Locus 654

Sequence ID 2L_DroMel_CAF1
Location 1,957,285 – 1,957,433
Length 148
Max. P 0.929336
window1073 window1074

overview

Window 3

Location 1,957,285 – 1,957,393
Length 108
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 80.59
Mean single sequence MFE -36.58
Consensus MFE -14.30
Energy contribution -16.78
Covariance contribution 2.48
Combinations/Pair 1.03
Mean z-score -2.45
Structure conservation index 0.39
SVM decision value 0.68
SVM RNA-class probability 0.819786
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 1957285 108 + 22407834
ACCUCGGGAAGGAACUGAACUUGGGCUGAUGCCCGAUUGCAGCAGAGAUU-UGGCCGA-UUUUUCCAGGGAAA--UGAAUCAAUGCUAUGGGAAAAUCGCUUU---CCGGG-----GGAA
.((((((((((...(((...((((((....))))))...)))........-....(((-((((((((.((...--((...))...)).)))))))))))))))---)))))-----)... ( -42.40)
>DroSim_CAF1 1672 108 + 1
ACCUCGGGAAGGAACUGAACUUGGGCUGAUGCCAGAUUGCAGCAGAGAUU-UGGCCGA-UUUUUCCAGGGAAA--UGAAUCAAUGCUAUGGGAAAAUCGCUUU---CCGGG-----GGAA
.((((((((((...................((((((((........))))-))))(((-((((((((.((...--((...))...)).)))))))))))))))---)))))-----)... ( -38.90)
>DroEre_CAF1 8979 109 + 1
ACCUCGGCCAGGAACUGAGCUUGGGCUGAUGCCAGAUUGCAGCAGAGAUUUUGGACGA-UUUUUCCAGGGAAA--UGAAUCAAUGCUAUGGGAAAAUCGCUUU---CCGGG-----GGAA
.((((((((((((.((..(((..(((....))).......)))..)).)))))).(((-((((((((.((...--((...))...)).)))))))))))....---)))))-----)... ( -36.00)
>DroYak_CAF1 6662 116 + 1
ACCUCGCUGAGGAACUGAGCUUGGGCUGAUGCCAGAUUGCAGCAGAGAUU-UGGCCGA-UUUUUCCAGGGAAA--UGAAUCAAUGCUAUGGGAAAAUCGCUUUUCCCCGGUGAAAGGAAG
.((((((((.((((..((((..........((((((((........))))-)))).((-((((((((.((...--((...))...)).)))))))))))))))))).))))))..))... ( -38.30)
>DroAna_CAF1 29375 92 + 1
ACCUCCGGGA----CGGAGAGAGUCCUGAUGCCAGAUUGCAACAGAGAUU-UGGCCGAGUUUUUCCUUGGAAAAUCGAAUCAAUUCUAUGGGAAAU-----------------------A
..((((((((----(.......))))))..((((((((........))))-)))).))).((((((.(((((...........))))).)))))).-----------------------. ( -27.30)
>consensus
ACCUCGGGAAGGAACUGAGCUUGGGCUGAUGCCAGAUUGCAGCAGAGAUU_UGGCCGA_UUUUUCCAGGGAAA__UGAAUCAAUGCUAUGGGAAAAUCGCUUU___CCGGG_____GGAA
..(((((.......)))))(((((.(((.(((......))).)))..........(((.((((((((.((...............)).))))))))))).......)))))......... (-14.30 = -16.78 +   2.48)

alignment

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secondary structure

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dotplot

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Window 4

Location 1,957,325 – 1,957,433
Length 108
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 83.78
Mean single sequence MFE -35.46
Consensus MFE -21.30
Energy contribution -23.10
Covariance contribution 1.80
Combinations/Pair 1.00
Mean z-score -2.85
Structure conservation index 0.60
SVM decision value 1.20
SVM RNA-class probability 0.929336
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 1957325 108 + 22407834
AGCAGAGAUU-UGGCCGA-UUUUUCCAGGGAAA--UGAAUCAAUGCUAUGGGAAAAUCGCUUU---CCGGG-----GGAAGGGAAGCAGAGCGGCUUGCAUAAUCUGCGGUAAGCCAGGA
.(((((....-.((((((-((((((((.((...--((...))...)).))))))))))(((((---((...-----....))))))).....)))).......)))))((....)).... ( -39.10)
>DroSim_CAF1 1712 108 + 1
AGCAGAGAUU-UGGCCGA-UUUUUCCAGGGAAA--UGAAUCAAUGCUAUGGGAAAAUCGCUUU---CCGGG-----GGAAGGGAAGCAGAGCGGCUUGCAUAAUCUGCGGUAAGCCAGGA
.(((((....-.((((((-((((((((.((...--((...))...)).))))))))))(((((---((...-----....))))))).....)))).......)))))((....)).... ( -39.10)
>DroEre_CAF1 9019 109 + 1
AGCAGAGAUUUUGGACGA-UUUUUCCAGGGAAA--UGAAUCAAUGCUAUGGGAAAAUCGCUUU---CCGGG-----GGAAGCGAAGCAGAGCGGCUUGCAUAAUCUGCGGUAAGCCAGGA
.(((((..((((((((((-((((((((.((...--((...))...)).)))))))))))...)---)))))-----)...((.((((......))))))....)))))((....)).... ( -33.30)
>DroYak_CAF1 6702 116 + 1
AGCAGAGAUU-UGGCCGA-UUUUUCCAGGGAAA--UGAAUCAAUGCUAUGGGAAAAUCGCUUUUCCCCGGUGAAAGGAAGGGGAAGCAGAGCGGCUUGCAUAAUCUGCGGUAAGCCAGAA
.(((((....-.((((((-((((((((.((...--((...))...)).))))))))))((((((((((...........))))))...)))))))).......)))))((....)).... ( -41.70)
>DroAna_CAF1 29411 92 + 1
AACAGAGAUU-UGGCCGAGUUUUUCCUUGGAAAAUCGAAUCAAUUCUAUGGGAAAU-----------------------AGAGAA----CACGGCUUGCAUAAUCUGCGGUAAGCCAGAA
......((((-((((((((......)))))....)))))))..((((((.....))-----------------------))))..----...(((((((..........))))))).... ( -24.10)
>consensus
AGCAGAGAUU_UGGCCGA_UUUUUCCAGGGAAA__UGAAUCAAUGCUAUGGGAAAAUCGCUUU___CCGGG_____GGAAGGGAAGCAGAGCGGCUUGCAUAAUCUGCGGUAAGCCAGGA
.(((((......(((((..((((((((.((...............)).))))))))..(((((...((........))....)))))....))))).......)))))((....)).... (-21.30 = -23.10 +   1.80)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:42:07 2006