Locus 230

Sequence ID	2L_DroMel_CAF1
Location	658,523 – 658,663
Length	140
Max. P	0.999936

overview

Window 5

Location	658,523 – 658,626
Length	103
Sequences	5
Columns	103
Reading direction	forward
Mean pairwise identity	92.78
Mean single sequence MFE	-40.06
Consensus MFE	-35.77
Energy contribution	-35.93
Covariance contribution	0.16
Combinations/Pair	1.03
Mean z-score	-2.31
Structure conservation index	0.89
SVM decision value	3.37
SVM RNA-class probability	0.999093
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 658523 103 + 22407834
UUAAACUCGUUUAACCCGGCCGGUGAAAUUGUCACCAGCGAAAUGGACGGAGGCAGUUCCAGUCCUGCGAUGCGAUGGGAUAUGGGCUGGAACUGGGCCGUCG
..................((.(((((.....))))).))......(((((...((((((((((((....((.(....).))..))))))))))))..))))). ( -40.90)
>DroSec_CAF1 47138 103 + 1
UUAAACUCGUUUAACCCGGCCGGUGAAAUUGUCACCAACGAAAUGGACGGGGGCAGUUCCAGUCCUGCGAUGGGGUGGGAUAUGGGCUGGAACUGGGCCGUCG
.....((((((((...((...(((((.....)))))..))...))))))))((((((((((((((..................)))))))))))..))).... ( -38.37)
>DroSim_CAF1 51669 103 + 1
UUAAACUCGUUUAACCCGGCCGGUGAAAUUGUCACCAACGAAAUGGACGGGGGCAGUUCCAGUCCUGCGAUGGGAUGGGAUAUGGGCUGGAACUGUGCCGUCG
.......((((((...((...(((((.....)))))..))...))))))((.(((((((((((((..................))))))))))))).)).... ( -39.87)
>DroEre_CAF1 52090 98 + 1
UUAAACUCGUUUAACCCGGUUGGUGAAAUUGUCACCAAUGAAAUGGACGGGGGCAGUUCCAGUCCUGCGA-----UGGGAUAUGGGCUGGAACUUGGCCGUCG
.....((((((((.....((((((((.....))))))))....))))))))((((((((((((((.....-----........)))))))))))..))).... ( -40.32)
>DroYak_CAF1 51496 98 + 1
UUAAACUCGUUUAACCCGGUCGGUGAAAUUGUCACCAAUGAAAUGGCCGGGGGCAGUUCCAGUCCUGCGG-----UGGGAUAUGGGCUGGAACUGGGCCGUCG
..............((((((((((((.....)))))........)))))))((((((((((((((.....-----........)))))))))))..))).... ( -40.82)
>consensus
UUAAACUCGUUUAACCCGGCCGGUGAAAUUGUCACCAACGAAAUGGACGGGGGCAGUUCCAGUCCUGCGAUG_G_UGGGAUAUGGGCUGGAACUGGGCCGUCG
.....((((((((...((...(((((.....)))))..))...))))))))((((((((((((((..................)))))))))))..))).... (-35.77 = -35.93 +   0.16)

alignment

secondary structure

dotplot

Window 6

Location	658,523 – 658,626
Length	103
Sequences	5
Columns	103
Reading direction	reverse
Mean pairwise identity	92.78
Mean single sequence MFE	-33.53
Consensus MFE	-31.65
Energy contribution	-31.89
Covariance contribution	0.24
Combinations/Pair	1.11
Mean z-score	-2.57
Structure conservation index	0.94
SVM decision value	4.67
SVM RNA-class probability	0.999936
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 658523 103 - 22407834
CGACGGCCCAGUUCCAGCCCAUAUCCCAUCGCAUCGCAGGACUGGAACUGCCUCCGUCCAUUUCGCUGGUGACAAUUUCACCGGCCGGGUUAAACGAGUUUAA
.(((((..(((((((((.((..................)).)))))))))...))))).(((..((((((((.....))))))))..)))............. ( -36.47)
>DroSec_CAF1 47138 103 - 1
CGACGGCCCAGUUCCAGCCCAUAUCCCACCCCAUCGCAGGACUGGAACUGCCCCCGUCCAUUUCGUUGGUGACAAUUUCACCGGCCGGGUUAAACGAGUUUAA
.(((((..(((((((((.((..................)).)))))))))...))))).(((..((((((((.....))))))))..)))............. ( -33.97)
>DroSim_CAF1 51669 103 - 1
CGACGGCACAGUUCCAGCCCAUAUCCCAUCCCAUCGCAGGACUGGAACUGCCCCCGUCCAUUUCGUUGGUGACAAUUUCACCGGCCGGGUUAAACGAGUUUAA
.(((((..(((((((((.((..................)).)))))))))...))))).(((..((((((((.....))))))))..)))............. ( -33.97)
>DroEre_CAF1 52090 98 - 1
CGACGGCCAAGUUCCAGCCCAUAUCCCA-----UCGCAGGACUGGAACUGCCCCCGUCCAUUUCAUUGGUGACAAUUUCACCAACCGGGUUAAACGAGUUUAA
.(((((...((((((((.((........-----.....)).))))))))....))))).......(((((((.....))))))).((.......))....... ( -30.02)
>DroYak_CAF1 51496 98 - 1
CGACGGCCCAGUUCCAGCCCAUAUCCCA-----CCGCAGGACUGGAACUGCCCCCGGCCAUUUCAUUGGUGACAAUUUCACCGACCGGGUUAAACGAGUUUAA
.((((((..((((((((.((........-----.....)).)))))))))))(((((........(((((((.....))))))))))))........)))... ( -33.22)
>consensus
CGACGGCCCAGUUCCAGCCCAUAUCCCA_C_CAUCGCAGGACUGGAACUGCCCCCGUCCAUUUCGUUGGUGACAAUUUCACCGGCCGGGUUAAACGAGUUUAA
.(((((..(((((((((.((..................)).)))))))))...))))).((((.((((((((.....)))))))).))))............. (-31.65 = -31.89 +   0.24)

alignment

secondary structure

dotplot

Window 7

Location	658,559 – 658,663
Length	104
Sequences	6
Columns	107
Reading direction	forward
Mean pairwise identity	78.59
Mean single sequence MFE	-35.66
Consensus MFE	-21.50
Energy contribution	-23.75
Covariance contribution	2.25
Combinations/Pair	1.12
Mean z-score	-2.12
Structure conservation index	0.60
SVM decision value	1.04
SVM RNA-class probability	0.905666
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 658559 104 + 22407834
AGCGAAAUGGACGGAGGCAGUUCCAGUCCUGCGAUGCGAUGGGAUAUG---GGCUGGAACUGGGCCGUCGUCAGUCCAGAGAUUGGCAAUUUUAUCUGUCAACAACA
...(((((.(((((...((((((((((((....((.(....).))..)---)))))))))))..)))))(((((((....))))))).))))).............. ( -40.00)
>DroSec_CAF1 47174 104 + 1
AACGAAAUGGACGGGGGCAGUUCCAGUCCUGCGAUGGGGUGGGAUAUG---GGCUGGAACUGGGCCGUCGUCAGUCCAGAGAUUGGCAAUUUUAUCUGUCAACAACA
...(((((.(((((...((((((((((((..................)---)))))))))))..)))))(((((((....))))))).))))).............. ( -37.57)
>DroSim_CAF1 51705 104 + 1
AACGAAAUGGACGGGGGCAGUUCCAGUCCUGCGAUGGGAUGGGAUAUG---GGCUGGAACUGUGCCGUCGUCAGUCCAGAGAUUGGCAAUUUUAUCUGUCAACAACA
...(((((.(((((.(.((((((((((((..................)---)))))))))))).)))))(((((((....))))))).))))).............. ( -39.57)
>DroEre_CAF1 52126 99 + 1
AAUGAAAUGGACGGGGGCAGUUCCAGUCCUGCGA-----UGGGAUAUG---GGCUGGAACUUGGCCGUCGUCAGUCCAGAGAUUGGGAAUUUUAUCUGUCAACAACA
.(((((((.(((((.((((((((((((((.....-----........)---))))))))))..))).)))))..(((........))))))))))............ ( -36.32)
>DroWil_CAF1 18009 85 + 1
AGAGUGUCGGUCGAAGACU-----------GG-------CAGGGCAUGAACGGCUGAA---GGGCUAUGG-CCGCCAGAAGACAGCCAACUUUAUCUGUCAACAACA
....((((((((...))))-----------))-------)).((((((((.(((((..---.(((.....-..)))......)))))...))))..))))....... ( -23.10)
>DroYak_CAF1 51532 99 + 1
AAUGAAAUGGCCGGGGGCAGUUCCAGUCCUGCGG-----UGGGAUAUG---GGCUGGAACUGGGCCGUCGUCAGUCCAGAGAUUGGCAAUUUUAUCUGUCAACAACU
.(((((((((((.....((((((((((((.....-----........)---)))))))))))))))...(((((((....))))))).)))))))............ ( -37.42)
>consensus
AACGAAAUGGACGGGGGCAGUUCCAGUCCUGCGA_____UGGGAUAUG___GGCUGGAACUGGGCCGUCGUCAGUCCAGAGAUUGGCAAUUUUAUCUGUCAACAACA
.........(((((((((((((((((((.......................))))))))))..)))...(((((((....))))))).......))))))....... (-21.50 = -23.75 +   2.25)

alignment

secondary structure

dotplot

Window 8

Location	658,559 – 658,663
Length	104
Sequences	6
Columns	107
Reading direction	reverse
Mean pairwise identity	78.59
Mean single sequence MFE	-27.32
Consensus MFE	-15.99
Energy contribution	-18.02
Covariance contribution	2.03
Combinations/Pair	1.15
Mean z-score	-1.56
Structure conservation index	0.59
SVM decision value	0.04
SVM RNA-class probability	0.552364
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 658559 104 - 22407834
UGUUGUUGACAGAUAAAAUUGCCAAUCUCUGGACUGACGACGGCCCAGUUCCAGCC---CAUAUCCCAUCGCAUCGCAGGACUGGAACUGCCUCCGUCCAUUUCGCU
.((((((.(.((((..........)))).).))).)))(((((..(((((((((.(---(..................)).)))))))))...)))))......... ( -28.17)
>DroSec_CAF1 47174 104 - 1
UGUUGUUGACAGAUAAAAUUGCCAAUCUCUGGACUGACGACGGCCCAGUUCCAGCC---CAUAUCCCACCCCAUCGCAGGACUGGAACUGCCCCCGUCCAUUUCGUU
.((((((.(.((((..........)))).).))).)))(((((..(((((((((.(---(..................)).)))))))))...)))))......... ( -28.17)
>DroSim_CAF1 51705 104 - 1
UGUUGUUGACAGAUAAAAUUGCCAAUCUCUGGACUGACGACGGCACAGUUCCAGCC---CAUAUCCCAUCCCAUCGCAGGACUGGAACUGCCCCCGUCCAUUUCGUU
.((((((.(.((((..........)))).).))).)))(((((..(((((((((.(---(..................)).)))))))))...)))))......... ( -28.17)
>DroEre_CAF1 52126 99 - 1
UGUUGUUGACAGAUAAAAUUCCCAAUCUCUGGACUGACGACGGCCAAGUUCCAGCC---CAUAUCCCA-----UCGCAGGACUGGAACUGCCCCCGUCCAUUUCAUU
.((((((.(.((((..........)))).).))).)))(((((...((((((((.(---(........-----.....)).))))))))....)))))......... ( -26.42)
>DroWil_CAF1 18009 85 - 1
UGUUGUUGACAGAUAAAGUUGGCUGUCUUCUGGCGG-CCAUAGCCC---UUCAGCCGUUCAUGCCCUG-------CC-----------AGUCUUCGACCGACACUCU
(((((((((.((((.....((((((((....)))))-)))..((..---....)).............-------..-----------.)))))))).))))).... ( -22.40)
>DroYak_CAF1 51532 99 - 1
AGUUGUUGACAGAUAAAAUUGCCAAUCUCUGGACUGACGACGGCCCAGUUCCAGCC---CAUAUCCCA-----CCGCAGGACUGGAACUGCCCCCGGCCAUUUCAUU
.(((((((.((((..............))))...)))))))(((((((((((((.(---(........-----.....)).))))))))).....))))........ ( -30.56)
>consensus
UGUUGUUGACAGAUAAAAUUGCCAAUCUCUGGACUGACGACGGCCCAGUUCCAGCC___CAUAUCCCA_____UCGCAGGACUGGAACUGCCCCCGUCCAUUUCGUU
.((((((.(.((((..........)))).).))).)))(((((..(((((((((((......................)).)))))))))...)))))......... (-15.99 = -18.02 +   2.03)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:30:38 2006