Locus 160

Sequence ID	2R_DroMel_CAF1
Location	1,422,631 – 1,423,023
Length	392
Max. P	0.999960

overview

Window 3

Location	1,422,631 – 1,422,743
Length	112
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	88.54
Mean single sequence MFE	-29.02
Consensus MFE	-23.08
Energy contribution	-23.20
Covariance contribution	0.12
Combinations/Pair	1.09
Mean z-score	-1.56
Structure conservation index	0.80
SVM decision value	0.27
SVM RNA-class probability	0.662981
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 1422631 112 + 20766785
--------UCCUUUGCCGUGGUCGUCGGUGAGUUUAAAAUGCAGUUAAAUAAUAGAUUUAACUCAUCUUGGGCUUGGGCACAGCGUAAUGUAAUUCAGGCAACUAGAUUAUGAAAAGCCC
--------......((((.......))))((((((((.(((.((((((((.....))))))))))).))))))))((((....((((((.(.....((....))).))))))....)))) ( -29.60)
>DroSec_CAF1 41084 112 + 1
--------UCCUUUGCCGUGGUCGUCGGUGAGUUUAAAAUGCAGUUAAAUAAUAGAUUUAACUCAUCUUGGGCUUGGGCACAUCGUAAUGUAAUUCAGGCAACUAGAUUAUGAAAAGCCC
--------......((((.......))))((((((((.(((.((((((((.....))))))))))).))))))))((((...(((((((.(.....((....))).)))))))...)))) ( -30.50)
>DroSim_CAF1 46135 112 + 1
--------UCCUUUGCCGUGGUCGUCGGUGAGUUUAAAAUGCAGUUAAAUAAUAGAUUUAACUCAUCUUGGGCUUGGGCACAUCGUAAUGUAAUUCAGGCAACUAGAUUAUGAAAAGCCC
--------......((((.......))))((((((((.(((.((((((((.....))))))))))).))))))))((((...(((((((.(.....((....))).)))))))...)))) ( -30.50)
>DroEre_CAF1 39289 97 + 1
-----------------------GUUGGUGAAUCUAAAAUGCAGUUAAAUAAUAGAUUUAACUCAUCUUGGGCUUGGGCACAGCGUAAUGUAAUUCGGGCAACUGGAUUAUGAAAAGCCC
-----------------------......((..((((.(((.((((((((.....))))))))))).))))..))(((((((......)))(((((((....))))))).......)))) ( -26.80)
>DroYak_CAF1 40442 120 + 1
AUGGUAUCUCCAUUGCCGUGGUCGUCGCUUACUUUAAAAUGCAGUUAAAUAAUAGAUUUAACUCAUCUUGGGCUUGGGCACAGCGUAAUGUAAUUCAGGCAACUAGAUUAUGAAAAGCCC
((((((.......))))))(((..(((((((.(((((.(((.((((((((.....))))))))))).)))))..)))))..........(((((..((....))..)))))))...))). ( -27.70)
>consensus
________UCCUUUGCCGUGGUCGUCGGUGAGUUUAAAAUGCAGUUAAAUAAUAGAUUUAACUCAUCUUGGGCUUGGGCACAGCGUAAUGUAAUUCAGGCAACUAGAUUAUGAAAAGCCC
.............................((((((((.(((.((((((((.....))))))))))).))))))))((((....((((((.(.....((....))).))))))....)))) (-23.08 = -23.20 +   0.12)

alignment

secondary structure

dotplot

Window 4

Location	1,422,663 – 1,422,783
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	97.50
Mean single sequence MFE	-34.54
Consensus MFE	-33.72
Energy contribution	-32.92
Covariance contribution	-0.80
Combinations/Pair	1.16
Mean z-score	-3.19
Structure conservation index	0.98
SVM decision value	4.89
SVM RNA-class probability	0.999960
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 1422663 120 + 20766785
GCAGUUAAAUAAUAGAUUUAACUCAUCUUGGGCUUGGGCACAGCGUAAUGUAAUUCAGGCAACUAGAUUAUGAAAAGCCCUCGCCUAGGGUUAAUUAACAUGACUAAUGCACUGGAAAUA
((((((((((.....)))))))..(((((((((..((((....((((((.(.....((....))).))))))....))))..)))))))))................))).......... ( -33.40)
>DroSec_CAF1 41116 120 + 1
GCAGUUAAAUAAUAGAUUUAACUCAUCUUGGGCUUGGGCACAUCGUAAUGUAAUUCAGGCAACUAGAUUAUGAAAAGCCCUCGCCUAGGGUUAAUUAACAUGACUAAUGCACUGGAAAUA
((((((((((.....)))))))..(((((((((..((((...(((((((.(.....((....))).)))))))...))))..)))))))))................))).......... ( -34.30)
>DroSim_CAF1 46167 120 + 1
GCAGUUAAAUAAUAGAUUUAACUCAUCUUGGGCUUGGGCACAUCGUAAUGUAAUUCAGGCAACUAGAUUAUGAAAAGCCCUCGCCUAGGGUUAAUUAACAUGACUAAUGCACUGGAAAUA
((((((((((.....)))))))..(((((((((..((((...(((((((.(.....((....))).)))))))...))))..)))))))))................))).......... ( -34.30)
>DroEre_CAF1 39306 120 + 1
GCAGUUAAAUAAUAGAUUUAACUCAUCUUGGGCUUGGGCACAGCGUAAUGUAAUUCGGGCAACUGGAUUAUGAAAAGCCCUCGCCCAGGGUUAAUUAACAUGACUAAUGCACUGGAAAUA
((((((((((.....)))))))..(((((((((..(((((((......)))(((((((....))))))).......))))..)))))))))................))).......... ( -39.80)
>DroYak_CAF1 40482 120 + 1
GCAGUUAAAUAAUAGAUUUAACUCAUCUUGGGCUUGGGCACAGCGUAAUGUAAUUCAGGCAACUAGAUUAUGAAAAGCCCUCGCUUAAGGUUAAUUAUCAUGACUAAUGCACUGGAAAUA
((((((((((.....)))))))..(((((((((..((((....((((((.(.....((....))).))))))....))))..)))))))))................))).......... ( -30.90)
>consensus
GCAGUUAAAUAAUAGAUUUAACUCAUCUUGGGCUUGGGCACAGCGUAAUGUAAUUCAGGCAACUAGAUUAUGAAAAGCCCUCGCCUAGGGUUAAUUAACAUGACUAAUGCACUGGAAAUA
((((((((((.....)))))))..(((((((((..((((....((((((.(.....((....))).))))))....))))..)))))))))................))).......... (-33.72 = -32.92 +  -0.80)

alignment

secondary structure

dotplot

Window 5

Location	1,422,783 – 1,422,903
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	93.42
Mean single sequence MFE	-43.66
Consensus MFE	-34.86
Energy contribution	-35.54
Covariance contribution	0.68
Combinations/Pair	1.03
Mean z-score	-2.34
Structure conservation index	0.80
SVM decision value	1.66
SVM RNA-class probability	0.970648
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 1422783 120 + 20766785
GCUGACACACUGCGGGCACUAAUCAGUCCUGGUCUUUCGCACUAGCGGCCAAGUAAGGCUUGAAAGCUCGGCAAUUAAGCCGUGCUGAUAAAACAGGACAAGUGAUUGUGCGAGUCAUAA
..((((...(....)((((.(((((((((((....(((((....))((((......)))).)))(((.((((......)))).))).......))))))...)))))))))..))))... ( -40.50)
>DroSec_CAF1 41236 120 + 1
GCUGACACACUGCGGGCACUAAUCAGUCCUGGGCCUUCGCACUAGCGGCCAAGUUGGGCUUGAAAGCUCGGCAAUUAAGCCGUGCUGAUAAAACAGGACAAGUGAUUGUGCGAGUCAUAA
..((((...(....)((((.((((((((((((((((((((....)))).......)))))....(((.((((......)))).))).......))))))...)))))))))..))))... ( -42.01)
>DroSim_CAF1 46287 120 + 1
GCUGACACACUGCGGGCACUAAUCAGUCCCGGGCCUUCGCACUAGCGGCCAAGUUGGGCUUGAAAGCUCGGCAAUUAAGCCGUGCUGAUAAAACAGGACAAGUGAUUGUGCGAGUCAUAA
..((((......((((.(((....))))))).....((((((..(((((...((((((((....))))))))......)))((.(((......))).))..))....))))))))))... ( -41.30)
>DroEre_CAF1 39426 119 + 1
ACUGACACACUGCGGGCACUAAUCAGUCCUGGACCUUCGCACUA-CGGCCAAGCCGGGCUUGAAAGCUCGGCAAUUAGGCCGGGCUGAUAAAGCGGGACAAGUGAUUGUGCGAGUCAUAA
..((((...(....)((((.(((((((((((.....((((....-(((((..((((((((....)))))))).....))))).)).)).....))))))...)))))))))..))))... ( -46.50)
>DroYak_CAF1 40602 120 + 1
GCUGACACACUGCGGGCACAAAUCAGUCCUGGGCCUUCGCACUAGCGGCCAUAGUGGUCUUGAAAGCUCGGCAAUUAAGCCGGGCUGAUAAAACAGCACAAGUGAUUGUGCGAGUCAUAA
..((((.(((((((((.((......))))))((((...((....)))))).)))))((.(((..((((((((......))))))))..))).)).((((((....))))))..))))... ( -48.00)
>consensus
GCUGACACACUGCGGGCACUAAUCAGUCCUGGGCCUUCGCACUAGCGGCCAAGUUGGGCUUGAAAGCUCGGCAAUUAAGCCGUGCUGAUAAAACAGGACAAGUGAUUGUGCGAGUCAUAA
..((((...(....)((((.(((((((((((....(((((....))((((......)))).)))(((.((((......)))).))).......))))))...)))))))))..))))... (-34.86 = -35.54 +   0.68)

alignment

secondary structure

dotplot

Window 6

Location	1,422,783 – 1,422,903
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	93.42
Mean single sequence MFE	-40.02
Consensus MFE	-33.76
Energy contribution	-34.36
Covariance contribution	0.60
Combinations/Pair	1.09
Mean z-score	-1.57
Structure conservation index	0.84
SVM decision value	0.86
SVM RNA-class probability	0.868838
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 1422783 120 - 20766785
UUAUGACUCGCACAAUCACUUGUCCUGUUUUAUCAGCACGGCUUAAUUGCCGAGCUUUCAAGCCUUACUUGGCCGCUAGUGCGAAAGACCAGGACUGAUUAGUGCCCGCAGUGUGUCAGC
...((((.(((..(((((...((((((.(((.((.(((((((......))).(((..(((((.....)))))..))).)))))).))).))))))))))).((....)).))).)))).. ( -41.00)
>DroSec_CAF1 41236 120 - 1
UUAUGACUCGCACAAUCACUUGUCCUGUUUUAUCAGCACGGCUUAAUUGCCGAGCUUUCAAGCCCAACUUGGCCGCUAGUGCGAAGGCCCAGGACUGAUUAGUGCCCGCAGUGUGUCAGC
...((((.(((..(((((...((((((...........((((......)))).((((((..(((......))).((....)))))))).))))))))))).((....)).))).)))).. ( -40.50)
>DroSim_CAF1 46287 120 - 1
UUAUGACUCGCACAAUCACUUGUCCUGUUUUAUCAGCACGGCUUAAUUGCCGAGCUUUCAAGCCCAACUUGGCCGCUAGUGCGAAGGCCCGGGACUGAUUAGUGCCCGCAGUGUGUCAGC
...((((.(((..(((((...((((((...........((((......)))).((((((..(((......))).((....)))))))).))))))))))).((....)).))).)))).. ( -39.80)
>DroEre_CAF1 39426 119 - 1
UUAUGACUCGCACAAUCACUUGUCCCGCUUUAUCAGCCCGGCCUAAUUGCCGAGCUUUCAAGCCCGGCUUGGCCG-UAGUGCGAAGGUCCAGGACUGAUUAGUGCCCGCAGUGUGUCAGU
...((((.(((((((....))))..((((..((((((((((((.....((((.(((....))).))))..)))))-..(..(....)..).)).))))).))))......))).)))).. ( -41.90)
>DroYak_CAF1 40602 120 - 1
UUAUGACUCGCACAAUCACUUGUGCUGUUUUAUCAGCCCGGCUUAAUUGCCGAGCUUUCAAGACCACUAUGGCCGCUAGUGCGAAGGCCCAGGACUGAUUUGUGCCCGCAGUGUGUCAGC
...((((.(((((((....)))))).((...(((((((((((......)))).((((((..(.((.....)).)((....))))))))...)).)))))....)).......).)))).. ( -36.90)
>consensus
UUAUGACUCGCACAAUCACUUGUCCUGUUUUAUCAGCACGGCUUAAUUGCCGAGCUUUCAAGCCCAACUUGGCCGCUAGUGCGAAGGCCCAGGACUGAUUAGUGCCCGCAGUGUGUCAGC
...((((.(((..(((((...((((((...........((((......)))).((((((..(((......))).((....)))))))).))))))))))).((....)).))).)))).. (-33.76 = -34.36 +   0.60)

alignment

secondary structure

dotplot

Window 7

Location	1,422,823 – 1,422,943
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	92.25
Mean single sequence MFE	-40.17
Consensus MFE	-28.18
Energy contribution	-29.36
Covariance contribution	1.18
Combinations/Pair	1.16
Mean z-score	-2.53
Structure conservation index	0.70
SVM decision value	0.16
SVM RNA-class probability	0.611154
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 1422823 120 + 20766785
ACUAGCGGCCAAGUAAGGCUUGAAAGCUCGGCAAUUAAGCCGUGCUGAUAAAACAGGACAAGUGAUUGUGCGAGUCAUAACUCAAAAGCACACGGAUACGGACAACAUGAGGGUGACGCC
....((((((......)))......(((((((......)))(((((.........(.((((....)))).)((((....))))...))))).((....))..........))))..))). ( -33.40)
>DroSec_CAF1 41276 120 + 1
ACUAGCGGCCAAGUUGGGCUUGAAAGCUCGGCAAUUAAGCCGUGCUGAUAAAACAGGACAAGUGAUUGUGCGAGUCAUAACUCAAAAGCACACGGAUACGGCCAACAUGAGGGUGACGCC
....((((((..((((((((....)))))))).......(((((.((........(.((((....)))).)((((....)))).....)))))))....))))........(....))). ( -39.70)
>DroSim_CAF1 46327 120 + 1
ACUAGCGGCCAAGUUGGGCUUGAAAGCUCGGCAAUUAAGCCGUGCUGAUAAAACAGGACAAGUGAUUGUGCGAGUCAUAACUCAAAAGCACACGGAUACGGCCAACAUGAGGGUGACGCC
....((((((..((((((((....)))))))).......(((((.((........(.((((....)))).)((((....)))).....)))))))....))))........(....))). ( -39.70)
>DroEre_CAF1 39466 119 + 1
ACUA-CGGCCAAGCCGGGCUUGAAAGCUCGGCAAUUAGGCCGGGCUGAUAAAGCGGGACAAGUGAUUGUGCGAGUCAUAACUCAAAAGAACACGGAUACGGCCAACAUGGGGGUGACGCC
....-.((((...(((.((((...((((((((......))))))))....)))).(.((((....)))).)((((....)))).........)))....)))).....((.(....).)) ( -46.30)
>DroYak_CAF1 40642 120 + 1
ACUAGCGGCCAUAGUGGUCUUGAAAGCUCGGCAAUUAAGCCGGGCUGAUAAAACAGCACAAGUGAUUGUGCGAGUCAUAACUUAAAAGAACACGGAUACGUGCAAUACGAGGGUGACGCU
...(((((((.....))))(((..((((((((......))))))))..)))....((((((....))))))..(((((..(((.......((((....)))).......))))))))))) ( -41.74)
>consensus
ACUAGCGGCCAAGUUGGGCUUGAAAGCUCGGCAAUUAAGCCGUGCUGAUAAAACAGGACAAGUGAUUGUGCGAGUCAUAACUCAAAAGCACACGGAUACGGCCAACAUGAGGGUGACGCC
......((((((((...)))))..(((.((((......)))).))).........(.((((....)))).)..(((((..((((........((....)).......)))).)))))))) (-28.18 = -29.36 +   1.18)

alignment

secondary structure

dotplot

Window 8

Location	1,422,863 – 1,422,983
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	93.58
Mean single sequence MFE	-42.06
Consensus MFE	-31.24
Energy contribution	-31.68
Covariance contribution	0.44
Combinations/Pair	1.17
Mean z-score	-1.93
Structure conservation index	0.74
SVM decision value	0.05
SVM RNA-class probability	0.559164
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 1422863 120 + 20766785
CGUGCUGAUAAAACAGGACAAGUGAUUGUGCGAGUCAUAACUCAAAAGCACACGGAUACGGACAACAUGAGGGUGACGCCCGUGCGCUCCAUCGUCAUUCAGAGGAUGACGCAGCGGGCG
.(((((.........(.((((....)))).)((((....))))...))))).((....))...........(....)(((((((((...((((.((.....)).)))).)))).))))). ( -41.50)
>DroSec_CAF1 41316 120 + 1
CGUGCUGAUAAAACAGGACAAGUGAUUGUGCGAGUCAUAACUCAAAAGCACACGGAUACGGCCAACAUGAGGGUGACGCCCGUGUGCUCCAUCGUCAUUCAGAGGAUGACGCAGCGGGCG
.(((((.........(.((((....)))).)((((....))))...))))).((....))(((........)))..(((((((.(((..((((.((.....)).))))..)))))))))) ( -43.20)
>DroSim_CAF1 46367 120 + 1
CGUGCUGAUAAAACAGGACAAGUGAUUGUGCGAGUCAUAACUCAAAAGCACACGGAUACGGCCAACAUGAGGGUGACGCCCGUGUGCUCCAUCGUCAUUCAGAGGAUGACGCAGCGGGCG
.(((((.........(.((((....)))).)((((....))))...))))).((....))(((........)))..(((((((.(((..((((.((.....)).))))..)))))))))) ( -43.20)
>DroEre_CAF1 39505 120 + 1
CGGGCUGAUAAAGCGGGACAAGUGAUUGUGCGAGUCAUAACUCAAAAGAACACGGAUACGGCCAACAUGGGGGUGACGCCCGUGUGCUCCAUCGUCAUUCAGAGAGUGACGCAGCGGGCG
..(((((........(.((((....)))).)((((....))))...............))))).((((((((....).)))))))(((((..((((((((...))))))))..).)))). ( -44.80)
>DroYak_CAF1 40682 120 + 1
CGGGCUGAUAAAACAGCACAAGUGAUUGUGCGAGUCAUAACUUAAAAGAACACGGAUACGUGCAAUACGAGGGUGACGCUCGUGUGUUCCAUCGACAUUCAGAGAAUGACGCAGCGGGCG
...((((........((((((....))))))..(((((.........(((((((....)))...((((((((....).)))))))))))..((........))..))))).))))..... ( -37.60)
>consensus
CGUGCUGAUAAAACAGGACAAGUGAUUGUGCGAGUCAUAACUCAAAAGCACACGGAUACGGCCAACAUGAGGGUGACGCCCGUGUGCUCCAUCGUCAUUCAGAGGAUGACGCAGCGGGCG
(((((.(((...((.......)).)))))))).(((((..((((........((....)).......)))).)))))((((((.(((..((((.((.....)).))))..))))))))). (-31.24 = -31.68 +   0.44)

alignment

secondary structure

dotplot

Window 9

Location	1,422,903 – 1,423,023
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	91.75
Mean single sequence MFE	-39.04
Consensus MFE	-28.74
Energy contribution	-29.58
Covariance contribution	0.84
Combinations/Pair	1.21
Mean z-score	-1.94
Structure conservation index	0.74
SVM decision value	0.23
SVM RNA-class probability	0.646070
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 1422903 120 + 20766785
CUCAAAAGCACACGGAUACGGACAACAUGAGGGUGACGCCCGUGCGCUCCAUCGUCAUUCAGAGGAUGACGCAGCGGGCGGCAAAAAAAAACCAAUGAACGAGUGUUGGGAUAAGCUCAA
((((...((((.((....)).....(((...(((..((((((((((...((((.((.....)).)))).)))).))))))..........))).))).....)))))))).......... ( -35.90)
>DroSec_CAF1 41356 120 + 1
CUCAAAAGCACACGGAUACGGCCAACAUGAGGGUGACGCCCGUGUGCUCCAUCGUCAUUCAGAGGAUGACGCAGCGGGCGACAGAAAAAAGCCAAUGAACGAGUGUUGGGAUAAGCUCAA
......(((...((....)).(((((((..((....)((((((.(((..((((.((.....)).))))..)))))))))....................)..))))))).....)))... ( -38.90)
>DroSim_CAF1 46407 120 + 1
CUCAAAAGCACACGGAUACGGCCAACAUGAGGGUGACGCCCGUGUGCUCCAUCGUCAUUCAGAGGAUGACGCAGCGGGCGGCAGAAAAAAGCCAAUGAACGAGUGUUGGGAUAAGCUCAA
......(((...((....)).(((((((..((....)((((((.(((..((((.((.....)).))))..)))))))))(((........)))......)..))))))).....)))... ( -43.10)
>DroEre_CAF1 39545 119 + 1
CUCAAAAGAACACGGAUACGGCCAACAUGGGGGUGACGCCCGUGUGCUCCAUCGUCAUUCAGAGAGUGACGCAGCGGGCGGCAAAA-AAAGCCAAUGGACGAGUGUUGGGAUAAGCUCAA
(((((....((.((..((..(((.((((((((....).)))))))(((....((((((((...)))))))).))).)))(((....-...)))..))..)).)).))))).......... ( -41.50)
>DroYak_CAF1 40722 119 + 1
CUUAAAAGAACACGGAUACGUGCAAUACGAGGGUGACGCUCGUGUGUUCCAUCGACAUUCAGAGAAUGACGCAGCGGGCGGCAAAAAAAAGCCAUUGGUUGAGUGU-GGGAUAAGCUCAA
..........((((....))))..((((((((....).)))))))(((((((...(((((...)))))((.((((.((.(((........))).)).)))).))))-)))))........ ( -35.80)
>consensus
CUCAAAAGCACACGGAUACGGCCAACAUGAGGGUGACGCCCGUGUGCUCCAUCGUCAUUCAGAGGAUGACGCAGCGGGCGGCAAAAAAAAGCCAAUGAACGAGUGUUGGGAUAAGCUCAA
............((....)).(((((((..(......((((((.(((..((((.((.....)).))))..)))))))))(((........)))......)..)))))))........... (-28.74 = -29.58 +   0.84)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:30:34 2006