Locus 4762

Sequence ID	2L_DroMel_CAF1
Location	13,577,628 – 13,577,745
Length	117
Max. P	0.877978

overview

Window 6

Location	13,577,628 – 13,577,745
Length	117
Sequences	4
Columns	119
Reading direction	forward
Mean pairwise identity	92.87
Mean single sequence MFE	-27.18
Consensus MFE	-21.02
Energy contribution	-20.64
Covariance contribution	-0.38
Combinations/Pair	1.06
Mean z-score	-1.86
Structure conservation index	0.77
SVM decision value	0.14
SVM RNA-class probability	0.602416
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 13577628 117 + 22407834
UUUUUUUUCUGCAUUUUUUGCCUUUGCCUUUAGGCCGCCAUAUGUGGGCUGU--AUGGAUAAACGAGCAAUUACGAUUAAUUGCAUUUGAUAAAAUGCCAUUAAAAAAUGUAAAACAGA
.........(((((((((((((((((((..(((.((((.....)))).))).--..)).)))).).))))......(((((.((((((....)))))).)))))))))))))....... ( -28.30)
>DroSec_CAF1 10796 114 + 1
UUU--UUUCUGCAUUUUUUGCCUUUGCCUUUGGGCCGCCAUAUGUGGGCUGU--AUGGAUAAACGAGCAAUUACGAUUAAUUGCGUUUGAUAAAAUGCCAUUAA-AAAUGUAAAACAGA
...--..((((......(((((((((((..(((.((((.....)))).))).--..)).)))).).))))(((((.(((((.((((((....)))))).)))))-...)))))..)))) ( -25.80)
>DroEre_CAF1 11168 111 + 1
UU--UUUUCUGUAUUUUU-GC---UGCCUUUAGGCCGCCAUAUGUGGGCUGU--AUGGAUAAACGAGCAAUUACGAUUAAUUGCAUUUGAUAAAAUGCCAUUAAAAAAUGUAAAACAGA
..--...(((((....((-((---((((....)))..((((((.......))--)))).......)))))(((((.(((((.((((((....)))))).)))))....))))).))))) ( -27.10)
>DroYak_CAF1 7905 114 + 1
UUU-UUUUCUGUAUUUUU-GC---UGCCUUUAGGCCGCCAUAUGUGGACUGUAUAUGGAUAAACGGGCAAUUACGAUUAAUUGCAUUUGAUAAAAUGCCAUUAAAAAAUGUAAAACAGA
...-...(((((....((-((---((((....)))..(((((((.......))))))).......)))))(((((.(((((.((((((....)))))).)))))....))))).))))) ( -27.50)
>consensus
UUU_UUUUCUGCAUUUUU_GC___UGCCUUUAGGCCGCCAUAUGUGGGCUGU__AUGGAUAAACGAGCAAUUACGAUUAAUUGCAUUUGAUAAAAUGCCAUUAAAAAAUGUAAAACAGA
.......((((........((.....((..(((.((((.....)))).))).....))........))..(((((.(((((.((((((....)))))).)))))....)))))..)))) (-21.02 = -20.64 +  -0.38)

alignment

secondary structure

dotplot

Window 7

Location	13,577,628 – 13,577,745
Length	117
Sequences	4
Columns	119
Reading direction	reverse
Mean pairwise identity	92.87
Mean single sequence MFE	-23.20
Consensus MFE	-19.66
Energy contribution	-19.23
Covariance contribution	-0.44
Combinations/Pair	1.08
Mean z-score	-2.01
Structure conservation index	0.85
SVM decision value	0.90
SVM RNA-class probability	0.877978
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 13577628 117 - 22407834
UCUGUUUUACAUUUUUUAAUGGCAUUUUAUCAAAUGCAAUUAAUCGUAAUUGCUCGUUUAUCCAU--ACAGCCCACAUAUGGCGGCCUAAAGGCAAAGGCAAAAAAUGCAGAAAAAAAA
(((((.((((.....(((((.((((((....)))))).)))))..))))(((((...........--...(((.......))).(((....)))...))))).....)))))....... ( -24.00)
>DroSec_CAF1 10796 114 - 1
UCUGUUUUACAUUU-UUAAUGGCAUUUUAUCAAACGCAAUUAAUCGUAAUUGCUCGUUUAUCCAU--ACAGCCCACAUAUGGCGGCCCAAAGGCAAAGGCAAAAAAUGCAGAAA--AAA
...........(((-((....(((((((.......(((((((....)))))))..((((......--...(((.......))).(((....)))..))))..)))))))..)))--)). ( -22.60)
>DroEre_CAF1 11168 111 - 1
UCUGUUUUACAUUUUUUAAUGGCAUUUUAUCAAAUGCAAUUAAUCGUAAUUGCUCGUUUAUCCAU--ACAGCCCACAUAUGGCGGCCUAAAGGCA---GC-AAAAAUACAGAAAA--AA
(((((.((((.....(((((.((((((....)))))).)))))..))))(((((...........--...(((.......))).(((....))))---))-))....)))))...--.. ( -23.70)
>DroYak_CAF1 7905 114 - 1
UCUGUUUUACAUUUUUUAAUGGCAUUUUAUCAAAUGCAAUUAAUCGUAAUUGCCCGUUUAUCCAUAUACAGUCCACAUAUGGCGGCCUAAAGGCA---GC-AAAAAUACAGAAAA-AAA
(((((.((((.....(((((.((((((....)))))).)))))..))))((((........((((((.........))))))..(((....))).---))-))....)))))...-... ( -22.50)
>consensus
UCUGUUUUACAUUUUUUAAUGGCAUUUUAUCAAAUGCAAUUAAUCGUAAUUGCUCGUUUAUCCAU__ACAGCCCACAUAUGGCGGCCUAAAGGCA___GC_AAAAAUACAGAAAA_AAA
(((((.((.((((....))))((............(((((((....))))))).................(((.......))).(((....)))....))....)).)))))....... (-19.66 = -19.23 +  -0.44)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:26:41 2006