Locus 2345

Sequence ID	3R_DroMel_CAF1
Location	6,676,174 – 6,676,302
Length	128
Max. P	0.995621

overview

Window 6

Location	6,676,174 – 6,676,273
Length	99
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	78.79
Mean single sequence MFE	-30.10
Consensus MFE	-19.41
Energy contribution	-19.82
Covariance contribution	0.42
Combinations/Pair	1.14
Mean z-score	-1.72
Structure conservation index	0.64
SVM decision value	0.68
SVM RNA-class probability	0.821222
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 6676174 99 - 27905053
AUAC-----------GUAUGCGAUGAUGAUAUACCAUCGAAAGUGGAUACUGCUACUUUCAGAUAGA--------AUGUGUCUGGGUACGGAUUCUCGUGCGGUUUGUUUACCUGCUC--
...(-----------((((.(...((((......))))((((((((......))))))))(((((..--------...)))))).))))).........(((((......))).))..-- ( -25.80)
>DroSec_CAF1 60776 99 - 1
GUAC-----------GGAUGCGAUGAUGAUAUACCAUCGAAAGUGGAUACUGCUACUUUCAGGUAGA--------AUGUGUCUGGGUACGGAUUCUCGUGCGGUUUGUUUACCUGCUC--
...(-----------(((((((..((((......))))((((((((......)))))))).......--------.)))))))).((((((....))))))(((......))).....-- ( -30.20)
>DroSim_CAF1 61772 99 - 1
GUAC-----------GGAUGCGAUGAUGAUAUACCAUCGAAAGUGGAUACUGCUACUUUCAGGUAGA--------AUGUGUCUGGGUACGGAUUCUCGUGCGGUUUGUUUACCUGCUC--
...(-----------(((((((..((((......))))((((((((......)))))))).......--------.)))))))).((((((....))))))(((......))).....-- ( -30.20)
>DroEre_CAF1 61940 109 - 1
GUAU-----------GGAUGCGAUGAUGAUACACCAUCGAAAGUGGAUACUGAUACUUUCAGGUAGAAUAACCGAAUGGAUCUGAGUACAGAUUCUCGUGCGGUUUGUUUACCUGCUCUC
....-----------(((.((...((((......))))(((((((........)))))))(((((((..(((((...(((((((....))))))).....)))))..)))))))))))). ( -35.00)
>DroYak_CAF1 62469 107 - 1
GUAU-----------GGAUGCGAUGAUGAUAUACCAUCGAAAGUGGAUACUGAUACUUCCAGGUAGAAGGGCUGAAUGGAUCUGAGUACAGAUUCUCGUGCGGUUUGUUUACCUGCUC--
((((-----------..((.(((((.........)))))...))..)))).........((((((((..(((((...(((((((....))))))).....)))))..))))))))...-- ( -31.70)
>DroAna_CAF1 67175 103 - 1
GAAAAAAAAGAAGUAAAAAGCGAUGAGAAUACAACGCCGAAAGUGGAAAC----ACUUUCAGGUAGA--------ACCAAUCUGAGAGCGGGUUU---CGAGGUUUGUUUACCUGCAC--
...................(((.((......)).))).(((((((....)----))))))(((((((--------...(((((((((.....)))---).)))))..)))))))....-- ( -27.70)
>consensus
GUAC___________GGAUGCGAUGAUGAUAUACCAUCGAAAGUGGAUACUGCUACUUUCAGGUAGA________AUGUAUCUGAGUACGGAUUCUCGUGCGGUUUGUUUACCUGCUC__
...................((((((.........))))(((((((........)))))))(((((((........(((.(((((....)))))...)))........))))))))).... (-19.41 = -19.82 +   0.42)

alignment

secondary structure

dotplot

Window 7

Location	6,676,212 – 6,676,302
Length	90
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	75.32
Mean single sequence MFE	-20.09
Consensus MFE	-10.66
Energy contribution	-10.92
Covariance contribution	0.25
Combinations/Pair	1.18
Mean z-score	-2.18
Structure conservation index	0.53
SVM decision value	1.41
SVM RNA-class probability	0.950803
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 6676212 90 + 27905053
CACAU--------UCUAUCUGAAAGUAGCAGUAUCCACUUUCGAUGGUAUAUCAUCAUCGCAUAC-----------GUAUA------AACAUUC-----AGCUGGUAGAAUGAAUUACUU
..(((--------((((((.((((((.(......).))))))((((((.....))))))......-----------.....------.......-----....)))))))))........ ( -20.40)
>DroSec_CAF1 60814 90 + 1
CACAU--------UCUACCUGAAAGUAGCAGUAUCCACUUUCGAUGGUAUAUCAUCAUCGCAUCC-----------GUACA------AACAUUC-----AGCUGGCAGAAUGAAUUACUU
..(((--------(((.((.((((((.(......).))))))((((((.....))))))......-----------.....------.......-----....)).))))))........ ( -18.40)
>DroSim_CAF1 61810 90 + 1
CACAU--------UCUACCUGAAAGUAGCAGUAUCCACUUUCGAUGGUAUAUCAUCAUCGCAUCC-----------GUACA------AACAUUU-----AGCUGGCAGAAUGAAUUACUU
..(((--------(((.((.((((((.(......).))))))((((((.....))))))......-----------.....------.......-----....)).))))))........ ( -18.40)
>DroEre_CAF1 61980 102 + 1
UCCAUUCGGUUAUUCUACCUGAAAGUAUCAGUAUCCACUUUCGAUGGUGUAUCAUCAUCGCAUCC-----------AUACAAA--CAAACAUUC-----AGAUGGCAGAAUGAAUUACUU
..(((((.((((((......((((((..........))))))(((((((...)))))))......-----------.......--.........-----.)))))).)))))........ ( -20.10)
>DroYak_CAF1 62507 104 + 1
UCCAUUCAGCCCUUCUACCUGGAAGUAUCAGUAUCCACUUUCGAUGGUAUAUCAUCAUCGCAUCC-----------AUACAAACACAAACAUUC-----AGCUGGCAGAAUGAAUUACUU
..(((((.((((((((....))))).....((((.......(((((((.....))))))).....-----------))))..............-----....))).)))))........ ( -20.70)
>DroAna_CAF1 67210 106 + 1
UUGGU--------UCUACCUGAAAGU----GUUUCCACUUUCGGCGUUGUAUUCUCAUCGCUUUUUACUUCUUUUUUUUCAAG--CUAAUGCUCAUACAAGCUGGUCGAAUAAAUUACUU
...((--------((.(((.((((((----(....)))))))(((.((((((...(((.((((.................)))--)..)))...)))))))))))).))))......... ( -22.53)
>consensus
CACAU________UCUACCUGAAAGUAGCAGUAUCCACUUUCGAUGGUAUAUCAUCAUCGCAUCC___________GUACA______AACAUUC_____AGCUGGCAGAAUGAAUUACUU
.............(((.((.((((((..........))))))((((((.....))))))............................................)).)))........... (-10.66 = -10.92 +   0.25)

alignment

secondary structure

dotplot

Window 8

Location	6,676,212 – 6,676,302
Length	90
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	75.32
Mean single sequence MFE	-27.24
Consensus MFE	-14.58
Energy contribution	-15.05
Covariance contribution	0.47
Combinations/Pair	1.12
Mean z-score	-2.90
Structure conservation index	0.54
SVM decision value	2.60
SVM RNA-class probability	0.995621
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 6676212 90 - 27905053
AAGUAAUUCAUUCUACCAGCU-----GAAUGUU------UAUAC-----------GUAUGCGAUGAUGAUAUACCAUCGAAAGUGGAUACUGCUACUUUCAGAUAGA--------AUGUG
........(((((((.(.((.-----..((((.------...))-----------))..))...((((......))))((((((((......)))))))).).))))--------))).. ( -22.50)
>DroSec_CAF1 60814 90 - 1
AAGUAAUUCAUUCUGCCAGCU-----GAAUGUU------UGUAC-----------GGAUGCGAUGAUGAUAUACCAUCGAAAGUGGAUACUGCUACUUUCAGGUAGA--------AUGUG
........(((((((((.((.-----...(((.------...))-----------)...))...((((......))))((((((((......)))))))).))))))--------))).. ( -28.40)
>DroSim_CAF1 61810 90 - 1
AAGUAAUUCAUUCUGCCAGCU-----AAAUGUU------UGUAC-----------GGAUGCGAUGAUGAUAUACCAUCGAAAGUGGAUACUGCUACUUUCAGGUAGA--------AUGUG
........(((((((((.((.-----...(((.------...))-----------)...))...((((......))))((((((((......)))))))).))))))--------))).. ( -28.40)
>DroEre_CAF1 61980 102 - 1
AAGUAAUUCAUUCUGCCAUCU-----GAAUGUUUG--UUUGUAU-----------GGAUGCGAUGAUGAUACACCAUCGAAAGUGGAUACUGAUACUUUCAGGUAGAAUAACCGAAUGGA
..(((..(((((...((((..-----((((....)--)))..))-----------))....)))))...))).((((((((((((........))))))).(((......)))).)))). ( -23.70)
>DroYak_CAF1 62507 104 - 1
AAGUAAUUCAUUCUGCCAGCU-----GAAUGUUUGUGUUUGUAU-----------GGAUGCGAUGAUGAUAUACCAUCGAAAGUGGAUACUGAUACUUCCAGGUAGAAGGGCUGAAUGGA
......(((((((.(((..((-----(..((...(((((.((((-----------..((.(((((.........)))))...))..)))).)))))...))..)))...))).))))))) ( -30.10)
>DroAna_CAF1 67210 106 - 1
AAGUAAUUUAUUCGACCAGCUUGUAUGAGCAUUAG--CUUGAAAAAAAAGAAGUAAAAAGCGAUGAGAAUACAACGCCGAAAGUGGAAAC----ACUUUCAGGUAGA--------ACCAA
..........(((.(((.((((((((...((((.(--(((.................))))))))...)))))).)).(((((((....)----)))))).))).))--------).... ( -30.33)
>consensus
AAGUAAUUCAUUCUGCCAGCU_____GAAUGUU______UGUAC___________GGAUGCGAUGAUGAUAUACCAUCGAAAGUGGAUACUGCUACUUUCAGGUAGA________AUGUA
...........((((((............................................((((.........))))(((((((........))))))).))))))............. (-14.58 = -15.05 +   0.47)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:33:05 2006