Locus 1144

Sequence ID	X_DroMel_CAF1
Location	3,426,601 – 3,426,745
Length	144
Max. P	0.998328

overview

Window 0

Location	3,426,601 – 3,426,706
Length	105
Sequences	5
Columns	108
Reading direction	forward
Mean pairwise identity	86.89
Mean single sequence MFE	-31.98
Consensus MFE	-26.74
Energy contribution	-26.74
Covariance contribution	0.00
Combinations/Pair	1.13
Mean z-score	-2.96
Structure conservation index	0.84
SVM decision value	3.07
SVM RNA-class probability	0.998328
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 3426601 105 + 22224390
CCA--UAGAUGAAGCUUUUGAAAAAGCUGUUUGCGUAGCAUACUUCUGGGCUCCAACCUUUUC-AAAAGUUAUGAAAACUUUGUAGCCCGCUUUUUGUCAGUUGCGAA
...--........((..((((((((((.((.(((...))).))....(((((.(((..(((((-(.......))))))..))).)))))))))))..))))..))... ( -28.40)
>DroSec_CAF1 2021 105 + 1
CCA--CAGAUUAAGCUUUUGAAAAAGCUGUUUGCGAAGCACACUUCUAGGCUCCAACCCUUUC-AAAAGUUAUGAAAGCUUUGGAGCCCGCUUUUUGUCAGUUGCGAA
...--........((..((((((((((.......((((....))))..((((((((..(((((-(.......))))))..)))))))).))))))..))))..))... ( -33.70)
>DroSim_CAF1 2019 105 + 1
CCA--CAGAUUAAGCUUUUGAAAAAGCUGUUUGCGUAGCACACUUCUAGGCUCCAACCCUUUC-AAAAGUUAUGAAAGCUUUGGAGCCCGCUUUUAGGCAGUUGCGAA
...--(((((..((((((....)))))))))))((((((.........((((((((..(((((-(.......))))))..)))))))).(((....))).)))))).. ( -36.40)
>DroEre_CAF1 594 107 + 1
CCAGUAAGAUUAAGCUUUUGAAAAAGCUGACUGUGAAGCACUCUUUUGGGCUCCAACCUUUUC-UAAGUGUAUGAGAACUUUGGAGCACGCUUUUUGUCAGUUGCGAA
................((((....(((((((...(((((.(......).(((((((..(((((-.........)))))..)))))))..)))))..))))))).)))) ( -29.80)
>DroYak_CAF1 690 108 + 1
CCAGUAAGAUUAAGCUUUUUAAAAAGCUGUUUGCGAAGCACACUUUCGGGCUCCAACCUUUUCCCAAAAGCAUGAGAACUUUGGAGCCCGCUUUUUAUCAGUUGCGAA
............((((...((((((((.((.(((...))).))....(((((((((..(((((..........)))))..)))))))))))))))))..))))..... ( -31.60)
>consensus
CCA__AAGAUUAAGCUUUUGAAAAAGCUGUUUGCGAAGCACACUUCUGGGCUCCAACCUUUUC_AAAAGUUAUGAAAACUUUGGAGCCCGCUUUUUGUCAGUUGCGAA
.............((..((((((((((.((.(((...))).))....(((((((((..(((((..........)))))..)))))))))))))))..))))..))... (-26.74 = -26.74 +   0.00)

alignment

secondary structure

dotplot

Window 1

Location	3,426,601 – 3,426,706
Length	105
Sequences	5
Columns	108
Reading direction	reverse
Mean pairwise identity	86.89
Mean single sequence MFE	-31.94
Consensus MFE	-26.48
Energy contribution	-26.84
Covariance contribution	0.36
Combinations/Pair	1.10
Mean z-score	-2.88
Structure conservation index	0.83
SVM decision value	2.88
SVM RNA-class probability	0.997564
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 3426601 105 - 22224390
UUCGCAACUGACAAAAAGCGGGCUACAAAGUUUUCAUAACUUUU-GAAAAGGUUGGAGCCCAGAAGUAUGCUACGCAAACAGCUUUUUCAAAAGCUUCAUCUA--UGG
...((...(((..(((((((((((.(((..((((((.......)-)))))..))).)))))....((.(((...))).)).)))))))))...))........--... ( -28.20)
>DroSec_CAF1 2021 105 - 1
UUCGCAACUGACAAAAAGCGGGCUCCAAAGCUUUCAUAACUUUU-GAAAGGGUUGGAGCCUAGAAGUGUGCUUCGCAAACAGCUUUUUCAAAAGCUUAAUCUG--UGG
..((((...........(((((((((((..((((((.......)-)))))..))))))))).((((....))))))....((((((....)))))).....))--)). ( -37.00)
>DroSim_CAF1 2019 105 - 1
UUCGCAACUGCCUAAAAGCGGGCUCCAAAGCUUUCAUAACUUUU-GAAAGGGUUGGAGCCUAGAAGUGUGCUACGCAAACAGCUUUUUCAAAAGCUUAAUCUG--UGG
...((((((((......))(((((((((..((((((.......)-)))))..)))))))))...))).)))..((((...((((((....)))))).....))--)). ( -35.40)
>DroEre_CAF1 594 107 - 1
UUCGCAACUGACAAAAAGCGUGCUCCAAAGUUCUCAUACACUUA-GAAAAGGUUGGAGCCCAAAAGAGUGCUUCACAGUCAGCUUUUUCAAAAGCUUAAUCUUACUGG
...((...(((..(((((((.(((((((..((((.........)-)))....))))))).)....((.((.....)).)).)))))))))...))............. ( -23.20)
>DroYak_CAF1 690 108 - 1
UUCGCAACUGAUAAAAAGCGGGCUCCAAAGUUCUCAUGCUUUUGGGAAAAGGUUGGAGCCCGAAAGUGUGCUUCGCAAACAGCUUUUUAAAAAGCUUAAUCUUACUGG
...((......(((((((((((((((((..((((((......))))))....)))))))))....((.(((...))).)).))))))))....))............. ( -35.90)
>consensus
UUCGCAACUGACAAAAAGCGGGCUCCAAAGUUUUCAUAACUUUU_GAAAAGGUUGGAGCCCAGAAGUGUGCUUCGCAAACAGCUUUUUCAAAAGCUUAAUCUG__UGG
...((...(((..(((((((((((((((..(((((..........)))))..)))))))))....((.(((...))).)).)))))))))...))............. (-26.48 = -26.84 +   0.36)

alignment

secondary structure

dotplot

Window 2

Location	3,426,627 – 3,426,745
Length	118
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	83.42
Mean single sequence MFE	-35.22
Consensus MFE	-22.79
Energy contribution	-22.23
Covariance contribution	-0.56
Combinations/Pair	1.23
Mean z-score	-2.67
Structure conservation index	0.65
SVM decision value	1.36
SVM RNA-class probability	0.945944
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 3426627 118 + 22224390
GUUUGCGUAGCAUACUUCUGGGCUCCAACCUUUUC-AAAAGUUAUGAAAACUUUGUAGCCCGCUUUUUGUCAGUUGCGAACCCUAGGCUAGGCUAUGACUUUGGUUUCAGCUUUCCA-AA
(((((((..(((......((((((.(((..(((((-(.......))))))..))).)))))).....)))....)))))))....((..(((((..(((....)))..))))).)).-.. ( -32.40)
>DroSec_CAF1 2047 113 + 1
GUUUGCGAAGCACACUUCUAGGCUCCAACCCUUUC-AAAAGUUAUGAAAGCUUUGGAGCCCGCUUUUUGUCAGUUGCGAACCCUGG-----GCUAUGGCUUUGGUUCCAGCUUUUCA-AA
....((((((....))))..((((((((..(((((-(.......))))))..)))))))).))..((((..(((((.(((((..((-----((....)))).))))))))))...))-)) ( -41.10)
>DroSim_CAF1 2045 113 + 1
GUUUGCGUAGCACACUUCUAGGCUCCAACCCUUUC-AAAAGUUAUGAAAGCUUUGGAGCCCGCUUUUAGGCAGUUGCGAACCCUGG-----GCUAUGGCUUUGGUUCCAGCUUUUCA-AA
....(((((((.........((((((((..(((((-(.......))))))..)))))))).(((....))).)))))(((((..((-----((....)))).)))))..))......-.. ( -40.00)
>DroEre_CAF1 622 113 + 1
GACUGUGAAGCACUCUUUUGGGCUCCAACCUUUUC-UAAGUGUAUGAGAACUUUGGAGCACGCUUUUUGUCAGUUGCGAAACCAAG-----GCUAUGUCCUUGCUAUCAGCUUUUCA-AA
(((...(((((.(......).(((((((..(((((-.........)))))..)))))))..)))))..)))(((((......((((-----(......)))))....))))).....-.. ( -29.90)
>DroYak_CAF1 718 115 + 1
GUUUGCGAAGCACACUUUCGGGCUCCAACCUUUUCCCAAAAGCAUGAGAACUUUGGAGCCCGCUUUUUAUCAGUUGCGAACCCUGU-----GCUAUGUCUUUGGUUUUAGCUUUUUAAAA
((((((((..........((((((((((..(((((..........)))))..))))))))))...........)))))))).....-----((((...(....)...))))......... ( -32.70)
>consensus
GUUUGCGAAGCACACUUCUGGGCUCCAACCUUUUC_AAAAGUUAUGAAAACUUUGGAGCCCGCUUUUUGUCAGUUGCGAACCCUGG_____GCUAUGGCUUUGGUUUCAGCUUUUCA_AA
((.(((...))).))...((((((((((..(((((..........)))))..)))))))))).........(((((.(((((....................))))))))))........ (-22.79 = -22.23 +  -0.56)

alignment

secondary structure

dotplot

Window 3

Location	3,426,627 – 3,426,745
Length	118
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	83.42
Mean single sequence MFE	-33.78
Consensus MFE	-21.37
Energy contribution	-21.45
Covariance contribution	0.08
Combinations/Pair	1.10
Mean z-score	-2.36
Structure conservation index	0.63
SVM decision value	0.83
SVM RNA-class probability	0.860767
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 3426627 118 - 22224390
UU-UGGAAAGCUGAAACCAAAGUCAUAGCCUAGCCUAGGGUUCGCAACUGACAAAAAGCGGGCUACAAAGUUUUCAUAACUUUU-GAAAAGGUUGGAGCCCAGAAGUAUGCUACGCAAAC
((-(((..........)))))......((.((((....(.(((((............))(((((.(((..((((((.......)-)))))..))).))))).))).)..)))).)).... ( -29.30)
>DroSec_CAF1 2047 113 - 1
UU-UGAAAAGCUGGAACCAAAGCCAUAGC-----CCAGGGUUCGCAACUGACAAAAAGCGGGCUCCAAAGCUUUCAUAACUUUU-GAAAGGGUUGGAGCCUAGAAGUGUGCUUCGCAAAC
((-((...((.(((((((...((....))-----....))))).)).))..))))..(((((((((((..((((((.......)-)))))..))))))))).((((....)))))).... ( -40.70)
>DroSim_CAF1 2045 113 - 1
UU-UGAAAAGCUGGAACCAAAGCCAUAGC-----CCAGGGUUCGCAACUGCCUAAAAGCGGGCUCCAAAGCUUUCAUAACUUUU-GAAAGGGUUGGAGCCUAGAAGUGUGCUACGCAAAC
..-......((..(((((...((....))-----....)))))((((((((......))(((((((((..((((((.......)-)))))..)))))))))...))).)))...)).... ( -38.10)
>DroEre_CAF1 622 113 - 1
UU-UGAAAAGCUGAUAGCAAGGACAUAGC-----CUUGGUUUCGCAACUGACAAAAAGCGUGCUCCAAAGUUCUCAUACACUUA-GAAAAGGUUGGAGCCCAAAAGAGUGCUUCACAGUC
..-((((..(((((.(.(((((......)-----)))).).))................(.(((((((..((((.........)-)))....))))))).).....)))..))))..... ( -25.00)
>DroYak_CAF1 718 115 - 1
UUUUAAAAAGCUAAAACCAAAGACAUAGC-----ACAGGGUUCGCAACUGAUAAAAAGCGGGCUCCAAAGUUCUCAUGCUUUUGGGAAAAGGUUGGAGCCCGAAAGUGUGCUUCGCAAAC
.....................(....(((-----(((...(((((............))(((((((((..((((((......))))))....))))))))))))..))))))...).... ( -35.80)
>consensus
UU_UGAAAAGCUGAAACCAAAGACAUAGC_____CCAGGGUUCGCAACUGACAAAAAGCGGGCUCCAAAGUUUUCAUAACUUUU_GAAAAGGUUGGAGCCCAGAAGUGUGCUUCGCAAAC
........(((................((........((........))........))(((((((((..(((((..........)))))..)))))))))........)))........ (-21.37 = -21.45 +   0.08)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:02:28 2006