Locus 1787

Sequence ID	2R_DroMel_CAF1
Location	6,695,287 – 6,695,388
Length	101
Max. P	0.703648

overview

Window 0

Location	6,695,287 – 6,695,388
Length	101
Sequences	6
Columns	111
Reading direction	forward
Mean pairwise identity	83.99
Mean single sequence MFE	-34.73
Consensus MFE	-26.70
Energy contribution	-26.37
Covariance contribution	-0.33
Combinations/Pair	1.12
Mean z-score	-2.04
Structure conservation index	0.77
SVM decision value	0.36
SVM RNA-class probability	0.703648
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 6695287 101 + 20766785
UGUACGA-GGUUGUUGCUGUGGCUGAAAGCAGUUCACUAGCAACAACAAGGG---------CCACAGCAACAGUGAGUGAGUGACGGCAACGACCGUGAAAGGCCAUUUGC
.......-..((((((((((((((....((((....)).))..(.....)))---------))))))))))))...(..((((.((....)).((......)).))))..) ( -33.90)
>DroSec_CAF1 43896 101 + 1
UGUACGA-GGUUGUUGCUGUGGCUGAAAGCAGUUCCUUAGCAACAACAAGGA---------CCACAGCAACAGUGAGUGAGUGACGGCAACGACCGUGAAAGGCCAUUUGC
.......-..(((((((((((((((....))).(((((.(......))))))---------))))))))))))...(..((((.((....)).((......)).))))..) ( -32.60)
>DroSim_CAF1 49235 101 + 1
UGUACGA-GGUUGUUGCUGGGGCUGAGAGCAGUUUCCUAGCAACAACAAGGA---------CCACAGCAACAGUGAGUGAGUGACGGGAACGACCGUGAAAGGCCAUUUGC
.((.(..-.((((((((((((((((....))))..))))))))))))..).)---------)....((((..(((.((...(.((((......)))).)...))))))))) ( -34.50)
>DroEre_CAF1 45636 102 + 1
UGUACAGAGGUUGUUGCUGCGGCUGAAAGCAGUUCAGCAGCAACAACAAGGG---------CCACAGCAACAGUAAGUGAGUGACGGCAACGACCGUGAAAGGCCAUUUGC
....((((.(((((((((((.((((....))))...)))))))))))...((---------((.((...((.....))...))((((......))))....)))).)))). ( -36.80)
>DroYak_CAF1 44234 101 + 1
UGUACCGA-GUUGUUGCUGUGGCUGAAAGCAGUUCAGCAGCAACAACAAGGG---------CCACAGCAACAGUGAGUGAGUGACGGCAACGACCGUGAAAGGCCAUUUGC
((..((..-(((((((((((.((((....))))...)))))))))))..)).---------.))..((((..(((.((...(.((((......)))).)...))))))))) ( -35.80)
>DroPer_CAF1 69270 102 + 1
---------GUUGUUGCCGGGGCAGAAAACUGUUCAACAGCGCCAACAAAGCAGGCAGAGGCAGAGGCAACGACGAGUGAGUGACGGCAACGACCGUGAAAGGCCAUUUGC
---------(((((((((.((((((....))))))......(((.........))).........)))))))))..(..((((.((....)).((......)).))))..) ( -34.80)
>consensus
UGUACGA_GGUUGUUGCUGUGGCUGAAAGCAGUUCACCAGCAACAACAAGGG_________CCACAGCAACAGUGAGUGAGUGACGGCAACGACCGUGAAAGGCCAUUUGC
.........((((((((((.(((((....)))))...)))))))))).............................(..((((.((....)).((......)).))))..) (-26.70 = -26.37 +  -0.33)

alignment

secondary structure

dotplot

Window 1

Location	6,695,287 – 6,695,388
Length	101
Sequences	6
Columns	111
Reading direction	reverse
Mean pairwise identity	83.99
Mean single sequence MFE	-32.90
Consensus MFE	-23.04
Energy contribution	-23.40
Covariance contribution	0.36
Combinations/Pair	1.12
Mean z-score	-2.54
Structure conservation index	0.70
SVM decision value	0.33
SVM RNA-class probability	0.692762
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 6695287 101 - 20766785
GCAAAUGGCCUUUCACGGUCGUUGCCGUCACUCACUCACUGUUGCUGUGG---------CCCUUGUUGUUGCUAGUGAACUGCUUUCAGCCACAGCAACAACC-UCGUACA
((((.(((((......)))))))))..............(((((((((((---------(...((.....((.((....))))...))))))))))))))...-....... ( -33.90)
>DroSec_CAF1 43896 101 - 1
GCAAAUGGCCUUUCACGGUCGUUGCCGUCACUCACUCACUGUUGCUGUGG---------UCCUUGUUGUUGCUAAGGAACUGCUUUCAGCCACAGCAACAACC-UCGUACA
((((.(((((......)))))))))..............(((((((((((---------(((((((....)).))))).(((....))))))))))))))...-....... ( -33.80)
>DroSim_CAF1 49235 101 - 1
GCAAAUGGCCUUUCACGGUCGUUCCCGUCACUCACUCACUGUUGCUGUGG---------UCCUUGUUGUUGCUAGGAAACUGCUCUCAGCCCCAGCAACAACC-UCGUACA
(..(((((((......)))))))..).............((((((((.((---------.....((((..((.((....))))...))))))))))))))...-....... ( -29.30)
>DroEre_CAF1 45636 102 - 1
GCAAAUGGCCUUUCACGGUCGUUGCCGUCACUCACUUACUGUUGCUGUGG---------CCCUUGUUGUUGCUGCUGAACUGCUUUCAGCCGCAGCAACAACCUCUGUACA
((((.(((((......))))))))).(((((..((.....))....))))---------)..((((((((((.((((((.....)))))).)))))))))).......... ( -36.50)
>DroYak_CAF1 44234 101 - 1
GCAAAUGGCCUUUCACGGUCGUUGCCGUCACUCACUCACUGUUGCUGUGG---------CCCUUGUUGUUGCUGCUGAACUGCUUUCAGCCACAGCAACAAC-UCGGUACA
((((.(((((......))))))))).(((((..((.....))....))))---------)((..(((((((((((((((.....))))))...)))))))))-..)).... ( -35.90)
>DroPer_CAF1 69270 102 - 1
GCAAAUGGCCUUUCACGGUCGUUGCCGUCACUCACUCGUCGUUGCCUCUGCCUCUGCCUGCUUUGUUGGCGCUGUUGAACAGUUUUCUGCCCCGGCAACAAC---------
((((.(((((......)))))))))...............((((((...((....(((.((...)).)))((((.....)))).....))...))))))...--------- ( -28.00)
>consensus
GCAAAUGGCCUUUCACGGUCGUUGCCGUCACUCACUCACUGUUGCUGUGG_________CCCUUGUUGUUGCUACUGAACUGCUUUCAGCCACAGCAACAACC_UCGUACA
((((.(((((......)))))))))..............(((((((((((..............((....)).......(((....))))))))))))))........... (-23.04 = -23.40 +   0.36)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:13:09 2006