Locus 7655

Sequence ID	2L_DroMel_CAF1
Location	21,312,375 – 21,312,507
Length	132
Max. P	0.959250

overview

Window 8

Location	21,312,375 – 21,312,467
Length	92
Sequences	6
Columns	93
Reading direction	forward
Mean pairwise identity	80.76
Mean single sequence MFE	-37.82
Consensus MFE	-24.76
Energy contribution	-26.93
Covariance contribution	2.17
Combinations/Pair	1.17
Mean z-score	-1.35
Structure conservation index	0.65
SVM decision value	-0.03
SVM RNA-class probability	0.515894
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 21312375 92 + 22407834
GCAGACGGCGGCGUCGUGAGGGCCAAAGG-GUAGCUCAUUUGCGGCCUGGUCAAAGCGGCGCCAAGCAGACGCCCAAGGAGACUGAAUCUCCC
......(((((((((((...(((((...(-((.((......)).))))))))...))))))))..(....))))...(((((.....))))). ( -38.20)
>DroSec_CAF1 13527 85 + 1
-------CCGGCGUCGUGAGGGCCAAAGG-UUCGCUCAUUUGCGGCCUGGUCAAAGCGGCGCCAAGCAGACGCCCAAGGAGACUGAAUCUCCC
-------..((((((((...(((((..((-(.(((......)))))))))))...))))))))..((....))....(((((.....))))). ( -37.50)
>DroSim_CAF1 12746 85 + 1
-------CCGGCGUCGUGAGGGCCAAAGG-UUCGCUCAUUUGCGGCCUGGUCAAAGCGGCGCCAAGCAGACGCCCAAGGAGACUGAAUCUCCC
-------..((((((((...(((((..((-(.(((......)))))))))))...))))))))..((....))....(((((.....))))). ( -37.50)
>DroEre_CAF1 13581 92 + 1
ACAGCCGGCGGGGUCGUGAGGGCCAAAGC-GUCGCUCAUUUGCGGCCUGGUCAAAGCGGCGCCGGGCAGGCGCCCAGGGAGACUGAAUCUCUC
.........((.(((((...(((((..(.-(((((......)))))))))))...))))).))((((....)))).((((((.....)))))) ( -40.50)
>DroYak_CAF1 16118 91 + 1
GCAGCCGGCGGACUUGUGAGGGCCAAAGG-GUCGCUCAUUUGCGGCCUGGUCAAAGCGGCGCCAGGCAGACGUCCAAGGAGACAGAA-CUCUC
...(((((((...((((...(((((...(-(((((......)))))))))))...)))))))).)))....(((......)))....-..... ( -34.10)
>DroAna_CAF1 10368 84 + 1
AGG---GGCGGUC---UG-GGGCCAGAGGCGUCGCUCAUUUGCGGCUUGGCCGAAGCGGCGCCAGUCCGCCGACCAAGCAAUCUGAUUCCC--
.((---(((((.(---((-(.(((...((((((((......)))))...))).....))).)))).)))))..))................-- ( -39.10)
>consensus
_CA___GGCGGCGUCGUGAGGGCCAAAGG_GUCGCUCAUUUGCGGCCUGGUCAAAGCGGCGCCAAGCAGACGCCCAAGGAGACUGAAUCUCCC
.........((((((((...(((((.....(((((......))))).)))))...))))))))..............(((((.....))))). (-24.76 = -26.93 +   2.17)

alignment

secondary structure

dotplot

Window 9

Location	21,312,399 – 21,312,507
Length	108
Sequences	6
Columns	109
Reading direction	reverse
Mean pairwise identity	74.38
Mean single sequence MFE	-43.53
Consensus MFE	-24.45
Energy contribution	-25.82
Covariance contribution	1.37
Combinations/Pair	1.19
Mean z-score	-2.07
Structure conservation index	0.56
SVM decision value	1.50
SVM RNA-class probability	0.959250
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 21312399 108 - 22407834
CCACCGCUCAGCAACUUGGUAUGGCGUGGUGAGAGCGAAAGGGAGAUUCAGUCUCCUUGGGCGUCUGCUUGGCGCCGCUUUGACCAGGCCGCAAA-UGAGCUACCCUUU
.....(((((((......))..(((.((((.(((((...((((((((...)))))))).((((((.....))))))))))).)))).))).....-)))))........ ( -48.50)
>DroGri_CAF1 16955 90 - 1
-----------------AAAGGGGGUGGG-CAGCUGAGGCGUGAGCUUUGGUUUGCCUGG-CGGCUGGAUGGCGCCGCUUUGACCAGCCCGCAAAACGAGUGACGCCGC
-----------------....((.(((((-((((..((((....))))..).)))))).(-(((((((..(((...)))....)))).))))..........)).)).. ( -39.40)
>DroSec_CAF1 13544 105 - 1
C---CGCUCAGCCACUUGGUAUGGCGCGGUGAGAGCGAAAGGGAGAUUCAGUCUCCUUGGGCGUCUGCUUGGCGCCGCUUUGACCAGGCCGCAAA-UGAGCGAACCUUU
.---(((((((((....)))..(((..(((.(((((...((((((((...)))))))).((((((.....))))))))))).)))..))).....-))))))....... ( -49.80)
>DroSim_CAF1 12763 105 - 1
C---CGCUCAGCCACUUGGUAUGGCGCGGUGAGAGCGAAAGGGAGAUUCAGUCUCCUUGGGCGUCUGCUUGGCGCCGCUUUGACCAGGCCGCAAA-UGAGCGAACCUUU
.---(((((((((....)))..(((..(((.(((((...((((((((...)))))))).((((((.....))))))))))).)))..))).....-))))))....... ( -49.80)
>DroEre_CAF1 13605 95 - 1
U---UG----------UGAGGUGGCACGGUGAGAGCGAAAGAGAGAUUCAGUCUCCCUGGGCGCCUGCCCGGCGCCGCUUUGACCAGGCCGCAAA-UGAGCGACGCUUU
(---((----------(...(((((..(((.(((((...((.(((((...))))).)).((((((.....))))))))))).)))..)))))...-...))))...... ( -41.20)
>DroYak_CAF1 16142 94 - 1
U---GG----------UGAGGUGGCACUGUGAGAGCGAAAGAGAG-UUCUGUCUCCUUGGACGUCUGCCUGGCGCCGCUUUGACCAGGCCGCAAA-UGAGCGACCCUUU
(---((----------(((((((((......(((((........)-))))((((....))))(((.....))))))))))).))))((.(((...-...))).)).... ( -32.50)
>consensus
C___CG__________UGAUAUGGCGCGGUGAGAGCGAAAGGGAGAUUCAGUCUCCUUGGGCGUCUGCUUGGCGCCGCUUUGACCAGGCCGCAAA_UGAGCGACCCUUU
......................(((..(((.(((((..(((.((((.....))))))).((((((.....))))))))))).)))..)))((.......))........ (-24.45 = -25.82 +   1.37)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:42:02 2006