Locus 490

Sequence ID	3L_DroMel_CAF1
Location	1,381,209 – 1,381,357
Length	148
Max. P	0.982950

overview

Window 6

Location	1,381,209 – 1,381,307
Length	98
Sequences	6
Columns	105
Reading direction	forward
Mean pairwise identity	83.11
Mean single sequence MFE	-32.38
Consensus MFE	-28.13
Energy contribution	-27.68
Covariance contribution	-0.44
Combinations/Pair	1.05
Mean z-score	-1.35
Structure conservation index	0.87
SVM decision value	0.07
SVM RNA-class probability	0.566864
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 1381209 98 + 23771897
---G--UCGAU--CUGCUAUCACAUCCCAUAUUGUCUAGUGGUUAGGAUAUCCGGCUCUCACCCGGAAGGCCCGGGUUCAAUUCCCGGUAUGGGAAUAUGGUGAA
---.--.....--......((((.(((((((.(((((........))))).((((.....((((((.....)))))).......))))))))))).....)))). ( -30.70)
>DroPse_CAF1 60582 98 + 1
UUUAACGUGAG--CACUUUCCAUAUCCCAUAUUGUCUAGUGGUUAGGAUACCCGGCUCUCACCCGGGAGGCCCGGGUUCAAUUCCCGGUAUGGGAAACUG-----
.....(....)--...((((((((((((((........))))...(((.(((((((((((....)))))..)))))).....))).))))))))))....----- ( -32.80)
>DroEre_CAF1 37949 98 + 1
---G--CCGGA--CCCCUAUCACAUCCCAUAUUGUCUAGUGGUUAGGAUAUCCGGCUCUCACCCGGAAGGCCCGGGUUCAAUUCCCGGUAUGGGAAAAUGGUGGA
---(--(((((--..((((((((...............)))).))))...))))))(((((.((....)).(((((.......)))))..))))).......... ( -34.26)
>DroYak_CAF1 39547 98 + 1
---G--GCAAU--CCCCUAUCACAUCCCAUAUUGUCUAGUGGUUAGGAUAUCCGGCUCUCACCCGGAAGGCCCGGGUUCAAUUCCCGGUAUGGGAAAGUAGUGAA
---.--.....--......((((.(((((((.(((((........))))).((((.....((((((.....)))))).......))))))))))).....)))). ( -29.60)
>DroAna_CAF1 38388 94 + 1
---G--GCAGACGCCAUUUUCAAGUCCCAUAUUGUCUAGUGGUUAGGAUAUCCGGCUCUCACCCGGAAGGCCCGGGUUCGAUUCCCGGUAUGGGAAACU------
---(--((....))).........(((((((.(((((........))))).((((.((..((((((.....))))))..))...)))))))))))....------ ( -33.10)
>DroPer_CAF1 61615 98 + 1
UUUGACGUGAG--CACUUUCCAUAUCCCAUAUUGUCUAGUGGUUAGGAUACCCGGCUCUCACCCGGGAGGCCCGGGUUCAAUUCCCGGUAUGGGAAACUG-----
..((.(....)--)).((((((((((((((........))))...(((.(((((((((((....)))))..)))))).....))).))))))))))....----- ( -33.80)
>consensus
___G__GCGAA__CCCCUAUCACAUCCCAUAUUGUCUAGUGGUUAGGAUAUCCGGCUCUCACCCGGAAGGCCCGGGUUCAAUUCCCGGUAUGGGAAACUG_____
........................(((((((.(((((........)))))(((((.......)))))....(((((.......)))))))))))).......... (-28.13 = -27.68 +  -0.44)

alignment

secondary structure

dotplot

Window 7

Location	1,381,209 – 1,381,307
Length	98
Sequences	6
Columns	105
Reading direction	reverse
Mean pairwise identity	83.11
Mean single sequence MFE	-33.35
Consensus MFE	-29.38
Energy contribution	-29.02
Covariance contribution	-0.36
Combinations/Pair	1.09
Mean z-score	-1.93
Structure conservation index	0.88
SVM decision value	0.92
SVM RNA-class probability	0.882574
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 1381209 98 - 23771897
UUCACCAUAUUCCCAUACCGGGAAUUGAACCCGGGCCUUCCGGGUGAGAGCCGGAUAUCCUAACCACUAGACAAUAUGGGAUGUGAUAGCAG--AUCGA--C---
.....(((((.((((((((((...((..((((((.....))))))..)).)))).....(((.....)))....))))))))))).......--.....--.--- ( -31.10)
>DroPse_CAF1 60582 98 - 1
-----CAGUUUCCCAUACCGGGAAUUGAACCCGGGCCUCCCGGGUGAGAGCCGGGUAUCCUAACCACUAGACAAUAUGGGAUAUGGAAAGUG--CUCACGUUAAA
-----((.(((((....((((...((..(((((((...)))))))..)).))))((((((((..............))))))))))))).))--........... ( -34.44)
>DroEre_CAF1 37949 98 - 1
UCCACCAUUUUCCCAUACCGGGAAUUGAACCCGGGCCUUCCGGGUGAGAGCCGGAUAUCCUAACCACUAGACAAUAUGGGAUGUGAUAGGGG--UCCGG--C---
.........(((((.....)))))((..((((((.....))))))..))(((((((.(((((..(((....(.....)....))).))))))--)))))--)--- ( -35.70)
>DroYak_CAF1 39547 98 - 1
UUCACUACUUUCCCAUACCGGGAAUUGAACCCGGGCCUUCCGGGUGAGAGCCGGAUAUCCUAACCACUAGACAAUAUGGGAUGUGAUAGGGG--AUUGC--C---
.........(((((...((((...((..((((((.....))))))..)).))))((((((((..............))))))))....))))--)....--.--- ( -32.34)
>DroAna_CAF1 38388 94 - 1
------AGUUUCCCAUACCGGGAAUCGAACCCGGGCCUUCCGGGUGAGAGCCGGAUAUCCUAACCACUAGACAAUAUGGGACUUGAAAAUGGCGUCUGC--C---
------....(((((((((((...((..((((((.....))))))..)).)))).....(((.....)))....))))))).........(((....))--)--- ( -32.10)
>DroPer_CAF1 61615 98 - 1
-----CAGUUUCCCAUACCGGGAAUUGAACCCGGGCCUCCCGGGUGAGAGCCGGGUAUCCUAACCACUAGACAAUAUGGGAUAUGGAAAGUG--CUCACGUCAAA
-----((.(((((....((((...((..(((((((...)))))))..)).))))((((((((..............))))))))))))).))--........... ( -34.44)
>consensus
_____CAGUUUCCCAUACCGGGAAUUGAACCCGGGCCUUCCGGGUGAGAGCCGGAUAUCCUAACCACUAGACAAUAUGGGAUGUGAAAAGGG__AUCGC__C___
..........(((((((((((...((..(((((((...)))))))..)).)))).....(((.....)))....)))))))........................ (-29.38 = -29.02 +  -0.36)

alignment

secondary structure

dotplot

Window 8

Location	1,381,227 – 1,381,343
Length	116
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	80.17
Mean single sequence MFE	-30.50
Consensus MFE	-25.70
Energy contribution	-25.70
Covariance contribution	-0.00
Combinations/Pair	1.00
Mean z-score	-1.50
Structure conservation index	0.84
SVM decision value	0.42
SVM RNA-class probability	0.729002
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 1381227 116 + 23771897
CCCAUAUUGUCUAGUGGUUAGGAUAUCCGGCUCUCACCCGGAAGGCCCGGGUUCAAUUCCCGGUAUGGGAAUAUGGUGAAGAAAU----AUUCUUUUUAGAAAUUUUCACUUUAAUUAUA
((((((.(((((........))))).((((.....((((((.....)))))).......))))))))))..((.((((((((...----.((((....)))).)))))))).))...... ( -33.40)
>DroSec_CAF1 36794 116 + 1
CCCAUAUUGUCUAGUGGUUAGGAUAUCCGGCUCUCACCCGGAAGGCCCGGGUUCAAUUCCCGGUAUGGGAAUAUGGUGAAGAAAU----AUUCUUUUUAGAAACUUUUACUUUAAUUUAA
.(((((((.((((.(((..(....(((((((..((.....))..).))))))....)..))).)).)).)))))))((((((((.----.((((....))))...))).)))))...... ( -29.70)
>DroEre_CAF1 37967 119 + 1
CCCAUAUUGUCUAGUGGUUAGGAUAUCCGGCUCUCACCCGGAAGGCCCGGGUUCAAUUCCCGGUAUGGGAAAAUGGUGGAAAUGUUUAUUUUCUUUUGAGAAACUUAAAAUAAAA-UUUA
((((((.(((((........))))).((((.....((((((.....)))))).......))))))))))..................(((((.(((((((...))))))).))))-)... ( -29.00)
>DroWil_CAF1 15473 102 + 1
CCCAUAUUGUCUAGUGGUUAGGAUAUCCGGCUCUCACCCGGAAGGCCCGGGUUCGAUUCCCGGUAUGGGAAACUU------------------UUUUUCCCUCGUAUUAUUAUAGUAUUA
...(((((((..((((((.(.((...((((.((..((((((.....))))))..))...))))...((((((...------------------..)))))))).)))))))))))))).. ( -27.90)
>DroYak_CAF1 39565 107 + 1
CCCAUAUUGUCUAGUGGUUAGGAUAUCCGGCUCUCACCCGGAAGGCCCGGGUUCAAUUCCCGGUAUGGGAAAGUAGUGAAAAUGU----UUUCUUUUAAGAAA--------ACAA-GUUA
((((((.(((((........))))).((((.....((((((.....)))))).......)))))))))).............(((----(((((....)))))--------))).-.... ( -32.50)
>consensus
CCCAUAUUGUCUAGUGGUUAGGAUAUCCGGCUCUCACCCGGAAGGCCCGGGUUCAAUUCCCGGUAUGGGAAAAUGGUGAAAAAAU____AUUCUUUUUAGAAACUUUUACUAUAAUUUUA
((((((.(((((........))))).((((.....((((((.....)))))).......))))))))))................................................... (-25.70 = -25.70 +  -0.00)

alignment

secondary structure

dotplot

Window 9

Location	1,381,227 – 1,381,343
Length	116
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	80.17
Mean single sequence MFE	-29.34
Consensus MFE	-26.12
Energy contribution	-25.96
Covariance contribution	-0.16
Combinations/Pair	1.05
Mean z-score	-2.26
Structure conservation index	0.89
SVM decision value	1.93
SVM RNA-class probability	0.982950
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 1381227 116 - 23771897
UAUAAUUAAAGUGAAAAUUUCUAAAAAGAAU----AUUUCUUCACCAUAUUCCCAUACCGGGAAUUGAACCCGGGCCUUCCGGGUGAGAGCCGGAUAUCCUAACCACUAGACAAUAUGGG
..........(((((...((((....)))).----.....)))))......((((((((((...((..((((((.....))))))..)).)))).....(((.....)))....)))))) ( -29.90)
>DroSec_CAF1 36794 116 - 1
UUAAAUUAAAGUAAAAGUUUCUAAAAAGAAU----AUUUCUUCACCAUAUUCCCAUACCGGGAAUUGAACCCGGGCCUUCCGGGUGAGAGCCGGAUAUCCUAACCACUAGACAAUAUGGG
..................((((....)))).----.........(((((((......((((...((..((((((.....))))))..)).)))).....(((.....)))..))))))). ( -26.20)
>DroEre_CAF1 37967 119 - 1
UAAA-UUUUAUUUUAAGUUUCUCAAAAGAAAAUAAACAUUUCCACCAUUUUCCCAUACCGGGAAUUGAACCCGGGCCUUCCGGGUGAGAGCCGGAUAUCCUAACCACUAGACAAUAUGGG
....-............(((((....)))))....................((((((((((...((..((((((.....))))))..)).)))).....(((.....)))....)))))) ( -27.00)
>DroWil_CAF1 15473 102 - 1
UAAUACUAUAAUAAUACGAGGGAAAAA------------------AAGUUUCCCAUACCGGGAAUCGAACCCGGGCCUUCCGGGUGAGAGCCGGAUAUCCUAACCACUAGACAAUAUGGG
.....(((((.........((((((..------------------...))))))...((((...((..((((((.....))))))..)).))))....................))))). ( -31.50)
>DroYak_CAF1 39565 107 - 1
UAAC-UUGU--------UUUCUUAAAAGAAA----ACAUUUUCACUACUUUCCCAUACCGGGAAUUGAACCCGGGCCUUCCGGGUGAGAGCCGGAUAUCCUAACCACUAGACAAUAUGGG
....-.(((--------(((((....)))))----))).............((((((((((...((..((((((.....))))))..)).)))).....(((.....)))....)))))) ( -32.10)
>consensus
UAAAAUUAUAGUAAAAGUUUCUAAAAAGAAA____ACAUCUUCACCAUUUUCCCAUACCGGGAAUUGAACCCGGGCCUUCCGGGUGAGAGCCGGAUAUCCUAACCACUAGACAAUAUGGG
...................................................((((((((((...((..((((((.....))))))..)).)))).....(((.....)))....)))))) (-26.12 = -25.96 +  -0.16)

alignment

secondary structure

dotplot

Window 0

Location	1,381,267 – 1,381,357
Length	90
Sequences	4
Columns	94
Reading direction	reverse
Mean pairwise identity	78.58
Mean single sequence MFE	-12.93
Consensus MFE	-9.88
Energy contribution	-9.88
Covariance contribution	0.00
Combinations/Pair	1.00
Mean z-score	-1.63
Structure conservation index	0.76
SVM decision value	0.48
SVM RNA-class probability	0.753631
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 1381267 90 - 23771897
GACCAAUAAAUAAAUAUAAUUAAAGUGAAAAUUUCUAAAAAGAAU----AUUUCUUCACCAUAUUCCCAUACCGGGAAUUGAACCCGGGCCUUC
..((....................(((((...((((....)))).----.....)))))((.((((((.....)))))))).....))...... ( -14.30)
>DroSec_CAF1 36834 90 - 1
GACCAAUAAAUAAAUUAAAUUAAAGUAAAAGUUUCUAAAAAGAAU----AUUUCUUCACCAUAUUCCCAUACCGGGAAUUGAACCCGGGCCUUC
..((............................((((....)))).----.....((((....((((((.....))))))))))...))...... ( -10.90)
>DroEre_CAF1 38007 93 - 1
GAUCAUUAAUUACAUAAA-UUUUAUUUUAAGUUUCUCAAAAGAAAAUAAACAUUUCCACCAUUUUCCCAUACCGGGAAUUGAACCCGGGCCUUC
..................-............(((((....)))))..........................(((((.......)))))...... ( -10.70)
>DroYak_CAF1 39605 80 - 1
GAUCAAUAAU-AAAUAAC-UUGU--------UUUCUUAAAAGAAA----ACAUUUUCACUACUUUCCCAUACCGGGAAUUGAACCCGGGCCUUC
..........-.......-.(((--------(((((....)))))----)))...................(((((.......)))))...... ( -15.80)
>consensus
GACCAAUAAAUAAAUAAA_UUAAAGU_AAAGUUUCUAAAAAGAAA____ACAUCUUCACCAUAUUCCCAUACCGGGAAUUGAACCCGGGCCUUC
................................((((....))))...........................(((((.......)))))...... ( -9.88 =  -9.88 +   0.00)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:43:19 2006