Locus 10315

Sequence ID	3R_DroMel_CAF1
Location	27,677,687 – 27,677,936
Length	249
Max. P	0.939538

overview

Window 8

Location	27,677,687 – 27,677,786
Length	99
Sequences	4
Columns	107
Reading direction	reverse
Mean pairwise identity	69.21
Mean single sequence MFE	-16.96
Consensus MFE	-12.27
Energy contribution	-13.15
Covariance contribution	0.88
Combinations/Pair	1.11
Mean z-score	-1.23
Structure conservation index	0.72
SVM decision value	0.78
SVM RNA-class probability	0.847632
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 27677687 99 - 27905053
AAUUU--UU--UUUCCCUUCUAUGUGUGCUAUUAAAACU----AUCGGAGCAACCACUAAUAACCUCGUCCUUUUUAUUUUACAGGAAGGACCGUAAAAUGGCACUG
.....--..--..............((((((((......----...((.....))............(((((((((.......))))))))).....)))))))).. ( -19.50)
>DroSec_CAF1 160 102 - 1
-UUUUUUAUUUUGCCAUUUGUAUGUGUGCUAUUAAAACU----AUCGGACCUACCACUAAAAACCUCAUCCUUUUUAUUUUUCAGGAAGGACCGUAAAAUGGCACUG
-..........((((((((.((((.((.((.........----...((.....)).............((((...........)))))).))))))))))))))... ( -18.60)
>DroEre_CAF1 153 82 - 1
---------------------AUAUGAGCUGUUAAAACUCUUUAACGGAAUCACCACUAA-AACCGUAUCCUUAU---CACACAGGAAAGACCGAAAAAUGGCACUG
---------------------......((((((.....((((..((((............-..)))).((((...---.....))))))))......)))))).... ( -11.14)
>DroYak_CAF1 153 83 - 1
---------------------AUGUGUGCUAUUAAAACUGCUUAACGGACUUACCACUAAAAACCGCAUCCUUUC---CCUACAGGAAGGACCGAAAAAUGGCACUG
---------------------....((((((((.............((.....)).........((..(((((((---......))))))).))...)))))))).. ( -18.60)
>consensus
_____________________AUGUGUGCUAUUAAAACU____AACGGACCUACCACUAAAAACCGCAUCCUUUU___CUUACAGGAAGGACCGAAAAAUGGCACUG
.........................((((((((.............((.....)).............((((((((.......))))))))......)))))))).. (-12.27 = -13.15 +   0.88)

alignment

secondary structure

dotplot

Window 9

Location	27,677,786 – 27,677,902
Length	116
Sequences	6
Columns	117
Reading direction	forward
Mean pairwise identity	78.52
Mean single sequence MFE	-27.78
Consensus MFE	-22.58
Energy contribution	-23.13
Covariance contribution	0.56
Combinations/Pair	1.18
Mean z-score	-1.10
Structure conservation index	0.81
SVM decision value	0.38
SVM RNA-class probability	0.711760
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 27677786 116 + 27905053
UUAAAAAUAGUUGUCUGUGC-GGCCAUUACUUACGGGAAAAAUUUGAAUGCCUUAACUUCAAAGCUGUUUGAGGUGAAAGCUUCUUUGAUGUCAUCCUCAGAGCAGGAUGAGCUGCA
......((((....))))((-(((((((..............((((((.(......))))))).(((((((((((((...(......)...))).))))))).))))))).))))). ( -29.60)
>DroVir_CAF1 223 112 + 1
-----AAUUGUUAUCUUUAUAUUCAUUUACUUACGGGAAAAAUUUGAAUGCUUUAACCUCGAAAUUGUUGGAGCUGAAGGCUUCUUUGAUGUCAUCCUCGGUACAGGAUGAGCUGUA
-----..........................(((((.........(((.(((((...(((.((....)).)))...)))))))).......(((((((......))))))).))))) ( -21.50)
>DroSec_CAF1 262 115 + 1
-AAAAAUUAGUUGUCUGUGC-GGGUUUUACUUACGGGAAAAAUUUGAAUGCUUUAACUUCGAAGCUGUUUGAGGUGAAAGCUUCUUUGAUGUCAUCCUCAGAGCAGGAUGAGCUGCA
-................(((-((......................(((.(((((.((((((((....)))))))).)))))))).......(((((((......))))))).))))) ( -28.10)
>DroWil_CAF1 230 108 + 1
----AGAAGGCUGAUUCUG-----CAUUACUUACGGGAAAAAUUUGAAUGCUUUGACUUCGAAACUGUUCGAGGUGAAGGCCUCUUUGAUGUCAUCCUCAGAGCAGGAUGAGCUGUA
----....((((.((((((-----(....((...((((.....(..((.(((((.((((((((....)))))))).)))))...))..).....)))).)).))))))).))))... ( -34.80)
>DroYak_CAF1 236 98 + 1
------------------GC-UGCCUUUACUUACGGGAAAAAUUUGAAUGCUUUAACUUCGAAGCUGUUUGAGGUGAAAGCUUCUUUGAUGUCAUCCUCAGAGCAGGAUGACCUGUG
------------------..-..........((((((........(((.(((((.((((((((....)))))))).)))))))).......(((((((......))))))))))))) ( -28.90)
>DroMoj_CAF1 215 112 + 1
-----AAUUUUGAAAAUCAUUAAUAUUAACUUACGGGAAAAAUUUGAAUGCUUUAACUUCAAAAUUGUUGGAGGUGAAGGCUUCUUUGAUGUCAUCCUCGGUGCAGGAUGAGCUGUA
-----..........................(((((.........(((.(((((..((((((.....))))))...)))))))).......(((((((......))))))).))))) ( -23.80)
>consensus
_____AAUAGUUGUCUGUGC_GGCCUUUACUUACGGGAAAAAUUUGAAUGCUUUAACUUCGAAACUGUUUGAGGUGAAAGCUUCUUUGAUGUCAUCCUCAGAGCAGGAUGAGCUGUA
...............................(((((.........(((.(((((.((((((((....)))))))).)))))))).......(((((((......))))))).))))) (-22.58 = -23.13 +   0.56)

alignment

secondary structure

dotplot

Window 0

Location	27,677,822 – 27,677,936
Length	114
Sequences	6
Columns	117
Reading direction	forward
Mean pairwise identity	78.72
Mean single sequence MFE	-32.23
Consensus MFE	-22.18
Energy contribution	-22.35
Covariance contribution	0.17
Combinations/Pair	1.13
Mean z-score	-2.10
Structure conservation index	0.69
SVM decision value	1.30
SVM RNA-class probability	0.939538
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 27677822 114 + 27905053
AAAAAUUUGAAUGCCUUAACUUCAAAGCUGUUUGAGGUGAAAGCUUCUUUGAUGUCAUCCUCAGAGCAGGAUGAGCUGCAGGGUAAG--AGAGAAGAUGUUGUUAGUUAC-CUUUAA
.....((((((.(......))))))).......(((((((.(((.(((((..(.(.((((((((..(.....)..))).))))).).--)..))))).))).....))))-)))... ( -25.10)
>DroPse_CAF1 262 113 + 1
AAAAACUUGAAUGCUUUGACUUCGAAACUGUUUGAGGUGAAGGCUUCUUUGAUGUCAUCCUCGGAGCAGGAUGAGCUGUGGGGAGCG--GGAG-UGAUA-GGUUAGAUUCGGUUUAA
..(((((.(((.(((((.((((((((....)))))))).))))).(((....((((.((((((.(((.......))).))))))((.--...)-)))))-....))))))))))).. ( -36.20)
>DroYak_CAF1 254 112 + 1
AAAAAUUUGAAUGCUUUAACUUCGAAGCUGUUUGAGGUGAAAGCUUCUUUGAUGUCAUCCUCAGAGCAGGAUGACCUGUGGGG-AC---AGAGAAGAUGUUGUUAGUUAG-CUUUAA
........(((.(((((.((((((((....)))))))).))))))))......((((((((......))))))))((.((...-.)---).)).....((((.....)))-)..... ( -31.60)
>DroMoj_CAF1 247 110 + 1
AAAAAUUUGAAUGCUUUAACUUCAAAAUUGUUGGAGGUGAAGGCUUCUUUGAUGUCAUCCUCGGUGCAGGAUGAGCUGUAAUAUGCAAGAGAAAGAACGUU---CGUUCG-C---UA
............(((((..((((((.....))))))...)))))((((((....(((((((......)))))))((........)).)))))).((((...---.)))).-.---.. ( -27.70)
>DroAna_CAF1 238 110 + 1
AAAAAUUUGAAUGCUUUGACUUCGAAGCUAUUCGAGGUGAAGGCUUCCUUGAUGUCAUCCUCAGAGCAGGAAGAGCUGUGGGGAAGA--GCAGGAGC----AUUAGUACG-GUUUCA
.......((((.(((((.((((((((....)))))))).)))))(((((.(...((.((((((.(((.......))).)))))).))--.)))))).----.........-..)))) ( -36.60)
>DroPer_CAF1 261 113 + 1
AAAAACUUGAAUGCUUUGACUUCGAAAGUGUUUGAGGUGAAGGCUUCUUUGAUGUCAUCCUCGGAGCAGGAUGAGCUGUGGGGAGCG--GGAG-UGAUA-GGUUAGAUUCGGUUUAA
..(((((.(((.(((((.((((((((....)))))))).))))).(((....((((.((((((.(((.......))).))))))((.--...)-)))))-....))))))))))).. ( -36.20)
>consensus
AAAAAUUUGAAUGCUUUAACUUCGAAACUGUUUGAGGUGAAGGCUUCUUUGAUGUCAUCCUCAGAGCAGGAUGAGCUGUGGGGAACG__AGAGAAGAUG_UGUUAGUUAC_CUUUAA
........(((.(((((.((((((((....)))))))).)))))))).......(((((((......)))))))........................................... (-22.18 = -22.35 +   0.17)

alignment

secondary structure

dotplot

Window 1

Location	27,677,822 – 27,677,936
Length	114
Sequences	6
Columns	117
Reading direction	reverse
Mean pairwise identity	78.72
Mean single sequence MFE	-20.00
Consensus MFE	-11.78
Energy contribution	-11.95
Covariance contribution	0.17
Combinations/Pair	1.00
Mean z-score	-1.54
Structure conservation index	0.59
SVM decision value	0.02
SVM RNA-class probability	0.541431
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 27677822 114 - 27905053
UUAAAG-GUAACUAACAACAUCUUCUCU--CUUACCCUGCAGCUCAUCCUGCUCUGAGGAUGACAUCAAAGAAGCUUUCACCUCAAACAGCUUUGAAGUUAAGGCAUUCAAAUUUUU
.....(-((((.................--.))))).....(.(((((((......))))))))......((((((((.((.(((((....))))).)).))))).)))........ ( -21.57)
>DroPse_CAF1 262 113 - 1
UUAAACCGAAUCUAACC-UAUCA-CUCC--CGCUCCCCACAGCUCAUCCUGCUCCGAGGAUGACAUCAAAGAAGCCUUCACCUCAAACAGUUUCGAAGUCAAAGCAUUCAAGUUUUU
.......((((((....-.....-....--.(((......)))(((((((......))))))).......(((((..............)))))........)).))))........ ( -15.54)
>DroYak_CAF1 254 112 - 1
UUAAAG-CUAACUAACAACAUCUUCUCU---GU-CCCCACAGGUCAUCCUGCUCUGAGGAUGACAUCAAAGAAGCUUUCACCUCAAACAGCUUCGAAGUUAAAGCAUUCAAAUUUUU
.....(-((...((((..........((---((-....))))((((((((......))))))))......((((((............))))))...)))).)))............ ( -25.70)
>DroMoj_CAF1 247 110 - 1
UA---G-CGAACG---AACGUUCUUUCUCUUGCAUAUUACAGCUCAUCCUGCACCGAGGAUGACAUCAAAGAAGCCUUCACCUCCAACAAUUUUGAAGUUAAAGCAUUCAAAUUUUU
..---(-(((((.---...))))....((((((........))(((((((......))))))).....)))).))................((((((((....)).))))))..... ( -19.40)
>DroAna_CAF1 238 110 - 1
UGAAAC-CGUACUAAU----GCUCCUGC--UCUUCCCCACAGCUCUUCCUGCUCUGAGGAUGACAUCAAGGAAGCCUUCACCUCGAAUAGCUUCGAAGUCAAAGCAUUCAAAUUUUU
......-......(((----(((.....--...(((.((.(((.......))).)).)))((((.((...(((((.(((.....)))..))))))).)))).))))))......... ( -22.50)
>DroPer_CAF1 261 113 - 1
UUAAACCGAAUCUAACC-UAUCA-CUCC--CGCUCCCCACAGCUCAUCCUGCUCCGAGGAUGACAUCAAAGAAGCCUUCACCUCAAACACUUUCGAAGUCAAAGCAUUCAAGUUUUU
.......((((((....-..((.-....--.(((......)))(((((((......))))))).......)).(.((((...............)))).)..)).))))........ ( -15.26)
>consensus
UUAAAC_CAAACUAACA_CAUCUUCUCC__CGCUCCCCACAGCUCAUCCUGCUCCGAGGAUGACAUCAAAGAAGCCUUCACCUCAAACAGCUUCGAAGUCAAAGCAUUCAAAUUUUU
.........................................(.(((((((......))))))))......(((((.((.((.((..........)).)).)).)).)))........ (-11.78 = -11.95 +   0.17)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:53:54 2006