Locus 1258

Sequence ID	2L_DroMel_CAF1
Location	3,322,380 – 3,322,522
Length	142
Max. P	0.989175

overview

Window 5

Location	3,322,380 – 3,322,500
Length	120
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	75.83
Mean single sequence MFE	-46.27
Consensus MFE	-30.68
Energy contribution	-31.88
Covariance contribution	1.20
Combinations/Pair	1.42
Mean z-score	-2.46
Structure conservation index	0.66
SVM decision value	2.15
SVM RNA-class probability	0.989175
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 3322380 120 + 22407834
AUCUUUGGCUGCUGGGCAACUGGGCAGAUCGGUAUCUGCCCAUUAUUCUGCUGGCCAUUCAGCUGGCUCUUGUCAGCUUUGGCCUUUAUCCCCUGGCCGCAGUCGUUAGCAGCGAAGUUC
...(((.((((((((.(...(((((((((....))))))))).....((((.(((((...(((((((....)))))))..((........)).)))))))))..))))))))).)))... ( -51.60)
>DroEre_CAF1 8250 120 + 1
ACCUUUGGCUGCUGGGCAACUGGGCGGAUCGCAAUUUGCCCAUUGUUCUGCUGGCCAUCCAGCUGGCUGUGGUCAGCUUUGGCCUUUAUCCCCUGGCCGCGGUUGUUAGCAGCGAGGUUU
(((((..((((((((.(((((((((((((....))))))))........((((((((..(((....)))))))))))...((((..........))))..)))))))))))))))))).. ( -55.00)
>DroWil_CAF1 118939 120 + 1
AAUCAUGGAUGUUGGGUUCGUGGUCGGAGCAAUAUCUUCCCAUUAUUUUACUGGCCGUGCAAUUGGCCUUUGUCAGCUUUGGGCUAUAUCCAUUGGCUGCUGUGGUAAGCAGCGAGCUUU
..((((((((((..(((((((((..(((......)))..)))).........(((((......)))))............)))))))))))))..((((((......))))))))..... ( -37.70)
>DroYak_CAF1 8573 120 + 1
AAUUUUGGUUGCUGGGCAACUGGGCUGAUCGGUAUUUGCCCAUUGUUUUGCUGGCCAUCCAGCUGGCUGUGGUCAGCUUUGGCCUUUAUCCCCUGGCCGCAGUUGUUAGCAGCGAGGUUC
...(((.((((((((.(((((((((((((.(((....))).)))........(((((...(((((((....))))))).)))))..........)))).)))))))))))))).)))... ( -49.00)
>DroMoj_CAF1 9397 120 + 1
AGAGCUGGUCUCUGGGCCCCUGGAGUGAGCGCACUGUUCCCAUCAUCCUGCUCGCCAUUCAGCUAUUCUUCGUCAGCUUUGGGCUCUAUCCCCUGGCCGCUGUCGUCAGCAGCGAAGUGC
..((((((..((..(....)..))(((((((...((.......))...)))))))...))))))...((((((..(((..(((......)))..))).((((....)))).))))))... ( -39.10)
>DroAna_CAF1 8475 120 + 1
AAAGUUGGCUGCUGGGUGAAUGGGCGGAUCGGUAUUUGCCCAUUAUCCUAUUGGCCAUCCAACUCGCCUUUGUUAGUUUCGGUCUAUAUCCACUGGCAGCUGUGGUGAGCAGCGAGGUUU
(((.((.((((((((((((((((((((((....)))))))))))..((....)).))))))..(((((.((((((((...((.......))))))))))....)))))))))).)).))) ( -45.20)
>consensus
AAAUUUGGCUGCUGGGCAACUGGGCGGAUCGGUAUUUGCCCAUUAUUCUGCUGGCCAUCCAGCUGGCCUUUGUCAGCUUUGGCCUUUAUCCCCUGGCCGCUGUCGUUAGCAGCGAGGUUC
.......((((((((((((.(((((((((....)))))))))))))))...((((((...(((((((....)))))))..((.......))..))))))........))))))....... (-30.68 = -31.88 +   1.20)

alignment

secondary structure

dotplot

Window 6

Location	3,322,380 – 3,322,500
Length	120
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	75.83
Mean single sequence MFE	-39.78
Consensus MFE	-21.29
Energy contribution	-21.77
Covariance contribution	0.48
Combinations/Pair	1.33
Mean z-score	-2.34
Structure conservation index	0.54
SVM decision value	1.64
SVM RNA-class probability	0.969501
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 3322380 120 - 22407834
GAACUUCGCUGCUAACGACUGCGGCCAGGGGAUAAAGGCCAAAGCUGACAAGAGCCAGCUGAAUGGCCAGCAGAAUAAUGGGCAGAUACCGAUCUGCCCAGUUGCCCAGCAGCCAAAGAU
...(((.((((((.....(((....)))((......(((((.(((((........)))))...))))).((((.....(((((((((....))))))))).))))))))))))..))).. ( -49.00)
>DroEre_CAF1 8250 120 - 1
AAACCUCGCUGCUAACAACCGCGGCCAGGGGAUAAAGGCCAAAGCUGACCACAGCCAGCUGGAUGGCCAGCAGAACAAUGGGCAAAUUGCGAUCCGCCCAGUUGCCCAGCAGCCAAAGGU
..((((.((((((.....((.(.....).)).....(((((.(((((........)))))...)))))...........((((((...(((...)))....))))))))))))...)))) ( -44.90)
>DroWil_CAF1 118939 120 - 1
AAAGCUCGCUGCUUACCACAGCAGCCAAUGGAUAUAGCCCAAAGCUGACAAAGGCCAAUUGCACGGCCAGUAAAAUAAUGGGAAGAUAUUGCUCCGACCACGAACCCAACAUCCAUGAUU
.......((((((......))))))..((((((.((((.....)))).....((((........))))..........((((..((......))((....))..))))..)))))).... ( -29.10)
>DroYak_CAF1 8573 120 - 1
GAACCUCGCUGCUAACAACUGCGGCCAGGGGAUAAAGGCCAAAGCUGACCACAGCCAGCUGGAUGGCCAGCAAAACAAUGGGCAAAUACCGAUCAGCCCAGUUGCCCAGCAACCAAAAUU
...(((.(((((........))))).)))((.....(((((.(((((........)))))...))))).((((.....(((((............))))).)))).......))...... ( -42.50)
>DroMoj_CAF1 9397 120 - 1
GCACUUCGCUGCUGACGACAGCGGCCAGGGGAUAGAGCCCAAAGCUGACGAAGAAUAGCUGAAUGGCGAGCAGGAUGAUGGGAACAGUGCGCUCACUCCAGGGGCCCAGAGACCAGCUCU
...(((((((((((....)))))))((((((......)))....)))..))))....(((....)))((((.((.(..((((..(((((....))))....)..))))..).)).)))). ( -40.30)
>DroAna_CAF1 8475 120 - 1
AAACCUCGCUGCUCACCACAGCUGCCAGUGGAUAUAGACCGAAACUAACAAAGGCGAGUUGGAUGGCCAAUAGGAUAAUGGGCAAAUACCGAUCCGCCCAUUCACCCAGCAGCCAACUUU
.......((((((..(((((((((((..((....(((.......))).))..))).)))))..)))......((..(((((((............)))))))...))))))))....... ( -32.90)
>consensus
AAACCUCGCUGCUAACAACAGCGGCCAGGGGAUAAAGGCCAAAGCUGACAAAAGCCAGCUGGAUGGCCAGCAGAAUAAUGGGCAAAUACCGAUCCGCCCAGUUGCCCAGCAGCCAAAAUU
...(((.(((((........))))).)))((.....(.(((.(((((........)))))...))).)..........(((((............))))).....))............. (-21.29 = -21.77 +   0.48)

alignment

secondary structure

dotplot

Window 7

Location	3,322,420 – 3,322,522
Length	102
Sequences	6
Columns	103
Reading direction	forward
Mean pairwise identity	79.67
Mean single sequence MFE	-31.83
Consensus MFE	-20.70
Energy contribution	-20.82
Covariance contribution	0.12
Combinations/Pair	1.35
Mean z-score	-1.68
Structure conservation index	0.65
SVM decision value	0.50
SVM RNA-class probability	0.761970
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 3322420 102 + 22407834
CAUUAUUCUGCUGGCCAUUCAGCUGGCUCUUGUCAGCUUUGGCCUUUAUCCCCUGGCCGCAGUCGUUAGCAGCGAAGUUCUGCCCACGAAGGUAAUCCAUUA-
.......((((.(((((...(((((((....)))))))..((........)).)))))))))((((..((((.......))))..)))).((....))....- ( -32.70)
>DroVir_CAF1 32054 102 + 1
CAUCGUUCUGCUCGCCGCUCAGCUGUUUUUUGUCAGCUUUGGUCUCUAUCCCCUGGCUGCUGUCGUCAGCAGCGAAGUGCUGCCCACAAAGGUAAGGAAUAU-
....(((((((.(((((...(((((........))))).))))............(((((((....)))))))...).))((((......)))).)))))..- ( -29.60)
>DroSim_CAF1 8737 102 + 1
CAUUGUCCUGCUGGCUAUCCAGCUGGCUCUUGUCAGCUUUGGCCUUUAUCCCCUGGCCGCAGUCGUUAGCAGCGAAGUUCUGCCCACAAAGGUAAUCCAUUA-
.....((((((((((.....(((((((....)))))))..((((..........))))......)))))))).)).....((((......))))........- ( -33.00)
>DroYak_CAF1 8613 102 + 1
CAUUGUUUUGCUGGCCAUCCAGCUGGCUGUGGUCAGCUUUGGCCUUUAUCCCCUGGCCGCAGUUGUUAGCAGCGAGGUUCUGCCCACUAAGGUAAGCCAGUU-
.........((((((.......((.(((((...(((((.(((((..........))))).)))))...))))).))....((((......)))).)))))).- ( -38.70)
>DroMoj_CAF1 9437 101 + 1
CAUCAUCCUGCUCGCCAUUCAGCUAUUCUUCGUCAGCUUUGGGCUCUAUCCCCUGGCCGCUGUCGUCAGCAGCGAAGUGCUGCCCACAAAGGUAAGCAAUA--
........((((..((.((((((....((((((..(((..(((......)))..))).((((....)))).)))))).)))).....)).))..))))...-- ( -31.90)
>DroAna_CAF1 8515 102 + 1
CAUUAUCCUAUUGGCCAUCCAACUCGCCUUUGUUAGUUUCGGUCUAUAUCCACUGGCAGCUGUGGUGAGCAGCGAGGUUUUGCCUACAAAGGUAAGUUU-UUG
.............(((.(((..((((((.((((((((...((.......))))))))))....))))))..).)))))(((((((....)))))))...-... ( -25.10)
>consensus
CAUUAUCCUGCUGGCCAUCCAGCUGGCUUUUGUCAGCUUUGGCCUUUAUCCCCUGGCCGCAGUCGUUAGCAGCGAAGUUCUGCCCACAAAGGUAAGCCAUUU_
.....((((((((((((...(((((((....))))))).)))))..........(((....)))...))))).)).....((((......))))......... (-20.70 = -20.82 +   0.12)

alignment

secondary structure

dotplot

Window 8

Location	3,322,420 – 3,322,522
Length	102
Sequences	6
Columns	103
Reading direction	reverse
Mean pairwise identity	79.67
Mean single sequence MFE	-31.83
Consensus MFE	-20.83
Energy contribution	-20.62
Covariance contribution	-0.22
Combinations/Pair	1.38
Mean z-score	-1.52
Structure conservation index	0.65
SVM decision value	0.31
SVM RNA-class probability	0.684176
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 3322420 102 - 22407834
-UAAUGGAUUACCUUCGUGGGCAGAACUUCGCUGCUAACGACUGCGGCCAGGGGAUAAAGGCCAAAGCUGACAAGAGCCAGCUGAAUGGCCAGCAGAAUAAUG
-.............((((.(((((.......))))).))))(((((((((.((........))..(((((........)))))...))))).))))....... ( -33.40)
>DroVir_CAF1 32054 102 - 1
-AUAUUCCUUACCUUUGUGGGCAGCACUUCGCUGCUGACGACAGCAGCCAGGGGAUAGAGACCAAAGCUGACAAAAAACAGCUGAGCGGCGAGCAGAACGAUG
-.............((((.((((((.....)))))).))))..((.(((..((........))..(((((........)))))....)))..))......... ( -30.40)
>DroSim_CAF1 8737 102 - 1
-UAAUGGAUUACCUUUGUGGGCAGAACUUCGCUGCUAACGACUGCGGCCAGGGGAUAAAGGCCAAAGCUGACAAGAGCCAGCUGGAUAGCCAGCAGGACAAUG
-..........(((((((.(((....(((.(((((........))))).)))((.......))...))).))))......(((((....))))))))...... ( -30.20)
>DroYak_CAF1 8613 102 - 1
-AACUGGCUUACCUUAGUGGGCAGAACCUCGCUGCUAACAACUGCGGCCAGGGGAUAAAGGCCAAAGCUGACCACAGCCAGCUGGAUGGCCAGCAAAACAAUG
-...(((((....(((((.(((....(((.(((((........))))).)))........)))...)))))....)))))(((((....)))))......... ( -37.00)
>DroMoj_CAF1 9437 101 - 1
--UAUUGCUUACCUUUGUGGGCAGCACUUCGCUGCUGACGACAGCGGCCAGGGGAUAGAGCCCAAAGCUGACGAAGAAUAGCUGAAUGGCGAGCAGGAUGAUG
--..((((((..((((((.(((....((..(((((((....))))))).))(((......)))...))).))))))....(((....)))))))))....... ( -36.40)
>DroAna_CAF1 8515 102 - 1
CAA-AAACUUACCUUUGUAGGCAAAACCUCGCUGCUCACCACAGCUGCCAGUGGAUAUAGACCGAAACUAACAAAGGCGAGUUGGAUGGCCAAUAGGAUAAUG
((.-.((((..(((((((.((((.......((((.......))))))))..(((.......)))......)))))))..))))...)).((....))...... ( -23.61)
>consensus
_AAAUGGCUUACCUUUGUGGGCAGAACUUCGCUGCUAACGACAGCGGCCAGGGGAUAAAGGCCAAAGCUGACAAAAGCCAGCUGAAUGGCCAGCAGAACAAUG
.............(((((.(((....(((.(((((........))))).))).............(((((........))))).....))).)))))...... (-20.83 = -20.62 +  -0.22)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:57:57 2006