Locus 1962

Sequence ID 2R_DroMel_CAF1
Location 7,409,490 – 7,409,690
Length 200
Max. P 0.854667
window3243 window3244 window3245

overview

Window 3

Location 7,409,490 – 7,409,610
Length 120
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 94.28
Mean single sequence MFE -38.87
Consensus MFE -32.86
Energy contribution -32.58
Covariance contribution -0.28
Combinations/Pair 1.16
Mean z-score -1.69
Structure conservation index 0.85
SVM decision value 0.21
SVM RNA-class probability 0.634004
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 7409490 120 - 20766785
CUCGAACUUCUCGAUGGUACGCUUGUCGAUACCACCGCACUUGUAGAUCAAGUGUCCGGUGGUGGUCGACUUACCGGAAUCGACGUGUCCGAUCACGACAAUGUUAAUGUGAAUCUUUUC
.(((.((...(((((((((.....(((((((((((((((((((.....))))))..))))))).)))))).))))...)))))...)).)))(((((..........)))))........ ( -39.50)
>DroPse_CAF1 25290 120 - 1
CUCGAACUUCUCGAUGGUACGCUUGUCGAUACCACCGCACUUGUAGAUCAAGUGACCGGUGGUCGUGGACUUGCCAGAAUCGACGUGUCCAAUGACGACAAUGUUGAUGUGAAUCUUUUC
............(((..(((((..(((.(((((((((((((((.....))))))..))))))).)).)))..))....(((((((((((.......))).))))))))))).)))..... ( -40.10)
>DroGri_CAF1 23959 120 - 1
CUCGAACUUCUCGAUGGUACGCUUGUCGAUGCCACCGCACUUGUAGAUCAAGUGACCGGUGGUGGUGGACUUGCCAGAGUCGACGUGUCCAAUCACGACAAUGUUGAUGUGAAUCUUUUC
.((((.....))))(((.((((..(((((((((((((((((((.....))))))..)))))))(((......)))...))))))))))))).(((((.((....)).)))))........ ( -42.80)
>DroWil_CAF1 27469 120 - 1
CUCGAACUUCUCAAUGGUACGCUUGUCGAUACCACCGCACUUGUAGAUCAAGUGACCAGUGGUGGUGGACUUGCCAGAGUCGACAUGUCCAAUGACGACAAUGUUAAUGUGAAUCUUUUC
....(((.(((((.(((.(((..((((..((((((((((((((.....))))).....)))))))))(((((....))))))))))))))).))).))....)))............... ( -34.00)
>DroAna_CAF1 24480 120 - 1
CUCGAACUUCUCGAUGGUACGCUUGUCGAUACCACCGCACUUGUAGAUCAAGUGACCGGUGGUGGUCGACUUACCGGAAUCGACGUGUCCGAUGACCACGAUGUUAAUGUGAAUCUUUUC
.(((.((...(((((((((.....(((((((((((((((((((.....))))))..))))))).)))))).))))...)))))...)).)))....((((.......))))......... ( -38.50)
>DroPer_CAF1 25242 120 - 1
CUCGAACUUCUCAAUGGUACGCUUGUCGAUACCACCGCACUUGUAGAUCAAGUGACCGGUGGUCGUGGACUUGCCAGAAUCGACGUGUCCAAUGACGACAAUGUUGAUGUGAAUCUUUUC
.((((...(((((.(((.((((..(((((((((((((((((((.....))))))..)))))))..(((.....)))..))))))))))))).))).)).....))))............. ( -38.30)
>consensus
CUCGAACUUCUCGAUGGUACGCUUGUCGAUACCACCGCACUUGUAGAUCAAGUGACCGGUGGUGGUGGACUUGCCAGAAUCGACGUGUCCAAUGACGACAAUGUUAAUGUGAAUCUUUUC
.......(((.((.(((.((((..(((((((((((((((((((.....))))))..)))))))(((......)))...))))))))))))).((((......)))).)).)))....... (-32.86 = -32.58 +  -0.28)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 4

Location 7,409,530 – 7,409,650
Length 120
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 94.28
Mean single sequence MFE -41.63
Consensus MFE -34.62
Energy contribution -34.23
Covariance contribution -0.39
Combinations/Pair 1.11
Mean z-score -1.79
Structure conservation index 0.83
SVM decision value 0.07
SVM RNA-class probability 0.570188
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 7409530 120 + 20766785
AUUCCGGUAAGUCGACCACCACCGGACACUUGAUCUACAAGUGCGGUGGUAUCGACAAGCGUACCAUCGAGAAGUUCGAGAAGGAGGCCCAGGAGAUGGGAAAGGGAUCCUUCAAGUACG
..........(((((..(((((((..((((((.....))))))))))))).)))))...(((((..(((((...)))))((((((..((((.....)))).......))))))..))))) ( -46.40)
>DroVir_CAF1 23871 120 + 1
ACUCUGGCAAGUCCACCACCACCGGUCACUUGAUCUACAAGUGCGGUGGUAUCGACAAGCGUACCAUUGAGAAGUUCGAGAAGGAGGCUCAGGAAAUGGGCAAGGGCUCGUUCAAGUACG
(((..(((.(((((.(((((((((..((((((.....))))))))))))).((((....((......))......))))...))..(((((.....)))))..))))).)))..)))... ( -39.50)
>DroGri_CAF1 23999 120 + 1
ACUCUGGCAAGUCCACCACCACCGGUCACUUGAUCUACAAGUGCGGUGGCAUCGACAAGCGUACCAUCGAGAAGUUCGAGAAGGAAGCUCAGGAAAUGGGCAAGGGCUCGUUCAAGUACG
(((..(((.(((((.((.((((((..((((((.....))))))))))))..((((....((......))......))))...))..(((((.....)))))..))))).)))..)))... ( -39.30)
>DroWil_CAF1 27509 120 + 1
ACUCUGGCAAGUCCACCACCACUGGUCACUUGAUCUACAAGUGCGGUGGUAUCGACAAGCGUACCAUUGAGAAGUUCGAGAAGGAAGCUCAGGAAAUGGGCAAGGGUUCCUUCAAGUACG
......((..(((....(((((((..((((((.....)))))))))))))...)))..))((((..(((((...)))))((((((((((((.....))))).....)))))))..)))). ( -38.60)
>DroMoj_CAF1 23830 120 + 1
ACUCCGGCAAGUCCACCACCACCGGUCACUUGAUCUACAAGUGCGGUGGUAUCGACAAGCGUACCAUUGAGAAGUUCGAGAAGGAAGCCCAGGAGAUGGGCAAGGGCUCGUUCAAGUACG
(((..(((.(((((.(((((((((..((((((.....))))))))))))).((((....((......))......))))...))..(((((.....)))))..))))).)))..)))... ( -42.40)
>DroPer_CAF1 25282 120 + 1
AUUCUGGCAAGUCCACGACCACCGGUCACUUGAUCUACAAGUGCGGUGGUAUCGACAAGCGUACCAUUGAGAAGUUCGAGAAGGAGGCUCAGGAGAUGGGCAAGGGCUCCUUCAAGUACG
......((..(((....(((((((..((((((.....)))))))))))))...)))..))((((..(((((...)))))((((((((((((.....))))).....)))))))..)))). ( -43.60)
>consensus
ACUCUGGCAAGUCCACCACCACCGGUCACUUGAUCUACAAGUGCGGUGGUAUCGACAAGCGUACCAUUGAGAAGUUCGAGAAGGAAGCUCAGGAAAUGGGCAAGGGCUCCUUCAAGUACG
......((..(((....(((((((..((((((.....)))))))))))))...)))..))((((..(((((...)))))(((.((.(((((.....)))))......)).)))..)))). (-34.62 = -34.23 +  -0.39)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 5

Location 7,409,570 – 7,409,690
Length 120
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 94.61
Mean single sequence MFE -39.57
Consensus MFE -34.06
Energy contribution -33.45
Covariance contribution -0.61
Combinations/Pair 1.11
Mean z-score -1.83
Structure conservation index 0.86
SVM decision value 0.80
SVM RNA-class probability 0.854667
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 7409570 120 + 20766785
GUGCGGUGGUAUCGACAAGCGUACCAUCGAGAAGUUCGAGAAGGAGGCCCAGGAGAUGGGAAAGGGAUCCUUCAAGUACGCCUGGGUUUUGGAUAAGUUGAAGGCUGAGCGCGAGCGUGG
...((((((((.((.....))))))))))....((((..((((((..((((.....)))).......))))))......((((.((((((.((....)).)))))).)).)))))).... ( -41.30)
>DroVir_CAF1 23911 120 + 1
GUGCGGUGGUAUCGACAAGCGUACCAUUGAGAAGUUCGAGAAGGAGGCUCAGGAAAUGGGCAAGGGCUCGUUCAAGUACGCAUGGGUUUUGGAUAAAUUGAAGGCCGAGCGUGAGCGUGG
...((((((((.((.....))))))))))....((((..(((.((((((((.....))))).....))).)))....((((.(.((((((.((....)).)))))).))))))))).... ( -37.70)
>DroGri_CAF1 24039 120 + 1
GUGCGGUGGCAUCGACAAGCGUACCAUCGAGAAGUUCGAGAAGGAAGCUCAGGAAAUGGGCAAGGGCUCGUUCAAGUACGCAUGGGUUUUGGAUAAAUUGAAGGCCGAGCGUGAGCGUGG
..(((.(.((.((..((.((((((....(((...(((.....)))..)))..(((.(((((....))))))))..)))))).))((((((.((....)).))))))))..)).).))).. ( -36.10)
>DroWil_CAF1 27549 120 + 1
GUGCGGUGGUAUCGACAAGCGUACCAUUGAGAAGUUCGAGAAGGAAGCUCAGGAAAUGGGCAAGGGUUCCUUCAAGUACGCAUGGGUUUUGGAUAAAUUGAAGGCCGAGCGUGAGCGUGG
...((((((((.((.....))))))))))....((((..((((((((((((.....))))).....)))))))....((((.(.((((((.((....)).)))))).))))))))).... ( -40.40)
>DroYak_CAF1 24122 120 + 1
GUGCGGUGGUAUCGACAAGCGUACCAUCGAGAAGUUCGAGAAGGAAGCCCAGGAGAUGGGCAAGGGAUCCUUCAAGUACGCCUGGGUUUUGGAUAAGUUGAAGGCUGAGCGCGAGCGUGG
...((((((((.((.....))))))))))....((((..((((((.(((((.....)))))......))))))......((((.((((((.((....)).)))))).)).)))))).... ( -42.70)
>DroMoj_CAF1 23870 120 + 1
GUGCGGUGGUAUCGACAAGCGUACCAUUGAGAAGUUCGAGAAGGAAGCCCAGGAGAUGGGCAAGGGCUCGUUCAAGUACGCAUGGGUUUUGGAUAAAUUGAAGGCCGAGCGUGAGCGUGG
(((((((((((.((.....))))))))......(..((((......(((((.....))))).....))))..).....))))).((((((.((....)).))))))..((....)).... ( -39.20)
>consensus
GUGCGGUGGUAUCGACAAGCGUACCAUCGAGAAGUUCGAGAAGGAAGCCCAGGAAAUGGGCAAGGGCUCCUUCAAGUACGCAUGGGUUUUGGAUAAAUUGAAGGCCGAGCGUGAGCGUGG
...((((((((.((.....))))))))))....(((((.(((.((.(((((.....)))))......)).))).....(((.(.((((((.((....)).)))))).))))))))).... (-34.06 = -33.45 +  -0.61)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:17:29 2006