Locus 9652

Sequence ID	3R_DroMel_CAF1
Location	25,520,497 – 25,520,597
Length	100
Max. P	0.836857

overview

Window 9

Location	25,520,497 – 25,520,597
Length	100
Sequences	6
Columns	116
Reading direction	forward
Mean pairwise identity	72.31
Mean single sequence MFE	-35.83
Consensus MFE	-15.62
Energy contribution	-17.12
Covariance contribution	1.51
Combinations/Pair	1.33
Mean z-score	-1.75
Structure conservation index	0.44
SVM decision value	0.04
SVM RNA-class probability	0.553887
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 25520497 100 + 27905053
UUCGACC-CCGCCUGCUUAUUAGGACUAUCGGCUGUGCAGAUGGGGGUUAUUACCCA---------------UAAGGUAACCCCAUGCCAAGGGUUCUGGCAGGCCAGAAACGUGA
.......-..(((((((....((((((...(((..........(((((((((.....---------------...)))))))))..)))...)))))))))))))........... ( -34.40)
>DroSec_CAF1 4365 100 + 1
UUCGACC-CCGCCUGCUUAUUAGGACUAUCUGCUGUGCAGAUGGGGGAUAUUACCCA---------------UAAGGUAACCCCAUGCCGAGGGUCCUGGCAGGGCAGAAACGUGA
(((..((-(.(((........((((((((((((...)))))).((((...(((((..---------------...)))))))))........))))))))).)))..)))...... ( -36.60)
>DroSim_CAF1 4364 99 + 1
UUCGACC-CUGCCUGCUUAUUAGGACUAUCUGCUGUGCAGAUGGGGGUUAUUACCCA---------------UAAGGUAACCCCAUGCCGAG-GUCCUGGCAGGGCAGAAACGUGA
(((..((-(((((........((((((((((((...)))))).(((((((((.....---------------...))))))))).......)-))))))))))))..)))...... ( -42.90)
>DroEre_CAF1 4379 96 + 1
UUCGACG-CCGCCUGCUUAUUAGGACUAUCUGCUGUGC---UG-GGGUUUUUGCCCA---------------UAGGAUAACCCCAUGCUGAGGCUCCUGGCAGGGUAGAAACGUGA
.....((-(..((((((....((((......(((..((---((-(((((....((..---------------..))..))))))).))...)))))))))))))((....))))). ( -31.50)
>DroAna_CAF1 1769 89 + 1
UUCAACCGUCACCCACUCAUUGGGACUAUCUGCUGUC---AUGGGGGG------------------------UAAGACAACCCCAUGCUGAGGGUCCUGAAAAGGGCGUAACGUGA
.....((((.((((.((..(..(((((.((....(.(---((((((..------------------------........)))))))).)).)))))..)..)))).)).))).). ( -31.30)
>DroPer_CAF1 1748 104 + 1
UUGUGCC-UCACCCACUCAUUAGGACUAUUCCCUGGC---AUGGGGGG--CGGCCCAGAAAAACUCGGGGAGUAAGACAACCCCAUGCUGAGGG------CGAGGGCGUAACGUGA
..((.((-((.(((.......(((.......)))(((---((((((.(--(..(((.((.....)).))).)).......)))))))))..)))------.))))))......... ( -38.30)
>consensus
UUCGACC_CCGCCUGCUUAUUAGGACUAUCUGCUGUGC__AUGGGGGUUAUUACCCA_______________UAAGAUAACCCCAUGCCGAGGGUCCUGGCAGGGCAGAAACGUGA
.........(((((((((.((((((((.((.((.......((((((..................................)))))))).)).)))))))).))).)))....))). (-15.62 = -17.12 +   1.51)

alignment

secondary structure

dotplot

Window 0

Location	25,520,497 – 25,520,597
Length	100
Sequences	6
Columns	116
Reading direction	reverse
Mean pairwise identity	72.31
Mean single sequence MFE	-35.15
Consensus MFE	-13.62
Energy contribution	-16.76
Covariance contribution	3.15
Combinations/Pair	1.34
Mean z-score	-2.09
Structure conservation index	0.39
SVM decision value	0.74
SVM RNA-class probability	0.836857
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 25520497 100 - 27905053
UCACGUUUCUGGCCUGCCAGAACCCUUGGCAUGGGGUUACCUUA---------------UGGGUAAUAACCCCCAUCUGCACAGCCGAUAGUCCUAAUAAGCAGGCGG-GGUCGAA
...((..(((.((((((.((.((..((((((((((((((((...---------------..)))))....)))))).......)))))..)).)).....)))))).)-)).)).. ( -35.01)
>DroSec_CAF1 4365 100 - 1
UCACGUUUCUGCCCUGCCAGGACCCUCGGCAUGGGGUUACCUUA---------------UGGGUAAUAUCCCCCAUCUGCACAGCAGAUAGUCCUAAUAAGCAGGCGG-GGUCGAA
......(((.(((((((((((((.........(((((((((...---------------..)))))....))))((((((...)))))).)))))........)))))-))).))) ( -39.70)
>DroSim_CAF1 4364 99 - 1
UCACGUUUCUGCCCUGCCAGGAC-CUCGGCAUGGGGUUACCUUA---------------UGGGUAAUAACCCCCAUCUGCACAGCAGAUAGUCCUAAUAAGCAGGCAG-GGUCGAA
......(((.(((((((((((((-........(((((((((...---------------..))))...))))).((((((...)))))).)))))........)))))-))).))) ( -40.70)
>DroEre_CAF1 4379 96 - 1
UCACGUUUCUACCCUGCCAGGAGCCUCAGCAUGGGGUUAUCCUA---------------UGGGCAAAAACCC-CA---GCACAGCAGAUAGUCCUAAUAAGCAGGCGG-CGUCGAA
(((((((.....(((((.((((...((.((.(((((((..((..---------------..))....)))))-))---.....)).))...)))).....))))).))-))).)). ( -26.50)
>DroAna_CAF1 1769 89 - 1
UCACGUUACGCCCUUUUCAGGACCCUCAGCAUGGGGUUGUCUUA------------------------CCCCCCAU---GACAGCAGAUAGUCCCAAUGAGUGGGUGACGGUUGAA
...((((((.(((((....((((..((..(((((((........------------------------..))))))---)......))..))))....))).))))))))...... ( -29.50)
>DroPer_CAF1 1748 104 - 1
UCACGUUACGCCCUCG------CCCUCAGCAUGGGGUUGUCUUACUCCCCGAGUUUUUCUGGGCCG--CCCCCCAU---GCCAGGGAAUAGUCCUAAUGAGUGGGUGA-GGCACAA
.........(((.(((------(((.(.((((((((..((((.((((...))))......))))..--..))))))---))..((((....)))).....).))))))-))).... ( -39.50)
>consensus
UCACGUUUCUGCCCUGCCAGGACCCUCAGCAUGGGGUUACCUUA_______________UGGGUAAUAACCCCCAU__GCACAGCAGAUAGUCCUAAUAAGCAGGCGG_GGUCGAA
......(((.(((((((((((((..((.((((((((((((((..................))))))....)))))).......)).))..)))))........))))).))).))) (-13.62 = -16.76 +   3.15)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:39:11 2006