Locus 6705

Sequence ID	3L_DroMel_CAF1
Location	17,902,087 – 17,902,230
Length	143
Max. P	0.730325

overview

Window 9

Location	17,902,087 – 17,902,206
Length	119
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	78.98
Mean single sequence MFE	-30.35
Consensus MFE	-18.72
Energy contribution	-20.28
Covariance contribution	1.56
Combinations/Pair	1.28
Mean z-score	-1.68
Structure conservation index	0.62
SVM decision value	0.42
SVM RNA-class probability	0.730325
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 17902087 119 - 23771897
AAUUCGCCUGGUAAAAGUGUACUUC-AUUUUGCCCUUUCCUUGGGUUAAUUAAUACUCUGGGGAUUGGGGUUGAUUUGCAGCCGAGUACAAAAUGCUAAUUUGGAGAAAUUAUUGUAAGA
..(((.(((((((....(((((((.-.......((..((((..(((........)).)..))))..))(((((.....))))))))))))...)))))....)).)))............ ( -32.20)
>DroSec_CAF1 25819 118 - 1
AAUUCGCCUGGUAAAAGUGUACUUC-AUUUUGCCCUUUCCCUGGGUUAAUUAAUACUCUGGGGAAUGGGCUUGCAAA-GAGCCGAGUACAAAAUGCUAAUUUGGAGAAAUUAUUGUAAGA
..(((.(((((((....(((((((.-.....((((.(((((..(((........)).)..))))).))))..((...-..)).)))))))...)))))....)).)))............ ( -34.50)
>DroSim_CAF1 26088 118 - 1
AAUUCGCCUGGUAAAAGUGUACUUC-AUUUUGCCCUUUCCCUGGGUUAAUUAAUACUCUGGGGAAUGGGGUUGCAAA-GAGCCGAGUACAAAAUGCUAAUUUGGAGAAAUUAUUGUAAGA
..(((.(((((((....(((((((.-.((((((((((((((..(((........)).)..))))).)))))....))-))...)))))))...)))))....)).)))............ ( -32.60)
>DroEre_CAF1 27055 117 - 1
AAUUCGCCUGGUAAAAGUGUGCUUC-AUUUUGCCCUUUCCCUGGGUUAAUUAGUACUCUGGGUACUGGGGUUGCAGA-GAGCCGAGUACAAAAUGCUAAUUUGGGGAAA-UAUUUUAAGA
..(((.(((((((....(((((((.-.(((((((((..(((.((((........)))).)))....)))))....))-))...)))))))...)))))....)).))).-.......... ( -31.70)
>DroYak_CAF1 27467 117 - 1
AAUUCGCCUGGUAAAAGUGUACUUC-AUUUCGCCCUUUCCCUGGGUUAAUUAAUACUCAGGGUAAUGGGGUUGCAAA-GAGCCGAGUGCGAAAUGCUAAUUUGGGGAAA-UAUUUUAAGA
..(((.(((((((....(((((((.-.....(((((..((((((((........))))))))....))))).((...-..)).)))))))...)))))....)).))).-.......... ( -34.90)
>DroAna_CAF1 24684 95 - 1
UAUUCGACGAGUAAAAGUCUAUUUCCAUUACUUUCAUUUCGGGGGUUAAUUAGAGGUCCAAGG---------------AAGUCAAGUAUGAAAUGCAAAUUUAAAGAAAA----------
..((((((........)))((((((...(((((...((((..((..(.......)..))..))---------------))...))))).))))))..........)))..---------- ( -16.20)
>consensus
AAUUCGCCUGGUAAAAGUGUACUUC_AUUUUGCCCUUUCCCUGGGUUAAUUAAUACUCUGGGGAAUGGGGUUGCAAA_GAGCCGAGUACAAAAUGCUAAUUUGGAGAAAUUAUUGUAAGA
..(((.(((((((....(((((((...((..(((((.((((.((((........)))).))))...))))).......))...)))))))...)))))....)).)))............ (-18.72 = -20.28 +   1.56)

alignment

secondary structure

dotplot

Window 0

Location	17,902,127 – 17,902,230
Length	103
Sequences	6
Columns	104
Reading direction	reverse
Mean pairwise identity	79.22
Mean single sequence MFE	-28.05
Consensus MFE	-15.03
Energy contribution	-18.20
Covariance contribution	3.17
Combinations/Pair	1.14
Mean z-score	-1.81
Structure conservation index	0.54
SVM decision value	-0.03
SVM RNA-class probability	0.518406
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 17902127 103 - 23771897
GGAGUAAGCAGACCAAGAAUUUGUAAUUCGCCUGGUAAAAGUGUACUUC-AUUUUGCCCUUUCCUUGGGUUAAUUAAUACUCUGGGGAUUGGGGUUGAUUUGCA
((((((.((..((((.((((.....))))...))))....)).))))))-..((.(((((.((((..(((........)).)..))))..))))).))...... ( -29.30)
>DroSec_CAF1 25859 102 - 1
GGAGUAAGCAGACCAAGAAUUUGUAAUUCGCCUGGUAAAAGUGUACUUC-AUUUUGCCCUUUCCCUGGGUUAAUUAAUACUCUGGGGAAUGGGCUUGCAAA-GA
((((((.((..((((.((((.....))))...))))....)).))))))-.....((((.(((((..(((........)).)..))))).)))).......-.. ( -33.80)
>DroSim_CAF1 26128 102 - 1
GCAGUAAGCAGACCAAGAAUUUGUAAUUCGCCUGGUAAAAGUGUACUUC-AUUUUGCCCUUUCCCUGGGUUAAUUAAUACUCUGGGGAAUGGGGUUGCAAA-GA
((((((.((..((((.((((.....))))...))))....)).)))...-.....((((((((((..(((........)).)..))))).))))))))...-.. ( -29.40)
>DroEre_CAF1 27094 102 - 1
GGAGUAAGCAGACCAAGAAUUUGUAAUUCGCCUGGUAAAAGUGUGCUUC-AUUUUGCCCUUUCCCUGGGUUAAUUAGUACUCUGGGUACUGGGGUUGCAGA-GA
((((((.((..((((.((((.....))))...))))....)).))))))-.((((((((((.(((.((((........)))).)))....))))..)))))-). ( -29.00)
>DroYak_CAF1 27506 102 - 1
GGAGUAAGCAGACCAAGAAUUUGUAAUUCGCCUGGUAAAAGUGUACUUC-AUUUCGCCCUUUCCCUGGGUUAAUUAAUACUCAGGGUAAUGGGGUUGCAAA-GA
((((((.((..((((.((((.....))))...))))....)).))))))-.....(((((..((((((((........))))))))....)))))......-.. ( -33.30)
>DroAna_CAF1 24714 79 - 1
----------AACCAAGAAUUCGUUAUUCGACGAGUAAAAGUCUAUUUCCAUUACUUUCAUUUCGGGGGUUAAUUAGAGGUCCAAGG---------------AA
----------.(((....(((((((....))))))).....((((........(((..(.....)..)))....)))))))......---------------.. ( -13.50)
>consensus
GGAGUAAGCAGACCAAGAAUUUGUAAUUCGCCUGGUAAAAGUGUACUUC_AUUUUGCCCUUUCCCUGGGUUAAUUAAUACUCUGGGGAAUGGGGUUGCAAA_GA
((((((.((..((((.((((.....))))...))))....)).))))))......(((((.((((.((((........)))).))))...)))))......... (-15.03 = -18.20 +   3.17)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:28:03 2006