Locus 1111

Sequence ID	2R_DroMel_CAF1
Location	4,442,220 – 4,442,319
Length	99
Max. P	0.988555

overview

Window 2

Location	4,442,220 – 4,442,319
Length	99
Sequences	6
Columns	118
Reading direction	forward
Mean pairwise identity	73.23
Mean single sequence MFE	-19.62
Consensus MFE	-13.26
Energy contribution	-13.07
Covariance contribution	-0.19
Combinations/Pair	1.11
Mean z-score	-1.63
Structure conservation index	0.68
SVM decision value	1.44
SVM RNA-class probability	0.954311
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 4442220 99 + 20766785
GAUAUUUAAU---UU----------------AUGCACACUCUCAGAACUGGAACCGAUUCAUUUUGCAUCAAAUGCAUUACGAAAUAUUCGAUUCUAGCAAGAACGCAUCCACCUACA
..........---..----------------((((....(((.....((((((.((((((.(..(((((...)))))..).)))....))).))))))..)))..))))......... ( -14.30)
>DroPse_CAF1 5421 114 + 1
--AUUAUCAUAAACUUUGGAGACAAACAUCUCUGCA--UCUACAGAACUGGAACCGAUUUAUACUGCAUCAAAUGCAUUACGAAAUCUUCGAUUCCAGCAAGAACUCAUCUGUGGGAG
--...............(((((......)))))...--((((((((.((((((.(((((..((.(((((...))))).))..))....))).))))))...(....).)))))))).. ( -26.60)
>DroEre_CAF1 7570 99 + 1
GAUAUUUAAU---UU----------------AUGCACUCUCUUAGAACUGGAACCGAUUCAUUUUGCAUCAAAUGCAUUACGAAAUUUUCGAUUCCAGCAAGAACCCAUACACCUUCA
..........---.(----------------(((.....((((....((((((.((((((.(..(((((...)))))..).)))....))).)))))).))))...))))........ ( -15.90)
>DroYak_CAF1 7426 99 + 1
GAUGUUUAAU---UU----------------AUGCACACUCUCAGAACUGGAACCGAUUCAUUUUGCAUCAAAUGCAUUACGAAAUUUUCGAUUCCAGCAAGAACACAUCCACCUCCA
(((((....(---((----------------.(((...(.....)...(((((.((((((.(..(((((...)))))..).)))....))).)))))))).))).)))))........ ( -17.00)
>DroAna_CAF1 7320 108 + 1
--UUUUUCAU---UUUUGCUAAUACA-----AUGCACGCCAUUAGAACUGGAACCGAUUCAUUCUGCAUCAAAUGCAUUACGAAAUCUUCGACUCCAGCAAGAACUCGUCCGCUUCAA
--.......(---(((((((.....(-----(((((......(((((.((((.....))))))))).......)))))).(((.....))).....)))))))).............. ( -17.32)
>DroPer_CAF1 5470 114 + 1
--AUUAUCAUAAACUUUGGAGACAAACAUCUCUGCA--UCUACAGAACUGGAACCGAUUUAUACUGCAUCAAAUGCAUUACGAAAUCUUCGAUUCCAGCAAGAACUCAUCUGUGGGAG
--...............(((((......)))))...--((((((((.((((((.(((((..((.(((((...))))).))..))....))).))))))...(....).)))))))).. ( -26.60)
>consensus
__UUUUUAAU___UU________________AUGCAC_CCCUCAGAACUGGAACCGAUUCAUUCUGCAUCAAAUGCAUUACGAAAUCUUCGAUUCCAGCAAGAACUCAUCCACCUCAA
...............................................((((((.((((((.(..(((((...)))))..).)))....))).)))))).................... (-13.26 = -13.07 +  -0.19)

alignment

secondary structure

dotplot

Window 3

Location	4,442,220 – 4,442,319
Length	99
Sequences	6
Columns	118
Reading direction	reverse
Mean pairwise identity	73.23
Mean single sequence MFE	-28.22
Consensus MFE	-19.45
Energy contribution	-19.82
Covariance contribution	0.36
Combinations/Pair	1.05
Mean z-score	-2.08
Structure conservation index	0.69
SVM decision value	2.13
SVM RNA-class probability	0.988555
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 4442220 99 - 20766785
UGUAGGUGGAUGCGUUCUUGCUAGAAUCGAAUAUUUCGUAAUGCAUUUGAUGCAAAAUGAAUCGGUUCCAGUUCUGAGAGUGUGCAU----------------AA---AUUAAAUAUC
.....(((.((((.(((..(((.(((((((....(((((..(((((...)))))..)))))))))))).)))...))).)))).)))----------------..---.......... ( -24.70)
>DroPse_CAF1 5421 114 - 1
CUCCCACAGAUGAGUUCUUGCUGGAAUCGAAGAUUUCGUAAUGCAUUUGAUGCAGUAUAAAUCGGUUCCAGUUCUGUAGA--UGCAGAGAUGUUUGUCUCCAAAGUUUAUGAUAAU--
.....(((((.........(((((((((((....((..((.(((((...))))).))..))))))))))))))))))(((--(...(((((....)))))....))))........-- ( -27.80)
>DroEre_CAF1 7570 99 - 1
UGAAGGUGUAUGGGUUCUUGCUGGAAUCGAAAAUUUCGUAAUGCAUUUGAUGCAAAAUGAAUCGGUUCCAGUUCUAAGAGAGUGCAU----------------AA---AUUAAAUAUC
.....((((((...((((((((((((((((....(((((..(((((...)))))..))))))))))))))))...))))).))))))----------------..---.......... ( -31.10)
>DroYak_CAF1 7426 99 - 1
UGGAGGUGGAUGUGUUCUUGCUGGAAUCGAAAAUUUCGUAAUGCAUUUGAUGCAAAAUGAAUCGGUUCCAGUUCUGAGAGUGUGCAU----------------AA---AUUAAACAUC
.....(((.(..(.(((..(((((((((((....(((((..(((((...)))))..))))))))))))))))...))).)..).)))----------------..---.......... ( -29.10)
>DroAna_CAF1 7320 108 - 1
UUGAAGCGGACGAGUUCUUGCUGGAGUCGAAGAUUUCGUAAUGCAUUUGAUGCAGAAUGAAUCGGUUCCAGUUCUAAUGGCGUGCAU-----UGUAUUAGCAAAA---AUGAAAAA--
.......(.(((.(((...((((((..(((....(((((..(((((...)))))..))))))))..))))))...)))..))).).(-----(((....))))..---........-- ( -28.80)
>DroPer_CAF1 5470 114 - 1
CUCCCACAGAUGAGUUCUUGCUGGAAUCGAAGAUUUCGUAAUGCAUUUGAUGCAGUAUAAAUCGGUUCCAGUUCUGUAGA--UGCAGAGAUGUUUGUCUCCAAAGUUUAUGAUAAU--
.....(((((.........(((((((((((....((..((.(((((...))))).))..))))))))))))))))))(((--(...(((((....)))))....))))........-- ( -27.80)
>consensus
UGCAGGCGGAUGAGUUCUUGCUGGAAUCGAAGAUUUCGUAAUGCAUUUGAUGCAAAAUGAAUCGGUUCCAGUUCUGAGAG_GUGCAU________________AA___AUGAAAAA__
...................(((((((((((....(((((..(((((...)))))..)))))))))))))))).............................................. (-19.45 = -19.82 +   0.36)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:56:48 2006