Locus 8336

Sequence ID	3L_DroMel_CAF1
Location	21,835,945 – 21,836,093
Length	148
Max. P	0.978162

overview

Window 3

Location	21,835,945 – 21,836,055
Length	110
Sequences	4
Columns	110
Reading direction	forward
Mean pairwise identity	90.91
Mean single sequence MFE	-30.71
Consensus MFE	-25.90
Energy contribution	-26.40
Covariance contribution	0.50
Combinations/Pair	1.00
Mean z-score	-2.63
Structure conservation index	0.84
SVM decision value	1.77
SVM RNA-class probability	0.976306
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 21835945 110 + 23771897
UUCCCUGCCCUGUUUUAACUUUUUCAUUCUGUCUGGCAUCAGCACAUCUCAGCAUCCUUUAUCAUACAUCCUCGUGUGGAUGAUGAUGACGGUGAUGUGGACAUGGCUUU
......(((.((((..............(((........)))((((((.......((.(((((((.(((((......)))))))))))).)).)))))))))).)))... ( -31.20)
>DroSec_CAF1 16824 110 + 1
UCCCCUGCCCUGUUUUAACUUUUUCAUUCUGCCUGGCAUCAGCACAUCUCAGCAUCCUUUAUCAUACAUCCUCGUGUGGAUGAUGAUGACGGUGAUGUGGACAUGGCUUU
.....((((..((.................))..))))..(((.(((.((.((((((((((((((.(((((......)))))))))))).)).))))).)).)))))).. ( -31.13)
>DroSim_CAF1 15488 109 + 1
UC-CCUGCCCUGUUUUAACUUUUUCAUUCUGCCUGGCAUCAGCACAUCUCAGCAUCCUUUAUCAUACAUCCUCGUGUGGAUGAUGAUGACGGUGAUGUGGACAUGGCUUU
..-..((((..((.................))..))))..(((.(((.((.((((((((((((((.(((((......)))))))))))).)).))))).)).)))))).. ( -31.13)
>DroEre_CAF1 15671 99 + 1
UCC-CUGCCCUGUUUUAACUUUUUCAUUUGGCCUGGCAUCA----------GCAUCCUUUAUCAUCCAUCCUCGUGUGGAUGAUGAUGAAGACGAUGUGGACAUGGCUUU
...-..(((.(((((...............((...))....----------(((((((((((((((.((((......))))))))))))))..)))))))))).)))... ( -29.40)
>consensus
UCCCCUGCCCUGUUUUAACUUUUUCAUUCUGCCUGGCAUCAGCACAUCUCAGCAUCCUUUAUCAUACAUCCUCGUGUGGAUGAUGAUGACGGUGAUGUGGACAUGGCUUU
......(((.(((((.................(((....))).........((((((((((((((.(((((......)))))))))))).)).)))))))))).)))... (-25.90 = -26.40 +   0.50)

alignment

secondary structure

dotplot

Window 4

Location	21,835,945 – 21,836,055
Length	110
Sequences	4
Columns	110
Reading direction	reverse
Mean pairwise identity	90.91
Mean single sequence MFE	-29.12
Consensus MFE	-22.91
Energy contribution	-23.10
Covariance contribution	0.19
Combinations/Pair	1.11
Mean z-score	-2.06
Structure conservation index	0.79
SVM decision value	0.72
SVM RNA-class probability	0.833822
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 21835945 110 - 23771897
AAAGCCAUGUCCACAUCACCGUCAUCAUCAUCCACACGAGGAUGUAUGAUAAAGGAUGCUGAGAUGUGCUGAUGCCAGACAGAAUGAAAAAGUUAAAACAGGGCAGGGAA
....((.(((((...(((.((((((((((((((......))))).)))))....)))).)))..(((.(((....))))))...................))))).)).. ( -29.20)
>DroSec_CAF1 16824 110 - 1
AAAGCCAUGUCCACAUCACCGUCAUCAUCAUCCACACGAGGAUGUAUGAUAAAGGAUGCUGAGAUGUGCUGAUGCCAGGCAGAAUGAAAAAGUUAAAACAGGGCAGGGGA
....((.(((((.((((......((((((((((......))))).)))))....))))(((...((.((....))))..)))..................))))).)).. ( -30.20)
>DroSim_CAF1 15488 109 - 1
AAAGCCAUGUCCACAUCACCGUCAUCAUCAUCCACACGAGGAUGUAUGAUAAAGGAUGCUGAGAUGUGCUGAUGCCAGGCAGAAUGAAAAAGUUAAAACAGGGCAGG-GA
....((.(((((.((((......((((((((((......))))).)))))....))))(((...((.((....))))..)))..................))))).)-). ( -30.00)
>DroEre_CAF1 15671 99 - 1
AAAGCCAUGUCCACAUCGUCUUCAUCAUCAUCCACACGAGGAUGGAUGAUAAAGGAUGC----------UGAUGCCAGGCCAAAUGAAAAAGUUAAAACAGGGCAG-GGA
....((.(((((.((((..(((.((((((((((......)))).)))))).)))))))(----------((....)))......................))))).-)). ( -27.10)
>consensus
AAAGCCAUGUCCACAUCACCGUCAUCAUCAUCCACACGAGGAUGUAUGAUAAAGGAUGCUGAGAUGUGCUGAUGCCAGGCAGAAUGAAAAAGUUAAAACAGGGCAGGGGA
...(((.((((..(((((((...((((((((((......))))).)))))...))..((........)))))))...))))..........((....))..)))...... (-22.91 = -23.10 +   0.19)

alignment

secondary structure

dotplot

Window 5

Location	21,835,978 – 21,836,093
Length	115
Sequences	6
Columns	118
Reading direction	reverse
Mean pairwise identity	77.34
Mean single sequence MFE	-29.92
Consensus MFE	-17.29
Energy contribution	-17.68
Covariance contribution	0.39
Combinations/Pair	1.09
Mean z-score	-2.55
Structure conservation index	0.58
SVM decision value	1.81
SVM RNA-class probability	0.978162
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 21835978 115 - 23771897
UGUGUCACAUAUAUCAUCAUUUUGUCUUCCUUUUUGACAAAGC-CAUGUCCACAUCACCGUCAUCAUCAUCCACACGAGGAUGU-AUGAUAAAGGAUGCUGAGAUGUGCU-GAUGCCA
.(((((((((((.(((.(((((((((.........))))))..-.............((...((((((((((......))))).-)))))...))))).))).))))).)-))))).. ( -31.40)
>DroPse_CAF1 52624 92 - 1
CGUGUCACA----UCAUCGUUUUGUCCUUCUCUUUGACAAAACACAUG---------------UCAUCAUCUCGUGGGGCAUGCAAUGAUAAAGGAUGCUG-------CUGGCUGCCA
...((((((----.((((((((((((.........)))))))).((((---------------((.((((...))))))))))...........)))).))-------.))))..... ( -24.70)
>DroSec_CAF1 16857 115 - 1
UGUGUCACAUAUAUCAUCGUUUUGUCUUCCUUUUUGACAAAGC-CAUGUCCACAUCACCGUCAUCAUCAUCCACACGAGGAUGU-AUGAUAAAGGAUGCUGAGAUGUGCU-GAUGCCA
.(((((((((((..(((.((((((((.........))))))))-.)))......(((.((((((((((((((......))))).-)))))....)))).))).))))).)-))))).. ( -34.30)
>DroSim_CAF1 15520 115 - 1
UGUGUCACAUAUAUCAUCGUUUUGUCUUCCUUUUUGACAAAGC-CAUGUCCACAUCACCGUCAUCAUCAUCCACACGAGGAUGU-AUGAUAAAGGAUGCUGAGAUGUGCU-GAUGCCA
.(((((((((((..(((.((((((((.........))))))))-.)))......(((.((((((((((((((......))))).-)))))....)))).))).))))).)-))))).. ( -34.30)
>DroEre_CAF1 15703 105 - 1
UGUGUCACAUAUAUCAUCGUUUUGUCUUCAUUUUUGACAAAGC-CAUGUCCACAUCGUCUUCAUCAUCAUCCACACGAGGAUGG-AUGAUAAAGGAUGC----------U-GAUGCCA
.(((((((((....(((.((((((((.........))))))))-.))).........((((.((((((((((......)))).)-))))).))))))).----------)-))))).. ( -30.10)
>DroPer_CAF1 51590 92 - 1
CGUGUCACA----UCAUCGUUUUGUCCUUCUCUUUGACAAAACACAUG---------------UCAUCAUCUCGUGGGGCAUGCAAUGAUAAAGGAUGCUG-------CUGGCUGCCA
...((((((----.((((((((((((.........)))))))).((((---------------((.((((...))))))))))...........)))).))-------.))))..... ( -24.70)
>consensus
UGUGUCACAUAUAUCAUCGUUUUGUCUUCCUUUUUGACAAAGC_CAUGUCCACAUCACCGUCAUCAUCAUCCACACGAGGAUGU_AUGAUAAAGGAUGCUG_______CU_GAUGCCA
.(((((............((((((((.........))))))))...................((((((((((......)))))..)))))....)))))................... (-17.29 = -17.68 +   0.39)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:12:56 2006