Locus 9266

Sequence ID	3R_DroMel_CAF1
Location	24,700,911 – 24,701,004
Length	93
Max. P	0.845126

overview

Window 0

Location	24,700,911 – 24,701,004
Length	93
Sequences	6
Columns	105
Reading direction	forward
Mean pairwise identity	78.77
Mean single sequence MFE	-27.40
Consensus MFE	-16.36
Energy contribution	-17.03
Covariance contribution	0.67
Combinations/Pair	1.15
Mean z-score	-1.97
Structure conservation index	0.60
SVM decision value	0.77
SVM RNA-class probability	0.845126
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 24700911 93 + 27905053
AGAAGGACAGGAACUUGUAGCCACUGUCCCAGGGCAUCAGUCCGGGCACGAUGGCCAGGAUGUAGAAGAUGGGUAUGGCUAAA----AUGGUAA--------GAU
............(((..((((((.((.((((...(.((.((((.(((......))).))))...)).).))))))))))))..----..)))..--------... ( -27.30)
>DroVir_CAF1 5224 100 + 1
AAAACGAAAGGAACUUGUAGCCACUGUCCCAUGGCAUCAGACCCGGCACAAUGGCCAGUAUAUAAAAUAUUGGUAUUGCUGCA----AAUAGAAGAUAUUAGC-A
....(....)...(((.((((((........))))..........((((((((.(((((((.....)))))))))))).))).----..)).)))........-. ( -23.00)
>DroPse_CAF1 1222 95 + 1
AGAACGACAGAAACUUGUAGCCACUGUCCCAGGGCAUCAGACCGGGCACAAUGGCCAGUAUAUAGAUGAUGGGUAUGGCUGCA----AGAAG-AAA----AGA-G
.............((((((((((.((.((((...((((..((.((.(.....).)).)).....)))).))))))))))))))----))...-...----...-. ( -31.30)
>DroWil_CAF1 5598 100 + 1
AAAACGAUAGAAACUUGUAACCGCUGUCCCAGGGCAUCAGUCCAGGCACAAUCGCCAGUAUAUAGAAGAUGGGUAUUGCUGGGGGGUAGAGGAGAA----AGA-G
.............(((....((.((..(((.((((....))))...........(((((((((.........))).)))))))))..)).))...)----)).-. ( -25.50)
>DroAna_CAF1 1961 95 + 1
AGAACGAUAGAAACUUGUAGCCGCUGUCCCAGGGCAUCAGGCCGGGCACAAUUGCCAGGAUAUAGAAGAUAGGUAUGGCUGCAAAA-AGGGCAG--------G-G
..............((((((((((((((....(((.....))).((((....))))...........)))))...)))))))))..-.......--------.-. ( -26.00)
>DroPer_CAF1 1210 96 + 1
AGAACGACAGAAACUUGUAGCCACUGUCCCAGGGCAUCAGACCGGGCACAAUGGCCAGUAUAUAGAUGAUGGGUAUGGCUGCA----AGAAAAAAA----AGA-G
.............((((((((((.((.((((...((((..((.((.(.....).)).)).....)))).))))))))))))))----)).......----...-. ( -31.30)
>consensus
AGAACGACAGAAACUUGUAGCCACUGUCCCAGGGCAUCAGACCGGGCACAAUGGCCAGUAUAUAGAAGAUGGGUAUGGCUGCA____AGAAGAAAA____AGA_G
...............((((((((.((.((((.(((....).)).(((......))).............))))))))))))))...................... (-16.36 = -17.03 +   0.67)

alignment

secondary structure

dotplot

Window 1

Location	24,700,911 – 24,701,004
Length	93
Sequences	6
Columns	105
Reading direction	reverse
Mean pairwise identity	78.77
Mean single sequence MFE	-22.27
Consensus MFE	-16.84
Energy contribution	-17.70
Covariance contribution	0.86
Combinations/Pair	1.07
Mean z-score	-1.26
Structure conservation index	0.76
SVM decision value	0.50
SVM RNA-class probability	0.759658
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 24700911 93 - 27905053
AUC--------UUACCAU----UUUAGCCAUACCCAUCUUCUACAUCCUGGCCAUCGUGCCCGGACUGAUGCCCUGGGACAGUGGCUACAAGUUCCUGUCCUUCU
...--------.......----............((((.......(((.(((......))).)))..))))....(((((((..((.....))..)))))))... ( -22.30)
>DroVir_CAF1 5224 100 - 1
U-GCUAAUAUCUUCUAUU----UGCAGCAAUACCAAUAUUUUAUAUACUGGCCAUUGUGCCGGGUCUGAUGCCAUGGGACAGUGGCUACAAGUUCCUUUCGUUUU
(-((.((((.....))))----.)))......................((((((((((.((((((.....))).))).))))))))))................. ( -25.20)
>DroPse_CAF1 1222 95 - 1
C-UCU----UUU-CUUCU----UGCAGCCAUACCCAUCAUCUAUAUACUGGCCAUUGUGCCCGGUCUGAUGCCCUGGGACAGUGGCUACAAGUUUCUGUCGUUCU
.-...----...-...((----((.((((((.((((.((((.....(((((.(.....).)))))..))))...))))...)))))).))))............. ( -25.60)
>DroWil_CAF1 5598 100 - 1
C-UCU----UUCUCCUCUACCCCCCAGCAAUACCCAUCUUCUAUAUACUGGCGAUUGUGCCUGGACUGAUGCCCUGGGACAGCGGUUACAAGUUUCUAUCGUUUU
.-...----.............(((((.......((((.((((......((((....))))))))..))))..)))))..((((((...........)))))).. ( -16.70)
>DroAna_CAF1 1961 95 - 1
C-C--------CUGCCCU-UUUUGCAGCCAUACCUAUCUUCUAUAUCCUGGCAAUUGUGCCCGGCCUGAUGCCCUGGGACAGCGGCUACAAGUUUCUAUCGUUCU
.-.--------((((...-....)))).....................((((..((((.((((((.....)))..)))))))..))))................. ( -18.20)
>DroPer_CAF1 1210 96 - 1
C-UCU----UUUUUUUCU----UGCAGCCAUACCCAUCAUCUAUAUACUGGCCAUUGUGCCCGGUCUGAUGCCCUGGGACAGUGGCUACAAGUUUCUGUCGUUCU
.-...----.......((----((.((((((.((((.((((.....(((((.(.....).)))))..))))...))))...)))))).))))............. ( -25.60)
>consensus
C_UCU____UUUUCCUCU____UGCAGCCAUACCCAUCUUCUAUAUACUGGCCAUUGUGCCCGGUCUGAUGCCCUGGGACAGUGGCUACAAGUUUCUGUCGUUCU
................................................((((((((((.((.((.(....).)).)).))))))))))................. (-16.84 = -17.70 +   0.86)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:30:21 2006