Locus 3785

Sequence ID 3R_DroMel_CAF1
Location 10,264,240 – 10,264,410
Length 170
Max. P 0.997087
window6069 window6070 window6071 window6072 window6073

overview

Window 9

Location 10,264,240 – 10,264,332
Length 92
Sequences 6
Columns 99
Reading direction forward
Mean pairwise identity 77.71
Mean single sequence MFE -28.17
Consensus MFE -14.65
Energy contribution -14.27
Covariance contribution -0.39
Combinations/Pair 1.13
Mean z-score -1.99
Structure conservation index 0.52
SVM decision value 0.46
SVM RNA-class probability 0.746186
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 10264240 92 + 27905053
-------CUCCUGCUCGCUAAUGUCUUGGCCAAGAUUAAGCGAAAAAGUGCGCAAUCUUUGCGCGCAGCUCUGAGCGGCAAACUGCUGUCAAUUUGACA
-------.....(((((((...(((((....)))))..)))))....(((((((.....))))))).))....(((((....)))))(((.....))). ( -30.90)
>DroPse_CAF1 131548 81 + 1
U----UCUU-CUGGG------------CGUCAAGAUUAAGCGCAAAAGUGCGCAAUCUGUGCGCUGAGCUUU-UGCGCAGAGCUGCUGUCAGUUUGACA
.----....-.....------------.(((........(((((((((((((((.....)))))...)))))-))))).((((((....))))))))). ( -30.50)
>DroSec_CAF1 121765 95 + 1
U----UCCUCCUGCUCGCCAAAGUCUUGGCCAAGAUUAAGCUAAAAAGUCCGCAAUCUUUGCGCGCAGCUCUGAGCGGCAAACUGCUGUCAAUUUGACA
.----.....(((((((((((....)))))........((((.....((.((((.....)))).))))))..)))))).........(((.....))). ( -24.40)
>DroSim_CAF1 120963 95 + 1
U----UCCUCCUGCUCGCCAAAGUCUUGGCCAAGAUUAAGCGAAAAAGUGCGCAAUCUUUGCGCGCAGCUCUGAGCGGCAAACUGCUGUCAAUUUGACA
.----.......((((((...((((((....))))))..))))....(((((((.....))))))).))....(((((....)))))(((.....))). ( -29.40)
>DroYak_CAF1 129233 99 + 1
UCCUUGCCUUCUCCACACCAAAGUCUUGGCCAAGAUUAAGCGAAAAAGUGCGCAAUCUUUGAGCGCAACUCUGAGCGGCAAACUGCUGUCAAUUUGACA
...(((((.............((((((....))))))..((.......(((((.........))))).......)))))))......(((.....))). ( -23.34)
>DroPer_CAF1 134172 81 + 1
U----UCUU-CUGGG------------CGUCAAGAUUAAGCGCAAAAGUGCGCAAUCUGUGCGCUGAGCUUU-UGCGCAGAGCUGCUGUCAGUUUGACA
.----....-.....------------.(((........(((((((((((((((.....)))))...)))))-))))).((((((....))))))))). ( -30.50)
>consensus
U____UCCUCCUGCUCGCCAAAGUCUUGGCCAAGAUUAAGCGAAAAAGUGCGCAAUCUUUGCGCGCAGCUCUGAGCGGCAAACUGCUGUCAAUUUGACA
......................................(((........(((((.....)))))((.((.....)).)).....)))(((.....))). (-14.65 = -14.27 +  -0.39)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 0

Location 10,264,240 – 10,264,332
Length 92
Sequences 6
Columns 99
Reading direction reverse
Mean pairwise identity 77.71
Mean single sequence MFE -29.17
Consensus MFE -16.85
Energy contribution -15.93
Covariance contribution -0.91
Combinations/Pair 1.22
Mean z-score -2.01
Structure conservation index 0.58
SVM decision value 0.92
SVM RNA-class probability 0.881733
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 10264240 92 - 27905053
UGUCAAAUUGACAGCAGUUUGCCGCUCAGAGCUGCGCGCAAAGAUUGCGCACUUUUUCGCUUAAUCUUGGCCAAGACAUUAGCGAGCAGGAG-------
((((.....))))(((((((........)))))))(((((.....))))).(((.((((((...((((....))))....)))))).)))..------- ( -31.40)
>DroPse_CAF1 131548 81 - 1
UGUCAAACUGACAGCAGCUCUGCGCA-AAAGCUCAGCGCACAGAUUGCGCACUUUUGCGCUUAAUCUUGACG------------CCCAG-AAGA----A
.(((((.(((....)))....(((((-((((....(((((.....))))).)))))))))......))))).------------.....-....----. ( -25.80)
>DroSec_CAF1 121765 95 - 1
UGUCAAAUUGACAGCAGUUUGCCGCUCAGAGCUGCGCGCAAAGAUUGCGGACUUUUUAGCUUAAUCUUGGCCAAGACUUUGGCGAGCAGGAGGA----A
((((.....)))).(..((((((((.(((((((..(.((.(((((((.((.((....))))))))))).))).)).)))))))).)))))..).----. ( -28.40)
>DroSim_CAF1 120963 95 - 1
UGUCAAAUUGACAGCAGUUUGCCGCUCAGAGCUGCGCGCAAAGAUUGCGCACUUUUUCGCUUAAUCUUGGCCAAGACUUUGGCGAGCAGGAGGA----A
((((.....))))(((((((........)))))))(((((.....))))).(((.((((((...((((....))))....)))))).)))....----. ( -31.40)
>DroYak_CAF1 129233 99 - 1
UGUCAAAUUGACAGCAGUUUGCCGCUCAGAGUUGCGCUCAAAGAUUGCGCACUUUUUCGCUUAAUCUUGGCCAAGACUUUGGUGUGGAGAAGGCAAGGA
((((.....))))((..(((.((((((((((((..(((..(((((((.((........)).))))))))))...)))))))).)))))))..))..... ( -32.20)
>DroPer_CAF1 134172 81 - 1
UGUCAAACUGACAGCAGCUCUGCGCA-AAAGCUCAGCGCACAGAUUGCGCACUUUUGCGCUUAAUCUUGACG------------CCCAG-AAGA----A
.(((((.(((....)))....(((((-((((....(((((.....))))).)))))))))......))))).------------.....-....----. ( -25.80)
>consensus
UGUCAAAUUGACAGCAGUUUGCCGCUCAGAGCUGCGCGCAAAGAUUGCGCACUUUUUCGCUUAAUCUUGGCCAAGACUUUGGCGAGCAGGAGGA____A
.(((((..(...(((.....((.((.....)).))(((((.....)))))........)))..)..)))))............................ (-16.85 = -15.93 +  -0.91)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 1

Location 10,264,255 – 10,264,372
Length 117
Sequences 6
Columns 118
Reading direction forward
Mean pairwise identity 75.55
Mean single sequence MFE -39.95
Consensus MFE -17.67
Energy contribution -17.83
Covariance contribution 0.17
Combinations/Pair 1.12
Mean z-score -3.30
Structure conservation index 0.44
SVM decision value 2.80
SVM RNA-class probability 0.997087
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 10264255 117 + 27905053
GUCUUGGCCAAGAUUAAGCGAAAAA-GUGCGCAAUCUUUGCGCGCAGCUCUGAGCGGCAAACUGCUGUCAAUUUGACAAAUGCGCCGCGCUCAGCGAUUGUGACAGUUUUAGCGAGCC
(((((....)))))...((..((((-.(((((((((.(((.((((.((....(((((....)))))(((.....)))......)).)))).))).))))))).)).)))).))..... ( -39.00)
>DroVir_CAF1 138950 102 + 1
GCGCCUGUCAAGAUUAAGCUCAAGAGCUGCGCAAUCGCU------------GAGCGG----CUGCUGUCAAUUUGACAAAUGCUCAGCUCUCAGCGAUUGUGACAGUUUUAGCGGAUU
.................(((..(((((((((((((((((------------(((.((----(((.((((.....))))......)))))))))))))))))).))))))))))..... ( -42.20)
>DroPse_CAF1 131558 111 + 1
-----CGUCAAGAUUAAGCGCAAAA-GUGCGCAAUCUGUGCGCUGAGCUUU-UGCGCAGAGCUGCUGUCAGUUUGACAAAUGCUCAGAGCUCAGCGAUUGUGACAGUUUUAGCGGAUU
-----.(((((((((..(((((...-.))))))))))...(((((((((((-.(((((....)))((((.....))))...))..)))))))))))....)))).............. ( -41.40)
>DroWil_CAF1 135405 98 + 1
CUCUUUCACAAGAUUAAGCGCAAAA-GUGCGCAAUCUUAG-------------------AGUUGCUGUCAAAUUGACAAAUGCUCAGCGUUCAGUGAUUGUGACAGUUUUAGUGAAUU
....(((((((((((..(((((...-.)))))))))))..-------------------....(((((((.(((((...((((...))))))))).....)))))))....))))).. ( -28.60)
>DroMoj_CAF1 135271 102 + 1
GCUCUCGUCAAGAUUAAGCGCAAAAGCUGCGCAAUCGCU------------GAGCGG----CUGCUGUCAAUUUGACAAAUGCUCAGCGCUCAGCGAUUGUGACAGUUUUAGCGGAUU
(((.((.....))...)))((.(((((((((((((((((------------(((((.----(((.((((.....))))......)))))))))))))))))).))))))).))..... ( -47.10)
>DroPer_CAF1 134182 111 + 1
-----CGUCAAGAUUAAGCGCAAAA-GUGCGCAAUCUGUGCGCUGAGCUUU-UGCGCAGAGCUGCUGUCAGUUUGACAAAUGCUCAGAGCUCAGCGAUUGUGACAGUUUUAGCGGAUU
-----.(((((((((..(((((...-.))))))))))...(((((((((((-.(((((....)))((((.....))))...))..)))))))))))....)))).............. ( -41.40)
>consensus
G___UCGUCAAGAUUAAGCGCAAAA_GUGCGCAAUCUCUG____________AGCGG__AGCUGCUGUCAAUUUGACAAAUGCUCAGCGCUCAGCGAUUGUGACAGUUUUAGCGGAUU
...........((((..(((((.....))))))))).........................((((((......(.((((.((((........)))).)))).)......))))))... (-17.67 = -17.83 +   0.17)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 2

Location 10,264,255 – 10,264,372
Length 117
Sequences 6
Columns 118
Reading direction reverse
Mean pairwise identity 75.55
Mean single sequence MFE -35.48
Consensus MFE -14.08
Energy contribution -15.13
Covariance contribution 1.06
Combinations/Pair 1.05
Mean z-score -3.03
Structure conservation index 0.40
SVM decision value 2.22
SVM RNA-class probability 0.990516
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 10264255 117 - 27905053
GGCUCGCUAAAACUGUCACAAUCGCUGAGCGCGGCGCAUUUGUCAAAUUGACAGCAGUUUGCCGCUCAGAGCUGCGCGCAAAGAUUGCGCAC-UUUUUCGCUUAAUCUUGGCCAAGAC
((((..................(((.....)))((((...((((.....))))(((((((........))))))))))).(((((((.((..-......)).)))))))))))..... ( -36.20)
>DroVir_CAF1 138950 102 - 1
AAUCCGCUAAAACUGUCACAAUCGCUGAGAGCUGAGCAUUUGUCAAAUUGACAGCAG----CCGCUC------------AGCGAUUGCGCAGCUCUUGAGCUUAAUCUUGACAGGCGC
....(((.....(((((((((((((((((.((((.....(((((.....))))))))----)..)))------------))))))))...((((....))))......))))))))). ( -39.00)
>DroPse_CAF1 131558 111 - 1
AAUCCGCUAAAACUGUCACAAUCGCUGAGCUCUGAGCAUUUGUCAAACUGACAGCAGCUCUGCGCA-AAAGCUCAGCGCACAGAUUGCGCAC-UUUUGCGCUUAAUCUUGACG-----
..............((((....((((((((((.((((..(((((.....)))))..)))).)....-..)))))))))...((((((((((.-...)))))..))))))))).----- ( -37.30)
>DroWil_CAF1 135405 98 - 1
AAUUCACUAAAACUGUCACAAUCACUGAACGCUGAGCAUUUGUCAAUUUGACAGCAACU-------------------CUAAGAUUGCGCAC-UUUUGCGCUUAAUCUUGUGAAAGAG
............((.((((..............(((...(((((.....)))))...))-------------------).(((((((((((.-...)))))..)))))))))).)).. ( -22.70)
>DroMoj_CAF1 135271 102 - 1
AAUCCGCUAAAACUGUCACAAUCGCUGAGCGCUGAGCAUUUGUCAAAUUGACAGCAG----CCGCUC------------AGCGAUUGCGCAGCUUUUGCGCUUAAUCUUGACGAGAGC
.....(((.....(((((.(((((((((((((((.....(((((.....))))))))----.)))))------------)))))))((((((...)))))).......)))))..))) ( -40.40)
>DroPer_CAF1 134182 111 - 1
AAUCCGCUAAAACUGUCACAAUCGCUGAGCUCUGAGCAUUUGUCAAACUGACAGCAGCUCUGCGCA-AAAGCUCAGCGCACAGAUUGCGCAC-UUUUGCGCUUAAUCUUGACG-----
..............((((....((((((((((.((((..(((((.....)))))..)))).)....-..)))))))))...((((((((((.-...)))))..))))))))).----- ( -37.30)
>consensus
AAUCCGCUAAAACUGUCACAAUCGCUGAGCGCUGAGCAUUUGUCAAAUUGACAGCAGCU__CCGCU____________CAAAGAUUGCGCAC_UUUUGCGCUUAAUCUUGACGA___C
..............((((.(((((((.(....).)))..(((((.....)))))............................))))(((((.....))))).......))))...... (-14.08 = -15.13 +   1.06)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 3

Location 10,264,293 – 10,264,410
Length 117
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 77.10
Mean single sequence MFE -32.18
Consensus MFE -16.98
Energy contribution -16.37
Covariance contribution -0.61
Combinations/Pair 1.22
Mean z-score -1.69
Structure conservation index 0.53
SVM decision value -0.01
SVM RNA-class probability 0.526216
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 10264293 117 + 27905053
-GCGCGCAGCUCUGAGCGGCAAACUGCUGUCAAUUUGACAAAUGCGCCGCGCUCAGCGAUUGUGACAGUUUUAGCGAGCCCGUAAUUAAGCAUGCGCGCACAUGCAUAAAUAGCAUAA--
-((((((((((.((((((((.....((((((.....))))...)))))))((((.(((((((...)))))...))))))......)))))).)))))))..((((.......))))..-- ( -40.70)
>DroGri_CAF1 127469 103 + 1
-------------GAACAG--CGCUGCUGUCACUUUGACAAAUGCUCAGCGCUCAGCGAUUGUGACAGUUUUAGCGGAUUCGUAAUUAAGCAUGCGCGCGCAUGCAUAAAUAGCAUAA--
-------------.....(--(.((((((..(((.(.((((.((((........)))).)))).).)))..))))))............((((((....)))))).......))....-- ( -30.50)
>DroEre_CAF1 122443 100 + 1
--------------------AAACUGCUGUCAAUUUGACAAAUGCGCCGGGCUCAGCGAUGGUGACAGUUUUAGCGGGCCCGUAAUUAAGCAUGCGCGCACAGGCAUAAAUAGCAUAAAU
--------------------...(((.((((.....))))..(((((.((((((.((..((....))......))))))))(((........)))))))))))((.......))...... ( -31.30)
>DroWil_CAF1 135443 98 + 1
-G-------------------AGUUGCUGUCAAAUUGACAAAUGCUCAGCGUUCAGUGAUUGUGACAGUUUUAGUGAAUUUGUAAUUAAGCAUGCGCGCACAUGCAUAAAUAGCAUAA--
-(-------------------(((...((((.....))))...)))).((((.((.((((((..(..((((....)))))..))))))....)).))))..((((.......))))..-- ( -23.10)
>DroAna_CAF1 109814 106 + 1
CACGGGCAGCUC------------UGCUGUCAAUUUGACAAAUGCUGCAGGCUCAGUGGUUGUGACAGUUUUAGCGAAUUCGUAAUUGAGAAUGCGCGCACAUGCACAAAUAGCAUAA--
.....(((((..------------...((((.....))))...))))).......((..(((((.((......(((.((((........)))).))).....)))))))...))....-- ( -28.30)
>DroPer_CAF1 134215 116 + 1
-GCGCUGAGCUUU-UGCGCAGAGCUGCUGUCAGUUUGACAAAUGCUCAGAGCUCAGCGAUUGUGACAGUUUUAGCGGAUUCGUAAUGAAGCAUGCGCGCACAUGCAUAAAUAGCAUAA--
-((((((((((((-.(((((....)))((((.....))))...))..))))))))))....(((.(((((((((((....)))..)))))).)))))))..((((.......))))..-- ( -39.20)
>consensus
_G___________________AGCUGCUGUCAAUUUGACAAAUGCUCAGCGCUCAGCGAUUGUGACAGUUUUAGCGAAUUCGUAAUUAAGCAUGCGCGCACAUGCAUAAAUAGCAUAA__
.........................(((((((..(((......((.....))....)))...)))))))....(((....((((........)))))))..((((.......)))).... (-16.98 = -16.37 +  -0.61)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:10:06 2006