Locus 5104

Sequence ID	2L_DroMel_CAF1
Location	14,530,827 – 14,530,961
Length	134
Max. P	0.999897

overview

Window 9

Location	14,530,827 – 14,530,925
Length	98
Sequences	5
Columns	101
Reading direction	forward
Mean pairwise identity	92.23
Mean single sequence MFE	-31.78
Consensus MFE	-30.86
Energy contribution	-31.06
Covariance contribution	0.20
Combinations/Pair	1.00
Mean z-score	-1.53
Structure conservation index	0.97
SVM decision value	1.94
SVM RNA-class probability	0.983412
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 14530827 98 + 22407834
UAAAUUAUGGUA--UAAAAAA-UGUAUUUUGCAUCGGCCGGGAAUCGAACCCAGGCCGCCCGCGUGGCAGGCGAGCAUUCUACCACUGAACCACCGAUGCU
........((((--((.....-))))))..(((((((..(((.......)))..((((((.((...)).)))).)).................))))))). ( -27.10)
>DroSec_CAF1 62907 100 + 1
UAAAUUUUGGUAUUUAAAAAA-UGUAGUAUGCAUCGGCCGGGAAUCGAACCCGGGCCGCCCGCGUGGCAGGCGAGCAUUCUACCACUGAACCACCGAUGCU
.....................-........((((((((((((.......)))))((((((.((...)).)))).)).................))))))). ( -32.20)
>DroSim_CAF1 48261 100 + 1
UACAUUUUGGUAUUUAAAAAA-UAUAGUAUGCAUCGGCCGGGAAUCGAACCCGGGCCGCCCGCGUGGCAGGCGAGCAUUCUACCACUGAACCACCGAUGCU
.....................-........((((((((((((.......)))))((((((.((...)).)))).)).................))))))). ( -32.20)
>DroEre_CAF1 58063 101 + 1
AAAAGUAUGGAACUUAAAAAAAAGUCGUAUGCAUCGGCCGGGAAUCGAACCCGGGCCGCCCGCGUGGCAGGCGAGCAUUCUACCACUGAACCACCGAUGCU
....(((((..((((......)))))))))((((((((((((.......)))))((((((.((...)).)))).)).................))))))). ( -35.20)
>DroYak_CAF1 53170 98 + 1
AAAAUUAUGGGAAUUAAAAAA---UCGUUUGCAUCGGCCGGGAAUCGAACCCGGGCCGCCCGCGUGGCAGGCGAGCAUUCUACCACUGAACCACCGAUGCU
.....................---......((((((((((((.......)))))((((((.((...)).)))).)).................))))))). ( -32.20)
>consensus
UAAAUUAUGGUAUUUAAAAAA_UGUAGUAUGCAUCGGCCGGGAAUCGAACCCGGGCCGCCCGCGUGGCAGGCGAGCAUUCUACCACUGAACCACCGAUGCU
..............................((((((((((((.......)))))((((((.((...)).)))).)).................))))))). (-30.86 = -31.06 +   0.20)

alignment

secondary structure

dotplot

Window 0

Location	14,530,827 – 14,530,925
Length	98
Sequences	5
Columns	101
Reading direction	reverse
Mean pairwise identity	92.23
Mean single sequence MFE	-36.70
Consensus MFE	-35.62
Energy contribution	-35.46
Covariance contribution	-0.16
Combinations/Pair	1.04
Mean z-score	-2.33
Structure conservation index	0.97
SVM decision value	4.43
SVM RNA-class probability	0.999897
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 14530827 98 - 22407834
AGCAUCGGUGGUUCAGUGGUAGAAUGCUCGCCUGCCACGCGGGCGGCCUGGGUUCGAUUCCCGGCCGAUGCAAAAUACA-UUUUUUA--UACCAUAAUUUA
.(((((....((((.(((((((.........)))))))..))))((((.(((.......))))))))))))........-.......--............ ( -35.00)
>DroSec_CAF1 62907 100 - 1
AGCAUCGGUGGUUCAGUGGUAGAAUGCUCGCCUGCCACGCGGGCGGCCCGGGUUCGAUUCCCGGCCGAUGCAUACUACA-UUUUUUAAAUACCAAAAUUUA
......((((........((((.((((((((((((...))))))((((.(((.......))))))))).)))).)))).-.........))))........ ( -37.77)
>DroSim_CAF1 48261 100 - 1
AGCAUCGGUGGUUCAGUGGUAGAAUGCUCGCCUGCCACGCGGGCGGCCCGGGUUCGAUUCCCGGCCGAUGCAUACUAUA-UUUUUUAAAUACCAAAAUGUA
.((((...((((......((((.((((((((((((...))))))((((.(((.......))))))))).)))).)))).-..........))))..)))). ( -37.13)
>DroEre_CAF1 58063 101 - 1
AGCAUCGGUGGUUCAGUGGUAGAAUGCUCGCCUGCCACGCGGGCGGCCCGGGUUCGAUUCCCGGCCGAUGCAUACGACUUUUUUUUAAGUUCCAUACUUUU
.(((((((..((((.......))))((.(((((((...)))))))))(((((.......))))))))))))....(((((......))))).......... ( -37.70)
>DroYak_CAF1 53170 98 - 1
AGCAUCGGUGGUUCAGUGGUAGAAUGCUCGCCUGCCACGCGGGCGGCCCGGGUUCGAUUCCCGGCCGAUGCAAACGA---UUUUUUAAUUCCCAUAAUUUU
.(((((((..((((.......))))((.(((((((...)))))))))(((((.......))))))))))))......---..................... ( -35.90)
>consensus
AGCAUCGGUGGUUCAGUGGUAGAAUGCUCGCCUGCCACGCGGGCGGCCCGGGUUCGAUUCCCGGCCGAUGCAUACUACA_UUUUUUAAAUACCAUAAUUUA
.(((((((..((((.......))))((.(((((((...)))))))))(((((.......)))))))))))).............................. (-35.62 = -35.46 +  -0.16)

alignment

secondary structure

dotplot

Window 1

Location	14,530,851 – 14,530,961
Length	110
Sequences	5
Columns	114
Reading direction	forward
Mean pairwise identity	89.13
Mean single sequence MFE	-33.01
Consensus MFE	-30.86
Energy contribution	-31.06
Covariance contribution	0.20
Combinations/Pair	1.00
Mean z-score	-1.39
Structure conservation index	0.93
SVM decision value	0.66
SVM RNA-class probability	0.813395
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 14530851 110 + 22407834
UUUGCAUCGGCCGGGAAUCGAACCCAGGCCGCCCGCGUGGCAGGCGAGCAUUCUACCACUGAACCACCGAUGCUUCUUUAUUU-CUUGCGUCAGCAUUUUCCAAUAAUA---AU
...(((((((..(((.......)))..((((((.((...)).)))).)).................)))))))..........-..(((....))).............---.. ( -29.40)
>DroSec_CAF1 62933 109 + 1
UAUGCAUCGGCCGGGAAUCGAACCCGGGCCGCCCGCGUGGCAGGCGAGCAUUCUACCACUGAACCACCGAUGCUUUU-UAGUU-UUUUCGUCAAAAUUUCCCAACAAUA---AU
...((((((((((((.......)))))((((((.((...)).)))).)).................)))))))....-.....-.........................---.. ( -32.20)
>DroSim_CAF1 48287 109 + 1
UAUGCAUCGGCCGGGAAUCGAACCCGGGCCGCCCGCGUGGCAGGCGAGCAUUCUACCACUGAACCACCGAUGCUUCU-UAGUU-UUUGCGUCAAAAUUUCCCAACUAUA---AU
...((((((((((((.......)))))((((((.((...)).)))).)).................)))))))....-.....-.........................---.. ( -32.20)
>DroEre_CAF1 58090 113 + 1
UAUGCAUCGGCCGGGAAUCGAACCCGGGCCGCCCGCGUGGCAGGCGAGCAUUCUACCACUGAACCACCGAUGCUUCA-UAUUUCGUUGCGUCAAAAUUUCCAAAUAAAAGCGAC
...((((((((((((.......)))))((((((.((...)).)))).)).................)))))))....-......(((((....................))))) ( -35.75)
>DroYak_CAF1 53194 113 + 1
UUUGCAUCGGCCGGGAAUCGAACCCGGGCCGCCCGCGUGGCAGGCGAGCAUUCUACCACUGAACCACCGAUGCUUCU-UAUUUUCUUUGGUCAAAAUUACCGAACAUAAACUAC
...((((((((((((.......)))))((((((.((...)).)))).)).................)))))))....-.......((((((.......)))))).......... ( -35.50)
>consensus
UAUGCAUCGGCCGGGAAUCGAACCCGGGCCGCCCGCGUGGCAGGCGAGCAUUCUACCACUGAACCACCGAUGCUUCU_UAUUU_CUUGCGUCAAAAUUUCCCAACAAUA___AU
...((((((((((((.......)))))((((((.((...)).)))).)).................)))))))......................................... (-30.86 = -31.06 +   0.20)

alignment

secondary structure

dotplot

Window 2

Location	14,530,851 – 14,530,961
Length	110
Sequences	5
Columns	114
Reading direction	reverse
Mean pairwise identity	89.13
Mean single sequence MFE	-39.32
Consensus MFE	-35.62
Energy contribution	-35.46
Covariance contribution	-0.16
Combinations/Pair	1.04
Mean z-score	-1.69
Structure conservation index	0.91
SVM decision value	1.42
SVM RNA-class probability	0.952586
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 14530851 110 - 22407834
AU---UAUUAUUGGAAAAUGCUGACGCAAG-AAAUAAAGAAGCAUCGGUGGUUCAGUGGUAGAAUGCUCGCCUGCCACGCGGGCGGCCUGGGUUCGAUUCCCGGCCGAUGCAAA
.(---((((((((((...((((((.((...-..........)).)))))).)))))))))))..(((((((((((...))))))((((.(((.......))))))))).))).. ( -42.42)
>DroSec_CAF1 62933 109 - 1
AU---UAUUGUUGGGAAAUUUUGACGAAAA-AACUA-AAAAGCAUCGGUGGUUCAGUGGUAGAAUGCUCGCCUGCCACGCGGGCGGCCCGGGUUCGAUUCCCGGCCGAUGCAUA
..---..((((..((....))..))))...-.....-....(((((((..((((.......))))((.(((((((...)))))))))(((((.......))))))))))))... ( -39.50)
>DroSim_CAF1 48287 109 - 1
AU---UAUAGUUGGGAAAUUUUGACGCAAA-AACUA-AGAAGCAUCGGUGGUUCAGUGGUAGAAUGCUCGCCUGCCACGCGGGCGGCCCGGGUUCGAUUCCCGGCCGAUGCAUA
..---....((..((....))..)).....-.....-....(((((((..((((.......))))((.(((((((...)))))))))(((((.......))))))))))))... ( -38.10)
>DroEre_CAF1 58090 113 - 1
GUCGCUUUUAUUUGGAAAUUUUGACGCAACGAAAUA-UGAAGCAUCGGUGGUUCAGUGGUAGAAUGCUCGCCUGCCACGCGGGCGGCCCGGGUUCGAUUCCCGGCCGAUGCAUA
.................((((((......)))))).-....(((((((..((((.......))))((.(((((((...)))))))))(((((.......))))))))))))... ( -37.70)
>DroYak_CAF1 53194 113 - 1
GUAGUUUAUGUUCGGUAAUUUUGACCAAAGAAAAUA-AGAAGCAUCGGUGGUUCAGUGGUAGAAUGCUCGCCUGCCACGCGGGCGGCCCGGGUUCGAUUCCCGGCCGAUGCAAA
....(((((.((((((.......)))...))).)))-))..(((((((..((((.......))))((.(((((((...)))))))))(((((.......))))))))))))... ( -38.90)
>consensus
AU___UAUUGUUGGGAAAUUUUGACGCAAA_AAAUA_AGAAGCAUCGGUGGUUCAGUGGUAGAAUGCUCGCCUGCCACGCGGGCGGCCCGGGUUCGAUUCCCGGCCGAUGCAUA
.........................................(((((((..((((.......))))((.(((((((...)))))))))(((((.......))))))))))))... (-35.62 = -35.46 +  -0.16)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:36:11 2006