Locus 9883

Sequence ID	3R_DroMel_CAF1
Location	26,376,302 – 26,376,409
Length	107
Max. P	0.689640

overview

Window 7

Location	26,376,302 – 26,376,409
Length	107
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	80.11
Mean single sequence MFE	-22.47
Consensus MFE	-14.73
Energy contribution	-15.29
Covariance contribution	0.56
Combinations/Pair	1.30
Mean z-score	-1.57
Structure conservation index	0.66
SVM decision value	0.33
SVM RNA-class probability	0.689640
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 26376302 107 + 27905053
UAGCUUAAGCCAUUAAA-AAGUGCAGUAAACAGGAAAUCACAAAAAAA----------UAGCUGUAGAAGUGAAAUCCUGGAUGA-GCACGGUGGUGAUACAAAUAUCCUU-UAAGGAAG
...(((((((((((...-..((((..((..(((((..((((.......----------...........))))..)))))..)).-))))))))))((((....))))..)-)))).... ( -22.87)
>DroSec_CAF1 105843 106 + 1
GAGCUUAAGCCAUUAAA-AAGUGCAGUAAACAGGAAAUCACAAA-AAA----------UAGCUGUAGAAGUGGAAUCCUGGAUGA-GCACGGUGGUGAUACAAAUAUCCUU-UAAGGAAG
...(((((((((((...-..((((..((..(((((..((((...-...----------...........))))..)))))..)).-))))))))))((((....))))..)-)))).... ( -22.03)
>DroSim_CAF1 103495 106 + 1
GAGCUUAAGCCAUUAAA-AAGUGCAGUAAACAGGAAAUCACAAA-AAA----------UAGCUGUAGAAGUGAAAUCCUGGAUGA-GCACGGUGGUGAUACAAAUAUCCUU-UAAGGAAG
...(((((((((((...-..((((..((..(((((..((((...-...----------...........))))..)))))..)).-))))))))))((((....))))..)-)))).... ( -22.93)
>DroEre_CAF1 109999 107 + 1
GAGCUUAAGCCAUUAAA-AAGUGCAGUAAACAGGAAAUCACAAAAAAA----------UAACAGCGGAAGUGAAAUCCUGGAUGA-GCACGAUGGGGCUACAAAUAUCCUU-UAAGGAAG
.((((....(((((...-..((((..((..(((((..((((.......----------...........))))..)))))..)).-))))))))))))).......(((..-...))).. ( -24.17)
>DroYak_CAF1 103924 117 + 1
UAGCUUAAGCCAUUAAA-AAGUGCAGUAAACAGGAAAUCACAAAAAAAUCCAACAGUAUAACAGCAGCAGUGGAAUCCUGGAUGA-GCUCGAUGGUGAUACAAAUAUCCUU-UAAGGAAG
...(((((((((((...-.(((.((.....(((((..((((............................))))..)))))..)).-))).))))))((((....))))..)-)))).... ( -18.99)
>DroAna_CAF1 118799 107 + 1
GGACUUGAGCCAUUAGAAGAAUGCAGUAAAUAGGAAAUCAUGGGAGGA----------GUUUUGUAA---AGAAACUCCGGUCGAGGCGGGGAGCUGAUGCCAAUAUUUGCCAAAGGAAG
...(((..((.(((.....))))).(((((((.............(((----------(((((....---.))))))))(((...(((.....)))...)))..)))))))..))).... ( -23.80)
>consensus
GAGCUUAAGCCAUUAAA_AAGUGCAGUAAACAGGAAAUCACAAAAAAA__________UAGCUGUAGAAGUGAAAUCCUGGAUGA_GCACGGUGGUGAUACAAAUAUCCUU_UAAGGAAG
........((((((......((((......(((((..((((............................))))..)))))......))))))))))..........((((....)))).. (-14.73 = -15.29 +   0.56)

alignment

secondary structure

dotplot

Window 8

Location	26,376,302 – 26,376,409
Length	107
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	80.11
Mean single sequence MFE	-19.69
Consensus MFE	-12.41
Energy contribution	-13.86
Covariance contribution	1.45
Combinations/Pair	1.20
Mean z-score	-1.64
Structure conservation index	0.63
SVM decision value	0.27
SVM RNA-class probability	0.663700
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 26376302 107 - 27905053
CUUCCUUA-AAGGAUAUUUGUAUCACCACCGUGC-UCAUCCAGGAUUUCACUUCUACAGCUA----------UUUUUUUGUGAUUUCCUGUUUACUGCACUU-UUUAAUGGCUUAAGCUA
.....(((-(((((((....))))......((((-..(..(((((..((((...........----------.......))))..)))))..)...)))).)-)))))((((....)))) ( -22.57)
>DroSec_CAF1 105843 106 - 1
CUUCCUUA-AAGGAUAUUUGUAUCACCACCGUGC-UCAUCCAGGAUUCCACUUCUACAGCUA----------UUU-UUUGUGAUUUCCUGUUUACUGCACUU-UUUAAUGGCUUAAGCUC
...(((((-(((((((....))))......((((-..(..(((((...(((...........----------...-...)))...)))))..)...)))).)-))))).))......... ( -18.33)
>DroSim_CAF1 103495 106 - 1
CUUCCUUA-AAGGAUAUUUGUAUCACCACCGUGC-UCAUCCAGGAUUUCACUUCUACAGCUA----------UUU-UUUGUGAUUUCCUGUUUACUGCACUU-UUUAAUGGCUUAAGCUC
...(((((-(((((((....))))......((((-..(..(((((..((((...........----------...-...))))..)))))..)...)))).)-))))).))......... ( -22.13)
>DroEre_CAF1 109999 107 - 1
CUUCCUUA-AAGGAUAUUUGUAGCCCCAUCGUGC-UCAUCCAGGAUUUCACUUCCGCUGUUA----------UUUUUUUGUGAUUUCCUGUUUACUGCACUU-UUUAAUGGCUUAAGCUC
..(((...-..)))..((((.((((.....((((-..(..(((((..((((...........----------.......))))..)))))..)...))))..-......))))))))... ( -23.39)
>DroYak_CAF1 103924 117 - 1
CUUCCUUA-AAGGAUAUUUGUAUCACCAUCGAGC-UCAUCCAGGAUUCCACUGCUGCUGUUAUACUGUUGGAUUUUUUUGUGAUUUCCUGUUUACUGCACUU-UUUAAUGGCUUAAGCUA
..(((...-..)))................((((-.(((.(((.......))).(((.((...((....(((..((.....))..))).))..)).)))...-....)))))))...... ( -15.80)
>DroAna_CAF1 118799 107 - 1
CUUCCUUUGGCAAAUAUUGGCAUCAGCUCCCCGCCUCGACCGGAGUUUCU---UUACAAAAC----------UCCUCCCAUGAUUUCCUAUUUACUGCAUUCUUCUAAUGGCUCAAGUCC
....(((.((((((((..((.((((((.....)).......(((((((..---.....))))----------))).....))))..)))))))....((((.....))))))).)))... ( -15.90)
>consensus
CUUCCUUA_AAGGAUAUUUGUAUCACCACCGUGC_UCAUCCAGGAUUUCACUUCUACAGCUA__________UUUUUUUGUGAUUUCCUGUUUACUGCACUU_UUUAAUGGCUUAAGCUC
..((((....))))................((((......(((((..((((............................))))..)))))......)))).........(((....))). (-12.41 = -13.86 +   1.45)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:44:11 2006