Locus 9368

Sequence ID	3R_DroMel_CAF1
Location	24,896,400 – 24,896,544
Length	144
Max. P	0.939879

overview

Window 3

Location	24,896,400 – 24,896,510
Length	110
Sequences	5
Columns	119
Reading direction	reverse
Mean pairwise identity	91.53
Mean single sequence MFE	-33.48
Consensus MFE	-27.50
Energy contribution	-27.70
Covariance contribution	0.20
Combinations/Pair	1.00
Mean z-score	-1.29
Structure conservation index	0.82
SVM decision value	-0.05
SVM RNA-class probability	0.509545
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 24896400 110 - 27905053
CCGGGGGAUUCCCCGCUCCGCCCGUGGA-UCGACCAAUGUGAAUGCGAAUGUCAAGUGGCAUUGUACCAUGCUCAAAU--------GCACAAAUGCAAAAUGCAGAGUGCACACAUGAG
.(((((....))))).((((....))))-.......(((((......((((((....))))))((((..(((.....(--------(((....))))....)))..)))).)))))... ( -33.10)
>DroSec_CAF1 9381 110 - 1
CCGGGGGUUUCCCCGCUCCGCCCGUGGA-UCGGCCAAUGUGAAUGCGAAUGUCAAGUGGCAUUGUACCAUGCUCAAAU--------GCACAAAUGCAAAAUGCAGAGUGCACACAUGAG
.(((((....)))))(((.(.(((....-.))).).(((((......((((((....))))))((((..(((.....(--------(((....))))....)))..)))).)))))))) ( -34.00)
>DroSim_CAF1 8854 110 - 1
CCGGGGGAUUCCCCGCUCCGCCCGUGGA-UCGGCCAAUGUGAAUGCGAAUGUCAAGUGGCAUUGUACCAUGCUCAAAU--------GCACAAAUGCAAAAUGCAGAGUGCACACAUGAG
.(((((....)))))(((.(.(((....-.))).).(((((......((((((....))))))((((..(((.....(--------(((....))))....)))..)))).)))))))) ( -34.00)
>DroEre_CAF1 9445 107 - 1
CCAGGGGAUUCCCCGCUC---CCAUGGA-UUGGCCAAUGUGAAUGCGAAUGUCAAGUAGCAUUGUACAAUGCACAAAU--------GCACAAAUGCAAAAUGCAGAGUGCACACAUGAA
(((.((((........))---)).))).-.......((((((((((............)))))((((..((((....(--------(((....))))...))))..)))).)))))... ( -29.90)
>DroYak_CAF1 9586 116 - 1
CCAGGGGAUUCCCCGCUC---CCGUGGAAUCGGCCAAUGUGAAUGCGAAUGUCAAGUGGCAUUGUACAAUGCACAAAUGCACAAAUGCACAAAUGCAAAAUGCAGAGUGCACACAUGAG
(((.((((........))---)).))).........(((((..(((.((((((....)))))))))...(((((...((((....((((....))))...))))..))))))))))... ( -36.40)
>consensus
CCGGGGGAUUCCCCGCUCCGCCCGUGGA_UCGGCCAAUGUGAAUGCGAAUGUCAAGUGGCAUUGUACCAUGCUCAAAU________GCACAAAUGCAAAAUGCAGAGUGCACACAUGAG
...((((...))))..........(((......)))(((((..(((.((((((....)))))))))....................((((...(((.....)))..)))).)))))... (-27.50 = -27.70 +   0.20)

alignment

secondary structure

dotplot

Window 4

Location	24,896,433 – 24,896,544
Length	111
Sequences	5
Columns	113
Reading direction	forward
Mean pairwise identity	93.90
Mean single sequence MFE	-35.54
Consensus MFE	-30.24
Energy contribution	-30.56
Covariance contribution	0.32
Combinations/Pair	1.14
Mean z-score	-1.71
Structure conservation index	0.85
SVM decision value	1.28
SVM RNA-class probability	0.939879
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 24896433 111 + 27905053
-AUUUGAGCAUGGUACAAUGCCACUUGACAUUCGCAUUCACAUUGGUCGA-UCCACGGGCGGAGCGGGGAAUCCCCCGGUUGUUAAUGGGUUAAUGGUCUUUGAAUGUUCAAC
-..((((((((....(((.((((.(((((..(((.(((......))))))-.(((..(((((..(((((....))))).)))))..))))))))))))..))).)))))))). ( -33.90)
>DroSec_CAF1 9414 111 + 1
-AUUUGAGCAUGGUACAAUGCCACUUGACAUUCGCAUUCACAUUGGCCGA-UCCACGGGCGGAGCGGGGAAACCCCCGGUUGUUAAUGGGUUAAUGGUCUUUGAAUGUUCAAC
-...((.((((......)))))).((((((((((......((((((((.(-(..((((.(((...(((....)))))).))))..)).)))))))).....)))))).)))). ( -38.70)
>DroSim_CAF1 8887 111 + 1
-AUUUGAGCAUGGUACAAUGCCACUUGACAUUCGCAUUCACAUUGGCCGA-UCCACGGGCGGAGCGGGGAAUCCCCCGGCUGUUAAUGGGUUAAUGGUCUUUGAAUGUUCAAC
-..(((((((((((.....)))..................((..((((((-((((..(((((..(((((....))))).)))))..))))))...))))..)).)))))))). ( -39.40)
>DroEre_CAF1 9478 108 + 1
-AUUUGUGCAUUGUACAAUGCUACUUGACAUUCGCAUUCACAUUGGCCAA-UCCAUGG---GAGCGGGGAAUCCCCUGGUUGUUAAUGGGUUAAUGGUCUUUGAAUGUUCAAC
-....(((((((....))))).))((((.....(((((((....((((((-(((((..---((.(((((....))))).))....))))))...)))))..))))))))))). ( -33.00)
>DroYak_CAF1 9626 110 + 1
CAUUUGUGCAUUGUACAAUGCCACUUGACAUUCGCAUUCACAUUGGCCGAUUCCACGG---GAGCGGGGAAUCCCCUGGUUGUUAAUGGGUUAAUGGUCUUUGAAUGUUCAAC
....((.(((((....))))))).((((((((((......((((((((.((((((.((---((........)))).))).....))).)))))))).....)))))).)))). ( -32.70)
>consensus
_AUUUGAGCAUGGUACAAUGCCACUUGACAUUCGCAUUCACAUUGGCCGA_UCCACGGGCGGAGCGGGGAAUCCCCCGGUUGUUAAUGGGUUAAUGGUCUUUGAAUGUUCAAC
....((.((((......)))))).((((.....(((((((....(((((..((((..(((((..(((((....))))).)))))..))))....)))))..))))))))))). (-30.24 = -30.56 +   0.32)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:32:51 2006