Locus 151

Sequence ID	4_DroMel_CAF1
Location	994,019 – 994,215
Length	196
Max. P	0.998841

overview

Window 0

Location	994,019 – 994,139
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	98.00
Mean single sequence MFE	-29.74
Consensus MFE	-27.32
Energy contribution	-27.36
Covariance contribution	0.04
Combinations/Pair	1.03
Mean z-score	-2.50
Structure conservation index	0.92
SVM decision value	3.25
SVM RNA-class probability	0.998841
Prediction	RNA

Download alignment: ClustalW | MAF

>4_DroMel_CAF1 994019 120 + 1281640
AUUCCUUAACUUCUGGAGAAUCCGAGGGUUGAACGAAUUACAAACCAGUGAGGUAAAUAAUGACAAAAUUAUGUUAGUAUUUAGAAAAACGGCAGAUUGUUAACAAUCUGGCAGAUGUAC
((((.((((((..(((.....)))..))))))..))))((((.....((....((((((.(((((......))))).)))))).....))(.(((((((....))))))).)...)))). ( -29.00)
>DroSec_CAF1 33082 120 + 1
AUUCGUUAACUUCUGGAGAAUCCGAGGGUUGAACGAAUUACAAACCAGUGAGGUAAAUAAUGACAAAAUUAUGUUAGUAUUUAGAAAAACGGCAGAUUGUUAACAAUCUGGCAGAUGUAC
(((((((((((..(((.....)))..))))).))))))((((.....((....((((((.(((((......))))).)))))).....))(.(((((((....))))))).)...)))). ( -32.80)
>DroSim_CAF1 27792 120 + 1
GUUCGUUAACUUCUGGAGAAUCCGAGGGUUGAACGAAUUACAAACCAGUGAGGUAAAUAAUGACAAAAUUAUGUUAGUAUUUAGAAAAACGGCAGAUUGUUAACAAUCUGGCAGAUGUAC
(((((((((((..(((.....)))..))))).))))))((((.....((....((((((.(((((......))))).)))))).....))(.(((((((....))))))).)...)))). ( -33.10)
>DroEre_CAF1 31520 120 + 1
AUUCCUUAACUUCUGGGGAAUCCGAGGGUUGAACGAAUUACAAACCAGUGAGGUAAAUAAUGACAAAAUUAUGUUAGUAUUUAGAAAAACGGCAGAUUGCUAACAAUCUGGCAGAUGUAC
((((.((((((..(((.....)))..))))))..))))((((.....((....((((((.(((((......))))).)))))).....))(.(((((((....))))))).)...)))). ( -27.30)
>DroYak_CAF1 29852 120 + 1
AUUCCUAAACUUCUGGGGAAUCCGAGGGUUGAACGAAUUACAAACCAGUGAGGUAAAUAAUGACAAAAUUAUGUUAGUAUUUAGAAAAACGGCAGAUUGUUAACAAUCUGGCAGAUGUAC
((((...((((..(((.....)))..))))....))))((((.....((....((((((.(((((......))))).)))))).....))(.(((((((....))))))).)...)))). ( -26.50)
>consensus
AUUCCUUAACUUCUGGAGAAUCCGAGGGUUGAACGAAUUACAAACCAGUGAGGUAAAUAAUGACAAAAUUAUGUUAGUAUUUAGAAAAACGGCAGAUUGUUAACAAUCUGGCAGAUGUAC
((((.((((((..(((.....)))..))))))..))))((((.....((....((((((.(((((......))))).)))))).....))(.(((((((....))))))).)...)))). (-27.32 = -27.36 +   0.04)

alignment

secondary structure

dotplot

Window 1

Location	994,019 – 994,139
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	98.00
Mean single sequence MFE	-21.38
Consensus MFE	-19.76
Energy contribution	-19.76
Covariance contribution	-0.00
Combinations/Pair	1.00
Mean z-score	-1.25
Structure conservation index	0.92
SVM decision value	0.13
SVM RNA-class probability	0.598885
Prediction	RNA

Download alignment: ClustalW | MAF

>4_DroMel_CAF1 994019 120 - 1281640
GUACAUCUGCCAGAUUGUUAACAAUCUGCCGUUUUUCUAAAUACUAACAUAAUUUUGUCAUUAUUUACCUCACUGGUUUGUAAUUCGUUCAACCCUCGGAUUCUCCAGAAGUUAAGGAAU
..........(((((((....)))))))((.......((((((.(.(((......))).).)))))).....((((...(.((((((.........))))))).)))).......))... ( -20.50)
>DroSec_CAF1 33082 120 - 1
GUACAUCUGCCAGAUUGUUAACAAUCUGCCGUUUUUCUAAAUACUAACAUAAUUUUGUCAUUAUUUACCUCACUGGUUUGUAAUUCGUUCAACCCUCGGAUUCUCCAGAAGUUAACGAAU
.((((...(((((((((....))))))..........((((((.(.(((......))).).)))))).......))).))))(((((((.(((..((((.....)).)).)))))))))) ( -22.50)
>DroSim_CAF1 27792 120 - 1
GUACAUCUGCCAGAUUGUUAACAAUCUGCCGUUUUUCUAAAUACUAACAUAAUUUUGUCAUUAUUUACCUCACUGGUUUGUAAUUCGUUCAACCCUCGGAUUCUCCAGAAGUUAACGAAC
.((((...(((((((((....))))))..........((((((.(.(((......))).).)))))).......))).)))).((((((.(((..((((.....)).)).))))))))). ( -21.90)
>DroEre_CAF1 31520 120 - 1
GUACAUCUGCCAGAUUGUUAGCAAUCUGCCGUUUUUCUAAAUACUAACAUAAUUUUGUCAUUAUUUACCUCACUGGUUUGUAAUUCGUUCAACCCUCGGAUUCCCCAGAAGUUAAGGAAU
..((.((((.(((((((....)))))))(((...............(((......))).(((((..(((.....)))..)))))............)))......)))).))........ ( -20.00)
>DroYak_CAF1 29852 120 - 1
GUACAUCUGCCAGAUUGUUAACAAUCUGCCGUUUUUCUAAAUACUAACAUAAUUUUGUCAUUAUUUACCUCACUGGUUUGUAAUUCGUUCAACCCUCGGAUUCCCCAGAAGUUUAGGAAU
........(.(((((((....))))))).)...(((((((((....(((......)))..............((((...(.((((((.........))))))).))))..))))))))). ( -22.00)
>consensus
GUACAUCUGCCAGAUUGUUAACAAUCUGCCGUUUUUCUAAAUACUAACAUAAUUUUGUCAUUAUUUACCUCACUGGUUUGUAAUUCGUUCAACCCUCGGAUUCUCCAGAAGUUAAGGAAU
..((.((((.(((((((....)))))))(((...............(((......))).(((((..(((.....)))..)))))............)))......)))).))........ (-19.76 = -19.76 +  -0.00)

alignment

secondary structure

dotplot

Window 2

Location	994,059 – 994,179
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	97.83
Mean single sequence MFE	-26.82
Consensus MFE	-26.66
Energy contribution	-26.46
Covariance contribution	-0.20
Combinations/Pair	1.06
Mean z-score	-2.01
Structure conservation index	0.99
SVM decision value	3.14
SVM RNA-class probability	0.998558
Prediction	RNA

Download alignment: ClustalW | MAF

>4_DroMel_CAF1 994059 120 + 1281640
CAAACCAGUGAGGUAAAUAAUGACAAAAUUAUGUUAGUAUUUAGAAAAACGGCAGAUUGUUAACAAUCUGGCAGAUGUACUCAAACUUUCGAUACAAAUCGAAUAAGCAGGGACGAGUGC
....((..((((.((((((.(((((......))))).)))))).......(.(((((((....))))))).).......))))....((((((....))))))......))......... ( -28.00)
>DroSec_CAF1 33122 120 + 1
CAAACCAGUGAGGUAAAUAAUGACAAAAUUAUGUUAGUAUUUAGAAAAACGGCAGAUUGUUAACAAUCUGGCAGAUGUACUCAAACUUUCGAUCAAAAUCGAAUAAGCAGGGACGAGUGC
....((..((((.((((((.(((((......))))).)))))).......(.(((((((....))))))).).......))))....((((((....))))))......))......... ( -27.70)
>DroSim_CAF1 27832 120 + 1
CAAACCAGUGAGGUAAAUAAUGACAAAAUUAUGUUAGUAUUUAGAAAAACGGCAGAUUGUUAACAAUCUGGCAGAUGUACUCAAACUUUCGAUCAAAAUCGAAUAAGCAGGGACGAGUGC
....((..((((.((((((.(((((......))))).)))))).......(.(((((((....))))))).).......))))....((((((....))))))......))......... ( -27.70)
>DroEre_CAF1 31560 120 + 1
CAAACCAGUGAGGUAAAUAAUGACAAAAUUAUGUUAGUAUUUAGAAAAACGGCAGAUUGCUAACAAUCUGGCAGAUGUACUCAAACUUCCGAUCAAAAUCGAGUAAGCAGGGACGAGUGC
....((..((((.((((((.(((((......))))).)))))).......(.(((((((....))))))).).......))))..((((((((....)))).).)))..))......... ( -25.30)
>DroYak_CAF1 29892 120 + 1
CAAACCAGUGAGGUAAAUAAUGACAAAAUUAUGUUAGUAUUUAGAAAAACGGCAGAUUGUUAACAAUCUGGCAGAUGUACUCAAACUUUUGAUCAAAAUCGAGUAAGCAGGGACGAGUGC
...(((.....)))(((((.(((((......))))).)))))........(.(((((((....))))))).)....((((((......(((((....)))))((........)))))))) ( -25.40)
>consensus
CAAACCAGUGAGGUAAAUAAUGACAAAAUUAUGUUAGUAUUUAGAAAAACGGCAGAUUGUUAACAAUCUGGCAGAUGUACUCAAACUUUCGAUCAAAAUCGAAUAAGCAGGGACGAGUGC
....((..((((.((((((.(((((......))))).)))))).......(.(((((((....))))))).).......))))....((((((....))))))......))......... (-26.66 = -26.46 +  -0.20)

alignment

secondary structure

dotplot

Window 3

Location	994,099 – 994,215
Length	116
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	94.28
Mean single sequence MFE	-31.12
Consensus MFE	-31.12
Energy contribution	-30.76
Covariance contribution	-0.36
Combinations/Pair	1.08
Mean z-score	-1.23
Structure conservation index	1.00
SVM decision value	1.07
SVM RNA-class probability	0.909695
Prediction	RNA

Download alignment: ClustalW | MAF

>4_DroMel_CAF1 994099 116 + 1281640
UUAGAAAAACGGCAGAUUGUUAACAAUCUGGCAGAUGUACUCAAACUUUCGAUACAAAUCGAAUAAGCAGGGACGAGUGCCUGAGGUUUAACGCACU----GCGGGGUUGUUUGUGAGAG
..........(.(((((((....))))))).).......((((....((((((....))))))(((((((...(((((((.(........).)))))----.))...))))))))))).. ( -31.60)
>DroSec_CAF1 33162 116 + 1
UUAGAAAAACGGCAGAUUGUUAACAAUCUGGCAGAUGUACUCAAACUUUCGAUCAAAAUCGAAUAAGCAGGGACGAGUGCCUGAGGUUUAACGCACU----GCGGGGUUGUUUGUAAGAG
................(((..((((((((.((((.(((....(((((((((((....))))).....((((.(....).))))))))))...)))))----)).))))))))..)))... ( -31.00)
>DroSim_CAF1 27872 116 + 1
UUAGAAAAACGGCAGAUUGUUAACAAUCUGGCAGAUGUACUCAAACUUUCGAUCAAAAUCGAAUAAGCAGGGACGAGUGCCUGAGGUUUAACGCACU----GCGGGGUUGUUUGUAAGAG
................(((..((((((((.((((.(((....(((((((((((....))))).....((((.(....).))))))))))...)))))----)).))))))))..)))... ( -31.00)
>DroEre_CAF1 31600 120 + 1
UUAGAAAAACGGCAGAUUGCUAACAAUCUGGCAGAUGUACUCAAACUUCCGAUCAAAAUCGAGUAAGCAGGGACGAGUGCCUGAGGUUUAACGCAUUAAAGGCGGGGUUGUUUGCAAGAG
............(((((((....)))))))(((((((.(((((((((((((((....)))).......(((.(....).))))))))))..(((.......))))))))))))))..... ( -31.90)
>DroYak_CAF1 29932 120 + 1
UUAGAAAAACGGCAGAUUGUUAACAAUCUGGCAGAUGUACUCAAACUUUUGAUCAAAAUCGAGUAAGCAGGGACGAGUGCCUGAGGUUUAACGCAUCAAAGGCGGGGUUGUUUGUAAGAG
............(((((((....)))))))(((((((.((((...(((((((((.(((((.......((((.(....).)))).)))))...).))))))))..)))))))))))..... ( -30.10)
>consensus
UUAGAAAAACGGCAGAUUGUUAACAAUCUGGCAGAUGUACUCAAACUUUCGAUCAAAAUCGAAUAAGCAGGGACGAGUGCCUGAGGUUUAACGCACU____GCGGGGUUGUUUGUAAGAG
............(((((((....)))))))(((((((.(((((((((((((((....))))))....((((.(....).)))).)))))..(((.......))))))))))))))..... (-31.12 = -30.76 +  -0.36)

alignment

secondary structure

dotplot

Window 4

Location	994,099 – 994,215
Length	116
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	94.28
Mean single sequence MFE	-25.20
Consensus MFE	-21.96
Energy contribution	-22.00
Covariance contribution	0.04
Combinations/Pair	1.03
Mean z-score	-1.49
Structure conservation index	0.87
SVM decision value	0.92
SVM RNA-class probability	0.882171
Prediction	RNA

Download alignment: ClustalW | MAF

>4_DroMel_CAF1 994099 116 - 1281640
CUCUCACAAACAACCCCGC----AGUGCGUUAAACCUCAGGCACUCGUCCCUGCUUAUUCGAUUUGUAUCGAAAGUUUGAGUACAUCUGCCAGAUUGUUAACAAUCUGCCGUUUUUCUAA
.......((((......((----(((((.((((((...(((((........))))).((((((....)))))).))))))))))...)))(((((((....)))))))..))))...... ( -26.90)
>DroSec_CAF1 33162 116 - 1
CUCUUACAAACAACCCCGC----AGUGCGUUAAACCUCAGGCACUCGUCCCUGCUUAUUCGAUUUUGAUCGAAAGUUUGAGUACAUCUGCCAGAUUGUUAACAAUCUGCCGUUUUUCUAA
.......((((......((----(((((.((((((...(((((........))))).((((((....)))))).))))))))))...)))(((((((....)))))))..))))...... ( -26.60)
>DroSim_CAF1 27872 116 - 1
CUCUUACAAACAACCCCGC----AGUGCGUUAAACCUCAGGCACUCGUCCCUGCUUAUUCGAUUUUGAUCGAAAGUUUGAGUACAUCUGCCAGAUUGUUAACAAUCUGCCGUUUUUCUAA
.......((((......((----(((((.((((((...(((((........))))).((((((....)))))).))))))))))...)))(((((((....)))))))..))))...... ( -26.60)
>DroEre_CAF1 31600 120 - 1
CUCUUGCAAACAACCCCGCCUUUAAUGCGUUAAACCUCAGGCACUCGUCCCUGCUUACUCGAUUUUGAUCGGAAGUUUGAGUACAUCUGCCAGAUUGUUAGCAAUCUGCCGUUUUUCUAA
.......((((.....(((.......)))..........((((((((.....((((.(.((((....))))))))).))))).........((((((....)))))))))))))...... ( -23.30)
>DroYak_CAF1 29932 120 - 1
CUCUUACAAACAACCCCGCCUUUGAUGCGUUAAACCUCAGGCACUCGUCCCUGCUUACUCGAUUUUGAUCAAAAGUUUGAGUACAUCUGCCAGAUUGUUAACAAUCUGCCGUUUUUCUAA
.......((((......((....((((..........((((........))))..(((((((((((.....)))).))))))))))).))(((((((....)))))))..))))...... ( -22.60)
>consensus
CUCUUACAAACAACCCCGC____AGUGCGUUAAACCUCAGGCACUCGUCCCUGCUUAUUCGAUUUUGAUCGAAAGUUUGAGUACAUCUGCCAGAUUGUUAACAAUCUGCCGUUUUUCUAA
.......((((.....(((.......)))..........((((((((.....((((..(((((....))))))))).))))).........((((((....)))))))))))))...... (-21.96 = -22.00 +   0.04)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:37:20 2006