Locus 8588

Sequence ID	3L_DroMel_CAF1
Location	22,372,560 – 22,372,703
Length	143
Max. P	0.959021

overview

Window 9

Location	22,372,560 – 22,372,677
Length	117
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	83.74
Mean single sequence MFE	-41.86
Consensus MFE	-30.52
Energy contribution	-31.88
Covariance contribution	1.36
Combinations/Pair	1.12
Mean z-score	-1.88
Structure conservation index	0.73
SVM decision value	0.52
SVM RNA-class probability	0.768700
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 22372560 117 - 23771897
AGCACAAUCUUGCAC--UUUUCGCCGAAGGUGAAUGGGCAAGACAAUCAUGGCCGAGUGCCUCUGGCGGCAUUUGGGCUUGCAAACACUCCAGUGGAAUUCCUCUGCA-UGUGCUAAGAG
((((((.((((((.(--(.((((((...)))))).))))))))....((.(.(((((((((......))))))))).).)).........(((.((....)).)))..-))))))..... ( -45.00)
>DroSec_CAF1 23700 117 - 1
GGCACAAUCUUGCAC--UUUUCGCCGAAGGUGAAUGGGCAAGACAAUCAUGGCCGAGUGCCUCUGGCGGCAUUUGGGCUUGCAAAUUCUCCAGUGGGAUUCCUCUGCA-UGUGCUAAGAG
((((((.((((((.(--(.((((((...)))))).)))))))).......(.(((((((((......))))))))).).((((.....(((....)))......))))-))))))..... ( -44.60)
>DroSim_CAF1 38132 117 - 1
GGCACAAUCUUGCAC--UUUUCGCCGAAGGUGAAUGGGCAAGACAAUCAUGGCCGAGUGCCUCUGGCGGCAUUUGGGCUUGCAAAUUCCCCAGUGGGAUUCCUCUGCA-UGUGCUAAGAG
((((((.((((((.(--(.((((((...)))))).)))))))).......(.(((((((((......))))))))).).((((...((((....))))......))))-))))))..... ( -47.20)
>DroEre_CAF1 40531 116 - 1
GGCACAAUCUUGCAAUCACUGCGCCGAAGGUGAAUGGGCAAGACCAUCAUGGCCGAGUGUCUCUGG---CAUCUGGGCUUUCAAGCAC-CCAGUGGGAUUCCCCUGCACUGGGCUAUGUG
((.....((((((..(((((........)))))....))))))))..(((((((.(((((......---...(((((..........)-)))).(((....))).))))).))))))).. ( -41.40)
>DroYak_CAF1 32100 109 - 1
GGCACAGUCUUGCAC--A-UUUUCCAAAGGUGAACGGGCAAGAAAAUCAUGGCCGAGUGUCUUUGG---CAUCUGGGC----AAAUAC-CCAGUGGGAUUUCAUUGAAGUGUACUAUUUG
.(((......)))((--(-((((((((((..(..(((.((.(.....).)).)))..)..))))))---((.(((((.----.....)-))))))..........)))))))........ ( -31.10)
>consensus
GGCACAAUCUUGCAC__UUUUCGCCGAAGGUGAAUGGGCAAGACAAUCAUGGCCGAGUGCCUCUGGCGGCAUUUGGGCUUGCAAAUAC_CCAGUGGGAUUCCUCUGCA_UGUGCUAAGAG
((((((.((((((......((((((...))))))...)))))).......(.(((((((((......))))))))).)............(((.((....)).)))...))))))..... (-30.52 = -31.88 +   1.36)

alignment

secondary structure

dotplot

Window 0

Location	22,372,599 – 22,372,703
Length	104
Sequences	5
Columns	109
Reading direction	reverse
Mean pairwise identity	81.61
Mean single sequence MFE	-40.74
Consensus MFE	-28.54
Energy contribution	-30.06
Covariance contribution	1.52
Combinations/Pair	1.07
Mean z-score	-2.38
Structure conservation index	0.70
SVM decision value	1.50
SVM RNA-class probability	0.959021
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 22372599 104 - 23771897
GUACAGCCACUAGCUCC---ACUCCUCGGAGCACAAUCUUGCAC--UUUUCGCCGAAGGUGAAUGGGCAAGACAAUCAUGGCCGAGUGCCUCUGGCGGCAUUUGGGCUU
....((((.((((((((---.......)))))....((((((.(--(.((((((...)))))).))))))))......))).((((((((......)))))))))))). ( -41.50)
>DroSec_CAF1 23739 107 - 1
GUACAGCCACUGGCCCCCCGACUCAUCGGGGCACAAUCUUGCAC--UUUUCGCCGAAGGUGAAUGGGCAAGACAAUCAUGGCCGAGUGCCUCUGGCGGCAUUUGGGCUU
....((((...((((((((((....)))))).....((((((.(--(.((((((...)))))).)))))))).......))))(((((((......))))))).)))). ( -48.10)
>DroSim_CAF1 38171 107 - 1
GUACAGCCACUGGCCCCCCGACUCCUCGGGGCACAAUCUUGCAC--UUUUCGCCGAAGGUGAAUGGGCAAGACAAUCAUGGCCGAGUGCCUCUGGCGGCAUUUGGGCUU
....((((...((((((((((....)))))).....((((((.(--(.((((((...)))))).)))))))).......))))(((((((......))))))).)))). ( -48.20)
>DroEre_CAF1 40570 92 - 1
GUG-----------CCC---ACUCCUCGGGGCACAAUCUUGCAAUCACUGCGCCGAAGGUGAAUGGGCAAGACCAUCAUGGCCGAGUGUCUCUGG---CAUCUGGGCUU
(((-----------(((---........))))))..((((((..(((((........)))))....)))))).......((((.(((((.....)---)).)).)))). ( -35.20)
>DroYak_CAF1 32137 98 - 1
AUACAGUCACUCGCCCC---ACUCUUUGGGGCACAGUCUUGCAC--A-UUUUCCAAAGGUGAACGGGCAAGAAAAUCAUGGCCGAGUGUCUUUGG---CAUCUGGGC--
.....(((....(((((---(.....)))))).(((...(((..--.-.....(((((..(..(((.((.(.....).)).)))..)..))))))---)).))))))-- ( -30.70)
>consensus
GUACAGCCACUGGCCCC___ACUCCUCGGGGCACAAUCUUGCAC__UUUUCGCCGAAGGUGAAUGGGCAAGACAAUCAUGGCCGAGUGCCUCUGGCGGCAUUUGGGCUU
............(((((..........)))))....((((((......((((((...))))))...)))))).......(.(((((((((......))))))))).).. (-28.54 = -30.06 +   1.52)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:19:42 2006