Locus 5019

Sequence ID	2L_DroMel_CAF1
Location	14,403,453 – 14,403,678
Length	225
Max. P	0.965002

overview

Window 8

Location	14,403,453 – 14,403,562
Length	109
Sequences	5
Columns	109
Reading direction	reverse
Mean pairwise identity	93.76
Mean single sequence MFE	-34.80
Consensus MFE	-28.68
Energy contribution	-29.44
Covariance contribution	0.76
Combinations/Pair	1.09
Mean z-score	-1.86
Structure conservation index	0.82
SVM decision value	1.25
SVM RNA-class probability	0.936017
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 14403453 109 - 22407834
CUUUUCGUGUUGCAAGCUGGUCUCAAUUUACGGCGAGCACCGAAAGUGAAAGUGACUUUCGACCGAUUGCGAUAAAGAAACUAUGGCCCGUUCGUCACACGAAGCAACA
..((((((((.((.(((.((((....((((..((((....(((((((.......))))))).....))))..))))........)))).))).)).))))))))..... ( -30.00)
>DroSec_CAF1 24557 109 - 1
CUUUUCGUGUUGCAAGCUGGUCUCAAUUUACGGCGAGCAACGAAAGUGAAAGUGACUUUCGACCGAUUGCGAUAAAGAAACUGAGGCCCGGUCGUCACACGAAGCAACA
..((((((((.((.(.(.(((((((.((((..((((....(((((((.......))))))).....))))..)))).....))))))).).).)).))))))))..... ( -33.80)
>DroSim_CAF1 23456 109 - 1
CUUUUCGUGUGGCAAGCUGGUCUCAAUUUACGGCGAGCAACGAAAGUGAAAGUGACUUUCGACCGAUUGCGAUAAAGAAACUGUGGCCCGGUCGUCACACGAAGCAACA
..(((((((((((..(((.(((.........))).)))...((((((.......))))))(((((...((.(((.......))).)).))))))))))))))))..... ( -39.80)
>DroEre_CAF1 24658 109 - 1
CUUUUCGUGUUGCAAGCCGGUCUCAAUUCACGACGAGCACCGAAAGUGAAAGUGCCUUUCGACCGAUUGCGAUAAAGAAAUUAUGGCCCGGUCGGCACACGGAGCAACA
.......((((((...(((.......(((((..((.....))...))))).(((((....(((((...((.((((.....)))).)).)))))))))).))).)))))) ( -36.30)
>DroYak_CAF1 24635 109 - 1
CUUUUCGUGUUGCAAGCUGGUCUCAAUUUACGGCGAGCAACGAAAGUGAAAGUGACUUUCGACCGAUUGCGAUACAGAAAUUAUGGCCCGGUCGUCACACUGCGCAACA
.......((((((..((((...........))))..(((((....))....(((((....(((((...((.(((.(....)))).)).))))))))))..))))))))) ( -34.10)
>consensus
CUUUUCGUGUUGCAAGCUGGUCUCAAUUUACGGCGAGCAACGAAAGUGAAAGUGACUUUCGACCGAUUGCGAUAAAGAAACUAUGGCCCGGUCGUCACACGAAGCAACA
..((((((((.((..(((.(((.........))).)))...((((((.......))))))(((((...((.(((.......))).)).))))))).))))))))..... (-28.68 = -29.44 +   0.76)

alignment

secondary structure

dotplot

Window 9

Location	14,403,562 – 14,403,678
Length	116
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	96.02
Mean single sequence MFE	-31.65
Consensus MFE	-28.64
Energy contribution	-29.08
Covariance contribution	0.45
Combinations/Pair	1.08
Mean z-score	-1.71
Structure conservation index	0.90
SVM decision value	1.57
SVM RNA-class probability	0.965002
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 14403562 116 - 22407834
UUCUAUCGCGAUGUUAAUCAUUUUAAUUGGCGCCACUUGAACGAGUCGCACUC----UGUGUGAGUGUCUGAUUGGUGUCCAUUAAUUUUGUGGCAGUCAUUUGAAAGCGUUUCAAAUUA
......((((((....))).((((((.(((((((((..((((.((((((((((----.....))))))..)))).)).........))..))))).)))).))))))))).......... ( -32.40)
>DroSec_CAF1 24666 116 - 1
UUCUAUCGCGAUGUUAAUCAUUUUAAUUGGCGCCACUUGAACGAGUCGCACUC----UGUGUGAGUGUCUGAUUGGUGUCCAUUAAUUUUGUGGCAGUCAUUUGAAAGCGUUUCAAAUUA
......((((((....))).((((((.(((((((((..((((.((((((((((----.....))))))..)))).)).........))..))))).)))).))))))))).......... ( -32.40)
>DroSim_CAF1 23565 116 - 1
UUCUAUCGCGAUGUUAAUCAUUUUAAUUGGCGCCACUUGAACGAGUCGCACUC----UGUGUGAGUGUCUGAUUGGUGUCCAUUAAUUUUGUGGCAGUCAUUUGAAAGCGUUUCAAAUUA
......((((((....))).((((((.(((((((((..((((.((((((((((----.....))))))..)))).)).........))..))))).)))).))))))))).......... ( -32.40)
>DroEre_CAF1 24767 116 - 1
UUCUAUCACGAUGUUAAUCAUUUUAAUUGGCGCCACUUGAACGAGUCGCACUC----UGUGUGAGUGUCUGAUUGGUGUCCAUUAAUUUUGUGGCAGUCAUUUGAAAGCGUUUCAAAUUA
..((..((((((....)))...(((((.(((((((.((..(((..((((((..----.)))))).)))..)).))))))).)))))....)))..))..(((((((.....))))))).. ( -30.70)
>DroYak_CAF1 24744 116 - 1
UUCUAUCGCGAUGUUAAUCAUUUUAAUUGGCGCCACUUGAACGAGUCGCACUC----UGUGUGAGUGUCUGAUUGGUGUCCAUUAAUUUUGUGGCAGUCAUUUGAAAGCGUUUCAAAUUA
......((((((....))).((((((.(((((((((..((((.((((((((((----.....))))))..)))).)).........))..))))).)))).))))))))).......... ( -32.40)
>DroAna_CAF1 38041 120 - 1
UUCUAUCGCGAUGUUAAUCAUUUUAAUUGGCGCCACUUGAACGGGUUUCUGUCGGUGUGUGCGAGUGUCUGAUUGGUGUCCAUUCAUUUUGGGGCAGUCGUUUGAAAGCGUUUCAAAUUA
......((((((....))).((((((...((((((((.((.(((....))))))))).))))((.(((((.(..((((......)))).).))))).))..))))))))).......... ( -29.60)
>consensus
UUCUAUCGCGAUGUUAAUCAUUUUAAUUGGCGCCACUUGAACGAGUCGCACUC____UGUGUGAGUGUCUGAUUGGUGUCCAUUAAUUUUGUGGCAGUCAUUUGAAAGCGUUUCAAAUUA
..((..((((((....)))...(((((.(((((((.((..(((..((((((.......)))))).)))..)).))))))).)))))....)))..))..(((((((.....))))))).. (-28.64 = -29.08 +   0.45)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:33:39 2006