Locus 4407

Sequence ID	X_DroMel_CAF1
Location	11,628,717 – 11,628,826
Length	109
Max. P	0.981966

overview

Window 1

Location	11,628,717 – 11,628,826
Length	109
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	73.03
Mean single sequence MFE	-25.40
Consensus MFE	-15.87
Energy contribution	-16.90
Covariance contribution	1.03
Combinations/Pair	1.22
Mean z-score	-1.56
Structure conservation index	0.62
SVM decision value	0.98
SVM RNA-class probability	0.893945
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 11628717 109 + 22224390
UCUGCCAGUGGUCUAAUCCUUUGAUUAUUAUCC----------UC-AGGUCUGUCGGACAUCCCCGGCGAGGCAAUGGUUAAGACCUAUUGCCCCAAGUGCAUUGACGUGUACACACCAA
...(((.(.((..(((((....)))))....))----------.)-.)))..(((((......)))))(.(((((((((....))).)))))).)..((((((....))))))....... ( -30.30)
>DroVir_CAF1 4328 89 + 1
-----------------UCUU--UAUAUUGUA-----------UU-AGGCCUUUCGGAUAUACCCGGCGAGGCAAUGGUGAAAACCUAUUGCCCCAAGUGCAUUGAUGUUUAUACACCAA
-----------------....--.....((((-----------((-.((....((((......))))...(((((((((....))).)))))))).))))))(((.(((....))).))) ( -23.80)
>DroGri_CAF1 1297 87 + 1
-----------------UC----UAUAUCGUA-----------UC-AGGCCUGUCGGAUAUACCCGGCGAGGCAAUGGUGAAAACCUAUUGCCCCAAGUGCAUUGAUGUUUAUACACCAA
-----------------..----((((...((-----------((-(((((((((((......)))))(.(((((((((....))).)))))).).)).)).))))))..))))...... ( -28.30)
>DroMoj_CAF1 1101 90 + 1
-----------------UCUU--UGCAUCGUG-----------UUCAGGACUGUCGGAUAUACCCGGCGAGGCAAUGGUGAAAACCUAUUGUCCCAAGUGCAUUGAUGUUUAUACACCAA
-----------------....--.((((((((-----------(...((..((((((......)))))).(((((((((....))).))))))))....))).))))))........... ( -26.70)
>DroAna_CAF1 1252 111 + 1
--------UCAAUUAAUAUUCUUUUUAUCAUCCCAUUCCCCCAAC-AGGUCUGUCCGACAUCCCCGGAGAGGCAAUGGUGAAGACCUAUUGCCCCAAGUGCAUUGAUGUUUACACACCAA
--------.....................................-.(((.(((..((((((........(((((((((....))).))))))...........)))))).))).))).. ( -20.41)
>DroPer_CAF1 1590 93 + 1
----------------UCGUUUCGUUUCGUUUU----------UU-AGGCCUUUCGGACAUACCCGGUGAGGCAAUGGUGAAGACCUAUUGCCCAAAGUGCAUUGAUGUCUAUACACCAA
----------------.................----------..-..(((((((((......)))).)))))..(((((.((((....(((.......))).....))))...))))). ( -22.90)
>consensus
_________________UCUU__UUUAUCGUA___________UC_AGGCCUGUCGGACAUACCCGGCGAGGCAAUGGUGAAAACCUAUUGCCCCAAGUGCAUUGAUGUUUAUACACCAA
...............................................((..(((.((((((.....(((.(((((((((....))).)))))).....)))....)))))))))..)).. (-15.87 = -16.90 +   1.03)

alignment

secondary structure

dotplot

Window 2

Location	11,628,717 – 11,628,826
Length	109
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	73.03
Mean single sequence MFE	-28.15
Consensus MFE	-20.06
Energy contribution	-20.33
Covariance contribution	0.28
Combinations/Pair	1.05
Mean z-score	-1.82
Structure conservation index	0.71
SVM decision value	1.90
SVM RNA-class probability	0.981966
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 11628717 109 - 22224390
UUGGUGUGUACACGUCAAUGCACUUGGGGCAAUAGGUCUUAACCAUUGCCUCGCCGGGGAUGUCCGACAGACCU-GA----------GGAUAAUAAUCAAAGGAUUAGACCACUGGCAGA
..(((((((........))))))).((((((((.(((....)))))))))))(((((((.(((((..((....)-).----------))))).(((((....)))))..)).)))))... ( -38.50)
>DroVir_CAF1 4328 89 - 1
UUGGUGUAUAAACAUCAAUGCACUUGGGGCAAUAGGUUUUCACCAUUGCCUCGCCGGGUAUAUCCGAAAGGCCU-AA-----------UACAAUAUA--AAGA-----------------
..(((((((........))))))).((((((((.(((....))))))))))).....((((..((....))...-.)-----------)))......--....----------------- ( -25.60)
>DroGri_CAF1 1297 87 - 1
UUGGUGUAUAAACAUCAAUGCACUUGGGGCAAUAGGUUUUCACCAUUGCCUCGCCGGGUAUAUCCGACAGGCCU-GA-----------UACGAUAUA----GA-----------------
..(((((((........))))))).((((((((.(((....)))))))))))(((.((.....))....)))..-..-----------.........----..----------------- ( -24.90)
>DroMoj_CAF1 1101 90 - 1
UUGGUGUAUAAACAUCAAUGCACUUGGGACAAUAGGUUUUCACCAUUGCCUCGCCGGGUAUAUCCGACAGUCCUGAA-----------CACGAUGCA--AAGA-----------------
(((((((....)))))))((((((..((((....(((....)))..(((((....))))).........))))..).-----------...).))))--....----------------- ( -22.00)
>DroAna_CAF1 1252 111 - 1
UUGGUGUGUAAACAUCAAUGCACUUGGGGCAAUAGGUCUUCACCAUUGCCUCUCCGGGGAUGUCGGACAGACCU-GUUGGGGGAAUGGGAUGAUAAAAAGAAUAUUAAUUGA--------
(((((((....)))))))(((.(....))))....(((.((.(((((.((((..((((..((.....))..)))-)..)))).))))))).)))..................-------- ( -34.60)
>DroPer_CAF1 1590 93 - 1
UUGGUGUAUAGACAUCAAUGCACUUUGGGCAAUAGGUCUUCACCAUUGCCUCACCGGGUAUGUCCGAAAGGCCU-AA----------AAAACGAAACGAAACGA----------------
(((((((....))))))).((.(((((((((((.(((....))))))))))...((((....))))))))))..-..----------.................---------------- ( -23.30)
>consensus
UUGGUGUAUAAACAUCAAUGCACUUGGGGCAAUAGGUCUUCACCAUUGCCUCGCCGGGUAUAUCCGACAGGCCU_AA___________GACGAUAAA__AAGA_________________
..(((((((........))))))).((((((((.(((....)))))))))))..((((....))))...................................................... (-20.06 = -20.33 +   0.28)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:24:17 2006