Locus 5658

Sequence ID	2L_DroMel_CAF1
Location	16,049,869 – 16,050,006
Length	137
Max. P	0.808201

overview

Window 8

Location	16,049,869 – 16,049,974
Length	105
Sequences	6
Columns	108
Reading direction	forward
Mean pairwise identity	83.44
Mean single sequence MFE	-36.18
Consensus MFE	-25.12
Energy contribution	-26.07
Covariance contribution	0.95
Combinations/Pair	1.08
Mean z-score	-2.87
Structure conservation index	0.69
SVM decision value	0.64
SVM RNA-class probability	0.808201
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 16049869 105 + 22407834
CCCCUCUACAAACUCACUUCAGUUUUGGGGCUUCUCCUGGGUUUUU--GGUAUCUGCAUCA-UGCAGUUAUUGCCGAUGCCCAGGAGCGUGGGCAGGAAAAUUAUGAA
((((((((.(((((......))))))))))...(((((((((..((--((((.((((....-.))))....)))))).)))))))))...)))............... ( -38.10)
>DroSec_CAF1 225423 103 + 1
GCCC--UACAAACUCACUUCAGUUUUCGGGCUUCUCCUGGGUUUUU--GGUAUCUGCAUCA-UGCAGUUAUUGCCGAUGCCCAGGAGCGUGGGCAGGAAAAUUAUGAA
((((--.(((((((......)))))........(((((((((..((--((((.((((....-.))))....)))))).))))))))).)))))).............. ( -39.90)
>DroSim_CAF1 232236 103 + 1
GUCC--UACAAACUCACUUCAGUUUUCGGGCUUCUCCUGGGUUUUU--GGUAUCUGCAUCA-UGCAGUUAUUGCCGAUGCCCAGGAGCGUGGGCAGGAAAAUUAUGAA
....--............(((((((((..(((((((((((((..((--((((.((((....-.))))....)))))).)))))))))...))))..))))))..))). ( -39.10)
>DroEre_CAF1 214322 105 + 1
CCCC--UGCAAACUCACUUCAGUUUUUGGGCUUCUCCUGGGUUUUUUGGGUAUCUGCAUCA-UGCAGUUAUUGCCGAUGCCCAGGAGCGUGGGCAGCAGAAUUAUGAA
...(--(((...(((((...((((....)))).(((((((((....(.((((.((((....-.))))....)))).).))))))))).)))))..))))......... ( -38.80)
>DroYak_CAF1 211614 103 + 1
CCCC--CACAAACUCACUUCAGUGUUCGGGCUUCUCCUGGGUUUUU--GGUAUCUGCAUCA-UGCAGUUAUUGCCGAUGCCCAGGAGCGUGGGCAGGAAAAUUAUGAA
((((--(((.....(((....))).........(((((((((..((--((((.((((....-.))))....)))))).))))))))).)))))..))........... ( -40.60)
>DroAna_CAF1 158278 93 + 1
CCUU--UAAAAACUC----CAGUA-UCGGGCUUCCUAUUGGUU-UG--GGUUUCUGCAUCUCUGCAGCUUUU-UAGAUUCACAGAGGCGUUGGCUCUGAAUGCA----
....--.........----..(((-(((((((.(((..(((((-((--((...(((((....)))))...))-)))).)))...)))....))).))).)))).---- ( -20.60)
>consensus
CCCC__UACAAACUCACUUCAGUUUUCGGGCUUCUCCUGGGUUUUU__GGUAUCUGCAUCA_UGCAGUUAUUGCCGAUGCCCAGGAGCGUGGGCAGGAAAAUUAUGAA
............(((((...(((......))).(((((((((......((((.(((((....))))).))))......))))))))).)))))............... (-25.12 = -26.07 +   0.95)

alignment

secondary structure

dotplot

Window 9

Location	16,049,869 – 16,049,974
Length	105
Sequences	6
Columns	108
Reading direction	reverse
Mean pairwise identity	83.44
Mean single sequence MFE	-29.61
Consensus MFE	-21.64
Energy contribution	-22.58
Covariance contribution	0.95
Combinations/Pair	1.10
Mean z-score	-1.74
Structure conservation index	0.73
SVM decision value	0.11
SVM RNA-class probability	0.587357
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 16049869 105 - 22407834
UUCAUAAUUUUCCUGCCCACGCUCCUGGGCAUCGGCAAUAACUGCA-UGAUGCAGAUACC--AAAAACCCAGGAGAAGCCCCAAAACUGAAGUGAGUUUGUAGAGGGG
.....................((((((((((((((((.....))).-)))))).(....)--......)))))))...((((.(((((......))))).....)))) ( -30.10)
>DroSec_CAF1 225423 103 - 1
UUCAUAAUUUUCCUGCCCACGCUCCUGGGCAUCGGCAAUAACUGCA-UGAUGCAGAUACC--AAAAACCCAGGAGAAGCCCGAAAACUGAAGUGAGUUUGUA--GGGC
.....................((((((((((((((((.....))).-)))))).(....)--......)))))))..((((..(((((......)))))...--)))) ( -33.00)
>DroSim_CAF1 232236 103 - 1
UUCAUAAUUUUCCUGCCCACGCUCCUGGGCAUCGGCAAUAACUGCA-UGAUGCAGAUACC--AAAAACCCAGGAGAAGCCCGAAAACUGAAGUGAGUUUGUA--GGAC
..........((((((.....((((((((((((((((.....))).-)))))).(....)--......)))))))........(((((......))))))))--))). ( -31.80)
>DroEre_CAF1 214322 105 - 1
UUCAUAAUUCUGCUGCCCACGCUCCUGGGCAUCGGCAAUAACUGCA-UGAUGCAGAUACCCAAAAAACCCAGGAGAAGCCCAAAAACUGAAGUGAGUUUGCA--GGGG
.......((((((.((.(((.((((((((((((((((.....))).-)))))).(.....).......))))))).....((.....))..))).))..)))--))). ( -32.60)
>DroYak_CAF1 211614 103 - 1
UUCAUAAUUUUCCUGCCCACGCUCCUGGGCAUCGGCAAUAACUGCA-UGAUGCAGAUACC--AAAAACCCAGGAGAAGCCCGAACACUGAAGUGAGUUUGUG--GGGG
...............(((((.((((((((((((((((.....))).-)))))).(....)--......))))))).........(((....))).....)))--)).. ( -33.70)
>DroAna_CAF1 158278 93 - 1
----UGCAUUCAGAGCCAACGCCUCUGUGAAUCUA-AAAAGCUGCAGAGAUGCAGAAACC--CA-AACCAAUAGGAAGCCCGA-UACUG----GAGUUUUUA--AAGG
----.((((.....((....))((((((.......-.......))))))))))(((((((--((-........((....))..-...))----).)))))).--.... ( -16.46)
>consensus
UUCAUAAUUUUCCUGCCCACGCUCCUGGGCAUCGGCAAUAACUGCA_UGAUGCAGAUACC__AAAAACCCAGGAGAAGCCCGAAAACUGAAGUGAGUUUGUA__GGGG
...............(((...((((((((............(((((....)))))............))))))))........(((((......))))).....))). (-21.64 = -22.58 +   0.95)

alignment

secondary structure

dotplot

Window 0

Location	16,049,898 – 16,050,006
Length	108
Sequences	6
Columns	119
Reading direction	forward
Mean pairwise identity	81.00
Mean single sequence MFE	-39.07
Consensus MFE	-24.35
Energy contribution	-24.77
Covariance contribution	0.42
Combinations/Pair	1.17
Mean z-score	-1.93
Structure conservation index	0.62
SVM decision value	0.39
SVM RNA-class probability	0.716192
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 16049898 108 + 22407834
GCUUCUCCUGGGUUUUU--GGUAUCUGCAUC-AUGCAGUUAUUGCCGAUGCCCAGGAGCGUGGGCAGGAAAAUUAUGAAGGAGAAUA--UCG--GGGGCACCUACC----ACGCCGCUU
((...((((((((..((--((((.((((...-..))))....)))))).))))))))((((((.................((.....--))(--((....))).))----)))).)).. ( -42.80)
>DroPse_CAF1 260585 107 + 1
-CUCCUCCUGUGUGUGU--GGUAUCUGCAUCUAUGCAGUUAUUGUAUGUGGCAAAGGGCGUAGGCAUUACGAUUAUCGAGGGA------UCGUACGAGUACCUGACUUUUAAAAUG---
-....((((.((((((.--.(((.(((((....))))).)))..)))...))).))))..((((.(((((((((.......))------)))))...)).))))............--- ( -25.10)
>DroSec_CAF1 225450 108 + 1
GCUUCUCCUGGGUUUUU--GGUAUCUGCAUC-AUGCAGUUAUUGCCGAUGCCCAGGAGCGUGGGCAGGAAAAUUAUGAAGGAGAAUA--UCG--GGGGCCACUACC----ACGGCGCUU
((..(((((((((..((--((((.((((...-..))))....)))))).)))))))))(((((...((.....(((........)))--...--....))....))----))))).... ( -40.10)
>DroSim_CAF1 232263 108 + 1
GCUUCUCCUGGGUUUUU--GGUAUCUGCAUC-AUGCAGUUAUUGCCGAUGCCCAGGAGCGUGGGCAGGAAAAUUAUGAAGGAGAAUA--UCG--GGGGCCACUACC----ACGGCGUUU
((..(((((((((..((--((((.((((...-..))))....)))))).)))))))))(((((...((.....(((........)))--...--....))....))----))))).... ( -40.10)
>DroEre_CAF1 214349 109 + 1
GCUUCUCCUGGGUUUUUUGGGUAUCUGCAUC-AUGCAGUUAUUGCCGAUGCCCAGGAGCGUGGGCAGCAGAAUUAUGAAGGGGA-UA--UCG--GGGGUCCCCACC----AAAGCGCUU
(((((((((((((....(.((((.((((...-..))))....)))).).)))))))))..(((....((......))..(((((-(.--...--...)))))).))----))))).... ( -43.20)
>DroYak_CAF1 211641 110 + 1
GCUUCUCCUGGGUUUUU--GGUAUCUGCAUC-AUGCAGUUAUUGCCGAUGCCCAGGAGCGUGGGCAGGAAAAUUAUGAAGGGGAAUAUUCUG--GGGGUCCCUACC----AUACUGCUU
....(((((((((..((--((((.((((...-..))))....)))))).)))))))))...((((((......((((..(((((...((...--.)).)))))..)----))))))))) ( -43.10)
>consensus
GCUUCUCCUGGGUUUUU__GGUAUCUGCAUC_AUGCAGUUAUUGCCGAUGCCCAGGAGCGUGGGCAGGAAAAUUAUGAAGGAGAAUA__UCG__GGGGCCCCUACC____ACAGCGCUU
(((((((((((((......((((.(((((....))))).))))......))))))))((....)).............................))))).................... (-24.35 = -24.77 +   0.42)

alignment

secondary structure

dotplot

Window 1

Location	16,049,898 – 16,050,006
Length	108
Sequences	6
Columns	119
Reading direction	reverse
Mean pairwise identity	81.00
Mean single sequence MFE	-30.19
Consensus MFE	-19.66
Energy contribution	-20.25
Covariance contribution	0.58
Combinations/Pair	1.17
Mean z-score	-1.50
Structure conservation index	0.65
SVM decision value	0.08
SVM RNA-class probability	0.574716
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 16049898 108 - 22407834
AAGCGGCGU----GGUAGGUGCCCC--CGA--UAUUCUCCUUCAUAAUUUUCCUGCCCACGCUCCUGGGCAUCGGCAAUAACUGCAU-GAUGCAGAUACC--AAAAACCCAGGAGAAGC
..((.((((----((((((......--.((--.........))........)))).))))))(((((((((((((((.....))).)-))))).(....)--......))))))...)) ( -34.16)
>DroPse_CAF1 260585 107 - 1
---CAUUUUAAAAGUCAGGUACUCGUACGA------UCCCUCGAUAAUCGUAAUGCCUACGCCCUUUGCCACAUACAAUAACUGCAUAGAUGCAGAUACC--ACACACACAGGAGGAG-
---..........((.(((((....(((((------(.........)))))).)))))))..(((((..............(((((....))))).....--.........)))))..- ( -19.89)
>DroSec_CAF1 225450 108 - 1
AAGCGCCGU----GGUAGUGGCCCC--CGA--UAUUCUCCUUCAUAAUUUUCCUGCCCACGCUCCUGGGCAUCGGCAAUAACUGCAU-GAUGCAGAUACC--AAAAACCCAGGAGAAGC
..((..(((----(((((.((...)--)((--.........)).........))).)))))((((((((((((((((.....))).)-))))).(....)--......)))))))..)) ( -30.30)
>DroSim_CAF1 232263 108 - 1
AAACGCCGU----GGUAGUGGCCCC--CGA--UAUUCUCCUUCAUAAUUUUCCUGCCCACGCUCCUGGGCAUCGGCAAUAACUGCAU-GAUGCAGAUACC--AAAAACCCAGGAGAAGC
....(((((----(((((.((...)--)((--.........)).........))).)))))((((((((((((((((.....))).)-))))).(....)--......)))))))..)) ( -29.50)
>DroEre_CAF1 214349 109 - 1
AAGCGCUUU----GGUGGGGACCCC--CGA--UA-UCCCCUUCAUAAUUCUGCUGCCCACGCUCCUGGGCAUCGGCAAUAACUGCAU-GAUGCAGAUACCCAAAAAACCCAGGAGAAGC
.((((...(----((.(((((....--...--..-))))).)))......)))).......((((((((((((((((.....))).)-))))).(.....).......))))))).... ( -33.50)
>DroYak_CAF1 211641 110 - 1
AAGCAGUAU----GGUAGGGACCCC--CAGAAUAUUCCCCUUCAUAAUUUUCCUGCCCACGCUCCUGGGCAUCGGCAAUAACUGCAU-GAUGCAGAUACC--AAAAACCCAGGAGAAGC
..((.((..----((((((((....--..(((........)))......)))))))).)).((((((((((((((((.....))).)-))))).(....)--......)))))))..)) ( -33.80)
>consensus
AAGCGCCGU____GGUAGGGACCCC__CGA__UAUUCCCCUUCAUAAUUUUCCUGCCCACGCUCCUGGGCAUCGGCAAUAACUGCAU_GAUGCAGAUACC__AAAAACCCAGGAGAAGC
.............(((((..................................)))))....((((((((............(((((....)))))............)))))))).... (-19.66 = -20.25 +   0.58)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:49:34 2006