Locus 7403

Sequence ID	3L_DroMel_CAF1
Location	19,912,150 – 19,912,270
Length	120
Max. P	0.894492

overview

Window 3

Location	19,912,150 – 19,912,270
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	86.26
Mean single sequence MFE	-41.58
Consensus MFE	-28.52
Energy contribution	-29.68
Covariance contribution	1.16
Combinations/Pair	1.11
Mean z-score	-1.74
Structure conservation index	0.69
SVM decision value	0.02
SVM RNA-class probability	0.541860
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 19912150 120 + 23771897
UCGAAAGGAGCUUGCUCAGCAUUCUCGGGAUCUCGAGUAGCCCCGCGGCCAUGGCUACACUCGUAUGUAUACACACGACGCAUGCGCAGACCUCGGGACUCCGCCGAGAUCCCUCCUCCA
.(....)(((..(((...)))..)))(((((((((.(.((.((((.((...((((.....((((.((....)).)))).....)).))..)).)))).)).)..)))))))))....... ( -43.70)
>DroSec_CAF1 48011 120 + 1
UCGAAAGGAGCUGGCUCAGCAUUCUCGGGAUCGCGAGUAGCCCCAUGGCCAUGGCUGCACUCGUAUGUAUACACACGACGCAUGCGGAGACCUCGGGACUCCGCCGAGAUCCCUACUCCA
......(((((((...))))......(((((((((.((((((..........))))))..((((.((....)).)))))))..((((((.((...)).))))))...))))))...))). ( -46.80)
>DroSim_CAF1 32376 120 + 1
UCGAAAGGAGCUGGCUCAGCAUUCUCGGGAUCGCGAGUAGCCCCAUGGACAUGGCUACACUCGUAUGUAUACACACGACGCAUGCGCAGACCUCGGGACUCCGCCGAGAUCCCUACUCCA
......((((..(((((.((..(((((((.(((((.((((((..........))))))..((((.((....)).))))......))).)).)))))))....)).)))...))..)))). ( -40.00)
>DroEre_CAF1 47224 106 + 1
UCGAAAGGAGCUGGCUCAGCGUUCUCGGGAUCUCGAGUAGC--------CGUGGCUACA------AGUAUACACACGACGCAUGCGCAGAGCUCGAGACUCCGCCGAGAUCGCUCCUCCA
.....((((((...(((.(((.(((((((.((((..(((((--------....))))).------.((((.(.......).))))).))).)))))))...))).)))...))))))... ( -40.30)
>DroYak_CAF1 47133 106 + 1
UCGAAAGGAGCUGGCUCAGCAUUCUCGGGAUCUCGAGUAGC--------CAUGGCUACA------UGUAUACACUCAACGCAUGCGCAGAUCGCGAGACUCCGAUGAGAUCCCUCCUCCA
......((((..((((((....(((((.(((((((.(((((--------....)))))(------(((...........)))).)).))))).)))))......))))...))..)))). ( -37.10)
>consensus
UCGAAAGGAGCUGGCUCAGCAUUCUCGGGAUCUCGAGUAGCCCC__GG_CAUGGCUACACUCGUAUGUAUACACACGACGCAUGCGCAGACCUCGGGACUCCGCCGAGAUCCCUCCUCCA
......(((((((...))))......(((((((((.((((((..........)))))).........................(((.((.(.....).)).))))))))))))...))). (-28.52 = -29.68 +   1.16)

alignment

secondary structure

dotplot

Window 4

Location	19,912,150 – 19,912,270
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	86.26
Mean single sequence MFE	-52.28
Consensus MFE	-33.24
Energy contribution	-39.00
Covariance contribution	5.76
Combinations/Pair	1.05
Mean z-score	-3.04
Structure conservation index	0.64
SVM decision value	0.98
SVM RNA-class probability	0.894492
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 19912150 120 - 23771897
UGGAGGAGGGAUCUCGGCGGAGUCCCGAGGUCUGCGCAUGCGUCGUGUGUAUACAUACGAGUGUAGCCAUGGCCGCGGGGCUACUCGAGAUCCCGAGAAUGCUGAGCAAGCUCCUUUCGA
.(((((.((((((((((...(((((((.((((((.((.(((((((((((....))))))).)))))))).)))).)))))))..))))))))))(((..(((...)))..)))))))).. ( -63.30)
>DroSec_CAF1 48011 120 - 1
UGGAGUAGGGAUCUCGGCGGAGUCCCGAGGUCUCCGCAUGCGUCGUGUGUAUACAUACGAGUGCAGCCAUGGCCAUGGGGCUACUCGCGAUCCCGAGAAUGCUGAGCCAGCUCCUUUCGA
.(((((.((...(((((((.(((((((.((((...((.(((((((((((....))))))).))))))...)))).))))))).((((......))))..))))))))).)))))...... ( -56.70)
>DroSim_CAF1 32376 120 - 1
UGGAGUAGGGAUCUCGGCGGAGUCCCGAGGUCUGCGCAUGCGUCGUGUGUAUACAUACGAGUGUAGCCAUGUCCAUGGGGCUACUCGCGAUCCCGAGAAUGCUGAGCCAGCUCCUUUCGA
.(((((.((...(((((((.(((((((.((.(((.((.(((((((((((....))))))).)))))))).).)).))))))).((((......))))..))))))))).)))))...... ( -52.60)
>DroEre_CAF1 47224 106 - 1
UGGAGGAGCGAUCUCGGCGGAGUCUCGAGCUCUGCGCAUGCGUCGUGUGUAUACU------UGUAGCCACG--------GCUACUCGAGAUCCCGAGAACGCUGAGCCAGCUCCUUUCGA
.((((((((...(((((((...(((((..(((((((((((...))))))))....------.(((((....--------)))))..)))....))))).)))))))...))))))))... ( -49.70)
>DroYak_CAF1 47133 106 - 1
UGGAGGAGGGAUCUCAUCGGAGUCUCGCGAUCUGCGCAUGCGUUGAGUGUAUACA------UGUAGCCAUG--------GCUACUCGAGAUCCCGAGAAUGCUGAGCCAGCUCCUUUCGA
....(((((((.((..((((..(((((.(((((.((.(((((.....)))))...------.(((((....--------))))).))))))).)))))...))))...)).))))))).. ( -39.10)
>consensus
UGGAGGAGGGAUCUCGGCGGAGUCCCGAGGUCUGCGCAUGCGUCGUGUGUAUACAUACGAGUGUAGCCAUG_CC__GGGGCUACUCGAGAUCCCGAGAAUGCUGAGCCAGCUCCUUUCGA
.(((...((((((((((...(((((((.((.(((.((.(((((((((((....))))))).)))))))).).)).)))))))..))))))))))......((((...)))))))...... (-33.24 = -39.00 +   5.76)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:46:05 2006