Locus 10287

Sequence ID	3R_DroMel_CAF1
Location	27,574,126 – 27,574,250
Length	124
Max. P	0.995131

overview

Window 2

Location	27,574,126 – 27,574,219
Length	93
Sequences	6
Columns	94
Reading direction	reverse
Mean pairwise identity	82.69
Mean single sequence MFE	-28.52
Consensus MFE	-23.00
Energy contribution	-23.75
Covariance contribution	0.75
Combinations/Pair	1.14
Mean z-score	-1.80
Structure conservation index	0.81
SVM decision value	0.51
SVM RNA-class probability	0.765157
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 27574126 93 - 27905053
GGCAGCGGCAAAACGUGAGCCUGAAAGGGAAUCGCCGAUUGCCC-UGCUUCUCUCGUCAUCUCCUCUUCUCUUCUUCUUCGGCGAGUAGCUACA
(((((((((....(....)(((....)))....)))).))))).-.(((...((((((......................)))))).))).... ( -29.55)
>DroSec_CAF1 1838 93 - 1
GGCAGCGGCAAAACGUGAGCCCGAAAGGGAAUCGCCGAUUGCCC-UGCUUCUAUCGUCAUCUCCUCUUCUCUUCUUCUUCGGCGAGUAGCUACA
(((((((((....(....)(((....)))....)))).))))).-.(((....(((((......................)))))..))).... ( -30.45)
>DroSim_CAF1 1839 93 - 1
GGCAGCGGCAAAACGUGAGCCCGAAAGGGAAUCGCCGAUUGCCC-UGCUUCUAUCGUCAUCUCCUCUUCUCUUCUUCUUCGGCGAGUAGCUACA
(((((((((....(....)(((....)))....)))).))))).-.(((....(((((......................)))))..))).... ( -30.45)
>DroEre_CAF1 1869 93 - 1
AGCAGCGGCAAAACGUGAGCCCGAAAGGGAAUCGCCGAUUGCCUCUG-UUCUCUCGUCAUCUCCUCUGCUCUUCUUCUUCGGCGAGUAGCUACA
(((((.(((((...((((.(((....)))..))))...))))).)))-))...............((((((.((......)).))))))..... ( -30.90)
>DroYak_CAF1 1871 94 - 1
GGCAGCGGCAAAACGUGAGCCCGAAAGGGAAUCGCCGAUUGCCUCUGCUUCUCUCGUCAUCUCAUCGUCUCUUCUUCUUCGGCGAGUAGCUACA
(((((((((....(....)(((....)))....)))).)))))...(((...((((((......................)))))).))).... ( -33.55)
>DroPer_CAF1 2482 70 - 1
--CAGCGGCAAAACGUGCGUCCAAAAGGGAAACGCCGAUUGCUU--GCU-----CACCAACCUAA--------------CGGC-AACAGCAACG
--.((((((((..((.((((((.....)))..))))).)))).)--)))-----......((...--------------.)).-.......... ( -16.20)
>consensus
GGCAGCGGCAAAACGUGAGCCCGAAAGGGAAUCGCCGAUUGCCC_UGCUUCUCUCGUCAUCUCCUCUUCUCUUCUUCUUCGGCGAGUAGCUACA
(((((((((....(....)(((....)))....)))).)))))...(((....(((((......................)))))..))).... (-23.00 = -23.75 +   0.75)

alignment

secondary structure

dotplot

Window 3

Location	27,574,146 – 27,574,250
Length	104
Sequences	5
Columns	105
Reading direction	reverse
Mean pairwise identity	95.99
Mean single sequence MFE	-34.50
Consensus MFE	-28.48
Energy contribution	-29.12
Covariance contribution	0.64
Combinations/Pair	1.04
Mean z-score	-2.98
Structure conservation index	0.83
SVM decision value	2.54
SVM RNA-class probability	0.995131
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 27574146 104 - 27905053
CAAGCAAAAAUAAAAACAAACGAGACGCGGCGGCAGCGGCAAAACGUGAGCCUGAAAGGGAAUCGCCGAUUGCCC-UGCUUCUCUCGUCAUCUCCUCUUCUCUUC
...................((((((.((((.(((((((((....(....)(((....)))....)))).))))))-)))...))))))................. ( -33.40)
>DroSec_CAF1 1858 104 - 1
CAAGCAAAAAUAAAAACAAACGAGACGCGGCGGCAGCGGCAAAACGUGAGCCCGAAAGGGAAUCGCCGAUUGCCC-UGCUUCUAUCGUCAUCUCCUCUUCUCUUC
...................((((((.((((.(((((((((....(....)(((....)))....)))).))))))-))).))..))))................. ( -33.90)
>DroSim_CAF1 1859 104 - 1
CAAGCAAAAAUAAAAACAAACGAGACGCGGCGGCAGCGGCAAAACGUGAGCCCGAAAGGGAAUCGCCGAUUGCCC-UGCUUCUAUCGUCAUCUCCUCUUCUCUUC
...................((((((.((((.(((((((((....(....)(((....)))....)))).))))))-))).))..))))................. ( -33.90)
>DroEre_CAF1 1889 104 - 1
CAAGCAAAAAUAAAAACAAACGAGACGCGGCAGCAGCGGCAAAACGUGAGCCCGAAAGGGAAUCGCCGAUUGCCUCUG-UUCUCUCGUCAUCUCCUCUGCUCUUC
..((((..........(....).((((.((.(((((.(((((...((((.(((....)))..))))...))))).)))-)).)).))))........)))).... ( -33.80)
>DroYak_CAF1 1891 105 - 1
CAAGCAAAAAUAAAAACAAACGAGACGCGGCGGCAGCGGCAAAACGUGAGCCCGAAAGGGAAUCGCCGAUUGCCUCUGCUUCUCUCGUCAUCUCAUCGUCUCUUC
...................((((((.((((.(((((((((....(....)(((....)))....)))).))))).))))...))))))................. ( -37.50)
>consensus
CAAGCAAAAAUAAAAACAAACGAGACGCGGCGGCAGCGGCAAAACGUGAGCCCGAAAGGGAAUCGCCGAUUGCCC_UGCUUCUCUCGUCAUCUCCUCUUCUCUUC
...................((((((.(.((((((((((((....(....)(((....)))....)))).)))))...))).)))))))................. (-28.48 = -29.12 +   0.64)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:53:20 2006