Locus 4387

Sequence ID	2L_DroMel_CAF1
Location	12,627,557 – 12,627,704
Length	147
Max. P	0.969716

overview

Window 1

Location	12,627,557 – 12,627,651
Length	94
Sequences	6
Columns	108
Reading direction	forward
Mean pairwise identity	79.85
Mean single sequence MFE	-23.40
Consensus MFE	-16.39
Energy contribution	-15.93
Covariance contribution	-0.47
Combinations/Pair	1.32
Mean z-score	-1.60
Structure conservation index	0.70
SVM decision value	0.59
SVM RNA-class probability	0.790658
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 12627557 94 + 22407834
A-UUCAAAAUAUUGCUGCUUAAGUGAACC-------GCUACUCAUU--CGGCAUUC-AAGUUCACUUGCUCAACAACAUUUUGUGGA--UGCAUAAGGAAAUGGU-AU
.-..((((((.(((.((..(((((((((.-------(((.......--.)))....-..)))))))))..)).))).))))))....--................-.. ( -16.60)
>DroPse_CAF1 8449 99 + 1
AACCAAAAAUAUUGCUAAUCAAGUGAACG-------GCUGCUGAUCGACGGCUCUG-CCGUUCACUCGAUCACCGACUUUUUUGGGAGGC-CAUGGGGAAAUCGAUAG
..(((((((..(((...(((.((((((((-------((.((((.....))))...)-))))))))).)))...)))..)))))))((..(-(....))...))..... ( -36.30)
>DroSec_CAF1 8504 95 + 1
A-UCCAAAAUAUUGCUGCUCAAGUGAACCGC-----GCUACUCAUU--CGGCAUUC-AAGUUCACUUGCUCAACAAGAUUUUGUGGA--U-CAUAAGGAAAUGGA-UU
(-((((.....(((.((..(((((((((...-----(((.......--.)))....-..)))))))))..)).)))((((.....))--)-).........))))-). ( -20.90)
>DroSim_CAF1 8589 95 + 1
A-UCCAAAAUAUUGCUGCUCAAGUGAACCGC-----GCUACUCAUU--UGGCAUUC-AAGUUCACUUGCUCAACAAGAUUUUGUGGA--U-CAUAAGGAAAUGGU-UU
.-..((((((.(((.((..(((((((((...-----((((......--))))....-..)))))))))..)).))).)))))).(((--(-(((......)))))-)) ( -23.00)
>DroEre_CAF1 8513 101 + 1
A-UCCGAAAUAGUGCUGCUCAAGUGAACAGCUAACAGCUACCCAUU--CGGCAUUUAAAGUUUACUUGAUCAACAACAUUUUGUGGA--U-CAUAAGGAAAUGGU-AU
.-((((((((..((.((.(((((((((((((.....)))..((...--.))........)))))))))).)).))..)))))).))(--(-(((......)))))-.. ( -23.90)
>DroYak_CAF1 8694 93 + 1
A-UCCAAAAUAUCGCUGCUCAAGUGAACA-------GCCACUCAUU--CGGCAUUC-AAGUUUACUUGAUCAACAACAUUUUGUGGA--U-CAUAAGGAAUUGGU-AU
.-......(((((((((....((((....-------..))))....--))))....-.(((((...(((((.((((....)))).))--)-))....))))))))-)) ( -19.70)
>consensus
A_UCCAAAAUAUUGCUGCUCAAGUGAACC_______GCUACUCAUU__CGGCAUUC_AAGUUCACUUGAUCAACAACAUUUUGUGGA__U_CAUAAGGAAAUGGU_AU
..((((((((.(((.((..(((((((((........(((..........))).......)))))))))..)).))).)))))).))...................... (-16.39 = -15.93 +  -0.47)

alignment

secondary structure

dotplot

Window 2

Location	12,627,557 – 12,627,651
Length	94
Sequences	6
Columns	108
Reading direction	reverse
Mean pairwise identity	79.85
Mean single sequence MFE	-28.93
Consensus MFE	-21.03
Energy contribution	-22.20
Covariance contribution	1.17
Combinations/Pair	1.20
Mean z-score	-3.14
Structure conservation index	0.73
SVM decision value	1.65
SVM RNA-class probability	0.969716
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 12627557 94 - 22407834
AU-ACCAUUUCCUUAUGCA--UCCACAAAAUGUUGUUGAGCAAGUGAACUU-GAAUGCCG--AAUGAGUAGC-------GGUUCACUUAAGCAGCAAUAUUUUGAA-U
..-................--....(((((((((((((...(((((((((.-...(((..--.....)))..-------)))))))))...)))))))))))))..-. ( -26.70)
>DroPse_CAF1 8449 99 - 1
CUAUCGAUUUCCCCAUG-GCCUCCCAAAAAAGUCGGUGAUCGAGUGAACGG-CAGAGCCGUCGAUCAGCAGC-------CGUUCACUUGAUUAGCAAUAUUUUUGGUU
.................-.....(((((((.((.(.(((((((((((((((-(...((.(.....).)).))-------)))))))))))))).).)).))))))).. ( -35.20)
>DroSec_CAF1 8504 95 - 1
AA-UCCAUUUCCUUAUG-A--UCCACAAAAUCUUGUUGAGCAAGUGAACUU-GAAUGCCG--AAUGAGUAGC-----GCGGUUCACUUGAGCAGCAAUAUUUUGGA-U
..-..............-(--((((..((((.((((((..((((((((((.-...(((..--.....)))..-----..))))))))))..)))))).))))))))-) ( -28.70)
>DroSim_CAF1 8589 95 - 1
AA-ACCAUUUCCUUAUG-A--UCCACAAAAUCUUGUUGAGCAAGUGAACUU-GAAUGCCA--AAUGAGUAGC-----GCGGUUCACUUGAGCAGCAAUAUUUUGGA-U
..-..............-(--((((..((((.((((((..((((((((((.-...((((.--...).)))..-----..))))))))))..)))))).))))))))-) ( -29.30)
>DroEre_CAF1 8513 101 - 1
AU-ACCAUUUCCUUAUG-A--UCCACAAAAUGUUGUUGAUCAAGUAAACUUUAAAUGCCG--AAUGGGUAGCUGUUAGCUGUUCACUUGAGCAGCACUAUUUCGGA-U
..-......(((...((-(--((.((((....)))).)))))(((.(((......((((.--....))))...))).(((((((....)))))))))).....)))-. ( -25.80)
>DroYak_CAF1 8694 93 - 1
AU-ACCAAUUCCUUAUG-A--UCCACAAAAUGUUGUUGAUCAAGUAAACUU-GAAUGCCG--AAUGAGUGGC-------UGUUCACUUGAGCAGCGAUAUUUUGGA-U
..-..............-(--((((..(((((((((((.((((((.(((..-....((((--......))))-------.))).)))))).)))))))))))))))-) ( -27.90)
>consensus
AU_ACCAUUUCCUUAUG_A__UCCACAAAAUGUUGUUGAGCAAGUGAACUU_GAAUGCCG__AAUGAGUAGC_______GGUUCACUUGAGCAGCAAUAUUUUGGA_U
.........................(((((((((((((..((((((((((......((............)).......))))))))))..))))))))))))).... (-21.03 = -22.20 +   1.17)

alignment

secondary structure

dotplot

Window 3

Location	12,627,614 – 12,627,704
Length	90
Sequences	6
Columns	94
Reading direction	forward
Mean pairwise identity	81.10
Mean single sequence MFE	-21.80
Consensus MFE	-13.15
Energy contribution	-13.05
Covariance contribution	-0.10
Combinations/Pair	1.27
Mean z-score	-2.62
Structure conservation index	0.60
SVM decision value	0.91
SVM RNA-class probability	0.879059
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 12627614 90 + 22407834
CUCAACAACAUUUUGUGGAUGCAUAAGGAAAUGGUAUUUAUUUGCCU-UG---AUAAGCAAAUGAAUUCGACUUCUUUAUAAGUCUUUUUGGCG
....((((....))))((((..((((((((.(.(.((((((((((..-..---....)))))))))).).).))))))))..))))........ ( -19.90)
>DroSec_CAF1 8563 89 + 1
CUCAACAAGAUUUUGUGGAU-CAUAAGGAAAUGGAUUUUAUUUGCCU-UG---AUAAGCAAAUAAAUUCGACUUCUUUAUAAUUAUUUUUGUCG
........(((......(((-.((((((((.(.((.(((((((((..-..---....))))))))).)).).)))))))).)))......))). ( -20.80)
>DroSim_CAF1 8648 89 + 1
CUCAACAAGAUUUUGUGGAU-CAUAAGGAAAUGGUUUUUAUUUGCCU-UG---AUAAGCAAAUAAAUUCGACUUCUUUAUAAUUCUUUUUGGCG
.....(((((......((((-.((((((((.(.(..(((((((((..-..---....)))))))))..).).)))))))).)))).)))))... ( -20.40)
>DroEre_CAF1 8578 88 + 1
AUCAACAACAUUUUGUGGAU-CAUAAGGAAAUGGUAUUUAUUUGCCU-UG---AUGGGCA-AUAAAUUCGGCUUCUUUAUGAGUCUUUGUGGCU
.((.((((....)))).))(-(((((((((.(((.(((((((.((((-..---..)))))-)))))))))..))))))))))(((.....))). ( -24.50)
>DroYak_CAF1 8751 89 + 1
AUCAACAACAUUUUGUGGAU-CAUAAGGAAUUGGUAUUUAUUUGCCU-UG---AUAAGCAAAUAAAUUCGGCUUUUUUAUGAUGCUUUGUGGCG
........(((.....(.((-(((((((((((((.((((((((((..-..---....)))))))))))))).))))))))))).)...)))... ( -22.40)
>DroAna_CAF1 3254 89 + 1
AUAACCAACAUUUUUGAGAU-CACAGGGAAAUGGAAUU-GCUUGCCAAUAAUUAUUUUCAAAUAAAUUCCAUUUCUCUGUCAGUAUA--UGGC-
....(((.((....))....-.((((((((((((((((-..(((..(((....)))..)))...)))))))))))))))).......--))).- ( -22.80)
>consensus
AUCAACAACAUUUUGUGGAU_CAUAAGGAAAUGGUAUUUAUUUGCCU_UG___AUAAGCAAAUAAAUUCGACUUCUUUAUAAGUCUUUUUGGCG
.((.((((....)))).))...((((((((.(.(.((((((((((............)))))))))).).).)))))))).............. (-13.15 = -13.05 +  -0.10)

alignment

secondary structure

dotplot

Window 4

Location	12,627,614 – 12,627,704
Length	90
Sequences	6
Columns	94
Reading direction	reverse
Mean pairwise identity	81.10
Mean single sequence MFE	-18.31
Consensus MFE	-12.73
Energy contribution	-13.82
Covariance contribution	1.09
Combinations/Pair	1.28
Mean z-score	-2.82
Structure conservation index	0.70
SVM decision value	1.23
SVM RNA-class probability	0.933772
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 12627614 90 - 22407834
CGCCAAAAAGACUUAUAAAGAAGUCGAAUUCAUUUGCUUAU---CA-AGGCAAAUAAAUACCAUUUCCUUAUGCAUCCACAAAAUGUUGUUGAG
.((......(((((......)))))..(((.((((((((..---..-)))))))).))).............)).((.((((....)))).)). ( -14.90)
>DroSec_CAF1 8563 89 - 1
CGACAAAAAUAAUUAUAAAGAAGUCGAAUUUAUUUGCUUAU---CA-AGGCAAAUAAAAUCCAUUUCCUUAUG-AUCCACAAAAUCUUGUUGAG
((((((.....(((((((.(((((.((.(((((((((((..---..-))))))))))).)).))))).)))))-))..........)))))).. ( -21.76)
>DroSim_CAF1 8648 89 - 1
CGCCAAAAAGAAUUAUAAAGAAGUCGAAUUUAUUUGCUUAU---CA-AGGCAAAUAAAAACCAUUUCCUUAUG-AUCCACAAAAUCUUGUUGAG
...(((.(((((((((((.(((((.(..(((((((((((..---..-)))))))))))..).))))).)))))-))........)))).))).. ( -19.20)
>DroEre_CAF1 8578 88 - 1
AGCCACAAAGACUCAUAAAGAAGCCGAAUUUAU-UGCCCAU---CA-AGGCAAAUAAAUACCAUUUCCUUAUG-AUCCACAAAAUGUUGUUGAU
............((((((.((((..(.((((((-((((...---..-.))).))))))).)..)))).)))))-)((.((((....)))).)). ( -16.10)
>DroYak_CAF1 8751 89 - 1
CGCCACAAAGCAUCAUAAAAAAGCCGAAUUUAUUUGCUUAU---CA-AGGCAAAUAAAUACCAAUUCCUUAUG-AUCCACAAAAUGUUGUUGAU
.((......)).((((((..((...(.((((((((((((..---..-)))))))))))).)...))..)))))-)((.((((....)))).)). ( -17.00)
>DroAna_CAF1 3254 89 - 1
-GCCA--UAUACUGACAGAGAAAUGGAAUUUAUUUGAAAAUAAUUAUUGGCAAGC-AAUUCCAUUUCCCUGUG-AUCUCAAAAAUGUUGGUUAU
-((((--.......((((.(((((((((((..((((..(((....)))..)))).-))))))))))).))))(-....)........))))... ( -20.90)
>consensus
CGCCAAAAAGAAUUAUAAAGAAGUCGAAUUUAUUUGCUUAU___CA_AGGCAAAUAAAUACCAUUUCCUUAUG_AUCCACAAAAUGUUGUUGAG
.............(((((.(((((.(.((((((((((((........)))))))))))).).))))).)))))..((.((((....)))).)). (-12.73 = -13.82 +   1.09)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:16:39 2006