Locus 164

Sequence ID 3R_DroMel_CAF1
Location 822,521 – 822,760
Length 239
Max. P 0.976561
window272 window273

overview

Window 2

Location 822,521 – 822,641
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 96.25
Mean single sequence MFE -37.22
Consensus MFE -34.16
Energy contribution -35.04
Covariance contribution 0.88
Combinations/Pair 1.06
Mean z-score -1.66
Structure conservation index 0.92
SVM decision value 1.77
SVM RNA-class probability 0.976561
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 822521 120 - 27905053
GAGUGCCUCGCCAGUUUGGUGACGAACUGAAAUGAGGCAUAGAACGCUGCACUUCAUGGGGCAUUGUAAAUAAAUGCGGAAGUGUGUUGAGCCUGACAUUUAAAUCGCAGAUGUGUUCGA
..((((((((.(((((((....)))))))...)))))))).((((((.(((((((.....(((((.......))))).)))))))(((......)))...............)))))).. ( -44.10)
>DroSec_CAF1 4994 120 - 1
GAGUGCCGCGCCAGUUUGGUGACGAACUGAAAUGAGGCAUAGAACGCUGCACUUCAUGGGGCAUUGUAAAUAAAUGCGGAAGUGUGUUGAGCCUGACAUUUAAAUCGCAGAUGUGUUCGA
..(((((.((.(((((((....)))))))...)).))))).((((((.(((((((.....(((((.......))))).)))))))(((......)))...............)))))).. ( -39.70)
>DroSim_CAF1 2173 120 - 1
GAGUGCCGCGCCAGUUUGGUGACGAACUGAAAUGAGGCAUAGAACGCUGCACUUCAUGGGGCAUUGUAAAUAAAUGCGGAAGUGUGUUGAGCCUGACAUUUAAAUCGCAGAUGUGUUCGA
..(((((.((.(((((((....)))))))...)).))))).((((((.(((((((.....(((((.......))))).)))))))(((......)))...............)))))).. ( -39.70)
>DroEre_CAF1 5764 119 - 1
GAGUGCCGCGCCAGCUUGGUGACGAUCUGAAAUGAGGCAUAGAACGCUGCACUUCAUGGG-CAUUGUAGAUAAAUGCGGAAGUGUGUUGAGCCUGACAUUUAAAUCGCAGAUGUGGUCGA
....((((((.(((.(((....))).)))(((((((((..((....))(((((((....(-((((.......))))).))))))).....))))..)))))..........))))))... ( -33.60)
>DroYak_CAF1 5420 120 - 1
AAGAGCCGCGCUAGUUUGGUGACGAUCUGAAAUGAGGCAUAGAACACUGCACUUCAUGGGACAUUGUAAAUAAAUGCGGAAGUGUGUUGAGCCUGACAUUUAAAUCGCAGAUGUGUUCGA
....(((.((.(((.(((....))).)))...)).)))...((((((.(((((((....(.((((.......))))).)))))))(((......)))...............)))))).. ( -29.00)
>consensus
GAGUGCCGCGCCAGUUUGGUGACGAACUGAAAUGAGGCAUAGAACGCUGCACUUCAUGGGGCAUUGUAAAUAAAUGCGGAAGUGUGUUGAGCCUGACAUUUAAAUCGCAGAUGUGUUCGA
..(((((.((.(((((((....)))))))...)).))))).((((((.(((((((.....(((((.......))))).)))))))(((......)))...............)))))).. (-34.16 = -35.04 +   0.88)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 3

Location 822,641 – 822,760
Length 119
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 76.55
Mean single sequence MFE -34.67
Consensus MFE -19.25
Energy contribution -19.97
Covariance contribution 0.72
Combinations/Pair 1.20
Mean z-score -1.92
Structure conservation index 0.56
SVM decision value 0.67
SVM RNA-class probability 0.817421
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 822641 119 + 27905053
GAAAUUAGUGGGACAAAUGUGAAGGAAAAGGGCGCAGCCAGUUCUGA-GCACCGAGGCUCGAAGCGAAAGACCCUGCACCCAGAAAAAUCCCAGCCAGGAACGCACCAAGCUUGGUCGAG
........(((((((....))........(((.((((....(((.((-((......))))))).(....)...)))).))).......)))))((((((...........)))))).... ( -30.70)
>DroSec_CAF1 5114 105 + 1
GAAAUUAGUGGGACAAAUGGGAAGGCAAAGGGUGCAGCCAGCUUU---------------GAAACGAAAGACCCUGCGCCCAGGUAAAUCCCAGCCAGGAACGCACUAAGAGUGUUCGAG
..........((.....(((((..((...((((((((....((((---------------......))))...))))))))..))...))))).))..((((((.......))))))... ( -34.70)
>DroSim_CAF1 2293 104 + 1
GAAAUUAGUGGGACAAAUGGGAAGGCAAAGGGUGCAGCCAGCUUU---------------GAAACGAAAGACCCUGCACCCACGAAAAUCCCAGCCAGGAACGCACUAA-AGUGUUCGAG
..........((.....(((((.......((((((((....((((---------------......))))...)))))))).......))))).))..((((((.....-.))))))... ( -33.34)
>DroEre_CAF1 5883 108 + 1
AAAGUUAGUGGGACAAAUGGGGAGGCAAGGGGUGCAGCCAGUUUUGAAGGAC------------CGCAGGACCCCGCACCCAGGAAAGUCCCAACUAGGAACGUACUGCGUUUACUUGAG
.(((((((((((((...((((...((..(((((.(.((..((((....))))------------.)).).))))))).)))).....))))).)))).(((((.....)))))))))... ( -38.60)
>DroYak_CAF1 5540 118 + 1
GAAAUUAGUGGAACAAAUGGAAGAGCAACGGGUGCAGCCAGUUUUGA-GCACCGAGGCUCGACACGAAAGACCCUGCACCCAG-AAAAUCCCAACCAGGAACGUACUGCGUUUAUUUGAG
.............((((((((...(((((((((((((......((((-((......))))))..(....)...))))))))..-....(((......)))..))..))).)))))))).. ( -36.00)
>consensus
GAAAUUAGUGGGACAAAUGGGAAGGCAAAGGGUGCAGCCAGUUUUGA_G_AC________GAAACGAAAGACCCUGCACCCAGGAAAAUCCCAGCCAGGAACGCACUAAGAUUGUUCGAG
.....((((((..(...(((((.......((((((((...(((((......................))))).)))))))).......))))).....)..).)))))............ (-19.25 = -19.97 +   0.72)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:35:28 2006