Locus 9334

Sequence ID	3R_DroMel_CAF1
Location	24,800,368 – 24,800,484
Length	116
Max. P	0.893961

overview

Window 5

Location	24,800,368 – 24,800,462
Length	94
Sequences	6
Columns	107
Reading direction	forward
Mean pairwise identity	80.34
Mean single sequence MFE	-22.75
Consensus MFE	-14.62
Energy contribution	-15.12
Covariance contribution	0.50
Combinations/Pair	1.00
Mean z-score	-1.57
Structure conservation index	0.64
SVM decision value	0.21
SVM RNA-class probability	0.636616
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 24800368 94 + 27905053
CUCCUU-------GGCAUCC--UUGAGAAACGGCGUUAUCGAGUUGAUUGAUAUUUUUAAAUUAUGUGCCGCAGUCGGCAUAAAUUUUAAA----UUUUUCGGCUAC
.....(-------(((....--.(((((((......((((((.....))))))..((((((...(((((((....)))))))...))))))----))))))))))). ( -19.70)
>DroVir_CAF1 44431 87 + 1
GUCC-U----------GUCCUGUCCACAAGCUUCGUUAUCGAGUUGAUUGAUAUUUUUAAAUUAUGUACCGCAGUCGGCAUAAAUUUAAA------UUUGCGGC---
...(-(----------((..((((....((((.((....))))))....))))..((((((((.(((.(((....))).)))))))))))------...)))).--- ( -13.30)
>DroGri_CAF1 44895 89 + 1
GUCC---------GUCGCCUUGCACACAAUCUGCGUUAUCGAGUUGAUUGAUAUUUUUAAAUUAUGUGCCGCAGUCGGCAUAAAUUUAAA------UUUUCGGC---
....---------...(((.......(((((.((........)).))))).....((((((((.(((((((....)))))))))))))))------.....)))--- ( -22.80)
>DroMoj_CAF1 43510 90 + 1
GUCC-U-------GCCGUCCUACACACAAUCUGCGUUAUCGAGUUGAUUGAUAUUUUUAAAUUAUGUGCCGCAGUCGGCAUAAAUUUAAA------UUUUCCGC---
....-.-------.............(((((.((........)).))))).....((((((((.(((((((....)))))))))))))))------........--- ( -18.90)
>DroAna_CAF1 10007 100 + 1
CUGCCUGGUAGCUGGUGGCU--GCCACAAUCUGCGUUAUCGAGUUGAUUGAUAUUUUUAAAUUAUGUGCCGCAGUCGGCAUAAAUUUAAAA-----UUUUCGGCUAC
..((((((((((.....)))--))))(((((.((........)).)))))....(((((((((.(((((((....))))))))))))))))-----.....)))... ( -34.90)
>DroPer_CAF1 11818 97 + 1
CUGC-U-------GGCUGCU--GCCACAUUCUGCGUUAUCGAGUUGAUUGAUAUUUUUAAAUUAUGUGCCGCAGUCGGCAUAAAUUUAAAAUUUUCCUUUCGGCUAC
.((.-(-------(((....--)))))).............((((((..((...(((((((((.(((((((....))))))))))))))))...))...)))))).. ( -26.90)
>consensus
CUCC_U_______GGCGUCC__CCCACAAUCUGCGUUAUCGAGUUGAUUGAUAUUUUUAAAUUAUGUGCCGCAGUCGGCAUAAAUUUAAA______UUUUCGGC___
................................((..((((((.....))))))..((((((((.(((((((....)))))))))))))))............))... (-14.62 = -15.12 +   0.50)

alignment

secondary structure

dotplot

Window 6

Location	24,800,386 – 24,800,484
Length	98
Sequences	6
Columns	116
Reading direction	forward
Mean pairwise identity	79.18
Mean single sequence MFE	-22.95
Consensus MFE	-16.35
Energy contribution	-16.72
Covariance contribution	0.36
Combinations/Pair	1.04
Mean z-score	-1.81
Structure conservation index	0.71
SVM decision value	0.98
SVM RNA-class probability	0.893961
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 24800386 98 + 27905053
AAACGGCGUUAUCGAGUUGAUUGAUAUUUUUAAAUUAUGUGCCGCAGUCGGCAUAAAUUUUAAAUUUUUCGGCUACCGC----UUC-AA-------------GAUGCUGAUGCUCU
....(((((((.((..((((..((.(..((((((...(((((((....)))))))...))))))..).))(((....))----)))-))-------------..)).))))))).. ( -23.70)
>DroVir_CAF1 44447 83 + 1
AAGCUUCGUUAUCGAGUUGAUUGAUAUUUUUAAAUUAUGUACCGCAGUCGGCAUAAAUUUAAA--UUUGCGGC-------------------------------UGCUGAUGCCGU
..((.((..((((((.....)))))).................(((((((.((..........--..))))))-------------------------------))).)).))... ( -17.70)
>DroGri_CAF1 44913 83 + 1
AAUCUGCGUUAUCGAGUUGAUUGAUAUUUUUAAAUUAUGUGCCGCAGUCGGCAUAAAUUUAAA--UUUUCGGC-------------------------------UGUUGAUGCUGU
.....((((((.(.((((((........((((((((.(((((((....)))))))))))))))--...)))))-------------------------------)).))))))... ( -23.30)
>DroWil_CAF1 10081 111 + 1
AAUCUGCGUUAUCGAAUUGAUUGAUAUUUUUAAAUUAUGUGCCGCAGUUGGCAUAAAUUUAAAA-UUUUAGGCUGCCUU----CUCUGAUGAUGGUGAUGUUGAGGCUGAUGCUCU
..((.(((((((((.............(((((((((.(((((((....))))))))))))))))-..(((((.......----.)))))...))))))))).))(((....))).. ( -24.80)
>DroMoj_CAF1 43529 83 + 1
AAUCUGCGUUAUCGAGUUGAUUGAUAUUUUUAAAUUAUGUGCCGCAGUCGGCAUAAAUUUAAA--UUUUCCGC-------------------------------UGCUGAUGCUGU
.....(((.((((((.....))))))..((((((((.(((((((....)))))))))))))))--.....)))-------------------------------.((....))... ( -20.40)
>DroAna_CAF1 10032 101 + 1
AAUCUGCGUUAUCGAGUUGAUUGAUAUUUUUAAAUUAUGUGCCGCAGUCGGCAUAAAUUUAAAA-UUUUCGGCUACCGCCGCUUCC-AA-------------GAUGUUGAUGCUCU
.....((((((.((..(((...((...(((((((((.(((((((....))))))))))))))))-...))(((....))).....)-))-------------..)).))))))... ( -27.80)
>consensus
AAUCUGCGUUAUCGAGUUGAUUGAUAUUUUUAAAUUAUGUGCCGCAGUCGGCAUAAAUUUAAA__UUUUCGGC_______________________________UGCUGAUGCUCU
.....((((((((((.....)))))...((((((((.(((((((....))))))))))))))).............................................)))))... (-16.35 = -16.72 +   0.36)

alignment

secondary structure

dotplot

Window 7

Location	24,800,386 – 24,800,484
Length	98
Sequences	6
Columns	116
Reading direction	reverse
Mean pairwise identity	79.18
Mean single sequence MFE	-17.90
Consensus MFE	-11.60
Energy contribution	-11.97
Covariance contribution	0.36
Combinations/Pair	1.05
Mean z-score	-1.95
Structure conservation index	0.65
SVM decision value	0.91
SVM RNA-class probability	0.880480
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 24800386 98 - 27905053
AGAGCAUCAGCAUC-------------UU-GAA----GCGGUAGCCGAAAAAUUUAAAAUUUAUGCCGACUGCGGCACAUAAUUUAAAAAUAUCAAUCAACUCGAUAACGCCGUUU
(((((....)).))-------------).-.((----(((((..........((((((.....(((((....))))).....))))))..((((.........))))..))))))) ( -18.70)
>DroVir_CAF1 44447 83 - 1
ACGGCAUCAGCA-------------------------------GCCGCAAA--UUUAAAUUUAUGCCGACUGCGGUACAUAAUUUAAAAAUAUCAAUCAACUCGAUAACGAAGCUU
..(((.......-------------------------------)))((...--((((((((..(((((....)))))...)))))))).............(((....))).)).. ( -16.60)
>DroGri_CAF1 44913 83 - 1
ACAGCAUCAACA-------------------------------GCCGAAAA--UUUAAAUUUAUGCCGACUGCGGCACAUAAUUUAAAAAUAUCAAUCAACUCGAUAACGCAGAUU
...((.......-------------------------------........--((((((((..(((((....)))))...))))))))..((((.........))))..))..... ( -14.60)
>DroWil_CAF1 10081 111 - 1
AGAGCAUCAGCCUCAACAUCACCAUCAUCAGAG----AAGGCAGCCUAAAA-UUUUAAAUUUAUGCCAACUGCGGCACAUAAUUUAAAAAUAUCAAUCAAUUCGAUAACGCAGAUU
.....(((.((((.....((..........)).----.)))).((......-(((((((((..((((......))))...))))))))).((((.........))))..)).))). ( -17.40)
>DroMoj_CAF1 43529 83 - 1
ACAGCAUCAGCA-------------------------------GCGGAAAA--UUUAAAUUUAUGCCGACUGCGGCACAUAAUUUAAAAAUAUCAAUCAACUCGAUAACGCAGAUU
...((....)).-------------------------------(((.....--((((((((..(((((....)))))...))))))))..((((.........)))).)))..... ( -18.00)
>DroAna_CAF1 10032 101 - 1
AGAGCAUCAACAUC-------------UU-GGAAGCGGCGGUAGCCGAAAA-UUUUAAAUUUAUGCCGACUGCGGCACAUAAUUUAAAAAUAUCAAUCAACUCGAUAACGCAGAUU
...((.........-------------..-.....((((....))))....-(((((((((..(((((....)))))...))))))))).((((.........))))..))..... ( -22.10)
>consensus
ACAGCAUCAGCA_______________________________GCCGAAAA__UUUAAAUUUAUGCCGACUGCGGCACAUAAUUUAAAAAUAUCAAUCAACUCGAUAACGCAGAUU
...((................................................((((((((..(((((....)))))...))))))))..((((.........))))..))..... (-11.60 = -11.97 +   0.36)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:32:02 2006