Locus 4173

Sequence ID	3R_DroMel_CAF1
Location	11,331,748 – 11,332,132
Length	384
Max. P	0.999441

overview

Window 6

Location	11,331,748 – 11,331,853
Length	105
Sequences	3
Columns	105
Reading direction	reverse
Mean pairwise identity	82.84
Mean single sequence MFE	-24.73
Consensus MFE	-15.52
Energy contribution	-15.63
Covariance contribution	0.11
Combinations/Pair	1.06
Mean z-score	-1.98
Structure conservation index	0.63
SVM decision value	0.00
SVM RNA-class probability	0.533925
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11331748 105 - 27905053
AUAAUGAAAUUCCUAGCUGCUUUGUGCCCACGACGGGCACAAGCCACUUGGCGGGAUGUCCCGAUCCCUGAUCCAUCCCCUACAUAUAUAUUCAUAUAUAUGUAU
...........((.((..((((.((((((.....))))))))))..)).)).((((((....((((...)))))))))).((((((((((....)))))))))). ( -36.10)
>DroEre_CAF1 66499 83 - 1
AUAAUGAAAUUCCUAGCUGCUUUGUGCCCACGACG-----AAGCCACUUGGCGGGAUGUCCCGAUCCCUGAUCUGUCCCCUACAUAUA-----------------
...(((.....((.((..(((((((.......)))-----))))..)).)).((((((....((((...))))))))))...)))...----------------- ( -17.70)
>DroYak_CAF1 68223 93 - 1
AUAAUGAAAUUCCUAGCUGCUUUGUGCCCACGACG-----AAGCCACUUGGCGGGAUGUCCCGAUCCCUGAUCCGUCGCCUACAUAUAUACACAUAUA-------
......................((((....(((((-----..(((....)))(((((......))))).....)))))....))))............------- ( -20.40)
>consensus
AUAAUGAAAUUCCUAGCUGCUUUGUGCCCACGACG_____AAGCCACUUGGCGGGAUGUCCCGAUCCCUGAUCCGUCCCCUACAUAUAUA__CAUAUA_______
...(((.........((........))....((((.......(((....)))(((((......))))).....)))).....))).................... (-15.52 = -15.63 +   0.11)

alignment

secondary structure

dotplot

Window 7

Location	11,331,853 – 11,331,972
Length	119
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	90.70
Mean single sequence MFE	-35.30
Consensus MFE	-28.52
Energy contribution	-29.52
Covariance contribution	1.00
Combinations/Pair	1.00
Mean z-score	-1.45
Structure conservation index	0.81
SVM decision value	0.21
SVM RNA-class probability	0.635763
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11331853 119 + 27905053
AUGCACCCCGGGCCAAAGGACAAAGACAUGUUUUUAAUAGUUUCGCAUGUUUGUGCAGCAGGCUUUGUUUUUUUUUUUUUUUUUGGCCCCUCCUU-GGAGGAGGCUGCAGGAACCCCUCU
.((((.(((((((((((((((((((...((((............((((....))))))))..)))))))...........)))))))))(((...-.)))).)).))))((....))... ( -34.20)
>DroSec_CAF1 71037 112 + 1
AUGCACCCCGGGCCAAAGGACAAAGACAUGUUUUUAAUAGUUUCGCAUGUUUGUGCAGCAGGGUUUGUUUUU-------UUUUUGGCCCCUCCUU-GGAGGAUUCUGCAUGAUCCCCCCU
(((((....(((((((((((..((((((..((((.....(((.((((....)))).)))))))..)))))))-------))))))))))(((...-.))).....))))).......... ( -31.30)
>DroSim_CAF1 69252 109 + 1
AUGCACCCCGGGCCAAAGGACAAAGACAUGUUUUUAAUAGUUUCGCAUGUUUGUGCAGCAGGCUUUGUUUUU--------UUUUGGCCCCUCC---GGAGGAGGCUGCAUGAUCCCCUCU
(((((((((((((((((((((((((...((((............((((....))))))))..)))))))...--------)))))))))(...---.).)).)).))))).......... ( -33.30)
>DroEre_CAF1 66582 110 + 1
AUGCACCCCGGGCCAAAGGACAAAGACAUGUUUUUAAUAGUUUCGCAUGUUUGUGCAGCAGGCUUUGUUUU---------UUUUGGCCCCUCCUC-GGAGGAGGCUGGAGGAUCCUGGCC
.(((((.((........))....((((((((.............)))))))))))))...((((..(..((---------(((..(((((((...-.)))).)))..)))))..).)))) ( -39.32)
>DroYak_CAF1 68316 113 + 1
AUGCACCCCGGGCCAAAGGACAAAGACAUGUUUUUAAUAGUUUCGCAUGUUUGUGCAGCAGGCUUUGUUUUU-------UUUUUGGCCCCUCCUCUGGAGGAGGCUGGAGGAUCCCCAGU
.........((((((((((((((((...((((............((((....))))))))..)))))))...-------.)))))))))(((((....)))))(((((.(....)))))) ( -38.40)
>consensus
AUGCACCCCGGGCCAAAGGACAAAGACAUGUUUUUAAUAGUUUCGCAUGUUUGUGCAGCAGGCUUUGUUUUU_______UUUUUGGCCCCUCCUC_GGAGGAGGCUGCAGGAUCCCCUCU
.((((.((.((((((((((((((((...((((............((((....))))))))..)))))))...........)))))))))((((...))))..)).))))........... (-28.52 = -29.52 +   1.00)

alignment

secondary structure

dotplot

Window 8

Location	11,331,972 – 11,332,092
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	93.16
Mean single sequence MFE	-35.20
Consensus MFE	-34.88
Energy contribution	-34.88
Covariance contribution	-0.00
Combinations/Pair	1.00
Mean z-score	-1.93
Structure conservation index	0.99
SVM decision value	3.61
SVM RNA-class probability	0.999441
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11331972 120 + 27905053
UCCCCUUUUAGUUUCCCCUUUCAGUUCCGAUUGUGUGCAGUAUGCGCAAAGUUGGCCAGAUUUUUGUGCUUGCACUUUGAAUAGUUGCAUUUUUGAGCAGUUCGUGGUGCAGAGCAUAAA
..........................((((((.(((((.....))))).)))))).......((((((((((((((.(((((.(((.((....))))).))))).)))))).)))))))) ( -35.50)
>DroSec_CAF1 71149 120 + 1
UCCCGUUUUAGUUUCCCCUUUCAGUUCCGAUUGUGUGCAGUAUGCGCAAAGUUGGUCAGAUUUUUGUGCUUGCACUUUGAAUAGUUGCAUUUUUGAGCAGUUCGUGGUGCAGAGCAUAAA
..........................((((((.(((((.....))))).)))))).......((((((((((((((.(((((.(((.((....))))).))))).)))))).)))))))) ( -35.70)
>DroSim_CAF1 69361 120 + 1
UCACCUUUUAGUUUCCUCUUUCAGUUCCGAUUGUGUGCAGUAUGCGCAAAGUUGGCCAGAUUUUUGUGCUUGCACUUUGAAUAGUUGCAUUUUUGAGCAGUUCGUGGUGCAGAGCAUAAA
..........................((((((.(((((.....))))).)))))).......((((((((((((((.(((((.(((.((....))))).))))).)))))).)))))))) ( -35.50)
>DroEre_CAF1 66692 118 + 1
CCC--UAUCCCUUUCCCCUCGCAGUUCCGAUUGUGUGCAGUAUGCGCAAAGUUGGCCAGAUUUUUGUGCUUGCACUUUGAAUAGUUGCAUUUUUGAGCAGUUCGUCGUGCAGAGCAUAAA
...--.....................((((((.(((((.....))))).)))))).......(((((((((((((..(((((.(((.((....))))).)))))..))))).)))))))) ( -34.10)
>DroYak_CAF1 68429 115 + 1
UCC--UA---GUUUCCCCUUUCAGUUCCGAUUGUGUGCAGUGCGCGCAAAGUUGGCCAGAUUUUUGUGCUUGCACUCUGAAUAGUUGCAUUUUUGAGCAGUUCGUGGUGCAGAGCAUAAA
...--..---................((((((.(((((.....))))).)))))).......((((((((((((((.(((((.(((.((....))))).))))).)))))).)))))))) ( -35.20)
>consensus
UCCC_UUUUAGUUUCCCCUUUCAGUUCCGAUUGUGUGCAGUAUGCGCAAAGUUGGCCAGAUUUUUGUGCUUGCACUUUGAAUAGUUGCAUUUUUGAGCAGUUCGUGGUGCAGAGCAUAAA
..........................((((((.(((((.....))))).)))))).......(((((((((((((..(((((.(((.((....))))).)))))..))))).)))))))) (-34.88 = -34.88 +  -0.00)

alignment

secondary structure

dotplot

Window 9

Location	11,332,012 – 11,332,132
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	95.67
Mean single sequence MFE	-32.98
Consensus MFE	-31.72
Energy contribution	-31.60
Covariance contribution	-0.12
Combinations/Pair	1.05
Mean z-score	-1.55
Structure conservation index	0.96
SVM decision value	1.96
SVM RNA-class probability	0.983971
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11332012 120 + 27905053
UAUGCGCAAAGUUGGCCAGAUUUUUGUGCUUGCACUUUGAAUAGUUGCAUUUUUGAGCAGUUCGUGGUGCAGAGCAUAAAUUGUGAGUCUGUCAGGAGUUAGUUGUAAUGAGUAAGGAAA
.....((((..(((((.(((((((((((((((((((.(((((.(((.((....))))).))))).)))))).))))))).....))))))))))).......)))).............. ( -31.10)
>DroSec_CAF1 71189 120 + 1
UAUGCGCAAAGUUGGUCAGAUUUUUGUGCUUGCACUUUGAAUAGUUGCAUUUUUGAGCAGUUCGUGGUGCAGAGCAUAAAUUGUGAGUCUGUCAGUAGUUAGUCGUAAUGAGUUAGGGAA
..(((((.((.(..(.((((((((((((((((((((.(((((.(((.((....))))).))))).)))))).))))))).....))))))).)...).)).).))))............. ( -33.20)
>DroSim_CAF1 69401 120 + 1
UAUGCGCAAAGUUGGCCAGAUUUUUGUGCUUGCACUUUGAAUAGUUGCAUUUUUGAGCAGUUCGUGGUGCAGAGCAUAAAUUGUGAGUCUGUCAGGAGUUAGUCGUAAUGAGUUAGGAAA
..(((((((..(((((.(((((((((((((((((((.(((((.(((.((....))))).))))).)))))).))))))).....)))))))))))...)).).))))............. ( -33.00)
>DroEre_CAF1 66730 120 + 1
UAUGCGCAAAGUUGGCCAGAUUUUUGUGCUUGCACUUUGAAUAGUUGCAUUUUUGAGCAGUUCGUCGUGCAGAGCAUAAAUUGUGAAUCUGUCAGGAGUUAGUCGUAAUGAGUUGGGAAA
..(((((((..(((((.((((((((((((((((((..(((((.(((.((....))))).)))))..))))).))))))).....)))))))))))...)).).))))............. ( -31.60)
>DroYak_CAF1 68464 120 + 1
UGCGCGCAAAGUUGGCCAGAUUUUUGUGCUUGCACUCUGAAUAGUUGCAUUUUUGAGCAGUUCGUGGUGCAGAGCAUAAAUUGUGAGUCUGUCAGGAGUUGGUCGUAAUGAGUUGGGGAA
(((((.(((..(((((.(((((((((((((((((((.(((((.(((.((....))))).))))).)))))).))))))).....)))))))))))...)))).))))............. ( -36.00)
>consensus
UAUGCGCAAAGUUGGCCAGAUUUUUGUGCUUGCACUUUGAAUAGUUGCAUUUUUGAGCAGUUCGUGGUGCAGAGCAUAAAUUGUGAGUCUGUCAGGAGUUAGUCGUAAUGAGUUAGGAAA
..(((((((..((((.(((((((((((((((((((..(((((.(((.((....))))).)))))..))))).))))))).....)))))))))))...)).).))))............. (-31.72 = -31.60 +  -0.12)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:20:17 2006