Locus 6526

Sequence ID	3L_DroMel_CAF1
Location	17,276,053 – 17,276,316
Length	263
Max. P	0.997381

overview

Window 5

Location	17,276,053 – 17,276,173
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	98.00
Mean single sequence MFE	-30.28
Consensus MFE	-28.00
Energy contribution	-28.12
Covariance contribution	0.12
Combinations/Pair	1.05
Mean z-score	-1.27
Structure conservation index	0.92
SVM decision value	0.21
SVM RNA-class probability	0.633872
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 17276053 120 + 23771897
CGUGGGUGGCCUGAACGUGAACGUGAACUUUUCACGUGCGCAAUUUGUGUUCGUAUUUAGUUUUCCUCUUUCUGCGCUCACCAGAAUGUGUGCUGUUUUAUUCAUAUAUAGUACAUUAUU
.(((((((......(((....)))(((((....(((.((((.....)))).)))....)))))...........)))))))......(((((((((...........))))))))).... ( -29.80)
>DroSec_CAF1 159395 120 + 1
CGUGGGUGGCCUGAACGUGAACGUGAACUUUUCACGUGCGCAAUUUGUGUUCGUAUUUAGUUUUCCUCUUUCUGCGCUCGCCAGAAUGUGUGCUGUUUUAUUCAUAUAUAGUACAUUAUU
.(.(((..((.((((..(((((((((.....))))))((((.....)))))))..))))))..))).).(((((.(....)))))).(((((((((...........))))))))).... ( -30.20)
>DroSim_CAF1 154737 120 + 1
CGUGGGUGGCCUGAACGUGAACGUGAACUUUUCACGUGCGCAAUUUGUGUUCGUAUUUAGUUUUCCUCUUUCUGCGCUCGCCAGAAUGUGUGCUGUUUUAUUCAUAUAUAGUACAUUAUU
.(.(((..((.((((..(((((((((.....))))))((((.....)))))))..))))))..))).).(((((.(....)))))).(((((((((...........))))))))).... ( -30.20)
>DroEre_CAF1 162390 120 + 1
CGUGGGUGGCCGGAACGUGAACGUGAACUUUUCACGUGCGCAAUUUGUGUUUGUAUUUAGCUUUCCUCUUUCUGCGCUCGCCAGAAUGUGUGCUGUUUUAUUCAUAUAUAGUACAUUAUU
....(((((((((((.(((.((((((.....)))))).))).......(((.......)))........))))).)).)))).....(((((((((...........))))))))).... ( -31.40)
>DroYak_CAF1 167348 120 + 1
CGUGGGUGUCCUGAACGUGAACGUGAACUUUUCACGUGCGCAAUUUGUGUUCGUAUUUAGUUUUCCUCUUUCUGCGUUCGCCAGAAUGUGUGCUGUUUUAUUCAUAUAUAGUACAUUAUU
...(((.(..(((((..(((((((((.....))))))((((.....)))))))..)))))..).)))......((((((....))))))(((((((...........)))))))...... ( -29.80)
>consensus
CGUGGGUGGCCUGAACGUGAACGUGAACUUUUCACGUGCGCAAUUUGUGUUCGUAUUUAGUUUUCCUCUUUCUGCGCUCGCCAGAAUGUGUGCUGUUUUAUUCAUAUAUAGUACAUUAUU
.(.(((.(((.((((..(((((((((.....))))))((((.....)))))))..))))))).))).).(((((.(....)))))).(((((((((...........))))))))).... (-28.00 = -28.12 +   0.12)

alignment

secondary structure

dotplot

Window 6

Location	17,276,093 – 17,276,205
Length	112
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	90.32
Mean single sequence MFE	-28.82
Consensus MFE	-27.14
Energy contribution	-26.78
Covariance contribution	-0.36
Combinations/Pair	1.10
Mean z-score	-1.97
Structure conservation index	0.94
SVM decision value	2.85
SVM RNA-class probability	0.997381
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 17276093 112 + 23771897
CAAUUUGUGUUCGUAUUUAGUUUUCCUCUUUCUGCGCUCACCAGAAUGUGUGCUGUUUUAUUCAUAUAUAGUACAUUAUUCGCCCCAACCUUUUGCACUGGGUGCUGGGCGA--------
......(((..((((...((.......))...))))..)))..(((((((((((((...........)))))))).)))))((((..((((........))))...))))..-------- ( -30.00)
>DroSec_CAF1 159435 117 + 1
CAAUUUGUGUUCGUAUUUAGUUUUCCUCUUUCUGCGCUCGCCAGAAUGUGUGCUGUUUUAUUCAUAUAUAGUACAUUAUUCGCCCCGACCUUUUCAACUGGGUUCUGGGCUA--C-CCCA
......(((..((((...((.......))...))))..)))..(((((((((((((...........)))))))).)))))((((.(((((........)))))..))))..--.-.... ( -29.30)
>DroSim_CAF1 154777 112 + 1
CAAUUUGUGUUCGUAUUUAGUUUUCCUCUUUCUGCGCUCGCCAGAAUGUGUGCUGUUUUAUUCAUAUAUAGUACAUUAUUCGCCCCGACCUUUUCAACUGGGUGCUGGGCGA--------
......(((..((((...((.......))...))))..)))..(((((((((((((...........)))))))).)))))((((.(((((........)))).).))))..-------- ( -29.70)
>DroEre_CAF1 162430 109 + 1
CAAUUUGUGUUUGUAUUUAGCUUUCCUCUUUCUGCGCUCGCCAGAAUGUGUGCUGUUUUAUUCAUAUAUAGUACAUUAUUCGCCCCGACCUU-UGCACUGGGUGCUGGGU----------
......(((..((((...((.......))...))))..)))..(((((((((((((...........)))))))).)))))((((.(((((.-......)))).).))))---------- ( -23.80)
>DroYak_CAF1 167388 120 + 1
CAAUUUGUGUUCGUAUUUAGUUUUCCUCUUUCUGCGUUCGCCAGAAUGUGUGCUGUUUUAUUCAUAUAUAGUACAUUAUUCGCCCCGACCUUCUGCACUGGGCGCUGGGUGCUGGGUUCU
......(((..((((...((.......))...))))..)))..(((((((((((((...........)))))))).)))))((((.(((((..(((.....)))..)))).).))))... ( -31.30)
>consensus
CAAUUUGUGUUCGUAUUUAGUUUUCCUCUUUCUGCGCUCGCCAGAAUGUGUGCUGUUUUAUUCAUAUAUAGUACAUUAUUCGCCCCGACCUUUUGCACUGGGUGCUGGGCGA________
......(((..((((...((.......))...))))..)))..(((((((((((((...........)))))))).)))))((((..((((........))))...)))).......... (-27.14 = -26.78 +  -0.36)

alignment

secondary structure

dotplot

Window 7

Location	17,276,133 – 17,276,236
Length	103
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	86.43
Mean single sequence MFE	-31.18
Consensus MFE	-21.78
Energy contribution	-21.74
Covariance contribution	-0.04
Combinations/Pair	1.05
Mean z-score	-2.19
Structure conservation index	0.70
SVM decision value	0.61
SVM RNA-class probability	0.799713
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 17276133 103 + 23771897
CCAGAAUGUGUGCUGUUUUAUUCAUAUAUAGUACAUUAUUCGCCCCAACCUUUUGCACUGGGUGCUGGGCGA-----------------GAACUACCCUUGUCCUAGCCGAACUCAACUC
...(((((((((((((...........)))))))).))))).................((((((((((((((-----------------(.......)))).))))))...))))).... ( -27.90)
>DroSec_CAF1 159475 117 + 1
CCAGAAUGUGUGCUGUUUUAUUCAUAUAUAGUACAUUAUUCGCCCCGACCUUUUCAACUGGGUUCUGGGCUA--C-CCCAAGGAACAAGGAACUACCCUUGUCCUAGCCGAACUCAACUC
...(((((((((((((...........)))))))).))))).................(((((((((((...--.-))))((((.(((((......)))))))))....))))))).... ( -35.30)
>DroSim_CAF1 154817 103 + 1
CCAGAAUGUGUGCUGUUUUAUUCAUAUAUAGUACAUUAUUCGCCCCGACCUUUUCAACUGGGUGCUGGGCGA-----------------GAACUACCCUUGUCCUAGCCGAACUCAACUC
...(((((((((((((...........)))))))).)))))....((((((........))))(((((((((-----------------(.......)))).)))))))).......... ( -28.10)
>DroEre_CAF1 162470 102 + 1
CCAGAAUGUGUGCUGUUUUAUUCAUAUAUAGUACAUUAUUCGCCCCGACCUU-UGCACUGGGUGCUGGGU-----------------AGGAACUACCCUUGUCCCGGCCGAACUCAACUC
...(((((((((((((...........)))))))).)))))(((..(((...-.((((...)))).((((-----------------((...))))))..)))..)))............ ( -29.20)
>DroYak_CAF1 167428 117 + 1
CCAGAAUGUGUGCUGUUUUAUUCAUAUAUAGUACAUUAUUCGCCCCGACCUUCUGCACUGGGCGCUGGGUGCUGGGUUCUGGG---AAGGAACUACCCUUGUCCUAGCCGAACUCAACUC
...(((((((((((((...........)))))))).)))))((((((.(((........)))...)))).))(((((((((((---((((......)))..)))))...))))))).... ( -35.40)
>consensus
CCAGAAUGUGUGCUGUUUUAUUCAUAUAUAGUACAUUAUUCGCCCCGACCUUUUGCACUGGGUGCUGGGCGA_______________AGGAACUACCCUUGUCCUAGCCGAACUCAACUC
...(((((((((((((...........)))))))).)))))((((..((((........))))...)))).................................................. (-21.78 = -21.74 +  -0.04)

alignment

secondary structure

dotplot

Window 8

Location	17,276,173 – 17,276,276
Length	103
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	86.43
Mean single sequence MFE	-34.34
Consensus MFE	-25.74
Energy contribution	-25.70
Covariance contribution	-0.04
Combinations/Pair	1.04
Mean z-score	-1.88
Structure conservation index	0.75
SVM decision value	0.54
SVM RNA-class probability	0.773948
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 17276173 103 + 23771897
CGCCCCAACCUUUUGCACUGGGUGCUGGGCGA-----------------GAACUACCCUUGUCCUAGCCGAACUCAACUCAAAUUAUAUUUUUAUGAGUGGGGCCAAGUUACGGCACUUA
.((((((...........)))).)).((((((-----------------(.......)))))))..((((((((...(((...(((((....)))))...)))...)))).))))..... ( -31.30)
>DroSec_CAF1 159515 117 + 1
CGCCCCGACCUUUUCAACUGGGUUCUGGGCUA--C-CCCAAGGAACAAGGAACUACCCUUGUCCUAGCCGAACUCAACUCAAAUUAUAUUUUUAUGAGUGGGGCCAAGUUACGGCACUUA
.((((.(((((........)))))..))))..--.-....((((.(((((......))))))))).((((((((...(((...(((((....)))))...)))...)))).))))..... ( -39.20)
>DroSim_CAF1 154857 103 + 1
CGCCCCGACCUUUUCAACUGGGUGCUGGGCGA-----------------GAACUACCCUUGUCCUAGCCGAACUCAACUCAAAUUAUAUUUUUAUGAGUGGGGCCAAGUUACGGCACUUA
.(((((............((((((((((((((-----------------(.......)))).))))))...)))))(((((.............)))))))))).((((......)))). ( -31.22)
>DroEre_CAF1 162510 102 + 1
CGCCCCGACCUU-UGCACUGGGUGCUGGGU-----------------AGGAACUACCCUUGUCCCGGCCGAACUCAACUCAAAUUAUAUUUUUAUGAGUGGGGCCAAGUUACGGCACUUA
.(((..(((...-......(((....((((-----------------((...))))))....)))((((..(((((..................)))))..))))..)))..)))..... ( -33.57)
>DroYak_CAF1 167468 117 + 1
CGCCCCGACCUUCUGCACUGGGCGCUGGGUGCUGGGUUCUGGG---AAGGAACUACCCUUGUCCUAGCCGAACUCAACUCAAAUUAUAUUUUUAUGAGUGGGGCCAAGUUACGGCACUUA
(((((.(..........).))))).(((((((((((..(((((---((((......)))..))))))))(..((((.((((.............))))))))..)......))))))))) ( -36.42)
>consensus
CGCCCCGACCUUUUGCACUGGGUGCUGGGCGA_______________AGGAACUACCCUUGUCCUAGCCGAACUCAACUCAAAUUAUAUUUUUAUGAGUGGGGCCAAGUUACGGCACUUA
.((((..((((........))))...))))....................................((((((((...(((...(((((....)))))...)))...)))).))))..... (-25.74 = -25.70 +  -0.04)

alignment

secondary structure

dotplot

Window 9

Location	17,276,173 – 17,276,276
Length	103
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	86.43
Mean single sequence MFE	-35.05
Consensus MFE	-27.86
Energy contribution	-27.78
Covariance contribution	-0.08
Combinations/Pair	1.11
Mean z-score	-1.48
Structure conservation index	0.79
SVM decision value	0.01
SVM RNA-class probability	0.536704
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 17276173 103 - 23771897
UAAGUGCCGUAACUUGGCCCCACUCAUAAAAAUAUAAUUUGAGUUGAGUUCGGCUAGGACAAGGGUAGUUC-----------------UCGCCCAGCACCCAGUGCAAAAGGUUGGGGCG
.....(((.((((((((((..(((((....((......))....)))))..)))).......((((.....-----------------..)))).((((...))))...)))))).))). ( -31.50)
>DroSec_CAF1 159515 117 - 1
UAAGUGCCGUAACUUGGCCCCACUCAUAAAAAUAUAAUUUGAGUUGAGUUCGGCUAGGACAAGGGUAGUUCCUUGUUCCUUGGG-G--UAGCCCAGAACCCAGUUGAAAAGGUCGGGGCG
(((((......)))))((((((((((.............)))))....(((((((.(((((((((....))))))))).(((((-.--...))))).....)))))))......))))). ( -41.02)
>DroSim_CAF1 154857 103 - 1
UAAGUGCCGUAACUUGGCCCCACUCAUAAAAAUAUAAUUUGAGUUGAGUUCGGCUAGGACAAGGGUAGUUC-----------------UCGCCCAGCACCCAGUUGAAAAGGUCGGGGCG
(((((......)))))((((((((((.............)))))....(((((((.((....((((.....-----------------..))))....)).)))))))......))))). ( -31.62)
>DroEre_CAF1 162510 102 - 1
UAAGUGCCGUAACUUGGCCCCACUCAUAAAAAUAUAAUUUGAGUUGAGUUCGGCCGGGACAAGGGUAGUUCCU-----------------ACCCAGCACCCAGUGCA-AAGGUCGGGGCG
(((((......)))))((((((((((....((......))....)))))..((((.......((((((...))-----------------)))).((((...)))).-..))))))))). ( -37.20)
>DroYak_CAF1 167468 117 - 1
UAAGUGCCGUAACUUGGCCCCACUCAUAAAAAUAUAAUUUGAGUUGAGUUCGGCUAGGACAAGGGUAGUUCCUU---CCCAGAACCCAGCACCCAGCGCCCAGUGCAGAAGGUCGGGGCG
(((((......)))))((((((((..................((((.((((((..(((((.......).)))).---.)).)))).)))).....((((...))))....))).))))). ( -33.90)
>consensus
UAAGUGCCGUAACUUGGCCCCACUCAUAAAAAUAUAAUUUGAGUUGAGUUCGGCUAGGACAAGGGUAGUUCCU_______________UCGCCCAGCACCCAGUGCAAAAGGUCGGGGCG
.((.((((.(..(((((((..(((((....((......))....)))))..)))))))...).)))).))....................((((...(((..........)))..)))). (-27.86 = -27.78 +  -0.08)

alignment

secondary structure

dotplot

Window 0

Location	17,276,205 – 17,276,316
Length	111
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	94.78
Mean single sequence MFE	-26.52
Consensus MFE	-22.76
Energy contribution	-22.96
Covariance contribution	0.20
Combinations/Pair	1.00
Mean z-score	-1.83
Structure conservation index	0.86
SVM decision value	1.61
SVM RNA-class probability	0.967603
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 17276205 111 + 23771897
---------GAACUACCCUUGUCCUAGCCGAACUCAACUCAAAUUAUAUUUUUAUGAGUGGGGCCAAGUUACGGCACUUAAUGAUGUUGCUUAGCAAAUUGUAGCAACUAAACACAAACA
---------.........((((....((((((((...(((...(((((....)))))...)))...)))).))))..........((((((..((.....)))))))).....))))... ( -23.10)
>DroSec_CAF1 159552 120 + 1
AGGAACAAGGAACUACCCUUGUCCUAGCCGAACUCAACUCAAAUUAUAUUUUUAUGAGUGGGGCCAAGUUACGGCACUUAAUGAUGUUGCUUAGCAAAUUGAAGCAACUAAACACAAACA
((((.(((((......))))))))).((((((((...(((...(((((....)))))...)))...)))).))))..........(((((((.........)))))))............ ( -33.30)
>DroSim_CAF1 154889 111 + 1
---------GAACUACCCUUGUCCUAGCCGAACUCAACUCAAAUUAUAUUUUUAUGAGUGGGGCCAAGUUACGGCACUUAAUGAUGUUGCUUAGCAAAUUGAAGCAACUAAACACAAACA
---------.........((((....((((((((...(((...(((((....)))))...)))...)))).))))..........(((((((.........))))))).....))))... ( -23.30)
>DroEre_CAF1 162539 113 + 1
-------AGGAACUACCCUUGUCCCGGCCGAACUCAACUCAAAUUAUAUUUUUAUGAGUGGGGCCAAGUUACGGCACUUAAUGAUGUUGCUUAGCAAAUUGAAGCAACUAAACACAAACA
-------.((.((.......)).)).((((((((...(((...(((((....)))))...)))...)))).))))..........(((((((.........)))))))............ ( -24.60)
>DroYak_CAF1 167508 117 + 1
GGG---AAGGAACUACCCUUGUCCUAGCCGAACUCAACUCAAAUUAUAUUUUUAUGAGUGGGGCCAAGUUACGGCACUUAAUGAUGUUGCUUAGCAAAUUGAAGCAACUAAACACAAACA
(((---((((......)))).)))..((((((((...(((...(((((....)))))...)))...)))).))))..........(((((((.........)))))))............ ( -28.30)
>consensus
_______AGGAACUACCCUUGUCCUAGCCGAACUCAACUCAAAUUAUAUUUUUAUGAGUGGGGCCAAGUUACGGCACUUAAUGAUGUUGCUUAGCAAAUUGAAGCAACUAAACACAAACA
..................((((....((((((((...(((...(((((....)))))...)))...)))).))))..........(((((((.........))))))).....))))... (-22.76 = -22.96 +   0.20)

alignment

secondary structure

dotplot

Window 1

Location	17,276,205 – 17,276,316
Length	111
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	94.78
Mean single sequence MFE	-28.30
Consensus MFE	-27.52
Energy contribution	-27.20
Covariance contribution	-0.32
Combinations/Pair	1.06
Mean z-score	-1.12
Structure conservation index	0.97
SVM decision value	0.45
SVM RNA-class probability	0.742199
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 17276205 111 - 23771897
UGUUUGUGUUUAGUUGCUACAAUUUGCUAAGCAACAUCAUUAAGUGCCGUAACUUGGCCCCACUCAUAAAAAUAUAAUUUGAGUUGAGUUCGGCUAGGACAAGGGUAGUUC---------
((....((((((((...........))))))))....))..((.((((.(..(((((((..(((((....((......))....)))))..)))))))...).)))).)).--------- ( -26.90)
>DroSec_CAF1 159552 120 - 1
UGUUUGUGUUUAGUUGCUUCAAUUUGCUAAGCAACAUCAUUAAGUGCCGUAACUUGGCCCCACUCAUAAAAAUAUAAUUUGAGUUGAGUUCGGCUAGGACAAGGGUAGUUCCUUGUUCCU
((....((((((((...........))))))))....))......((((.((((..((.....(((.............)))))..))))))))..(((((((((....))))))))).. ( -32.42)
>DroSim_CAF1 154889 111 - 1
UGUUUGUGUUUAGUUGCUUCAAUUUGCUAAGCAACAUCAUUAAGUGCCGUAACUUGGCCCCACUCAUAAAAAUAUAAUUUGAGUUGAGUUCGGCUAGGACAAGGGUAGUUC---------
((....((((((((...........))))))))....))..((.((((.(..(((((((..(((((....((......))....)))))..)))))))...).)))).)).--------- ( -26.90)
>DroEre_CAF1 162539 113 - 1
UGUUUGUGUUUAGUUGCUUCAAUUUGCUAAGCAACAUCAUUAAGUGCCGUAACUUGGCCCCACUCAUAAAAAUAUAAUUUGAGUUGAGUUCGGCCGGGACAAGGGUAGUUCCU-------
((....((((((((...........))))))))....))..((.((((.(..(((((((..(((((....((......))....)))))..)))))))...).)))).))...------- ( -28.40)
>DroYak_CAF1 167508 117 - 1
UGUUUGUGUUUAGUUGCUUCAAUUUGCUAAGCAACAUCAUUAAGUGCCGUAACUUGGCCCCACUCAUAAAAAUAUAAUUUGAGUUGAGUUCGGCUAGGACAAGGGUAGUUCCUU---CCC
((....((((((((...........))))))))....))..((.((((.(..(((((((..(((((....((......))....)))))..)))))))...).)))).))....---... ( -26.90)
>consensus
UGUUUGUGUUUAGUUGCUUCAAUUUGCUAAGCAACAUCAUUAAGUGCCGUAACUUGGCCCCACUCAUAAAAAUAUAAUUUGAGUUGAGUUCGGCUAGGACAAGGGUAGUUCCU_______
((....((((((((...........))))))))....))..((.((((.(..(((((((..(((((....((......))....)))))..)))))))...).)))).)).......... (-27.52 = -27.20 +  -0.32)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:22:56 2006