Locus 3368

Sequence ID	3L_DroMel_CAF1
Location	9,841,831 – 9,841,973
Length	142
Max. P	0.967441

overview

Window 2

Location	9,841,831 – 9,841,936
Length	105
Sequences	5
Columns	106
Reading direction	reverse
Mean pairwise identity	89.29
Mean single sequence MFE	-20.68
Consensus MFE	-18.08
Energy contribution	-18.12
Covariance contribution	0.04
Combinations/Pair	1.06
Mean z-score	-1.68
Structure conservation index	0.87
SVM decision value	1.18
SVM RNA-class probability	0.927348
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 9841831 105 - 23771897
CUCUGGAGGCCGCUUGGAUAAUCUUGCACCAAGUGCUCUCCUCCCUCCUCCU-UUUCGCAUUCAGAUUUUCGAUGCCUCACUGAAUCUCACAGUUCGUUCACAUUA
....((((..(((((((...........)))))))..))))...........-....(((((.........)))))...((((.......))))............ ( -20.50)
>DroSec_CAF1 2793 105 - 1
CUCUGGAGGCCGCUUGGAUAAUCUUACACCAAGUGCUCUCCUCCCUCCUCCU-UUUCGCAUUCAGAUUUUAGAUGCCUCACUGAAUCUCACAGUUUGUUCACAUUA
....((((..(((((((...........)))))))..))))...........-....(((((.........)))))...((((.......))))............ ( -20.60)
>DroSim_CAF1 2676 105 - 1
CUCUGGAGGCCGCUUGGAUAAUCUUACACCAAGUGCUCUCCUCCCUCCUCCU-UUUCGCAUUCAGAUUUUAGAUGCCUCACUGAAUCUCACAGUUUGUUCACAUUA
....((((..(((((((...........)))))))..))))...........-....(((((.........)))))...((((.......))))............ ( -20.60)
>DroEre_CAF1 2826 97 - 1
CUCUGAAGGCCGCUUGGUUAAUCUGGCACCAAGUGCUCUCCUC----CUCCU-UUUCGCAUUUAGAUUUUAGAUUCCUUACUGAAUCUCACAGU----UCACAUUA
.((((((.((((((((((.........))))))))........----.....-....)).))))))....((((((......))))))......----........ ( -17.02)
>DroYak_CAF1 2913 98 - 1
CUCUGGAGGCCGCUUGGUUAAUCUGGCACCAAGUGCUCUCCUC----CUCCGCAUUCGCAUUCAGUUUUUAGAUUCCUUGCUGAAUCUCACAGU----UCACAUUA
....((((..((((((((.........))))))))..))))..----....((....))(((((((....((....)).)))))))........----........ ( -24.70)
>consensus
CUCUGGAGGCCGCUUGGAUAAUCUUGCACCAAGUGCUCUCCUCCCUCCUCCU_UUUCGCAUUCAGAUUUUAGAUGCCUCACUGAAUCUCACAGUU_GUUCACAUUA
....((((..(((((((...........)))))))..))))................(.((((((...............)))))))................... (-18.08 = -18.12 +   0.04)

alignment

secondary structure

dotplot

Window 3

Location	9,841,857 – 9,841,973
Length	116
Sequences	5
Columns	117
Reading direction	reverse
Mean pairwise identity	88.24
Mean single sequence MFE	-32.08
Consensus MFE	-26.36
Energy contribution	-26.56
Covariance contribution	0.20
Combinations/Pair	1.08
Mean z-score	-2.13
Structure conservation index	0.82
SVM decision value	1.61
SVM RNA-class probability	0.967441
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 9841857 116 - 23771897
CACAUGGAUAGUAUUUGAUCUACGAAGAUGGGAGUUUCUCUGGAGGCCGCUUGGAUAAUCUUGCACCAAGUGCUCUCCUCCCUCCUCCU-UUUCGCAUUCAGAUUUUCGAUGCCUCA
..(((.((....((((((....((((((.(((((.......((((..(((((((...........)))))))..))))...)))).).)-)))))...))))))..)).)))..... ( -34.40)
>DroSec_CAF1 2819 112 - 1
CACAUG----GUAUUUGAUCUACGAAGAUGGGAGUUUCUCUGGAGGCCGCUUGGAUAAUCUUACACCAAGUGCUCUCCUCCCUCCUCCU-UUUCGCAUUCAGAUUUUAGAUGCCUCA
.....(----(((((((((((.((((((.(((((.......((((..(((((((...........)))))))..))))...)))).).)-))))).....)))))..)))))))... ( -34.50)
>DroSim_CAF1 2702 112 - 1
CACAUG----GUAUUUGAUCUACGAAGAUGGGAGUUUCUCUGGAGGCCGCUUGGAUAAUCUUACACCAAGUGCUCUCCUCCCUCCUCCU-UUUCGCAUUCAGAUUUUAGAUGCCUCA
.....(----(((((((((((.((((((.(((((.......((((..(((((((...........)))))))..))))...)))).).)-))))).....)))))..)))))))... ( -34.50)
>DroEre_CAF1 2848 112 - 1
CACAUGGAUAGUUUUUGAGCUACGAAGAAUGGAGUUUCUCUGAAGGCCGCUUGGUUAAUCUGGCACCAAGUGCUCUCCUC----CUCCU-UUUCGCAUUUAGAUUUUAGAUUCCUUA
.....((((((..((((((...((((((..((((.......((..((.(((((((.........)))))))))..)))))----)...)-)))))..))))))..)))...)))... ( -25.31)
>DroYak_CAF1 2935 112 - 1
CAC-UGGAUAGUAUUUGAGCUACGAAGAAUGGAGUUUCUCUGGAGGCCGCUUGGUUAAUCUGGCACCAAGUGCUCUCCUC----CUCCGCAUUCGCAUUCAGUUUUUAGAUUCCUUG
.((-((((((((......))).((((...(((((.......((((..((((((((.........))))))))..))))..----)))))..)))).))))))).............. ( -31.70)
>consensus
CACAUGGAUAGUAUUUGAUCUACGAAGAUGGGAGUUUCUCUGGAGGCCGCUUGGAUAAUCUUGCACCAAGUGCUCUCCUCCCUCCUCCU_UUUCGCAUUCAGAUUUUAGAUGCCUCA
.............(((((....((((...(((((.......((((..(((((((...........)))))))..))))......)))))..))))...))))).............. (-26.36 = -26.56 +   0.20)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:56:23 2006