Locus 2800

Sequence ID	X_DroMel_CAF1
Location	7,484,850 – 7,485,073
Length	223
Max. P	0.978583

overview

Window 6

Location	7,484,850 – 7,484,958
Length	108
Sequences	3
Columns	109
Reading direction	forward
Mean pairwise identity	97.54
Mean single sequence MFE	-26.20
Consensus MFE	-25.90
Energy contribution	-25.90
Covariance contribution	0.00
Combinations/Pair	1.00
Mean z-score	-2.56
Structure conservation index	0.99
SVM decision value	1.82
SVM RNA-class probability	0.978583
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 7484850 108 + 22224390
AGGGUUUAGGGGCGGGGCU-UCUAAUCAUUAUUUGUAUGGCCUGACCGAACACACACAUCCCCCCGCACCCCAAAACCCCAACCCCAGCCCCCUUUAACCCACACAAUG
.(((((..(((((((((..-.............(((.(((.....))).))).............(.....)..........)))).)))))....)))))........ ( -26.80)
>DroSec_CAF1 17918 107 + 1
AGGGUUUAGGGGCGGGGCUUUCUAAUCAUUAUUUGUAUGGCCUGACCGAACACACACAUCCC-CCACACCCCA-AACCCCAACCCCAGCCCCCUUUAACCCACACAAUG
.(((((..(((((((((.....((.....))..(((.(((.....))).)))..........-..........-........)))).)))))....)))))........ ( -25.90)
>DroSim_CAF1 19603 107 + 1
AGGGUUUAGGGGCGGGGCUUUCUAAUCAUUAUUUGUAUGGCCUGACCGAACACACACAUCCC-CCACACCCCA-AACCCCAACCCCAGCCCCCUUUAACCCACACAAUG
.(((((..(((((((((.....((.....))..(((.(((.....))).)))..........-..........-........)))).)))))....)))))........ ( -25.90)
>consensus
AGGGUUUAGGGGCGGGGCUUUCUAAUCAUUAUUUGUAUGGCCUGACCGAACACACACAUCCC_CCACACCCCA_AACCCCAACCCCAGCCCCCUUUAACCCACACAAUG
.(((((..(((((((((.....((.....))..(((.(((.....))).)))..............................)))).)))))....)))))........ (-25.90 = -25.90 +   0.00)

alignment

secondary structure

dotplot

Window 7

Location	7,484,850 – 7,484,958
Length	108
Sequences	3
Columns	109
Reading direction	reverse
Mean pairwise identity	97.54
Mean single sequence MFE	-38.96
Consensus MFE	-37.67
Energy contribution	-38.00
Covariance contribution	0.33
Combinations/Pair	1.00
Mean z-score	-2.00
Structure conservation index	0.97
SVM decision value	0.87
SVM RNA-class probability	0.870260
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 7484850 108 - 22224390
CAUUGUGUGGGUUAAAGGGGGCUGGGGUUGGGGUUUUGGGGUGCGGGGGGAUGUGUGUGUUCGGUCAGGCCAUACAAAUAAUGAUUAGA-AGCCCCGCCCCUAAACCCU
................((((..(((((.(((((((((..(((.((..(.....((((((..(.....)..))))))..)..))))).))-))))))).)))))..)))) ( -37.20)
>DroSec_CAF1 17918 107 - 1
CAUUGUGUGGGUUAAAGGGGGCUGGGGUUGGGGUU-UGGGGUGUGG-GGGAUGUGUGUGUUCGGUCAGGCCAUACAAAUAAUGAUUAGAAAGCCCCGCCCCUAAACCCU
........(((((...((((((.((((((...(((-((.(((.(((-.((((......))))..))).)))...)))))...........)))))))))))).))))). ( -39.84)
>DroSim_CAF1 19603 107 - 1
CAUUGUGUGGGUUAAAGGGGGCUGGGGUUGGGGUU-UGGGGUGUGG-GGGAUGUGUGUGUUCGGUCAGGCCAUACAAAUAAUGAUUAGAAAGCCCCGCCCCUAAACCCU
........(((((...((((((.((((((...(((-((.(((.(((-.((((......))))..))).)))...)))))...........)))))))))))).))))). ( -39.84)
>consensus
CAUUGUGUGGGUUAAAGGGGGCUGGGGUUGGGGUU_UGGGGUGUGG_GGGAUGUGUGUGUUCGGUCAGGCCAUACAAAUAAUGAUUAGAAAGCCCCGCCCCUAAACCCU
........(((((...((((((.((((((..((((.....((((((...(((.((......)))))...)))))).......))))....)))))))))))).))))). (-37.67 = -38.00 +   0.33)

alignment

secondary structure

dotplot

Window 8

Location	7,484,958 – 7,485,073
Length	115
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	97.44
Mean single sequence MFE	-21.45
Consensus MFE	-19.84
Energy contribution	-19.84
Covariance contribution	-0.00
Combinations/Pair	1.00
Mean z-score	-1.31
Structure conservation index	0.93
SVM decision value	0.47
SVM RNA-class probability	0.748937
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 7484958 115 + 22224390
CCCACAUAUGAGUUAUAUUUAUUUGUAUUUGUCUGGGCCCGUUUUCUGCCUUGACUUGACCAUUCC-----CACACCCUUUGCUUUGUGCUAUUUGGUCAGUGUAAUGCUUAAUUAUUUA
........((((((((((............(((.((((.........)))).))).((((((....-----((((..........)))).....)))))))))))..)))))........ ( -21.80)
>DroSec_CAF1 18025 115 + 1
CCCACAUAUGAGUUAUAUUUAUUUGUAUUUGUCUGGGCCCGUUUUCUGCCUUGACUUGACCAUUCC-----CACACCCUUUGCUUUGUGCUAUUUGGUCAGUGUAAUGCUUAAUUAUUUA
........((((((((((............(((.((((.........)))).))).((((((....-----((((..........)))).....)))))))))))..)))))........ ( -21.80)
>DroSim_CAF1 19710 115 + 1
CCCACAUAUGAGUUAUAUUUAUUUGUAUUUGUCUGGGCCCGUUUUCUGCCUUGACUUGACCAUUCC-----CACACCCUUUGCUUUGUGCUAUUUGGUCAGUGUAAUGCUUAAUUAUUUA
........((((((((((............(((.((((.........)))).))).((((((....-----((((..........)))).....)))))))))))..)))))........ ( -21.80)
>DroEre_CAF1 19041 115 + 1
CCCACAUAUGAGUUAUAUUUAUUUGUAUUUGUCUGGGCCCGUUUUCUGCCUUGACUUGACCAUUUC-----CACACCCUUUGCUUUGUGCUAUUUGGUCAGUGUAAUGCUUAAUUAUUUA
........((((((((((............(((.((((.........)))).))).((((((....-----((((..........)))).....)))))))))))..)))))........ ( -21.80)
>DroYak_CAF1 21492 120 + 1
CCCACAUAUGAGUUAUAUUUAUUUGUAUUUGUCUGGGCCUGUUUUCUGCCUUGACUUGACCAUUUCCCCCCCACACCCUUUGCUUUGUGCUAUUUGGUCAGUGUAAUGCUUAAUUAUUUA
........((((((((((............(((.((((..(....).)))).))).((((((.........((((..........)))).....)))))))))))..)))))........ ( -20.04)
>consensus
CCCACAUAUGAGUUAUAUUUAUUUGUAUUUGUCUGGGCCCGUUUUCUGCCUUGACUUGACCAUUCC_____CACACCCUUUGCUUUGUGCUAUUUGGUCAGUGUAAUGCUUAAUUAUUUA
........((((((((((............(((.((((.........)))).))).((((((.........((((..........)))).....)))))))))))..)))))........ (-19.84 = -19.84 +  -0.00)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:43:43 2006