Locus 6229

Sequence ID	2R_DroMel_CAF1
Location	19,576,104 – 19,576,211
Length	107
Max. P	0.993018

overview

Window 9

Location	19,576,104 – 19,576,211
Length	107
Sequences	5
Columns	111
Reading direction	forward
Mean pairwise identity	84.07
Mean single sequence MFE	-33.08
Consensus MFE	-20.18
Energy contribution	-21.70
Covariance contribution	1.52
Combinations/Pair	1.10
Mean z-score	-3.00
Structure conservation index	0.61
SVM decision value	1.36
SVM RNA-class probability	0.945829
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 19576104 107 + 20766785
UUCCUCAUGUAAUCGGCUUCGUGGCUGCACCUGCGGAAUGCCAGGGGUAUUCCGCAAGCCGAUUACGACUUUUGUCGAUUU---CCU-UUAGCUAUAGCUAAAGAUUUAUU
........(((((((((((.(((....)))..((((((((((...)))))))))))))))))))))(((....))).....---.((-(((((....)))))))....... ( -45.70)
>DroSec_CAF1 2419 107 + 1
UUCCUCAUGUAAUCGGCUUCGUGGCUGCACCUGCGGAAUGCCAGGGGUAUUCCGAAAACCGAUUACGAUUUUUGUCGAUUU---CUU-UUAGCUAUAGCUAAAGAUAUAUU
........((((((((.((((..(......)..)((((((((...)))))))))))..))))))))(((....))).....---.((-(((((....)))))))....... ( -32.10)
>DroSim_CAF1 2921 110 + 1
UUCCUCAUGUAAUCGGCUUCGUGGCUGCACCUGCGGAAUGCCAGGGGUAUUCCGGAAACCGAUAACGAUUUUUGUCGUUUUUUUUUU-UUAGCUAUAGCUAAAGAUAUAUU
......((((((((((.((((((....)))...(((((((((...)))))))))))).)))))((((((....)))))).....(((-(((((....))))))))))))). ( -34.40)
>DroEre_CAF1 2299 100 + 1
UACCCUGUGUAAUCGGCUUCGUGGCUACACCUGCAGCAGGUCAGGGGUAUUCC--------AUUACGAUUUUUAUCGAUUU---UGUUUUAGCUUUAGCUAAAGAUUUAUU
..(((((.......((((....))))..(((((...)))))))))).......--------....((((....))))....---..(((((((....)))))))....... ( -24.40)
>DroYak_CAF1 2279 106 + 1
UACCCUGUGUAAUCGGCUUCGUGGCUGCACCUGCGGAAUGUCAGGGGUAUUCCGCAAACCGAUUACGAUUUUUGCCAAUAU---UAC-UUAGCUUUUGCCA-AGAUUUAUU
.......(((((((((....(((....))).((((((((..(...)..))))))))..)))))))))..............---..(-((.((....)).)-))....... ( -28.80)
>consensus
UUCCUCAUGUAAUCGGCUUCGUGGCUGCACCUGCGGAAUGCCAGGGGUAUUCCGCAAACCGAUUACGAUUUUUGUCGAUUU___UUU_UUAGCUAUAGCUAAAGAUUUAUU
........((((((((.((((.(..(((.(((((.....).)))).)))..))).)).))))))))(((....)))............(((((....)))))......... (-20.18 = -21.70 +   1.52)

alignment

secondary structure

dotplot

Window 0

Location	19,576,104 – 19,576,211
Length	107
Sequences	5
Columns	111
Reading direction	reverse
Mean pairwise identity	84.07
Mean single sequence MFE	-32.38
Consensus MFE	-21.22
Energy contribution	-22.18
Covariance contribution	0.96
Combinations/Pair	1.16
Mean z-score	-3.67
Structure conservation index	0.66
SVM decision value	2.37
SVM RNA-class probability	0.993018
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 19576104 107 - 20766785
AAUAAAUCUUUAGCUAUAGCUAA-AGG---AAAUCGACAAAAGUCGUAAUCGGCUUGCGGAAUACCCCUGGCAUUCCGCAGGUGCAGCCACGAAGCCGAUUACAUGAGGAA
......((((((((....)))))-)))---...(((((....)))((((((((((((((((((.((...)).))))))).((.....))...)))))))))))..)).... ( -43.00)
>DroSec_CAF1 2419 107 - 1
AAUAUAUCUUUAGCUAUAGCUAA-AAG---AAAUCGACAAAAAUCGUAAUCGGUUUUCGGAAUACCCCUGGCAUUCCGCAGGUGCAGCCACGAAGCCGAUUACAUGAGGAA
......((((((((....))).)-)))---)..............((((((((((((((((((.((...)).))))))..((.....))..))))))))))))........ ( -31.10)
>DroSim_CAF1 2921 110 - 1
AAUAUAUCUUUAGCUAUAGCUAA-AAAAAAAAAACGACAAAAAUCGUUAUCGGUUUCCGGAAUACCCCUGGCAUUCCGCAGGUGCAGCCACGAAGCCGAUUACAUGAGGAA
........((((((....)))))-).......(((((......)))))(((((((((((((((.((...)).))))))..((.....))..)))))))))........... ( -29.20)
>DroEre_CAF1 2299 100 - 1
AAUAAAUCUUUAGCUAAAGCUAAAACA---AAAUCGAUAAAAAUCGUAAU--------GGAAUACCCCUGACCUGCUGCAGGUGUAGCCACGAAGCCGAUUACACAGGGUA
........((((((....)))))).((---....((((....))))...)--------)......(((((....(((((....)))))..((....))......))))).. ( -21.70)
>DroYak_CAF1 2279 106 - 1
AAUAAAUCU-UGGCAAAAGCUAA-GUA---AUAUUGGCAAAAAUCGUAAUCGGUUUGCGGAAUACCCCUGACAUUCCGCAGGUGCAGCCACGAAGCCGAUUACACAGGGUA
.....((((-((......(((((-...---...))))).......((((((((((((((((((.........))))))).((.....))...))))))))))).)))))). ( -36.90)
>consensus
AAUAAAUCUUUAGCUAUAGCUAA_AAA___AAAUCGACAAAAAUCGUAAUCGGUUUGCGGAAUACCCCUGGCAUUCCGCAGGUGCAGCCACGAAGCCGAUUACAUGAGGAA
......((((((((....)))).......................(((((((((((..((......((((........)))).....))...)))))))))))..)))).. (-21.22 = -22.18 +   0.96)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:06:12 2006