Locus 3168

Sequence ID	3L_DroMel_CAF1
Location	9,205,683 – 9,205,780
Length	97
Max. P	0.977282

overview

Window 2

Location	9,205,683 – 9,205,780
Length	97
Sequences	6
Columns	109
Reading direction	forward
Mean pairwise identity	79.93
Mean single sequence MFE	-32.77
Consensus MFE	-17.96
Energy contribution	-18.47
Covariance contribution	0.50
Combinations/Pair	1.32
Mean z-score	-2.63
Structure conservation index	0.55
SVM decision value	1.07
SVM RNA-class probability	0.910292
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 9205683 97 + 23771897
GGAGAUGGUGAUGGAGAUGGAACUGGUGCUCGAGCUGGACAAACA--GUCCAGUGAGCCCCAGUGCC------AGUGCC--AACUAAUAAAAAGUUUUUUGCUGGC--A
.....((((..(((...(((.(((((.((((..(((((((.....--))))))))))).))))).))------)...))--)))))......(((.....)))...--. ( -35.90)
>DroSec_CAF1 59473 97 + 1
GGUGAUGGUGAUGGAGAUGGAACUGCUGCUGGAGCUGGACAAACA--GUCCAGUGAGCCCCAGUGCC------AGUGCC--AACUAAUAAAAAGUUUUUUGCUGGC--A
.((..((((..(((...(((.((((..(((...(((((((.....--))))))).)))..)))).))------)...))--)))))......(((.....))).))--. ( -30.00)
>DroSim_CAF1 60030 97 + 1
GGAGAUGGUGAUGGAGAUGGAACUGGUGCUGGAGCUGGACAAACA--GUCCAGUGAGCCCCAGUGCC------AGUGCC--AACUAAUAAAAAGUUUUUUGCUGGC--A
((((((..(.....((.(((.(((((..((((.(((((((.....--))))))).....))))..))------))).))--).)).....)..)))))).......--. ( -36.80)
>DroEre_CAF1 77174 96 + 1
GGAGAUGGAGAUGGAGAUGGAGCUGGU------GCUGGACAAACA--GUCCAGUGAGCCCCAGUGCCAGUGCCAGUGCC--AACUAAUAAAAAGUU-UUUGCUGGC--A
...........(((...(((.(((..(------(((((((.....--))))))))))).)))...))).((((((((..--((((.......))))-..)))))))--) ( -34.70)
>DroYak_CAF1 76339 94 + 1
--GGAUGUAAAUGGAGAUGGAGUUGGU------GCUGGACAAAUA--GUCCAGUGAGCCCCAGUGCCAGUGCCAGUGCC--AACUAAUAAAAAGUU-UUUGCUGGC--A
--.........(((...(((.((...(------(((((((.....--)))))))).)).)))...))).((((((((..--((((.......))))-..)))))))--) ( -32.50)
>DroPer_CAF1 69735 99 + 1
GAAGCUAGAGUUUGAGAUGGAGUUGAAGUUGCAGAUGGACAAACAGAGUCCAU--AGUCCGGGCAGC------AGCGUCGAAACUAAUAAAAAGUU--UUGCUGGCACA
...(((((...................(((((..((((((.......))))))--.((....)).))------)))..(((((((.......))))--))))))))... ( -26.70)
>consensus
GGAGAUGGAGAUGGAGAUGGAACUGGUGCUGGAGCUGGACAAACA__GUCCAGUGAGCCCCAGUGCC______AGUGCC__AACUAAUAAAAAGUU_UUUGCUGGC__A
..................((.(((((.(((...(((((((.......))))))).))).))))).))......((((....((((.......))))...))))...... (-17.96 = -18.47 +   0.50)

alignment

secondary structure

dotplot

Window 3

Location	9,205,683 – 9,205,780
Length	97
Sequences	6
Columns	109
Reading direction	reverse
Mean pairwise identity	79.93
Mean single sequence MFE	-29.37
Consensus MFE	-14.91
Energy contribution	-15.86
Covariance contribution	0.95
Combinations/Pair	1.16
Mean z-score	-3.52
Structure conservation index	0.51
SVM decision value	1.79
SVM RNA-class probability	0.977282
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 9205683 97 - 23771897
U--GCCAGCAAAAAACUUUUUAUUAGUU--GGCACU------GGCACUGGGGCUCACUGGAC--UGUUUGUCCAGCUCGAGCACCAGUUCCAUCUCCAUCACCAUCUCC
(--((((((................)))--)))).(------((.(((((.((((.((((((--.....))))))...)))).))))).)))................. ( -35.99)
>DroSec_CAF1 59473 97 - 1
U--GCCAGCAAAAAACUUUUUAUUAGUU--GGCACU------GGCACUGGGGCUCACUGGAC--UGUUUGUCCAGCUCCAGCAGCAGUUCCAUCUCCAUCACCAUCACC
(--((((((................)))--)))).(------((.((((..(((..((((((--.....))))))....)))..)))).)))................. ( -29.69)
>DroSim_CAF1 60030 97 - 1
U--GCCAGCAAAAAACUUUUUAUUAGUU--GGCACU------GGCACUGGGGCUCACUGGAC--UGUUUGUCCAGCUCCAGCACCAGUUCCAUCUCCAUCACCAUCUCC
.--((((((................)))--)))(((------((..((((((((....((((--.....))))))))))))..)))))..................... ( -33.49)
>DroEre_CAF1 77174 96 - 1
U--GCCAGCAAA-AACUUUUUAUUAGUU--GGCACUGGCACUGGCACUGGGGCUCACUGGAC--UGUUUGUCCAGC------ACCAGCUCCAUCUCCAUCUCCAUCUCC
(--((((((...-............)))--)))).(((...(((...(((((((..((((((--.....)))))).------...)))))))...)))...)))..... ( -33.46)
>DroYak_CAF1 76339 94 - 1
U--GCCAGCAAA-AACUUUUUAUUAGUU--GGCACUGGCACUGGCACUGGGGCUCACUGGAC--UAUUUGUCCAGC------ACCAACUCCAUCUCCAUUUACAUCC--
(--(((((....-((((.......))))--....)))))).(((...(((((....((((((--.....)))))).------.....)))))...))).........-- ( -28.10)
>DroPer_CAF1 69735 99 - 1
UGUGCCAGCAA--AACUUUUUAUUAGUUUCGACGCU------GCUGCCCGGACU--AUGGACUCUGUUUGUCCAUCUGCAACUUCAACUCCAUCUCAAACUCUAGCUUC
...((((((((--((((.......)))))......)------))))..((((..--.(((((.......)))))))))..........................))... ( -15.50)
>consensus
U__GCCAGCAAA_AACUUUUUAUUAGUU__GGCACU______GGCACUGGGGCUCACUGGAC__UGUUUGUCCAGCUCCAGCACCAGCUCCAUCUCCAUCACCAUCUCC
.......((....((((.......))))...)).........((.(((((......((((((.......))))))........))))).)).................. (-14.91 = -15.86 +   0.95)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:51:14 2006