Locus 5552

Sequence ID	2L_DroMel_CAF1
Location	15,819,589 – 15,819,753
Length	164
Max. P	0.938808

overview

Window 7

Location	15,819,589 – 15,819,680
Length	91
Sequences	5
Columns	95
Reading direction	forward
Mean pairwise identity	78.75
Mean single sequence MFE	-19.78
Consensus MFE	-8.30
Energy contribution	-8.30
Covariance contribution	-0.00
Combinations/Pair	1.24
Mean z-score	-2.20
Structure conservation index	0.42
SVM decision value	0.70
SVM RNA-class probability	0.826896
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 15819589 91 + 22407834
CGAUUUAUCUACCGGAGUUGUAGGGAUCUAUCUCCCUAU--ACGAGUAGACGAGUAUGUAUUUAAUAUGAAUAUAU--AUAUACUCAUGUAUUGU
.......(((((((....((((((((......)))))))--))).))))).((((((((((.((.......)).))--))))))))......... ( -25.90)
>DroSec_CAF1 14143 84 + 1
CGAUUUAACUGCAGGAGGUGCAGAGAUCUAUCUCUCAAU--ACG--------AGUAUGUAUUUAAUAUGAAUAUAUAUAUAUACUCAUGUAUUG-
.(((((..(((((.....)))))))))).......((((--(((--------(((((((((...(((....)))..))))))))))..))))))- ( -20.80)
>DroSim_CAF1 14149 80 + 1
CGAUUUAUCAGCAGGAGGUGCAGAGAUCUAUCUCCCUAU--ACG--------AGUAUGUAUUUAAUAUGAAUAUA----UAUACUCAUGUAUUG-
..........((((((((((........)))))))....--..(--------(((((((((...........)))----))))))).)))....- ( -18.50)
>DroEre_CAF1 13939 76 + 1
CGCUUUAUCUACAGGAGGCGCAGAGAUC----UCCCAAUAUGCG--------AAUAUGUGUUUAAUAUGAAUAU------AUACUCAUGUAUUG-
.............((((((.....).))----)))((((((..(--------(.(((((((((.....))))))------))).))..))))))- ( -16.90)
>DroYak_CAF1 40606 76 + 1
CGAUUGAUCUACAGGAGGUGCAGGGAUC----UCCUUAUAUGCG--------AAUAUGUGUUUAAUAUGAAUAU------AUACUCAUGUAUCG-
(((.........(((((((......)))----))))((((((.(--------..(((((((((.....))))))------)))).)))))))))- ( -16.80)
>consensus
CGAUUUAUCUACAGGAGGUGCAGAGAUCUAUCUCCCUAU__ACG________AGUAUGUAUUUAAUAUGAAUAUA____UAUACUCAUGUAUUG_
.........((((.(((.....((((......)))).....................((((((.....)))))).........))).)))).... ( -8.30 =  -8.30 +  -0.00)

alignment

secondary structure

dotplot

Window 8

Location	15,819,615 – 15,819,720
Length	105
Sequences	5
Columns	109
Reading direction	forward
Mean pairwise identity	83.00
Mean single sequence MFE	-19.48
Consensus MFE	-10.30
Energy contribution	-10.24
Covariance contribution	-0.06
Combinations/Pair	1.05
Mean z-score	-2.57
Structure conservation index	0.53
SVM decision value	0.61
SVM RNA-class probability	0.799461
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 15819615 105 + 22407834
UCUAUCUCCCUAU--ACGAGUAGACGAGUAUGUAUUUAAUAUGAAUAUAU--AUAUACUCAUGUAUUGUGUACGCACAUACGCACAUCUGGCCAAAAAAAAGCCAUCAG
((((.(((.....--..))))))).((((((((((.((.......)).))--))))))))..((((.(((....))))))).......((((.........)))).... ( -22.90)
>DroSec_CAF1 14169 95 + 1
UCUAUCUCUCAAU--ACG--------AGUAUGUAUUUAAUAUGAAUAUAUAUAUAUACUCAUGUAUUG--UACGCACAUACGCACAUCUGGCCAAA--AAAGCCAUCAG
.........((((--(((--------(((((((((...(((....)))..))))))))))..))))))--...((......)).....((((....--...)))).... ( -19.10)
>DroSim_CAF1 14175 91 + 1
UCUAUCUCCCUAU--ACG--------AGUAUGUAUUUAAUAUGAAUAUA----UAUACUCAUGUAUUG--UACGCACAUACGCACAUCUGGCCAAA--AAAGCCAUCAG
..........(((--(.(--------(((((((((...........)))----))))))).)))).((--(.((......)).)))..((((....--...)))).... ( -16.60)
>DroEre_CAF1 13965 87 + 1
UC----UCCCAAUAUGCG--------AAUAUGUGUUUAAUAUGAAUAU------AUACUCAUGUAUUG--UUCGCACAUUCGCACAUCUGGCCAAA--AAAGCCAUCAG
..----........((((--------(((.((((..((((((((....------....))))))..))--..)))).)))))))....((((....--...)))).... ( -21.10)
>DroYak_CAF1 40632 87 + 1
UC----UCCUUAUAUGCG--------AAUAUGUGUUUAAUAUGAAUAU------AUACUCAUGUAUCG--AACGCACAUACGCACAUCUGGCCAAA--AAAGCUAUCAG
..----.((..((.((((--------.((.(((((((.((((((....------....))))))...)--)))))).)).)))).))..)).....--........... ( -17.70)
>consensus
UCUAUCUCCCUAU__ACG________AGUAUGUAUUUAAUAUGAAUAUA____UAUACUCAUGUAUUG__UACGCACAUACGCACAUCUGGCCAAA__AAAGCCAUCAG
.............................((((.....((((((.((((....)))).)))))).........((......)))))).((((.........)))).... (-10.30 = -10.24 +  -0.06)

alignment

secondary structure

dotplot

Window 9

Location	15,819,615 – 15,819,720
Length	105
Sequences	5
Columns	109
Reading direction	reverse
Mean pairwise identity	83.00
Mean single sequence MFE	-24.48
Consensus MFE	-15.94
Energy contribution	-16.36
Covariance contribution	0.42
Combinations/Pair	1.08
Mean z-score	-2.51
Structure conservation index	0.65
SVM decision value	1.23
SVM RNA-class probability	0.933528
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 15819615 105 - 22407834
CUGAUGGCUUUUUUUUGGCCAGAUGUGCGUAUGUGCGUACACAAUACAUGAGUAUAU--AUAUAUUCAUAUUAAAUACAUACUCGUCUACUCGU--AUAGGGAGAUAGA
....(((((.......)))))..(((((((....)))))))........((((((.(--((.((.......)).))).))))))((((.(((..--...)))))))... ( -25.80)
>DroSec_CAF1 14169 95 - 1
CUGAUGGCUUU--UUUGGCCAGAUGUGCGUAUGUGCGUA--CAAUACAUGAGUAUAUAUAUAUAUUCAUAUUAAAUACAUACU--------CGU--AUUGAGAGAUAGA
....(((((..--...)))))..(((((((....)))))--))....(((((((((....)))))))))............((--------(..--.....)))..... ( -23.80)
>DroSim_CAF1 14175 91 - 1
CUGAUGGCUUU--UUUGGCCAGAUGUGCGUAUGUGCGUA--CAAUACAUGAGUAUA----UAUAUUCAUAUUAAAUACAUACU--------CGU--AUAGGGAGAUAGA
....(((((..--...)))))..(((((((....)))))--))....((((((((.----(((...........))).)))))--------)))--............. ( -21.90)
>DroEre_CAF1 13965 87 - 1
CUGAUGGCUUU--UUUGGCCAGAUGUGCGAAUGUGCGAA--CAAUACAUGAGUAU------AUAUUCAUAUUAAACACAUAUU--------CGCAUAUUGGGA----GA
....(((((..--...)))))((((((((((((((.(..--.((((..(((((..------..)))))))))...).))))))--------))))))))....----.. ( -27.40)
>DroYak_CAF1 40632 87 - 1
CUGAUAGCUUU--UUUGGCCAGAUGUGCGUAUGUGCGUU--CGAUACAUGAGUAU------AUAUUCAUAUUAAACACAUAUU--------CGCAUAUAAGGA----GA
...........--.....((..(((((((.(((((.(((--..(((..(((((..------..))))))))..))).))))).--------)))))))..)).----.. ( -23.50)
>consensus
CUGAUGGCUUU__UUUGGCCAGAUGUGCGUAUGUGCGUA__CAAUACAUGAGUAUA____UAUAUUCAUAUUAAAUACAUACU________CGU__AUAGGGAGAUAGA
....(((((.......))))).......(((((((.(((.....)))(((((((((....)))))))))......)))))))........................... (-15.94 = -16.36 +   0.42)

alignment

secondary structure

dotplot

Window 0

Location	15,819,642 – 15,819,753
Length	111
Sequences	5
Columns	115
Reading direction	reverse
Mean pairwise identity	89.85
Mean single sequence MFE	-25.50
Consensus MFE	-20.02
Energy contribution	-20.12
Covariance contribution	0.10
Combinations/Pair	1.07
Mean z-score	-2.13
Structure conservation index	0.78
SVM decision value	1.27
SVM RNA-class probability	0.938808
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 15819642 111 - 22407834
--GCCCUACCCUUCUUUUUCCAGUUUCUUUGCUGGCUGAUGGCUUUUUUUUGGCCAGAUGUGCGUAUGUGCGUACACAAUACAUGAGUAUAU--AUAUAUUCAUAUUAAAUACAU
--.................(((((......)))))....(((((.......)))))..(((((((....)))))))......((((((((..--..))))))))........... ( -25.60)
>DroSec_CAF1 14188 109 - 1
--GCCCUACCCUUCUUUUUCCAGUUUCUUUGCUGGCUGAUGGCUUU--UUUGGCCAGAUGUGCGUAUGUGCGUA--CAAUACAUGAGUAUAUAUAUAUAUUCAUAUUAAAUACAU
--.................(((((......)))))....(((((..--...)))))..(((((((....)))))--))....(((((((((....)))))))))........... ( -27.30)
>DroSim_CAF1 14194 105 - 1
--GCCCUACCCUUCUUUUUCCAGUUUCUUUGCUGGCUGAUGGCUUU--UUUGGCCAGAUGUGCGUAUGUGCGUA--CAAUACAUGAGUAUA----UAUAUUCAUAUUAAAUACAU
--.................(((((......)))))....(((((..--...)))))..(((((((....)))))--))....(((((((..----..)))))))........... ( -24.90)
>DroEre_CAF1 13982 105 - 1
UCGCCCUUCGCCUGCUUUUCCAGUUUCUUUGCUGGCUGAUGGCUUU--UUUGGCCAGAUGUGCGAAUGUGCGAA--CAAUACAUGAGUAU------AUAUUCAUAUUAAACACAU
(((((.(((((........(((((......)))))....(((((..--...))))).....))))).).)))).--......((((((..------..))))))........... ( -27.80)
>DroYak_CAF1 40649 103 - 1
--GCCCUUUUCUUCUUUUUCCAGUUUCUUUGCUGGCUGAUAGCUUU--UUUGGCCAGAUGUGCGUAUGUGCGUU--CGAUACAUGAGUAU------AUAUUCAUAUUAAACACAU
--....................((((.....(((((..(.......--.)..)))))(((((.((((((((...--..........))))------)))).))))).)))).... ( -21.92)
>consensus
__GCCCUACCCUUCUUUUUCCAGUUUCUUUGCUGGCUGAUGGCUUU__UUUGGCCAGAUGUGCGUAUGUGCGUA__CAAUACAUGAGUAUA____UAUAUUCAUAUUAAAUACAU
...................(((((......)))))....(((((.......))))).(((((.((((.((......))))))(((((((((....)))))))))......))))) (-20.02 = -20.12 +   0.10)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:46:59 2006