Locus 4862

Sequence ID	2R_DroMel_CAF1
Location	15,923,387 – 15,923,561
Length	174
Max. P	0.836745

overview

Window 5

Location	15,923,387 – 15,923,486
Length	99
Sequences	6
Columns	109
Reading direction	forward
Mean pairwise identity	82.02
Mean single sequence MFE	-39.68
Consensus MFE	-26.52
Energy contribution	-26.58
Covariance contribution	0.06
Combinations/Pair	1.32
Mean z-score	-1.53
Structure conservation index	0.67
SVM decision value	0.02
SVM RNA-class probability	0.544908
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 15923387 99 + 20766785
UAGCCGGCCGAACGUGUCAUAACACACAAGCUGGGGGCUCACAGG---GAGAGCUAGAGCUGUUGGCUUCGGGCUGCAGGAUUCUGUUUUCGGAGUCCUGAC-------
(((((((((((..((((......)))).((((...(((((.....---..)))))..)))).))))))...)))))((((((((((....))))))))))..------- ( -42.80)
>DroSec_CAF1 51096 99 + 1
UAUCCGGCCGAACGUGUCAUAACACACAAGCUGGGGGCUCACAGG---GAGAGCCAGGUCUGCUGGCUUCGGGCUGCAGGAUCCUGUUUUCGGAGUCCUGUC-------
...(((((.....((((....))))....)))))((((((.....---((((((.((((((((.(.(....).).)))))..))))))))).))))))....------- ( -37.70)
>DroSim_CAF1 49187 99 + 1
UAGCCGGCCGAACGUGUCAUAACACACAAGCUGGGGGCUCACAGG---GAGAGCCCCACCUGCUGGCUUCGGGCUGCAGGAUCCUGUUUUCGGAGUCCUGAC-------
(((((((((....((((......)))).(((..(((((((.....---..)))))))....)))))))...)))))(((((..(((....)))..)))))..------- ( -44.60)
>DroEre_CAF1 50550 99 + 1
UAGCCGGUCGAACGUGUCAUAACACACAAGCUGGGGGCUCACAGG---GAGAGCCAGAGCUUCUGGCCUGGGGCUGCAGGAUCCUGUUUUCGGAGUCCUGAC-------
(((((........((((....)))).((.((..(((((((....(---(....)).)))))))..)).)).)))))(((((..(((....)))..)))))..------- ( -40.40)
>DroYak_CAF1 52670 102 + 1
UAGCCGGCCGAACGUGUCAUAACACACAAGCUGGGGGCUCACAGGGCGGAGAGCCAGCGCUUCUGGCUUGGGGCAACAGGAUCCUGUUUUCGGAGUCCUGAC-------
..(((........((((....)))).(((((..(((((.(....(((.....))).).)))))..))))).)))..(((((..(((....)))..)))))..------- ( -43.40)
>DroAna_CAF1 43958 96 + 1
UAGCCAGACGAACGUGUCAUAACACACAAGCCGGGGGCUCACUGG---GAGAGUUC----------CUUCUAGCUGACGGAUCCCGAGAUGGGAGCUAGGACCUGGGGA
...((........((((......))))...(((((..((((((((---(((.....----------))))))).))).((.((((.....)))).)).)..))))))). ( -29.20)
>consensus
UAGCCGGCCGAACGUGUCAUAACACACAAGCUGGGGGCUCACAGG___GAGAGCCAGAGCUGCUGGCUUCGGGCUGCAGGAUCCUGUUUUCGGAGUCCUGAC_______
(((((((((....((((......))))........(((((.(......).))))).........))))...)))))((((((.(((....))).))))))......... (-26.52 = -26.58 +   0.06)

alignment

secondary structure

dotplot

Window 6

Location	15,923,453 – 15,923,561
Length	108
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	83.04
Mean single sequence MFE	-41.05
Consensus MFE	-25.02
Energy contribution	-25.33
Covariance contribution	0.31
Combinations/Pair	1.23
Mean z-score	-3.28
Structure conservation index	0.61
SVM decision value	0.74
SVM RNA-class probability	0.836745
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 15923453 108 + 20766785
CGGGCUGCAGGAUUCUGUUUUCGGAGUCCUGAC--------UCCACACCAC----ACUCCAUCACAACAAAGUGACACGACGUGUGCAUAAGAAAGCAGGCGAGAGUGUGGCACAUAACA
.(((...((((((((((....))))))))))..--------)))...((((----((((..((((......)))).....(((.(((........))).))).))))))))......... ( -43.70)
>DroSec_CAF1 51162 108 + 1
CGGGCUGCAGGAUCCUGUUUUCGGAGUCCUGUC--------UCCACACCGC----ACUCCAUCACAACAAAGUGACACGACGUGUGCAUAAGAAAGCAGGCGAGAGUGUGGCCCAUAACA
.((((.((((((..(((....)))..)))))).--------.......(((----((((..((((......)))).....(((.(((........))).))).)))))))))))...... ( -42.90)
>DroSim_CAF1 49253 108 + 1
CGGGCUGCAGGAUCCUGUUUUCGGAGUCCUGAC--------UCCACACCGC----ACUCCAUCACAACAAAGUGACACGACGUGUGCAUAAGAAAGCAGGCGAGAGUGUGGCCCAUAACA
.((((..((....((((((((((((((....))--------)))....(((----((((..((((......))))...)).))))).....)))))))))......))..))))...... ( -43.40)
>DroEre_CAF1 50616 108 + 1
GGGGCUGCAGGAUCCUGUUUUCGGAGUCCUGAC--------UCCACACCAC----ACUCCAUCACAACAAAGUGACACGACGUGUGCAUAAGAAAGCAGACGAGAGUGUGGGCCAUAACA
((((...(((((..(((....)))..))))).)--------)))...((((----((((..((((......)))).....(((.(((........))).))).))))))))......... ( -42.60)
>DroYak_CAF1 52739 107 + 1
GGGGCAACAGGAUCCUGUUUUCGGAGUCCUGAC--------UCCACACCACACACACUCCAUCACAACAACGUGACACGACGUGUGCAUAAGAAAGCAGACGAGAGUGUGUGCC-----A
((((.(((((....))))).))(((((....))--------)))...)).(((((((((..((((......)))).....(((.(((........))).))).)))))))))..-----. ( -41.70)
>DroAna_CAF1 44014 115 + 1
CUAGCUGACGGAUCCCGAGAUGGGAGCUAGGACCUGGGGAGCCUGCAACA-----GCUCCAUCACAACAAAGUGCUACGACGUGUGCAUAAGAAAGCAGGCGAGUGUUCGAGUCAAAACA
.....((((((.((((.....)))).)).((((((..(((((........-----)))))..(((......)))......(((.(((........))).))))).))))..))))..... ( -32.00)
>consensus
CGGGCUGCAGGAUCCUGUUUUCGGAGUCCUGAC________UCCACACCAC____ACUCCAUCACAACAAAGUGACACGACGUGUGCAUAAGAAAGCAGGCGAGAGUGUGGCCCAUAACA
.......((((((.(((....))).))))))...........(((((((............((((......)))).....(((.(((........))).))).).))))))......... (-25.02 = -25.33 +   0.31)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:31:01 2006