Locus 8419

Sequence ID	X_DroMel_CAF1
Location	20,902,230 – 20,902,391
Length	161
Max. P	0.896537

overview

Window 1

Location	20,902,230 – 20,902,329
Length	99
Sequences	5
Columns	104
Reading direction	forward
Mean pairwise identity	81.06
Mean single sequence MFE	-14.60
Consensus MFE	-4.76
Energy contribution	-5.40
Covariance contribution	0.64
Combinations/Pair	1.08
Mean z-score	-2.46
Structure conservation index	0.33
SVM decision value	0.44
SVM RNA-class probability	0.736946
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 20902230 99 + 22224390
UGUCUGUGUGCAUUGGCAAACAUUUGACAGUUGCAACAGCA-----ACAAAAUAACAACAAAUUAAUGCAACAAAAUAAAUAAAAGAGAAAAAAAAGACAAAGC
(((((.(((((((((((((....)))...(((((....)))-----))..............))))))).)))......................))))).... ( -16.20)
>DroSec_CAF1 21472 98 + 1
UGUCUGUGUGCAUUGGCAAACAUUUAACAGUUGCAACAGCA-----ACAAAAUAACAACAAAUUAAUACAACAAAAUAAAUAAACGAGAAA-AAAAGACAAAGC
(((((((.(((....))).))........(((((....)))-----))...........................................-...))))).... ( -14.90)
>DroSim_CAF1 23354 98 + 1
UGUCUGUGUGCAUUGGCAAACAUUUGACAGUUGCAACAGCA-----ACAAAAUAACAACAAAUUAAUACAACAAAAUAAAUAAACGAGAAA-AAAAGACAAAGC
(((((((.(((....))).))........(((((....)))-----))...........................................-...))))).... ( -14.90)
>DroEre_CAF1 14393 97 + 1
UGUCUGUGUGCAUUGGCAAACAUUUGACAGUUGCAACAGCA-----ACAAAAUAACAACAAAUUAAUACAAAAAAAUAAAUAAAUGAGA-G-AAAAGCCAAAGC
.........((.(((((............(((((....)))-----))....................................(....-)-....))))).)) ( -14.00)
>DroAna_CAF1 12665 85 + 1
UCGGUGUGUGGAUUGGCAAGCAUUUGACA----CAAAAACACACACAAAAAAUAACAAAAAGUUGAC----UAAAAUAA---AAUGGGC-U-A------AAAGU
...(((((((..(((.(((....)))...----)))...)))))))......((((.....))))..----........---.......-.-.------..... ( -13.00)
>consensus
UGUCUGUGUGCAUUGGCAAACAUUUGACAGUUGCAACAGCA_____ACAAAAUAACAACAAAUUAAUACAACAAAAUAAAUAAACGAGAAA_AAAAGACAAAGC
....(((.(((((((.(((....))).))).))))...)))............................................................... ( -4.76 =  -5.40 +   0.64)

alignment

secondary structure

dotplot

Window 2

Location	20,902,295 – 20,902,391
Length	96
Sequences	4
Columns	96
Reading direction	forward
Mean pairwise identity	92.67
Mean single sequence MFE	-15.78
Consensus MFE	-12.05
Energy contribution	-12.42
Covariance contribution	0.37
Combinations/Pair	1.05
Mean z-score	-3.28
Structure conservation index	0.76
SVM decision value	0.81
SVM RNA-class probability	0.856187
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 20902295 96 + 22224390
ACAAAAUAAAUAAAAGAGAAAAAAAAGACAAAGCAAACUGCCAAAAGGCACAACACAAACAAAAAUGCAAACAUUUUGUUAGUCCUCUCUUGUUAA
........(((((.((((....................((((....))))....((.(((((((.((....))))))))).)).)))).))))).. ( -15.00)
>DroSec_CAF1 21537 95 + 1
ACAAAAUAAAUAAACGAGAAA-AAAAGACAAAGCAAACUGCCAAAAGGCACAACACAAACAAAAAUGCGAACAUUUGGUUAGUUCUCUCUUGUUAA
............(((((((..-................((((....))))....((.(((..(((((....))))).))).))....))))))).. ( -13.50)
>DroSim_CAF1 23419 95 + 1
ACAAAAUAAAUAAACGAGAAA-AAAAGACAAAGCAAACUGCCAAAAGGCACAACACAAACAAAAAUGCGAACAUUUUGUUAGUUCUCUCUUGUUCC
............(((((((..-................((((....))))....((.(((((((.((....))))))))).))....))))))).. ( -14.60)
>DroEre_CAF1 14458 94 + 1
AAAAAAUAAAUAAAUGAGA-G-AAAAGCCAAAGCAAACUGCCAAAAGGCACAACACAAACAAAAAUGCGAACAUUUUGUUGGUCCUCUCUUGUUCU
............((..(((-(-(...(((((.......((((....))))...........((((((....)))))).)))))..)))))..)).. ( -20.00)
>consensus
ACAAAAUAAAUAAACGAGAAA_AAAAGACAAAGCAAACUGCCAAAAGGCACAACACAAACAAAAAUGCGAACAUUUUGUUAGUCCUCUCUUGUUAA
............(((((((...................((((....))))....((.(((((((.((....))))))))).))....))))))).. (-12.05 = -12.42 +   0.37)

alignment

secondary structure

dotplot

Window 3

Location	20,902,295 – 20,902,391
Length	96
Sequences	4
Columns	96
Reading direction	reverse
Mean pairwise identity	92.67
Mean single sequence MFE	-19.05
Consensus MFE	-16.29
Energy contribution	-16.35
Covariance contribution	0.06
Combinations/Pair	1.10
Mean z-score	-2.02
Structure conservation index	0.85
SVM decision value	0.99
SVM RNA-class probability	0.896537
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 20902295 96 - 22224390
UUAACAAGAGAGGACUAACAAAAUGUUUGCAUUUUUGUUUGUGUUGUGCCUUUUGGCAGUUUGCUUUGUCUUUUUUUUCUCUUUUAUUUAUUUUGU
.....((((((((((.(((((((((....)).))))))).))....((((....))))...................))))))))........... ( -18.60)
>DroSec_CAF1 21537 95 - 1
UUAACAAGAGAGAACUAACCAAAUGUUCGCAUUUUUGUUUGUGUUGUGCCUUUUGGCAGUUUGCUUUGUCUUUU-UUUCUCGUUUAUUUAUUUUGU
.......(((((((..(..((((.((.((((........))))...((((....))))....))))))..)..)-))))))............... ( -17.10)
>DroSim_CAF1 23419 95 - 1
GGAACAAGAGAGAACUAACAAAAUGUUCGCAUUUUUGUUUGUGUUGUGCCUUUUGGCAGUUUGCUUUGUCUUUU-UUUCUCGUUUAUUUAUUUUGU
.((((.(((((((((.(((((((((....)).))))))).))....((((....))))..............))-))))).))))........... ( -19.30)
>DroEre_CAF1 14458 94 - 1
AGAACAAGAGAGGACCAACAAAAUGUUCGCAUUUUUGUUUGUGUUGUGCCUUUUGGCAGUUUGCUUUGGCUUUU-C-UCUCAUUUAUUUAUUUUUU
.......((((((((.(((((((((....)).))))))).)).....(((....(((.....)))..)))...)-)-))))............... ( -21.20)
>consensus
UGAACAAGAGAGAACUAACAAAAUGUUCGCAUUUUUGUUUGUGUUGUGCCUUUUGGCAGUUUGCUUUGUCUUUU_UUUCUCGUUUAUUUAUUUUGU
.......((((((((.(((((((((....)).))))))).))....((((....)))).................))))))............... (-16.29 = -16.35 +   0.06)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:03:34 2006