Locus 324

Sequence ID	X_DroMel_CAF1
Location	1,024,109 – 1,024,240
Length	131
Max. P	0.780926

overview

Window 4

Location	1,024,109 – 1,024,212
Length	103
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	78.26
Mean single sequence MFE	-26.57
Consensus MFE	-14.87
Energy contribution	-15.98
Covariance contribution	1.11
Combinations/Pair	1.13
Mean z-score	-1.60
Structure conservation index	0.56
SVM decision value	-0.06
SVM RNA-class probability	0.500000
Prediction	OTHER

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 1024109 103 - 22224390
UCUGUGG----GUGCGGGCAUUUUAAUUCAAUGCCCAAGUAAAUCAGCUUAAAGUGCAUGAAUAGUCUUUUCAUGGACGAUUUCAUCAAUUAUUCAAAGC---UG---G-ACCA------
......(----((..(((((((.......))))))).......(((((((...((.((((((.......)))))).))(((...))).........))))---))---)-))).------ ( -30.30)
>DroSec_CAF1 9623 103 - 1
UCUGUGG----GUGCGGGCAUUUUAAUUCAAUGCCCGAGUAAAUCAGCUUAAAGUGCAUGAAUAGUCUUUUCAUGGACGAUUUCAUCAAUUAUUCAAAGC---UG---G-ACCA------
......(----((.((((((((.......))))))))......(((((((...((.((((((.......)))))).))(((...))).........))))---))---)-))).------ ( -32.00)
>DroSim_CAF1 9186 103 - 1
UCUGUGG----GUGCGGGCAUUUUAAUUCAAUGCCCGAGUAAAUCAGCUUAAAGUGCAUGAAUAGUCUUUUCAUGGACGAUUUCAUCAAUUAUUCAAAGC---UG---G-ACCA------
......(----((.((((((((.......))))))))......(((((((...((.((((((.......)))))).))(((...))).........))))---))---)-))).------ ( -32.00)
>DroYak_CAF1 9977 107 - 1
UCUGUGGGUGGGUGCGGGCAUUUUAAUUCAAUGCCCGAGUAAAUCAGCUUAAAGUGCAUGAAUAGUCUUUUCAUGGACGAUUUCAUCAAUUAUUCAAAGC---UG---G-ACCA------
..........(((.((((((((.......))))))))......(((((((...((.((((((.......)))))).))(((...))).........))))---))---)-))).------ ( -32.00)
>DroAna_CAF1 14853 105 - 1
UCCUUG-----------GCAUUUUAAUUCGUUGG-CAAGUAAAUCAGCUUAAAGUGCAUGAAUGGCCACUUCAUGGACGAUUUCAUCAAUUAUUCAAAGC---CCAUAGCCCCAGCUCCG
.....(-----------((..........(((((-........))))).....((.((((((.(....))))))).))....................))---)...(((....)))... ( -17.00)
>DroPer_CAF1 128900 88 - 1
AGUGUAC----GUGUG-----------------G-UGUGUGCAUCAGCUUAAAGUGCAUGACUGGCCAAUUCAUGGACGAUUUCAUCAAUUAUUCAAAGCCUUUC---G-ACGG------
......(----((.((-----------------(-((....)))))((((...((.(((((.(.....).))))).))(((...))).........)))).....---.-))).------ ( -16.10)
>consensus
UCUGUGG____GUGCGGGCAUUUUAAUUCAAUGCCCGAGUAAAUCAGCUUAAAGUGCAUGAAUAGUCUUUUCAUGGACGAUUUCAUCAAUUAUUCAAAGC___UG___G_ACCA______
..............((((((((.......)))))))).........((((...((.((((((.......)))))).))(((...))).........)))).................... (-14.87 = -15.98 +   1.11)

alignment

secondary structure

dotplot

Window 5

Location	1,024,136 – 1,024,240
Length	104
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	82.97
Mean single sequence MFE	-26.59
Consensus MFE	-19.64
Energy contribution	-20.41
Covariance contribution	0.77
Combinations/Pair	1.09
Mean z-score	-1.85
Structure conservation index	0.74
SVM decision value	0.56
SVM RNA-class probability	0.780926
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 1024136 104 + 22224390
UCGUCCAUGAAAAGACUAUUCAUGCACUUUAAGCUGAUUUACUUGGGCAUUGAAUUAAAAUGCCCGCAC----CCACAGAGUGCAUUGACUGCCAAAGCAACACGACU------------
..(((..............((((((((((((((........)))(((((((.......)))))))....----....)))))))).))).(((....)))....))).------------ ( -25.80)
>DroSec_CAF1 9650 104 + 1
UCGUCCAUGAAAAGACUAUUCAUGCACUUUAAGCUGAUUUACUCGGGCAUUGAAUUAAAAUGCCCGCAC----CCACAGAGUGCAUUGACUGCCAAAGCAACACGACU------------
..(((((((((.......))))))........(((.......(((((((((.......)))))))((((----.......))))...)).......))).....))).------------ ( -26.44)
>DroSim_CAF1 9213 104 + 1
UCGUCCAUGAAAAGACUAUUCAUGCACUUUAAGCUGAUUUACUCGGGCAUUGAAUUAAAAUGCCCGCAC----CCACAGAGUGCAUUGACUGCCAAAGCAACACGACU------------
..(((((((((.......))))))........(((.......(((((((((.......)))))))((((----.......))))...)).......))).....))).------------ ( -26.44)
>DroYak_CAF1 10004 112 + 1
UCGUCCAUGAAAAGACUAUUCAUGCACUUUAAGCUGAUUUACUCGGGCAUUGAAUUAAAAUGCCCGCACCCACCCACAGAGUGCAUUGACUGGCAAAGCAACACGACUCGAC--------
((((...((....(.(((.(((((((((((.............((((((((.......))))))))...........)))))))).))).))))....))..))))......-------- ( -27.65)
>DroAna_CAF1 14890 108 + 1
UCGUCCAUGAAGUGGCCAUUCAUGCACUUUAAGCUGAUUUACUUG-CCAACGAAUUAAAAUGC-----------CAAGGAGUGCAUUGACUGGCUAGGAUAUAUAUGUAGAGGAUGUAGU
.(((((......((((((.(((((((((((..((((((((.....-.....))))))....))-----------...)))))))).))).))))))...(((....)))..))))).... ( -26.60)
>consensus
UCGUCCAUGAAAAGACUAUUCAUGCACUUUAAGCUGAUUUACUCGGGCAUUGAAUUAAAAUGCCCGCAC____CCACAGAGUGCAUUGACUGCCAAAGCAACACGACU____________
..(((.(((((.......)))))(((((((.............((((((((.......))))))))...........)))))))...))).............................. (-19.64 = -20.41 +   0.77)

alignment

secondary structure

dotplot

Window 6

Location	1,024,136 – 1,024,240
Length	104
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	82.97
Mean single sequence MFE	-31.82
Consensus MFE	-20.93
Energy contribution	-21.18
Covariance contribution	0.25
Combinations/Pair	1.08
Mean z-score	-2.03
Structure conservation index	0.66
SVM decision value	0.54
SVM RNA-class probability	0.774266
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 1024136 104 - 22224390
------------AGUCGUGUUGCUUUGGCAGUCAAUGCACUCUGUGG----GUGCGGGCAUUUUAAUUCAAUGCCCAAGUAAAUCAGCUUAAAGUGCAUGAAUAGUCUUUUCAUGGACGA
------------..((((((.((((((((.......(((((.....)----))))(((((((.......)))))))..........)).))))))))))))...((((......)))).. ( -34.50)
>DroSec_CAF1 9650 104 - 1
------------AGUCGUGUUGCUUUGGCAGUCAAUGCACUCUGUGG----GUGCGGGCAUUUUAAUUCAAUGCCCGAGUAAAUCAGCUUAAAGUGCAUGAAUAGUCUUUUCAUGGACGA
------------..((((((.((((((((.......(((((.....)----))))(((((((.......)))))))..........)).))))))))))))...((((......)))).. ( -34.50)
>DroSim_CAF1 9213 104 - 1
------------AGUCGUGUUGCUUUGGCAGUCAAUGCACUCUGUGG----GUGCGGGCAUUUUAAUUCAAUGCCCGAGUAAAUCAGCUUAAAGUGCAUGAAUAGUCUUUUCAUGGACGA
------------..((((((.((((((((.......(((((.....)----))))(((((((.......)))))))..........)).))))))))))))...((((......)))).. ( -34.50)
>DroYak_CAF1 10004 112 - 1
--------GUCGAGUCGUGUUGCUUUGCCAGUCAAUGCACUCUGUGGGUGGGUGCGGGCAUUUUAAUUCAAUGCCCGAGUAAAUCAGCUUAAAGUGCAUGAAUAGUCUUUUCAUGGACGA
--------..........((((.((((((.......((((((.......))))))(((((((.......)))))))).))))).)))).....((.((((((.......)))))).)).. ( -35.80)
>DroAna_CAF1 14890 108 - 1
ACUACAUCCUCUACAUAUAUAUCCUAGCCAGUCAAUGCACUCCUUG-----------GCAUUUUAAUUCGUUGG-CAAGUAAAUCAGCUUAAAGUGCAUGAAUGGCCACUUCAUGGACGA
.....................(((..((((.(((.((((((.((((-----------.((...........)).-))))(((......))).))))))))).))))........)))... ( -19.80)
>consensus
____________AGUCGUGUUGCUUUGGCAGUCAAUGCACUCUGUGG____GUGCGGGCAUUUUAAUUCAAUGCCCGAGUAAAUCAGCUUAAAGUGCAUGAAUAGUCUUUUCAUGGACGA
..............................(((...(((((..............(((((((.......)))))))((((......))))..)))))(((((.......))))).))).. (-20.93 = -21.18 +   0.25)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:41:48 2006