Locus 7812

Sequence ID	3R_DroMel_CAF1
Location	20,931,357 – 20,931,470
Length	113
Max. P	0.940272

overview

Window 7

Location	20,931,357 – 20,931,470
Length	113
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	78.38
Mean single sequence MFE	-28.57
Consensus MFE	-15.08
Energy contribution	-15.92
Covariance contribution	0.84
Combinations/Pair	1.28
Mean z-score	-2.51
Structure conservation index	0.53
SVM decision value	1.29
SVM RNA-class probability	0.940272
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 20931357 113 + 27905053
GAAUAUUUAGGCAUAGGGUUUUGUCCUUAUGAGGGCAAUUAUCCAACGCAUUCAUAGUCACUGGAAGAUAUCCCAAUCCUUUGAUGCUUCUAGUUU----CUAACCCUUU---AAUACUA
...((((.(((....((((.(((((((....)))))))..))))..........(((..((((((((.((((..........))))))))))))..----)))..)))..---))))... ( -28.30)
>DroSec_CAF1 14859 113 + 1
GAAUAUUUAGGCAUAGGGUUUUGUCCUUAUGAGGGCAAUUAUCCAGCGCAUUCAUAGUAACUGGAAGAUAUCCCAAUCCUUUGAUGCUUCUAGUUU----CUAAGCCUUU---AAUACUA
...((((.((((...((((.(((((((....)))))))..))))..........(((.(((((((((.((((..........))))))))))))).----))).))))..---))))... ( -33.80)
>DroSim_CAF1 23222 113 + 1
GAAUAUUUAGGCAUAGGGUUUUGUCCUUAUGAGGGCAAUUAUCCAGCGCAUUCAUAGUCACUGGAAGAUAUCCCAAUCCCUUGAUGCUUCUAGUUU----CUAAGCCUUU---AUUCCUA
(((((...((((...((((.(((((((....)))))))..))))..........(((..((((((((.((((..........))))))))))))..----))).)))).)---))))... ( -35.80)
>DroEre_CAF1 23220 113 + 1
GAAUAUUUAGGCAUAGGGUUUUGUCCUUAUGAGGACAAUUAUCCAGCGCAUUCAUAGAAACUGGUAAAUAUCCCAAUCCUUUGAUGCUUCUACUAG----CCAAGCCUUU---CAUACUU
(((......(((...((((.(((((((....)))))))..))))...((((.((.((....(((........)))...)).))))))........)----))......))---)...... ( -26.40)
>DroYak_CAF1 21558 113 + 1
GAAUAUUUAGGCAUAGGGUUUUGUCCUUAUGUGGACAAUUAUCCAGCGCAUUCAUAGAAACUGGAAAAUAUCCCAAUCCUUUGAUGCUUUUAGUUU----CUUGGCCUUU---AAUACUU
...((((.((((...((((.((((((......))))))..))))........((.(((((((((((..((((..........)))).)))))))))----))))))))..---))))... ( -29.60)
>DroPer_CAF1 63950 120 + 1
GCAUUUUAAAGUACAAGGGUUUCUCAUUAUUUGGAAAUUUCUUCAACUUAGUUAUCGAAGCUGUAUAGUCUCUAAGGUUUUCUAUGCUUUUAAUUGAAACUUUGGAUUUUUCUGACUCCU
..........(((((...(((((..((((.(((((......)))))..))))....))))))))))(((((((((((((((..((.......)).))))))))))).......))))... ( -17.51)
>consensus
GAAUAUUUAGGCAUAGGGUUUUGUCCUUAUGAGGACAAUUAUCCAGCGCAUUCAUAGAAACUGGAAAAUAUCCCAAUCCUUUGAUGCUUCUAGUUU____CUAAGCCUUU___AAUACUA
........((((...((((.((((((......))))))..))))...(((.(((.((....(((........)))...)).)))))).................))))............ (-15.08 = -15.92 +   0.84)

alignment

secondary structure

dotplot

Window 8

Location	20,931,357 – 20,931,470
Length	113
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	78.38
Mean single sequence MFE	-26.83
Consensus MFE	-12.72
Energy contribution	-14.28
Covariance contribution	1.56
Combinations/Pair	1.34
Mean z-score	-2.17
Structure conservation index	0.47
SVM decision value	0.31
SVM RNA-class probability	0.682380
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 20931357 113 - 27905053
UAGUAUU---AAAGGGUUAG----AAACUAGAAGCAUCAAAGGAUUGGGAUAUCUUCCAGUGACUAUGAAUGCGUUGGAUAAUUGCCCUCAUAAGGACAAAACCCUAUGCCUAAAUAUUC
..((((.---..((((((..----...((((..((((((.((.(((((((....)))))))..)).)).)))).))))....(((.(((....))).))))))))))))).......... ( -26.10)
>DroSec_CAF1 14859 113 - 1
UAGUAUU---AAAGGCUUAG----AAACUAGAAGCAUCAAAGGAUUGGGAUAUCUUCCAGUUACUAUGAAUGCGCUGGAUAAUUGCCCUCAUAAGGACAAAACCCUAUGCCUAAAUAUUC
.((((((---..((((.(((----...((((..((((((.((((((((((....)))))))).)).)).)))).))))....(((.(((....))).)))....))).)))).)))))). ( -29.00)
>DroSim_CAF1 23222 113 - 1
UAGGAAU---AAAGGCUUAG----AAACUAGAAGCAUCAAGGGAUUGGGAUAUCUUCCAGUGACUAUGAAUGCGCUGGAUAAUUGCCCUCAUAAGGACAAAACCCUAUGCCUAAAUAUUC
...((((---(.((((.(((----...((((..((((((((..(((((((....)))))))..)).)).)))).))))....(((.(((....))).)))....))).))))...))))) ( -29.70)
>DroEre_CAF1 23220 113 - 1
AAGUAUG---AAAGGCUUGG----CUAGUAGAAGCAUCAAAGGAUUGGGAUAUUUACCAGUUUCUAUGAAUGCGCUGGAUAAUUGUCCUCAUAAGGACAAAACCCUAUGCCUAAAUAUUC
.(((((.---..((((..((----(((((....((((((.((((((((........)))).)))).)).)))))))))....(((((((....)))))))...))...))))..))))). ( -33.00)
>DroYak_CAF1 21558 113 - 1
AAGUAUU---AAAGGCCAAG----AAACUAAAAGCAUCAAAGGAUUGGGAUAUUUUCCAGUUUCUAUGAAUGCGCUGGAUAAUUGUCCACAUAAGGACAAAACCCUAUGCCUAAAUAUUC
.((((((---..((((..((----...(((...((((((.((((((((((....)))))).)))).)).))))..)))....((((((......))))))....))..)))).)))))). ( -29.10)
>DroPer_CAF1 63950 120 - 1
AGGAGUCAGAAAAAUCCAAAGUUUCAAUUAAAAGCAUAGAAAACCUUAGAGACUAUACAGCUUCGAUAACUAAGUUGAAGAAAUUUCCAAAUAAUGAGAAACCCUUGUACUUUAAAAUGC
.(((..........)))..((((((.......................)))))).((((((((((((......)))))))...((((((.....)).))))...)))))........... ( -14.10)
>consensus
AAGUAUU___AAAGGCUUAG____AAACUAGAAGCAUCAAAGGAUUGGGAUAUCUUCCAGUUACUAUGAAUGCGCUGGAUAAUUGCCCUCAUAAGGACAAAACCCUAUGCCUAAAUAUUC
............((((.(((.......((((..((((((.((((((((((....)))))))).)).))).))).))))....(((.((......)).)))....))).))))........ (-12.72 = -14.28 +   1.56)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:55:20 2006