Locus 2603

Sequence ID	X_DroMel_CAF1
Location	6,993,010 – 6,993,247
Length	237
Max. P	0.989101

overview

Window 3

Location	6,993,010 – 6,993,130
Length	120
Sequences	3
Columns	120
Reading direction	forward
Mean pairwise identity	94.38
Mean single sequence MFE	-31.67
Consensus MFE	-28.45
Energy contribution	-28.57
Covariance contribution	0.11
Combinations/Pair	1.03
Mean z-score	-2.02
Structure conservation index	0.90
SVM decision value	0.47
SVM RNA-class probability	0.747761
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 6993010 120 + 22224390
UGAUUUGCUCAGUCAGGGUGGGAAAAAAUACACACCCAUAUAUAUGUAUGUAUGUAUAUUAUAUAUGUACUUACUCUUGGGUAGUUGGGGUAACCCGGCUUAUAAGCGUGAUAAUGAUGA
...........(((((((((............)))))........(((((((((((...)))))))))))((((.((((...(((((((....)))))))..)))).))))...)))).. ( -34.30)
>DroSec_CAF1 15414 116 + 1
UGAUUUGCUCAGUCAGGGUGGGAAAAAAUACACACCCAUCUAUAUGUAUGCAUG----UUAUAUAUGUACAUACUUUUGGGUAGUUGGGGGAACCCGGCUUAUAAGCGUGAUAAUGAUGA
...((..(((.....)))..))........((((((((....(((((..(((((----(...)))))))))))....)))))(((((((....))))))).......))).......... ( -32.20)
>DroSim_CAF1 518 116 + 1
UGAUUUGCUCAGUCAGGGUGGGAAAAAAUACACACCAAUAUAUAUGUAUGCAUG----UUAUAUAUGUACAUACUUUUGGGUAGUUGGGGGAACCCGGCUUAUAAGCGUGAUAAUGAUGA
.....(((((((..((((((............))))..((((((((((......----.))))))))))....)).)))))))((((((....))))))..................... ( -28.50)
>consensus
UGAUUUGCUCAGUCAGGGUGGGAAAAAAUACACACCCAUAUAUAUGUAUGCAUG____UUAUAUAUGUACAUACUUUUGGGUAGUUGGGGGAACCCGGCUUAUAAGCGUGAUAAUGAUGA
...........(((((((((............)))))...((((((((((.........))))))))))..(((.((((...(((((((....)))))))..)))).)))....)))).. (-28.45 = -28.57 +   0.11)

alignment

secondary structure

dotplot

Window 4

Location	6,993,010 – 6,993,130
Length	120
Sequences	3
Columns	120
Reading direction	reverse
Mean pairwise identity	94.38
Mean single sequence MFE	-22.43
Consensus MFE	-19.68
Energy contribution	-20.13
Covariance contribution	0.45
Combinations/Pair	1.05
Mean z-score	-1.98
Structure conservation index	0.88
SVM decision value	0.24
SVM RNA-class probability	0.650553
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 6993010 120 - 22224390
UCAUCAUUAUCACGCUUAUAAGCCGGGUUACCCCAACUACCCAAGAGUAAGUACAUAUAUAAUAUACAUACAUACAUAUAUAUGGGUGUGUAUUUUUUCCCACCCUGACUGAGCAAAUCA
.............(((((..((..((((..........))))..(((.((((((((((...(((((.((......)).)))))..)))))))))).))).....))...)))))...... ( -22.70)
>DroSec_CAF1 15414 116 - 1
UCAUCAUUAUCACGCUUAUAAGCCGGGUUCCCCCAACUACCCAAAAGUAUGUACAUAUAUAA----CAUGCAUACAUAUAGAUGGGUGUGUAUUUUUUCCCACCCUGACUGAGCAAAUCA
.............(((((......((((..........))))....(((((((.........----..)))))))........(((((.(........).)))))....)))))...... ( -23.20)
>DroSim_CAF1 518 116 - 1
UCAUCAUUAUCACGCUUAUAAGCCGGGUUCCCCCAACUACCCAAAAGUAUGUACAUAUAUAA----CAUGCAUACAUAUAUAUUGGUGUGUAUUUUUUCCCACCCUGACUGAGCAAAUCA
.............(((((....(.((((..................((((((.........)----)))))((((((((......))))))))........)))).)..)))))...... ( -21.40)
>consensus
UCAUCAUUAUCACGCUUAUAAGCCGGGUUCCCCCAACUACCCAAAAGUAUGUACAUAUAUAA____CAUGCAUACAUAUAUAUGGGUGUGUAUUUUUUCCCACCCUGACUGAGCAAAUCA
.............(((((......((((..........))))....(((((((...............)))))))........(((((.(........).)))))....)))))...... (-19.68 = -20.13 +   0.45)

alignment

secondary structure

dotplot

Window 5

Location	6,993,050 – 6,993,167
Length	117
Sequences	3
Columns	120
Reading direction	forward
Mean pairwise identity	93.26
Mean single sequence MFE	-38.17
Consensus MFE	-36.25
Energy contribution	-36.03
Covariance contribution	-0.22
Combinations/Pair	1.03
Mean z-score	-2.69
Structure conservation index	0.95
SVM decision value	1.86
SVM RNA-class probability	0.980192
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 6993050 117 + 22224390
UAUAUGUAUGUAUGUAUAUUAUAUAUGUACUUACUCUUGGGUAGUUGGGGUAACCCGGCUUAUAAGCGUGAUAAUGAUGAUGGCUGACCUCUGGGCUGUUUCCCAGCUU---GUCAGCUG
.....(((((((((((...)))))))))))((((.((((...(((((((....)))))))..)))).))))..........(((((((..(((((......)))))...---))))))). ( -42.10)
>DroSec_CAF1 15454 116 + 1
UAUAUGUAUGCAUG----UUAUAUAUGUACAUACUUUUGGGUAGUUGGGGGAACCCGGCUUAUAAGCGUGAUAAUGAUGAUGGCUGACCUCUGGGCUCUUUCCCAGCUUGUUGUCAGCUG
((((((((((....----.))))))))))..(((.((((...(((((((....)))))))..)))).)))...........(((((((..(((((......)))))......))))))). ( -36.20)
>DroSim_CAF1 558 116 + 1
UAUAUGUAUGCAUG----UUAUAUAUGUACAUACUUUUGGGUAGUUGGGGGAACCCGGCUUAUAAGCGUGAUAAUGAUGAUGGCUGACCUCUGGGCUCUUUCCCAGCUUGUUGUCAGCUG
((((((((((....----.))))))))))..(((.((((...(((((((....)))))))..)))).)))...........(((((((..(((((......)))))......))))))). ( -36.20)
>consensus
UAUAUGUAUGCAUG____UUAUAUAUGUACAUACUUUUGGGUAGUUGGGGGAACCCGGCUUAUAAGCGUGAUAAUGAUGAUGGCUGACCUCUGGGCUCUUUCCCAGCUUGUUGUCAGCUG
((((((((((.........))))))))))..(((.((((...(((((((....)))))))..)))).)))...........(((((((..(((((......)))))......))))))). (-36.25 = -36.03 +  -0.22)

alignment

secondary structure

dotplot

Window 6

Location	6,993,050 – 6,993,167
Length	117
Sequences	3
Columns	120
Reading direction	reverse
Mean pairwise identity	93.26
Mean single sequence MFE	-29.70
Consensus MFE	-27.91
Energy contribution	-28.03
Covariance contribution	0.11
Combinations/Pair	1.04
Mean z-score	-3.30
Structure conservation index	0.94
SVM decision value	2.15
SVM RNA-class probability	0.989101
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 6993050 117 - 22224390
CAGCUGAC---AAGCUGGGAAACAGCCCAGAGGUCAGCCAUCAUCAUUAUCACGCUUAUAAGCCGGGUUACCCCAACUACCCAAGAGUAAGUACAUAUAUAAUAUACAUACAUACAUAUA
..((((((---...(((((......)))))..))))))...........((..(((....))).((((..........))))..))(((.(((..((((...))))..))).)))..... ( -29.50)
>DroSec_CAF1 15454 116 - 1
CAGCUGACAACAAGCUGGGAAAGAGCCCAGAGGUCAGCCAUCAUCAUUAUCACGCUUAUAAGCCGGGUUCCCCCAACUACCCAAAAGUAUGUACAUAUAUAA----CAUGCAUACAUAUA
..((((((......(((((......)))))..))))))...............(((....))).((((..........))))....(((((((.........----..)))))))..... ( -29.80)
>DroSim_CAF1 558 116 - 1
CAGCUGACAACAAGCUGGGAAAGAGCCCAGAGGUCAGCCAUCAUCAUUAUCACGCUUAUAAGCCGGGUUCCCCCAACUACCCAAAAGUAUGUACAUAUAUAA----CAUGCAUACAUAUA
..((((((......(((((......)))))..))))))...............(((....))).((((..........))))....(((((((.........----..)))))))..... ( -29.80)
>consensus
CAGCUGACAACAAGCUGGGAAAGAGCCCAGAGGUCAGCCAUCAUCAUUAUCACGCUUAUAAGCCGGGUUCCCCCAACUACCCAAAAGUAUGUACAUAUAUAA____CAUGCAUACAUAUA
..((((((......(((((......)))))..))))))...............(((....))).((((..........))))....(((((((...............)))))))..... (-27.91 = -28.03 +   0.11)

alignment

secondary structure

dotplot

Window 7

Location	6,993,090 – 6,993,207
Length	117
Sequences	3
Columns	120
Reading direction	forward
Mean pairwise identity	97.22
Mean single sequence MFE	-42.57
Consensus MFE	-41.90
Energy contribution	-41.90
Covariance contribution	-0.00
Combinations/Pair	1.00
Mean z-score	-1.66
Structure conservation index	0.98
SVM decision value	0.46
SVM RNA-class probability	0.744880
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 6993090 117 + 22224390
GUAGUUGGGGUAACCCGGCUUAUAAGCGUGAUAAUGAUGAUGGCUGACCUCUGGGCUGUUUCCCAGCUU---GUCAGCUGGUCAAAAUGGCCGACAUUGCCUUGGCGGCGACUUAACUUU
..(((((((....)))))))..(((((((......((((..(((((((..(((((......)))))...---)))))))((((.....))))..))))((....)).))).))))..... ( -42.90)
>DroSec_CAF1 15490 120 + 1
GUAGUUGGGGGAACCCGGCUUAUAAGCGUGAUAAUGAUGAUGGCUGACCUCUGGGCUCUUUCCCAGCUUGUUGUCAGCUGGUCAAAAUGGCCGACAUUGCCUUGGCGGCGACUUAACUUU
..(((((((....)))))))..(((((((......((((..(((((((..(((((......)))))......)))))))((((.....))))..))))((....)).))).))))..... ( -42.40)
>DroSim_CAF1 594 120 + 1
GUAGUUGGGGGAACCCGGCUUAUAAGCGUGAUAAUGAUGAUGGCUGACCUCUGGGCUCUUUCCCAGCUUGUUGUCAGCUGGUCAAAAUGGCCGACAUUGCCUUGGCGGCGACUUAACUUU
..(((((((....)))))))..(((((((......((((..(((((((..(((((......)))))......)))))))((((.....))))..))))((....)).))).))))..... ( -42.40)
>consensus
GUAGUUGGGGGAACCCGGCUUAUAAGCGUGAUAAUGAUGAUGGCUGACCUCUGGGCUCUUUCCCAGCUUGUUGUCAGCUGGUCAAAAUGGCCGACAUUGCCUUGGCGGCGACUUAACUUU
..(((((((....)))))))..(((((((......((((..(((((((..(((((......)))))......)))))))((((.....))))..))))((....)).))).))))..... (-41.90 = -41.90 +  -0.00)

alignment

secondary structure

dotplot

Window 8

Location	6,993,090 – 6,993,207
Length	117
Sequences	3
Columns	120
Reading direction	reverse
Mean pairwise identity	97.22
Mean single sequence MFE	-35.03
Consensus MFE	-33.13
Energy contribution	-33.13
Covariance contribution	-0.00
Combinations/Pair	1.00
Mean z-score	-1.67
Structure conservation index	0.95
SVM decision value	0.19
SVM RNA-class probability	0.627606
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 6993090 117 - 22224390
AAAGUUAAGUCGCCGCCAAGGCAAUGUCGGCCAUUUUGACCAGCUGAC---AAGCUGGGAAACAGCCCAGAGGUCAGCCAUCAUCAUUAUCACGCUUAUAAGCCGGGUUACCCCAACUAC
...((((((..((((.((......)).))))...))))))..((((((---...(((((......)))))..))))))...............(((....))).(((....)))...... ( -35.50)
>DroSec_CAF1 15490 120 - 1
AAAGUUAAGUCGCCGCCAAGGCAAUGUCGGCCAUUUUGACCAGCUGACAACAAGCUGGGAAAGAGCCCAGAGGUCAGCCAUCAUCAUUAUCACGCUUAUAAGCCGGGUUCCCCCAACUAC
..((((.(((.(((.....)))..(((((((...........)))))))....)))(((...((((((.((((....)).))...........(((....))).)))))).))))))).. ( -34.80)
>DroSim_CAF1 594 120 - 1
AAAGUUAAGUCGCCGCCAAGGCAAUGUCGGCCAUUUUGACCAGCUGACAACAAGCUGGGAAAGAGCCCAGAGGUCAGCCAUCAUCAUUAUCACGCUUAUAAGCCGGGUUCCCCCAACUAC
..((((.(((.(((.....)))..(((((((...........)))))))....)))(((...((((((.((((....)).))...........(((....))).)))))).))))))).. ( -34.80)
>consensus
AAAGUUAAGUCGCCGCCAAGGCAAUGUCGGCCAUUUUGACCAGCUGACAACAAGCUGGGAAAGAGCCCAGAGGUCAGCCAUCAUCAUUAUCACGCUUAUAAGCCGGGUUCCCCCAACUAC
...((((((..((((.((......)).))))...))))))..((((((......(((((......)))))..))))))...............(((....))).(((....)))...... (-33.13 = -33.13 +  -0.00)

alignment

secondary structure

dotplot

Window 9

Location	6,993,130 – 6,993,247
Length	117
Sequences	3
Columns	120
Reading direction	forward
Mean pairwise identity	97.21
Mean single sequence MFE	-46.23
Consensus MFE	-42.17
Energy contribution	-42.17
Covariance contribution	-0.00
Combinations/Pair	1.00
Mean z-score	-1.80
Structure conservation index	0.91
SVM decision value	0.15
SVM RNA-class probability	0.608606
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 6993130 117 + 22224390
UGGCUGACCUCUGGGCUGUUUCCCAGCUU---GUCAGCUGGUCAAAAUGGCCGACAUUGCCUUGGCGGCGACUUAACUUUUGACCAUUGGUCAGGAGCAAGACGGGAGCAGCACGUGUCC
.(((((((..(((((......)))))...---)))))))((((.....))))((((((((....((..((.(((..(((((((((...))))))))).))).))...)).))).))))). ( -45.30)
>DroSec_CAF1 15530 119 + 1
UGGCUGACCUCUGGGCUCUUUCCCAGCUUGUUGUCAGCUGGUCAAAAUGGCCGACAUUGCCUUGGCGGCGACUUAACUUUUGACCAUUGGUCAGGAGCAAGA-GGGAGCAGCACGUGUCC
..((((.(((((..((((((..((((((.......)))((((((((((.((((.((......)).)))).)......))))))))).)))..)))))).)))-))...))))........ ( -46.70)
>DroSim_CAF1 634 119 + 1
UGGCUGACCUCUGGGCUCUUUCCCAGCUUGUUGUCAGCUGGUCAAAAUGGCCGACAUUGCCUUGGCGGCGACUUAACUUUUGACCAUUGGUCAGGAGCAAGA-GGGAGCAGCACGUGUCC
..((((.(((((..((((((..((((((.......)))((((((((((.((((.((......)).)))).)......))))))))).)))..)))))).)))-))...))))........ ( -46.70)
>consensus
UGGCUGACCUCUGGGCUCUUUCCCAGCUUGUUGUCAGCUGGUCAAAAUGGCCGACAUUGCCUUGGCGGCGACUUAACUUUUGACCAUUGGUCAGGAGCAAGA_GGGAGCAGCACGUGUCC
.(((((((..(((((......)))))......)))))))((((.....))))((((((((....)))((..((...(((((((((...)))))))))......))..)).....))))). (-42.17 = -42.17 +  -0.00)

alignment

secondary structure

dotplot

Window 0

Location	6,993,130 – 6,993,247
Length	117
Sequences	3
Columns	120
Reading direction	reverse
Mean pairwise identity	97.21
Mean single sequence MFE	-40.93
Consensus MFE	-37.83
Energy contribution	-37.83
Covariance contribution	0.00
Combinations/Pair	1.00
Mean z-score	-1.59
Structure conservation index	0.92
SVM decision value	-0.07
SVM RNA-class probability	0.500000
Prediction	OTHER

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 6993130 117 - 22224390
GGACACGUGCUGCUCCCGUCUUGCUCCUGACCAAUGGUCAAAAGUUAAGUCGCCGCCAAGGCAAUGUCGGCCAUUUUGACCAGCUGAC---AAGCUGGGAAACAGCCCAGAGGUCAGCCA
.((((..((((((...((.((((((..(((((...)))))..)).)))).))..))...)))).))))((.(.....).)).((((((---...(((((......)))))..)))))).. ( -41.20)
>DroSec_CAF1 15530 119 - 1
GGACACGUGCUGCUCCC-UCUUGCUCCUGACCAAUGGUCAAAAGUUAAGUCGCCGCCAAGGCAAUGUCGGCCAUUUUGACCAGCUGACAACAAGCUGGGAAAGAGCCCAGAGGUCAGCCA
......(.((((...((-(((.((((.(..(((.((((((((((......)((((.((......)).))))..)))))))))(((.......))))))..).))))..))))).))))). ( -40.80)
>DroSim_CAF1 634 119 - 1
GGACACGUGCUGCUCCC-UCUUGCUCCUGACCAAUGGUCAAAAGUUAAGUCGCCGCCAAGGCAAUGUCGGCCAUUUUGACCAGCUGACAACAAGCUGGGAAAGAGCCCAGAGGUCAGCCA
......(.((((...((-(((.((((.(..(((.((((((((((......)((((.((......)).))))..)))))))))(((.......))))))..).))))..))))).))))). ( -40.80)
>consensus
GGACACGUGCUGCUCCC_UCUUGCUCCUGACCAAUGGUCAAAAGUUAAGUCGCCGCCAAGGCAAUGUCGGCCAUUUUGACCAGCUGACAACAAGCUGGGAAAGAGCCCAGAGGUCAGCCA
((.((.(.((............)).).)).))..((((((((((......)((((.((......)).))))..)))))))))((((((......(((((......)))))..)))))).. (-37.83 = -37.83 +   0.00)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:38:53 2006