Locus 7006

Sequence ID	3R_DroMel_CAF1
Location	18,473,075 – 18,473,235
Length	160
Max. P	0.851283

overview

Window 6

Location	18,473,075 – 18,473,195
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	92.47
Mean single sequence MFE	-38.22
Consensus MFE	-31.57
Energy contribution	-31.49
Covariance contribution	-0.08
Combinations/Pair	1.12
Mean z-score	-1.52
Structure conservation index	0.83
SVM decision value	0.54
SVM RNA-class probability	0.775455
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 18473075 120 + 27905053
CUAGGCAGCUUUGCCGGCGGACUGAAUGUCCUGGAGCCGAAAGCCAUUUGGCCAGAGACAAAACUACACGGCCAGUCAAUGGCGGCAUACAGUUUCAGGCAACGAAAACAAAACUUGGCA
.......(((.(((((((((((.....))))....)))....(((((((((((..((......))....)))))...))))))))))....((((..(....)..)))).......))). ( -38.90)
>DroSec_CAF1 28286 117 + 1
---GGCUGCUUUGUCGGCGGACUGAAUGUCCUGGAGCCGAAAGCCAUUUGGCCAGAGACAAAACUACACGGCCAGUCAAUGGCGGCAUACAGUUUCGGGCAACGCAAACAAAACUUGGCA
---(..(((.(((((.(.((((((.(((((.((....))...(((((((((((..((......))....)))))...))))))))))).))))))).))))).)))..)........... ( -37.90)
>DroSim_CAF1 27996 117 + 1
---GGCUGCUUUGCCGGCGGACUGAAUGUCCUGGAGCCGAAAGCCAUUUGGCCAGAGACAAAACUACACGGCCAGUCAAUGGCGGCAUACAGUUUCAGGCAACGCAAACAAAACUUGGCA
---(..(((.(((((...((((((.(((((.((....))...(((((((((((..((......))....)))))...))))))))))).))))))..))))).)))..)........... ( -39.60)
>DroEre_CAF1 28554 117 + 1
---GGCAGCUCUGCCAGCGGCCUGAAUGUCCUGGACCCGAAAGCCAUUUGGCCACAGACAAAACUACACGGCCAGUCAAUGGCGGCAUACAAUUUCAGGCAGCGAACACAAGACUUGGCA
---((((....)))).((.(((((((((((.((....))...(((((((((((................)))))...)))))))))))......)))))).))................. ( -36.79)
>DroYak_CAF1 29261 117 + 1
---GCCAGCUUUGCCGGCGGGCUGAAUGUCCUGGACCCGAAAGCCAUUUGGCCAGAGACAAAACUACACGGCCAGUCAAUGGCGGCAUACAAUUUCAGGCAGAGAAAACAGAACUUGGCA
---((((((((((((..((((((.........)).))))...(((((((((((..((......))....)))))...))))))..............)))))))..........))))). ( -37.90)
>consensus
___GGCAGCUUUGCCGGCGGACUGAAUGUCCUGGAGCCGAAAGCCAUUUGGCCAGAGACAAAACUACACGGCCAGUCAAUGGCGGCAUACAGUUUCAGGCAACGAAAACAAAACUUGGCA
.......((((((((...((((((.(((((.((....))...(((((((((((..((......))....)))))...))))))))))).))))))..)))))..............))). (-31.57 = -31.49 +  -0.08)

alignment

secondary structure

dotplot

Window 7

Location	18,473,115 – 18,473,235
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	93.47
Mean single sequence MFE	-32.66
Consensus MFE	-26.91
Energy contribution	-27.99
Covariance contribution	1.08
Combinations/Pair	1.03
Mean z-score	-1.65
Structure conservation index	0.82
SVM decision value	0.79
SVM RNA-class probability	0.851283
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 18473115 120 + 27905053
AAGCCAUUUGGCCAGAGACAAAACUACACGGCCAGUCAAUGGCGGCAUACAGUUUCAGGCAACGAAAACAAAACUUGGCAACUUGAAGCAUAAAUGUCGGCCGAAUGCCAAGUCGAGACG
..(.(((((((((.................((((.....))))(((((...((((((((...(((.........)))....))))))))....)))))))))))))).)........... ( -33.90)
>DroSec_CAF1 28323 119 + 1
AAGCCAUUUGGCCAGAGACAAAACUACACGGCCAGUCAAUGGCGGCAUACAGUUUCGGGCAACGCAAACAAAACUUGGCAACUUGAAGCAUAAAUGUCGGCCGACUGCCAAGUC-AGACG
..(((((((((((..((......))....)))))...))))))(((..(((((((((((...(.(((.......))))...)))))))).....)))..)))((((....))))-..... ( -32.60)
>DroSim_CAF1 28033 119 + 1
AAGCCAUUUGGCCAGAGACAAAACUACACGGCCAGUCAAUGGCGGCAUACAGUUUCAGGCAACGCAAACAAAACUUGGCAACUUGAAGCAUAAAUGUCGGCCGACUGCCAAGUC-AGACG
..(((((((((((..((......))....)))))...))))))(((..(((((((((((...(.(((.......))))...)))))))).....)))..)))((((....))))-..... ( -33.40)
>DroEre_CAF1 28591 119 + 1
AAGCCAUUUGGCCACAGACAAAACUACACGGCCAGUCAAUGGCGGCAUACAAUUUCAGGCAGCGAACACAAGACUUGGCAACACGAACCAUAAAUGUCGGCUGUGUGCCAAGUC-AGACG
..(((((((((((................)))))...))))))............................(((((((((.((((..((.........)).)))))))))))))-..... ( -34.89)
>DroYak_CAF1 29298 119 + 1
AAGCCAUUUGGCCAGAGACAAAACUACACGGCCAGUCAAUGGCGGCAUACAAUUUCAGGCAGAGAAAACAGAACUUGGCAACUUGAACCAUAAAUGUCGGCUGAAUGCCAAGUC-AGACG
..(((((((((((..((......))....)))))...))))))(((((.....((((((..(((.........))).....))))))......)))))(((.....))).....-..... ( -28.50)
>consensus
AAGCCAUUUGGCCAGAGACAAAACUACACGGCCAGUCAAUGGCGGCAUACAGUUUCAGGCAACGAAAACAAAACUUGGCAACUUGAAGCAUAAAUGUCGGCCGAAUGCCAAGUC_AGACG
..(((((((((((..((......))....)))))...))))))(((((...((((((((......................))))))))....)))))(((.....)))........... (-26.91 = -27.99 +   1.08)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:35:21 2006