Locus 2557

Sequence ID	2R_DroMel_CAF1
Location	9,073,820 – 9,074,020
Length	200
Max. P	0.998014

overview

Window 0

Location	9,073,820 – 9,073,940
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	92.67
Mean single sequence MFE	-29.12
Consensus MFE	-26.30
Energy contribution	-25.62
Covariance contribution	-0.68
Combinations/Pair	1.21
Mean z-score	-2.08
Structure conservation index	0.90
SVM decision value	2.98
SVM RNA-class probability	0.998014
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 9073820 120 - 20766785
UGCCCAUUUUCCAGGGUAGCAGAGUGCUAUUUUGAAGGACAUAUAGAAAACCCAUCGACAAUCUUACCAAAUGUCUGGCCUAUUUCGUGGGCCUUGCAUUUCCUUUAAAUUGUCAAACAA
......((((.(((((((((.....))))))))).)))).................((((((......((((((..(((((((...)))))))..)))))).......))))))...... ( -30.62)
>DroSec_CAF1 38766 120 - 1
UGCCUAUUUUCCAGGGUAGCAGAGUGCUAUUUUGAAGGACACAUAGUAAACCCAUCGACAAUCUUACCAAAUGUCUGGCCUAUUUCCUGGACCUUGCAUUUCUUUUAAAUUGUCAAACAA
(((((......(((((((((.....))))))))).))).))...............((((((......((((((..((((........)).))..)))))).......))))))...... ( -25.02)
>DroSim_CAF1 40549 120 - 1
UGCCCAUUUUCCAGGGUAGCAGAGUGCUAUUUUGAAGGACACAUAGAAAACCCAUCGACAAUCUUACCAAAUGUCUGGCCUAUUUCCUGGGCCUUGCAUUUCUUUUAAAUUGUCAAACAA
......((((((((((((((.....)))))))))..(....)...)))))......((((((......((((((..((((((.....))))))..)))))).......))))))...... ( -30.42)
>DroEre_CAF1 44452 120 - 1
UGCCCAUUUUCCAGGGUAGCAGAGUGCUAUUUUGAAGGACACAUAGCAAACCCAUCGACAAUCUUACCAAAUGCUUGACCUAAUUCCUGGUCUUUGCGUUUCAUUUAAAUUGUCAAACAA
(((((........)))))......((((((..((.....)).))))))........((((((......((((((..((((........))))...)))))).......))))))...... ( -28.12)
>DroYak_CAF1 40904 120 - 1
UGCCCACUUUCCAGGGCAGCAGAGUGCUAUUUCGAAGGACAUAUAGAAAACCCAUCGACAAUCUUACCAAAUGCUUGACCUAAUUCCUGGGUUUUGCGUUUCAUUUAAAUUGUCAAACAA
(((((........)))))...(.((.((((.((....))...))))...)).)...((((((......((((((..((((((.....))))))..)))))).......))))))...... ( -31.42)
>consensus
UGCCCAUUUUCCAGGGUAGCAGAGUGCUAUUUUGAAGGACACAUAGAAAACCCAUCGACAAUCUUACCAAAUGUCUGGCCUAUUUCCUGGGCCUUGCAUUUCAUUUAAAUUGUCAAACAA
.((((........))))(((.....))).....((.((.............)).))((((((......((((((..((((((.....))))))..)))))).......))))))...... (-26.30 = -25.62 +  -0.68)

alignment

secondary structure

dotplot

Window 1

Location	9,073,860 – 9,073,980
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	91.83
Mean single sequence MFE	-29.77
Consensus MFE	-24.20
Energy contribution	-23.60
Covariance contribution	-0.60
Combinations/Pair	1.25
Mean z-score	-1.61
Structure conservation index	0.81
SVM decision value	0.63
SVM RNA-class probability	0.804148
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 9073860 120 - 20766785
UUAUCUUUCAGAACCACGUGUUGUCCAAUGCACGCUCAACUGCCCAUUUUCCAGGGUAGCAGAGUGCUAUUUUGAAGGACAUAUAGAAAACCCAUCGACAAUCUUACCAAAUGUCUGGCC
...((((((((((....((((........))))((((..((((((........))))))..))))....))))))))))............(((..((((...........))))))).. ( -31.00)
>DroSec_CAF1 38806 120 - 1
UUAUCUUUCAGAACCACAUGUUGUCCAAUGCACGCUCAACUGCCUAUUUUCCAGGGUAGCAGAGUGCUAUUUUGAAGGACACAUAGUAAACCCAUCGACAAUCUUACCAAAUGUCUGGCC
...((((((((((.....(((........)))(((((..((((((........))))))..)))))...))))))))))............(((..((((...........))))))).. ( -26.70)
>DroSim_CAF1 40589 120 - 1
UUAUCUUUCAGAACCACGUGUUGUCCAAUGCACGCUCAACUGCCCAUUUUCCAGGGUAGCAGAGUGCUAUUUUGAAGGACACAUAGAAAACCCAUCGACAAUCUUACCAAAUGUCUGGCC
...((((((((((....((((........))))((((..((((((........))))))..))))....))))))))))............(((..((((...........))))))).. ( -31.00)
>DroEre_CAF1 44492 120 - 1
UCAUUUUCUGGAACCACGUGUUGUCCUAUGCACGCUCUACUGCCCAUUUUCCAGGGUAGCAGAGUGCUAUUUUGAAGGACACAUAGCAAACCCAUCGACAAUCUUACCAAAUGCUUGACC
........(((......((((.(((((...((((((((.((((((........)))))).))))))......)).))))))))).......))).......................... ( -28.02)
>DroYak_CAF1 40944 120 - 1
UCAUUUUCUGGAACCACGUGUUGUCCUAUGCACGCUCGGCUGCCCACUUUCCAGGGCAGCAGAGUGCUAUUUCGAAGGACAUAUAGAAAACCCAUCGACAAUCUUACCAAAUGCUUGACC
...(((((((...........((((((.((..(((((.(((((((........))))))).)))))......)).))))))..))))))).............................. ( -32.12)
>consensus
UUAUCUUUCAGAACCACGUGUUGUCCAAUGCACGCUCAACUGCCCAUUUUCCAGGGUAGCAGAGUGCUAUUUUGAAGGACACAUAGAAAACCCAUCGACAAUCUUACCAAAUGUCUGGCC
...((((((((((....((((........))))((((..((((((........))))))..))))....))))))))))......................................... (-24.20 = -23.60 +  -0.60)

alignment

secondary structure

dotplot

Window 2

Location	9,073,900 – 9,074,020
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	88.42
Mean single sequence MFE	-35.81
Consensus MFE	-30.65
Energy contribution	-30.77
Covariance contribution	0.12
Combinations/Pair	1.11
Mean z-score	-1.93
Structure conservation index	0.86
SVM decision value	1.54
SVM RNA-class probability	0.962464
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 9073900 120 - 20766785
AUCCAAUUCGGUUUAUUGCUCGUGGAGAUGGCCUCAUCUCUUAUCUUUCAGAACCACGUGUUGUCCAAUGCACGCUCAACUGCCCAUUUUCCAGGGUAGCAGAGUGCUAUUUUGAAGGAC
........((((.....)).)).(((((((....)))))))..((((((((((....((((........))))((((..((((((........))))))..))))....)))))))))). ( -35.70)
>DroSec_CAF1 38846 120 - 1
AUCAAAUCCGGUUAAUAACUCGUGGAGAUGGCCUCAUCUCUUAUCUUUCAGAACCACAUGUUGUCCAAUGCACGCUCAACUGCCUAUUUUCCAGGGUAGCAGAGUGCUAUUUUGAAGGAC
......(((((((..........(((((((....)))))))..........))))..........(((....(((((..((((((........))))))..))))).....)))..))). ( -31.35)
>DroSim_CAF1 40629 120 - 1
AUCCAAUCCGGUUUAUUGCUCGUGGAGAUGGCCUCAUCUCUUAUCUUUCAGAACCACGUGUUGUCCAAUGCACGCUCAACUGCCCAUUUUCCAGGGUAGCAGAGUGCUAUUUUGAAGGAC
........((((.....)).)).(((((((....)))))))..((((((((((....((((........))))((((..((((((........))))))..))))....)))))))))). ( -35.90)
>DroEre_CAF1 44532 120 - 1
AUCCAAAUCGGUUUAUUUCUCGUGGAGAUGGUUGAAUCUCUCAUUUUCUGGAACCACGUGUUGUCCUAUGCACGCUCUACUGCCCAUUUUCCAGGGUAGCAGAGUGCUAUUUUGAAGGAC
.(((.....(((((.......((((((((......))))).)))......)))))..((((........))))(((((.((((((........)))))).)))))...........))). ( -36.62)
>DroYak_CAF1 40984 120 - 1
AUUCAAUUCGGUUUAUUUUUGGUGGAGGUCGUUGCAUCUCUCAUUUUCUGGAACCACGUGUUGUCCUAUGCACGCUCGGCUGCCCACUUUCCAGGGCAGCAGAGUGCUAUUUCGAAGGAC
.........(((((......(((((((((......))))).)))).....))))).......(((((.((..(((((.(((((((........))))))).)))))......)).))))) ( -39.50)
>consensus
AUCCAAUUCGGUUUAUUGCUCGUGGAGAUGGCCUCAUCUCUUAUCUUUCAGAACCACGUGUUGUCCAAUGCACGCUCAACUGCCCAUUUUCCAGGGUAGCAGAGUGCUAUUUUGAAGGAC
.........(((((.........(((((((....))))))).........))))).......((((......(((((..((((((........))))))..)))))(......)..)))) (-30.65 = -30.77 +   0.12)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:33:01 2006