Locus 3572

Sequence ID	3R_DroMel_CAF1
Location	9,670,823 – 9,671,004
Length	181
Max. P	0.999954

overview

Window 0

Location	9,670,823 – 9,670,942
Length	119
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	96.24
Mean single sequence MFE	-38.16
Consensus MFE	-31.50
Energy contribution	-31.58
Covariance contribution	0.08
Combinations/Pair	1.06
Mean z-score	-1.90
Structure conservation index	0.83
SVM decision value	0.98
SVM RNA-class probability	0.894205
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 9670823 119 - 27905053
AACGGCCACACAAUCGCCAUAAGUUUUGGCCGCUCUGCAAUUAUUUGCGGAAUUCCUUUUGGAAUAUAUAUUGACUCGGACUGGAGUGCUCGGC-CAGACUGGUCAACUCAACCAGGAGA
...((((........((((.......)))).(((((((((....)))))))(((((....)))))........((((......))))))..)))-)...(((((.......))))).... ( -37.70)
>DroSec_CAF1 62623 119 - 1
AACGGCCACACAAUCGCCAUAAGUUUUGGCCGCUCUGCAAUUAUUUGCGGAAUUCCUUUUGGAAUAUAUAUUGACUCGGACUGGAGUGCCCGGC-CAGACUGGCCAACUCAACCAGGAGA
...(((((.......((.....))((((((((.(((((((....)))))))(((((....)))))........((((......))))...))))-)))).)))))..(((......))). ( -38.10)
>DroSim_CAF1 65534 119 - 1
AACGGCCACACAAUCGCCAUAAGUUUUGGCCGCUCUGCAAUUAUUUGCGGAAUUCCUUUUGGAAUAUAUAUUGACUCGGACUGAAGUGCCCGGC-CAGACUGGCCAACUCAACCAGGAGA
...(((((.......((.....))((((((((.(((((((....)))))))(((((....)))))............((((....)).))))))-)))).)))))..(((......))). ( -35.90)
>DroEre_CAF1 63815 120 - 1
AGCGGGCACACAAUCGCCAUAAGUUUUGGCCGCUCUGCAAUUAUUUGCGGAAUUCCUUUCGGAAUAUAUAUUGACUCGCACUGGAGUGCCAGGCCCAGACUGGCCAACUCAACCAGGAGA
.(((((((.......((((.......))))...(((((((....)))))))(((((....)))))......)).))))).((((((((((((.......)))))..)))...)))).... ( -39.50)
>DroYak_CAF1 67519 120 - 1
AGCGGCCACACAAUCGCCAUAAGUUUUGGCCGCUCUGCAAUUAUUUGCGGAAUUCCUUUCGGAAUAUAUAUUGACUCGGACUGGAGUGCCUGGCCCAGACUGGCCAACUCAACCAGGAGA
.(((((((.((...........))..)))))))(((((((....)))))))(((((....))))).........(((((....((((...(((((......)))))))))..))..))). ( -39.60)
>consensus
AACGGCCACACAAUCGCCAUAAGUUUUGGCCGCUCUGCAAUUAUUUGCGGAAUUCCUUUUGGAAUAUAUAUUGACUCGGACUGGAGUGCCCGGC_CAGACUGGCCAACUCAACCAGGAGA
...(((((.......(((....((((..((((.(((((((....)))))))(((((....)))))...........))).)..))))....)))......)))))..(((......))). (-31.50 = -31.58 +   0.08)

alignment

secondary structure

dotplot

Window 1

Location	9,670,862 – 9,670,982
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	89.72
Mean single sequence MFE	-35.54
Consensus MFE	-33.04
Energy contribution	-32.84
Covariance contribution	-0.20
Combinations/Pair	1.07
Mean z-score	-3.05
Structure conservation index	0.93
SVM decision value	4.83
SVM RNA-class probability	0.999954
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 9670862 120 + 27905053
UCCGAGUCAAUAUAUAUUCCAAAAGGAAUUCCGCAAAUAAUUGCAGAGCGGCCAAAACUUAUGGCGAUUGUGUGGCCGUUCGGCCAGGCGAUGCUCACUGAAAAAAAAAAUGUUUACACA
.....((.(((((...((((....))))(((.((((....)))).((((.((((.......)))).(((((.(((((....))))).)))))))))...))).......))))).))... ( -36.40)
>DroSec_CAF1 62662 120 + 1
UCCGAGUCAAUAUAUAUUCCAAAAGGAAUUCCGCAAAUAAUUGCAGAGCGGCCAAAACUUAUGGCGAUUGUGUGGCCGUUCGGCCAGGCAAAGCUCACUGAAAAAAAAAAGUUUUACAAA
......(((......(((((....)))))...((((....)))).((((.((((.......))))..((((.(((((....))))).)))).))))..)))................... ( -33.90)
>DroSim_CAF1 65573 117 + 1
UCCGAGUCAAUAUAUAUUCCAAAAGGAAUUCCGCAAAUAAUUGCAGAGCGGCCAAAACUUAUGGCGAUUGUGUGGCCGUUCGGCCAGGCAAAGCUCAGUGAAA---AAAAGUUUAACAAA
......(((......(((((....)))))...((((....)))).((((.((((.......))))..((((.(((((....))))).)))).))))..)))..---.............. ( -34.00)
>DroEre_CAF1 63855 113 + 1
UGCGAGUCAAUAUAUAUUCCGAAAGGAAUUCCGCAAAUAAUUGCAGAGCGGCCAAAACUUAUGGCGAUUGUGUGCCCGCUCGGCCAGGCGAGGCUCACUGAAAGAAAAC-GUA------A
((((((((.......(((((....)))))((.((((....)))).))...((((.......))))))))(((.(((((((......)))).))).)))..........)-)))------. ( -35.50)
>DroYak_CAF1 67559 116 + 1
UCCGAGUCAAUAUAUAUUCCGAAAGGAAUUCCGCAAAUAAUUGCAGAGCGGCCAAAACUUAUGGCGAUUGUGUGGCCGCUCGGCUAAGCGAGGCUCACUGAAAGAAAAU-GUU-UA--AA
...(((((.......(((((....))))).((((((....)))).(((((((((..((...........)).)))))))))))........))))).............-...-..--.. ( -37.90)
>consensus
UCCGAGUCAAUAUAUAUUCCAAAAGGAAUUCCGCAAAUAAUUGCAGAGCGGCCAAAACUUAUGGCGAUUGUGUGGCCGUUCGGCCAGGCGAAGCUCACUGAAAAAAAAAAGUUUUACAAA
......(((......(((((....)))))...((((....)))).((((.((((.......))))..((((.(((((....))))).)))).))))..)))................... (-33.04 = -32.84 +  -0.20)

alignment

secondary structure

dotplot

Window 2

Location	9,670,862 – 9,670,982
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	89.72
Mean single sequence MFE	-33.06
Consensus MFE	-27.96
Energy contribution	-28.56
Covariance contribution	0.60
Combinations/Pair	1.00
Mean z-score	-2.22
Structure conservation index	0.85
SVM decision value	2.24
SVM RNA-class probability	0.990858
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 9670862 120 - 27905053
UGUGUAAACAUUUUUUUUUUCAGUGAGCAUCGCCUGGCCGAACGGCCACACAAUCGCCAUAAGUUUUGGCCGCUCUGCAAUUAUUUGCGGAAUUCCUUUUGGAAUAUAUAUUGACUCGGA
(((....))).........((((((.((...(..(((((....)))))..)....((((.......)))).))(((((((....)))))))(((((....)))))...))))))...... ( -32.50)
>DroSec_CAF1 62662 120 - 1
UUUGUAAAACUUUUUUUUUUCAGUGAGCUUUGCCUGGCCGAACGGCCACACAAUCGCCAUAAGUUUUGGCCGCUCUGCAAUUAUUUGCGGAAUUCCUUUUGGAAUAUAUAUUGACUCGGA
...................((((((.((.(((..(((((....)))))..)))..((((.......)))).))(((((((....)))))))(((((....)))))...))))))...... ( -33.10)
>DroSim_CAF1 65573 117 - 1
UUUGUUAAACUUUU---UUUCACUGAGCUUUGCCUGGCCGAACGGCCACACAAUCGCCAUAAGUUUUGGCCGCUCUGCAAUUAUUUGCGGAAUUCCUUUUGGAAUAUAUAUUGACUCGGA
..............---.....(((((..(((..(((((....)))))..)))((((((.......))))...(((((((....)))))))(((((....))))).......))))))). ( -33.40)
>DroEre_CAF1 63855 113 - 1
U------UAC-GUUUUCUUUCAGUGAGCCUCGCCUGGCCGAGCGGGCACACAAUCGCCAUAAGUUUUGGCCGCUCUGCAAUUAUUUGCGGAAUUCCUUUCGGAAUAUAUAUUGACUCGCA
.------...-...........(((((....((..((((((((.(((........)))....).)))))))))(((((((....)))))))(((((....))))).........))))). ( -34.00)
>DroYak_CAF1 67559 116 - 1
UU--UA-AAC-AUUUUCUUUCAGUGAGCCUCGCUUAGCCGAGCGGCCACACAAUCGCCAUAAGUUUUGGCCGCUCUGCAAUUAUUUGCGGAAUUCCUUUCGGAAUAUAUAUUGACUCGGA
..--..-...-............(((((...))))).(((((((((((.((...........))..)))))))(((((((....)))))))(((((....)))))..........)))). ( -32.30)
>consensus
UUUGUAAAACUUUUUUCUUUCAGUGAGCCUCGCCUGGCCGAACGGCCACACAAUCGCCAUAAGUUUUGGCCGCUCUGCAAUUAUUUGCGGAAUUCCUUUUGGAAUAUAUAUUGACUCGGA
...................((((((.((...(..(((((....)))))..)....((((.......)))).))(((((((....)))))))(((((....)))))...))))))...... (-27.96 = -28.56 +   0.60)

alignment

secondary structure

dotplot

Window 3

Location	9,670,902 – 9,671,004
Length	102
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	76.39
Mean single sequence MFE	-30.37
Consensus MFE	-26.04
Energy contribution	-25.60
Covariance contribution	-0.44
Combinations/Pair	1.12
Mean z-score	-2.04
Structure conservation index	0.86
SVM decision value	2.23
SVM RNA-class probability	0.990772
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 9670902 102 + 27905053
UUGCAGAGCGGCCAAAACUUAUGGCGAUUGUGUGGCCGUUCGGCCAGGCGAUGCUCACUGAAAAAAAAAAUGUUUACACAUA-AUUUAAUACUAAAGGUAUAU-----------------
.....((((.((((.......)))).(((((.(((((....))))).))))))))).............((((....)))).-.....((((.....))))..----------------- ( -29.30)
>DroSec_CAF1 62702 120 + 1
UUGCAGAGCGGCCAAAACUUAUGGCGAUUGUGUGGCCGUUCGGCCAGGCAAAGCUCACUGAAAAAAAAAAGUUUUACAAAAAGAAUUAAUACUUAAGGUAGUUUGAAGCGGAAUGUGUAA
.((((((((.((((.......))))..((((.(((((....))))).)))).)))).(((....(((..((((((......))))))..(((.....))).)))....)))....)))). ( -31.70)
>DroSim_CAF1 65613 117 + 1
UUGCAGAGCGGCCAAAACUUAUGGCGAUUGUGUGGCCGUUCGGCCAGGCAAAGCUCAGUGAAA---AAAAGUUUAACAAAAAGAAUUAAUACUUAAGGUAGUUUGAAGCGGAAUGUGUAA
((((.((((.((((.......))))..((((.(((((....))))).)))).)))).......---................((((((...(....).))))))...))))......... ( -30.80)
>DroYak_CAF1 67599 116 + 1
UUGCAGAGCGGCCAAAACUUAUGGCGAUUGUGUGGCCGCUCGGCUAAGCGAGGCUCACUGAAAGAAAAU-GUU-UA--AACACAGUAAAUGCCUAAUGAAAUACGAUGAGAAAUGCGACG
((((((((((((((..((...........)).))))))))).........((((..((((.........-...-..--....))))....))))...................))))).. ( -29.67)
>consensus
UUGCAGAGCGGCCAAAACUUAUGGCGAUUGUGUGGCCGUUCGGCCAGGCAAAGCUCACUGAAAAAAAAAAGUUUUACAAAAAGAAUUAAUACUUAAGGUAGUUUGAAGCGGAAUGUGUAA
.....((((.((((.......))))..((((.(((((....))))).)))).))))................................................................ (-26.04 = -25.60 +  -0.44)

alignment

secondary structure

dotplot

Window 4

Location	9,670,902 – 9,671,004
Length	102
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	76.39
Mean single sequence MFE	-25.58
Consensus MFE	-18.27
Energy contribution	-18.53
Covariance contribution	0.25
Combinations/Pair	1.00
Mean z-score	-1.92
Structure conservation index	0.71
SVM decision value	1.37
SVM RNA-class probability	0.947176
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 9670902 102 - 27905053
-----------------AUAUACCUUUAGUAUUAAAU-UAUGUGUAAACAUUUUUUUUUUCAGUGAGCAUCGCCUGGCCGAACGGCCACACAAUCGCCAUAAGUUUUGGCCGCUCUGCAA
-----------------...........(....(((.-.((((....))))..)))....).((((((...(..(((((....)))))..)....((((.......)))).)))).)).. ( -23.80)
>DroSec_CAF1 62702 120 - 1
UUACACAUUCCGCUUCAAACUACCUUAAGUAUUAAUUCUUUUUGUAAAACUUUUUUUUUUCAGUGAGCUUUGCCUGGCCGAACGGCCACACAAUCGCCAUAAGUUUUGGCCGCUCUGCAA
...........((.......(((...(((........)))...)))..................((((.(((..(((((....)))))..)))..((((.......)))).)))).)).. ( -24.10)
>DroSim_CAF1 65613 117 - 1
UUACACAUUCCGCUUCAAACUACCUUAAGUAUUAAUUCUUUUUGUUAAACUUUU---UUUCACUGAGCUUUGCCUGGCCGAACGGCCACACAAUCGCCAUAAGUUUUGGCCGCUCUGCAA
...........((.............((((.(((((.......)))))))))..---.......((((.(((..(((((....)))))..)))..((((.......)))).)))).)).. ( -24.80)
>DroYak_CAF1 67599 116 - 1
CGUCGCAUUUCUCAUCGUAUUUCAUUAGGCAUUUACUGUGUU--UA-AAC-AUUUUCUUUCAGUGAGCCUCGCUUAGCCGAGCGGCCACACAAUCGCCAUAAGUUUUGGCCGCUCUGCAA
....((....(((((.(.....).((((((((.....)))))--))-)..-...........)))))....))...((.(((((((((.((...........))..))))))))).)).. ( -29.60)
>consensus
UUACACAUUCCGCUUCAAACUACCUUAAGUAUUAAUUCUUUUUGUAAAACUUUUUUUUUUCAGUGAGCUUCGCCUGGCCGAACGGCCACACAAUCGCCAUAAGUUUUGGCCGCUCUGCAA
................................................................((((...(..(((((....)))))..)....((((.......)))).))))..... (-18.27 = -18.53 +   0.25)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:04:36 2006