Locus 7603

Sequence ID	3R_DroMel_CAF1
Location	20,386,246 – 20,386,385
Length	139
Max. P	0.876596

overview

Window 4

Location	20,386,246 – 20,386,345
Length	99
Sequences	6
Columns	104
Reading direction	reverse
Mean pairwise identity	81.43
Mean single sequence MFE	-27.19
Consensus MFE	-19.11
Energy contribution	-20.47
Covariance contribution	1.36
Combinations/Pair	1.15
Mean z-score	-2.34
Structure conservation index	0.70
SVM decision value	0.90
SVM RNA-class probability	0.876596
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 20386246 99 - 27905053
AGAAGGCGCAGCACGAGGCCAACAAAAUUAAGUUGUUCGGCCUUGAAAUUGAACACAGUGAGUUCAAUGUG-AAAGCUGUGG-AAAUAUCUUAUAA---UCCUU
..((((((((((.((((((((((((.......))))).)))))))..(((((((.......)))))))...-...))))))(-(....))......---.)))) ( -31.60)
>DroSec_CAF1 9137 102 - 1
AGAAGGCGCAGCACGAGGCCAACAAAAUUAAGCUUUUCGGCCUUGAAAUUGAACACAGUAAGUUCGAUGUG-AAUGCUUUGG-CAUUACCUUAUAAUAAUGCAU
..((((((..((.(((((((..................)))))))..(((((((.......))))))))).-..)))))).(-(((((........)))))).. ( -27.17)
>DroSim_CAF1 12083 102 - 1
AGAAGGCGCAGCACGAGGCCAACAAAAUUAAGCUUUUCGGCCUUGAAAUUGAACACAGUAAGUUUGAUGUG-AAAGCUGUGG-CAUUACCUUAUAAUAAUGCAU
......((((((.(((((((..................)))))))..((..(((.......)))..))...-...))))))(-(((((........)))))).. ( -29.27)
>DroEre_CAF1 8605 102 - 1
AGAAGGCGCAGCACGAGGCCAACAAAAUUAAGCUUUUCGGCCUUGAAAUUGAACACAGUAAGUGCGAUGCG-CAAGCUGUGG-AAUUACCUUAAAGUAAUCUUU
.((((.((((((.(((((((..................)))))))................((((...)))-)..)))))).-.(((((......))))))))) ( -26.47)
>DroYak_CAF1 12533 102 - 1
AGAAGGCGCAGCACGAGGCCAAUAAAAUUAAGCUAUUUGGCCUUGAAAUUGAACACAGUAAGUUGGAUGUG-CAAGCUGUGG-AAUUACCAUAUAAUAAUCCUU
..((((((((((.(((((((((..............)))))))))..(((.(((.......))).)))...-...)))))).-.((((.....))))...)))) ( -26.34)
>DroMoj_CAF1 28188 100 - 1
AGAAGGCCCAGCACGAGGCCAACAAAAUCAAACUAUAUGGCCUGGAAAUUGAGCACAGUGAGUGCA---UGCAAUACUAUAUUGAUG-UAAUUGAACUAUAUCA
..........((((.((((((................)))))).).......((((.....)))).---)))..........(((((-((.......))))))) ( -22.29)
>consensus
AGAAGGCGCAGCACGAGGCCAACAAAAUUAAGCUUUUCGGCCUUGAAAUUGAACACAGUAAGUUCGAUGUG_AAAGCUGUGG_AAUUACCUUAUAAUAAUCCUU
......((((((.(((((((..................)))))))..(((((((.......))))))).......))))))....................... (-19.11 = -20.47 +   1.36)

alignment

secondary structure

dotplot

Window 5

Location	20,386,274 – 20,386,385
Length	111
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	79.70
Mean single sequence MFE	-31.67
Consensus MFE	-20.55
Energy contribution	-20.22
Covariance contribution	-0.33
Combinations/Pair	1.35
Mean z-score	-1.79
Structure conservation index	0.65
SVM decision value	0.62
SVM RNA-class probability	0.802921
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 20386274 111 + 27905053
C-ACAUUG--------AACUCACUGUGUUCAAUUUCAAGGCCGAACAACUUAAUUUUGUUGGCCUCGUGCUGCGCCUUCUUCUUCAGGCGACAGGCGCGUGAGGCCAGCUUGUUCUUCUC
.-..((((--------(((.......))))))).........((((((.........((((((((((((((.(((((........)))))...)))))..)))))))))))))))..... ( -41.10)
>DroVir_CAF1 10806 110 + 1
C-AAC-UC--------GACUCACUGUGCUCAAUUUCCAACCCAUAUAGUUUGAUCUUAUUAGCCUCAUGCUGGGCCUUCUUCUUCAGACGGCAGGCGCGAGAGGCUAAUUUGUUCUUCUC
.-...-..--------.....((((((................))))))..((.(..(((((((((.((((..(((.(((.....))).))).))))...)))))))))..).))..... ( -26.49)
>DroGri_CAF1 30407 111 + 1
C-AACUUC--------GACUCACUGUGCUCAAUUUCCAGGCCAUAGAGCUUGAUCUUGUUGGCCUCGUGCUGGGCCUUCUUCUUCAGGCGACAGGCGCGCGAGGCCAGCUUAUUCUUCUC
.-....((--------(((((..((.(((.........)))))..))).))))....(((((((((((((...((((((.((....)).)).)))))))))))))))))........... ( -39.10)
>DroWil_CAF1 12313 112 + 1
CUUUUUUG--------AACUUACUAUGUUCAAUUUCCAGUCCAUAUAGCUUUAUCUUGUUGGCCUCAUGCUGGGCUUUCUUCUUCAGACGACAAGCACGCGAUGCCAGCUUAUUCUUCUC
.....(((--------(((.......)))))).........................((((((.((..((...((((((.((....)).)).))))..)))).))))))........... ( -22.00)
>DroMoj_CAF1 28220 108 + 1
C-A---UG--------CACUCACUGUGCUCAAUUUCCAGGCCAUAUAGUUUGAUUUUGUUGGCCUCGUGCUGGGCCUUCUUCUUCAGCCGGCAGGCACGCGAUGCCAACUUGUUCUUCUC
.-.---.(--------(((.....))))........(((((......))))).....(((((((.((((((..(((..((.....))..))).)))))).)..))))))........... ( -31.40)
>DroAna_CAF1 9999 119 + 1
A-AGAUAUAUCUCCUAUACAUACUGUGUUCUAUUUCAAGGCCAAAGAGCUUGAUUUUGUUCGCCUCGUGCUGGGCUUUCUUCUUCAAGCGGCAGGCGCGGGAGGCCAGCUUGUUCUUCUC
(-(((..........((((.....))))..........((((...((((........))))..((((((((..(((..(((....))).))).)))))))).)))).......))))... ( -29.90)
>consensus
C_AAAUUG________AACUCACUGUGCUCAAUUUCCAGGCCAUAUAGCUUGAUCUUGUUGGCCUCGUGCUGGGCCUUCUUCUUCAGGCGACAGGCGCGCGAGGCCAGCUUGUUCUUCUC
.........................................................(((((((((.(((...((((((.((....)).)).))))))).)))))))))........... (-20.55 = -20.22 +  -0.33)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:49:53 2006