Locus 2447

Sequence ID	3L_DroMel_CAF1
Location	6,913,022 – 6,913,161
Length	139
Max. P	0.961146

overview

Window 2

Location	6,913,022 – 6,913,135
Length	113
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	92.83
Mean single sequence MFE	-23.17
Consensus MFE	-22.57
Energy contribution	-22.43
Covariance contribution	-0.14
Combinations/Pair	1.03
Mean z-score	-1.24
Structure conservation index	0.97
SVM decision value	1.52
SVM RNA-class probability	0.961146
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 6913022 113 + 23771897
UUUUGCUCACUGGCGCGUUGACAUCGCCAUCAAAAUGCUUUGACGUGGUUUUUGAUUGACAGGAAACUCAUAAAUAAUUCAUGUCAUUAAAUCAUGUUACAUUUUUU---CUUCUC----
..........(((((.........)))))..((((((...(((((((((((.....(((((.(((............))).)))))..)))))))))))))))))..---......---- ( -22.60)
>DroVir_CAF1 208050 113 + 1
UUUUGCUCGCUGGCGCGUUGACAUCGCCAUCAAAAUGCUUUGACGUGGUUUUUGAUUGACAGGAAACUCAUAAAUAAUUCAUGUCAUUAAAUCAUGUUACAUUUUUU---UUUCUC----
........(.(((((.........))))).)((((((...(((((((((((.....(((((.(((............))).)))))..)))))))))))))))))..---......---- ( -23.30)
>DroPse_CAF1 189863 120 + 1
UUUUGCUCAGUGGCGCGUUGACAUCGCCAUCAAAAUGCUUUGACGUGGUUUUUGAUUGACAGGAAACUCAUAAAUAAUUCAUGUCAUUAAAUCAUGUUACAUUUUUUUCUCUUCUCCUCU
.........((((((.........)))))).((((((...(((((((((((.....(((((.(((............))).)))))..)))))))))))))))))............... ( -23.70)
>DroGri_CAF1 180063 109 + 1
UUUUGUGCAGUGGCGCGUUGACAUCGCCAUCAAAAUGCUUUGACGUGGUUUUUGAUUGACAGGAAACUCAUAAAUAAUUCAUGUCAUUAAAUCAUGUUACAUUUUUU---UU--------
.........((((((.........)))))).((((((...(((((((((((.....(((((.(((............))).)))))..)))))))))))))))))..---..-------- ( -23.70)
>DroMoj_CAF1 192544 113 + 1
UUUUGCUCGCUGGCGCGUUGACAUUGCCAUCAAAAUGCUUUGACGUGGUUUUUGAUUGACAGGAAACUCAUAAAUAAUUCAUGUCAUUAAAUCAUGUUACAUUUUUU---UCUCUU----
........(.(((((.........))))).)((((((...(((((((((((.....(((((.(((............))).)))))..)))))))))))))))))..---......---- ( -22.00)
>DroPer_CAF1 187929 120 + 1
UUUUGCUCAGUGGCGCGUUGACAUCGCCAUCAAAAUGCUUUGACGUGGUUUUUGAUUGACAGGAAACUCAUAAAUAAUUCAUGUCAUUAAAUCAUGUUACAUUUUUUUCUCUUCUCCUCU
.........((((((.........)))))).((((((...(((((((((((.....(((((.(((............))).)))))..)))))))))))))))))............... ( -23.70)
>consensus
UUUUGCUCACUGGCGCGUUGACAUCGCCAUCAAAAUGCUUUGACGUGGUUUUUGAUUGACAGGAAACUCAUAAAUAAUUCAUGUCAUUAAAUCAUGUUACAUUUUUU___CUUCUC____
..........(((((.........)))))..((((((...(((((((((((.....(((((.(((............))).)))))..)))))))))))))))))............... (-22.57 = -22.43 +  -0.14)

alignment

secondary structure

dotplot

Window 3

Location	6,913,062 – 6,913,161
Length	99
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	78.79
Mean single sequence MFE	-17.27
Consensus MFE	-15.00
Energy contribution	-15.00
Covariance contribution	0.00
Combinations/Pair	1.00
Mean z-score	-1.20
Structure conservation index	0.87
SVM decision value	0.47
SVM RNA-class probability	0.750017
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 6913062 99 + 23771897
UGACGUGGUUUUUGAUUGACAGGAAACUCAUAAAUAAUUCAUGUCAUUAAAUCAUGUUACAUUUUUU---CUUCUC------UC--------UGGGACGAGCUCCUCAGCUUUC-GG---
(((((((((((.....(((((.(((............))).)))))..)))))))))))........---......------.(--------(((((.....))).))).....-..--- ( -19.50)
>DroVir_CAF1 208090 86 + 1
UGACGUGGUUUUUGAUUGACAGGAAACUCAUAAAUAAUUCAUGUCAUUAAAUCAUGUUACAUUUUUU---UUUCUC------C---------------------UUCAGCUUUC-UG---
(((((((((((.....(((((.(((............))).)))))..)))))))))))........---......------.---------------------..........-..--- ( -15.00)
>DroGri_CAF1 180103 83 + 1
UGACGUGGUUUUUGAUUGACAGGAAACUCAUAAAUAAUUCAUGUCAUUAAAUCAUGUUACAUUUUUU---UU----------AU--------------------GCCAGCUUUC-UG---
(((((((((((.....(((((.(((............))).)))))..)))))))))))........---..----------..--------------------..........-..--- ( -15.00)
>DroMoj_CAF1 192584 88 + 1
UGACGUGGUUUUUGAUUGACAGGAAACUCAUAAAUAAUUCAUGUCAUUAAAUCAUGUUACAUUUUUU---UCUCUU------CU--------------------UUCAGCUUUCCAG---
(((((((((((.....(((((.(((............))).)))))..)))))))))))........---......------..--------------------.............--- ( -15.00)
>DroAna_CAF1 189118 107 + 1
UGACGUGGUUUUUGAUUGACAGGAAACUCAUAAAUAAUUCAUGUCAUUAAAUCAUGUUACAUUUUUU---CUUCUC------CCAGCUCAGCUCGACCGAGGUCCUCUGCUUUC-GG---
(((((((((((.....(((((.(((............))).)))))..)))))))))))........---.....(------(.((..(((...(((....)))..)))..)).-))--- ( -20.10)
>DroPer_CAF1 187969 107 + 1
UGACGUGGUUUUUGAUUGACAGGAAACUCAUAAAUAAUUCAUGUCAUUAAAUCAUGUUACAUUUUUUUCUCUUCUCCUCUCAUC--------UGGG----GCUCCUCCUCUUCC-UUCCU
(((((((((((.....(((((.(((............))).)))))..)))))))))))................((((.....--------.)))----).............-..... ( -19.00)
>consensus
UGACGUGGUUUUUGAUUGACAGGAAACUCAUAAAUAAUUCAUGUCAUUAAAUCAUGUUACAUUUUUU___CUUCUC______CC____________________CUCAGCUUUC_UG___
(((((((((((.....(((((.(((............))).)))))..)))))))))))............................................................. (-15.00 = -15.00 +   0.00)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:32:30 2006