCUCGUCCUUCAUUCUGGAACAUGGUCCA-CACAUGGCCGUCUGUC
.............(((((.(((((((((....))).((((....((((---(...((((..(((.......))).))))..))))).....))))..-.....))))))))))) ( -36.60)
>DroSec_CAF1 5121 109 + 1
UAUUUGUAUUUGUGACAGGAUGGCCGCCGAGAGGAUGACCUCCACCAG---ACUAGAAGCCACGCAUUGCUCGUCCUUCAUUCUGCAAUAUGGUCCA-CG-AUGGCCUUCUGUC
.............(((((((.(((((((....))..((((.....(((---(...((((..(((.......))).))))..))))......))))..-..-.)))))))))))) ( -31.40)
>DroSim_CAF1 5110 110 + 1
UAUUUGUAUUUGUGACAGGACGGCCGCCGAGAGGAUGACCUCCACCAG---ACUAGAAGCCACGCAUUGCUCGUCCUUCAUUCUGCAAUAUGGUCCA-CACAUGGCCGUCUGUC
.............(((((.(((((((((....))..((((.....(((---(...((((..(((.......))).))))..))))......))))..-....)))))))))))) ( -33.50)
>DroEre_CAF1 5125 110 + 1
UAUUUGUAUUUGUGACAGGACGGCCGCCGAGAGAAUGACCUCCACCAG---ACUAGAACCCAAGCAUUGCUCGACCUUCUUUCUGGAACAUGGUCCA-AACACGGUCGUCUGUC
.............(((((.(((((((.(....)...((((....((((---(..((((..(.(((...))).)...)))).))))).....))))..-....)))))))))))) ( -32.70)
>DroYak_CAF1 5148 111 + 1
UAUUUGUAUUUGUGACAGGACGGCCGCCGAGAGGAUGACCUCCACCAG---ACUUGAAGCCACGCAUUACUCGGACUUCUUUCUGGAUCAUGGUUCAAAACGCGGUCGUCUGUC
.............(((((.((((((((.(.((((....))))).((((---(...((((((...........)).))))..)))))...............))))))))))))) ( -38.80)
>DroPer_CAF1 5275 90 + 1
UAUUUGUAUUUGUGGCACGACGGCCACC-ACAGAAUGAUCUUGAUCGUGUGUACCGUACCCAUGCAUCGG------AUCAUUUG-----------------GGGGCCGUCGGUC
.............(((.((((((((.((-...(((((((((.(((((((.(((...))).)))).)))))------))))))).-----------------))))))))))))) ( -39.30)
>consensus
UAUUUGUAUUUGUGACAGGACGGCCGCCGAGAGGAUGACCUCCACCAG___ACUAGAAGCCACGCAUUGCUCGUCCUUCAUUCUGGAACAUGGUCCA_CACAUGGCCGUCUGUC
.............(((.(((((((((....((((....)))).((((......(((((......................))))).....))))........)))))))))))) (-19.08 = -19.58 +   0.51)

alignment

secondary structure

dotplot

Window 6

Location	3,141,145 – 3,141,255
Length	110
Sequences	6
Columns	114
Reading direction	reverse
Mean pairwise identity	77.53
Mean single sequence MFE	-36.32
Consensus MFE	-21.42
Energy contribution	-23.21
Covariance contribution	1.79
Combinations/Pair	1.18
Mean z-score	-1.88
Structure conservation index	0.59
SVM decision value	0.80
SVM RNA-class probability	0.854058
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 3141145 110 - 23771897
GACAGACGGCCAUGUG-UGGACCAUGUUCCAGAAUGAAGGACGAGCAAUGCGUGGCUUCUAGU---CUGAUGGAGGUCAACCUUUCGGCGGCCGUCCUGUCACAAAUACAAAUA
(((((((((((...(.-((((......)))).).((((((((((....).)))((((((((..---....))))))))...))))))..)))))).)))))............. ( -39.80)
>DroSec_CAF1 5121 109 - 1
GACAGAAGGCCAU-CG-UGGACCAUAUUGCAGAAUGAAGGACGAGCAAUGCGUGGCUUCUAGU---CUGGUGGAGGUCAUCCUCUCGGCGGCCAUCCUGUCACAAAUACAAAUA
(((((..((((..-((-.(((...((((((..............))))))..(((((((((..---....))))))))))))...))..))))...)))))............. ( -34.14)
>DroSim_CAF1 5110 110 - 1
GACAGACGGCCAUGUG-UGGACCAUAUUGCAGAAUGAAGGACGAGCAAUGCGUGGCUUCUAGU---CUGGUGGAGGUCAUCCUCUCGGCGGCCGUCCUGUCACAAAUACAAAUA
(((((((((((.((.(-.(((...((((((..............))))))..(((((((((..---....)))))))))))).).))..)))))).)))))............. ( -38.54)
>DroEre_CAF1 5125 110 - 1
GACAGACGACCGUGUU-UGGACCAUGUUCCAGAAAGAAGGUCGAGCAAUGCUUGGGUUCUAGU---CUGGUGGAGGUCAUUCUCUCGGCGGCCGUCCUGUCACAAAUACAAAUA
((((((((.((((...-..((((.....(((((.((((..((((((...)))))).))))..)---))))....)))).........)))).))).)))))............. ( -35.24)
>DroYak_CAF1 5148 111 - 1
GACAGACGACCGCGUUUUGAACCAUGAUCCAGAAAGAAGUCCGAGUAAUGCGUGGCUUCAAGU---CUGGUGGAGGUCAUCCUCUCGGCGGCCGUCCUGUCACAAAUACAAAUA
((((((((.((((...............(((((..(((((((((....).)).))))))...)---)))).(((((....)))))..)))).))).)))))............. ( -40.70)
>DroPer_CAF1 5275 90 - 1
GACCGACGGCCCC-----------------CAAAUGAU------CCGAUGCAUGGGUACGGUACACACGAUCAAGAUCAUUCUGU-GGUGGCCGUCGUGCCACAAAUACAAAUA
...((((((((((-----------------((((((((------(.(((.(.((.(((...))).)).))))..))))))).)).-)).))))))))................. ( -29.50)
>consensus
GACAGACGGCCAUGUG_UGGACCAUGUUCCAGAAUGAAGGACGAGCAAUGCGUGGCUUCUAGU___CUGGUGGAGGUCAUCCUCUCGGCGGCCGUCCUGUCACAAAUACAAAUA
(((((((((((..........((...............)).((((....(.((((((((((.........)))))))))).).))))..))))))).))))............. (-21.42 = -23.21 +   1.79)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:58:17 2006