Locus 4069

Sequence ID	3R_DroMel_CAF1
Location	11,080,449 – 11,080,542
Length	93
Max. P	0.969355

overview

Window 9

Location	11,080,449 – 11,080,542
Length	93
Sequences	6
Columns	99
Reading direction	forward
Mean pairwise identity	80.73
Mean single sequence MFE	-40.12
Consensus MFE	-25.26
Energy contribution	-25.90
Covariance contribution	0.64
Combinations/Pair	1.17
Mean z-score	-1.76
Structure conservation index	0.63
SVM decision value	0.30
SVM RNA-class probability	0.679429
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11080449 93 + 27905053
GG------UCAGCGCAAGGAGCAGACUCCCUCGCUGACUCUGCCGCCGGCCAGUCCAGCCGCAGGACAGUCCGGCGAGAAGCUGACCAGCGGCAAGAUC
((------((((((...((((....))))..)))))))).((((((.((.((((....((((.((.....)).))).)..)))).)).))))))..... ( -43.60)
>DroGri_CAF1 11536 96 + 1
AGCAUGCAUCAGCGUAAGGAGCAAACGCCCACAUUGACCCUGCCCCCCGCCAGUCCGUCGGC---CAGUUGCAGCGAGAAGUCGGCAGGUGGCAAAAUA
...((((....))))..((.((....))))..........((((.((.(((..(((((..((---.....)).))).))....))).)).))))..... ( -25.30)
>DroSec_CAF1 10307 93 + 1
GG------UCAGCGCAAGGAGCAGACUCCCUCGCUGACCCUGCCGCCGGCAAGUCCAGCCGCAGGCCAGUCCGGCGAGAAGCUGACCAGCGGCAAGAUC
((------(((((....((((....))))((((((((((((((.((.((.....)).)).)))))...)).)))))))..)))))))............ ( -43.30)
>DroSim_CAF1 10538 93 + 1
GG------UCAGCGCAAGGAGCAGACUCCCUCGCUGACCCUGCCGCCGGCAAGUCCAGCCGCAGGCCAGUCCGGCGAGAAGCUGACCAGCGGCAAGAUC
((------(((((....((((....))))((((((((((((((.((.((.....)).)).)))))...)).)))))))..)))))))............ ( -43.30)
>DroEre_CAF1 11832 90 + 1
GG------CCAGCGCAAGGAGCAGACUCCCUCGCUGACCCUGCCGCCGGCCAGCCCUGCCGCAGGA---GCUGGAGAGAAGCUGGCCAGCGGCAAGAUC
((------.(((((...((((....))))..))))).)).((((((.(((((((.((.((((....---)).))..))..))))))).))))))..... ( -46.30)
>DroYak_CAF1 10289 90 + 1
UG------CCAGCGCAAGGAGCAGACUCCAUCUCUGACCCUGCCGCCGGCCAGCCCUGCCGCAGCA---GCCGGAGAGAAGCUGGCCAGCGGCAAGAUC
((------(....)))(((..((((.......))))..)))(((((.(((((((.((.((((....---).)))..))..))))))).)))))...... ( -38.90)
>consensus
GG______UCAGCGCAAGGAGCAGACUCCCUCGCUGACCCUGCCGCCGGCCAGUCCAGCCGCAGGACAGUCCGGCGAGAAGCUGACCAGCGGCAAGAUC
.........(((((...((((....))))..)))))....((((((((((.......))))..........((((.....))))....))))))..... (-25.26 = -25.90 +   0.64)

alignment

secondary structure

dotplot

Window 0

Location	11,080,449 – 11,080,542
Length	93
Sequences	6
Columns	99
Reading direction	reverse
Mean pairwise identity	80.73
Mean single sequence MFE	-53.10
Consensus MFE	-44.82
Energy contribution	-46.80
Covariance contribution	1.98
Combinations/Pair	1.17
Mean z-score	-3.95
Structure conservation index	0.84
SVM decision value	1.64
SVM RNA-class probability	0.969355
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11080449 93 - 27905053
GAUCUUGCCGCUGGUCAGCUUCUCGCCGGACUGUCCUGCGGCUGGACUGGCCGGCGGCAGAGUCAGCGAGGGAGUCUGCUCCUUGCGCUGA------CC
..(((.((((((((((((((..((((.((.....)).))))..)).)))))))))))))))(((((((((((((....)))))).))))))------). ( -59.00)
>DroGri_CAF1 11536 96 - 1
UAUUUUGCCACCUGCCGACUUCUCGCUGCAACUG---GCCGACGGACUGGCGGGGGGCAGGGUCAAUGUGGGCGUUUGCUCCUUACGCUGAUGCAUGCU
.((((((((.(((((((..((((((((......)---).))).))).))))))).))))))))....((..(((((.((.......)).)))))..)). ( -33.00)
>DroSec_CAF1 10307 93 - 1
GAUCUUGCCGCUGGUCAGCUUCUCGCCGGACUGGCCUGCGGCUGGACUUGCCGGCGGCAGGGUCAGCGAGGGAGUCUGCUCCUUGCGCUGA------CC
...((((((((((((.((((..((((.((.....)).))))..)).)).))))))))))))(((((((((((((....)))))).))))))------). ( -55.50)
>DroSim_CAF1 10538 93 - 1
GAUCUUGCCGCUGGUCAGCUUCUCGCCGGACUGGCCUGCGGCUGGACUUGCCGGCGGCAGGGUCAGCGAGGGAGUCUGCUCCUUGCGCUGA------CC
...((((((((((((.((((..((((.((.....)).))))..)).)).))))))))))))(((((((((((((....)))))).))))))------). ( -55.50)
>DroEre_CAF1 11832 90 - 1
GAUCUUGCCGCUGGCCAGCUUCUCUCCAGC---UCCUGCGGCAGGGCUGGCCGGCGGCAGGGUCAGCGAGGGAGUCUGCUCCUUGCGCUGG------CC
...(((((((((((((((((...((((.((---....)))).)))))))))))))))))))(((((((((((((....)))))).))))))------). ( -61.10)
>DroYak_CAF1 10289 90 - 1
GAUCUUGCCGCUGGCCAGCUUCUCUCCGGC---UGCUGCGGCAGGGCUGGCCGGCGGCAGGGUCAGAGAUGGAGUCUGCUCCUUGCGCUGG------CA
...(((((((((((((((((...(((((.(---....)))).)))))))))))))))))))(((((.(..((((....))))...).))))------). ( -54.50)
>consensus
GAUCUUGCCGCUGGCCAGCUUCUCGCCGGACUGGCCUGCGGCUGGACUGGCCGGCGGCAGGGUCAGCGAGGGAGUCUGCUCCUUGCGCUGA______CC
((((((((((((((((((((..((((.((.....)).))))..)).))))))))))))))))))((((((((((....)))))).)))).......... (-44.82 = -46.80 +   1.98)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:17:22 2006