Locus 3390

Sequence ID	3L_DroMel_CAF1
Location	9,935,825 – 9,936,023
Length	198
Max. P	0.997769

overview

Window 8

Location	9,935,825 – 9,935,924
Length	99
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	71.25
Mean single sequence MFE	-31.11
Consensus MFE	-15.84
Energy contribution	-15.70
Covariance contribution	-0.13
Combinations/Pair	1.25
Mean z-score	-2.79
Structure conservation index	0.51
SVM decision value	2.93
SVM RNA-class probability	0.997769
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 9935825 99 + 23771897
GUGUCCGUCACUCAAUAUCACAUUCAGUCAAUAAUACGAUCUGAACGAAAUCGGCGAGGCUA---CGGCCAACGCCGAUUCCAGCAGAUA------CGGUUC------AGCC------AG
(((((.((..............(((((((........)).))))).(.((((((((.(((..---..)))..)))))))).).)).))))------)((...------..))------.. ( -32.20)
>DroVir_CAF1 88248 85 + 1
GUGUCCGUCACUCAAUAUAACAUUCAGUCAAUAAUAUAACCUGAACGAAAUCGGCGGGGCCC---AACCUCCGGCUGAUUACAACAAU--------------------------------
(((.....)))...........(((((.............))))).(.(((((((((((...---...)))).))))))).)......-------------------------------- ( -16.42)
>DroPse_CAF1 88108 105 + 1
GUGUCCGUCACUCAAUAUCACAUUCAGUCAAUAAUAUAACCUGAACGAAAUCGGCGGGGCCC---AGCCCCCCGCCGAUUCGCUCAGAUU------CGGGUA------CGUCAAUCCAAG
((..(((..(((.(((.....))).)))............((((.((((.(((((((((...---....))))))))))))).))))...------)))..)------)........... ( -35.60)
>DroWil_CAF1 133471 102 + 1
GUGUCCGUCACUCAAUAUAACAUUCAGUCAAUAGUAUAAUCUGAACGAAAUCGGUGAAUCGAGGCAAUCGAUCACCGAUUCGAUUAACAA------CAGCAG------GGAC------AG
.(((((................(((((.............)))))((((.(((((((.((((.....)))))))))))))))........------......------))))------). ( -29.52)
>DroAna_CAF1 85105 111 + 1
GUGUCCGUCACUCAAUAUUACAUUCAGUCAAUAGUACGAUCUGAACGAAAUCGGCGGGGCUC---CGGCCAUCGCCGAUUCCAGCAGAUAUUCGUACCGAUUGGCCCAAUCC------AG
(((.....)))...............((((((.((((((((((...(.((((((((((((..---..))).))))))))).)..))))...))))))..)))))).......------.. ( -37.30)
>DroPer_CAF1 89220 105 + 1
GUGUCCGUCACUCAAUAUCACAUUCAGUCAAUAAUAUAACCUGAACGAAAUCGGCGGGGCCC---AGCCCCCCGCCGAUUCGCUCAGAUU------CGGGUA------CGUCAAUCCAAG
((..(((..(((.(((.....))).)))............((((.((((.(((((((((...---....))))))))))))).))))...------)))..)------)........... ( -35.60)
>consensus
GUGUCCGUCACUCAAUAUCACAUUCAGUCAAUAAUAUAACCUGAACGAAAUCGGCGGGGCCC___AGCCCACCGCCGAUUCCAUCAGAUA______CGGGUA______AGCC______AG
(((.....))).........(.(((((.............))))).).(((((((((((.........)).)))))))))........................................ (-15.84 = -15.70 +  -0.13)

alignment

secondary structure

dotplot

Window 9

Location	9,935,825 – 9,935,924
Length	99
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	71.25
Mean single sequence MFE	-35.38
Consensus MFE	-19.90
Energy contribution	-20.12
Covariance contribution	0.23
Combinations/Pair	1.21
Mean z-score	-2.24
Structure conservation index	0.56
SVM decision value	2.16
SVM RNA-class probability	0.989302
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 9935825 99 - 23771897
CU------GGCU------GAACCG------UAUCUGCUGGAAUCGGCGUUGGCCG---UAGCCUCGCCGAUUUCGUUCAGAUCGUAUUAUUGACUGAAUGUGAUAUUGAGUGACGGACAC
..------....------...(((------(.((....((((((((((..(((..---..))).))))))))))((((((.(((......)))))))))........))...)))).... ( -35.20)
>DroVir_CAF1 88248 85 - 1
--------------------------------AUUGUUGUAAUCAGCCGGAGGUU---GGGCCCCGCCGAUUUCGUUCAGGUUAUAUUAUUGACUGAAUGUUAUAUUGAGUGACGGACAC
--------------------------------...((((....))))..((((((---((......))))))))((((.(((((......)))))....(((((.....))))))))).. ( -20.20)
>DroPse_CAF1 88108 105 - 1
CUUGGAUUGACG------UACCCG------AAUCUGAGCGAAUCGGCGGGGGGCU---GGGCCCCGCCGAUUUCGUUCAGGUUAUAUUAUUGACUGAAUGUGAUAUUGAGUGACGGACAC
............------...(((------(((((((((((((((((((((....---...))))))))).)))))))))))).........(((.((((...)))).)))..))).... ( -42.60)
>DroWil_CAF1 133471 102 - 1
CU------GUCC------CUGCUG------UUGUUAAUCGAAUCGGUGAUCGAUUGCCUCGAUUCACCGAUUUCGUUCAGAUUAUACUAUUGACUGAAUGUUAUAUUGAGUGACGGACAC
.(------((((------(....)------..((((.((((((((((((((((.....)))).))))))))))(((((((.(((......)))))))))).......)).))))))))). ( -32.50)
>DroAna_CAF1 85105 111 - 1
CU------GGAUUGGGCCAAUCGGUACGAAUAUCUGCUGGAAUCGGCGAUGGCCG---GAGCCCCGCCGAUUUCGUUCAGAUCGUACUAUUGACUGAAUGUAAUAUUGAGUGACGGACAC
.(------(.(((.((.((((.(((((((...((((.(((((((((((..(((..---..))).)))))))))))..))))))))))))))).)).))).)).................. ( -39.20)
>DroPer_CAF1 89220 105 - 1
CUUGGAUUGACG------UACCCG------AAUCUGAGCGAAUCGGCGGGGGGCU---GGGCCCCGCCGAUUUCGUUCAGGUUAUAUUAUUGACUGAAUGUGAUAUUGAGUGACGGACAC
............------...(((------(((((((((((((((((((((....---...))))))))).)))))))))))).........(((.((((...)))).)))..))).... ( -42.60)
>consensus
CU______GACG______UACCCG______UAUCUGAUCGAAUCGGCGGGGGGCU___GGGCCCCGCCGAUUUCGUUCAGAUUAUAUUAUUGACUGAAUGUGAUAUUGAGUGACGGACAC
................................((((...((((((((((..............))))))))))(((((((.(((......)))))))))).............))))... (-19.90 = -20.12 +   0.23)

alignment

secondary structure

dotplot

Window 0

Location	9,935,865 – 9,935,964
Length	99
Sequences	6
Columns	111
Reading direction	reverse
Mean pairwise identity	87.95
Mean single sequence MFE	-39.90
Consensus MFE	-29.63
Energy contribution	-30.49
Covariance contribution	0.86
Combinations/Pair	1.03
Mean z-score	-3.31
Structure conservation index	0.74
SVM decision value	0.44
SVM RNA-class probability	0.738294
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 9935865 99 - 23771897
AUUGUAGCCGGUAUUGUAGCCGGUAUUGAAAUUGCUGGUGCUGGCU------GAACCG------UAUCUGCUGGAAUCGGCGUUGGCCGUAGCCUCGCCGAUUUCGUUCAG
...((((.((((....(((((((((((.........))))))))))------).))))------...)))).((((((((((..(((....))).))))))))))...... ( -42.70)
>DroSec_CAF1 87864 93 - 1
AUUGUAGCCGGUAUUGUA------AUUGAAAUUGCUGGUGCUGGCU------GAACCG------UAUCUGCUGGAAUCGGCGUUGGCCGUAGCCUCGCCGAUUUCGUUCAG
.....(((((((((((((------((....))))).))))))))))------((((.(------(....)).((((((((((..(((....))).)))))))))))))).. ( -39.80)
>DroSim_CAF1 91423 93 - 1
AUUGUAGCCGGUAUUGUA------AUUGAAAUUGCUGGUGCUGGCU------GAACCG------UAUCUGCUGGAAUCGGCGUUGGCCGUAGCCUCGCCGAUUUCGUUCAG
.....(((((((((((((------((....))))).))))))))))------((((.(------(....)).((((((((((..(((....))).)))))))))))))).. ( -39.80)
>DroEre_CAF1 90484 93 - 1
AUUGUAGCCGGGAUUGUA------AUUGAAAUUGCUGGUGCUGGCU------GAACCG------UAUCUGCUGGAAUCGGCGUUGGCCGUAGCCUCGCCGAUUUCGUUCAG
.....((((((.((((((------((....))))).))).))))))------((((.(------(....)).((((((((((..(((....))).)))))))))))))).. ( -37.30)
>DroYak_CAF1 91946 93 - 1
AUUGUAGCCGGUAUUGUA------AUUGAAAUUGCUGGUGCUGGCU------GAACCG------UAUCUGCUGGAAUCGGCGUUGGCCGUAGCCUCGCCGAUUUCGUUCAG
.....(((((((((((((------((....))))).))))))))))------((((.(------(....)).((((((((((..(((....))).)))))))))))))).. ( -39.80)
>DroAna_CAF1 85145 105 - 1
AUUGUAGCCGGAUUGGUA------GCCGGAAUUGUAGCUGCUGGAUUGGGCCAAUCGGUACGAAUAUCUGCUGGAAUCGGCGAUGGCCGGAGCCCCGCCGAUUUCGUUCAG
.(((((.(((.((((((.------.((((...........)))).....))))))))))))))....(((.(((((((((((..(((....))).)))))))))))..))) ( -40.00)
>consensus
AUUGUAGCCGGUAUUGUA______AUUGAAAUUGCUGGUGCUGGCU______GAACCG______UAUCUGCUGGAAUCGGCGUUGGCCGUAGCCUCGCCGAUUUCGUUCAG
.....(((((((((((((..............))).)))))))))).....................(((.(((((((((((..(((....))).)))))))))))..))) (-29.63 = -30.49 +   0.86)

alignment

secondary structure

dotplot

Window 1

Location	9,935,924 – 9,936,023
Length	99
Sequences	6
Columns	99
Reading direction	forward
Mean pairwise identity	78.95
Mean single sequence MFE	-17.32
Consensus MFE	-8.75
Energy contribution	-8.67
Covariance contribution	-0.08
Combinations/Pair	1.56
Mean z-score	-2.04
Structure conservation index	0.51
SVM decision value	0.19
SVM RNA-class probability	0.626912
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 9935924 99 + 23771897
CACCAGCAAUUUCAAUACCGGCUACAAUACCGGCUACAAUUACGGGCCCCAAAGUUACGGGCCACAAACAUACGGCCACAAUCUCAAUCAGAGCCUCAA
...................(((.........((((.........(((((.........)))))..........))))....(((.....)))))).... ( -19.91)
>DroSec_CAF1 87923 93 + 1
CACCAGCAAUUUCAAU------UACAAUACCGGCUACAAUUACGGCCCCCAAAGUUACGGGCCCCAAACAUACGGCCACAAUCUCAAUCAGAGCCUCAA
................------.........((((........(((((..........)))))((........))................)))).... ( -15.00)
>DroSim_CAF1 91482 93 + 1
CACCAGCAAUUUCAAU------UACAAUACCGGCUACAAUUACGGCCCCCAAAGUUACGGGCCCCAAACAUACGGCCACAAUCUCAAUCAGAGCCUCAA
................------.........((((........(((((..........)))))((........))................)))).... ( -15.00)
>DroEre_CAF1 90543 93 + 1
CACCAGCAAUUUCAAU------UACAAUCCCGGCUACAAUUACGGCCCCCAAAGUUACGGGCCCCAAAGUUACGGCCACAAUCUCAAUCAGAGUCUCAA
................------.........((((..((((..(((((..........)))))....))))..)))).....(((.....)))...... ( -16.00)
>DroWil_CAF1 133573 87 + 1
ACACAGAAAUAGCUAU------CACAAUAUAUAUGGCAGUAACUGUG-CCAAUGCCAGUGGC-----AGUGGCAGUGGCAAUUACAAUUACAAUUACAA
...........(((((------..........))))).((((...((-(((.(((((.....-----..))))).))))).)))).............. ( -20.70)
>DroYak_CAF1 92005 93 + 1
CACCAGCAAUUUCAAU------UACAAUACCGGCUACAAUUACGGCCCCCAAAGUUACGGGCCCCAAAGCUAUGGCUACAAUCUCAAUCAGAGCCUCAA
................------.........((((........(((((..........)))))....(((....)))..............)))).... ( -17.30)
>consensus
CACCAGCAAUUUCAAU______UACAAUACCGGCUACAAUUACGGCCCCCAAAGUUACGGGCCCCAAACAUACGGCCACAAUCUCAAUCAGAGCCUCAA
...............................((((........(((((..........)))))..........))))...................... ( -8.75 =  -8.67 +  -0.08)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:56:59 2006